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(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 (19 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></select></div></div><input type="hidden" name="start" form="facetForm" value="0"/><nav class="c-pagination"><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></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/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/20p263cq"><div class="c-clientmarkup">The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AShi%2C%20Shengjing">Shi, Shengjing</a>; </li><li><a href="/search/?q=author%3ANuccio%2C%20Erin%20E">Nuccio, Erin E</a>; </li><li><a href="/search/?q=author%3AShi%2C%20Zhou%20J">Shi, Zhou J</a>; </li><li><a href="/search/?q=author%3AHe%2C%20Zhili">He, Zhili</a>; </li><li><a href="/search/?q=author%3AZhou%2C%20Jizhong">Zhou, Jizhong</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AFirestone%2C%20Mary%20K">Firestone, Mary K</a> </li><li class="c-authorlist__begin"><span class="c-authorlist__heading">Editor(s):</span> <a href="/search/?q=author%3AJohnson%2C%20Nancy">Johnson, Nancy</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">While interactions between roots and microorganisms have been intensively studied, we know little about interactions among root-associated microbes. We used random matrix theory-based network analysis of 16S rRNA genes to identify bacterial networks associated with wild oat (Avena fatua) over two seasons in greenhouse microcosms. Rhizosphere networks were substantially more complex than those in surrounding soils, indicating the rhizosphere has a greater potential for interactions and niche-sharing. Network complexity increased as plants grew, even as diversity decreased, highlighting that community organisation is not captured by univariate diversity. Covariations were predominantly positive (> 80%), suggesting that extensive mutualistic interactions may occur among rhizosphere bacteria; we identified quorum-based signalling as one potential strategy. Putative keystone taxa often had low relative abundances, suggesting low-abundance taxa may significantly contribute to rhizosphere function. Network complexity, a previously undescribed property of the rhizosphere microbiome, appears to be a defining characteristic of this habitat.</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/20p263cq"><img src="/cms-assets/ae090fbf97bf07a6148cf186ff72c6896c39eb9c496bd1496ab6d10f3c4515bd" alt="Cover page: The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages"/></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/5hk8t192"><div class="c-clientmarkup">Soil Candidate Phyla Radiation Bacteria Encode Components of Aerobic Metabolism and Co-occur with Nanoarchaea in the Rare Biosphere of Rhizosphere Grassland Communities</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3ANicolas%2C%20Alexa%20M">Nicolas, Alexa M</a>; </li><li><a href="/search/?q=author%3AJaffe%2C%20Alexander%20L">Jaffe, Alexander L</a>; </li><li><a href="/search/?q=author%3ANuccio%2C%20Erin%20E">Nuccio, Erin E</a>; </li><li><a href="/search/?q=author%3ATaga%2C%20Michiko%20E">Taga, Michiko E</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%3ABanfield%2C%20Jillian%20F">Banfield, Jillian F</a> </li><li class="c-authorlist__begin"><span class="c-authorlist__heading">Editor(s):</span> <a href="/search/?q=author%3AChu%2C%20Haiyan">Chu, Haiyan</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">Candidate Phyla Radiation (CPR) bacteria and nanoarchaea populate most ecosystems but are rarely detected in soil. We concentrated particles of less than 0.2鈥壩糾 in size from grassland soil, enabling targeted metagenomic analysis of these organisms, which are almost totally unexplored in largely oxic environments such as soil. We recovered a diversity of CPR bacterial and some archaeal sequences but no sequences from other cellular organisms. The sampled sequences include Doudnabacteria (SM2F11) and Pacearchaeota, organisms rarely reported in soil, as well as Saccharibacteria, Parcubacteria, and Microgenomates. CPR and archaea of the phyla Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) were enriched 100- to 1,000-fold compared to that in bulk soil, in which we estimate each of these organisms comprises approximately 1 to 100 cells per gram of soil. Like most CPR and DPANN sequenced to date, we predict these microorganisms live symbiotic anaerobic lifestyles. However, Saccharibacteria, Parcubacteria, and Doudnabacteria genomes sampled here also harbor ubiquinol oxidase operons that may have been acquired from other bacteria, likely during adaptation to aerobic soil environments. We conclude that CPR bacteria and DPANN archaea are part of the rare soil biosphere and harbor unique metabolic platforms that potentially evolved to live symbiotically under relatively oxic conditions. <b>IMPORTANCE</b> Here, we investigated