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class="social-profile-avatar-container"><img class="profile-avatar u-positionAbsolute" border="0" alt="" src="//a.academia-assets.com/images/s200_no_pic.png" /></div><div class="title-container"><h1 class="ds2-5-heading-sans-serif-sm">Brandon Swan</h1><div class="affiliations-container fake-truncate js-profile-affiliations"></div></div></div><div class="sidebar-cta-container"><button class="ds2-5-button hidden profile-cta-button grow js-profile-follow-button" data-broccoli-component="user-info.follow-button" data-click-track="profile-user-info-follow-button" data-follow-user-fname="Brandon" data-follow-user-id="31550655" data-follow-user-source="profile_button" data-has-google="false"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">add</span>Follow</button><button class="ds2-5-button hidden profile-cta-button grow js-profile-unfollow-button" data-broccoli-component="user-info.unfollow-button" data-click-track="profile-user-info-unfollow-button" 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js-section-heading" data-section="Papers" id="Papers"><h3 class="profile--tab_heading_container">Papers by Brandon Swan</h3></div><div class="js-work-strip profile--work_container" data-work-id="12605995"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/12605995/Depth_Distribution_of_Archaeal_Diversity_and_Community_Composition_Across_Steep_Geochemical_Gradients_in_Anoxic_Sediments_of_a_Hypersaline_Lake"><img alt="Research paper thumbnail of Depth Distribution of Archaeal Diversity and Community Composition Across Steep Geochemical Gradients in Anoxic Sediments of a Hypersaline Lake" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605995/Depth_Distribution_of_Archaeal_Diversity_and_Community_Composition_Across_Steep_Geochemical_Gradients_in_Anoxic_Sediments_of_a_Hypersaline_Lake">Depth Distribution of Archaeal Diversity and Community Composition Across Steep Geochemical Gradients in Anoxic Sediments of a Hypersaline Lake</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Patterns in Archaeal diversity and community composition were investigated in the anoxic sediment...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Patterns in Archaeal diversity and community composition were investigated in the anoxic sediments of the Salton Sea, California&#39;s largest lake. The sediments of this lake contain strong gradients in salinity and organic carbon, which provide a natural setting to examine the influence of these gradients on Archaeal communities. Measurements of sediment and porewater geochemistry and Archaeal diversity were made within</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605995"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="12605995"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 12605995; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=12605995]").text(description); $(".js-view-count[data-work-id=12605995]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 12605995; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='12605995']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 12605995, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=12605995]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":12605995,"title":"Depth Distribution of Archaeal Diversity and Community Composition Across Steep Geochemical Gradients in Anoxic Sediments of a Hypersaline Lake","translated_title":"","metadata":{"abstract":"Patterns in Archaeal diversity and community composition were investigated in the anoxic sediments of the Salton Sea, California\u0026#39;s largest lake. 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Luo</a>, and <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/JessicaLabont%C3%A9">Jessica Labonté</a></span></div><div class="wp-workCard_item"><span>The ISME journal</span><span>, Jan 7, 2015</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Viral infections dynamically alter the composition and metabolic potential of marine microbial co...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Viral infections dynamically alter the composition and metabolic potential of marine microbial communities and the evolutionary trajectories of host populations with resulting feedback on biogeochemical cycles. It is quite possible that all microbial populations in the ocean are impacted by viral infections. Our knowledge of virus-host relationships, however, has been limited to a minute fraction of cultivated host groups. Here, we utilized single-cell sequencing to obtain genomic blueprints of viruses inside or attached to individual bacterial and archaeal cells captured in their native environment, circumventing the need for host and virus cultivation. A combination of comparative genomics, metagenomic fragment recruitment, sequence anomalies and irregularities in sequence coverage depth and genome recovery were utilized to detect viruses and to decipher modes of virus-host interactions. Members of all three tailed phage families were identified in 20 out of 58 phylogenetically an...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="6fa5325e94dfff31cbd251cc3eea3313" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055146,"asset_id":12605994,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055146/download_file?st=MTczMjc5MDQwOSw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605994"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="12605994"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 12605994; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=12605994]").text(description); $(".js-view-count[data-work-id=12605994]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 12605994; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='12605994']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 12605994, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "6fa5325e94dfff31cbd251cc3eea3313" } } $('.js-work-strip[data-work-id=12605994]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":12605994,"title":"Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton","translated_title":"","metadata":{"abstract":"Viral infections dynamically alter the composition and metabolic potential of marine microbial communities and the evolutionary trajectories of host populations with resulting feedback on biogeochemical cycles. 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Total abundance was highest in summer following late winter/early spring phytoplankton blooms. At this time, metazooplankton consisted mostly of the copepod, Apocyclops dengizicus, and the rotifer, Brachionus rotundiformis. In August or September, severe crashes in the metazooplankton populations occurred each year in mid-lake due to strong wind events which increased mixing and caused low oxygen and high sulfide concentrations throughout the water column. Larvae of the polychaete worm, Neanthes succinea and the barnacle, Balanus amphitrite were present mostly in late winter and spring. Their scarcity in summer is due in part to persistent anoxic bottom conditions that decrease adult populations and in part to predation by tilapia, an omnivorous fish that has become abundant in the lake since the 1960s. Two Synchaeta species, rotifers not previously reported from the Sea, were abundant in winter and spring and predation on these may have permitted the copepod to persist at low levels through the winter. There were two major changes in metazooplankton dynamics since 1954-1956 in addition to the appearance of the two synchaetid rotifers in the fauna. First, there are now much lower densities of barnacle and polychaete larvae in the fall, probably due to the invasion of the zooplanktivorous fish, tilapia. Second the precipitous crashes now seen in metazooplankton densities, especially the copepod, in late summer-early fall did not occur in the 1950s possibly because fall overturn events did not result in such high sulfide levels.","publication_date":{"day":1,"month":4,"year":2002,"errors":{}},"grobid_abstract_attachment_id":46055087},"translated_abstract":null,"internal_url":"https://www.academia.edu/12605993/Metazooplankton_dynamics_in_the_Salton_Sea_California_1997_1999","translated_internal_url":"","created_at":"2015-05-26T06:21:42.030-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":31550655,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":46055087,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/46055087/thumbnails/1.jpg","file_name":"Metazooplankton_dynamics_in_the_Salton_S20160529-32630-1r10a7n.pdf","download_url":"https://www.academia.edu/attachments/46055087/download_file?st=MTczMjc5MDQwOSw4LjIyMi4yMDguMTQ2&","bulk_download_file_name":"Metazooplankton_dynamics_in_the_Salton_S.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/46055087/Metazooplankton_dynamics_in_the_Salton_S20160529-32630-1r10a7n-libre.pdf?1464574042=\u0026response-content-disposition=attachment%3B+filename%3DMetazooplankton_dynamics_in_the_Salton_S.pdf\u0026Expires=1732794009\u0026Signature=UThpG7jryPOyj7Ja9lJ3ZTJAm2~addmyCWXacLXpP0JOlMn0sdb5QNMXHQ-WPWT4Z9t0j8RW27j3PkB7t9-XQKgnhkp08CMNERyqPbz8vMJ6sy08EPuB~xbmUiUgMc6k9qC2t7MxH9OYrqahD8gibikn67wkwpdEACwlHqr6DgBbVJlgl8oOm2eF7XPMdqDQV6WVlzrXdbUEtwgu43aOAet-BMkrwgwBfAWUDL2vCjDM-C1YBziS2EMSOPaGCK-vSoCJx7pyWiNDIHPuSHevMZtyRPTiDctDAg8MTgfLjYKfupLgMiAUJ4~qPnEvySqxGXpwncLLrCLk5t14N7aqhw__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"Metazooplankton_dynamics_in_the_Salton_Sea_California_1997_1999","translated_slug":"","page_count":18,"language":"en","content_type":"Work","owner":{"id":31550655,"first_name":"Brandon","middle_initials":null,"last_name":"Swan","page_name":"SwanBrandon","domain_name":"independent","created_at":"2015-05-26T06:21:03.429-07:00","display_name":"Brandon Swan","url":"https://independent.academia.edu/SwanBrandon"},"attachments":[{"id":46055087,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/46055087/thumbnails/1.jpg","file_name":"Metazooplankton_dynamics_in_the_Salton_S20160529-32630-1r10a7n.pdf","download_url":"https://www.academia.edu/attachments/46055087/download_file?st=MTczMjc5MDQwOSw4LjIyMi4yMDguMTQ2&","bulk_download_file_name":"Metazooplankton_dynamics_in_the_Salton_S.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/46055087/Metazooplankton_dynamics_in_the_Salton_S20160529-32630-1r10a7n-libre.pdf?1464574042=\u0026response-content-disposition=attachment%3B+filename%3DMetazooplankton_dynamics_in_the_Salton_S.pdf\u0026Expires=1732794009\u0026Signature=UThpG7jryPOyj7Ja9lJ3ZTJAm2~addmyCWXacLXpP0JOlMn0sdb5QNMXHQ-WPWT4Z9t0j8RW27j3PkB7t9-XQKgnhkp08CMNERyqPbz8vMJ6sy08EPuB~xbmUiUgMc6k9qC2t7MxH9OYrqahD8gibikn67wkwpdEACwlHqr6DgBbVJlgl8oOm2eF7XPMdqDQV6WVlzrXdbUEtwgu43aOAet-BMkrwgwBfAWUDL2vCjDM-C1YBziS2EMSOPaGCK-vSoCJx7pyWiNDIHPuSHevMZtyRPTiDctDAg8MTgfLjYKfupLgMiAUJ4~qPnEvySqxGXpwncLLrCLk5t14N7aqhw__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":400,"name":"Earth Sciences","url":"https://www.academia.edu/Documents/in/Earth_Sciences"},{"id":8060,"name":"Saline Lake","url":"https://www.academia.edu/Documents/in/Saline_Lake"},{"id":47884,"name":"Biological Sciences","url":"https://www.academia.edu/Documents/in/Biological_Sciences"},{"id":58054,"name":"Environmental Sciences","url":"https://www.academia.edu/Documents/in/Environmental_Sciences"},{"id":770327,"name":"Oreochromis mossambicus","url":"https://www.academia.edu/Documents/in/Oreochromis_mossambicus"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="12605992"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/12605992/Marine_viruses_a_genetic_reservoir_revealed_by_targeted_viromics"><img alt="Research paper thumbnail of Marine viruses, a genetic reservoir revealed by targeted viromics" class="work-thumbnail" src="https://attachments.academia-assets.com/46055133/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605992/Marine_viruses_a_genetic_reservoir_revealed_by_targeted_viromics">Marine viruses, a genetic reservoir revealed by targeted viromics</a></div><div class="wp-workCard_item"><span>The ISME journal</span><span>, 2014</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Metagenomics has opened new windows on investigating viral diversity and functions. Viromic studi...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Metagenomics has opened new windows on investigating viral diversity and functions. Viromic studies typically require large sample volumes and filtration through 0.2 μm pore-size filters, consequently excluding or under-sampling tailed and very large viruses. We have optimized a targeted viromic approach that employs fluorescence-activated sorting and whole genome amplification to produce dsDNA-enriched libraries from discrete viral populations from a 1-ml water sample. Using this approach on an environmental sample from the Patagonian Shelf, we produced three distinct libraries. One of the virus libraries was dominated (79.65% of sequences with known viral homology) by giant viruses from the Mimiviridae and Phycodnaviridae families, while the two other viromes were dominated by smaller phycodnaviruses, cyanophages and other bacteriophages. The estimated genotypic richness and diversity in our sorted viromes, with 52-163 estimated genotypes, was much lower than in previous virome re...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="6893ecd79cc017c68691da770ef27a74" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055133,"asset_id":12605992,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055133/download_file?st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605992"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="12605992"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 12605992; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=12605992]").text(description); $(".js-view-count[data-work-id=12605992]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 12605992; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='12605992']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 12605992, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "6893ecd79cc017c68691da770ef27a74" } } $('.js-work-strip[data-work-id=12605992]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":12605992,"title":"Marine viruses, a genetic reservoir revealed by targeted viromics","translated_title":"","metadata":{"abstract":"Metagenomics has opened new windows on investigating viral diversity and functions. Viromic studies typically require large sample volumes and filtration through 0.2 μm pore-size filters, consequently excluding or under-sampling tailed and very large viruses. We have optimized a targeted viromic approach that employs fluorescence-activated sorting and whole genome amplification to produce dsDNA-enriched libraries from discrete viral populations from a 1-ml water sample. Using this approach on an environmental sample from the Patagonian Shelf, we produced three distinct libraries. One of the virus libraries was dominated (79.65% of sequences with known viral homology) by giant viruses from the Mimiviridae and Phycodnaviridae families, while the two other viromes were dominated by smaller phycodnaviruses, cyanophages and other bacteriophages. The estimated genotypic richness and diversity in our sorted viromes, with 52-163 estimated genotypes, was much lower than in previous virome re...","publication_date":{"day":null,"month":null,"year":2014,"errors":{}},"publication_name":"The ISME journal"},"translated_abstract":"Metagenomics has opened new windows on investigating viral diversity and functions. Viromic studies typically require large sample volumes and filtration through 0.2 μm pore-size filters, consequently excluding or under-sampling tailed and very large viruses. We have optimized a targeted viromic approach that employs fluorescence-activated sorting and whole genome amplification to produce dsDNA-enriched libraries from discrete viral populations from a 1-ml water sample. Using this approach on an environmental sample from the Patagonian Shelf, we produced three distinct libraries. One of the virus libraries was dominated (79.65% of sequences with known viral homology) by giant viruses from the Mimiviridae and Phycodnaviridae families, while the two other viromes were dominated by smaller phycodnaviruses, cyanophages and other bacteriophages. 