Pangenomic insights into Dehalobacter evolution and acquisition of functional genes for bioremediation

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value="0e42663a6c3bd85498fcb88798998fed7bfdc45d457db35281e41afe13cc0524" /> </form> </div> </div> <div id="collections-action-panel" class="collections-action-panel action-panel in-progress-dots-panel" aria-hidden="true" data-collections-open-panel-enabled="false" data-collections-open-panel-url-hash="#open-collections-panel"> <div class="inner-wrap"> <h3 class="action-panel-heading"> Add to Collections </h3> <form id="collections-action-panel-form" class="collections-action-panel-form action-panel-content action-form action-panel-smaller-selectors" data-existing-collections-url="/list-existing-collections/" data-add-to-existing-collection-url="/add-to-existing-collection/" data-create-and-add-to-new-collection-url="/create-and-add-to-new-collection/" data-get-article-ids-by-search-url="/get-article-ids-by-search/" data-myncbi-max-collection-name-length="100" data-add-to-collection-max-amount="1000" data-collections-root-url="https://www.ncbi.nlm.nih.gov/myncbi/collections/"> <input type="hidden" name="csrfmiddlewaretoken" value="izzarUzilUAiTq1dnBLUCTzUN8L7194C9CUHFMPuzMyhvZU1UtDtKptfu9kdB4HM"> <div class="choice-group" role="radiogroup"> <ul class="radio-group-items"> <li> <input type="radio" id="collections-action-panel-new" class="collections-new" name="collections" value="new" data-ga-category="save_share" data-ga-action="collections" data-ga-label="collections_radio_new"> <label for="collections-action-panel-new">Create a new collection</label> </li> <li> <input type="radio" id="collections-action-panel-existing" class="collections-existing" name="collections" value="existing" checked="true" data-ga-category="save_share" data-ga-action="collections" data-ga-label="collections_radio_existing"> <label for="collections-action-panel-existing">Add to an existing collection</label> </li> </ul> </div> <div class="controls-wrapper"> <div class="action-panel-control-wrap new-collections-controls"> <label for="collections-action-panel-add-to-new" class="action-panel-label required-field-asterisk"> Name your collection: </label> <input type="text" name="add-to-new-collection" id="collections-action-panel-add-to-new" class="collections-action-add-to-new" pattern="[^"&=<>\/]*" title="The following characters are not allowed in the Name field: "&=<>/" maxlength="100" data-ga-category="save_share" data-ga-action="create_collection" data-ga-label="non_favorties_collection"> <div class="collections-new-name-too-long usa-input-error-message selection-validation-message"> Name must be less than 100 characters </div> </div> <div class="action-panel-control-wrap existing-collections-controls"> <label for="collections-action-panel-add-to-existing" class="action-panel-label"> Choose a collection: </label> <select id="collections-action-panel-add-to-existing" class="action-panel-selector collections-action-add-to-existing" data-ga-category="save_share" data-ga-action="select_collection" data-ga-label="($('#collections-action-add-to-existing').val() === 'Favorites') ? 'Favorites' : 'non_favorites_collection'"> </select> <div class="collections-retry-load-on-error usa-input-error-message selection-validation-message"> Unable to load your collection due to an error<br> <a href="#">Please try again</a> </div> </div> </div> <div class="action-panel-actions"> <button class="action-panel-submit" type="submit" data-loading-label="Adding..." data-pinger-ignore data-ga-category="save_share" data-ga-action="collections" data-ga-label="add"> Add </button> <button class="action-panel-cancel" aria-label="Close 'Add to Collections' panel" ref="linksrc=close_collections_panel" aria-controls="collections-action-panel" aria-expanded="false" data-ga-category="save_share" data-ga-action="collections" data-ga-label="cancel"> Cancel </button> </div> </form> </div> </div> <div id="bibliography-action-panel" class="bibliography-action-panel action-panel in-progress-dots-panel" aria-hidden="true" data-bibliography-open-panel-enabled="false" data-bibliography-open-panel-url-hash="#open-bibliography-panel"> <div class="inner-wrap"> <h3 class="action-panel-heading"> Add to My Bibliography </h3> <form id="bibliography-action-panel-form" class="bibliography-action-panel-form action-panel-content action-form action-panel-smaller-selectors" data-add-to-bibliography-max-amount="100" data-add-to-bibliography-batch-size="10" data-bibliography-delegates-url="/list-bibliography-delegates/" data-add-to-bibliography-url="/add-to-bibliography/" data-get-article-ids-by-search-url="/get-article-ids-by-search/" data-mybib-root-url="https://www.ncbi.nlm.nih.gov/myncbi/collections/mybibliography/"> <input type="hidden" name="csrfmiddlewaretoken" value="izzarUzilUAiTq1dnBLUCTzUN8L7194C9CUHFMPuzMyhvZU1UtDtKptfu9kdB4HM"> <div class="action-panel-control-wrap bibliographies-controls"> <div class="choice-group"> <ul class="bibliographies-action-add radio-group-items"> <li> <input name="bibliography" id="my-bibliography" class="my-bibliography" type="radio" checked/> <label for="my-bibliography">My Bibliography</label> </li> </ul> </div> </div> <div class="bibliographies-retry-load-on-error usa-input-error-message selection-validation-message"> Unable to load your delegates due to an error<br> <a href="#">Please try again</a> </div> <div class="action-panel-actions"> <button