overlooked microbes in soil, Candidate Phyla Radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, by size fractionating small particles from soil, an approach typically used for the recovery of viral metagenomes. Concentration of these small cells (<0.2鈥壩糾) allowed us to identify these organisms as part of the rare soil biosphere and to sample genomes that were absent from non-size-fractionated metagenomes. We found that some of these predicted symbionts, which have been largely studied in anaerobic systems, have acquired aerobic capacity via lateral transfer that may enable adaptation to oxic soil environments. We estimate that there are approximately 1 to 100 cells of each of these lineages per gram of soil, highlighting that the approach provides a window into the rare soil biosphere and its associated genetic potential.</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/5hk8t192"><img src="/cms-assets/23553ea5bb128f03f372c34f7d48fd9b79b5cf12d859b8b35ab6e53fefa7415a" alt="Cover page: Soil Candidate Phyla Radiation Bacteria Encode Components of Aerobic Metabolism and Co-occur with Nanoarchaea in the Rare Biosphere of Rhizosphere Grassland Communities"/></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/07n8f4kn"><div class="c-clientmarkup">Fungal-Bacterial Cooccurrence Patterns Differ between Arbuscular Mycorrhizal Fungi and Nonmycorrhizal Fungi across Soil Niches</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AYuan%2C%20Mengting%20Maggie">Yuan, Mengting Maggie</a>; </li><li><a href="/search/?q=author%3AKakouridis%2C%20Anne">Kakouridis, Anne</a>; </li><li><a href="/search/?q=author%3AStarr%2C%20Evan">Starr, Evan</a>; </li><li><a href="/search/?q=author%3ANguyen%2C%20Nhu">Nguyen, Nhu</a>; </li><li><a href="/search/?q=author%3AShi%2C%20Shengjing">Shi, Shengjing</a>; </li><li><a href="/search/?q=author%3APett-Ridge%2C%20Jennifer">Pett-Ridge, Jennifer</a>; </li><li><a href="/search/?q=author%3ANuccio%2C%20Erin">Nuccio, Erin</a>; </li><li><a href="/search/?q=author%3AZhou%2C%20Jizhong">Zhou, Jizhong</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AFirestone%2C%20Mary">Firestone, Mary</a> </li><li class="c-authorlist__begin"><span class="c-authorlist__heading">Editor(s):</span> <a href="/search/?q=author%3AGiovannoni%2C%20Stephen%20J">Giovannoni, Stephen J</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">Soil bacteria and fungi are known to form niche-specific communities that differ between actively growing and decaying roots. Yet almost nothing is known about the cross-kingdom interactions that frame these communities and the environmental filtering that defines these potentially friendly or competing neighbors. We explored the temporal and spatial patterns of soil fungal (mycorrhizal and nonmycorrhizal) and bacterial cooccurrence near roots of wild oat grass, Avena fatua, growing in its naturalized soil in a greenhouse experiment. Amplicon sequences of the fungal internal transcribed spacer (ITS) and bacterial 16S rRNA genes from rhizosphere and bulk soils collected at multiple plant growth stages were used to construct covariation-based networks as a step toward identifying fungal-bacterial associations. Corresponding stable-isotope-enabled metagenome-assembled genomes (MAGs) of bacteria identified in cooccurrence networks were used to inform potential mechanisms underlying the observed links. Bacterial-fungal networks were significantly different in rhizosphere versus bulk soils and between arbuscular mycorrhizal fungi (AMF) and nonmycorrhizal fungi. Over 12鈥墂eeks of plant growth, nonmycorrhizal fungi formed increasingly complex networks with bacteria in rhizosphere soils, while AMF more frequently formed networks with bacteria in bulk soils. Analysis of network-associated bacterial MAGs suggests that some of the fungal-bacterial links that we identified are potential indicators of bacterial breakdown and consumption of fungal biomass, while others intimate shared ecological niches.IMPORTANCE Soils near living and decomposing roots form distinct niches that promote microorganisms with distinctive environmental preferences and interactions. Yet few studies have assessed the community-level cooccurrence of bacteria and fungi in these soil niches as plant roots grow and senesce. With plant growth, we observed increasingly complex cooccurrence networks between nonmycorrhizal fungi and bacteria in the rhizosphere, while mycorrhizal fungal (AMF) and bacterial cooccurrence was more pronounced in soil further from roots, in the presence of decaying root litter. This rarely documented phenomenon suggests niche sharing of nonmycorrhizal fungi and bacteria, versus niche partitioning between AMF and bacteria; both patterns are likely driven by C substrate availability and quality. Although the implications of species cooccurrence are fiercely debated, MAGs matching the bacterial nodes in our networks possess the functional potential to interact with the fungi that they are linked to, suggesting an ecological significance of fungal-bacterial cooccurrence patterns.