Biology subjects

Kimbrel, J.

Publications and source records attributed to Kimbrel, J..

15 recordsLinked to original sources

bioRxiv2026

Microbial communities in tropical soils are highly resilient to fluctuating redox conditions

Many wet tropical soils alternate frequently between fully oxygenated and anaerobic conditions, constraining the terminal electron acceptors available for microbial metabolism, and the mineral-organic matter interactions that regulate many aspects of soil carbon (C) cycling. However, it is still unclear how fluctuating soil redox conditions influence the microbial community composition and if microbially mediated C flux is sensitive to extended oxic or anoxic periods like those observed during drought and flooding respectively. Using a 44-day redox manipulation of tropical soils that experience daily-to-weekly oxygen (O2) fluctuations in the field, we measured how different redox regimes shape soil biogeochemistry and microbial and metabolite composition. Replicate microcosms were exposed to four treatments (static oxic, static anoxic, high frequency fluctuation (4 day oxic/4 day anoxic), or low frequency fluctuation (8 day oxic/4 day anoxic)) regimes, and harvested for microbial, metabolite, carbon dioxide (CO2) flux, and biogeochemical assays at multiple timepoints. Oxic and fluctuating redox conditions caused the microbial community to shift in a manner correlated with soil iron content and directly orthogonal to communities from anoxic soils. The identity of both iron oxidizers and iron reducers was distinct in static anoxic soils but was resilient to redox fluctuation and prolonged O2 exposure. The total amount of CO2 respired was similar across all four redox regimes. Water-extractable organic matter composition was distinct across redox treatments, with anoxic soils accumulating higher levels of carbohydrate-, proteins-, amino sugar-, and lignin-like compounds consistent with reduced enzymatic decomposition and release of mineral-associated organic matter via iron reduction, while oxic soils showed elevated lipid- and unsaturated hydrocarbon-like compounds indicative of greater microbial biomass turnover. The microbial community adapted to dynamic redox conditions and the results substantiate cycling of distinct C compounds under varying redox conditions resulting from varying bioavailability (driven by mineral-OM dynamics) and/or shifted microbial metabolism.

microbiology↗

bioRxiv2026

Iron limitation alters diatom carbon flow through shifts in microbiome exometabolite consumption

Iron is required for photosynthesis, and thus affects biogeochemical cycling in widespread regions where its availability is limited. Turnover of aquatic photosynthetically-derived carbon is largely constrained by bacterial activity, but we lack a mechanistic understanding of how iron limitation influences this activity. We examined a bacterial enrichment community dependent on carbon from the diatom Phaeodactylum tricornutum to investigate how iron limitation alters the flow of carbon to bacteria, and exometabolite and community composition. Using stable isotope tracing, we quantified diatom exudate incorporation with single-cell-resolution. We identified a population of bacteria under iron limitation with high metabolic activity yet low incorporation of newly-fixed diatom carbon, indicating a shift in metabolism relative to the iron-replete control. Ultra-high-resolution exometabolomics revealed bacterial consumption of aromatics, lipid-like compounds, and purines and pyrimidines occurred under iron-limitation, when these compounds also exhibited increased exudation. We identified gene pathways for utilization of these compounds in taxa with increased abundance under iron limitation which may be responsible for carbon flow shifts. These results provide a mechanistic link between iron-limitation driven shifts in exudate composition and flow of carbon to the microbiome. This has important implications for predicting carbon flow in surface oceans and manipulating algal-bacterial interactions in engineered systems.

