CINXE.COM
Search
<!DOCTYPE html> <html lang="en" class="no-js"> <head> <meta charset="UTF-8"> <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes"> <title>Search</title> <meta id="meta-title" property="citation_title" content="Search"/> <meta id="og-title" property="og:title" content="Search"/> <meta name="twitter:widgets:autoload" content="off"/> <meta name="twitter:dnt" content="on"/> <meta name="twitter:widgets:csp" content="on"/> <meta name="google-site-verification" content="lQbRRf0vgPqMbnbCsgELjAjIIyJjiIWo917M7hBshvI"/> <meta id="og-image" property="og:image" content="https://escholarship.org/images/escholarship-facebook2.jpg"/> <meta id="og-image-width" property="og:image:width" content="1242"/> <meta id="og-image-height" property="og:image:height" content="1242"/> <link rel="stylesheet" href="/css/main-62e3023ddd136de2.css"> <link rel="resource" type="application/l10n" href="/node_modules/pdfjs-embed2/dist/locale/locale.properties"> <noscript><style> .jsonly { display: none } </style></noscript> <!-- Matomo --> <!-- TBD Configure Matomo for SPA https://developer.matomo.org/guides/spa-tracking --> <script> var _paq = window._paq = window._paq || []; /* tracker methods like "setCustomDimension" should be called before "trackPageView" */ _paq.push(['trackPageView']); _paq.push(['enableLinkTracking']); (function() { var u="//matomo.cdlib.org/"; _paq.push(['setTrackerUrl', u+'matomo.php']); _paq.push(['setSiteId', '7']); var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0]; g.async=true; g.src=u+'matomo.js'; s.parentNode.insertBefore(g,s); })(); </script> <!-- End Matomo Code --> </head> <body> <div id="main"><div data-reactroot=""><div class="body"><a href="#maincontent" class="c-skipnav">Skip to main content</a><div class="l_search"><div><div style="margin-top:-10px"></div><header id="#top" class="c-header"><a class="c-header__logo2" href="/"><picture><source srcSet="/images/logo_eschol-small.svg" media="(min-width: 870px)"/><img src="/images/logo_eschol-mobile.svg" alt="eScholarship"/></picture><div class="c-header__logo2-tagline">Open Access Publications from the University of California</div></a><div class="c-header__search"><form class="c-search1"><label class="c-search1__label" for="c-search1__field">search</label><input type="search" id="c-search1__field" name="q" class="c-search1__field" placeholder="Search over 500,000 items" autoCapitalize="off" value="author:Pett-Ridge, Jennifer"/><button type="submit" class="c-search1__submit-button" aria-label="submit search"></button><button type="button" class="c-search1__search-close-button" aria-label="close search field"></button></form></div><button class="c-header__search-open-button" aria-label="open search field"></button></header></div><div class="c-navbar"><nav class="c-nav"><details open="" class="c-nav__main"><summary class="c-nav__main-button">Menu</summary><ul class="c-nav__main-items"><li><details class="c-nav__sub"><summary class="c-nav__sub-button">About eScholarship</summary><div class="c-nav__sub-items"><button class="c-nav__sub-items-button" aria-label="return to menu">Main Menu</button><ul><li><a href="/aboutEschol">About eScholarship</a></li><li><a href="/repository">eScholarship Repository</a></li><li><a href="/publishing">eScholarship Publishing</a></li><li><a href="/policies">Site policies</a></li><li><a href="/terms">Terms of Use and Copyright Information</a></li><li><a href="/privacyPolicy">Privacy statement</a></li></ul></div></details></li><li><details class="c-nav__sub"><summary class="c-nav__sub-button">Campus Sites</summary><div class="c-nav__sub-items"><button class="c-nav__sub-items-button" aria-label="return to menu">Main Menu</button><ul><li><a href="/uc/ucb">UC Berkeley</a></li><li><a href="/uc/ucd">UC Davis</a></li><li><a href="/uc/uci">UC Irvine</a></li><li><a href="/uc/ucla">UCLA</a></li><li><a href="/uc/ucm">UC Merced</a></li><li><a href="/uc/ucr">UC Riverside</a></li><li><a href="/uc/ucsd">UC San Diego</a></li><li><a href="/uc/ucsf">UCSF</a></li><li><a href="/uc/ucsb">UC Santa Barbara</a></li><li><a href="/uc/ucsc">UC Santa Cruz</a></li><li><a href="/uc/ucop">UC Office of the President</a></li><li><a href="/uc/lbnl">Lawrence Berkeley National Laboratory</a></li><li><a href="/uc/anrcs">UC Agriculture & Natural Resources</a></li></ul></div></details></li><li><a href="/ucoapolicies">UC Open Access Policies</a></li><li><a href="/publishing">eScholarship Publishing</a></li></ul></details></nav></div><form id="facetForm" class="c-columns"><aside><div><div class="c-filter"><h1 class="c-filter__heading">Your search: "author:Pett-Ridge, Jennifer"</h1><input type="hidden" name="q" value="author:Pett-Ridge, Jennifer"/><div class="c-filter__results">66<!-- --> results</div><div class="c-filter__inactive-note">No filters applied</div><details class="c-filter__active" open=""><summary><span><strong></strong> filter<!-- -->s<!-- --> applied</span></summary><button class="c-filter__clear-all">clear all</button><ul class="c-filter__active-list"></ul></details><a href="https://help.escholarship.org/support/solutions/articles/9000148939-using-advanced-search-beta-" class="c-filter__tips">Search tips</a></div><div class="c-refine--has-drawer"><button class="c-refine__button--open">Refine Results</button><button class="c-refine__button--close" hidden="">Back to Results</button><div class="c-refine__drawer--closed"><details class="c-facetbox" open=""><summary class="c-facetbox__summary"><span id="facetbox0">Type of Work</span></summary><fieldset aria-labelledby="facetbox0"><ul class="c-checkbox"><li class=""><input type="checkbox" id="type_of_work-article" class="c-checkbox__input" name="type_of_work" value="article"/><label for="type_of_work-article" class="c-checkbox__label">Article<!-- --> (<!-- -->65<!-- -->)</label></li><li class=""><input type="checkbox" id="type_of_work-monograph" class="c-checkbox__input" name="type_of_work" value="monograph"/><label for="type_of_work-monograph" class="c-checkbox__label">Book<!-- --> (<!-- -->0<!-- -->)</label></li><li class=""><input type="checkbox" id="type_of_work-dissertation" class="c-checkbox__input" name="type_of_work" value="dissertation"/><label for="type_of_work-dissertation" class="c-checkbox__label">Theses<!-- --> (<!-- -->0<!-- -->)</label></li><li class=""><input type="checkbox" id="type_of_work-multimedia" class="c-checkbox__input" name="type_of_work" value="multimedia"/><label for="type_of_work-multimedia" class="c-checkbox__label">Multimedia<!-- --> (<!-- -->0<!-- -->)</label></li></ul></fieldset></details><details class="c-facetbox" open=""><summary class="c-facetbox__summary"><span id="facetbox1">Peer Review</span></summary><fieldset aria-labelledby="facetbox1"><ul class="c-checkbox"><li class=""><input type="checkbox" id="peer_reviewed-1" class="c-checkbox__input" name="peer_reviewed" value="1"/><label for="peer_reviewed-1" class="c-checkbox__label">Peer-reviewed only<!-- --> (<!-- -->66<!-- -->)</label></li></ul></fieldset></details><details class="c-facetbox"><summary class="c-facetbox__summary"><span id="facetbox2">Supplemental Material</span></summary><fieldset aria-labelledby="facetbox2"><ul class="c-checkbox--2column"><li class=""><input type="checkbox" id="supp_file_types-video" class="c-checkbox__input" name="supp_file_types" value="video"/><label for="supp_file_types-video" class="c-checkbox__label">Video<!-- --> (<!-- -->0<!-- -->)</label></li><li class=""><input type="checkbox" id="supp_file_types-audio" class="c-checkbox__input" name="supp_file_types" value="audio"/><label for="supp_file_types-audio" class="c-checkbox__label">Audio<!-- --> (<!-- -->0<!-- -->)</label></li><li class=""><input type="checkbox" id="supp_file_types-images" class="c-checkbox__input" name="supp_file_types" value="images"/><label for="supp_file_types-images" class="c-checkbox__label">Images<!-- --> (<!-- -->0<!-- -->)</label></li><li class=""><input type="checkbox" id="supp_file_types-zip" class="c-checkbox__input" name="supp_file_types" value="zip"/><label for="supp_file_types-zip" class="c-checkbox__label">Zip<!-- --> (<!-- -->0<!-- -->)</label></li><li class=""><input type="checkbox" id="supp_file_types-other_files" class="c-checkbox__input" name="supp_file_types" value="other files"/><label for="supp_file_types-other_files" class="c-checkbox__label">Other files<!-- --> (<!-- -->0<!-- -->)</label></li></ul></fieldset></details><details class="c-facetbox"><summary class="c-facetbox__summary"><span id="facetbox3">Publication Year</span></summary><fieldset aria-labelledby="facetbox3"><div class="c-pubyear"><div class="c-pubyear__field"><label for="c-pubyear__textfield1">From:</label><input type="text" id="c-pubyear__textfield1" name="pub_year_start" maxLength="4" placeholder="1900" value=""/></div><div class="c-pubyear__field"><label for="c-pubyear__textfield2">To:</label><input type="text" id="c-pubyear__textfield2" name="pub_year_end" maxLength="4" placeholder="2024" value=""/></div><button class="c-pubyear__button">Apply</button></div></fieldset></details><details class="c-facetbox"><summary class="c-facetbox__summary"><span id="facetbox4">Campus</span></summary><fieldset aria-labelledby="facetbox4"><ul class="c-checkbox"><li class=""><input type="checkbox" id="campuses-ucb" class="c-checkbox__input" name="campuses" value="ucb"/><label for="campuses-ucb" class="c-checkbox__label">UC Berkeley<!-- --> (<!-- -->52<!-- -->)</label></li><li class=""><input type="checkbox" id="campuses-ucd" class="c-checkbox__input" name="campuses" value="ucd"/><label for="campuses-ucd" class="c-checkbox__label">UC Davis<!-- --> (<!-- -->7<!-- -->)</label></li><li class=""><input type="checkbox" id="campuses-uci" class="c-checkbox__input" name="campuses" value="uci"/><label for="campuses-uci" class="c-checkbox__label">UC Irvine<!-- --> (<!-- -->1<!