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="12605991"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/12605991/Evolutionary_analysis_of_a_streamlined_lineage_of_surface_ocean_Roseobacters"><img alt="Research paper thumbnail of Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters" class="work-thumbnail" src="https://attachments.academia-assets.com/46055084/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605991/Evolutionary_analysis_of_a_streamlined_lineage_of_surface_ocean_Roseobacters">Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/SwanBrandon">Brandon Swan</a> and <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/AustinHughes2">Austin Hughes</a></span></div><div class="wp-workCard_item"><span>The ISME Journal</span><span>, 2014</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="8e634a30b2e97939469d967690d20f29" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055084,"asset_id":12605991,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055084/download_file?st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605991"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="12605991"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 12605991; 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dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "8e634a30b2e97939469d967690d20f29" } } $('.js-work-strip[data-work-id=12605991]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":12605991,"title":"Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters","translated_title":"","metadata":{"publication_date":{"day":null,"month":null,"year":2014,"errors":{}},"publication_name":"The ISME Journal"},"translated_abstract":null,"internal_url":"https://www.academia.edu/12605991/Evolutionary_analysis_of_a_streamlined_lineage_of_surface_ocean_Roseobacters","translated_internal_url":"","created_at":"2015-05-26T06:21:41.628-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":31550655,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[{"id":649291,"work_id":12605991,"tagging_user_id":31550655,"tagged_user_id":34775074,"co_author_invite_id":245284,"email":"a***n@biol.sc.edu","display_order":0,"name":"Austin Hughes","title":"Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters"},{"id":649292,"work_id":12605991,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":245285,"email":"a***n@biols.sc.edu","display_order":null,"name":"Austin Hughes","title":"Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters"},{"id":649332,"work_id":12605991,"tagging_user_id":31550655,"tagged_user_id":31620842,"co_author_invite_id":236704,"email":"h***6@gmail.com","display_order":null,"name":"H. Luo","title":"Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters"},{"id":649293,"work_id":12605991,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":245286,"email":"a***l@blogmail.cc","display_order":null,"name":"Hughes Al","title":"Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters"},{"id":649290,"work_id":12605991,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":245283,"email":"a***n@biol.ac.edu","display_order":null,"name":"Austin Hughes","title":"Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters"},{"id":649330,"work_id":12605991,"tagging_user_id":31550655,"tagged_user_id":124681449,"co_author_invite_id":147185,"email":"m***n@uga.edu","affiliation":"The University of Georgia","display_order":null,"name":"Mary Ann Moran","title":"Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters"}],"downloadable_attachments":[{"id":46055084,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/46055084/thumbnails/1.jpg","file_name":"Evolutionary_analysis_of_a_streamlined_l20160529-20889-6j8jw7.pdf","download_url":"https://www.academia.edu/attachments/46055084/download_file?st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&","bulk_download_file_name":"Evolutionary_analysis_of_a_streamlined_l.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/46055084/Evolutionary_analysis_of_a_streamlined_l20160529-20889-6j8jw7-libre.pdf?1464574042=\u0026response-content-disposition=attachment%3B+filename%3DEvolutionary_analysis_of_a_streamlined_l.pdf\u0026Expires=1732769385\u0026Signature=FfnWeS-SvEGYZSF-w4ANt3ZRt0C7Wufdai48l8d1M8noyu2aIcQ3b1orxtXbGqE-GxKfkPNXQ0uggT-CaKEljWIHmjwELd9ca3IbpgB3FLUfDbYZoI~704YlHjYBJzMxgqCKo3V28fuak2DGH0kq9FiGgBSXMkCkC77DWk5u5wcUM3r4HiRzk1G03~-HZLUJZh8INb5Z6fIKnZrZihNNHMBicMdni7Prr8qm4KRT8qLD7tMAdIZsRcgrkMuB124zMmF5UMmo7yNXBv6IhYIKXArZ1QkGhAU6KCm0RyxgaypUZFtJtLJDu3QiiAH6I6nXC3TsiD7EotiC5q~SvwSLhg__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"Evolutionary_analysis_of_a_streamlined_lineage_of_surface_ocean_Roseobacters","translated_slug":"","page_count":19,"language":"en","content_type":"Work","owner":{"id":31550655,"first_name":"Brandon","middle_initials":null,"last_name":"Swan","page_name":"SwanBrandon","domain_name":"independent","created_at":"2015-05-26T06:21:03.429-07:00","display_name":"Brandon Swan","url":"https://independent.academia.edu/SwanBrandon"},"attachments":[{"id":46055084,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/46055084/thumbnails/1.jpg","file_name":"Evolutionary_analysis_of_a_streamlined_l20160529-20889-6j8jw7.pdf","download_url":"https://www.academia.edu/attachments/46055084/download_file?st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&","bulk_download_file_name":"Evolutionary_analysis_of_a_streamlined_l.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/46055084/Evolutionary_analysis_of_a_streamlined_l20160529-20889-6j8jw7-libre.pdf?1464574042=\u0026response-content-disposition=attachment%3B+filename%3DEvolutionary_analysis_of_a_streamlined_l.pdf\u0026Expires=1732769385\u0026Signature=FfnWeS-SvEGYZSF-w4ANt3ZRt0C7Wufdai48l8d1M8noyu2aIcQ3b1orxtXbGqE-GxKfkPNXQ0uggT-CaKEljWIHmjwELd9ca3IbpgB3FLUfDbYZoI~704YlHjYBJzMxgqCKo3V28fuak2DGH0kq9FiGgBSXMkCkC77DWk5u5wcUM3r4HiRzk1G03~-HZLUJZh8INb5Z6fIKnZrZihNNHMBicMdni7Prr8qm4KRT8qLD7tMAdIZsRcgrkMuB124zMmF5UMmo7yNXBv6IhYIKXArZ1QkGhAU6KCm0RyxgaypUZFtJtLJDu3QiiAH6I6nXC3TsiD7EotiC5q~SvwSLhg__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":923,"name":"Technology","url":"https://www.academia.edu/Documents/in/Technology"},{"id":4312,"name":"Genetic Drift","url":"https://www.academia.edu/Documents/in/Genetic_Drift"},{"id":4967,"name":"Molecular Evolution","url":"https://www.academia.edu/Documents/in/Molecular_Evolution"},{"id":20256,"name":"Genome Size","url":"https://www.academia.edu/Documents/in/Genome_Size"},{"id":47884,"name":"Biological Sciences","url":"https://www.academia.edu/Documents/in/Biological_Sciences"},{"id":54433,"name":"Phylogeny","url":"https://www.academia.edu/Documents/in/Phylogeny"},{"id":58054,"name":"Environmental Sciences","url":"https://www.academia.edu/Documents/in/Environmental_Sciences"},{"id":143622,"name":"Roseobacter","url":"https://www.academia.edu/Documents/in/Roseobacter"},{"id":184467,"name":"Seawater","url":"https://www.academia.edu/Documents/in/Seawater"},{"id":377566,"name":"Aquatic organisms","url":"https://www.academia.edu/Documents/in/Aquatic_organisms"},{"id":880279,"name":"Bayes Theorem","url":"https://www.academia.edu/Documents/in/Bayes_Theorem-1"},{"id":1795281,"name":"Oceans and Seas","url":"https://www.academia.edu/Documents/in/Oceans_and_Seas"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="12605989"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/12605989/Single_cell_enabled_comparative_genomics_of_a_deep_ocean_SAR11_bathytype"><img alt="Research paper thumbnail of Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype" class="work-thumbnail" src="https://attachments.academia-assets.com/46055141/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605989/Single_cell_enabled_comparative_genomics_of_a_deep_ocean_SAR11_bathytype">Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/SwanBrandon">Brandon Swan</a> and <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/BenTemperton">Ben Temperton</a></span></div><div class="wp-workCard_item"><span>The ISME Journal</span><span>, 2014</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="f57e1ade6a98d676221347750cfec00b" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055141,"asset_id":12605989,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055141/download_file?st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605989"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="12605989"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 12605989; 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dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "f57e1ade6a98d676221347750cfec00b" } } $('.js-work-strip[data-work-id=12605989]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":12605989,"title":"Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype","translated_title":"","metadata":{"grobid_abstract":"Bacterioplankton of the SAR11 clade are the most abundant microorganisms in marine systems, usually representing 25% or more of the total bacterial cells in seawater worldwide. SAR11 is divided into subclades with distinct spatiotemporal distributions (ecotypes), some of which appear to be specific to deep water. Here we examine the genomic basis for deep ocean distribution of one SAR11 bathytype (depth-specific ecotype), subclade Ic. Four single-cell Ic genomes, with estimated completeness of 55%-86%, were isolated from 770 m at station ALOHA and compared with eight SAR11 surface genomes and metagenomic datasets. Subclade Ic genomes dominated metagenomic fragment recruitment below the euphotic zone. They had similar COG distributions, high local synteny and shared a large number (69%) of orthologous clusters with SAR11 surface genomes, yet were distinct at the 16S rRNA gene and amino-acid level, and formed a separate, monophyletic group in phylogenetic trees. Subclade Ic genomes were enriched in genes associated with membrane/cell wall/envelope biosynthesis and showed evidence of unique phage defenses. The majority of subclade Ic-specfic genes were hypothetical, and some were highly abundant in deep ocean metagenomic data, potentially masking mechanisms for niche differentiation. However, the evidence suggests these organisms have a similar metabolism to their surface counterparts, and that subclade Ic adaptations to the deep ocean do not involve large variations in gene content, but rather more subtle differences previously observed deep ocean genomic data, like preferential amino-acid substitutions, larger coding regions among SAR11 clade orthologs, larger intergenic regions and larger estimated average genome size.","publication_date":{"day":null,"month":null,"year":2014,"errors":{}},"publication_name":"The ISME Journal","grobid_abstract_attachment_id":46055141},"translated_abstract":null,"internal_url":"https://www.academia.edu/12605989/Single_cell_enabled_comparative_genomics_of_a_deep_ocean_SAR11_bathytype","translated_internal_url":"","created_at":"2015-05-26T06:21:41.500-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":31550655,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[{"id":649288,"work_id":12605989,"tagging_user_id":31550655,"tagged_user_id":56223722,"co_author_invite_id":189821,"email":"s***i@oregonstate.edu","display_order":0,"name":"S. Giovannoni","title":"Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype"},{"id":649340,"work_id":12605989,"tagging_user_id":31550655,"tagged_user_id":6765232,"co_author_invite_id":null,"email":"t***e@lbl.gov","affiliation":"Lawrence Berkeley National Laboratory","display_order":null,"name":"Tanja Woyke","title":"Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype"},{"id":649289,"work_id":12605989,"tagging_user_id":31550655,"tagged_user_id":31607602,"co_author_invite_id":245282,"email":"b***n@gmail.com","display_order":null,"name":"Ben Temperton","title":"Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype"},{"id":649310,"work_id":12605989,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":212180,"email":"e***g@hawaii.edu","display_order":null,"name":"Edward DeLong","title":"Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype"},{"id":649312,"work_id":12605989,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":212181,"email":"d***g@mit.edu","display_order":null,"name":"Edward DeLong","title":"Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype"},{"id":649287,"work_id":12605989,"tagging_user_id":31550655,"tagged_user_id":63834471,"co_author_invite_id":236706,"email":"z***y@gmail.com","display_order":null,"name":"Zachary Landry","title":"Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype"}],"downloadable_attachments":[{"id":46055141,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/46055141/thumbnails/1.jpg","file_name":"Single-cell_enabled_comparative_genomics20160529-5431-1cwxuyp.pdf","download_url":"https://www.academia.edu/attachments/46055141/download_file?st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&","bulk_download_file_name":"Single_cell_enabled_comparative_genomics.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/46055141/Single-cell_enabled_comparative_genomics20160529-5431-1cwxuyp-libre.pdf?1464574132=\u0026response-content-disposition=attachment%3B+filename%3DSingle_cell_enabled_comparative_genomics.pdf\u0026Expires=1732794010\u0026Signature=abPnN6FSWsrgnVg1LWcOg6rVeKTPsLuIKICM6oC2naHt7c2bBk~dUwrV1uIDo0Axo8baX6phqWa21X1yUDNgRnssRhgT8WnmoV4DO6LTMLQvre1~cTiFhyM8agDvY8BpIRR7SSBxYELdMaxXORvn~S5ribrDSmWfpQHZqWK-6sSQrtQ1rasEkRsSy-KRK6yq6mL6ZI9rGNFWz3SmVYq1GR~KEXMG6tPVwCBqJD4yRY-mIfhN9VCyZiy94pQNa5YQ3W5JvNqnQzEpWq5HuL3qV-eZScqDu4LscbvJKg89S1q73YRxwrnMk9TKqBTRDr01yY82ZHVtXdj8Kg6LxjjMNQ__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"Single_cell_enabled_comparative_genomics_of_a_deep_ocean_SAR11_bathytype","translated_slug":"","page_count":56,"language":"en","content_type":"Work","owner":{"id":31550655,"first_name":"Brandon","middle_initials":null,"last_name":"Swan","page_name":"SwanBrandon","domain_name":"independent","created_at":"2015-05-26T06:21:03.429-07:00","display_name":"Brandon Swan","url":"https://independent.academia.edu/SwanBrandon"},"attachments":[{"id":46055141,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/46055141/thumbnails/1.jpg","file_name":"Single-cell_enabled_comparative_genomics20160529-5431-1cwxuyp.pdf","download_url":"https://www.academia.edu/attachments/46055141/download_file?st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&","bulk_download_file_name":"Single_cell_enabled_comparative_genomics.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/46055141/Single-cell_enabled_comparative_genomics20160529-5431-1cwxuyp-libre.pdf?1464574132=\u0026response-content-disposition=attachment%3B+filename%3DSingle_cell_enabled_comparative_genomics.pdf\u0026Expires=1732794010\u0026Signature=abPnN6FSWsrgnVg1LWcOg6rVeKTPsLuIKICM6oC2naHt7c2bBk~dUwrV1uIDo0Axo8baX6phqWa21X1yUDNgRnssRhgT8WnmoV4DO6LTMLQvre1~cTiFhyM8agDvY8BpIRR7SSBxYELdMaxXORvn~S5ribrDSmWfpQHZqWK-6sSQrtQ1rasEkRsSy-KRK6yq6mL6ZI9rGNFWz3SmVYq1GR~KEXMG6tPVwCBqJD4yRY-mIfhN9VCyZiy94pQNa5YQ3W5JvNqnQzEpWq5HuL3qV-eZScqDu4LscbvJKg89S1q73YRxwrnMk9TKqBTRDr01yY82ZHVtXdj8Kg6LxjjMNQ__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":923,"name":"Technology","url":"https://www.academia.edu/Documents/in/Technology"},{"id":3216,"name":"Genomics","url":"https://www.academia.edu/Documents/in/Genomics"},{"id":47884,"name":"Biological Sciences","url":"https://www.academia.edu/Documents/in/Biological_Sciences"},{"id":54433,"name":"Phylogeny","url":"https://www.academia.edu/Documents/in/Phylogeny"},{"id":58054,"name":"Environmental Sciences","url":"https://www.academia.edu/Documents/in/Environmental_Sciences"},{"id":58564,"name":"Single cell analysis","url":"https://www.academia.edu/Documents/in/Single_cell_analysis"},{"id":184467,"name":"Seawater","url":"https://www.academia.edu/Documents/in/Seawater"},{"id":360394,"name":"Alphaproteobacteria","url":"https://www.academia.edu/Documents/in/Alphaproteobacteria"},{"id":1710970,"name":"Metagenome","url":"https://www.academia.edu/Documents/in/Metagenome"},{"id":2007776,"name":"Synteny","url":"https://www.academia.edu/Documents/in/Synteny"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="12605988"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/12605988/Single_cell_genomics_shedding_light_on_marine_Thaumarchaeota_diversification"><img alt="Research paper thumbnail of Single-cell genomics shedding light on marine Thaumarchaeota diversification" class="work-thumbnail" src="https://attachments.academia-assets.com/46055091/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605988/Single_cell_genomics_shedding_light_on_marine_Thaumarchaeota_diversification">Single-cell genomics shedding light on marine Thaumarchaeota diversification</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/SwanBrandon">Brandon Swan</a> and <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/JamesHollibaugh">James Hollibaugh</a></span></div><div class="wp-workCard_item"><span>The ISME Journal</span><span>, 2014</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="194328cd829dd2d5546d6354b892e8d8" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055091,"asset_id":12605988,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055091/download_file?st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605988"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="12605988"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 12605988; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=12605988]").text(description); $(".js-view-count[data-work-id=12605988]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 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_.