microbiology↗

bioRxiv2025

Direct and diffuse cross-kingdom interactions in plant microbiome assembly

Studies of plant-associated microbial communities consistently indicate a role for classic assembly mechanisms, such as environmental and host filters, but often leave substantial unexplained variation. Biotic interactions within microbial communities may help to fill this gap, specifically cross-kingdom interactions between fungi and bacteria, as these are increasingly found to be important to both assembly and function. We hypothesized that direct interactions between bacteria and fungi are an important driver of composition in low-diversity leaf habitats, where pairwise interactions are more likely. In high-diversity root habitats, we expected diffuse, indirect interactions to be more relevant to composition. To test these hypotheses, we characterized bacterial and fungal communities of switchgrass (Panicum virgatum L.) leaves and roots at 14 sites spanning mountain to coastal ecoregions of North Carolina, USA. We analyzed putative direct and diffuse interactions using ecological network inference and partitioned variance explained in microbial community composition by spatial, environmental, and biotic interactions. We found that cross-kingdom biotic interactions contributed to microbial community structure. The largest improvements to variance explained (5-11%) were from direct interactions, except for root fungal communities where diffuse interactions (7.5%) explained more than double that of direct interactions (2.8%). These contributions were comparable to those from environmental and spatial factors. The joint effects of putative biotic interactions and environmental conditions also contributed to the explained variation, highlighting the importance of environmental tracking in microbes. These findings suggest that using network inference for identifying cross-kingdom ecological interactions can improve our fundamental understanding of how plant-associated microbiomes assemble, which is also directly relevant to applied efforts such as the effective development of synthetic communities.

ecology↗

bioRxiv2025

Marine bacteria cross-feeding controls the fate of extracellular glycolate carbon

Glycolate is a major product of phytoplankton photorespiration, but its fate in the microbial food web is not well constrained. Here, we used stable isotope probing and mass spectrometry combined with genomic analyses and microscopy to quantify glycolate metabolism by a taxonomically diverse set of heterotrophic marine bacteria. We found that 9 of 16 tested strains with the genomic capability to metabolize glycolate directly assimilated and respired glycolate carbon in monoculture. We next co-cultivated glycolate-incorporating strains with non-incorporating strains and found that several cross-feeders incorporated more glycolate carbon into their biomass than direct incorporators. Carbon use efficiency, reflecting proportional differences in movement of glycolate carbon into biomass versus into carbon dioxide, were distinct across co-cultures and ranged from 0.01 -3.15% depending on the strain mixtures. These results suggest that the fate of glycolate carbon is not limited to microbial taxa with the genetic capability for direct assimilation, and that bacterial metabolic interactions via cross-feeding play a critical role in influencing the efficiency of carbon transfer. Such information is critical to refine conceptual and numerical models of heterotrophic processing and transfer of organic carbon in an era of global change with predicted increases in photorespiration.

microbiology↗

bioRxiv2025

Reduced legacy precipitation decreases microbial community growth efficiency and alters soil organic carbon in a California grassland

Changes in global patterns can leave a lasting legacy in semi-arid grasslands by reshaping microbial growth dynamics and carbon cycling during the first wet-up in the autumn--a period known for intense microbial activity and significant carbon emissions. To study the lasting impacts of decreased winter rain, we implemented two precipitation regimes (100% vs. 50% mean annual precipitation) in California Mediterranean-climate grassland field plots. After the dry season, soils were rewetted in the laboratory with H218O, and sampled at 0 h, 3 h, 24 h, 48 h, 72 h, and 168 h post rewet. We quantified CO2 efflux; measured microbial growth and mortality via quantitative 18O stable isotope probing and 16S rRNA gene amplicon sequencing; and characterized the soil organic carbon chemical composition, metagenomes, and metatranscriptomes. We found that reduced winter precipitation imposed a strong legacy effect on microbial turnover; despite maintaining similar respiration rates, microbial growth declined by [~]1 order of magnitude, yielding decreased community growth efficiency (CGE = gross community growth/net respiration), and microbial mortality declined by [~]2 orders of magnitude. Soil organic carbon also shifted from lipid-like, amino-sugar-like, and protein-like compounds (indicative of microbial necromass) to more oxidized lignin-like and tannin-like compounds (indicative of decomposing plant-derived compounds). Meta-omics revealed distinct metabolic strategies linked to CGE. At high-CGE, microbes appeared to consume more energetically favorable N-rich necromass (released via high microbial turnover), this allowed for increased amino acids and peptidoglycan biosynthesis and greater aromatic compound degradation, fueling further energy production and growth efficiency. At low-CGE, communities had elevated carbohydrate metabolism and lipid turnover, consistent with increased investment in plant detritus degradation and membrane repair and maintenance rather than growth. Together, our findings demonstrate that reduced winter rainfall decreases microbial turnover following rewetting. Persistent decreases in CGE due to reduced winter rainfall result in consistent carbon loss as CO2, which, if sustained over multiple years, could ultimately lead to a net decline in total soil organic carbon.