-- -->)</label></li><li class=""><input type="checkbox" id="campuses-ucla" class="c-checkbox__input" name="campuses" value="ucla"/><label for="campuses-ucla" class="c-checkbox__label">UCLA<!-- --> (<!-- -->5<!-- -->)</label></li><li class=""><input type="checkbox" id="campuses-ucm" class="c-checkbox__input" name="campuses" value="ucm"/><label for="campuses-ucm" class="c-checkbox__label">UC Merced<!-- --> (<!-- -->10<!-- -->)</label></li><li class=""><input type="checkbox" id="campuses-ucr" class="c-checkbox__input" name="campuses" value="ucr"/><label for="campuses-ucr" class="c-checkbox__label">UC Riverside<!-- --> (<!-- -->2<!-- -->)</label></li><li class=""><input type="checkbox" id="campuses-ucsd" class="c-checkbox__input" name="campuses" value="ucsd"/><label for="campuses-ucsd" class="c-checkbox__label">UC San Diego<!-- --> (<!-- -->1<!-- -->)</label></li><li class=""><input type="checkbox" id="campuses-ucsf" class="c-checkbox__input" name="campuses" value="ucsf"/><label for="campuses-ucsf" class="c-checkbox__label">UCSF<!-- --> (<!-- -->0<!-- -->)</label></li><li class=""><input type="checkbox" id="campuses-ucsb" class="c-checkbox__input" name="campuses" value="ucsb"/><label for="campuses-ucsb" class="c-checkbox__label">UC Santa Barbara<!-- --> (<!-- -->0<!-- -->)</label></li><li class=""><input type="checkbox" id="campuses-ucsc" class="c-checkbox__input" name="campuses" value="ucsc"/><label for="campuses-ucsc" class="c-checkbox__label">UC Santa Cruz<!-- --> (<!-- -->0<!-- -->)</label></li><li class=""><input type="checkbox" id="campuses-ucop" class="c-checkbox__input" name="campuses" value="ucop"/><label for="campuses-ucop" class="c-checkbox__label">UC Office of the President<!-- --> (<!-- -->22<!-- -->)</label></li><li class=""><input type="checkbox" id="campuses-lbnl" class="c-checkbox__input" name="campuses" value="lbnl"/><label for="campuses-lbnl" class="c-checkbox__label">Lawrence Berkeley National Laboratory<!-- --> (<!-- -->56<!-- -->)</label></li><li class=""><input type="checkbox" id="campuses-anrcs" class="c-checkbox__input" name="campuses" value="anrcs"/><label for="campuses-anrcs" class="c-checkbox__label">UC Agriculture & Natural Resources<!-- --> (<!-- -->0<!-- -->)</label></li></ul></fieldset></details><details class="c-facetbox"><summary class="c-facetbox__summary"><span id="facetbox5">Department</span></summary><fieldset aria-labelledby="facetbox5"><ul class="c-checkbox"><li class=""><input type="checkbox" id="departments-lbnl_bs" class="c-checkbox__input" name="departments" value="lbnl_bs"/><label for="departments-lbnl_bs" class="c-checkbox__label">BioSciences<!-- --> (<!-- -->28<!-- -->)</label></li><li class=""><input type="checkbox" id="departments-rgpo" class="c-checkbox__input" name="departments" value="rgpo"/><label for="departments-rgpo" class="c-checkbox__label">Research Grants Program Office<!-- --> (<!-- -->22<!-- -->)</label></li><li class=""><input type="checkbox" id="departments-lbnl_ees" class="c-checkbox__input" name="departments" value="lbnl_ees"/><label for="departments-lbnl_ees" class="c-checkbox__label">Earth & Environmental Sciences<!-- --> (<!-- -->15<!-- -->)</label></li><li class=""><input type="checkbox" id="departments-lbnl_es" class="c-checkbox__input" name="departments" value="lbnl_es"/><label for="departments-lbnl_es" class="c-checkbox__label">Energy Sciences<!-- --> (<!-- -->6<!-- -->)</label></li><li class=""><input type="checkbox" id="departments-ucb_chemistry" class="c-checkbox__input" name="departments" value="ucb_chemistry"/><label for="departments-ucb_chemistry" class="c-checkbox__label">College of Chemistry<!-- --> (<!-- -->3<!-- -->)</label></li><li class=""><input type="checkbox" id="departments-ucb_eps" class="c-checkbox__input" name="departments" value="ucb_eps"/><label for="departments-ucb_eps" class="c-checkbox__label">Department of Earth and Planetary Science<!-- --> (<!-- -->3<!-- -->)</label></li></ul><div id="facetModalBase-departments"><button class="c-facetbox__show-more">Show more</button></div></fieldset></details><details class="c-facetbox"><summary class="c-facetbox__summary"><span id="facetbox6">Journal</span></summary><fieldset aria-labelledby="facetbox6"><ul class="c-checkbox"></ul></fieldset></details><details class="c-facetbox"><summary class="c-facetbox__summary"><span id="facetbox7">Discipline</span></summary><fieldset aria-labelledby="facetbox7"><ul class="c-checkbox"><li class=""><input type="checkbox" id="disciplines-Life_Sciences" class="c-checkbox__input" name="disciplines" value="Life Sciences"/><label for="disciplines-Life_Sciences" class="c-checkbox__label">Life Sciences<!-- --> (<!-- -->1<!-- -->)</label></li><li class=""><input type="checkbox" id="disciplines-Physical_Sciences_and_Mathematics" class="c-checkbox__input" name="disciplines" value="Physical Sciences and Mathematics"/><label for="disciplines-Physical_Sciences_and_Mathematics" class="c-checkbox__label">Physical Sciences and Mathematics<!-- --> (<!-- -->1<!-- -->)</label></li></ul></fieldset></details><details class="c-facetbox"><summary class="c-facetbox__summary"><span id="facetbox8">Reuse License</span></summary><fieldset aria-labelledby="facetbox8"><ul class="c-checkbox"><li class="c-checkbox__attrib-cc-by"><input type="checkbox" id="rights-CC_BY" class="c-checkbox__input" name="rights" value="CC BY"/><label for="rights-CC_BY" class="c-checkbox__label">BY - Attribution required<!-- --> (<!-- -->10<!-- -->)</label></li><li class="c-checkbox__attrib-cc-by-nc"><input type="checkbox" id="rights-CC_BY-NC" class="c-checkbox__input" name="rights" value="CC BY-NC"/><label for="rights-CC_BY-NC" class="c-checkbox__label">BY-NC - Attribution; NonCommercial use only<!-- --> (<!-- -->2<!-- -->)</label></li><li class="c-checkbox__attrib-cc-by-nc-nd"><input type="checkbox" id="rights-CC_BY-NC-ND" class="c-checkbox__input" name="rights" value="CC BY-NC-ND"/><label for="rights-CC_BY-NC-ND" class="c-checkbox__label">BY-NC-ND - Attribution; NonCommercial use; No derivatives<!-- --> (<!-- -->1<!-- -->)</label></li></ul></fieldset></details></div></div><button type="submit" id="facet-form-submit" style="display:none">Search</button></div></aside><main id="maincontent"><section class="o-columnbox1"><header><h2 class="o-columnbox1__heading" aria-live="polite">Scholarly Works (<!-- -->66 results<!-- -->)</h2></header><div class="c-sortpagination"><div class="c-sort"><div class="o-input__droplist1"><label for="c-sort1">Sort By:</label><select name="sort" id="c-sort1" form="facetForm"><option selected="" value="rel">Relevance</option><option value="a-title">A-Z By Title</option><option value="z-title">Z-A By Title</option><option value="a-author">A-Z By Author</option><option value="z-author">Z-A By Author</option><option value="asc">Date Ascending</option><option value="desc">Date Descending</option></select></div><div class="o-input__droplist1 c-sort__page-input"><label for="c-sort2">Show:</label><select name="rows" id="c-sort2" form="facetForm"><option selected="" value="10">10</option><option value="20">20</option><option value="30">30</option><option value="40">40</option><option value="50">50</option></select></div></div><input type="hidden" name="start" form="facetForm" value="0"/><nav class="c-pagination--next"><ul><li><a href="" aria-label="you are on result set 1" class="c-pagination__item--current">1</a></li><li><a href="" aria-label="go to result set 2" class="c-pagination__item">2</a></li><li><a href="" aria-label="go to result set 3" class="c-pagination__item">3</a></li><li><a href="" aria-label="go to result set 4" class="c-pagination__item">4</a></li><li><a href="" aria-label="go to result set 7" class="c-pagination__item">7</a></li><li class="c-pagination__next"><a href="" aria-label="go to Next result set">Next</a></li></ul></nav></div><section class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li><li class="c-scholworks__tag-peer">Peer Reviewed</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/1bw9p4dj"><div class="c-clientmarkup">Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development.</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3ASieradzki%2C%20Ella">Sieradzki, Ella</a>; </li><li><a href="/search/?q=author%3ANuccio%2C%20Erin">Nuccio, Erin</a>; </li><li><a href="/search/?q=author%3APett-Ridge%2C%20Jennifer">Pett-Ridge, Jennifer</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AFirestone%2C%20Mary">Firestone, Mary</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/ucb_postprints">UC Berkeley Previously Published Works</a> (<!-- -->2023<!