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "194328cd829dd2d5546d6354b892e8d8" } } $('.js-work-strip[data-work-id=12605988]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":12605988,"title":"Single-cell genomics shedding light on marine Thaumarchaeota diversification","translated_title":"","metadata":{"grobid_abstract":"Previous studies based on analysis of amoA, 16S ribosomal RNA or accA gene sequences have established that marine Thaumarchaeota fall into two phylogenetically distinct groups corresponding to shallow-and deep-water clades, but it is not clear how water depth interacts with other environmental factors, including light, temperature and location, to affect this pattern of diversification. Earlier studies focused on single-gene distributions were not able to link phylogenetic structure to other aspects of functional adaptation. Here, we analyzed the genome content of 46 uncultivated single Thaumarchaeota cells sampled from epi-and mesopelagic waters of subtropical, temperate and polar oceans. Phylogenomic analysis showed that populations diverged by depth, as expected, and that mesopelagic populations from different locations were well mixed. Functional analysis showed that some traits, including putative DNA photolyase and catalase genes that may be related to adaptive mechanisms to reduce light-induced damage, were found exclusively in members of the epipelagic clade. Our analysis of partial genomes has thus confirmed the depth differentiation of Thaumarchaeota populations observed previously, consistent with the distribution of putative mechanisms to reduce light-induced damage in shallow-and deep-water populations.","publication_date":{"day":null,"month":null,"year":2014,"errors":{}},"publication_name":"The ISME Journal","grobid_abstract_attachment_id":46055091},"translated_abstract":null,"internal_url":"https://www.academia.edu/12605988/Single_cell_genomics_shedding_light_on_marine_Thaumarchaeota_diversification","translated_internal_url":"","created_at":"2015-05-26T06:21:41.349-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":31550655,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[{"id":649331,"work_id":12605988,"tagging_user_id":31550655,"tagged_user_id":31620842,"co_author_invite_id":236704,"email":"h***6@gmail.com","display_order":null,"name":"H. Luo","title":"Single-cell genomics shedding light on marine Thaumarchaeota diversification"},{"id":649285,"work_id":12605988,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":245280,"email":"a***g@gmail.com","display_order":null,"name":"Chuanlun Zhang","title":"Single-cell genomics shedding light on marine Thaumarchaeota diversification"},{"id":649286,"work_id":12605988,"tagging_user_id":31550655,"tagged_user_id":31607436,"co_author_invite_id":245281,"email":"a***c@uga.edu","display_order":null,"name":"James Hollibaugh","title":"Single-cell genomics shedding light on marine Thaumarchaeota diversification"},{"id":649329,"work_id":12605988,"tagging_user_id":31550655,"tagged_user_id":124681449,"co_author_invite_id":147185,"email":"m***n@uga.edu","affiliation":"The University of Georgia","display_order":null,"name":"Mary Ann Moran","title":"Single-cell genomics shedding light on marine Thaumarchaeota diversification"}],"downloadable_attachments":[{"id":46055091,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/46055091/thumbnails/1.jpg","file_name":"Single-cell_genomics_shedding_light_on_m20160529-5313-1e8dgtl.pdf","download_url":"https://www.academia.edu/attachments/46055091/download_file?st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&","bulk_download_file_name":"Single_cell_genomics_shedding_light_on_m.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/46055091/Single-cell_genomics_shedding_light_on_m20160529-5313-1e8dgtl-libre.pdf?1464574044=\u0026response-content-disposition=attachment%3B+filename%3DSingle_cell_genomics_shedding_light_on_m.pdf\u0026Expires=1732794010\u0026Signature=gtoef74iiGGqWDNvohOMjSxg~YWazEPQ~mcCr2y-Ths2p88HcnhHp6Rs~MT5J1eFlRr6-3SWQFTEALVgZ~tj26TQA4CyzC9qotdsh9H1yunGkNXLdl5AMV3ypOO9eZjaC0jxCv93ggvUSK2TljQH--qC4aFcoJDVnQqUOyj49Q6x8LmLlMWvNTGmFtBiZL1-ymZY5n2ZVyQbHqeDLj6t5bC2~xu4SUNxWcQPtXOGqwPmoXQheJHW1mLcowme-xPcgNF-aTuDH2-R9iKRQ6NPzSYw~5itkbQ9ySXm96VxeWu6j9V2zzPWed05vqcM9DnphswDdJKeKGYv4bijLGW0dg__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"Single_cell_genomics_shedding_light_on_marine_Thaumarchaeota_diversification","translated_slug":"","page_count":24,"language":"en","content_type":"Work","owner":{"id":31550655,"first_name":"Brandon","middle_initials":null,"last_name":"Swan","page_name":"SwanBrandon","domain_name":"independent","created_at":"2015-05-26T06:21:03.429-07:00","display_name":"Brandon Swan","url":"https://independent.academia.edu/SwanBrandon"},"attachments":[{"id":46055091,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/46055091/thumbnails/1.jpg","file_name":"Single-cell_genomics_shedding_light_on_m20160529-5313-1e8dgtl.pdf","download_url":"https://www.academia.edu/attachments/46055091/download_file?st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&","bulk_download_file_name":"Single_cell_genomics_shedding_light_on_m.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/46055091/Single-cell_genomics_shedding_light_on_m20160529-5313-1e8dgtl-libre.pdf?1464574044=\u0026response-content-disposition=attachment%3B+filename%3DSingle_cell_genomics_shedding_light_on_m.pdf\u0026Expires=1732794010\u0026Signature=gtoef74iiGGqWDNvohOMjSxg~YWazEPQ~mcCr2y-Ths2p88HcnhHp6Rs~MT5J1eFlRr6-3SWQFTEALVgZ~tj26TQA4CyzC9qotdsh9H1yunGkNXLdl5AMV3ypOO9eZjaC0jxCv93ggvUSK2TljQH--qC4aFcoJDVnQqUOyj49Q6x8LmLlMWvNTGmFtBiZL1-ymZY5n2ZVyQbHqeDLj6t5bC2~xu4SUNxWcQPtXOGqwPmoXQheJHW1mLcowme-xPcgNF-aTuDH2-R9iKRQ6NPzSYw~5itkbQ9ySXm96VxeWu6j9V2zzPWed05vqcM9DnphswDdJKeKGYv4bijLGW0dg__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":923,"name":"Technology","url":"https://www.academia.edu/Documents/in/Technology"},{"id":3216,"name":"Genomics","url":"https://www.academia.edu/Documents/in/Genomics"},{"id":47884,"name":"Biological Sciences","url":"https://www.academia.edu/Documents/in/Biological_Sciences"},{"id":54433,"name":"Phylogeny","url":"https://www.academia.edu/Documents/in/Phylogeny"},{"id":58054,"name":"Environmental Sciences","url":"https://www.academia.edu/Documents/in/Environmental_Sciences"},{"id":58564,"name":"Single cell analysis","url":"https://www.academia.edu/Documents/in/Single_cell_analysis"},{"id":104196,"name":"Archaea","url":"https://www.academia.edu/Documents/in/Archaea"},{"id":1795281,"name":"Oceans and Seas","url":"https://www.academia.edu/Documents/in/Oceans_and_Seas"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="12605987"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/12605987/High_throughput_single_cell_sequencing_identifies_photoheterotrophs_and_chemoautotrophs_in_freshwater_bacterioplankton"><img alt="Research paper thumbnail of High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton" class="work-thumbnail" src="https://attachments.academia-assets.com/46055097/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605987/High_throughput_single_cell_sequencing_identifies_photoheterotrophs_and_chemoautotrophs_in_freshwater_bacterioplankton">High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/SwanBrandon">Brandon Swan</a> and <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/DashiellMasland">Dashiell Masland</a></span></div><div class="wp-workCard_item"><span>The ISME Journal</span><span>, 2012</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="43ff456256dd843034b7d8bd0f5b028f" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055097,"asset_id":12605987,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055097/download_file?st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605987"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="12605987"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 12605987; 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However, their abundance and taxonomic identities remain largely unknown. We used a combination of single-cell and metagenomic DNA sequencing to study the predominant photoheterotrophs and chemoautotrophs inhabiting the euphotic zone of temperate, physicochemically diverse freshwater lakes. Multi-locus sequencing of 712 single amplified genomes, generated by fluorescence-activated cell sorting and whole genome multiple displacement amplification, showed that most of the cosmopolitan freshwater clusters contain photoheterotrophs. These comprised at least 10-23% of bacterioplankton, and RBs were the dominant fraction. Our data demonstrate that Actinobacteria, including clusters acI, Luna and acSTL, are the predominant freshwater RBs. We significantly broaden the known taxonomic range of freshwater RBs, to include Alpha-, Beta-, Gamma-and Deltaproteobacteria, Verrucomicrobia and Sphingobacteria. By sequencing single cells, we found evidence for inter-phyla horizontal gene transfer and recombination of rhodopsin genes and identified specific taxonomic groups involved in these evolutionary processes. Our data suggest that members of the ubiquitous betaproteobacteria Polynucleobacter spp. are the dominant AAPs in temperate freshwater lakes. Furthermore, the RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) gene was found in several single cells of Betaproteobacteria, Bacteroidetes and Gammaproteobacteria, suggesting that chemoautotrophs may be more prevalent among aerobic bacterioplankton than previously thought. This study demonstrates the power of single-cell DNA sequencing addressing previously unresolved questions about the metabolic potential and evolutionary histories of uncultured microorganisms, which dominate most natural environments.","publication_date":{"day":null,"month":null,"year":2012,"errors":{}},"publication_name":"The ISME Journal","grobid_abstract_attachment_id":46055097},"translated_abstract":null,"internal_url":"https://www.academia.edu/12605987/High_throughput_single_cell_sequencing_identifies_photoheterotrophs_and_chemoautotrophs_in_freshwater_bacterioplankton","translated_internal_url":"","created_at":"2015-05-26T06:21:41.227-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":31550655,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[{"id":649327,"work_id":12605987,"tagging_user_id":31550655,"tagged_user_id":52993821,"co_author_invite_id":245294,"email":"m***i@bigelow.org","display_order":0,"name":"Michael Sieracki","title":"High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton"},{"id":649351,"work_id":12605987,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":215686,"email":"m***z@ua.es","display_order":null,"name":"M. 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Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres" class="work-thumbnail" src="https://attachments.academia-assets.com/46055079/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605986/Genomic_and_Metabolic_Diversity_of_Marine_Group_I_Thaumarchaeota_in_the_Mesopelagic_of_Two_Subtropical_Gyres">Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/SwanBrandon">Brandon Swan</a> and <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/DashiellMasland">Dashiell Masland</a></span></div><div class="wp-workCard_item"><span>PLoS ONE</span><span>, 2014</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="cac0b6fcb12dace81d42d6f1fbb42edd" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055079,"asset_id":12605986,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055079/download_file?st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605986"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span 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WowProfile.WorkStripView({ el: this, workJSON: {"id":12605986,"title":"Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres","translated_title":"","metadata":{"grobid_abstract":"Marine Group I (MGI) Thaumarchaeota are one of the most abundant and cosmopolitan chemoautotrophs within the global dark ocean. To date, no representatives of this archaeal group retrieved from the dark ocean have been successfully cultured. We used single cell genomics to investigate the genomic and metabolic diversity of thaumarchaea within the mesopelagic of the subtropical North Pacific and South Atlantic Ocean. Phylogenetic and metagenomic recruitment analysis revealed that MGI single amplified genomes (SAGs) are genetically and biogeographically distinct from existing thaumarchaea cultures obtained from surface waters. Confirming prior studies, we found genes encoding proteins for aerobic ammonia oxidation and the hydrolysis of urea, which may be used for energy production, as well as genes involved in 3-hydroxypropionate/4-hydroxybutyrate and oxidative tricarboxylic acid pathways. A large proportion of protein sequences identified in MGI SAGs were absent in the marine cultures Cenarchaeum symbiosum and Nitrosopumilus maritimus, thus expanding the predicted protein space for this archaeal group. Identifiable genes located on genomic islands with low metagenome recruitment capacity were enriched in cellular defense functions, likely in response to viral infections or grazing. We show that MGI Thaumarchaeota in the dark ocean may have more flexibility in potential energy sources and adaptations to biotic interactions than the existing, surface-ocean cultures.","publication_date":{"day":null,"month":null,"year":2014,"errors":{}},"publication_name":"PLoS ONE","grobid_abstract_attachment_id":46055079},"translated_abstract":null,"internal_url":"https://www.academia.edu/12605986/Genomic_and_Metabolic_Diversity_of_Marine_Group_I_Thaumarchaeota_in_the_Mesopelagic_of_Two_Subtropical_Gyres","translated_internal_url":"","created_at":"2015-05-26T06:21:41.051-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":31550655,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[{"id":649339,"work_id":12605986,"tagging_user_id":31550655,"tagged_user_id":6765232,"co_author_invite_id":null,"email":"t***e@lbl.gov","affiliation":"Lawrence Berkeley National Laboratory","display_order":null,"name":"Tanja Woyke","title":"Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres"},{"id":649350,"work_id":12605986,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":215686,"email":"m***z@ua.es","display_order":null,"name":"M. 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href="https://www.academia.edu/12554217/Insights_into_the_phylogeny_and_coding_potential_of_microbial_dark_matter">Insights into the phylogeny and coding potential of microbial dark matter</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/EstherGies">Esther Gies</a>, <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/SwanBrandon">Brandon Swan</a>, and <a class="" data-click-track="profile-work-strip-authors" href="https://lbl.academia.edu/PatrickSchwientek">Patrick Schwientek</a></span></div><div class="wp-workCard_item"><span>Nature</span><span>, 2013</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="e41041950c0aaaab6df45b215a33c330" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" 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"profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="12605985"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/12605985/Biodiversity_and_biogeography_of_phages_in_modern_stromatolites_and_thrombolites"><img alt="Research paper thumbnail of Biodiversity and biogeography of phages in modern stromatolites and thrombolites" class="work-thumbnail" src="https://attachments.academia-assets.com/46055090/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605985/Biodiversity_and_biogeography_of_phages_in_modern_stromatolites_and_thrombolites">Biodiversity and biogeography of phages in modern stromatolites and thrombolites</a></div><div class="wp-workCard_item"><span>Nature</span><span>, 2008</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="ad26795ecc6f691eb2113623ab2c7edf" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055090,"asset_id":12605985,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055090/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605985"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span 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Sediments","url":"https://www.academia.edu/Documents/in/Geologic_Sediments"},{"id":2467566,"name":"Molecular Sequence Data","url":"https://www.academia.edu/Documents/in/Molecular_Sequence_Data"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="12605984"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/12605984/Functional_metagenomic_profiling_of_nine_biomes"><img alt="Research paper thumbnail of Functional metagenomic profiling of nine biomes" class="work-thumbnail" src="https://attachments.academia-assets.com/46055078/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605984/Functional_metagenomic_profiling_of_nine_biomes">Functional metagenomic profiling of nine biomes</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/SwanBrandon">Brandon Swan</a> and <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/JohnPaul155">John Paul</a></span></div><div class="wp-workCard_item"><span>Nature</span><span>, 2008</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="24bd69374efb8f192d26de28422b761b" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055078,"asset_id":12605984,"asset_type":"Work","button_location":"profile"}" 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$(".js-view-count[data-work-id=12605984]").text(description); $(".js-view-count[data-work-id=12605984]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 12605984; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='12605984']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 12605984, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "24bd69374efb8f192d26de28422b761b" } } $('.js-work-strip[data-work-id=12605984]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":12605984,"title":"Functional metagenomic profiling of nine biomes","translated_title":"","metadata":{"grobid_abstract":"Microbial activities shape the biogeochemistry of the planet 1,2 and macroorganism health 3 . Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for example, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is hampered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional diversity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.","publication_date":{"day":null,"month":null,"year":2008,"errors":{}},"publication_name":"Nature","grobid_abstract_attachment_id":46055078},"translated_abstract":null,"internal_url":"https://www.academia.edu/12605984/Functional_metagenomic_profiling_of_nine_biomes","translated_internal_url":"","created_at":"2015-05-26T06:21:40.343-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":31550655,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[{"id":649344,"work_id":12605984,"tagging_user_id":31550655,"tagged_user_id":189133207,"co_author_invite_id":245295,"email":"d***e@gmail.com","affiliation":"University of California, Santa Barbara","display_order":0,"name":"David Valentine","title":"Functional metagenomic profiling of nine biomes"},{"id":649280,"work_id":12605984,"tagging_user_id":31550655,"tagged_user_id":32737043,"co_author_invite_id":245276,"email":"l***r@icr.ac.uk","display_order":null,"name":"L. L","title":"Functional metagenomic profiling of nine biomes"},{"id":649277,"work_id":12605984,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":245275,"email":"a***f@udc.es","display_order":null,"name":"Angly F","title":"Functional metagenomic profiling of nine biomes"},{"id":649272,"work_id":12605984,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":233773,"email":"j***l@seas.marine.usf.edu","display_order":null,"name":"John Paul","title":"Functional metagenomic profiling of nine biomes"},{"id":649319,"work_id":12605984,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":245291,"email":"r***s@mail.sdsu.edu","display_order":null,"name":"Genivaldo Silva","title":"Functional metagenomic profiling of nine biomes"},{"id":649279,"work_id":12605984,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":214821,"email":"c***2@dgeec.mec.pt","display_order":null,"name":"Desnues C","title":"Functional metagenomic profiling of nine biomes"},{"id":649281,"work_id":12605984,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":245277,"email":"p***s@effem.com","display_order":null,"name":"Paul J","title":"Functional metagenomic profiling of nine biomes"},{"id":649278,"work_id":12605984,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":232411,"email":"m***e@anu.edu.au","display_order":null,"name":"Breitbart M","title":"Functional metagenomic profiling of nine biomes"},{"id":649321,"work_id":12605984,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":245292,"email":"m***s@lbl.gov","display_order":null,"name":"Matthew Haynes","title":"Functional metagenomic profiling of nine biomes"},{"id":649273,"work_id":12605984,"tagging_user_id":31550655,"tagged_user_id":31610185,"co_author_invite_id":189838,"email":"j***l@marine.usf.edu","display_order":null,"name":"John Paul","title":"Functional metagenomic profiling of nine 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$a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="12605983"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/12605983/Zooplankton_life_cycles_Direct_documentation_of_pelagic_births_and_deaths_relative_to_diapausing_egg_production"><img alt="Research paper thumbnail of Zooplankton life cycles: Direct documentation of pelagic births and deaths relative to diapausing egg production" class="work-thumbnail" src="https://attachments.academia-assets.com/46055032/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605983/Zooplankton_life_cycles_Direct_documentation_of_pelagic_births_and_deaths_relative_to_diapausing_egg_production">Zooplankton life cycles: Direct documentation of pelagic births and deaths relative to diapausing egg production</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/SwanBrandon">Brandon Swan</a> and <a class="" data-click-track="profile-work-strip-authors" href="https://epa.academia.edu/TaylorJarnagin">Taylor Jarnagin</a></span></div><div class="wp-workCard_item"><span>Limnology and Oceanography</span><span>, 2004</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="3234b142969c5407088977578fa61847" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" 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waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "3234b142969c5407088977578fa61847" } } $('.js-work-strip[data-work-id=12605983]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":12605983,"title":"Zooplankton life cycles: Direct documentation of pelagic births and deaths relative to diapausing egg production","translated_title":"","metadata":{"grobid_abstract":"Zooplankton demographics operate over multiple time scales corresponding to pelagic parthenogenetic generations, an overwintering stage, and an ''egg bank.'' Comparisons of pelagic birth and death rates with seasonal diapausing egg production provide insights into local species persistence. The spiny cladoceran (Bythotrephes) possesses morphological adaptations (spines and thick-walled diapausing eggs) that lessen, but do not eliminate, predation effects by fish. Because caudal spines are retained throughout life and are indigestible in fish guts, spine accumulation in sediment traps directly documents patterns of seasonal mortality. Here, we contrast deposition of spines and diapausing eggs in a recently colonized inland lake (Lake Michigamme) with deposition in a larger source lake (Lake Michigan). Direct mortality estimates at the inland lake correspond well with traditional indirect estimates from egg ratio techniques. Although spines are effective against abundant small fish in the inland lake, individuals are susceptible to ingestion by late-season young of year and larger fish. Laboratory experiments confirm that fish are responsible for spine breakage in the water column, accounting for an estimated 62-71% of seasonal mortality. Effects of late-season predation are lessened because diapausing eggs survive gut passage, yet yearly production of diapausing eggs is low in Lake Michigamme. A more balanced pelagic birth(death) to diapausing egg relationship exists in Lake Michigan, probably because egg-carrying adults find better refuge in central, deeper waters. Since spines catch on seines and diapausing eggs survive gut passage, use of bait fish and live wells promotes Bythotrephes dispersal.","publication_date":{"day":null,"month":null,"year":2004,"errors":{}},"publication_name":"Limnology and Oceanography","grobid_abstract_attachment_id":46055032},"translated_abstract":null,"internal_url":"https://www.academia.edu/12605983/Zooplankton_life_cycles_Direct_documentation_of_pelagic_births_and_deaths_relative_to_diapausing_egg_production","translated_internal_url":"","created_at":"2015-05-26T06:21:40.193-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":31550655,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[{"id":649302,"work_id":12605983,"tagging_user_id":31550655,"tagged_user_id":12177307,"co_author_invite_id":null,"email":"j***r@epa.gov","affiliation":"United States Environmental Protection Agency","display_order":0,"name":"Taylor Jarnagin","title":"Zooplankton life cycles: Direct documentation of pelagic births and deaths relative to diapausing egg production"},{"id":649304,"work_id":12605983,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":245289,"email":"t***n@aol.com","display_order":null,"name":"S. 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="12605982"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/12605982/Spatial_and_temporal_patterns_of_transparency_and_light_attenuation_in_the_Salton_Sea_California_1997_1999"><img alt="Research paper thumbnail of Spatial and temporal patterns of transparency and light attenuation in the Salton Sea, California, 1997–1999" class="work-thumbnail" src="https://attachments.academia-assets.com/46055074/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605982/Spatial_and_temporal_patterns_of_transparency_and_light_attenuation_in_the_Salton_Sea_California_1997_1999">Spatial and temporal patterns of transparency and light attenuation in the Salton Sea, California, 1997–1999</a></div><div class="wp-workCard_item"><span>Lake and Reservoir Management</span><span>, 2007</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="9b70b6447d4f32500703aac6ad586fe0" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055074,"asset_id":12605982,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055074/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605982"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="12605982"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 12605982; 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dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "9b70b6447d4f32500703aac6ad586fe0" } } $('.js-work-strip[data-work-id=12605982]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":12605982,"title":"Spatial and temporal patterns of transparency and light attenuation in the Salton Sea, California, 1997–1999","translated_title":"","metadata":{"grobid_abstract":"Swan, B.K., K.M. Reifel, M.A. Tiffany, J.M. Watts and S.H. Hurlbert. 2007. Spatial and temporal patterns of transparency and light attenuation in the Salton Sea, California -1999 Transparency, as measured by Secchi disk depth (SD), and light attenuation (K d (PAR)) were measured in the Salton Sea in 1997-1999. Linear regression models were used to evaluate the relative importance of phytoplankton and non-phytoplankton substances in determining SD and K d (PAR). Paired measurements of SD and K d (PAR) made in 1999 were used to track relative changes in the importance of light absorption and scattering processes. Phytoplankton biomass was a poor predictor of both SD and K d (PAR) at mid-lake stations, and this is most likely due to high concentrations of non-phytoplankton substances such as inorganic particulate matter in the Salton Sea. During strong windstorms in the warmer part of the year, the upper water column mixes with hydrogen sulfide-laden bottom waters, causing large crashes in plankton populations. This previously reported phenomenon also strongly affects the light regime through the production of gypsum crystals, which scatter large portions of penetrating light. 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="12605979"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/12605979/Potential_for_chemolithoautotrophy_among_ubiquitous_bacteria_lineages_in_the_dark_ocean"><img alt="Research paper thumbnail of Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean" class="work-thumbnail" src="https://attachments.academia-assets.com/46055100/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605979/Potential_for_chemolithoautotrophy_among_ubiquitous_bacteria_lineages_in_the_dark_ocean">Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/SwanBrandon">Brandon Swan</a>, <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/PoultonN">Nicole Poulton</a>, <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/DashiellMasland">Dashiell Masland</a>, and <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/ChristinaPreston1">Christina Preston</a></span></div><div class="wp-workCard_item"><span>Science (New York, N.Y.)</span><span>, Jan 2, 2011</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Recent studies suggest that unidentified prokaryotes fix inorganic carbon at globally significant...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Recent studies suggest that unidentified prokaryotes fix inorganic carbon at globally significant rates in the immense dark ocean. Using single-cell sorting and whole-genome amplification of prokaryotes from two subtropical gyres, we obtained genomic DNA from 738 cells representing most cosmopolitan lineages. Multiple cells of Deltaproteobacteria cluster SAR324, Gammaproteobacteria clusters ARCTIC96BD-19 and Agg47, and some Oceanospirillales from the lower mesopelagic contained ribulose-1,5-bisphosphate carboxylase-oxygenase and sulfur oxidation genes. These results corroborated community DNA and RNA profiling from diverse geographic regions. The SAR324 genomes also suggested C(1) metabolism and a particle-associated life-style. Microautoradiography and fluorescence in situ hybridization confirmed bicarbonate uptake and particle association of SAR324 cells. Our study suggests potential chemolithoautotrophy in several uncultured Proteobacteria lineages that are ubiquitous in the dark...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="c7e589a4dc5965916a4ce4c43946e4ff" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055100,"asset_id":12605979,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055100/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605979"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="12605979"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 12605979; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=12605979]").text(description); $(".js-view-count[data-work-id=12605979]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 12605979; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='12605979']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 12605979, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "c7e589a4dc5965916a4ce4c43946e4ff" } } $('.js-work-strip[data-work-id=12605979]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":12605979,"title":"Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean","translated_title":"","metadata":{"abstract":"Recent studies suggest that unidentified prokaryotes fix inorganic carbon at globally significant rates in the immense dark ocean. Using single-cell sorting and whole-genome amplification of prokaryotes from two subtropical gyres, we obtained genomic DNA from 738 cells representing most cosmopolitan lineages. Multiple cells of Deltaproteobacteria cluster SAR324, Gammaproteobacteria clusters ARCTIC96BD-19 and Agg47, and some Oceanospirillales from the lower mesopelagic contained ribulose-1,5-bisphosphate carboxylase-oxygenase and sulfur oxidation genes. These results corroborated community DNA and RNA profiling from diverse geographic regions. The SAR324 genomes also suggested C(1) metabolism and a particle-associated life-style. Microautoradiography and fluorescence in situ hybridization confirmed bicarbonate uptake and particle association of SAR324 cells. 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dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="12605978"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/12605978/Unveiling_in_situ_interactions_between_marine_protists_and_bacteria_through_single_cell_sequencing"><img alt="Research paper thumbnail of Unveiling in situ interactions between marine protists and bacteria through single cell sequencing" class="work-thumbnail" src="https://attachments.academia-assets.com/46055066/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605978/Unveiling_in_situ_interactions_between_marine_protists_and_bacteria_through_single_cell_sequencing">Unveiling in situ interactions between marine protists and bacteria through single cell sequencing</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/SwanBrandon">Brandon Swan</a> and <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/DashiellMasland">Dashiell Masland</a></span></div><div class="wp-workCard_item"><span>The ISME journal</span><span>, 2012</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Heterotrophic protists are a highly diverse and biogeochemically significant component of marine ...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Heterotrophic protists are a highly diverse and biogeochemically significant component of marine ecosystems, yet little is known about their species-specific prey preferences and symbiotic interactions in situ. Here we demonstrate how these previously unresolved questions can be addressed by sequencing the eukaryote and bacterial SSU rRNA genes from individual, uncultured protist cells collected from their natural marine environment and sorted by flow cytometry. We detected Pelagibacter ubique in association with a MAST-4 protist, an actinobacterium in association with a chrysophyte and three bacteroidetes in association with diverse protist groups. The presence of identical phylotypes among the putative prey and the free bacterioplankton in the same sample provides evidence for predator-prey interactions. Our results also suggest a discovery of novel symbionts, distantly related to Rickettsiales and the candidate divisions ZB3 and TG2, associated with Cercozoa and Chrysophyta cells...