microbiology↗

bioRxiv2025

Tracking Persistence and Dynamics of Active Soil Viruses with SIP-Viromics

Viruses are abundant and ecologically important in soils, yet the persistence and production dynamics of extracellular virions remain poorly understood. We applied a genome-resolved stable isotope probing viromics (SIP-viromics) approach, combining H 18O labeling with viral metagenomics, to track virion turnover in seasonally dry grassland soils following rewetting. We identified 354 viral populations (vOTUs) using individual-sample and combined metagenome assemblies. Only 22% of vOTUs exhibited significant 18O enrichment, indicating active replication and new virion production during the 1-week incubation; the majority (78%) persisted without detectable replication, consistent with a viral seed bank. Active vOTUs accounted for 4.76-5.15% of total virions per gram of soil, with viral loads ranging from 3.15 x 1010 to 6.59 x 1010 virions per gram. Probabilistic and deterministic sensitivity analyses spanning viral DNA fraction and genome length reinforced that persistent virions represented the majority of the extracellular viral pool post-wet-up, regardless of parameter assumptions. Host predictions linked both active and persistent vOTUs primarily to Actinomycetota and Pseudomonadota--bacterial groups known to rapidly resuscitate following rewetting--suggesting that some viruses exhibit rapid turnover while others persist over longer timescales, forming a stable viral pool capable of reinitiating infections during favorable conditions. These results demonstrate that SIP-viromics can distinguish newly produced from persistent virions and reveal host-associated patterns of lytic infection and virion production. Our findings advance understanding of soil virus-host interactions and highlight the ecological role of persistent virions as a genetic reservoir contributing to microbial turnover and biogeochemical cycling following environmental disturbance. ImportanceUnderstanding the persistence and production dynamics of soil viruses is critical for elucidating their roles in microbial community dynamics and nutrient cycling, yet these processes have remained largely uncharacterized due to methodological limitations. By integrating stable isotope probing with viromics, this study provides a robust framework for directly distinguishing newly produced from persistent virions in situ. Unlike conventional viromics, which only catalogs viral diversity, SIP-viromics enables quantification of active viral replication and persistence under natural soil conditions. Our results demonstrate that most virions in a seasonally dry soil persisted through a rewetting event, with active replication limited to a minority of viral populations. Persistent virions were primarily linked to dominant bacterial groups, indicating that host ecophysiology and environmental stability strongly influence lytic infection. Collectively, these findings highlight viruses as long-term reservoirs of genetic material, capable of shaping microbial dynamics and ecosystem processes over time. This work establishes SIP-viromics as a powerful approach for studying virus-host interactions and their ecological significance in terrestrial environments.