class="action-panel-submit" type="submit" data-loading-label="Adding..." data-pinger-ignore> Add </button> <button class="action-panel-cancel" aria-label="Close 'Add to bibliography' panel" ref="linksrc=close_bibliography_panel" aria-controls="bibliography-action-panel" aria-expanded="false" data-ga-category="save_share" data-ga-action="mybib" data-ga-label="cancel"> Cancel </button> </div> </form> </div> </div> <div id="saved-search-action-panel" class="saved-search-action-panel action-panel " aria-hidden="true" data-saved-search-open-panel-enabled="false" data-saved-search-open-panel-url-hash="#open-saved-search-panel"> <div class="inner-wrap"> <h2 class="action-panel-heading"> Your saved search </h2> <form id="saved-search-action-panel-form" class="saved-search-action-panel-form action-panel-content action-form" data-create-saved-search-url="/create-saved-search/" data-try-search-terms-url="/try-search-term/" data-saved-search-root-url="https://www.ncbi.nlm.nih.gov/myncbi/searches/"> <input type="hidden" name="csrfmiddlewaretoken" value="izzarUzilUAiTq1dnBLUCTzUN8L7194C9CUHFMPuzMyhvZU1UtDtKptfu9kdB4HM"> <div class="action-panel-control-wrap"> <label for="saved-search-name" class="action-panel-label saved-search-name-label required-field-asterisk"> Name of saved search: </label> <input maxlength="200" type="text" name="saved-search-name" id="saved-search-name" class="saved-search-name" value="" required pattern="[^"&=<>\/]*" title="The following characters are not allowed in the Name field: "&=<>/"> </div> <div class="action-panel-control-wrap"> <label for="saved-search-term" class="action-panel-label required-field-asterisk"> Search terms: </label> <textarea name="saved-search-term" id="saved-search-term" class="saved-search-term" required></textarea> </div> <div class="test-search-term-wrap"> <a href="#" class="try-search-term">Test search terms</a> </div> <div class="choice-group action-panel-extra-margin-top"> <span class="action-panel-label" id="fieldset-label"> Would you like email updates of new search results? </span> <fieldset id="saved-search-alert" aria-describedby="fieldset-label"> <legend class="usa-sr-only">Saved Search Alert Radio Buttons</legend> <ul class="radio-group-items"> <li> <input type="radio" id="saved-search-alert-yes" class="saved-search-alert-yes" name="saved-search-alert" value="yes" checked> <label for="saved-search-alert-yes" class="action-panel-label">Yes</label> </li> <li> <input aria-label="No radio input" type="radio" id="saved-search-alert-no" class="saved-search-alert-no" name="saved-search-alert" value="no"> <label for="saved-search-alert-no" class="action-panel-label">No</label> </li> </ul> </fieldset> </div> <div class="alert-schedule-wrap"> <div class="action-panel-control-wrap"> <label class="action-panel-label"> Email: </label> <span aria-label="Email address" id="saved-search-email" class="action-panel-label"><span class="action-panel-label-bold"></span> (<a class="myncbi-account-settings" href="https://www.ncbi.nlm.nih.gov/account/settings/">change</a>)</span> </div> <div class="action-panel-control-wrap action-panel-extra-margin-top"> <label for="saved-search-frequency" class="action-panel-label"> Frequency: </label> <select id="saved-search-frequency" class="no-border-panel-selector saved-search-frequency"> <option value="monthly">Monthly</option> <option value="weekly">Weekly</option> <option value="daily">Daily</option> </select> </div> <div class="action-panel-control-wrap saved-search-monthly-additional"> <label for="saved-search-monthly-on-day" class="action-panel-label"> Which day? </label> <select id="saved-search-monthly-on-day" class="no-border-panel-selector"> <option value="Sunday">The first Sunday</option> <option value="Monday">The first Monday</option> <option value="Tuesday">The first Tuesday</option> <option value="Wednesday">The first Wednesday</option> <option value="Thursday">The first Thursday</option> <option value="Friday">The first Friday</option> <option value="Saturday">The first Saturday</option> <option value="day">The first day</option> <option value="weekday">The first weekday</option> </select> </div> <div class="action-panel-control-wrap saved-search-weekly-additional"> <label for="saved-search-weekly-on-day" class="action-panel-label"> Which day? </label> <select id="saved-search-weekly-on-day" class="no-border-panel-selector saved-search-weekly-on-day"> <option value="Sunday">Sunday</option> <option value="Monday">Monday</option> <option value="Tuesday">Tuesday</option> <option value="Wednesday">Wednesday</option> <option value="Thursday">Thursday</option> <option value="Friday">Friday</option> <option value="Saturday">Saturday</option> </select> </div> <div class="action-panel-control-wrap"> <label for="saved-search-report" class="action-panel-label"> Report format: </label> <select id="saved-search-report" class="no-border-panel-selector saved-search-report"> <option value="DocSum">Summary</option> <option value="DocSumText">Summary (text)</option> <option value="Abstract">Abstract</option> <option value="AbstractText">Abstract (text)</option> <option value="MEDLINE">PubMed</option> </select> </div> <div class="action-panel-control-wrap"> <label for="saved-search-amount" class="action-panel-label"> Send at most: </label> <select id="saved-search-amount" class="no-border-panel-selector saved-search-amount"> <option value="1">1 item</option> <option