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="0fd9dd311b540563e2dbf7a4822489dc" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055066,"asset_id":12605978,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055066/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605978"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="12605978"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 12605978; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=12605978]").text(description); $(".js-view-count[data-work-id=12605978]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 12605978; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='12605978']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 12605978, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "0fd9dd311b540563e2dbf7a4822489dc" } } $('.js-work-strip[data-work-id=12605978]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":12605978,"title":"Unveiling in situ interactions between marine protists and bacteria through single cell sequencing","translated_title":"","metadata":{"abstract":"Heterotrophic protists are a highly diverse and biogeochemically significant component of marine ecosystems, yet little is known about their species-specific prey preferences and symbiotic interactions in situ. 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genomes of active polysaccharide degraders: an unexpected contribution of verrucomicrobia" class="work-thumbnail" src="https://attachments.academia-assets.com/46055108/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605977/Capturing_single_cell_genomes_of_active_polysaccharide_degraders_an_unexpected_contribution_of_verrucomicrobia">Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of verrucomicrobia</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/SwanBrandon">Brandon Swan</a>, <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/ChrisDetter">Chris Detter</a>, <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/WendyBellows">Wendy Bellows</a>, and <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/DashiellMasland">Dashiell Masland</a></span></div><div class="wp-workCard_item"><span>PloS one</span><span>, 2012</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Microbial hydrolysis of polysaccharides is critical to ecosystem functioning and is of great inte...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Microbial hydrolysis of polysaccharides is critical to ecosystem functioning and is of great interest in diverse biotechnological applications, such as biofuel production and bioremediation. Here we demonstrate the use of a new, efficient approach to recover genomes of active polysaccharide degraders from natural, complex microbial assemblages, using a combination of fluorescently labeled substrates, fluorescence-activated cell sorting, and single cell genomics. We employed this approach to analyze freshwater and coastal bacterioplankton for degraders of laminarin and xylan, two of the most abundant storage and structural polysaccharides in nature. Our results suggest that a few phylotypes of Verrucomicrobia make a considerable contribution to polysaccharide degradation, although they constituted only a minor fraction of the total microbial community. 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hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/12605995/Depth_Distribution_of_Archaeal_Diversity_and_Community_Composition_Across_Steep_Geochemical_Gradients_in_Anoxic_Sediments_of_a_Hypersaline_Lake"><img alt="Research paper thumbnail of Depth Distribution of Archaeal Diversity and Community Composition Across Steep Geochemical Gradients in Anoxic Sediments of a Hypersaline Lake" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605995/Depth_Distribution_of_Archaeal_Diversity_and_Community_Composition_Across_Steep_Geochemical_Gradients_in_Anoxic_Sediments_of_a_Hypersaline_Lake">Depth Distribution of Archaeal Diversity and Community Composition Across Steep Geochemical Gradients in Anoxic Sediments of a Hypersaline Lake</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Patterns in Archaeal diversity and community composition were investigated in the anoxic sediment...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Patterns in Archaeal diversity and community composition were investigated in the anoxic sediments of the Salton Sea, California&#39;s largest lake. The sediments of this lake contain strong gradients in salinity and organic carbon, which provide a natural setting to examine the influence of these gradients on Archaeal communities. 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Luo</a>, and <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/JessicaLabont%C3%A9">Jessica Labonté</a></span></div><div class="wp-workCard_item"><span>The ISME journal</span><span>, Jan 7, 2015</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Viral infections dynamically alter the composition and metabolic potential of marine microbial co...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Viral infections dynamically alter the composition and metabolic potential of marine microbial communities and the evolutionary trajectories of host populations with resulting feedback on biogeochemical cycles. It is quite possible that all microbial populations in the ocean are impacted by viral infections. Our knowledge of virus-host relationships, however, has been limited to a minute fraction of cultivated host groups. Here, we utilized single-cell sequencing to obtain genomic blueprints of viruses inside or attached to individual bacterial and archaeal cells captured in their native environment, circumventing the need for host and virus cultivation. A combination of comparative genomics, metagenomic fragment recruitment, sequence anomalies and irregularities in sequence coverage depth and genome recovery were utilized to detect viruses and to decipher modes of virus-host interactions. Members of all three tailed phage families were identified in 20 out of 58 phylogenetically an...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="6fa5325e94dfff31cbd251cc3eea3313" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055146,"asset_id":12605994,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055146/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&st=MTczMjc5MDQwOSw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605994"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="12605994"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 12605994; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=12605994]").text(description); $(".js-view-count[data-work-id=12605994]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 12605994; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='12605994']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 12605994, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "6fa5325e94dfff31cbd251cc3eea3313" } } $('.js-work-strip[data-work-id=12605994]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":12605994,"title":"Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton","translated_title":"","metadata":{"abstract":"Viral infections dynamically alter the composition and metabolic potential of marine microbial communities and the evolutionary trajectories of host populations with resulting feedback on biogeochemical cycles. 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Two Synchaeta species, rotifers not previously reported from the Sea, were abundant in winter and spring and predation on these may have permitted the copepod to persist at low levels through the winter. There were two major changes in metazooplankton dynamics since 1954-1956 in addition to the appearance of the two synchaetid rotifers in the fauna. First, there are now much lower densities of barnacle and polychaete larvae in the fall, probably due to the invasion of the zooplanktivorous fish, tilapia. 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Viromic studi...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Metagenomics has opened new windows on investigating viral diversity and functions. Viromic studies typically require large sample volumes and filtration through 0.2 μm pore-size filters, consequently excluding or under-sampling tailed and very large viruses. We have optimized a targeted viromic approach that employs fluorescence-activated sorting and whole genome amplification to produce dsDNA-enriched libraries from discrete viral populations from a 1-ml water sample. Using this approach on an environmental sample from the Patagonian Shelf, we produced three distinct libraries. One of the virus libraries was dominated (79.65% of sequences with known viral homology) by giant viruses from the Mimiviridae and Phycodnaviridae families, while the two other viromes were dominated by smaller phycodnaviruses, cyanophages and other bacteriophages. The estimated genotypic richness and diversity in our sorted viromes, with 52-163 estimated genotypes, was much lower than in previous virome re...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="6893ecd79cc017c68691da770ef27a74" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055133,"asset_id":12605992,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055133/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605992"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="12605992"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 12605992; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=12605992]").text(description); $(".js-view-count[data-work-id=12605992]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 12605992; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='12605992']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 12605992, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "6893ecd79cc017c68691da770ef27a74" } } $('.js-work-strip[data-work-id=12605992]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":12605992,"title":"Marine viruses, a genetic reservoir revealed by targeted viromics","translated_title":"","metadata":{"abstract":"Metagenomics has opened new windows on investigating viral diversity and functions. 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The estimated genotypic richness and diversity in our sorted viromes, with 52-163 estimated genotypes, was much lower than in previous virome re...","publication_date":{"day":null,"month":null,"year":2014,"errors":{}},"publication_name":"The ISME journal"},"translated_abstract":"Metagenomics has opened new windows on investigating viral diversity and functions. Viromic studies typically require large sample volumes and filtration through 0.2 μm pore-size filters, consequently excluding or under-sampling tailed and very large viruses. We have optimized a targeted viromic approach that employs fluorescence-activated sorting and whole genome amplification to produce dsDNA-enriched libraries from discrete viral populations from a 1-ml water sample. Using this approach on an environmental sample from the Patagonian Shelf, we produced three distinct libraries. One of the virus libraries was dominated (79.65% of sequences with known viral homology) by giant viruses from the Mimiviridae and Phycodnaviridae families, while the two other viromes were dominated by smaller phycodnaviruses, cyanophages and other bacteriophages. The estimated genotypic richness and diversity in our sorted viromes, with 52-163 estimated genotypes, was much lower than in previous virome re...","internal_url":"https://www.academia.edu/12605992/Marine_viruses_a_genetic_reservoir_revealed_by_targeted_viromics","translated_internal_url":"","created_at":"2015-05-26T06:21:41.790-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":31550655,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[{"id":649294,"work_id":12605992,"tagging_user_id":31550655,"tagged_user_id":30766012,"co_author_invite_id":null,"email":"w***w@pml.ac.uk","display_order":null,"name":"William Wilson","title":"Marine viruses, a genetic reservoir revealed by targeted viromics"},{"id":649295,"work_id":12605992,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":245287,"email":"j***z@bigelow.org","display_order":null,"name":"Joaquín Martínez Martínez","title":"Marine viruses, a genetic reservoir revealed by targeted viromics"}],"downloadable_attachments":[{"id":46055133,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/46055133/thumbnails/1.jpg","file_name":"Marine_viruses_a_genetic_reservoir_revea20160529-733-6o9g7u.pdf","download_url":"https://www.academia.edu/attachments/46055133/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&","bulk_download_file_name":"Marine_viruses_a_genetic_reservoir_revea.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/46055133/Marine_viruses_a_genetic_reservoir_revea20160529-733-6o9g7u-libre.pdf?1464574039=\u0026response-content-disposition=attachment%3B+filename%3DMarine_viruses_a_genetic_reservoir_revea.pdf\u0026Expires=1732794009\u0026Signature=IjttxquEw9rrxWBndzPXJ7yNT8~qUdepVg52jaK8h4IdHBPdxxrm9jySW~kPsY71tJqCDARkxDcN9mM7KiTqIjh1B1rWXGHufh71Vq~Cxb3VKEXqVjhwb0swDpkOAY2YMKpYi0Niuy0RsadfmQ4jwUnH8e8x5O0V3rLzjBo97TQ-SjgjkniHZ9Mjn4bMqBh1p-BKZeLF8Hj3gX6mRECp9gAxyo0P1Ys2fTPPdsRG1PJ2RpdhCR-We4fUmRqtFGpDHShy8hv2tTArRhEHmt-HePARLO0eWlQRPUcpm~zNbKznjg1jngDd~PGxJvtCmuVGQq4yzE2teq~z1RN3l7vdUw__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"Marine_viruses_a_genetic_reservoir_revealed_by_targeted_viromics","translated_slug":"","page_count":29,"language":"en","content_type":"Work","owner":{"id":31550655,"first_name":"Brandon","middle_initials":null,"last_name":"Swan","page_name":"SwanBrandon","domain_name":"independent","created_at":"2015-05-26T06:21:03.429-07:00","display_name":"Brandon Swan","url":"https://independent.academia.edu/SwanBrandon"},"attachments":[{"id":46055133,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/46055133/thumbnails/1.jpg","file_name":"Marine_viruses_a_genetic_reservoir_revea20160529-733-6o9g7u.pdf","download_url":"https://www.academia.edu/attachments/46055133/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&","bulk_download_file_name":"Marine_viruses_a_genetic_reservoir_revea.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/46055133/Marine_viruses_a_genetic_reservoir_revea20160529-733-6o9g7u-libre.pdf?1464574039=\u0026response-content-disposition=attachment%3B+filename%3DMarine_viruses_a_genetic_reservoir_revea.pdf\u0026Expires=1732794010\u0026Signature=L-0ygEB3TVGBb1Ca1DEu3-mtld3-UHV1A-SJxN1Hj26qhEi3Czf03bmmZRjAEKx8GHjf0MVby9aVUH8IK-9e1jCS3I54pNDZ7CiQHsaHXFhNr4QGTLuGFJ~3uKgrI1V6B5qEKNYlLtKdppWonU-J~yEuvT4-r3heOKsp-dibdrOS1hvxsmhNnpFWXzxPDoyNIclk66rhdmZsRz6ssPVEWu9n54RkcRVfGtJWEUB8x0yG5k3hLqwjSmkuDYEDq8jThKINmNj3RnXzwc-peFVbC~E~pJsL2NsOyuDR52mEUHSK0aMMf9eFZFlrOnyQ-W3~nVg9pCIOeAxZgYQNIxDKGw__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":923,"name":"Technology","url":"https://www.academia.edu/Documents/in/Technology"},{"id":8090,"name":"Bacteriophages","url":"https://www.academia.edu/Documents/in/Bacteriophages"},{"id":21948,"name":"Metagenomics","url":"https://www.academia.edu/Documents/in/Metagenomics"},{"id":47884,"name":"Biological Sciences","url":"https://www.academia.edu/Documents/in/Biological_Sciences"},{"id":54433,"name":"Phylogeny","url":"https://www.academia.edu/Documents/in/Phylogeny"},{"id":58054,"name":"Environmental Sciences","url":"https://www.academia.edu/Documents/in/Environmental_Sciences"},{"id":93497,"name":"Atlantic Ocean","url":"https://www.academia.edu/Documents/in/Atlantic_Ocean"},{"id":184467,"name":"Seawater","url":"https://www.academia.edu/Documents/in/Seawater"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="12605991"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/12605991/Evolutionary_analysis_of_a_streamlined_lineage_of_surface_ocean_Roseobacters"><img alt="Research paper thumbnail of Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters" class="work-thumbnail" src="https://attachments.academia-assets.com/46055084/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605991/Evolutionary_analysis_of_a_streamlined_lineage_of_surface_ocean_Roseobacters">Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/SwanBrandon">Brandon Swan</a> and <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/AustinHughes2">Austin Hughes</a></span></div><div class="wp-workCard_item"><span>The ISME Journal</span><span>, 2014</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="8e634a30b2e97939469d967690d20f29" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055084,"asset_id":12605991,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055084/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605991"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="12605991"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 12605991; 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dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "8e634a30b2e97939469d967690d20f29" } } $('.js-work-strip[data-work-id=12605991]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":12605991,"title":"Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters","translated_title":"","metadata":{"publication_date":{"day":null,"month":null,"year":2014,"errors":{}},"publication_name":"The ISME Journal"},"translated_abstract":null,"internal_url":"https://www.academia.edu/12605991/Evolutionary_analysis_of_a_streamlined_lineage_of_surface_ocean_Roseobacters","translated_internal_url":"","created_at":"2015-05-26T06:21:41.628-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":31550655,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[{"id":649291,"work_id":12605991,"tagging_user_id":31550655,"tagged_user_id":34775074,"co_author_invite_id":245284,"email":"a***n@biol.sc.edu","display_order":0,"name":"Austin Hughes","title":"Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters"},{"id":649292,"work_id":12605991,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":245285,"email":"a***n@biols.sc.edu","display_order":null,"name":"Austin Hughes","title":"Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters"},{"id":649332,"work_id":12605991,"tagging_user_id":31550655,"tagged_user_id":31620842,"co_author_invite_id":236704,"email":"h***6@gmail.com","display_order":null,"name":"H. Luo","title":"Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters"},{"id":649293,"work_id":12605991,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":245286,"email":"a***l@blogmail.cc","display_order":null,"name":"Hughes Al","title":"Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters"},{"id":649290,"work_id":12605991,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":245283,"email":"a***n@biol.ac.edu","display_order":null,"name":"Austin Hughes","title":"Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters"},{"id":649330,"work_id":12605991,"tagging_user_id":31550655,"tagged_user_id":124681449,"co_author_invite_id":147185,"email":"m***n@uga.edu","affiliation":"The University of Georgia","display_order":null,"name":"Mary Ann Moran","title":"Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters"}],"downloadable_attachments":[{"id":46055084,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/46055084/thumbnails/1.jpg","file_name":"Evolutionary_analysis_of_a_streamlined_l20160529-20889-6j8jw7.pdf","download_url":"https://www.academia.edu/attachments/46055084/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&","bulk_download_file_name":"Evolutionary_analysis_of_a_streamlined_l.