microbiology↗

bioRxiv2025

Specialist Generalist Trade Offs in Microbial Growth Rates Across Soil Habitats

Microbial ecological strategies are shaped by a fundamental trade-off: is it better to specialize and thrive in a narrow niche or generalize and persist across diverse environments? In soils, this trade-off is particularly relevant in the rhizosphere and detritusphere, where microorganisms encounter distinct resource inputs from living and decaying roots. Using H {superscript 1} O quantitative stable isotope probing (qSIP), we measured in situ bacterial and fungal growth rates in the rhizosphere, the root detritusphere, and in the combined presence of rhizosphere + root detritus to test whether specialists--microbes growing in a single habitat--grow faster than generalists that persist across multiple environments. Specialists grew consistently faster than generalists, suggesting a trade-off between the breadth of environmental conditions a microorganism can tolerate and its ability to grow quickly in a specific habitat. This cost to broad niche adaptation was apparent for bacteria, but growth rates of fungal saprotrophs varied little between specialists and generalists, reflecting how fundamental differences in life-history strategies between bacteria and fungi can shape microbial responses to resource availability and habitat heterogeneity. Net relatedness and nearest taxon indices indicated total bacterial communities were phylogenetically clustered while specialist and generalist communities were phylogenetically random, suggesting that functional traits, not lineage, best predict ecological strategy. In annual grassland soils, fast-growing specialists may dominate ecosystem processes when resources abound, and slow-growing generalists may sustain element transformations when conditions shift; understanding this interplay is key to predicting soil-carbon trajectories.

microbiology↗

bioRxiv2024

Coastal bacteria and protists assimilate viral carbon and nitrogen

Free viruses are the most abundant type of biological particles in the biosphere, but the lack of quantitative knowledge about their consumption by heterotrophic protists and bacterial degradation has hindered the inclusion of virovory in biogeochemical models. Here, using isotope-labeled viruses added to three independent microcosm experiments with natural microbial communities followed by isotope measurements with single-cell resolution and flow cytometry, we quantified the flux of viral C and N into virovorous protists and bacteria and compared the loss of viruses due to abiotic vs biotic factors. We found that some protists can obtain most of their C and N requirements from viral particles and that viral C and N get incorporated into bacterial biomass. We found that bacteria and protists were responsible for increasing the daily removal rate of viruses by 33% to 85%, respectively, compared to abiotic processes alone. Our laboratory incubation experiments showed that abiotic processes removed roughly 50% of the viruses within a week, and adding biotic processes led to a removal of 83% to 91%. Our data provide direct evidence for the transfer of viral C and N back into the microbial loop through protist grazing and bacterial breakdown, representing a globally significant flux that needs to be investigated further to better understand and predictably model the C and N cycles of the hydrosphere.

ecology↗

bioRxiv2023

Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro assessment of neutralizing antibodies

Viral populations in natural infections can have a high degree of sequence diversity, which can directly impact immune escape. However, antibody potency is often tested in vitro with a relatively clonal viral populations, such as laboratory virus or pseudotyped virus stocks, which may not accurately represent the genetic diversity of circulating viral genotypes. This can affect the validity of viral phenotype assays, such as antibody neutralization assays. To address this issue, we tested whether recombinant virus carrying SARS-CoV-2 spike (VSV-SARS-CoV-2-S) stocks could be made more genetically diverse by passage, and if a stock passaged under selective pressure was more capable of escaping monoclonal antibody (mAb) neutralization than unpassaged stock or than viral stock passaged without selective pressures. We passaged VSV-SARS-CoV-2-S four times concurrently in three cell lines and then six times with or without polyclonal antiserum selection pressure. All three of the monoclonal antibodies tested neutralized the viral population present in the unpassaged stock. The viral inoculum derived from serial passage without antiserum selection pressure was neutralized by two of the three mAbs. However, the viral inoculum derived from serial passage under antiserum selection pressure escaped neutralization by all three mAbs. Deep sequencing revealed the rapid acquisition of multiple mutations associated with antibody escape in the VSV-SARS-CoV-2-S that had been passaged in the presence of antiserum, including key mutations present in currently circulating Omicron subvariants. These data indicate that viral stock that was generated under polyclonal antiserum selection pressure better reflects the natural environment of the circulating virus and may yield more biologically relevant outcomes in phenotypic assays.

molecular biology↗

bioRxiv2022

Divergent microbial traits influence the transformation of living versus dead root inputs to soil carbon