-- -->)</div><div class="c-scholworks__abstract"><div class="c-clientmarkup">Interactions between plant roots and rhizosphere bacteria modulate nitrogen (N)-cycling processes and create habitats rich in low molecular weight compounds (exudates) and complex organic molecules (decaying root litter) compared to those of bulk soil. Microbial N-cycling is regulated by edaphic conditions and genes from many interconnected metabolic pathways, but most studies of soil N-cycling gene expression have focused on single pathways. Currently, we lack a comprehensive understanding of the interplay between soil N-cycling gene regulation, spatial habitat, and time. We present results from a replicated time series of soil metatranscriptomes; we followed gene expression of multiple N transformations in four soil habitats (rhizosphere, detritusphere, rhizo-detritusphere, and bulk soil) during active root growth for the annual grass, Avena fatua. The presence of root litter and living roots significantly altered the trajectories of N-cycling gene expression. Upregulation of assimilatory nitrate reduction in the rhizosphere suggests that rhizosphere bacteria were actively competing with roots for nitrate. Simultaneously, ammonium assimilatory pathways were upregulated in both rhizosphere and detritusphere soil, which could have limited N availability to plants. The detritusphere supported dissimilatory processes DNRA and denitrification. Expression of nitrification genes was dominated by three phylotypes of Thaumarchaeota and was upregulated in bulk soil. Unidirectional ammonium assimilation and its regulatory genes (GS/GOGAT) were upregulated near relatively young roots and highly decayed root litter, suggesting N may have been limiting in these habitats (GS/GOGAT is typically activated under N limitation). Our comprehensive analysis indicates that differences in carbon and inorganic N availability control contemporaneous transcription of N-cycling pathways in soil habitats. IMPORTANCE Plant roots modulate microbial nitrogen (N) cycling by regulating the supply of root-derived carbon and nitrogen uptake. These differences in resource availability cause distinct micro-habitats to develop: soil near living roots, decaying roots, near both, or outside the direct influence of roots. While many environmental factors and genes control the microbial processes involved in the nitrogen cycle, most research has focused on single genes and pathways, neglecting the interactive effects these pathways have on each other. The processes controlled by these pathways determine consumption and production of N by soil microorganisms. We followed the expression of N-cycling genes in four soil microhabitats over a period of active root growth for an annual grass. We found that the presence of root litter and living roots significantly altered gene expression involved in multiple nitrogen pathways, as well as tradeoffs between pathways, which ultimately regulate N availability to plants.</div></div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/1bw9p4dj"><img src="/cms-assets/c95204361f486b527ca8c4d0567d31b42d6301e0ee620eb34f33575651914ffe" alt="Cover page: Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development."/></a></div></section><section class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li><li class="c-scholworks__tag-peer">Peer Reviewed</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/9g04p5md"><div class="c-clientmarkup">Mineral protection of soil carbon counteracted by root exudates</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AKeiluweit%2C%20Marco">Keiluweit, Marco</a>; </li><li><a href="/search/?q=author%3ABougoure%2C%20Jeremy%20J">Bougoure, Jeremy J</a>; </li><li><a href="/search/?q=author%3ANico%2C%20Peter%20S">Nico, Peter S</a>; </li><li><a href="/search/?q=author%3APett-Ridge%2C%20Jennifer">Pett-Ridge, Jennifer</a>; </li><li><a href="/search/?q=author%3AWeber%2C%20Peter%20K">Weber, Peter K</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AKleber%2C%20Markus">Kleber, Markus</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/ucb_postprints">UC Berkeley Previously Published Works</a> (<!-- -->2015<!-- -->)</div><div class="c-scholworks__abstract"><div class="c-clientmarkup">Multiple lines of existing evidence suggest that climate change enhances root exudation of organic compounds into soils. Recent experimental studies show that increased exudate inputs may cause a net loss of soil carbon. This stimulation of microbial carbon mineralization ('priming') is commonly rationalized by the assumption that exudates provide a readily bioavailable supply of energy for the decomposition of native soil carbon (co-metabolism). Here we show that an alternate mechanism can cause carbon loss of equal or greater magnitude. We find that a common root exudate, oxalic acid, promotes carbon loss by liberating organic compounds from protective associations with minerals. By enhancing microbial access to previously mineral-protected compounds, this indirect mechanism accelerated carbon loss more than simply increasing the supply of energetically more favourable substrates. Our results provide insights into the coupled biotic-abiotic mechanisms underlying the 'priming'phenomenon and challenge the assumption that mineral-associated carbon is protected from microbial cycling over millennial timescales.</div></div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/9g04p5md"><img src="/cms-assets/806fe413ebff7d8828cc6166b302fc58ed5401fd85da59893759d6e3ba715cf8" alt="Cover page: Mineral protection of soil carbon counteracted by root exudates"/></a></div></section><section class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li><li class="c-scholworks__tag-peer">Peer Reviewed</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/4kt6d5gt"><div class="c-clientmarkup">Long-term litter decomposition controlled by manganese redox cycling</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AKeiluweit%2C%20Marco">Keiluweit, Marco</a>; </li><li><a href="/search/?q=author%3ANico%2C%20Peter">Nico, Peter</a>; </li><li><a href="/search/?q=author%3AHarmon%2C%20Mark%20E">Harmon, Mark E</a>; </li><li><a href="/search/?q=author%3AMao%2C%20Jingdong">Mao, Jingdong</a>; </li><li><a href="/search/?q=author%3APett-Ridge%2C%20Jennifer">Pett-Ridge, Jennifer</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AKleber%2C%20Markus">Kleber, Markus</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/ucb_postprints">UC Berkeley Previously Published Works</a> (<!-- -->2015<!-- -->)</div><div class="c-scholworks__abstract"><div class="c-clientmarkup">Litter decomposition is a keystone ecosystem process impacting nutrient cycling and productivity, soil properties, and the terrestrial carbon (C) balance, but the factors regulating decomposition rate are still poorly understood. Traditional models assume that the rate is controlled by litter quality, relying on parameters such as lignin content as predictors. However, a strong correlation has been observed between the manganese (Mn) content of litter and decomposition rates across a variety of forest ecosystems. Here, we show that long-term litter decomposition in forest ecosystems is tightly coupled to Mn redox cycling. Over 7 years of litter decomposition, microbial transformation of litter was paralleled by variations in Mn oxidation state and concentration. A detailed chemical imaging analysis of the litter revealed that fungi recruit and redistribute unreactive Mn(2+) provided by fresh plant litter to produce oxidative Mn(3+) species at sites of active decay, with Mn eventually accumulating as insoluble Mn(3+/4+) oxides. Formation of reactive Mn(3+) species coincided with the generation of aromatic oxidation products, providing direct proof of the previously posited role of Mn(3+)-based oxidizers in the breakdown of litter. Our results suggest that the litter-decomposing machinery at our coniferous forest site depends on the ability of plants and microbes to supply, accumulate, and regenerate short-lived Mn(3+) species in the litter layer. This observation indicates that biogeochemical constraints on bioavailability, mobility, and reactivity of Mn in the plant-soil system may have a profound impact on litter decomposition rates.</div></div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/4kt6d5gt"><img src="/cms-assets/69aacc806284dd3c275df6d1e1ac681fd8a100b36e39c000ca840f1c98cb2ce5" alt="Cover page: Long-term litter decomposition controlled by manganese redox cycling"/></a></div></section><section class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li><li class="c-scholworks__tag-peer">Peer Reviewed</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/2k51w8rn"><div class="c-clientmarkup">Fast redox switches lead to rapid transformation of goethite in humid tropical soils: A Mössbauer spectroscopy study</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3ABhattacharyya%2C%20Amrita">Bhattacharyya, Amrita</a>; </li><li><a href="/search/?q=author%3AKukkadapu%2C%20Ravi%20K">Kukkadapu, Ravi K</a>; </li><li><a href="/search/?q=author%3ABowden%2C%20Mark">Bowden, Mark</a>; </li><li><a href="/search/?q=author%3APett%E2%80%90Ridge%2C%20Jennifer">Pett‐Ridge, Jennifer</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3ANico%2C%20Peter%20S">Nico, Peter S</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/ucb_postprints">UC Berkeley Previously Published Works</a> (<!-- -->2022<!-- -->)</div><div class="c-scholworks__abstract"><div class="c-clientmarkup">Humid tropical forest soils experience frequent rainfall, which limits oxygen diffusion and creates redox heterogeneity in upland soils. In this study we gauged the effect of short-term anoxic conditions on Fe mineralogy of relatively Fe- and C-rich surface soils (C/Fe mole ratio ∼5) from a humid tropical forest in Puerto Rico. Soils subjected to 4-d oxic/anoxic oscillation were characterized by selective chemical extractions, Mössbauer spectroscopy (MBS), and X-ray diffraction. Chemical extraction data suggested that rapidly switching redox conditions had subtle effects on bulk Fe mineralogy. Mössbauer, on the other hand, indicated that (a) the soil Fe is a mixture of goethites of varying characteristics with minor contributions from ferrihydrite (<5%) and Fe(III)-organic matter (OM) phases (∼10%), and (b) anoxic conditions rapidly transformed all forms of goethite to relatively stable Fe oxides. Such fast changes in goethite features could be due to rapid depletion and sorption of bio-released structural Al or sorbed OM onto residual soil components. The rapid temporal changes in MBS parameters and corresponding pore water nominal oxidation state of C values suggest that Fe-C transformations in these upland tropical soils are complex and intricately coupled. A comprehensive understanding of the fate of Fe, Al, and OM (Fe-organic moieties) during redox switches and concurrent changes in pore water chemistry is critical for development of robust transport models in humid tropical soils, which are subject to episodic low-redox events.