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/46055084/Evolutionary_analysis_of_a_streamlined_l20160529-20889-6j8jw7-libre.pdf?1464574042=\u0026response-content-disposition=attachment%3B+filename%3DEvolutionary_analysis_of_a_streamlined_l.pdf\u0026Expires=1732769385\u0026Signature=FfnWeS-SvEGYZSF-w4ANt3ZRt0C7Wufdai48l8d1M8noyu2aIcQ3b1orxtXbGqE-GxKfkPNXQ0uggT-CaKEljWIHmjwELd9ca3IbpgB3FLUfDbYZoI~704YlHjYBJzMxgqCKo3V28fuak2DGH0kq9FiGgBSXMkCkC77DWk5u5wcUM3r4HiRzk1G03~-HZLUJZh8INb5Z6fIKnZrZihNNHMBicMdni7Prr8qm4KRT8qLD7tMAdIZsRcgrkMuB124zMmF5UMmo7yNXBv6IhYIKXArZ1QkGhAU6KCm0RyxgaypUZFtJtLJDu3QiiAH6I6nXC3TsiD7EotiC5q~SvwSLhg__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"Evolutionary_analysis_of_a_streamlined_lineage_of_surface_ocean_Roseobacters","translated_slug":"","page_count":19,"language":"en","content_type":"Work","owner":{"id":31550655,"first_name":"Brandon","middle_initials":null,"last_name":"Swan","page_name":"SwanBrandon","domain_name":"independent","created_at":"2015-05-26T06:21:03.429-07:00","display_name":"Brandon Swan","url":"https://independent.academia.edu/SwanBrandon"},"attachments":[{"id":46055084,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/46055084/thumbnails/1.jpg","file_name":"Evolutionary_analysis_of_a_streamlined_l20160529-20889-6j8jw7.pdf","download_url":"https://www.academia.edu/attachments/46055084/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&","bulk_download_file_name":"Evolutionary_analysis_of_a_streamlined_l.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/46055084/Evolutionary_analysis_of_a_streamlined_l20160529-20889-6j8jw7-libre.pdf?1464574042=\u0026response-content-disposition=attachment%3B+filename%3DEvolutionary_analysis_of_a_streamlined_l.pdf\u0026Expires=1732769385\u0026Signature=FfnWeS-SvEGYZSF-w4ANt3ZRt0C7Wufdai48l8d1M8noyu2aIcQ3b1orxtXbGqE-GxKfkPNXQ0uggT-CaKEljWIHmjwELd9ca3IbpgB3FLUfDbYZoI~704YlHjYBJzMxgqCKo3V28fuak2DGH0kq9FiGgBSXMkCkC77DWk5u5wcUM3r4HiRzk1G03~-HZLUJZh8INb5Z6fIKnZrZihNNHMBicMdni7Prr8qm4KRT8qLD7tMAdIZsRcgrkMuB124zMmF5UMmo7yNXBv6IhYIKXArZ1QkGhAU6KCm0RyxgaypUZFtJtLJDu3QiiAH6I6nXC3TsiD7EotiC5q~SvwSLhg__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":923,"name":"Technology","url":"https://www.academia.edu/Documents/in/Technology"},{"id":4312,"name":"Genetic Drift","url":"https://www.academia.edu/Documents/in/Genetic_Drift"},{"id":4967,"name":"Molecular Evolution","url":"https://www.academia.edu/Documents/in/Molecular_Evolution"},{"id":20256,"name":"Genome Size","url":"https://www.academia.edu/Documents/in/Genome_Size"},{"id":47884,"name":"Biological Sciences","url":"https://www.academia.edu/Documents/in/Biological_Sciences"},{"id":54433,"name":"Phylogeny","url":"https://www.academia.edu/Documents/in/Phylogeny"},{"id":58054,"name":"Environmental Sciences","url":"https://www.academia.edu/Documents/in/Environmental_Sciences"},{"id":143622,"name":"Roseobacter","url":"https://www.academia.edu/Documents/in/Roseobacter"},{"id":184467,"name":"Seawater","url":"https://www.academia.edu/Documents/in/Seawater"},{"id":377566,"name":"Aquatic organisms","url":"https://www.academia.edu/Documents/in/Aquatic_organisms"},{"id":880279,"name":"Bayes Theorem","url":"https://www.academia.edu/Documents/in/Bayes_Theorem-1"},{"id":1795281,"name":"Oceans and Seas","url":"https://www.academia.edu/Documents/in/Oceans_and_Seas"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="12605989"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/12605989/Single_cell_enabled_comparative_genomics_of_a_deep_ocean_SAR11_bathytype"><img alt="Research paper thumbnail of Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype" class="work-thumbnail" src="https://attachments.academia-assets.com/46055141/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605989/Single_cell_enabled_comparative_genomics_of_a_deep_ocean_SAR11_bathytype">Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/SwanBrandon">Brandon Swan</a> and <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/BenTemperton">Ben Temperton</a></span></div><div class="wp-workCard_item"><span>The ISME Journal</span><span>, 2014</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="f57e1ade6a98d676221347750cfec00b" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055141,"asset_id":12605989,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055141/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605989"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="12605989"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 12605989; 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dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "f57e1ade6a98d676221347750cfec00b" } } $('.js-work-strip[data-work-id=12605989]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":12605989,"title":"Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype","translated_title":"","metadata":{"grobid_abstract":"Bacterioplankton of the SAR11 clade are the most abundant microorganisms in marine systems, usually representing 25% or more of the total bacterial cells in seawater worldwide. SAR11 is divided into subclades with distinct spatiotemporal distributions (ecotypes), some of which appear to be specific to deep water. Here we examine the genomic basis for deep ocean distribution of one SAR11 bathytype (depth-specific ecotype), subclade Ic. Four single-cell Ic genomes, with estimated completeness of 55%-86%, were isolated from 770 m at station ALOHA and compared with eight SAR11 surface genomes and metagenomic datasets. Subclade Ic genomes dominated metagenomic fragment recruitment below the euphotic zone. They had similar COG distributions, high local synteny and shared a large number (69%) of orthologous clusters with SAR11 surface genomes, yet were distinct at the 16S rRNA gene and amino-acid level, and formed a separate, monophyletic group in phylogenetic trees. Subclade Ic genomes were enriched in genes associated with membrane/cell wall/envelope biosynthesis and showed evidence of unique phage defenses. The majority of subclade Ic-specfic genes were hypothetical, and some were highly abundant in deep ocean metagenomic data, potentially masking mechanisms for niche differentiation. However, the evidence suggests these organisms have a similar metabolism to their surface counterparts, and that subclade Ic adaptations to the deep ocean do not involve large variations in gene content, but rather more subtle differences previously observed deep ocean genomic data, like preferential amino-acid substitutions, larger coding regions among SAR11 clade orthologs, larger intergenic regions and larger estimated average genome size.","publication_date":{"day":null,"month":null,"year":2014,"errors":{}},"publication_name":"The ISME Journal","grobid_abstract_attachment_id":46055141},"translated_abstract":null,"internal_url":"https://www.academia.edu/12605989/Single_cell_enabled_comparative_genomics_of_a_deep_ocean_SAR11_bathytype","translated_internal_url":"","created_at":"2015-05-26T06:21:41.500-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":31550655,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[{"id":649288,"work_id":12605989,"tagging_user_id":31550655,"tagged_user_id":56223722,"co_author_invite_id":189821,"email":"s***i@oregonstate.edu","display_order":0,"name":"S. Giovannoni","title":"Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype"},{"id":649340,"work_id":12605989,"tagging_user_id":31550655,"tagged_user_id":6765232,"co_author_invite_id":null,"email":"t***e@lbl.gov","affiliation":"Lawrence Berkeley National Laboratory","display_order":null,"name":"Tanja Woyke","title":"Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype"},{"id":649289,"work_id":12605989,"tagging_user_id":31550655,"tagged_user_id":31607602,"co_author_invite_id":245282,"email":"b***n@gmail.com","display_order":null,"name":"Ben Temperton","title":"Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype"},{"id":649310,"work_id":12605989,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":212180,"email":"e***g@hawaii.edu","display_order":null,"name":"Edward DeLong","title":"Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype"},{"id":649312,"work_id":12605989,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":212181,"email":"d***g@mit.edu","display_order":null,"name":"Edward DeLong","title":"Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype"},{"id":649287,"work_id":12605989,"tagging_user_id":31550655,"tagged_user_id":63834471,"co_author_invite_id":236706,"email":"z***y@gmail.com","display_order":null,"name":"Zachary Landry","title":"Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype"}],"downloadable_attachments":[{"id":46055141,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/46055141/thumbnails/1.jpg","file_name":"Single-cell_enabled_comparative_genomics20160529-5431-1cwxuyp.pdf","download_url":"https://www.academia.edu/attachments/46055141/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&","bulk_download_file_name":"Single_cell_enabled_comparative_genomics.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/46055141/Single-cell_enabled_comparative_genomics20160529-5431-1cwxuyp-libre.pdf?1464574132=\u0026response-content-disposition=attachment%3B+filename%3DSingle_cell_enabled_comparative_genomics.pdf\u0026Expires=1732794010\u0026Signature=abPnN6FSWsrgnVg1LWcOg6rVeKTPsLuIKICM6oC2naHt7c2bBk~dUwrV1uIDo0Axo8baX6phqWa21X1yUDNgRnssRhgT8WnmoV4DO6LTMLQvre1~cTiFhyM8agDvY8BpIRR7SSBxYELdMaxXORvn~S5ribrDSmWfpQHZqWK-6sSQrtQ1rasEkRsSy-KRK6yq6mL6ZI9rGNFWz3SmVYq1GR~KEXMG6tPVwCBqJD4yRY-mIfhN9VCyZiy94pQNa5YQ3W5JvNqnQzEpWq5HuL3qV-eZScqDu4LscbvJKg89S1q73YRxwrnMk9TKqBTRDr01yY82ZHVtXdj8Kg6LxjjMNQ__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"Single_cell_enabled_comparative_genomics_of_a_deep_ocean_SAR11_bathytype","translated_slug":"","page_count":56,"language":"en","content_type":"Work","owner":{"id":31550655,"first_name":"Brandon","middle_initials":null,"last_name":"Swan","page_name":"SwanBrandon","domain_name":"independent","created_at":"2015-05-26T06:21:03.429-07:00","display_name":"Brandon Swan","url":"https://independent.academia.edu/SwanBrandon"},"attachments":[{"id":46055141,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/46055141/thumbnails/1.jpg","file_name":"Single-cell_enabled_comparative_genomics20160529-5431-1cwxuyp.pdf","download_url":"https://www.academia.edu/attachments/46055141/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&","bulk_download_file_name":"Single_cell_enabled_comparative_genomics.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/46055141/Single-cell_enabled_comparative_genomics20160529-5431-1cwxuyp-libre.pdf?1464574132=\u0026response-content-disposition=attachment%3B+filename%3DSingle_cell_enabled_comparative_genomics.pdf\u0026Expires=1732794010\u0026Signature=abPnN6FSWsrgnVg1LWcOg6rVeKTPsLuIKICM6oC2naHt7c2bBk~dUwrV1uIDo0Axo8baX6phqWa21X1yUDNgRnssRhgT8WnmoV4DO6LTMLQvre1~cTiFhyM8agDvY8BpIRR7SSBxYELdMaxXORvn~S5ribrDSmWfpQHZqWK-6sSQrtQ1rasEkRsSy-KRK6yq6mL6ZI9rGNFWz3SmVYq1GR~KEXMG6tPVwCBqJD4yRY-mIfhN9VCyZiy94pQNa5YQ3W5JvNqnQzEpWq5HuL3qV-eZScqDu4LscbvJKg89S1q73YRxwrnMk9TKqBTRDr01yY82ZHVtXdj8Kg6LxjjMNQ__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":923,"name":"Technology","url":"https://www.academia.edu/Documents/in/Technology"},{"id":3216,"name":"Genomics","url":"https://www.academia.edu/Documents/in/Genomics"},{"id":47884,"name":"Biological Sciences","url":"https://www.academia.edu/Documents/in/Biological_Sciences"},{"id":54433,"name":"Phylogeny","url":"https://www.academia.edu/Documents/in/Phylogeny"},{"id":58054,"name":"Environmental Sciences","url":"https://www.academia.edu/Documents/in/Environmental_Sciences"},{"id":58564,"name":"Single cell analysis","url":"https://www.academia.edu/Documents/in/Single_cell_analysis"},{"id":184467,"name":"Seawater","url":"https://www.academia.edu/Documents/in/Seawater"},{"id":360394,"name":"Alphaproteobacteria","url":"https://www.academia.edu/Documents/in/Alphaproteobacteria"},{"id":1710970,"name":"Metagenome","url":"https://www.academia.edu/Documents/in/Metagenome"},{"id":2007776,"name":"Synteny","url":"https://www.academia.edu/Documents/in/Synteny"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="12605988"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/12605988/Single_cell_genomics_shedding_light_on_marine_Thaumarchaeota_diversification"><img alt="Research paper thumbnail of Single-cell genomics shedding light on marine Thaumarchaeota diversification" class="work-thumbnail" src="https://attachments.academia-assets.com/46055091/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605988/Single_cell_genomics_shedding_light_on_marine_Thaumarchaeota_diversification">Single-cell genomics shedding light on marine Thaumarchaeota diversification</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/SwanBrandon">Brandon Swan</a> and <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/JamesHollibaugh">James Hollibaugh</a></span></div><div class="wp-workCard_item"><span>The ISME Journal</span><span>, 2014</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="194328cd829dd2d5546d6354b892e8d8" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055091,"asset_id":12605988,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055091/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" 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Earlier studies focused on single-gene distributions were not able to link phylogenetic structure to other aspects of functional adaptation. Here, we analyzed the genome content of 46 uncultivated single Thaumarchaeota cells sampled from epi-and mesopelagic waters of subtropical, temperate and polar oceans. Phylogenomic analysis showed that populations diverged by depth, as expected, and that mesopelagic populations from different locations were well mixed. Functional analysis showed that some traits, including putative DNA photolyase and catalase genes that may be related to adaptive mechanisms to reduce light-induced damage, were found exclusively in members of the epipelagic clade. Our analysis of partial genomes has thus confirmed the depth differentiation of Thaumarchaeota populations observed previously, consistent with the distribution of putative mechanisms to reduce light-induced damage in shallow-and deep-water populations.","publication_date":{"day":null,"month":null,"year":2014,"errors":{}},"publication_name":"The ISME Journal","grobid_abstract_attachment_id":46055091},"translated_abstract":null,"internal_url":"https://www.academia.edu/12605988/Single_cell_genomics_shedding_light_on_marine_Thaumarchaeota_diversification","translated_internal_url":"","created_at":"2015-05-26T06:21:41.349-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":31550655,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[{"id":649331,"work_id":12605988,"tagging_user_id":31550655,"tagged_user_id":31620842,"co_author_invite_id":236704,"email":"h***6@gmail.com","display_order":null,"name":"H. Luo","title":"Single-cell genomics shedding light on marine Thaumarchaeota diversification"},{"id":649285,"work_id":12605988,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":245280,"email":"a***g@gmail.com","display_order":null,"name":"Chuanlun Zhang","title":"Single-cell genomics shedding light on marine Thaumarchaeota diversification"},{"id":649286,"work_id":12605988,"tagging_user_id":31550655,"tagged_user_id":31607436,"co_author_invite_id":245281,"email":"a***c@uga.edu","display_order":null,"name":"James Hollibaugh","title":"Single-cell genomics shedding light on marine Thaumarchaeota diversification"},{"id":649329,"work_id":12605988,"tagging_user_id":31550655,"tagged_user_id":124681449,"co_author_invite_id":147185,"email":"m***n@uga.edu","affiliation":"The University of Georgia","display_order":null,"name":"Mary Ann Moran","title":"Single-cell genomics shedding light on marine Thaumarchaeota diversification"}],"downloadable_attachments":[{"id":46055091,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/46055091/thumbnails/1.jpg","file_name":"Single-cell_genomics_shedding_light_on_m20160529-5313-1e8dgtl.pdf","download_url":"https://www.academia.edu/attachments/46055091/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&","bulk_download_file_name":"Single_cell_genomics_shedding_light_on_m.