Soil microorganisms influence the global carbon cycle by transforming plant inputs into soil organic carbon (SOC), but the microbial traits that facilitate this process are unresolved. While current theory and biogeochemical models suggest microbial carbon-use efficiency and growth rate are positive predictors of SOC, recent observations demonstrate these relationships can be positive, negative, or neutral. To parse these contradictory effects, we used a 13C-labeling experiment to test whether different microbial traits influenced the transformation of plant C into SOC within the microbial habitats surrounding living root inputs (rhizosphere) versus decaying root litter (detritusphere), under both normal soil moisture and droughted conditions. In the rhizosphere, bacterial-dominated communities with fast growth, high carbon-use efficiency, and high production of extracellular polymeric substances formed microbial-derived SOC under normal moisture conditions. However, in the detritusphere - and the rhizosphere under drought - more fungal-dominated communities with slower growth but higher exoenzyme activity formed plant-derived SOC. These findings emphasize that microbial traits linked with SOC accrual are not universal, but contingent on how microorganisms allocate carbon under different resource conditions and environmental stressors.

ecology↗

bioRxiv2022

Single cell carbon and nitrogen incorporation and remineralization profiles are uncoupled from phylogenetic groupings of diatom-associated bacteria

Bacterial remineralization of algal organic matter is thought to fuel algal growth, but this has not been quantified. Consequently, we cannot currently predict whether some bacterial taxa may provide more remineralized nutrients to algae than others, nor whether this is linked their incorporation. We quantified bacterial incorporation of algal-derived complex dissolved organic C (DOC) and N (DON) and net algal incorporation of remineralized C and N at the single cell level using isotope tracing and NanoSIMS for fifteen bacterial co-cultures growing with the diatom Phaeodactylum tricornutum. We found unexpected variability in the net C and N fluxes between algae and bacteria, including non-ubiquitous complex DON utilization and remineralization. We identified three distinct functional categories of metabolic interactions, which we termed macromolecule remineralizers, macromolecule users, and small-molecule users, the latter exhibiting efficient growth under low carbon availability. The functional categories were not linked to phylogeny and could not be elucidated strictly from metabolic capacity as predicted by comparative genomics. Using comparative proteogenomic analyses, we show that a complex DON incorporating strain expressed proteins related to growth and peptide transport, and a non-incorporator prioritized reactive oxygen species scavenging and inorganic nutrient uptake. Our analysis suggests that phylogeny does not predict the extent of algae-bacteria metabolite exchange, and activity-based measurements are indispensable to classify the high diversity of microbes into functional groups. These categorizations are useful for conceptual understanding and mechanistic numerical modeling to ultimately predict the fate of elemental cycles in response to environmental change.

microbiology↗

bioRxiv2022

Dynamic Phaeodactylum tricornutum Exometabolites Shape Surrounding Bacterial Communities

The roles of exometabolites in mediating algal-bacterial interactions and regulating microbial community composition are not well understood. Here, we identified specific exometabolites from the model diatom Phaeodactylum tricornutum affecting abundance of specific bacterial taxa in isolation and in a community setting. We examined the response of a P. tricornutum-adapted enrichment community and found that both algal exudates and algal presence drove similar changes in community composition compared to controls. Using LC-MS/MS, we identified 50 metabolites produced by axenic P. tricornutum and found that different exometabolites accumulated during different algal growth phases. Profiling growth of 12 bacterial isolates representative of the enrichment community uncovered two algal exometabolites (out of 12 tested) which supported growth of a subset of isolates as a primary carbon source. We compared enrichment community response with and without the addition of two contrasting metabolites: 4-hydroxybenzoic acid, which supported isolate growth, and lumichrome, which did not. Exogenous metabolite additions did promote increased abundances of taxa that were able to utilize the metabolite in the isolate study, but also revealed the importance of factors relating to algal presence in regulating community composition. Collectively, this work demonstrates the influence of specific algal exometabolites in driving microbial community composition.