value="5" selected>5 items</option> <option value="10">10 items</option> <option value="20">20 items</option> <option value="50">50 items</option> <option value="100">100 items</option> <option value="200">200 items</option> </select> </div> <div> <input type="checkbox" id="saved-search-send-if-no-result" class="saved-search-send-if-no-result" name="saved-search-send-if-no-result"> <label for="saved-search-send-if-no-result" class="action-panel-label smaller-checkbox"> Send even when there aren't any new results </label> </div> <div class="action-panel-control-wrap option-text-in-email-wrap"> <label for="saved-search-email-text" class="action-panel-label"> Optional text in email: </label> <textarea name="saved-search-email-text" id="saved-search-email-text" class="saved-search-email-text"></textarea> </div> </div> <div class="action-panel-actions"> <button class="action-panel-submit" type="submit" data-loading-label="Saving..." data-ga-category="save_share" data-ga-action="alert" data-ga-label="save"> Save </button> <button class="action-panel-cancel" aria-label="Close 'Your saved search' panel" ref="linksrc=close_saved_search_panel" aria-controls="saved-search-action-panel" aria-expanded="false" data-ga-category="save_share" data-ga-action="alert" data-ga-label="cancel"> Cancel </button> </div> </form> </div> </div> <div id="citation-manager-action-panel" class="citation-manager-action-panel action-panel" aria-hidden="true"> <div class="inner-wrap"> <h2 class="action-panel-heading"> Create a file for external citation management software </h2> <form id="citation-manager-action-panel-form" class="action-panel-content action-form" action="/results-export-ids/" data-by-search-action="/results-export-search-data/" data-by-ids-action="/results-export-ids/" method="post" data-by-search-method="post" data-by-ids-method="post"> <input type="hidden" name="csrfmiddlewaretoken" value="izzarUzilUAiTq1dnBLUCTzUN8L7194C9CUHFMPuzMyhvZU1UtDtKptfu9kdB4HM"> <input name="results-format" type="hidden" value="pubmed"/> <div class="action-panel-actions"> <button class="action-panel-submit" type="submit" data-loading-label="Sending..." data-ga-category="save_share" data-ga-action="citation_manager" data-ga-label="save"> Create file </button> <button class="action-panel-cancel" aria-label="Close 'Send citations to citation manager' panel" ref="linksrc=close_citation_manager_panel" aria-controls="citation-manager-action-panel" aria-expanded="false" data-ga-category="save_share" data-ga-action="citation_manager" data-ga-label="cancel"> Cancel </button> </div> </form> </div> </div> <div id="rss-action-panel" class="rss-action-panel action-panel " aria-hidden="true"> <div class="inner-wrap"> <h2 class="action-panel-heading"> Your RSS Feed </h2> <form id="rss-action-panel-form" class="rss-action-panel-form action-panel-content action-form" data-create-rss-feed-url="/create-rss-feed-url/" data-search-form-term-value=""> <input type="hidden" name="csrfmiddlewaretoken" value="izzarUzilUAiTq1dnBLUCTzUN8L7194C9CUHFMPuzMyhvZU1UtDtKptfu9kdB4HM"> <div class="action-panel-control-wrap"> <label for="rss-name" class="action-panel-label required-field-asterisk"> Name of RSS Feed: </label> <input maxlength="200" placeholder="Name" type="text" name="rss-name" id="rss-name" class="rss-name" value='' required pattern="[^"&=<>\/]*" title="The following characters are not allowed in the Name field: "&=<>/"> </div> <div class="rss-limit-wrap"> <div class="action-panel-control-wrap action-panel-extra-margin-top"> <label for="rss-limit" class="action-panel-label"> Number of items displayed: </label> <select id="rss-limit" class="no-border-panel-selector rss-limit"> <option value="5">5</option> <option value="10">10</option> <option value="15" selected="selected">15</option> <option value="20">20</option> <option value="50">50</option> <option value="100">100</option> </select> </div> </div> <div class="action-panel-actions"> <button class="action-panel-submit" type="submit" data-loading-label="Creating..." data-ga-category="save_share" data-ga-action="alert" data-ga-label="save"> Create RSS </button> <button class="action-panel-cancel" aria-label="Close 'Your RSS' panel" ref="linksrc=close_rss_panel" aria-controls="rss-action-panel" aria-expanded="false" data-ga-category="save_share" data-ga-action="alert" data-ga-label="cancel"> Cancel </button> </div> <div class="action-panel-control-wrap rss-link-copy-wrap"> <label for="rss-link" class="usa-sr-only">RSS Link</label> <input placeholder="Your RSS Feed Link" type="text" name="rss-link" id="rss-link" class="rss-link" title="RSS Link"> <button type="button" disabled class="rss-link-copy-button disabled" data-ga-category="save_share" data-ga-action="rss" data-ga-label="copy"> Copy </button> </div> </form> </div> </div> </div> </div> <div class="article-page" id="article-page" data-article-pmid="39565095"> <aside class="page-sidebar"> <div class="inner-wrap"> <div class="full-text-links"> <div class="full-view"> <h3 class="title"> Full text links </h3> <div class="full-text-links-list"> <a class="link-item dialog-focus" 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data-create-and-add-to-new-collection-url="/create-and-add-to-new-collection/" data-myncbi-max-collection-name-length="100" data-collections-root-url="https://www.ncbi.nlm.nih.gov/myncbi/collections/"><input type="hidden" name="csrfmiddlewaretoken" value="izzarUzilUAiTq1dnBLUCTzUN8L7194C9CUHFMPuzMyhvZU1UtDtKptfu9kdB4HM"><div