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/46055091/Single-cell_genomics_shedding_light_on_m20160529-5313-1e8dgtl-libre.pdf?1464574044=\u0026response-content-disposition=attachment%3B+filename%3DSingle_cell_genomics_shedding_light_on_m.pdf\u0026Expires=1732794010\u0026Signature=gtoef74iiGGqWDNvohOMjSxg~YWazEPQ~mcCr2y-Ths2p88HcnhHp6Rs~MT5J1eFlRr6-3SWQFTEALVgZ~tj26TQA4CyzC9qotdsh9H1yunGkNXLdl5AMV3ypOO9eZjaC0jxCv93ggvUSK2TljQH--qC4aFcoJDVnQqUOyj49Q6x8LmLlMWvNTGmFtBiZL1-ymZY5n2ZVyQbHqeDLj6t5bC2~xu4SUNxWcQPtXOGqwPmoXQheJHW1mLcowme-xPcgNF-aTuDH2-R9iKRQ6NPzSYw~5itkbQ9ySXm96VxeWu6j9V2zzPWed05vqcM9DnphswDdJKeKGYv4bijLGW0dg__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"Single_cell_genomics_shedding_light_on_marine_Thaumarchaeota_diversification","translated_slug":"","page_count":24,"language":"en","content_type":"Work","owner":{"id":31550655,"first_name":"Brandon","middle_initials":null,"last_name":"Swan","page_name":"SwanBrandon","domain_name":"independent","created_at":"2015-05-26T06:21:03.429-07:00","display_name":"Brandon Swan","url":"https://independent.academia.edu/SwanBrandon"},"attachments":[{"id":46055091,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/46055091/thumbnails/1.jpg","file_name":"Single-cell_genomics_shedding_light_on_m20160529-5313-1e8dgtl.pdf","download_url":"https://www.academia.edu/attachments/46055091/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&","bulk_download_file_name":"Single_cell_genomics_shedding_light_on_m.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/46055091/Single-cell_genomics_shedding_light_on_m20160529-5313-1e8dgtl-libre.pdf?1464574044=\u0026response-content-disposition=attachment%3B+filename%3DSingle_cell_genomics_shedding_light_on_m.pdf\u0026Expires=1732794010\u0026Signature=gtoef74iiGGqWDNvohOMjSxg~YWazEPQ~mcCr2y-Ths2p88HcnhHp6Rs~MT5J1eFlRr6-3SWQFTEALVgZ~tj26TQA4CyzC9qotdsh9H1yunGkNXLdl5AMV3ypOO9eZjaC0jxCv93ggvUSK2TljQH--qC4aFcoJDVnQqUOyj49Q6x8LmLlMWvNTGmFtBiZL1-ymZY5n2ZVyQbHqeDLj6t5bC2~xu4SUNxWcQPtXOGqwPmoXQheJHW1mLcowme-xPcgNF-aTuDH2-R9iKRQ6NPzSYw~5itkbQ9ySXm96VxeWu6j9V2zzPWed05vqcM9DnphswDdJKeKGYv4bijLGW0dg__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":923,"name":"Technology","url":"https://www.academia.edu/Documents/in/Technology"},{"id":3216,"name":"Genomics","url":"https://www.academia.edu/Documents/in/Genomics"},{"id":47884,"name":"Biological Sciences","url":"https://www.academia.edu/Documents/in/Biological_Sciences"},{"id":54433,"name":"Phylogeny","url":"https://www.academia.edu/Documents/in/Phylogeny"},{"id":58054,"name":"Environmental Sciences","url":"https://www.academia.edu/Documents/in/Environmental_Sciences"},{"id":58564,"name":"Single cell analysis","url":"https://www.academia.edu/Documents/in/Single_cell_analysis"},{"id":104196,"name":"Archaea","url":"https://www.academia.edu/Documents/in/Archaea"},{"id":1795281,"name":"Oceans and Seas","url":"https://www.academia.edu/Documents/in/Oceans_and_Seas"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="12605987"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/12605987/High_throughput_single_cell_sequencing_identifies_photoheterotrophs_and_chemoautotrophs_in_freshwater_bacterioplankton"><img alt="Research paper thumbnail of High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton" class="work-thumbnail" src="https://attachments.academia-assets.com/46055097/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605987/High_throughput_single_cell_sequencing_identifies_photoheterotrophs_and_chemoautotrophs_in_freshwater_bacterioplankton">High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/SwanBrandon">Brandon Swan</a> and <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/DashiellMasland">Dashiell Masland</a></span></div><div class="wp-workCard_item"><span>The ISME Journal</span><span>, 2012</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="43ff456256dd843034b7d8bd0f5b028f" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055097,"asset_id":12605987,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055097/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605987"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="12605987"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 12605987; 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However, their abundance and taxonomic identities remain largely unknown. We used a combination of single-cell and metagenomic DNA sequencing to study the predominant photoheterotrophs and chemoautotrophs inhabiting the euphotic zone of temperate, physicochemically diverse freshwater lakes. Multi-locus sequencing of 712 single amplified genomes, generated by fluorescence-activated cell sorting and whole genome multiple displacement amplification, showed that most of the cosmopolitan freshwater clusters contain photoheterotrophs. These comprised at least 10-23% of bacterioplankton, and RBs were the dominant fraction. Our data demonstrate that Actinobacteria, including clusters acI, Luna and acSTL, are the predominant freshwater RBs. We significantly broaden the known taxonomic range of freshwater RBs, to include Alpha-, Beta-, Gamma-and Deltaproteobacteria, Verrucomicrobia and Sphingobacteria. By sequencing single cells, we found evidence for inter-phyla horizontal gene transfer and recombination of rhodopsin genes and identified specific taxonomic groups involved in these evolutionary processes. Our data suggest that members of the ubiquitous betaproteobacteria Polynucleobacter spp. are the dominant AAPs in temperate freshwater lakes. Furthermore, the RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) gene was found in several single cells of Betaproteobacteria, Bacteroidetes and Gammaproteobacteria, suggesting that chemoautotrophs may be more prevalent among aerobic bacterioplankton than previously thought. This study demonstrates the power of single-cell DNA sequencing addressing previously unresolved questions about the metabolic potential and evolutionary histories of uncultured microorganisms, which dominate most natural environments.","publication_date":{"day":null,"month":null,"year":2012,"errors":{}},"publication_name":"The ISME Journal","grobid_abstract_attachment_id":46055097},"translated_abstract":null,"internal_url":"https://www.academia.edu/12605987/High_throughput_single_cell_sequencing_identifies_photoheterotrophs_and_chemoautotrophs_in_freshwater_bacterioplankton","translated_internal_url":"","created_at":"2015-05-26T06:21:41.227-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":31550655,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[{"id":649327,"work_id":12605987,"tagging_user_id":31550655,"tagged_user_id":52993821,"co_author_invite_id":245294,"email":"m***i@bigelow.org","display_order":0,"name":"Michael Sieracki","title":"High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton"},{"id":649351,"work_id":12605987,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":215686,"email":"m***z@ua.es","display_order":null,"name":"M. 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Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres" class="work-thumbnail" src="https://attachments.academia-assets.com/46055079/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605986/Genomic_and_Metabolic_Diversity_of_Marine_Group_I_Thaumarchaeota_in_the_Mesopelagic_of_Two_Subtropical_Gyres">Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/SwanBrandon">Brandon Swan</a> and <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/DashiellMasland">Dashiell Masland</a></span></div><div class="wp-workCard_item"><span>PLoS ONE</span><span>, 2014</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="cac0b6fcb12dace81d42d6f1fbb42edd" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055079,"asset_id":12605986,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055079/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&st=MTczMjc5MDQxMCw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605986"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa 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href="https://www.academia.edu/12554217/Insights_into_the_phylogeny_and_coding_potential_of_microbial_dark_matter">Insights into the phylogeny and coding potential of microbial dark matter</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/EstherGies">Esther Gies</a>, <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/SwanBrandon">Brandon Swan</a>, and <a class="" data-click-track="profile-work-strip-authors" href="https://lbl.academia.edu/PatrickSchwientek">Patrick Schwientek</a></span></div><div class="wp-workCard_item"><span>Nature</span><span>, 2013</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="e41041950c0aaaab6df45b215a33c330" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" 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providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called 'microbial dark matter'. With this additional genomic information, we are able to resolve many intra-and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.","publication_date":{"day":null,"month":null,"year":2013,"errors":{}},"publication_name":"Nature","grobid_abstract_attachment_id":46091269},"translated_abstract":null,"internal_url":"https://www.academia.edu/12554217/Insights_into_the_phylogeny_and_coding_potential_of_microbial_dark_matter","translated_internal_url":"","created_at":"2015-05-23T23:24:28.105-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":31462878,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[{"id":620790,"work_id":12554217,"tagging_user_id":31462878,"tagged_user_id":56009143,"co_author_invite_id":236722,"email":"s***t@whoi.edu","display_order":-7098052,"name":"Stefan Sievert","title":"Insights into the phylogeny and coding potential of microbial dark 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text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605984/Functional_metagenomic_profiling_of_nine_biomes">Functional metagenomic profiling of nine biomes</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/SwanBrandon">Brandon Swan</a> and <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/JohnPaul155">John Paul</a></span></div><div class="wp-workCard_item"><span>Nature</span><span>, 2008</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="24bd69374efb8f192d26de28422b761b" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055078,"asset_id":12605984,"asset_type":"Work","button_location":"profile"}" 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window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=12605984]").text(description); $(".js-view-count[data-work-id=12605984]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 12605984; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='12605984']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 12605984, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "24bd69374efb8f192d26de28422b761b" } } $('.js-work-strip[data-work-id=12605984]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":12605984,"title":"Functional metagenomic profiling of nine biomes","translated_title":"","metadata":{"grobid_abstract":"Microbial activities shape the biogeochemistry of the planet 1,2 and macroorganism health 3 . Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for example, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is hampered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional diversity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.","publication_date":{"day":null,"month":null,"year":2008,"errors":{}},"publication_name":"Nature","grobid_abstract_attachment_id":46055078},"translated_abstract":null,"internal_url":"https://www.academia.edu/12605984/Functional_metagenomic_profiling_of_nine_biomes","translated_internal_url":"","created_at":"2015-05-26T06:21:40.343-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":31550655,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[{"id":649344,"work_id":12605984,"tagging_user_id":31550655,"tagged_user_id":189133207,"co_author_invite_id":245295,"email":"d***e@gmail.com","affiliation":"University of California, Santa Barbara","display_order":0,"name":"David Valentine","title":"Functional metagenomic profiling of nine biomes"},{"id":649280,"work_id":12605984,"tagging_user_id":31550655,"tagged_user_id":32737043,"co_author_invite_id":245276,"email":"l***r@icr.ac.uk","display_order":null,"name":"L. 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$a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="12605983"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/12605983/Zooplankton_life_cycles_Direct_documentation_of_pelagic_births_and_deaths_relative_to_diapausing_egg_production"><img alt="Research paper thumbnail of Zooplankton life cycles: Direct documentation of pelagic births and deaths relative to diapausing egg production" class="work-thumbnail" src="https://attachments.academia-assets.com/46055032/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605983/Zooplankton_life_cycles_Direct_documentation_of_pelagic_births_and_deaths_relative_to_diapausing_egg_production">Zooplankton life cycles: Direct documentation of pelagic births and deaths relative to diapausing egg production</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/SwanBrandon">Brandon Swan</a> and <a class="" data-click-track="profile-work-strip-authors" href="https://epa.academia.edu/TaylorJarnagin">Taylor Jarnagin</a></span></div><div class="wp-workCard_item"><span>Limnology and Oceanography</span><span>, 2004</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="3234b142969c5407088977578fa61847" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" 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id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "3234b142969c5407088977578fa61847" } } $('.js-work-strip[data-work-id=12605983]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":12605983,"title":"Zooplankton life cycles: Direct documentation of pelagic births and deaths relative to diapausing egg production","translated_title":"","metadata":{"grobid_abstract":"Zooplankton demographics operate over multiple time scales corresponding to pelagic parthenogenetic generations, an overwintering stage, and an ''egg bank.'' Comparisons of pelagic birth and death rates with seasonal diapausing egg production provide insights into local species persistence. The spiny cladoceran (Bythotrephes) possesses morphological adaptations (spines and thick-walled diapausing eggs) that lessen, but do not eliminate, predation effects by fish. Because caudal spines are retained throughout life and are indigestible in fish guts, spine accumulation in sediment traps directly documents patterns of seasonal mortality. Here, we contrast deposition of spines and diapausing eggs in a recently colonized inland lake (Lake Michigamme) with deposition in a larger source lake (Lake Michigan). Direct mortality estimates at the inland lake correspond well with traditional indirect estimates from egg ratio techniques. Although spines are effective against abundant small fish in the inland lake, individuals are susceptible to ingestion by late-season young of year and larger fish. Laboratory experiments confirm that fish are responsible for spine breakage in the water column, accounting for an estimated 62-71% of seasonal mortality. Effects of late-season predation are lessened because diapausing eggs survive gut passage, yet yearly production of diapausing eggs is low in Lake Michigamme. A more balanced pelagic birth(death) to diapausing egg relationship exists in Lake Michigan, probably because egg-carrying adults find better refuge in central, deeper waters. Since spines catch on seines and diapausing eggs survive gut passage, use of bait fish and live wells promotes Bythotrephes dispersal.","publication_date":{"day":null,"month":null,"year":2004,"errors":{}},"publication_name":"Limnology and Oceanography","grobid_abstract_attachment_id":46055032},"translated_abstract":null,"internal_url":"https://www.academia.edu/12605983/Zooplankton_life_cycles_Direct_documentation_of_pelagic_births_and_deaths_relative_to_diapausing_egg_production","translated_internal_url":"","created_at":"2015-05-26T06:21:40.193-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":31550655,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[{"id":649302,"work_id":12605983,"tagging_user_id":31550655,"tagged_user_id":12177307,"co_author_invite_id":null,"email":"j***r@epa.gov","affiliation":"United States Environmental Protection Agency","display_order":0,"name":"Taylor Jarnagin","title":"Zooplankton life cycles: Direct documentation of pelagic births and deaths relative to diapausing egg production"},{"id":649304,"work_id":12605983,"tagging_user_id":31550655,"tagged_user_id":null,"co_author_invite_id":245289,"email":"t***n@aol.com","display_order":null,"name":"S. 