</div></div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/2k51w8rn"><img src="/cms-assets/e7a0c93e31f96541a88bb284724a51642cba8f158ab36f27d5b6f8e6142825d3" alt="Cover page: Fast redox switches lead to rapid transformation of goethite in humid tropical soils: A Mössbauer spectroscopy study"/></a><a href="https://creativecommons.org/licenses/by/4.0/" class="c-scholworks__license"><img class="c-lazyimage" data-src="/images/cc-by-small.svg" alt="Creative Commons 'BY' version 4.0 license"/></a></div></section><section class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li><li class="c-scholworks__tag-peer">Peer Reviewed</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/5d64r4sk"><div class="c-clientmarkup">Phosphorus fractionation responds to dynamic redox conditions in a humid tropical forest soil</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3ALin%2C%20Yang">Lin, Yang</a>; </li><li><a href="/search/?q=author%3ABhattacharyya%2C%20Amrita">Bhattacharyya, Amrita</a>; </li><li><a href="/search/?q=author%3ACampbell%2C%20Ashley%20N">Campbell, Ashley N</a>; </li><li><a href="/search/?q=author%3ANico%2C%20Peter%20S">Nico, Peter S</a>; </li><li><a href="/search/?q=author%3APett-Ridge%2C%20Jennifer">Pett-Ridge, Jennifer</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3ASilver%2C%20Whendee%20L">Silver, Whendee L</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/ucb_postprints">UC Berkeley Previously Published Works</a> (<!-- -->2018<!-- -->)</div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/5d64r4sk"><img src="/cms-assets/4de1a17e6e17cb7f57d443bd417d316fafd7c8724779a42d6341e4365402784b" alt="Cover page: Phosphorus fractionation responds to dynamic redox conditions in a humid tropical forest soil"/></a></div></section><section class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li><li class="c-scholworks__tag-peer">Peer Reviewed</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/5954v7s7"><div class="c-clientmarkup">Managing Plant Microbiomes for Sustainable Biofuel Production</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AZhalnina%2C%20Kateryna">Zhalnina, Kateryna</a>; </li><li><a href="/search/?q=author%3AHawkes%2C%20Christine">Hawkes, Christine</a>; </li><li><a href="/search/?q=author%3AShade%2C%20Ashley">Shade, Ashley</a>; </li><li><a href="/search/?q=author%3AFirestone%2C%20Mary%20K">Firestone, Mary K</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3APett-Ridge%2C%20Jennifer">Pett-Ridge, Jennifer</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/ucb_postprints">UC Berkeley Previously Published Works</a> (<!-- -->2021<!-- -->)</div><div class="c-scholworks__abstract"><div class="c-clientmarkup">The development of environmentally sustainable, economical, and reliable sources of energy is one of the great challenges of the 21st century. Large-scale cultivation of cellulosic feedstock crops (henceforth, bioenergy crops) is considered one of themost promising renewable sources for liquid transportation fuels. However, the mandate to develop a viable cellulosic bioenergy industry is accompanied by an equally urgent mandate to deliver not only cheap reliable biomass but also ecosystembenefits, including efficient use of water, nitrogen, and phosphorous; restored soil health; and net negative carbon emissions. Thus, sustainable bioenergy crop production may involve new agricultural practices or feedstocks and should be reliable, cost effective, and minimal input,without displacing crops currently grown for food production on fertile land. In this editorial perspective for the Phytobiomes Journal Focus Issue on Phytobiomes of Bioenergy Crops and Agroecosystems, we consider the microbiomes associated with bioenergy crops, the effects beneficial microbes have on their hosts, and potential ecosystem impacts of these interactions.We also address outstanding questions, major advances, and emerging biotechnological strategies to design and manipulate bioenergy crop microbiomes. This approach could simultaneously increase crop yields and provide important ecosystem services for a sustainable energy future.</div></div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/5954v7s7"><img src="/cms-assets/93a6995432625f08402197574b7adb16ae774a3327c4542c1758839145d362ea" alt="Cover page: Managing Plant Microbiomes for Sustainable Biofuel Production"/></a></div></section><section class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li><li class="c-scholworks__tag-peer">Peer Reviewed</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/58m9d2d9"><div class="c-clientmarkup">Initial soil organic carbon stocks govern changes in soil carbon: Reality or artifact?</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3ASlessarev%2C%20Eric">Slessarev, Eric</a>; </li><li><a href="/search/?q=author%3AMayer%2C%20Allegra">Mayer, Allegra</a>; </li><li><a href="/search/?q=author%3AKelly%2C%20Courtland">Kelly, Courtland</a>; </li><li><a href="/search/?q=author%3AGeorgiou%2C%20Katerina">Georgiou, Katerina</a>; </li><li><a href="/search/?q=author%3APett-Ridge%2C%20Jennifer">Pett-Ridge, Jennifer</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3ANuccio%2C%20Erin">Nuccio, Erin</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/lbnl_rw">LBL Publications</a> (<!-- -->2023<!-- -->)</div><div class="c-scholworks__abstract"><div class="c-clientmarkup">Changes in soil organic carbon (SOC) storage have the potential to affect global climate; hence identifying environments with a high capacity to gain or lose SOC is of broad interest. Many cross-site studies have found that SOC-poor soils tend to gain or retain carbon more readily than SOC-rich soils. While this pattern may partly reflect reality, here we argue that it can also be created by a pair of statistical artifacts. First, soils that appear SOC-poor purely due to random variation will tend to yield more moderate SOC estimates upon resampling and hence will appear to accrue or retain more SOC than SOC-rich soils. This phenomenon is an example of regression to the mean. Second, normalized metrics of SOC change-such as relative rates and response ratios-will by definition show larger changes in SOC at lower initial SOC levels, even when the absolute change in SOC does not depend on initial SOC. These two artifacts create an exaggerated impression that initial SOC stocks are a major control on SOC dynamics. To address this problem, we recommend applying statistical corrections to eliminate the effect of regression to the mean, and avoiding normalized metrics when testing relationships between SOC change and initial SOC. Careful consideration of these issues in future cross-site studies will support clearer scientific inference that can better inform environmental management.</div></div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/58m9d2d9"><img src="/cms-assets/dfb88c3baa921826f65e21eb051c13817b9ec66e4985017056962dff662456b9" alt="Cover page: Initial soil organic carbon stocks govern changes in soil carbon: Reality or artifact?"/></a></div></section><section class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li><li class="c-scholworks__tag-peer">Peer Reviewed</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/438035xq"><div class="c-clientmarkup">Expression of macromolecular organic nitrogen degrading enzymes identifies potential mediators of soil organic N availability to an annual grass</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3ASieradzki%2C%20Ella%20T">Sieradzki, Ella T</a>; </li><li><a href="/search/?q=author%3ANuccio%2C%20Erin%20E">Nuccio, Erin E</a>; </li><li><a href="/search/?q=author%3APett-Ridge%2C%20Jennifer">Pett-Ridge, Jennifer</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AFirestone%2C%20Mary%20K">Firestone, Mary K</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/ucb_postprints">UC Berkeley Previously Published Works</a> (<!-- -->2023<!-- -->)</div><div class="c-scholworks__abstract"><div class="c-clientmarkup">Nitrogen (N) is frequently limiting to plant growth, in part because most soil N is present as polymeric organic compounds that are not readily taken up by plants. Microbial depolymerization of these large macromolecular N-substrates gradually releases available inorganic N. While many studies have researched and modeled controls on soil organic matter formation and bulk N mineralization, the ecological-spatial, temporal and phylogenetic-patterns underlying organic N degradation remain unclear. We analyzed 48 time-resolved metatranscriptomes and quantified N-depolymerization gene expression to resolve differential expression by soil habitat and time in specific taxonomic groups and gene-based guilds. We observed much higher expression of extracellular serine-type proteases than other extracellular N-degrading enzymes, with protease expression of predatory bacteria declining with time and other taxonomic patterns driven by the presence (Gammaproteobacteria) or absence (Thermoproteota) of live roots and root detritus (Deltaproteobacteria and Fungi). The primary chitinase chit1 gene was more highly expressed by eukaryotes near root detritus, suggesting predation of fungi. In some lineages, increased gene expression over time suggests increased competitiveness with rhizosphere age (Chloroflexi). Phylotypes from some genera had protease expression patterns that could benefit plant N nutrition, for example, we identified a Janthinobacterium phylotype and two Burkholderiales that depolymerize organic N near young roots and a Rhizobacter with elevated protease levels near mature roots. These taxon-resolved gene expression results provide an ecological read-out of microbial interactions and controls on N dynamics in specific soil microhabitats and could be used to target potential plant N bioaugmentation strategies.