Biology subjects

Brodie, E. L.

Publications and source records attributed to Brodie, E. L..

18 recordsLinked to original sources

bioRxiv2026

Establishment of microbial strains from the river, groundwater, and soil in the hyporheic zone is limited despite connectivity

Microbial diversity across ecosystems may be impacted by dispersal pathways and selection due to physiochemical conditions, and so it is hard to predict the extent of strain sharing across heterogeneous environmental compartments. Evaluation of patterns of strain-level overlap requires genome-level comparisons using extensive datasets collected over large spatial scales. Here, we sampled microbiomes beneath (hyporheic zone) and within the East River (Colorado, USA) and found little or no strain overlap at sites along the river corridor, despite connection by river flow, suggesting selection due to the local environment. Comparisons involving microbiomes from hillslopes and riparian zone soil yielded essentially no strain-level overlap with the microbiomes of river and hyporheic zones. We also sampled a nearby groundwater well and found near-perfect genotypic overlap with strains in one hyporheic zone location that exhibited active groundwater upwelling. Given an absence of direct connectivity between these two locations via discrete hydrologic flow paths, we conclude that groundwater strains are widely dispersed in the aquifer. As hyporheic zone microbiomes in zones with low river flow share no strains with groundwater microbiomes, we infer that strains introduced by groundwater mixing in the hyporheic zone are transitory. We conclude that despite evidence for mixing of river-and-hyporheic zone water, and river-and-groundwater on short time scales, establishment of transported strains in the hyporheic zone is minimal.

microbiology↗

bioRxiv2025

The long-term application of composted organic wastes caused a lasting increase in vineyard soil health and multifunctionality

As a consequence of climate change and unsustainable management practices, agricultural soils in the Mediterranean region are often degraded. The application of composted organic wastes is traditionally considered a beneficial practice to improve soil health. We studied the permanence of the beneficial effects of the long-term (20 years) application of composted organic wastes, versus mineral fertilization or no fertilization, on Mediterranean vineyard soil health. To this aim, four years after ceasing fertilization, a comprehensive analysis of soil physicochemical and biological properties, including prokaryotic diversity and functional traits by genome-centric metagenomics, was conducted to ascertain whether the beneficial effects of organic fertilization were maintained 4 years after its end. In general, but not always, soils treated with composted organic wastes showed significantly higher values of many physicochemical and biological properties (e.g., organic matter, Olsen phosphorus and extractable potassium), resulting in improved soil multifunctionality. However, despite such statistical significance, the quantitative magnitude of many of those differences was small. Fertilization regimes had a lasting strong influence on soil prokaryotic communities, as 70% of the 200 metagenome-assembled genomes and 86% of the prokaryotic functional traits showed significant differences among treatments. Organic amendments promoted nitrifying taxa such as Nitrosocosmicus oleophilus and Nitrospira japonica. In minerally-fertilized soils, resource acquisition and stress tolerance strategies were fostered among prokaryotic communities, possibly due to resource limitation and soil degradation, respectively. Stress tolerance traits were lower under organic fertilization, likely due to the improved soil properties and functions. The results obtained suggest that soil functions are influenced by microbial genes involved in nitrogen and carbon cycling, underscoring the central role of microbial metabolism in sustaining soil health and ecosystem functioning. This study demonstrates the lasting benefits of composted organic amendments in promoting soil multifunctionality in vineyard soils.

genomics↗

bioRxiv2024

Coordinated organic and inorganic nitrogen transformations fuel soil microbial blooms and increase nitrogen retention during snowmelt