</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/07n8f4kn"><img src="/cms-assets/9eb07765054fee5499711e30392cd64ff5a4cd2730e52ff1a6eb0aba84bbe410" alt="Cover page: Fungal-Bacterial Cooccurrence Patterns Differ between Arbuscular Mycorrhizal Fungi and Nonmycorrhizal Fungi across Soil Niches"/></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/3824k1sw"><div class="c-clientmarkup">Climate and edaphic controllers influence rhizosphere community assembly for a wild 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%3ANuccio%2C%20Erin%20E">Nuccio, Erin E</a>; </li><li><a href="/search/?q=author%3AAnderson%E2%80%90Furgeson%2C%20James">Anderson鈥怓urgeson, James</a>; </li><li><a href="/search/?q=author%3AEstera%2C%20Katerina%20Y">Estera, Katerina Y</a>; </li><li><a href="/search/?q=author%3APett%E2%80%90Ridge%2C%20Jennifer">Pett鈥怰idge, Jennifer</a>; </li><li><a href="/search/?q=author%3Ade%20Valpine%2C%20Perry">de Valpine, Perry</a>; </li><li><a href="/search/?q=author%3ABrodie%2C%20Eoin%20L">Brodie, Eoin L</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> (2016)</div><div class="c-scholworks__abstract"><div class="c-clientmarkup">The interface between roots and soil, known as the rhizosphere, is a dynamic habitat in the soil ecosystem. Unraveling the factors that control rhizosphere community assembly is a key starting point for understanding the diversity of plant-microbial interactions that occur in soil. The goals of this study were to determine how environmental factors shape rhizosphere microbial communities, such as local soil characteristics and the regional climate, and to determine the relative influence of the rhizosphere on microbial community assembly compared to the pressures imposed by the local and regional environment. We identified the bacteria present in the soil immediately adjacent to the roots of wild oat (A vena spp.) in three California grasslands using deep Illumina 16S sequencing. Rhizosphere communities were more similar to each other than to the surrounding soil communities from which they were derived, despite the fact that the grasslands studied were separated by hundreds of kilometers. The rhizosphere was the dominant factor structuring bacterial community composition (38% variance explained), and was comparable in magnitude to the combined local and regional effects (22% and 21%, respectively). Rhizosphere communities were most influenced by factors related to the regional climate (soil moisture and temperature), while background soil communities were more influenced by soil characteristics (pH, CEC, exchangeable cations, clay content). The Avena core microbiome was strongly phylogenetically clustered according to the metrics NRI and NTI, which indicates that selective processes likely shaped these communities. Furthermore, 17% of these taxa were not detectable in the background soil, even with a robust sequencing depth of approximately 70,000 sequences per sample. These results support the hypothesis that roots select less abundant or possibly rare populations in the soil microbial community, which appear to be lineages of bacteria that have made a physiological tradeoff for rhizosphere competence at the expense of their competitiveness in non-rhizosphere soil.</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/3824k1sw"><img src="/cms-assets/5cf768e39315ab53e6bfd4ac5363c748ea9a42efc5620ad45c886d1d4c18d2c6" alt="Cover page: Climate and edaphic controllers influence rhizosphere community assembly for a wild 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/5mq7x3xt"><div class="c-clientmarkup">Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil.</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3ABlazewicz%2C%20Steven%20J">Blazewicz, Steven J</a>; </li><li><a href="/search/?q=author%3AHungate%2C%20Bruce%20A">Hungate, Bruce A</a>; </li><li><a href="/search/?q=author%3AKoch%2C%20Benjamin%20J">Koch, Benjamin J</a>; </li><li><a href="/search/?q=author%3ANuccio%2C%20Erin%20E">Nuccio, Erin E</a>; </li><li><a href="/search/?q=author%3AMorrissey%2C%20Ember">Morrissey, Ember</a>; </li><li><a href="/search/?q=author%3ABrodie%2C%20Eoin%20L">Brodie, Eoin L</a>; </li><li><a href="/search/?q=author%3ASchwartz%2C%20Egbert">Schwartz, Egbert</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> (2020)</div><div class="c-scholworks__abstract"><div class="c-clientmarkup">Microbial activity increases after rewetting dry soil, resulting in a pulse of carbon mineralization and nutrient availability. The biogeochemical responses to wet-up are reasonably well understood and known to be microbially mediated. Yet, the population level dynamics, and the resulting changes in microbial community patterns, are not well understood as ecological phenomena. Here, we used sequencing