class="choice-group" role="radiogroup"><ul class="radio-group-items"><li><input type="radio" id="collections-action-dialog-new" class="collections-new" name="collections" value="new" data-ga-category="collections_button" data-ga-action="click" data-ga-label="collections_radio_new"><label for="collections-action-dialog-new">Create a new collection</label></li><li><input type="radio" id="collections-action-dialog-existing" class="collections-existing" name="collections" value="existing" checked="true" data-ga-category="collections_button" data-ga-action="click" data-ga-label="collections_radio_existing"><label for="collections-action-dialog-existing">Add to an 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class="authors-list-item "><a class="full-name" href="/?term=Bulka+O&cauthor_id=39565095" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Olivia Bulka">Olivia Bulka</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada." href="#full-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Mahadevan+R&cauthor_id=39565095" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Radhakrishnan Mahadevan">Radhakrishnan Mahadevan</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada." href="#full-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Edwards+EA&cauthor_id=39565095" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Elizabeth A Edwards">Elizabeth A Edwards</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada." href="#full-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup></span> </div> </div> </div> <div class="short-article-details"> Affiliations <button class="more-details" id="toggle-authors" data-alt-text="Collapse" aria-controls="expanded-authors" aria-expanded="false" data-pinger-ignore data-fetch-url="/39565095/long-authors/" data-id-prefix=""> <span class="title"> Expand </span> </button> </div> <div 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</li> <li> <span class="identifier doi"> <span class="id-label"> DOI: </span> <a class="id-link" target="_blank" rel="noopener" ref="linksrc=article_id_link&article_id=10.1099/mgen.0.001324&id_type=DOI" href="https://doi.org/10.1099/mgen.0.001324" data-ga-category="full_text" data-ga-action="DOI" > 10.1099/mgen.0.001324 </a> </span> </li> </ul> <div class="in-clipboard-label " hidden> Item in Clipboard </div> </div> <div class="short-view" id="short-view-heading"> <h1 class="heading-title"> Pangenomic insights into <i>Dehalobacter</i> evolution and acquisition of functional genes for bioremediation </h1> <div class="short-citation"> <span class="authors-list"> <span class="authors-list-item "><span class="full-name">Olivia Bulka</span><span class="citation-separator"> et al.</span></span> </span> <span class="citation-journal"> Microb Genom<span class="citation-separator">.</span> </span> <span class="date"> <span class="citation-year">2024 Nov</span><span 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Nov;10(11):001324.</span> </div> <span class="citation-doi"> doi: 10.1099/mgen.0.001324. </span> </div> <div class="expanded-authors" id="short-view-expanded-authors"> <div class="authors"> <h3 class="title"> Authors </h3> <div class="authors-list"> <span class="authors-list-item "><a class="full-name" href="/?term=Bulka+O&cauthor_id=39565095" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Olivia Bulka">Olivia Bulka</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada." href="#short-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Mahadevan+R&cauthor_id=39565095" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Radhakrishnan Mahadevan">Radhakrishnan Mahadevan</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada." href="#short-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Edwards+EA&cauthor_id=39565095" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Elizabeth A Edwards">Elizabeth A Edwards</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada." href="#short-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup></span> </div> </div> <div class="affiliations"> <h3 class="title"> Affiliation </h3> <ul class="item-list"> <li data-affiliation-id="short-view-affiliation-1" id="short-view-affiliation-1" ><sup class="key">1</sup> Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.</li> </ul> </div> </div> <ul class="identifiers" id="short-view-identifiers"> <li> <span class="identifier pubmed"> <span class="id-label"> PMID: </span> <strong class="current-id" title="PubMed ID">39565095</strong> </span> </li> <li> <span class="identifier pmc"> <span class="id-label"> PMCID: </span> <a class="id-link" target="_blank" rel="noopener" ref="linksrc=article_id_link&article_id=PMC11578063&id_type=PMC" href="https://pmc.ncbi.nlm.nih.gov/articles/PMC11578063/" data-ga-category="full_text" data-ga-action="PMCID" > PMC11578063 </a> </span> </li> <li> <span class="identifier doi"> <span class="id-label"> DOI: </span> <a class="id-link" target="_blank" rel="noopener" ref="linksrc=article_id_link&article_id=10.1099/mgen.0.001324&id_type=DOI" href="https://doi.org/10.1099/mgen.0.001324" data-ga-category="full_text" data-ga-action="DOI" > 10.1099/mgen.0.001324 </a> </span> </li> </ul> <div class="in-clipboard-label " hidden> Item in Clipboard </div> </div> </div> </header> <div class="actions-buttons inline"><div class="inner-wrap"><button class="full-text-links-button full-text-links-dialog-trigger" title="Open