</div></div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/438035xq"><img src="/cms-assets/4b9ed7370856d260ba760481990d37708b8179ad61c85afb3c117f38e6ee5c1c" alt="Cover page: Expression of macromolecular organic nitrogen degrading enzymes identifies potential mediators of soil organic N availability to an annual grass"/></a></div></section><section class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li><li class="c-scholworks__tag-peer">Peer Reviewed</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/3zz110xz"><div class="c-clientmarkup">Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AStarr%2C%20Evan%20P">Starr, Evan P</a>; </li><li><a href="/search/?q=author%3ANuccio%2C%20Erin%20E">Nuccio, Erin E</a>; </li><li><a href="/search/?q=author%3APett-Ridge%2C%20Jennifer">Pett-Ridge, Jennifer</a>; </li><li><a href="/search/?q=author%3ABanfield%2C%20Jillian%20F">Banfield, Jillian F</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AFirestone%2C%20Mary%20K">Firestone, Mary K</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/ucb_postprints">UC Berkeley Previously Published Works</a> (<!-- -->2019<!-- -->)</div><div class="c-scholworks__abstract"><div class="c-clientmarkup">Viruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health, and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in soil, 1 of the most complex microbial systems. Here, we assembled 48 individual metatranscriptomes from 4 habitats within a planted soil sampled over a 22-d time series: Rhizosphere alone, detritosphere alone, rhizosphere with added root detritus, and unamended soil (4 time points and 3 biological replicates). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker genes. Based on viral phylogeny, much of the diversity was <i>Narnaviridae</i> that may parasitize fungi or <i>Leviviridae</i>, which may infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral and host communities were structured based on the presence of root litter. Clear temporal dynamics by <i>Leviviridae</i> and their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant, and active in soil. When viral infection causes host cell death, it may mobilize cell carbon in a process that may represent an overlooked component of soil carbon cycling.</div></div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/3zz110xz"><img src="/cms-assets/51c6b8ac693c082a3abedc30b2a0233013d4b027bffe5f5845b81af7ea9fd00a" alt="Cover page: Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil"/></a></div></section><section class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li><li class="c-scholworks__tag-peer">Peer Reviewed</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/4s82s0d8"><div class="c-clientmarkup">Evidence for foliar endophytic nitrogen fixation in a widely distributed subalpine conifer</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AMoyes%2C%20Andrew%20B">Moyes, Andrew B</a>; </li><li><a href="/search/?q=author%3AKueppers%2C%20Lara%20M">Kueppers, Lara M</a>; </li><li><a href="/search/?q=author%3APett-Ridge%2C%20Jennifer">Pett-Ridge, Jennifer</a>; </li><li><a href="/search/?q=author%3ACarper%2C%20Dana%20L">Carper, Dana L</a>; </li><li><a href="/search/?q=author%3AVandehey%2C%20Nick">Vandehey, Nick</a>; </li><li><a href="/search/?q=author%3AO'Neil%2C%20James">O'Neil, James</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AFrank%2C%20A%20Carolin">Frank, A Carolin</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/ucb_postprints">UC Berkeley Previously Published Works</a> (<!-- -->2016<!-- -->)</div><div class="c-scholworks__abstract"><div class="c-clientmarkup">Coniferous forest nitrogen (N) budgets indicate unknown sources of N. A consistent association between limber pine (Pinus flexilis) and potential N2 -fixing acetic acid bacteria (AAB) indicates that native foliar endophytes may supply subalpine forests with N. To assess whether the P. flexilis-AAB association is consistent across years, we re-sampled P. flexilis twigs at Niwot Ridge, CO and characterized needle endophyte communities via 16S rRNA Illumina sequencing. To investigate whether endophytes have access to foliar N2 , we incubated twigs with (13) N2 -enriched air and imaged radioisotope distribution in needles, the first experiment of its kind using (13) N. We used the acetylene reduction assay to test for nitrogenase activity within P. flexilis twigs four times from June to September. We found evidence for N2 fixation in P. flexilis foliage. N2 diffused readily into needles and nitrogenase activity was positive across sampling dates. We estimate that this association could provide 6.8-13.6 μg N m(-2) d(-1) to P. flexilis stands. AAB dominated the P. flexilis needle endophyte community. We propose that foliar endophytes represent a low-cost, evolutionarily stable N2 -fixing strategy for long-lived conifers. This novel source of biological N2 fixation has fundamental implications for understanding forest N budgets.</div></div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/4s82s0d8"><img src="/cms-assets/89c83d51b8fd094542876775bdb306565a9c1adf8082d9390cc98bf0f2182dab" alt="Cover page: Evidence for foliar endophytic nitrogen fixation in a widely distributed subalpine conifer"/></a></div></section><nav class="c-pagination--next"><ul><li><a href="" aria-label="you are on result set 1" class="c-pagination__item--current">1</a></li><li><a href="" aria-label="go to result set 2" class="c-pagination__item">2</a></li><li><a href="" aria-label="go to result set 3" class="c-pagination__item">3</a></li><li><a href="" aria-label="go to result set 4" class="c-pagination__item">4</a></li><li><a href="" aria-label="go to result set 7" class="c-pagination__item">7</a></li><li class="c-pagination__next"><a href="" aria-label="go to Next result set">Next</a></li></ul></nav></section></main></form></div><div><div class="c-toplink"><a href="javascript:window.scrollTo(0, 0)">Top</a></div><footer class="c-footer"><nav class="c-footer__nav"><ul><li><a href="/">Home</a></li><li><a href="/aboutEschol">About eScholarship</a></li><li><a href="/campuses">Campus Sites</a></li><li><a href="/ucoapolicies">UC Open Access Policy</a></li><li><a href="/publishing">eScholarship Publishing</a></li><li><a href="https://www.cdlib.org/about/accessibility.html">Accessibility</a></li><li><a href="/privacypolicy">Privacy Statement</a></li><li><a href="/policies">Site Policies</a></li><li><a href="/terms">Terms of Use</a></li><li><a href="/login"><strong>Admin Login</strong></a></li><li><a href="https://help.escholarship.org"><strong>Help</strong></a></li></ul></nav><div class="c-footer__logo"><a href="/"><img class="c-lazyimage" data-src="/images/logo_footer-eschol.svg" alt="eScholarship, University of California"/></a></div><div class="c-footer__copyright">Powered by the<br/><a href="http://www.cdlib.org">California Digital Library</a><br/>Copyright © 2017<br/>The Regents of the University of California</div></footer></div></div></div></div> <script>window.jscholApp_initialPageData = {"header":{"campusID":"root","campusName":"eScholarship","ancestorID":null,"ancestorName":null,"campuses":[{"id":"","name":"eScholarship at..."},{"id":"ucb","name":"UC Berkeley"},{"id":"ucd","name":"UC Davis"},{"id":"uci","name":"UC Irvine"},{"id":"ucla","name":"UCLA"},{"id":"ucm","name":"UC Merced"},{"id":"ucr","name":"UC Riverside"},{"id":"ucsd","name":"UC San Diego"},{"id":"ucsf","name":"UCSF"},{"id":"ucsb","name":"UC Santa Barbara"},{"id":"ucsc","name":"UC Santa Cruz"},{"id":"ucop","name":"UC Office of the President"},{"id":"lbnl","name":"Lawrence Berkeley National Laboratory"},{"id":"anrcs","name":"UC Agriculture & Natural Resources"}],"logo":null,"bgColor":null,"elColor":null,"directSubmit":null,"directSubmitURL":null,"directManageURLauthor":null,"directManageURLeditor":null,"nav_bar":[{"id":1,"name":"About eScholarship","type":"folder","sub_nav":[{"id":5,"name":"About eScholarship","slug":"aboutEschol","type":"page","url":"/aboutEschol"},{"id":11,"name":"eScholarship Repository","slug":"repository","type":"page","url":"/repository"},{"id":28,"url":"/publishing","name":"eScholarship Publishing","type":"link"},{"id":29,"name":"Site policies","slug":"policies","type":"page","url":"/policies"},{"id":13,"name":"Terms of Use and Copyright Information","slug":"terms","type":"page","url":"/terms"},{"id":26,"name":"Coming soon","slug":"comingSoon","type":"page","hidden":true,"url":"/comingSoon"},{"id":27,"name":"Privacy statement","slug":"privacyPolicy","type":"page","url":"/privacyPolicy"}]},{"id":2,"name":"Campus Sites","type":"folder","sub_nav":[{"id":15,"url":"/uc/ucb","name":"UC Berkeley","type":"link"},{"id":16,"url":"/uc/ucd","name":"UC Davis","type":"link"},{"id":17,"url":"/uc/uci","name":"UC Irvine","type":"link"},{"id":6,"url":"/uc/ucla","name":"UCLA","type":"link"},{"id":18,"url":"/uc/ucm","name":"UC Merced","type":"link"},{"id":19,"url":"/uc/ucr","name":"UC Riverside","type":"link"},{"id":20,"url":"/uc/ucsd","name":"UC San Diego","type":"link"},{"id":9,"url":"/uc/ucsf","name":"UCSF","type":"link"},{"id":21,"url":"/uc/ucsb","name":"UC Santa Barbara","type":"link"},{"id":22,"url":"/uc/ucsc","name":"UC Santa Cruz","type":"link"},{"id":23,"url":"/uc/ucop","name":"UC Office of the President","type":"link"},{"id":24,"url":"/uc/lbnl","name":"Lawrence Berkeley National Laboratory","type":"link"},{"id":25,"url":"/uc/anrcs","name":"UC Agriculture & Natural Resources","type":"link"}]},{"id":10,"name":"UC Open Access Policies","slug":"ucoapolicies","type":"page","url":"/ucoapolicies"},{"id":12,"name":"eScholarship Publishing","slug":"publishing","type":"page","url":"/publishing"}],"social":{"facebook":null,"twitter":null,"rss":"/rss/unit/root"},"breadcrumb":[{"name":"eScholarship","id":"root","url":"/"}]},"campuses":[{"id":"","name":"eScholarship at..."