of 16S rRNA genes coupled with heavy water (H<sub>2</sub><sup>18</sup>O) DNA quantitative stable isotope probing to estimate population-specific rates of growth and mortality in response to a simulated wet-up event in a California annual grassland soil. Bacterial growth and mortality responded rapidly to wet-up, within 3鈥塰, and continued throughout the 168鈥塰 incubation, with patterns of sequential growth observed at the phylum level. Of the 37 phyla detected in the prewet community, growth was found in 18 phyla while mortality was measured in 26 phyla. Rapid growth and mortality rates were measurable within 3鈥塰 of wet-up but had contrasting characteristics; growth at 3鈥塰 was dominated by select taxa within the Proteobacteria and Firmicutes, whereas mortality was taxonomically widespread. Furthermore, across the community, mortality exhibited density-independence, consistent with the indiscriminate shock resulting from dry-down and wet-up, whereas growth was density-dependent, consistent with control by competition or predation. Total aggregated growth across the community was highly correlated with total soil CO<sub>2</sub> production. Together, these results illustrate how previously "invisible" population responses can translate quantitatively to emergent observations of ecosystem-scale biogeochemistry.</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/5mq7x3xt"><img src="/cms-assets/416aa9588c294a4961133697218257eeeecab6daed46d525237cf8f7497ae3fb" alt="Cover page: Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland 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/0d62v85p"><div class="c-clientmarkup">Community RNA-Seq: multi-kingdom responses to living versus decaying roots 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%3ANuccio%2C%20Erin%20E">Nuccio, Erin E</a>; </li><li><a href="/search/?q=author%3ANguyen%2C%20Nhu%20H">Nguyen, Nhu H</a>; </li><li><a href="/search/?q=author%3ANunes%20da%20Rocha%2C%20Ulisses">Nunes da Rocha, Ulisses</a>; </li><li><a href="/search/?q=author%3AMayali%2C%20Xavier">Mayali, Xavier</a>; </li><li><a href="/search/?q=author%3ABougoure%2C%20Jeremy">Bougoure, Jeremy</a>; </li><li><a href="/search/?q=author%3AWeber%2C%20Peter%20K">Weber, Peter K</a>; </li><li><a href="/search/?q=author%3ABrodie%2C%20Eoin">Brodie, Eoin</a>; </li><li><a href="/search/?q=author%3AFirestone%2C%20Mary">Firestone, Mary</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">Roots are a primary source of organic carbon input in most soils. The consumption of living and detrital root inputs involves multi-trophic processes and multiple kingdoms of microbial life, but typical microbial ecology studies focus on only one or two major lineages. We used Illumina shotgun RNA sequencing to conduct PCR-independent SSU rRNA community analysis ("community RNA-Seq") and simultaneously assess the bacteria, archaea, fungi, and microfauna surrounding both living and decomposing roots of the annual grass, Avena fatua. Plants were grown in <sup>13</sup>CO<sub>2</sub>-labeled microcosms amended with <sup>15</sup>N-root litter to identify the preferences of rhizosphere organisms for root exudates (<sup>13</sup>C) versus decaying root biomass (<sup>15</sup>N) using NanoSIMS microarray imaging (Chip-SIP). When litter was available, rhizosphere and bulk soil had significantly more Amoebozoa, which are potentially important yet often overlooked top-down drivers of detritusphere community dynamics and nutrient cycling. Bulk soil containing litter was depleted in Actinobacteria but had significantly more Bacteroidetes and Proteobacteria. While Actinobacteria were abundant in the rhizosphere, Chip-SIP showed Actinobacteria preferentially incorporated litter relative to root exudates, indicating this group's more prominent role in detritus elemental cycling in the rhizosphere. Our results emphasize that decomposition is a multi-trophic process involving complex interactions, and our methodology can be used to track the trajectory of carbon through multi-kingdom soil food webs.</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/0d62v85p"><img src="/cms-assets/0aa4b9ff6b6e3cf12aae565458d0cf50dd9a62e808fa226760bd13fee4db5d63" alt="Cover page: Community RNA-Seq: multi-kingdom responses to living versus decaying roots in soil."