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="12605982"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/12605982/Spatial_and_temporal_patterns_of_transparency_and_light_attenuation_in_the_Salton_Sea_California_1997_1999"><img alt="Research paper thumbnail of Spatial and temporal patterns of transparency and light attenuation in the Salton Sea, California, 1997–1999" class="work-thumbnail" src="https://attachments.academia-assets.com/46055074/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605982/Spatial_and_temporal_patterns_of_transparency_and_light_attenuation_in_the_Salton_Sea_California_1997_1999">Spatial and temporal patterns of transparency and light attenuation in the Salton Sea, California, 1997–1999</a></div><div class="wp-workCard_item"><span>Lake and Reservoir Management</span><span>, 2007</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="9b70b6447d4f32500703aac6ad586fe0" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055074,"asset_id":12605982,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055074/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605982"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="12605982"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 12605982; 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Reifel, M.A. Tiffany, J.M. Watts and S.H. Hurlbert. 2007. Spatial and temporal patterns of transparency and light attenuation in the Salton Sea, California -1999 Transparency, as measured by Secchi disk depth (SD), and light attenuation (K d (PAR)) were measured in the Salton Sea in 1997-1999. Linear regression models were used to evaluate the relative importance of phytoplankton and non-phytoplankton substances in determining SD and K d (PAR). Paired measurements of SD and K d (PAR) made in 1999 were used to track relative changes in the importance of light absorption and scattering processes. Phytoplankton biomass was a poor predictor of both SD and K d (PAR) at mid-lake stations, and this is most likely due to high concentrations of non-phytoplankton substances such as inorganic particulate matter in the Salton Sea. During strong windstorms in the warmer part of the year, the upper water column mixes with hydrogen sulfide-laden bottom waters, causing large crashes in plankton populations. This previously reported phenomenon also strongly affects the light regime through the production of gypsum crystals, which scatter large portions of penetrating light. Since a large amount of variation in both SD and K d (PAR) is not explained by phytoplankton biomass, any use of this relationship to forecast future changes in water clarity through nutrient reductions must be done with caution.","publication_date":{"day":null,"month":null,"year":2007,"errors":{}},"publication_name":"Lake and Reservoir Management","grobid_abstract_attachment_id":46055074},"translated_abstract":null,"internal_url":"https://www.academia.edu/12605982/Spatial_and_temporal_patterns_of_transparency_and_light_attenuation_in_the_Salton_Sea_California_1997_1999","translated_internal_url":"","created_at":"2015-05-26T06:21:40.082-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":31550655,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":46055074,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/46055074/thumbnails/1.jpg","file_name":"Spatial_and_temporal_patterns_of_transpa20160529-20903-1hoka3l.pdf","download_url":"https://www.academia.edu/attachments/46055074/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&","bulk_download_file_name":"Spatial_and_temporal_patterns_of_transpa.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/46055074/Spatial_and_temporal_patterns_of_transpa20160529-20903-1hoka3l-libre.pdf?1464574040=\u0026response-content-disposition=attachment%3B+filename%3DSpatial_and_temporal_patterns_of_transpa.pdf\u0026Expires=1732794011\u0026Signature=QbgYwOAwkia-8LE1SeYjzk1UjCQsKEvMg9ULbfOhuOWwK35ZNOU03Zpx-9NXbue3eo1fUHcD6G2Hz3EIKKNmwbjZCJVCNn26~a-XTPANvCc1fDAfgvRf1jx2D5QHKyp~ZVnYustQLCNi5F5V4vySx0dS-LhiGmVAE4cA7alkAK6ZFzCZOStX5rdsPnN80aVovnIYdku9hVg7iOVzC-FPqiVc7ku0pRYGdM4MCZaWKYIrZaiR1OAQDk8~EDI8nsyRS7XhxPmRTOIpsr~jBesAm6fLfBxuhhcip85y1I512u-bGVoCHMoKH0uW~OY7ldqRvU4SQSeGpvAUcW-0Psm4Ew__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"Spatial_and_temporal_patterns_of_transparency_and_light_attenuation_in_the_Salton_Sea_California_1997_1999","translated_slug":"","page_count":10,"language":"en","content_type":"Work","owner":{"id":31550655,"first_name":"Brandon","middle_initials":null,"last_name":"Swan","page_name":"SwanBrandon","domain_name":"independent","created_at":"2015-05-26T06:21:03.429-07:00","display_name":"Brandon Swan","url":"https://independent.academia.edu/SwanBrandon"},"attachments":[{"id":46055074,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/46055074/thumbnails/1.jpg","file_name":"Spatial_and_temporal_patterns_of_transpa20160529-20903-1hoka3l.pdf","download_url":"https://www.academia.edu/attachments/46055074/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&","bulk_download_file_name":"Spatial_and_temporal_patterns_of_transpa.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/46055074/Spatial_and_temporal_patterns_of_transpa20160529-20903-1hoka3l-libre.pdf?1464574040=\u0026response-content-disposition=attachment%3B+filename%3DSpatial_and_temporal_patterns_of_transpa.pdf\u0026Expires=1732794011\u0026Signature=QbgYwOAwkia-8LE1SeYjzk1UjCQsKEvMg9ULbfOhuOWwK35ZNOU03Zpx-9NXbue3eo1fUHcD6G2Hz3EIKKNmwbjZCJVCNn26~a-XTPANvCc1fDAfgvRf1jx2D5QHKyp~ZVnYustQLCNi5F5V4vySx0dS-LhiGmVAE4cA7alkAK6ZFzCZOStX5rdsPnN80aVovnIYdku9hVg7iOVzC-FPqiVc7ku0pRYGdM4MCZaWKYIrZaiR1OAQDk8~EDI8nsyRS7XhxPmRTOIpsr~jBesAm6fLfBxuhhcip85y1I512u-bGVoCHMoKH0uW~OY7ldqRvU4SQSeGpvAUcW-0Psm4Ew__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":8060,"name":"Saline Lake","url":"https://www.academia.edu/Documents/in/Saline_Lake"},{"id":476869,"name":"Hydrogen Sulfide","url":"https://www.academia.edu/Documents/in/Hydrogen_Sulfide"},{"id":518609,"name":"Particulate Matter","url":"https://www.academia.edu/Documents/in/Particulate_Matter"},{"id":990608,"name":"Linear Regression Model","url":"https://www.academia.edu/Documents/in/Linear_Regression_Model"},{"id":1431418,"name":"Chlorophyll a","url":"https://www.academia.edu/Documents/in/Chlorophyll_a"},{"id":1914073,"name":"Light Attenuation","url":"https://www.academia.edu/Documents/in/Light_Attenuation"}],"urls":[]}, dispatcherData: dispatcherData }); 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Using single-cell sorting and whole-genome amplification of prokaryotes from two subtropical gyres, we obtained genomic DNA from 738 cells representing most cosmopolitan lineages. Multiple cells of Deltaproteobacteria cluster SAR324, Gammaproteobacteria clusters ARCTIC96BD-19 and Agg47, and some Oceanospirillales from the lower mesopelagic contained ribulose-1,5-bisphosphate carboxylase-oxygenase and sulfur oxidation genes. These results corroborated community DNA and RNA profiling from diverse geographic regions. The SAR324 genomes also suggested C(1) metabolism and a particle-associated life-style. Microautoradiography and fluorescence in situ hybridization confirmed bicarbonate uptake and particle association of SAR324 cells. Our study suggests potential chemolithoautotrophy in several uncultured Proteobacteria lineages that are ubiquitous in the dark...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="c7e589a4dc5965916a4ce4c43946e4ff" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055100,"asset_id":12605979,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055100/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605979"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="12605979"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 12605979; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=12605979]").text(description); $(".js-view-count[data-work-id=12605979]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 12605979; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='12605979']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 12605979, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "c7e589a4dc5965916a4ce4c43946e4ff" } } $('.js-work-strip[data-work-id=12605979]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":12605979,"title":"Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean","translated_title":"","metadata":{"abstract":"Recent studies suggest that unidentified prokaryotes fix inorganic carbon at globally significant rates in the immense dark ocean. Using single-cell sorting and whole-genome amplification of prokaryotes from two subtropical gyres, we obtained genomic DNA from 738 cells representing most cosmopolitan lineages. Multiple cells of Deltaproteobacteria cluster SAR324, Gammaproteobacteria clusters ARCTIC96BD-19 and Agg47, and some Oceanospirillales from the lower mesopelagic contained ribulose-1,5-bisphosphate carboxylase-oxygenase and sulfur oxidation genes. These results corroborated community DNA and RNA profiling from diverse geographic regions. The SAR324 genomes also suggested C(1) metabolism and a particle-associated life-style. Microautoradiography and fluorescence in situ hybridization confirmed bicarbonate uptake and particle association of SAR324 cells. 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dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="12605978"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/12605978/Unveiling_in_situ_interactions_between_marine_protists_and_bacteria_through_single_cell_sequencing"><img alt="Research paper thumbnail of Unveiling in situ interactions between marine protists and bacteria through single cell sequencing" class="work-thumbnail" src="https://attachments.academia-assets.com/46055066/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605978/Unveiling_in_situ_interactions_between_marine_protists_and_bacteria_through_single_cell_sequencing">Unveiling in situ interactions between marine protists and bacteria through single cell sequencing</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/SwanBrandon">Brandon Swan</a> and <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/DashiellMasland">Dashiell Masland</a></span></div><div class="wp-workCard_item"><span>The ISME journal</span><span>, 2012</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Heterotrophic protists are a highly diverse and biogeochemically significant component of marine ...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Heterotrophic protists are a highly diverse and biogeochemically significant component of marine ecosystems, yet little is known about their species-specific prey preferences and symbiotic interactions in situ. Here we demonstrate how these previously unresolved questions can be addressed by sequencing the eukaryote and bacterial SSU rRNA genes from individual, uncultured protist cells collected from their natural marine environment and sorted by flow cytometry. We detected Pelagibacter ubique in association with a MAST-4 protist, an actinobacterium in association with a chrysophyte and three bacteroidetes in association with diverse protist groups. The presence of identical phylotypes among the putative prey and the free bacterioplankton in the same sample provides evidence for predator-prey interactions. Our results also suggest a discovery of novel symbionts, distantly related to Rickettsiales and the candidate divisions ZB3 and TG2, associated with Cercozoa and Chrysophyta cells...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="0fd9dd311b540563e2dbf7a4822489dc" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055066,"asset_id":12605978,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055066/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605978"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="12605978"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 12605978; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=12605978]").text(description); $(".js-view-count[data-work-id=12605978]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 12605978; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='12605978']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 12605978, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "0fd9dd311b540563e2dbf7a4822489dc" } } $('.js-work-strip[data-work-id=12605978]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":12605978,"title":"Unveiling in situ interactions between marine protists and bacteria through single cell sequencing","translated_title":"","metadata":{"abstract":"Heterotrophic protists are a highly diverse and biogeochemically significant component of marine ecosystems, yet little is known about their species-specific prey preferences and symbiotic interactions in situ. 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genomes of active polysaccharide degraders: an unexpected contribution of verrucomicrobia" class="work-thumbnail" src="https://attachments.academia-assets.com/46055108/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/12605977/Capturing_single_cell_genomes_of_active_polysaccharide_degraders_an_unexpected_contribution_of_verrucomicrobia">Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of verrucomicrobia</a></div><div class="wp-workCard_item wp-workCard--coauthors"><span>by </span><span><a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/SwanBrandon">Brandon Swan</a>, <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/ChrisDetter">Chris Detter</a>, <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/WendyBellows">Wendy Bellows</a>, and <a class="" data-click-track="profile-work-strip-authors" href="https://independent.academia.edu/DashiellMasland">Dashiell Masland</a></span></div><div class="wp-workCard_item"><span>PloS one</span><span>, 2012</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Microbial hydrolysis of polysaccharides is critical to ecosystem functioning and is of great inte...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Microbial hydrolysis of polysaccharides is critical to ecosystem functioning and is of great interest in diverse biotechnological applications, such as biofuel production and bioremediation. Here we demonstrate the use of a new, efficient approach to recover genomes of active polysaccharide degraders from natural, complex microbial assemblages, using a combination of fluorescently labeled substrates, fluorescence-activated cell sorting, and single cell genomics. We employed this approach to analyze freshwater and coastal bacterioplankton for degraders of laminarin and xylan, two of the most abundant storage and structural polysaccharides in nature. Our results suggest that a few phylotypes of Verrucomicrobia make a considerable contribution to polysaccharide degradation, although they constituted only a minor fraction of the total microbial community. Genomic sequencing of five cells, representing the most predominant, polysaccharide-active Verrucomicrobia phylotype, revealed signif...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="1a0a49a3f25c7c73984bca8b3c0cb433" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":46055108,"asset_id":12605977,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/46055108/download_file?st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&st=MTczMjc5MDQxMSw4LjIyMi4yMDguMTQ2&s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="12605977"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span><span id="work-strip-rankings-button-container"></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="12605977"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 12605977; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=12605977]").text(description); $(".js-view-count[data-work-id=12605977]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 12605977; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='12605977']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span><span><script>$(function() { new Works.PaperRankView({ workId: 12605977, container: "", }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-f77ea15d77ce96025a6048a514272ad8becbad23c641fc2b3bd6e24ca6ff1932.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "1a0a49a3f25c7c73984bca8b3c0cb433" } } $('.js-work-strip[data-work-id=12605977]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":12605977,"title":"Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of verrucomicrobia","translated_title":"","metadata":{"abstract":"Microbial hydrolysis of polysaccharides is critical to ecosystem functioning and is of great interest in diverse biotechnological applications, such as biofuel production and bioremediation. 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