},{"id":"ucb","name":"UC Berkeley"},{"id":"ucd","name":"UC Davis"},{"id":"uci","name":"UC Irvine"},{"id":"ucla","name":"UCLA"},{"id":"ucm","name":"UC Merced"},{"id":"ucr","name":"UC Riverside"},{"id":"ucsd","name":"UC San Diego"},{"id":"ucsf","name":"UCSF"},{"id":"ucsb","name":"UC Santa Barbara"},{"id":"ucsc","name":"UC Santa Cruz"},{"id":"ucop","name":"UC Office of the President"},{"id":"lbnl","name":"Lawrence Berkeley National Laboratory"},{"id":"anrcs","name":"UC Agriculture & Natural Resources"}],"query":{"q":"author:Pett-Ridge, Jennifer","sort":"rel","rows":"10","info_start":"0","start":"0","filters":{}},"count":66,"info_count":0,"infoResults":[],"searchResults":[{"id":"qt1bw9p4dj","title":"Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development.","abstract":"Interactions between plant roots and rhizosphere bacteria modulate nitrogen (N)-cycling processes and create habitats rich in low molecular weight compounds (exudates) and complex organic molecules (decaying root litter) compared to those of bulk soil. Microbial N-cycling is regulated by edaphic conditions and genes from many interconnected metabolic pathways, but most studies of soil N-cycling gene expression have focused on single pathways. Currently, we lack a comprehensive understanding of the interplay between soil N-cycling gene regulation, spatial habitat, and time. We present results from a replicated time series of soil metatranscriptomes; we followed gene expression of multiple N transformations in four soil habitats (rhizosphere, detritusphere, rhizo-detritusphere, and bulk soil) during active root growth for the annual grass, Avena fatua. The presence of root litter and living roots significantly altered the trajectories of N-cycling gene expression. Upregulation of assimilatory nitrate reduction in the rhizosphere suggests that rhizosphere bacteria were actively competing with roots for nitrate. Simultaneously, ammonium assimilatory pathways were upregulated in both rhizosphere and detritusphere soil, which could have limited N availability to plants. The detritusphere supported dissimilatory processes DNRA and denitrification. Expression of nitrification genes was dominated by three phylotypes of Thaumarchaeota and was upregulated in bulk soil. Unidirectional ammonium assimilation and its regulatory genes (GS/GOGAT) were upregulated near relatively young roots and highly decayed root litter, suggesting N may have been limiting in these habitats (GS/GOGAT is typically activated under N limitation). Our comprehensive analysis indicates that differences in carbon and inorganic N availability control contemporaneous transcription of N-cycling pathways in soil habitats. IMPORTANCE Plant roots modulate microbial nitrogen (N) cycling by regulating the supply of root-derived carbon and nitrogen uptake. These differences in resource availability cause distinct micro-habitats to develop: soil near living roots, decaying roots, near both, or outside the direct influence of roots. While many environmental factors and genes control the microbial processes involved in the nitrogen cycle, most research has focused on single genes and pathways, neglecting the interactive effects these pathways have on each other. The processes controlled by these pathways determine consumption and production of N by soil microorganisms. We followed the expression of N-cycling genes in four soil microhabitats over a period of active root growth for an annual grass. We found that the presence of root litter and living roots significantly altered gene expression involved in multiple nitrogen pathways, as well as tradeoffs between pathways, which ultimately regulate N availability to plants.","content_type":"application/pdf","author_hide":null,"authors":[{"name":"Sieradzki, Ella","fname":"Ella","lname":"Sieradzki"},{"name":"Nuccio, Erin","fname":"Erin","lname":"Nuccio"},{"name":"Pett-Ridge, Jennifer","fname":"Jennifer","lname":"Pett-Ridge"},{"name":"Firestone, Mary","email":"mkfstone@berkeley.edu","fname":"Mary","lname":"Firestone"}],"supp_files":[{"type":"pdf","count":0},{"type":"image","count":0},{"type":"video","count":0},{"type":"audio","count":0},{"type":"zip","count":0},{"type":"other","count":0}],"thumbnail":{"width":121,"height":171,"asset_id":"c95204361f486b527ca8c4d0567d31b42d6301e0ee620eb34f33575651914ffe","timestamp":1700925177,"image_type":"jpeg"},"pub_year":2023,"genre":"article","rights":null,"peerReviewed":true,"unitInfo":{"displayName":"UC Berkeley Previously Published Works","link_path":"ucb_postprints"}},{"id":"qt9g04p5md","title":"Mineral protection of soil carbon counteracted by root exudates","abstract":"Multiple lines of existing evidence suggest that climate change enhances root exudation of organic compounds into soils. Recent experimental studies show that increased exudate inputs may cause a net loss of soil carbon. This stimulation of microbial carbon mineralization ('priming') is commonly rationalized by the assumption that exudates provide a readily bioavailable supply of energy for the decomposition of native soil carbon (co-metabolism). Here we show that an alternate mechanism can cause carbon loss of equal or greater magnitude. We find that a common root exudate, oxalic acid, promotes carbon loss by liberating organic compounds from protective associations with minerals. By enhancing microbial access to previously mineral-protected compounds, this indirect mechanism accelerated carbon loss more than simply increasing the supply of energetically more favourable substrates. Our results provide insights into the coupled biotic-abiotic mechanisms underlying the 'priming'phenomenon and challenge the assumption that mineral-associated carbon is protected from microbial cycling over millennial timescales.","content_type":"application/pdf","author_hide":null,"authors":[{"name":"Keiluweit, Marco","fname":"Marco","lname":"Keiluweit"},{"name":"Bougoure, Jeremy J","fname":"Jeremy J","lname":"Bougoure"},{"name":"Nico, Peter S","email":"pnico@berkeley.edu","fname":"Peter S","lname":"Nico"},{"name":"Pett-Ridge, Jennifer","fname":"Jennifer","lname":"Pett-Ridge"},{"name":"Weber, Peter K","fname":"Peter K","lname":"Weber"},{"name":"Kleber, Markus","fname":"Markus","lname":"Kleber"}],"supp_files":[{"type":"pdf","count":0},{"type":"image","count":0},{"type":"video","count":0},{"type":"audio","count":0},{"type":"zip","count":0},{"type":"other","count":0}],"thumbnail":{"width":121,"height":160,"asset_id":"806fe413ebff7d8828cc6166b302fc58ed5401fd85da59893759d6e3ba715cf8","timestamp":1537827646,"image_type":"png"},"pub_year":2015,"genre":"article","rights":null,"peerReviewed":true,"unitInfo":{"displayName":"UC Berkeley Previously Published Works","link_path":"ucb_postprints"}},{"id":"qt4kt6d5gt","title":"Long-term litter decomposition controlled by manganese redox cycling","abstract":"Litter decomposition is a keystone ecosystem process impacting nutrient cycling and productivity, soil properties, and the terrestrial carbon (C) balance, but the factors regulating decomposition rate are still poorly understood. Traditional models assume that the rate is controlled by litter quality, relying on parameters such as lignin content as predictors. However, a strong correlation has been observed between the manganese (Mn) content of litter and decomposition rates across a variety of forest ecosystems. Here, we show that long-term litter decomposition in forest ecosystems is tightly coupled to Mn redox cycling. Over 7 years of litter decomposition, microbial transformation of litter was paralleled by variations in Mn oxidation state and concentration. A detailed chemical imaging analysis of the litter revealed that fungi recruit and redistribute unreactive Mn(2+) provided by fresh plant litter to produce oxidative Mn(3+) species at sites of active decay, with Mn eventually accumulating as insoluble Mn(3+/4+) oxides. Formation of reactive Mn(3+) species coincided with the generation of aromatic oxidation products, providing direct proof of the previously posited role of Mn(3+)-based oxidizers in the breakdown of litter. Our results suggest that the litter-decomposing machinery at our coniferous forest site depends on the ability of plants and microbes to supply, accumulate, and regenerate short-lived Mn(3+) species in the litter layer. This observation indicates that biogeochemical constraints on bioavailability, mobility, and reactivity of Mn in the plant-soil system may have a profound impact on litter decomposition rates.","content_type":"application/pdf","author_hide":null,"authors":[{"name":"Keiluweit, Marco","fname":"Marco","lname":"Keiluweit"},{"name":"Nico, Peter","email":"pnico@berkeley.edu","fname":"Peter","lname":"Nico"},{"name":"Harmon, Mark E","fname":"Mark E","lname":"Harmon"},{"name":"Mao, Jingdong","fname":"Jingdong","lname":"Mao"},{"name":"Pett-Ridge, Jennifer","fname":"Jennifer","lname":"Pett-Ridge"},{"name":"Kleber, Markus","fname":"Markus","lname":"Kleber"}],"supp_files":[{"type":"pdf","count":0},{"type":"image","count":0},{"type":"video","count":0},{"type":"audio","count":0},{"type":"zip","count":0},{"type":"other","count":0}],"thumbnail":{"width":121,"height":161,"asset_id":"69aacc806284dd3c275df6d1e1ac681fd8a100b36e39c000ca840f1c98cb2ce5","timestamp":1537827758,"image_type":"png"},"pub_year":2015,"genre":"article","rights":null,"peerReviewed":true,"unitInfo":{"displayName":"UC Berkeley Previously Published Works","link_path":"ucb_postprints"}},{"id":"qt2k51w8rn","title":"Fast redox switches lead to rapid transformation of goethite in humid tropical soils: A M\u00F6ssbauer spectroscopy study","abstract":"Humid tropical forest soils experience frequent rainfall, which limits oxygen diffusion and creates redox heterogeneity in upland soils. In this