dialog with full text links" ref="linksrc=full_text_links"> Full text links </button><button class="citation-button citation-dialog-trigger" aria-label="Open dialog with citation text in different styles" data-ga-category="save_share" data-ga-action="cite" data-ga-label="open" data-all-citations-url="/39565095/citations/" data-citation-style="nlm" data-pubmed-format-link="/39565095/export/"><span class="button-label">Cite</span></button><button class="more-actions-button more-actions-dialog-trigger" title="Open dialog with more actions to take" ref="linksrc=more_actions_btn"></button><div class="display-options" data-format-key="format" data-default-format-value="abstract" data-current-format-value="abstract" role="region"><button class="trigger usa-button" title="Change format" data-ga-category="display_options" data-ga-action="display_options_dialog"><span class="button-label">Display options</span></button><div class="dropdown" hidden><div class="title"> Display options </div><div class="content"><div class="format-container"><span class="option-label"> Format </span><select name="format" data-initial-value="abstract" aria-label="Display format" id="inline-actions-display-format"><option value="abstract">Abstract</option><option value="pubmed">PubMed</option><option value="pmid">PMID</option></select></div></div></div></div></div></div> <div class="abstract" id="abstract"> <h2 class="title"> Abstract </h2> <div class="abstract-content selected" id="eng-abstract"> <p> <i>Dehalobacter</i> is a genus of organohalide-respiring bacteria that is recognized for its fastidious growth using reductive dehalogenases (RDases). In the SC05 culture, however, a <i>Dehalobacter</i> population also mineralizes dichloromethane (DCM) produced by chloroform dechlorination using the <i>mec</i> cassette, just downstream of its active RDase. A closed genome of this DCM-mineralizing lineage has previously evaded assembly. Here, we present the genomes of two novel <i>Dehalobacter</i> strains, each of which was assembled from the metagenome of a distinct subculture from SC05. A pangenomic analysis of the <i>Dehalobacter</i> genus, including RDase synteny and phylogenomics, reveals at least five species of <i>Dehalobacter</i> based on average nucleotide identity, RDase and core gene synteny, as well as differential functional genes. An integration hotspot is also pinpointed in the <i>Dehalobacter</i> genome, in which many recombinase islands have accumulated. This nested recombinase island encodes the active RDase and <i>mec</i> cassette in both SC05 <i>Dehalobacter</i> genomes, indicating the transfer of key functional genes between species of <i>Dehalobacter</i>. Horizontal gene transfer between these two novel <i>Dehalobacter</i> strains has implications for the evolutionary history within the SC05 subcultures and of the <i>Dehalobacter</i> genus as a whole, especially regarding adaptation to anthropogenic chemicals. </p> </div> <p> <strong class="sub-title"> Keywords: </strong> Dehalobacter; bioremediation; pangenome; reductive dehalogenase. </p> </div> <p class="disclaimer" id="disclaimer"> <a href="/disclaimer/" target="_blank" ga_category="literature_resources" ga_action="disclaimer_link" ga_label="under_abstract">PubMed Disclaimer</a> </p> <div class="conflict-of-interest" id="conflict-of-interest"> <h2 class="title"> Conflict of interest statement </h2> <div class="statement"> <p xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:p1="http://pubmed.gov/pub-one">The authors declare that there are no conflicts of interest.</p> </div> </div> <div class="figures" id="figures"> <h2 class="title"> Figures </h2> <div class="figures-list" id="slides-container" itemscope itemtype="http://schema.org/ImageGallery"> <figure class="figure-item " itemscope itemtype="http://schema.org/ImageObject" itemprop="associatedMedia" data-slide-index="0" data-label-slug="fig-1"> <a class="figure-link" href="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/02d9/11578063/2203f0bb40c7/mgen-10-01324-g001.jpg" itemprop="contentUrl" aria-describedby="figure-caption-0" role="button" data-image-width="735" data-image-height="374" data-image-alt="Fig. 1." data-pmc-id="PMC11578063" data-figure-id="F1"> <img class="figure-thumb" itemprop="thumbnail" id="article-image-0" src="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/02d9/11578063/29467ea2c6f1/mgen-10-01324-g001.gif" alt="Fig. 1." /> </a> <meta itemprop="width" itemtype="http://schema.org/ImageObject" content="735"> <meta itemprop="height" itemtype="http://schema.org/ImageObject" content="374"> <div class="figure-caption figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="caption" aria-hidden="true"> <div class="caption-wrap"> <strong class="figure-label"> <p> Fig. 1.. Genome map of <i> Dehalobacter </i> strains… </p> </strong> </div> </div> <div class="figure-caption-medium figure-caption-text" aria-hidden="true"> <strong class="figure-label"> <p> Fig. 1.. Genome map of <i> Dehalobacter </i> strains SAD and DAD. From inside outwards: (1) GC… </p> </strong> </div> <figcaption id="figure-caption-0" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description"> <strong class="figure-label"> Fig. 1.. Genome map of <i>Dehalobacter</i> strains SAD and DAD. From inside outwards: (1) GC skew; (2) %GC; – strand: (3) select coding sequences (CDSs), (4) all CDS and (5) RNA genes; + strand: (6) RNA genes, (7) all CDS