/></a></div></section><nav class="c-pagination"><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></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 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(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":"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":"qt20p263cq","title":"The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages","abstract":"While interactions between roots and microorganisms have been intensively studied, we know little about interactions among root-associated microbes. We used random matrix theory-based network analysis of 16S rRNA genes to identify bacterial networks associated with wild oat (Avena fatua) over two seasons in greenhouse microcosms. Rhizosphere networks were substantially more complex than those in surrounding soils, indicating the rhizosphere has a greater potential for interactions and niche-sharing. Network complexity increased as plants grew, even as diversity decreased, highlighting that community organisation is not captured by univariate diversity. Covariations were predominantly positive (> 80%), suggesting that extensive mutualistic interactions may occur among rhizosphere bacteria; we identified quorum-based signalling as one potential strategy. Putative keystone taxa often had low relative abundances, suggesting low-abundance taxa may significantly contribute to rhizosphere function. Network complexity, a previously undescribed property of the rhizosphere microbiome, appears to be a defining characteristic of this habitat.","content_type":"application/pdf","author_hide":null,"authors":[{"name":"Shi, Shengjing","fname":"Shengjing","lname":"Shi"},{"name":"Nuccio, Erin E","fname":"Erin E","lname":"Nuccio"},{"name":"Shi, Zhou J","fname":"Zhou J","lname":"Shi"},{"name":"He, Zhili","fname":"Zhili","lname":"He"},{"name":"Zhou, Jizhong","email":"JZZhou@lbl.gov","fname":"Jizhong","lname":"Zhou","ORCID_id":"0000-0003-2014-0564"},{"name":"Firestone, Mary K","email":"mkfstone@berkeley.edu","fname":"Mary K","lname":"Firestone"}],"editors":[{"name":"Johnson, Nancy","fname":"Nancy","lname":"Johnson"}],"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":"ae090fbf97bf07a6148cf186ff72c6896c39eb9c496bd1496ab6d10f3c4515bd","timestamp":1536699011,"image_type":"png"},"pub_year":2016,"genre":"article","rights":null,"peerReviewed":true,"unitInfo":{"displayName":"UC Berkeley Previously Published Works","link_path":"ucb_postprints"}},{"id":"qt5hk8t192","title":"Soil Candidate Phyla Radiation Bacteria Encode Components of Aerobic Metabolism and Co-occur with Nanoarchaea in the Rare Biosphere of Rhizosphere Grassland Communities","abstract":"Candidate Phyla Radiation (CPR) bacteria and nanoarchaea populate most ecosystems but are rarely detected in soil. We concentrated particles of less than 0.2\u2009\u03BCm in size from grassland soil, enabling targeted metagenomic analysis of these organisms, which are almost totally unexplored in largely oxic environments such as soil. We recovered a diversity of CPR bacterial and some archaeal sequences but no sequences from other cellular organisms. The sampled sequences include Doudnabacteria (SM2F11) and Pacearchaeota, organisms rarely reported in soil, as well as Saccharibacteria, Parcubacteria, and Microgenomates. CPR and archaea of the phyla Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) were enriched 100- to 1,000-fold compared to that in bulk soil, in which we estimate each of these organisms comprises approximately 1 to 100 cells per gram of soil. Like most CPR and DPANN sequenced to date, we predict these microorganisms live symbiotic anaerobic lifestyles. However, Saccharibacteria, Parcubacteria, and Doudnabacteria genomes sampled here also harbor ubiquinol oxidase operons that may have been acquired from other bacteria, likely during adaptation to aerobic soil environments. We conclude that CPR bacteria and DPANN archaea are part of the rare soil biosphere and harbor unique metabolic platforms that potentially evolved to live symbiotically under relatively oxic conditions. <b>IMPORTANCE</b> Here, we investigated overlooked microbes in soil, Candidate Phyla Radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, by size fractionating small particles from soil, an approach typically used for the recovery of viral metagenomes. Concentration of these small cells (<0.2\u2009\u03BCm) allowed us to identify these organisms as part of the rare soil biosphere and to sample genomes that were absent from non-size-fractionated metagenomes. We found that some of these predicted symbionts, which have been largely studied in anaerobic systems, have acquired aerobic capacity via lateral transfer that may enable adaptation to oxic soil environments. We estimate that there are approximately 1 to 100 cells of each of these lineages per gram of soil, highlighting that the approach provides a window into the rare soil biosphere and its associated genetic potential.","content_type":"application/pdf","author_hide":null,"authors":[{"name":"Nicolas, Alexa M","fname":"Alexa M","lname":"Nicolas"},{"name":"Jaffe, Alexander L","fname":"Alexander L","lname":"Jaffe"},{"name":"Nuccio, Erin E","fname":"Erin E","lname":"Nuccio"},{"name":"Taga, Michiko E","fname":"Michiko E","lname":"Taga"},{"name":"Firestone, Mary K","email":"mkfstone@berkeley.edu","fname":"Mary K","lname":"Firestone"},{"name":"Banfield, Jillian F","email":"jbanfield@berkeley.edu","fname":"Jillian