microbiology↗

bioRxiv2022

Mycorrhizal fungi stabilize bacterial growth and diversity in water-limited soils

Drought disrupts soil microbial activity and many biogeochemical processes. Although plant-associated fungi can support plant performance and nutrient cycling during drought, their effects on nearby drought-exposed soil microbial communities are not well resolved. We used H 18O quantitative stable isotope probing (qSIP) and 16S rRNA gene profiling to investigate bacterial community dynamics following water limitation in the hyphospheres of two distinct fungal lineages (Rhizophagus irregularis and Serendipita bescii) grown with the bioenergy model grass Panicum hallii. In uninoculated soil, a history of water limitation resulted in significantly lower bacterial growth potential and growth efficiency, as well as lower diversity in the actively growing bacterial community. In contrast, both fungal lineages had a protective effect on hyphosphere bacterial communities exposed to water limitation: bacterial growth potential, growth efficiency, and the diversity of the actively growing bacterial community were not suppressed by a history of water limitation in soils inoculated with either fungus. Despite their similar effects at the community level, the two fungal lineages did elicit different taxon-specific responses, and bacterial growth potential was greater in R. irregularis- compared in S. bescii- inoculated soils. Several of the bacterial taxa that responded positively to fungal inocula belong to lineages that are considered drought-susceptible. Overall, H 18O qSIP highlighted treatment effects on bacterial community structure that were less pronounced using traditional 16S rRNA gene profiling. Together, these results indicate that fungal-bacterial synergies may support bacterial resilience to moisture limitation.

ecology↗

bioRxiv2021

Active viral population dynamics in frozen Arctic peat soil revealed with H218O stable isotope probing metagenomics

Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake. However, most ecosystem carbon measurements neglect winter months since carbon losses (primarily driven by microbial decomposers) are assumed to be negligible at low temperatures. We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under winter conditions, with an emphasis on viruses and virus-host dynamics. Peat soils from the Bonanza Creek LTER site in Alaska were incubated under subzero anoxic conditions with H218O for 184 and 370 days. We identified 46 bacterial populations (MAGs; spanning 9 bacterial phyla) and 243 viral populations (vOTUs) that actively took up 18O and produced significant CO2 throughout the incubation. Active hosts, predicted for 33% of the active vOTUs, were some of the most abundant MAGs and capable of fermentation and organic matter degradation. Approximately three-quarters of the active vOTUs carried auxiliary metabolic genes that spanned five functional categories, including carbon utilization, highlighting the potential impact of viruses in this peat soils microbial biogeochemistry. These results illustrate significant bacterial and viral activity and interactions occur in frozen soils, revealing viruses are a major community-structuring agent throughout winter months.

microbiology↗

bioRxiv2020

MultiPhATE2: Code for Functional Annotation and Comparison of Bacteriophage Genomes

To address the need for improved tools for annotation and comparative genomics of bacteriophage genomes, we developed multiPhATE2. As an extension of the multiPhATE code, multiPhATE2 performs gene finding and functional sequence annotation of predicted gene and protein sequences, and additional search algorithms and databases extend the search space of the original functional annotation subsystem. MultiPhATE2 includes comparative genomics codes for gene matching among sets of input bacteriophage genomes, and scales well to large input data sets with the incorporation of multiprocessing in the functional annotation and comparative genomics subsystems. MultiPhATE2 was implemented in Python 3.7 and runs as a command-line code under Linux or MAC-OS. MultiPhATE2 is freely available under an open-source GPL-3 license at https://github.com/carolzhou/multiPhATE2. Instructions for acquiring the databases and third party codes used by multiPhATE2 are found in the README file included with the distribution. Users may report bugs by submitting issues to the project GitHub repository webpage. Contact: zhou4@llnl.gov or multiphate@gmail.com. Supplementary materials, which demonstrate the outputs of multiPhATE2, are available in a GitHub repository, at https://github.com/carolzhou/multiPhATE2_supplementaryData/.

bioinformatics↗