and (8) select CDS. Select CDS include <i>mec</i> genes (orange) and RDases (purple). Highlighted regions include predicted prophages (yellow), RDase-dense regions (purple) and a predicted genomic island (blue). </strong> </figcaption> </figure> <figure class="figure-item " itemscope itemtype="http://schema.org/ImageObject" itemprop="associatedMedia" data-slide-index="1" data-label-slug="fig-2"> <a class="figure-link" href="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/02d9/11578063/a7802571ca72/mgen-10-01324-g002.jpg" itemprop="contentUrl" aria-describedby="figure-caption-1" role="button" data-image-width="735" data-image-height="352" data-image-alt="Fig. 2." data-pmc-id="PMC11578063" data-figure-id="F2"> <img class="figure-thumb" itemprop="thumbnail" id="article-image-1" src="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/02d9/11578063/553199211340/mgen-10-01324-g002.gif" alt="Fig. 2." /> </a> <meta itemprop="width" itemtype="http://schema.org/ImageObject" content="735"> <meta itemprop="height" itemtype="http://schema.org/ImageObject" content="352"> <div class="figure-caption figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="caption" aria-hidden="true"> <div class="caption-wrap"> <strong class="figure-label"> <p> Fig. 2.. Pangenomic analysis of the <i> Dehalobacter… </i> </p> </strong> </div> </div> <div class="figure-caption-medium figure-caption-text" aria-hidden="true"> <strong class="figure-label"> <p> Fig. 2.. Pangenomic analysis of the <i> Dehalobacter </i> genus. Homologous gene clusters are shown in blue,… </p> </strong> </div> <figcaption id="figure-caption-1" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description"> <strong class="figure-label"> Fig. 2.. Pangenomic analysis of the <i>Dehalobacter</i> genus. Homologous gene clusters are shown in blue, with single-copy core genes (SCGs) and clade-specific genes highlighted in their respective colours. Closed genomes are dark blue, while multi-contig genomes are light blue. The outgroup (<i>Ca</i>. D. elyunquensis: LNDB000000000) is shown in grey. ANI is in red, and multi-strain clades of the phylogenomic tree are highlighted on the right. The active RDase OG in each strain is shown with a shaded box; an open box represents the gene presence of an OG expected to be active but lacking characterization data. Geographic origins are abbreviated as follows: CAN, Canada; NED, Netherlands; CHI, China; GUAD, Guadeloupe; and AUS, Australia. </strong> </figcaption> </figure> <figure class="figure-item " itemscope itemtype="http://schema.org/ImageObject" itemprop="associatedMedia" data-slide-index="2" data-label-slug="fig-3"> <a class="figure-link" href="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/02d9/11578063/f25b12f43ee0/mgen-10-01324-g003.jpg" itemprop="contentUrl" aria-describedby="figure-caption-2" role="button" data-image-width="735" data-image-height="237" data-image-alt="Fig. 3." data-pmc-id="PMC11578063" data-figure-id="F3"> <img class="figure-thumb" itemprop="thumbnail" id="article-image-2" src="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/02d9/11578063/6e41a4a92974/mgen-10-01324-g003.gif" alt="Fig. 3." /> </a> <meta itemprop="width" itemtype="http://schema.org/ImageObject" content="735"> <meta itemprop="height" itemtype="http://schema.org/ImageObject" content="237"> <div class="figure-caption figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="caption" aria-hidden="true"> <div class="caption-wrap"> <strong class="figure-label"> <p> Fig. 3.. Alignment of closed <i> Dehalobacter </i> genomes… </p> </strong> </div> </div> <div class="figure-caption-medium figure-caption-text" aria-hidden="true"> <strong class="figure-label"> <p> Fig. 3.. Alignment of closed <i> Dehalobacter </i> genomes representing two clades. Each coloured brick represents one… </p> </strong> </div> <figcaption id="figure-caption-2" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description"> <strong class="figure-label"> Fig. 3.. Alignment of closed <i>Dehalobacter</i> genomes representing two clades. Each coloured brick represents one LCB. Highlights in yellow and orange mark inversions between strain DAD and strains in clades A and B, respectively. Highlighted in blue is a region common only to strains SAD and DAD. </strong> </figcaption> </figure> <figure class="figure-item " itemscope itemtype="http://schema.org/ImageObject" itemprop="associatedMedia" data-slide-index="3" data-label-slug="fig-4"> <a class="figure-link" href="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/02d9/11578063/7fff87c87f52/mgen-10-01324-g004.jpg" itemprop="contentUrl" aria-describedby="figure-caption-3" role="button" data-image-width="735" data-image-height="710" data-image-alt="Fig. 4." data-pmc-id="PMC11578063" data-figure-id="F4"> <img class="figure-thumb" itemprop="thumbnail" id="article-image-3" src="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/02d9/11578063/e906d5be1e27/mgen-10-01324-g004.gif" alt="Fig. 4." /> </a> <meta itemprop="width" itemtype="http://schema.org/ImageObject" content="735"> <meta itemprop="height" itemtype="http://schema.org/ImageObject" content="710"> <div class="figure-caption figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="caption" aria-hidden="true"> <div class="caption-wrap"> <strong class="figure-label"> <p> Fig. 4.. Phylogenetic tree of all <i> Dehalobacter… </i> </p> </strong> </div> </div> <div class="figure-caption-medium