F","lname":"Banfield"}],"editors":[{"name":"Chu, Haiyan","fname":"Haiyan","lname":"Chu"}],"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":"23553ea5bb128f03f372c34f7d48fd9b79b5cf12d859b8b35ab6e53fefa7415a","timestamp":1632144286,"image_type":"jpeg"},"pub_year":2021,"genre":"article","rights":null,"peerReviewed":true,"unitInfo":{"displayName":"UC Berkeley Previously Published Works","link_path":"ucb_postprints"}},{"id":"qt07n8f4kn","title":"Fungal-Bacterial Cooccurrence Patterns Differ between Arbuscular Mycorrhizal Fungi and Nonmycorrhizal Fungi across Soil Niches","abstract":"Soil bacteria and fungi are known to form niche-specific communities that differ between actively growing and decaying roots. Yet almost nothing is known about the cross-kingdom interactions that frame these communities and the environmental filtering that defines these potentially friendly or competing neighbors. We explored the temporal and spatial patterns of soil fungal (mycorrhizal and nonmycorrhizal) and bacterial cooccurrence near roots of wild oat grass, Avena fatua, growing in its naturalized soil in a greenhouse experiment. Amplicon sequences of the fungal internal transcribed spacer (ITS) and bacterial 16S rRNA genes from rhizosphere and bulk soils collected at multiple plant growth stages were used to construct covariation-based networks as a step toward identifying fungal-bacterial associations. Corresponding stable-isotope-enabled metagenome-assembled genomes (MAGs) of bacteria identified in cooccurrence networks were used to inform potential mechanisms underlying the observed links. Bacterial-fungal networks were significantly different in rhizosphere versus bulk soils and between arbuscular mycorrhizal fungi (AMF) and nonmycorrhizal fungi. Over 12\u2009weeks of plant growth, nonmycorrhizal fungi formed increasingly complex networks with bacteria in rhizosphere soils, while AMF more frequently formed networks with bacteria in bulk soils. Analysis of network-associated bacterial MAGs suggests that some of the fungal-bacterial links that we identified are potential indicators of bacterial breakdown and consumption of fungal biomass, while others intimate shared ecological niches.IMPORTANCE Soils near living and decomposing roots form distinct niches that promote microorganisms with distinctive environmental preferences and interactions. Yet few studies have assessed the community-level cooccurrence of bacteria and fungi in these soil niches as plant roots grow and senesce. With plant growth, we observed increasingly complex cooccurrence networks between nonmycorrhizal fungi and bacteria in the rhizosphere, while mycorrhizal fungal (AMF) and bacterial cooccurrence was more pronounced in soil further from roots, in the presence of decaying root litter. This rarely documented phenomenon suggests niche sharing of nonmycorrhizal fungi and bacteria, versus niche partitioning between AMF and bacteria; both patterns are likely driven by C substrate availability and quality. Although the implications of species cooccurrence are fiercely debated, MAGs matching the bacterial nodes in our networks possess the functional potential to interact with the fungi that they are linked to, suggesting an ecological significance of fungal-bacterial cooccurrence patterns.","content_type":"application/pdf","author_hide":null,"authors":[{"name":"Yuan, Mengting Maggie","fname":"Mengting Maggie","lname":"Yuan"},{"name":"Kakouridis, Anne","fname":"Anne","lname":"Kakouridis"},{"name":"Starr, Evan","fname":"Evan","lname":"Starr"},{"name":"Nguyen, Nhu","fname":"Nhu","lname":"Nguyen"},{"name":"Shi, Shengjing","fname":"Shengjing","lname":"Shi"},{"name":"Pett-Ridge, Jennifer","fname":"Jennifer","lname":"Pett-Ridge"},{"name":"Nuccio, Erin","fname":"Erin","lname":"Nuccio"},{"name":"Zhou, Jizhong","fname":"Jizhong","lname":"Zhou"},{"name":"Firestone, Mary","email":"mkfstone@berkeley.edu","fname":"Mary","lname":"Firestone"}],"editors":[{"name":"Giovannoni, Stephen J","fname":"Stephen J","lname":"Giovannoni"}],"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":"9eb07765054fee5499711e30392cd64ff5a4cd2730e52ff1a6eb0aba84bbe410","timestamp":1658449664,"image_type":"png"},"pub_year":2021,"genre":"article","rights":null,"peerReviewed":true,"unitInfo":{"displayName":"UC Berkeley Previously Published Works","link_path":"ucb_postprints"}},{"id":"qt3824k1sw","title":"Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass","abstract":"The interface between roots and soil, known as the rhizosphere, is a dynamic habitat in the soil ecosystem. Unraveling the factors that control rhizosphere community assembly is a key starting point for understanding the diversity of plant-microbial interactions that occur in soil. The goals of this study were to determine how environmental factors shape rhizosphere microbial communities, such as local soil characteristics and the regional climate, and to determine the relative influence of the rhizosphere on microbial community assembly