study we gauged the effect of short-term anoxic conditions on Fe mineralogy of relatively Fe- and C-rich surface soils (C/Fe mole ratio \u223C5) from a humid tropical forest in Puerto Rico. Soils subjected to 4-d oxic/anoxic oscillation were characterized by selective chemical extractions, M\u00F6ssbauer spectroscopy (MBS), and X-ray diffraction. Chemical extraction data suggested that rapidly switching redox conditions had subtle effects on bulk Fe mineralogy. M\u00F6ssbauer, on the other hand, indicated that (a) the soil Fe is a mixture of goethites of varying characteristics with minor contributions from ferrihydrite (<5%) and Fe(III)-organic matter (OM) phases (\u223C10%), and (b) anoxic conditions rapidly transformed all forms of goethite to relatively stable Fe oxides. Such fast changes in goethite features could be due to rapid depletion and sorption of bio-released structural Al or sorbed OM onto residual soil components. The rapid temporal changes in MBS parameters and corresponding pore water nominal oxidation state of C values suggest that Fe-C transformations in these upland tropical soils are complex and intricately coupled. A comprehensive understanding of the fate of Fe, Al, and OM (Fe-organic moieties) during redox switches and concurrent changes in pore water chemistry is critical for development of robust transport models in humid tropical soils, which are subject to episodic low-redox events.","content_type":"application/pdf","author_hide":null,"authors":[{"name":"Bhattacharyya, Amrita","fname":"Amrita","lname":"Bhattacharyya"},{"name":"Kukkadapu, Ravi K","fname":"Ravi K","lname":"Kukkadapu"},{"name":"Bowden, Mark","fname":"Mark","lname":"Bowden"},{"name":"Pett\u2010Ridge, Jennifer","fname":"Jennifer","lname":"Pett\u2010Ridge"},{"name":"Nico, Peter S","email":"pnico@berkeley.edu","fname":"Peter S","lname":"Nico"}],"supp_files":[{"type":"pdf","count":0},{"type":"image","count":0},{"type":"video","count":0},{"type":"audio","count":0},{"type":"zip","count":0},{"type":"other","count":0}],"thumbnail":{"width":121,"height":168,"asset_id":"e7a0c93e31f96541a88bb284724a51642cba8f158ab36f27d5b6f8e6142825d3","timestamp":1677785609,"image_type":"png"},"pub_year":2022,"genre":"article","rights":"https://creativecommons.org/licenses/by/4.0/","peerReviewed":true,"unitInfo":{"displayName":"UC Berkeley Previously Published Works","link_path":"ucb_postprints"}},{"id":"qt5d64r4sk","title":"Phosphorus fractionation responds to dynamic redox conditions in a humid tropical forest soil","abstract":null,"content_type":"application/pdf","author_hide":null,"authors":[{"name":"Lin, Yang","fname":"Yang","lname":"Lin"},{"name":"Bhattacharyya, Amrita","fname":"Amrita","lname":"Bhattacharyya"},{"name":"Campbell, Ashley N","fname":"Ashley","lname":"Campbell","mname":"N"},{"name":"Nico, Peter S","fname":"Peter","lname":"Nico","mname":"S"},{"name":"Pett-Ridge, Jennifer","fname":"Jennifer","lname":"Pett-Ridge"},{"name":"Silver, Whendee L","fname":"Whendee","lname":"Silver","mname":"L"}],"supp_files":[{"type":"pdf","count":0},{"type":"image","count":0},{"type":"video","count":0},{"type":"audio","count":0},{"type":"zip","count":0},{"type":"other","count":0}],"thumbnail":{"width":121,"height":166,"asset_id":"4de1a17e6e17cb7f57d443bd417d316fafd7c8724779a42d6341e4365402784b","timestamp":1535384730,"image_type":"png"},"pub_year":2018,"genre":"article","rights":null,"peerReviewed":true,"unitInfo":{"displayName":"UC Berkeley Previously Published Works","link_path":"ucb_postprints"}},{"id":"qt5954v7s7","title":"Managing Plant Microbiomes for Sustainable Biofuel Production","abstract":"The development of environmentally sustainable, economical, and reliable sources of energy is one of the great challenges of the 21st century. Large-scale cultivation of cellulosic feedstock crops (henceforth, bioenergy crops) is considered one of themost promising renewable sources for liquid transportation fuels. However, the mandate to develop a viable cellulosic bioenergy industry is accompanied by an equally urgent mandate to deliver not only cheap reliable biomass but also ecosystembenefits, including efficient use of water, nitrogen, and phosphorous; restored soil health; and net negative carbon emissions. Thus, sustainable bioenergy crop production may involve new agricultural practices or feedstocks and should be reliable, cost effective, and minimal input,without displacing crops currently grown for food production on fertile land. In this editorial perspective for the Phytobiomes Journal Focus Issue on Phytobiomes of Bioenergy Crops and Agroecosystems, we consider the microbiomes associated with bioenergy crops, the effects beneficial microbes have on their hosts, and potential ecosystem impacts of these interactions.We also address outstanding questions, major advances, and emerging biotechnological strategies to design and manipulate bioenergy crop microbiomes. This approach could simultaneously increase crop yields and provide important ecosystem services for a sustainable energy future.","content_type":"application/pdf","author_hide":null,"authors":[{"name":"Zhalnina, Kateryna","email":"KZhalnina@lbl.gov","fname":"Kateryna","lname":"Zhalnina"},{"name":"Hawkes, Christine","fname":"Christine","lname":"Hawkes"},{"name":"Shade, Ashley","fname":"Ashley","lname":"Shade"},{"name":"Firestone, Mary K","email":"mkfstone@berkeley.edu","fname":"Mary K","lname":"Firestone"},{"name":"Pett-Ridge, Jennifer","fname":"Jennifer","lname":"Pett-Ridge"}],"supp_files":[{"type":"pdf","count":0},{"type":"image","count":0},{"type":"video","count":0},{"type":"audio","count":0},{"type":"zip","count":0},{"type":"other","count":0}],"thumbnail":{"width":121,"height":173,"asset_id":"93a6995432625f08402197574b7adb16ae774a3327c4542c1758839145d362ea","timestamp":1625843329,"image_type":"jpeg"},"pub_year":2021,"genre":"article","rights":null,"peerReviewed":true,"unitInfo":{"displayName":"UC Berkeley Previously Published Works","link_path":"ucb_postprints"}},{"id":"qt58m9d2d9","title":"Initial soil organic carbon stocks govern changes in soil carbon: Reality or artifact?","abstract":"Changes in soil organic carbon (SOC) storage have the potential to affect global climate; hence identifying environments with a high capacity to gain or lose SOC is of broad interest. Many cross-site studies have found that SOC-poor soils tend to gain or retain carbon more readily than SOC-rich soils. While this pattern may partly reflect reality, here we argue that it can also be created by a pair of statistical artifacts. First, soils that appear SOC-poor purely due to random variation will tend to yield more moderate SOC estimates upon resampling and hence will appear to accrue or retain more SOC than SOC-rich soils. This phenomenon is an example of regression to the mean. Second, normalized metrics of SOC change-such as relative rates and response ratios-will by definition show larger changes in SOC at lower initial SOC levels, even when the absolute change in SOC does not depend on initial SOC. These two artifacts create an exaggerated impression that initial SOC stocks are a major control on SOC dynamics. To address this problem, we recommend applying statistical corrections to eliminate the effect of regression to the mean, and avoiding normalized metrics when testing relationships between SOC change and initial SOC. Careful consideration of these issues in future cross-site studies will support clearer scientific inference that can better inform environmental management.","content_type":"application/pdf","author_hide":null,"authors":[{"name":"Slessarev, Eric","fname":"Eric","lname":"Slessarev"},{"name":"Mayer, Allegra","fname":"Allegra","lname":"Mayer"},{"name":"Kelly, Courtland","fname":"Courtland","lname":"Kelly"},{"name":"Georgiou, Katerina","email":"KGeorgiou@lbl.gov","fname":"Katerina","lname":"Georgiou"},{"name":"Pett-Ridge, Jennifer","fname":"Jennifer","lname":"Pett-Ridge"},{"name":"Nuccio, Erin","fname":"Erin","lname":"Nuccio"}],"supp_files":[{"type":"pdf","count":0},{"type":"image","count":0},{"type":"video","count":0},{"type":"audio","count":0},{"type":"zip","count":0},{"type":"other","count":0}],"thumbnail":{"width":121,"height":176,"asset_id":"dfb88c3baa921826f65e21eb051c13817b9ec66e4985017056962dff662456b9","timestamp":1719672626,"image_type":"png"},"pub_year":2023,"genre":"article","rights":null,"peerReviewed":true,"unitInfo":{"displayName":"LBL Publications","link_path":"lbnl_rw"}},{"id":"qt438035xq","title":"Expression of macromolecular organic nitrogen degrading enzymes identifies potential mediators of soil organic N availability to an annual grass","abstract":"Nitrogen (N) is frequently limiting to plant growth, in part because most soil N is present as polymeric organic compounds that are not readily taken up by plants. Microbial depolymerization of these large macromolecular N-substrates gradually releases available inorganic N. While many studies have researched and modeled controls on soil organic matter formation and bulk N mineralization, the ecological-spatial, temporal and phylogenetic-patterns underlying organic N degradation remain unclear. We analyzed 48 time-resolved metatranscriptomes and quantified N-depolymerization gene expression to resolve differential expression by soil habitat and time in specific taxonomic groups and gene-based guilds. We observed much higher expression of extracellular serine-type proteases than other extracellular N-degrading enzymes, with protease expression of predatory bacteria declining with time and other taxonomic patterns driven by the presence (Gammaproteobacteria) or absence (Thermoproteota) of live roots and root detritus (Deltaproteobacteria and Fungi). The primary chitinase chit1 gene was more highly expressed by eukaryotes near root detritus, suggesting predation