figure-caption-text" aria-hidden="true"> <strong class="figure-label"> <p> Fig. 4.. Phylogenetic tree of all <i> Dehalobacter </i> RdhA sequences from high-quality genomes. Leaves are labelled… </p> </strong> </div> <figcaption id="figure-caption-3" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description"> <strong class="figure-label"> Fig. 4.. Phylogenetic tree of all <i>Dehalobacter</i> RdhA sequences from high-quality genomes. Leaves are labelled with the RdhA accession and <i>Dehalobacter</i> strain and are coloured by <i>Dehalobacter</i> clade and OG classification. Singletons are shown in grey and labelled A–Q. Stars indicate an OG including at least one characterized RDase; outer yellow highlights denote OG umbrellas; orange highlights indicate singleton umbrellas. </strong> </figcaption> </figure> <figure class="figure-item " itemscope itemtype="http://schema.org/ImageObject" itemprop="associatedMedia" data-slide-index="4" data-label-slug="fig-5"> <a class="figure-link" href="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/02d9/11578063/064cda01b06c/mgen-10-01324-g005.jpg" itemprop="contentUrl" aria-describedby="figure-caption-4" role="button" data-image-width="735" data-image-height="464" data-image-alt="Fig. 5." data-pmc-id="PMC11578063" data-figure-id="F5"> <img class="figure-thumb" itemprop="thumbnail" id="article-image-4" src="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/02d9/11578063/72c08c8a7a92/mgen-10-01324-g005.gif" alt="Fig. 5." /> </a> <meta itemprop="width" itemtype="http://schema.org/ImageObject" content="735"> <meta itemprop="height" itemtype="http://schema.org/ImageObject" content="464"> <div class="figure-caption figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="caption" aria-hidden="true"> <div class="caption-wrap"> <strong class="figure-label"> <p> Fig. 5.. Reconciled species-aware phylogenetic gene tree… </p> </strong> </div> </div> <div class="figure-caption-medium figure-caption-text" aria-hidden="true"> <strong class="figure-label"> <p> Fig. 5.. Reconciled species-aware phylogenetic gene tree of selected OGs. Each reconciled RDase gene tree… </p> </strong> </div> <figcaption id="figure-caption-4" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description"> <strong class="figure-label"> Fig. 5.. Reconciled species-aware phylogenetic gene tree of selected OGs. Each reconciled RDase gene tree is mapped inside the <i>Dehalobacter</i> species tree, which is coloured by clade. Each gene tree begins with an acquisition event represented by a downward triangle and has a symbol at each node representing an evolutionary event; speciation nodes are represented as circles, duplication nodes are squares and gene losses are crosses. Horizontal transfers are dotted lines starting from a diamond and ending with a downward triangular arrow. </strong> </figcaption> </figure> <figure class="figure-item " itemscope itemtype="http://schema.org/ImageObject" itemprop="associatedMedia" data-slide-index="5" data-label-slug="fig-6"> <a class="figure-link" href="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/02d9/11578063/ed018c6477fc/mgen-10-01324-g006.jpg" itemprop="contentUrl" aria-describedby="figure-caption-5" role="button" data-image-width="735" data-image-height="859" data-image-alt="Fig. 6." data-pmc-id="PMC11578063" data-figure-id="F6"> <img class="figure-thumb" itemprop="thumbnail" id="article-image-5" src="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/02d9/11578063/cfdeca076ee0/mgen-10-01324-g006.gif" alt="Fig. 6." /> </a> <meta itemprop="width" itemtype="http://schema.org/ImageObject" content="735"> <meta itemprop="height" itemtype="http://schema.org/ImageObject" content="859"> <div class="figure-caption figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="caption" aria-hidden="true"> <div class="caption-wrap"> <strong class="figure-label"> <p> Fig. 6.. Alignment of concatenated adjacent RdhA… </p> </strong> </div> </div> <div class="figure-caption-medium figure-caption-text" aria-hidden="true"> <strong class="figure-label"> <p> Fig. 6.. Alignment of concatenated adjacent RdhA sequences in RDase clusters. Each RDase is coloured… </p> </strong> </div> <figcaption id="figure-caption-5" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description"> <strong class="figure-label"> Fig. 6.. Alignment of concatenated adjacent RdhA sequences in RDase clusters. Each RDase is coloured by OG as in Fig. 4. Grey RDases represent singleton sequences (i.e. not a part of any OG). Solid lines represent >90% aa identity (RDases within the same OG); grey dashed lines represent connections between OG/singleton umbrellas (75–90% similarity). Each clade of <i>Dehalobacter</i> is demarcated by colour. </strong> </figcaption> </figure> <figure class="figure-item tail" itemscope itemtype="http://schema.org/ImageObject" itemprop="associatedMedia" data-slide-index="6" data-label-slug="fig-7"> <a class="figure-link" href="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/02d9/11578063/b1ba69fe3e3f/mgen-10-01324-g007.jpg" itemprop="contentUrl" aria-describedby="figure-caption-6" role="button" data-image-width="735" data-image-height="272" data-image-alt="Fig. 7." data-pmc-id="PMC11578063" data-figure-id="F7"> <img class="figure-thumb" itemprop="thumbnail" id="article-image-6" src="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/02d9/11578063/b6f9dc4f123a/mgen-10-01324-g007.gif" alt="Fig. 