compared to the pressures imposed by the local and regional environment. We identified the bacteria present in the soil immediately adjacent to the roots of wild oat (A vena spp.) in three California grasslands using deep Illumina 16S sequencing. Rhizosphere communities were more similar to each other than to the surrounding soil communities from which they were derived, despite the fact that the grasslands studied were separated by hundreds of kilometers. The rhizosphere was the dominant factor structuring bacterial community composition (38% variance explained), and was comparable in magnitude to the combined local and regional effects (22% and 21%, respectively). Rhizosphere communities were most influenced by factors related to the regional climate (soil moisture and temperature), while background soil communities were more influenced by soil characteristics (pH, CEC, exchangeable cations, clay content). The Avena core microbiome was strongly phylogenetically clustered according to the metrics NRI and NTI, which indicates that selective processes likely shaped these communities. Furthermore, 17% of these taxa were not detectable in the background soil, even with a robust sequencing depth of approximately 70,000 sequences per sample. These results support the hypothesis that roots select less abundant or possibly rare populations in the soil microbial community, which appear to be lineages of bacteria that have made a physiological tradeoff for rhizosphere competence at the expense of their competitiveness in non-rhizosphere soil.","content_type":"application/pdf","author_hide":null,"authors":[{"name":"Nuccio, Erin E","fname":"Erin E","lname":"Nuccio"},{"name":"Anderson\u2010Furgeson, James","fname":"James","lname":"Anderson\u2010Furgeson"},{"name":"Estera, Katerina Y","fname":"Katerina Y","lname":"Estera"},{"name":"Pett\u2010Ridge, Jennifer","fname":"Jennifer","lname":"Pett\u2010Ridge"},{"name":"de Valpine, Perry","email":"pdevalpine@berkeley.edu","fname":"Perry","lname":"de Valpine","ORCID_id":"0000-0002-8329-6796"},{"name":"Brodie, Eoin L","email":"eoin_brodie@berkeley.edu","fname":"Eoin L","lname":"Brodie","ORCID_id":"0000-0002-8453-8435"},{"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":167,"asset_id":"5cf768e39315ab53e6bfd4ac5363c748ea9a42efc5620ad45c886d1d4c18d2c6","timestamp":1574096501,"image_type":"png"},"pub_year":2016,"genre":"article","rights":null,"peerReviewed":true,"unitInfo":{"displayName":"UC Berkeley Previously Published Works","link_path":"ucb_postprints"}},{"id":"qt5mq7x3xt","title":"Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil.","abstract":"Microbial activity increases after rewetting dry soil, resulting in a pulse of carbon mineralization and nutrient availability. The biogeochemical responses to wet-up are reasonably well understood and known to be microbially mediated. Yet, the population level dynamics, and the resulting changes in microbial community patterns, are not well understood as ecological phenomena. Here, we used sequencing of 16S rRNA genes coupled with heavy water (H<sub>2</sub><sup>18</sup>O) DNA quantitative stable isotope probing to estimate population-specific rates of growth and mortality in response to a simulated wet-up event in a California annual grassland soil. Bacterial growth and mortality responded rapidly to wet-up, within 3\u2009h, and continued throughout the 168\u2009h incubation, with patterns of sequential growth observed at the phylum level. Of the 37 phyla detected in the prewet community, growth was found in 18 phyla while mortality was measured in 26 phyla. Rapid growth and mortality rates were measurable within 3\u2009h of wet-up but had contrasting characteristics; growth at 3\u2009h was dominated by select taxa within the Proteobacteria and Firmicutes, whereas mortality was taxonomically widespread. Furthermore, across the community, mortality exhibited density-independence, consistent with the indiscriminate shock resulting from dry-down and wet-up, whereas growth was density-dependent, consistent with control by competition or predation. Total aggregated growth across the community was highly correlated with total soil CO<sub>2</sub> production. Together, these results illustrate how previously \"invisible\" population responses can translate quantitatively to emergent observations of ecosystem-scale biogeochemistry.","content_type":"application/pdf","author_hide":null,"authors":[{"name":"Blazewicz, Steven J","fname":"Steven J","lname":"Blazewicz","ORCID_id":"0000-0001-7517-1750"},{"name":"Hungate, Bruce A","fname":"Bruce A","lname":"Hungate","ORCID_id":"0000-0002-7337-1887"},{"name":"Koch, Benjamin J","fname":"Benjamin J","lname":"Koch"},{"name":"Nuccio, Erin E","fname":"Erin E","lname":"Nuccio","ORCID_id":"0000-0003-0189-183X"},{"name":"Morrissey, Ember","fname":"Ember","lname":"Morrissey","ORCID_id":"0000-0002-5810-1096"},{"name":"Brodie, Eoin