of fungi. In some lineages, increased gene expression over time suggests increased competitiveness with rhizosphere age (Chloroflexi). Phylotypes from some genera had protease expression patterns that could benefit plant N nutrition, for example, we identified a Janthinobacterium phylotype and two Burkholderiales that depolymerize organic N near young roots and a Rhizobacter with elevated protease levels near mature roots. These taxon-resolved gene expression results provide an ecological read-out of microbial interactions and controls on N dynamics in specific soil microhabitats and could be used to target potential plant N bioaugmentation strategies.","content_type":"application/pdf","author_hide":null,"authors":[{"name":"Sieradzki, Ella T","fname":"Ella T","lname":"Sieradzki"},{"name":"Nuccio, Erin E","fname":"Erin E","lname":"Nuccio"},{"name":"Pett-Ridge, Jennifer","fname":"Jennifer","lname":"Pett-Ridge"},{"name":"Firestone, Mary K","email":"mkfstone@berkeley.edu","fname":"Mary K","lname":"Firestone"}],"supp_files":[{"type":"pdf","count":0},{"type":"image","count":0},{"type":"video","count":0},{"type":"audio","count":0},{"type":"zip","count":0},{"type":"other","count":0}],"thumbnail":{"width":121,"height":162,"asset_id":"4b9ed7370856d260ba760481990d37708b8179ad61c85afb3c117f38e6ee5c1c","timestamp":1689420140,"image_type":"png"},"pub_year":2023,"genre":"article","rights":null,"peerReviewed":true,"unitInfo":{"displayName":"UC Berkeley Previously Published Works","link_path":"ucb_postprints"}},{"id":"qt3zz110xz","title":"Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil","abstract":"Viruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health, and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in soil, 1 of the most complex microbial systems. Here, we assembled 48 individual metatranscriptomes from 4 habitats within a planted soil sampled over a 22-d time series: Rhizosphere alone, detritosphere alone, rhizosphere with added root detritus, and unamended soil (4 time points and 3 biological replicates). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker genes. Based on viral phylogeny, much of the diversity was <i>Narnaviridae</i> that may parasitize fungi or <i>Leviviridae</i>, which may infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral and host communities were structured based on the presence of root litter. Clear temporal dynamics by <i>Leviviridae</i> and their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant, and active in soil. When viral infection causes host cell death, it may mobilize cell carbon in a process that may represent an overlooked component of soil carbon cycling.","content_type":"application/pdf","author_hide":null,"authors":[{"name":"Starr, Evan P","fname":"Evan P","lname":"Starr"},{"name":"Nuccio, Erin E","fname":"Erin E","lname":"Nuccio"},{"name":"Pett-Ridge, Jennifer","fname":"Jennifer","lname":"Pett-Ridge"},{"name":"Banfield, Jillian F","email":"jbanfield@berkeley.edu","fname":"Jillian F","lname":"Banfield"},{"name":"Firestone, Mary K","email":"mkfstone@berkeley.edu","fname":"Mary K","lname":"Firestone"}],"supp_files":[{"type":"pdf","count":0},{"type":"image","count":0},{"type":"video","count":0},{"type":"audio","count":0},{"type":"zip","count":0},{"type":"other","count":0}],"thumbnail":{"width":121,"height":164,"asset_id":"51c6b8ac693c082a3abedc30b2a0233013d4b027bffe5f5845b81af7ea9fd00a","timestamp":1579040188,"image_type":"png"},"pub_year":2019,"genre":"article","rights":null,"peerReviewed":true,"unitInfo":{"displayName":"UC Berkeley Previously Published Works","link_path":"ucb_postprints"}},{"id":"qt4s82s0d8","title":"Evidence for foliar endophytic nitrogen fixation in a widely distributed subalpine conifer","abstract":"Coniferous forest nitrogen (N) budgets indicate unknown sources of N. A consistent association between limber pine (Pinus flexilis) and potential N2 -fixing acetic acid bacteria (AAB) indicates that native foliar endophytes may supply subalpine forests with N. To assess whether the P. flexilis-AAB association is consistent across years, we re-sampled P. flexilis twigs at Niwot Ridge, CO and characterized needle endophyte communities via 16S rRNA Illumina sequencing. To investigate whether endophytes have access to foliar N2 , we incubated twigs with (13) N2 -enriched air and imaged radioisotope distribution in needles, the first experiment of its kind using (13) N. We used the acetylene reduction assay to test for nitrogenase activity within P. flexilis twigs four times from June to September. We found evidence for N2 fixation in P. flexilis foliage. N2 diffused readily into needles and nitrogenase activity was positive across sampling dates. We estimate that this association could provide 6.8-13.6 \u03BCg N m(-2) d(-1) to P. flexilis stands. AAB dominated the P. flexilis needle endophyte community. We propose that foliar endophytes represent a low-cost, evolutionarily stable N2 -fixing strategy for long-lived conifers. This novel source of biological N2 fixation has fundamental implications for understanding forest N budgets.","content_type":"application/pdf","author_hide":null,"authors":[{"name":"Moyes, Andrew B","email":"ABMoyes@lbl.gov","fname":"Andrew B","lname":"Moyes","ORCID_id":"0000-0002-9137-8118"},{"name":"Kueppers, Lara M","email":"lmkueppers@berkeley.edu","fname":"Lara M","lname":"Kueppers","ORCID_id":"0000-0002-8134-3579"},{"name":"Pett-Ridge, Jennifer","fname":"Jennifer","lname":"Pett-Ridge"},{"name":"Carper, Dana L","fname":"Dana L","lname":"Carper"},{"name":"Vandehey, Nick","fname":"Nick","lname":"Vandehey"},{"name":"O'Neil, James","fname":"James","lname":"O'Neil"},{"name":"Frank, A Carolin","fname":"A Carolin","lname":"Frank"}],"supp_files":[{"type":"pdf","count":0},{"type":"image","count":0},{"type":"video","count":0},{"type":"audio","count":0},{"type":"zip","count":0},{"type":"other","count":0}],"thumbnail":{"width":121,"height":156,"asset_id":"89c83d51b8fd094542876775bdb306565a9c1adf8082d9390cc98bf0f2182dab","timestamp":1525299170,"image_type":"jpeg"},"pub_year":2016,"genre":"article","rights":null,"peerReviewed":true,"unitInfo":{"displayName":"UC Berkeley Previously Published Works","link_path":"ucb_postprints"}}],"facets":[{"display":"Type of Work","fieldName":"type_of_work","facets":[{"value":"article","count":65,"displayName":"Article"},{"value":"monograph","count":0,"displayName":"Book"},{"value":"dissertation","count":0,"displayName":"Theses"},{"value":"multimedia","count":0,"displayName":"Multimedia"}]},{"display":"Peer Review","fieldName":"peer_reviewed","facets":[{"value":"1","count":66,"displayName":"Peer-reviewed only"}]},{"display":"Supplemental Material","fieldName":"supp_file_types","facets":[{"value":"video","count":0,"displayName":"Video"},{"value":"audio","count":0,"displayName":"Audio"},{"value":"images","count":0,"displayName":"Images"},{"value":"zip","count":0,"displayName":"Zip"},{"value":"other files","count":0,"displayName":"Other files"}]},{"display":"Publication Year","fieldName":"pub_year","range":{"pub_year_start":null,"pub_year_end":null}},{"display":"Campus","fieldName":"campuses","facets":[{"value":"ucb","count":52,"displayName":"UC Berkeley"},{"value":"ucd","count":7,"displayName":"UC Davis"},{"value":"uci","count":1,"displayName":"UC Irvine"},{"value":"ucla","count":5,"displayName":"UCLA"},{"value":"ucm","count":10,"displayName":"UC Merced"},{"value":"ucr","count":2,"displayName":"UC Riverside"},{"value":"ucsd","count":1,"displayName":"UC San Diego"},{"value":"ucsf","count":0,"displayName":"UCSF"},{"value":"ucsb","count":0,"displayName":"UC Santa Barbara"},{"value":"ucsc","count":0,"displayName":"UC Santa Cruz"},{"value":"ucop","count":22,"displayName":"UC Office of the President"},{"value":"lbnl","count":56,"displayName":"Lawrence Berkeley National Laboratory"},{"value":"anrcs","count":0,"displayName":"UC Agriculture & Natural Resources"}]},{"display":"Department","fieldName":"departments","facets":[{"value":"lbnl_bs","count":28,"displayName":"BioSciences"},{"value":"ucb_chemistry","count":3,"displayName":"College of Chemistry"},{"value":"lbnl_cs","count":1,"displayName":"Computing Sciences"},{"value":"ucd_animalscience","count":2,"displayName":"Department of Animal Science"},{"value":"uclabiolchem","count":2,"displayName":"Department of Biological Chemistry, UCLA, David Geffen School of Medicine"},{"value":"ucb_eps","count":3,"displayName":"Department of Earth and Planetary Science"},{"value":"plantpath_ucd","count":2,"displayName":"Department of Plant Pathology"},{"value":"ipnc","count":3,"displayName":"Department of Plant Sciences"},{"value":"lbnl_ees","count":15,"displayName":"Earth & Environmental Sciences"},{"value":"lbnl_es","count":6,"displayName":"Energy Sciences"},{"value":"ucr_plantpathmicro","count":2,"displayName":"Microbiology and Plant Pathology"},{"value":"rgpo","count":22,"displayName":"Research Grants Program Office"},{"value":"sio","count":1,"displayName":"Scripps Institution of Oceanography","descendents":[{"value":"sio_iod","count":1,"displayName":"Integrative Oceanography Division","ancestor_in_list":true}]}]},{"display":"Journal","fieldName":"journals","facets":[]},{"display":"Discipline","fieldName":"disciplines","facets":[{"value":"Life Sciences","count":1},{"value":"Physical Sciences and Mathematics","count":1}]},{"display":"Reuse License","fieldName":"rights","facets":[{"value":"CC BY","count":10,"displayName":"BY - Attribution required"},{"value":"CC BY-NC","count":2,"displayName":"BY-NC - Attribution; NonCommercial use only"},{"value":"CC BY-NC-ND","count":1,"displayName":"BY-NC-ND - Attribution; NonCommercial use; No derivatives"}]}]};</script> <script src="/js/vendors~app-bundle-7424603c338d723fd773.js"></script> <script src="/js/app-bundle-8362e6d7829414ab4baa.js"></script> </body> </html>