7." /> </a> <meta itemprop="width" itemtype="http://schema.org/ImageObject" content="735"> <meta itemprop="height" itemtype="http://schema.org/ImageObject" content="272"> <div class="figure-caption figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="caption" aria-hidden="true"> <div class="caption-wrap"> <strong class="figure-label"> <p> Fig. 7.. Alignment of nested recombinase island… </p> </strong> </div> </div> <div class="figure-caption-medium figure-caption-text" aria-hidden="true"> <strong class="figure-label"> <p> Fig. 7.. Alignment of nested recombinase island extracted from all closed <i> Dehalobacter </i> genomes from <i> rdhB… </i> </p> </strong> </div> <figcaption id="figure-caption-6" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description"> <strong class="figure-label"> Fig. 7.. Alignment of nested recombinase island extracted from all closed <i>Dehalobacter</i> genomes from <i>rdhB</i> to <i>rumA</i>. Each coloured rectangle represents an LCB, and highlighted regions represent consistently consecutive blocks. CE, conjugative element; Tn, transposon; IS, insertion sequence. </strong> </figcaption> </figure> <figure class="figure-item tail" itemscope itemtype="http://schema.org/ImageObject" itemprop="associatedMedia" data-slide-index="7" data-label-slug="fig-8"> <a class="figure-link" href="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/02d9/11578063/2c03ccfb1049/mgen-10-01324-g008.jpg" itemprop="contentUrl" aria-describedby="figure-caption-7" role="button" data-image-width="732" data-image-height="374" data-image-alt="Fig. 8." data-pmc-id="PMC11578063" data-figure-id="F8"> <img class="figure-thumb" itemprop="thumbnail" id="article-image-7" src="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/02d9/11578063/cde018a3bab7/mgen-10-01324-g008.gif" alt="Fig. 8." /> </a> <meta itemprop="width" itemtype="http://schema.org/ImageObject" content="732"> <meta itemprop="height" itemtype="http://schema.org/ImageObject" content="374"> <div class="figure-caption figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="caption" aria-hidden="true"> <div class="caption-wrap"> <strong class="figure-label"> <p> Fig. 8.. Relative strain composition of <i> Dehalobacter… </i> </p> </strong> </div> </div> <div class="figure-caption-medium figure-caption-text" aria-hidden="true"> <strong class="figure-label"> <p> Fig. 8.. Relative strain composition of <i> Dehalobacter </i> population in (a) SC05-UT and (b) DCME during… </p> </strong> </div> <figcaption id="figure-caption-7" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description"> <strong class="figure-label"> Fig. 8.. Relative strain composition of <i>Dehalobacter</i> population in (a) SC05-UT and (b) DCME during enrichment (T<sub>0</sub>=DCME inoculation, Fig. S1). Strain SAD is in orange, and strain DAD is in blue. </strong> </figcaption> </figure> </div> <div class="see-all actions-bar"> <button class="show-more" aria-controls="slides-container" data-ga-category="figure" data-ga-action="show_all"> All figures (8) </button> </div>  <div class="pswp figures-dialog" id="figures-dialog" tabindex="-1" role="dialog" aria-hidden="true" data-image-gallery-uid="article-figures" aria-label="Figures Dialog">  <div class="pswp__bg"></div>  <div class="pswp__scroll-wrap">  <div class="pswp__container"> <div class="pswp__item"></div> <div class="pswp__item"></div> <div class="pswp__item"></div> </div>  <div class="pswp__ui pswp__ui--hidden"> <div class="pswp__top-bar">  <div class="pswp__counter"></div> <button class="pswp__button pswp__button--close" title="Close (Esc)"></button> <button class="pswp__button pswp__button--share" title="Share"></button> <button class="pswp__button pswp__button--fs" title="Toggle fullscreen"></button> <button class="pswp__button pswp__button--zoom" title="Zoom in/out"></button>   <div class="pswp__preloader"> <div class="pswp__preloader__icn"> <div class="pswp__preloader__cut"> <div class="pswp__preloader__donut"></div> </div> </div> </div> </div> <div class="pswp__share-modal pswp__share-modal--hidden pswp__single-tap"> <div class="pswp__share-tooltip"></div> </div> <button class="pswp__button pswp__button--arrow--left" title="Previous (arrow left)"> </button> <button class="pswp__button pswp__button--arrow--right" title="Next (arrow right)"> </button> <div class="pswp__caption"> <div class="pswp__caption__center"></div> </div> </div> </div> </div> <div class="figure-dialog-caption"> <div class="figure-caption-link-container"> <a class="figure-caption-link" href="#">See this image and copyright information in PMC</a> </div> <div class="figure-caption-center" data-expand-title="click to show full caption" data-collapse-title="click to hide full caption"> </div> <button class="figure-caption-toggle-btn" aria-label="show full caption" data-expand-text="show full caption" data-collapse-text="hide full caption">  </button> </div> </div> <div class="references" id="references"> <h2 class="title"> References </h2> <div id='top-references-list' class="references-lists-container"> <div class="refs-list"> <ol id="top-references-list-1" class="references-list"> <li> <ol class="references-and-notes-list"> <li class="skip-numbering" value="1"> Holliger C, Hahn D, Harmsen H, Ludwig W, Schumacher W, et al. 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Pangenomic insights into Dehalobacter evolution and acquisition of functional genes for bioremediation - PubMed