L","email":"eoin_brodie@berkeley.edu","fname":"Eoin L","lname":"Brodie","ORCID_id":"0000-0002-8453-8435"},{"name":"Schwartz, Egbert","fname":"Egbert","lname":"Schwartz"},{"name":"Pett-Ridge, Jennifer","fname":"Jennifer","lname":"Pett-Ridge","ORCID_id":"0000-0002-4439-2398"},{"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":174,"asset_id":"416aa9588c294a4961133697218257eeeecab6daed46d525237cf8f7497ae3fb","timestamp":1686191011,"image_type":"png"},"pub_year":2020,"genre":"article","rights":null,"peerReviewed":true,"unitInfo":{"displayName":"UC Berkeley Previously Published Works","link_path":"ucb_postprints"}},{"id":"qt0d62v85p","title":"Community RNA-Seq: multi-kingdom responses to living versus decaying roots in soil.","abstract":"Roots are a primary source of organic carbon input in most soils. The consumption of living and detrital root inputs involves multi-trophic processes and multiple kingdoms of microbial life, but typical microbial ecology studies focus on only one or two major lineages. We used Illumina shotgun RNA sequencing to conduct PCR-independent SSU rRNA community analysis (\"community RNA-Seq\") and simultaneously assess the bacteria, archaea, fungi, and microfauna surrounding both living and decomposing roots of the annual grass, Avena fatua. Plants were grown in <sup>13</sup>CO<sub>2</sub>-labeled microcosms amended with <sup>15</sup>N-root litter to identify the preferences of rhizosphere organisms for root exudates (<sup>13</sup>C) versus decaying root biomass (<sup>15</sup>N) using NanoSIMS microarray imaging (Chip-SIP). When litter was available, rhizosphere and bulk soil had significantly more Amoebozoa, which are potentially important yet often overlooked top-down drivers of detritusphere community dynamics and nutrient cycling. Bulk soil containing litter was depleted in Actinobacteria but had significantly more Bacteroidetes and Proteobacteria. While Actinobacteria were abundant in the rhizosphere, Chip-SIP showed Actinobacteria preferentially incorporated litter relative to root exudates, indicating this group's more prominent role in detritus elemental cycling in the rhizosphere. Our results emphasize that decomposition is a multi-trophic process involving complex interactions, and our methodology can be used to track the trajectory of carbon through multi-kingdom soil food webs.","content_type":"application/pdf","author_hide":null,"authors":[{"name":"Nuccio, Erin E","fname":"Erin E","lname":"Nuccio","ORCID_id":"0000-0003-0189-183X"},{"name":"Nguyen, Nhu H","fname":"Nhu H","lname":"Nguyen","ORCID_id":"0000-0001-8276-7042"},{"name":"Nunes da Rocha, Ulisses","fname":"Ulisses","lname":"Nunes da Rocha","ORCID_id":"0000-0001-6972-6692"},{"name":"Mayali, Xavier","fname":"Xavier","lname":"Mayali","ORCID_id":"0000-0002-2170-0773"},{"name":"Bougoure, Jeremy","fname":"Jeremy","lname":"Bougoure"},{"name":"Weber, Peter K","fname":"Peter K","lname":"Weber","ORCID_id":"0000-0001-6022-6050"},{"name":"Brodie, Eoin","email":"eoin_brodie@berkeley.edu","fname":"Eoin","lname":"Brodie","ORCID_id":"0000-0002-8453-8435"},{"name":"Firestone, Mary","fname":"Mary","lname":"Firestone"},{"name":"Pett-Ridge, Jennifer","email":"pettridge2@llnl.gov","fname":"Jennifer","lname":"Pett-Ridge","ORCID_id":"0000-0002-4439-2398"}],"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":"0aa4b9ff6b6e3cf12aae565458d0cf50dd9a62e808fa226760bd13fee4db5d63","timestamp":1687895533,"image_type":"png"},"pub_year":2021,"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":18,"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":19,"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":16,"displayName":"UC Berkeley"},{"value":"ucd","count":0,"displayName":"UC Davis"},{"value":"uci","count":0,"displayName":"UC Irvine"},{"value":"ucla","count":0,"displayName":"UCLA"},{"value":"ucm","count":1,"displayName":"UC Merced"},{"value":"ucr","count":0,"displayName":"UC Riverside"},{"value":"ucsd","count":0,"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":5,"displayName":"UC Office of the President"},{"value":"lbnl","count":15,"displayName":"Lawrence Berkeley National Laboratory"},{"value":"anrcs","count":0,"displayName":"UC Agriculture & Natural Resources"}]},{"display":"Department","fieldName":"departments","facets":[{"value":"lbnl_bs","count":6,"displayName":"BioSciences"},{"value":"ucb_eps","count":3,"displayName":"Department of Earth and Planetary Science"},{"value":"lbnl_ees","count":5,"displayName":"Earth & Environmental Sciences"},{"value":"lbnl_es","count":1,"displayName":"Energy Sciences"},{"value":"rgpo","count":5,"displayName":"Research Grants Program Office"}]},{"display":"Journal","fieldName":"journals","facets":[]},{"display":"Discipline","fieldName":"disciplines","facets":[]},{"display":"Reuse License","fieldName":"rights","facets":[{"value":"CC BY","count":3,"displayName":"BY - Attribution required"},{"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>