Snowmelt in high-elevation watersheds triggers a microbial bloom and crash that affects nitrogen (N) export. Predicting watershed N dynamics as snowpack declines is a challenge because the mechanisms that underlie this microbial bloom and crash are uncertain. Using a multi-omic approach, we show that the dynamic molecular properties of dissolved organic N, plus high gene expression for peptidases that recycle microbial biomass, suggested that microbial turnover provided N for biosynthesis during the microbial bloom. Amino acid fermentation by Bradyrhizobia produced organic acids that also fueled denitrification and dissimilatory nitrate reduction to ammonia (DNRA) during snowmelt. Nitrification in spring was driven by Spring-Adapted Nitrososphaerales, which utilized ammonium derived from osmolyte degradation by Winter-Adapted Solirubrobacteraceae. High DNRA gene expression after snowmelt suggested significant nitrate retention, increasing watershed N retention potential. However, declining snowfall may compromise microbial regulation of soil N retention, with implications for watershed N export.

microbiology↗

bioRxiv2024

Bacterial population-level trade-offs between drought tolerance and resource acquisition traits impact decomposition

Microbes drive fundamental ecosystem processes such as decomposition. Environmental stressors are known to affect microbes, their fitness, and the ecosystem functions that they perform, yet understanding the causal mechanisms behind this influence has been difficult. We used leaf litter on soil surface as a model in situ system to assess changes in bacterial genomic traits and decomposition rates over 18 months with drought as a stressor. We hypothesized that genome-scale trade-offs due to investment in stress tolerance traits under drought reduce the capacity for bacterial populations to carry out decomposition; and that these population-level trade-offs scale up to impact emergent community traits thereby reducing decomposition rates. We observed drought tolerance mechanisms that were heightened in bacterial populations under drought, identified as higher gene copy numbers in metagenome-assembled genomes. A subset of populations under drought had reduced carbohydrate-active enzyme genes which suggested - as a trade-off - a decline in decomposition capabilities. These trade-offs were taxonomically structured as distinct patterns appeared in populations across families. We show that trait-tradeoffs in bacterial populations under drought could scale up to reduce overall decomposition capabilities and litter decay rates. Using a trait-based approach to assess the population ecology of soil bacteria, we demonstrate genome-level trade-offs in response to drought with consequences for decomposition rates.

ecology↗

bioRxiv2023

Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates

Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions. Corrinoids--the vitamin B12 family of cofactors--are critical for microbial metabolism, yet they are synthesized by only a subset of microbiome members. Here, we evaluated corrinoid production and dependence in soil bacteria as a model to investigate the ecological roles of microbes involved in metabolic interactions. We isolated and characterized a taxonomically diverse collection of 161 soil bacteria from a single study site. Most corrinoid-dependent bacteria in the collection prefer B12 over other corrinoids, while all tested producers synthesize B12, indicating metabolic compatibility between producers and dependents in the collection. Furthermore, a subset of producers release B12 at levels sufficient to support dependent isolates in laboratory culture at estimated ratios of up to 1,000 dependents per producer. Within our isolate collection, we did not find strong phylogenetic patterns in corrinoid production or dependence. Upon investigating trends in the phylogenetic dispersion of corrinoid metabolism categories across sequenced bacteria from various environments, we found that these traits are conserved in 47 out of 85 genera. Together, these phenotypic and genomic results provide evidence for corrinoid-based metabolic interactions among bacteria and provide a framework for the study of nutrient-sharing ecological interactions in microbial communities.

microbiology↗

bioRxiv2023

Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

Viruses, including phages, impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time, and their response to strong seasonal change in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental DNA and RNA viruses, including phages, across dynamics seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes. We identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of RNA viruses target fungal hosts and a large and unsuspected diversity of positive single-stranded RNA phages (Leviviricetes), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active phages which changed across seasons, consistent with a "seed-bank" viral community structure in which new phage activity, for example replication and host lysis, is sequentially triggered by changes in environmental conditions. Zooming in at the population level, we further identified virus-host dynamics matching two existing ecological models: "Kill-The-Winner" which proposes that lytic phages are actively infecting abundant bacteria, and "Piggyback-The-Persistent" which argues that when the host is growing slowly it is more beneficial to remain in a lysogenic state. The former was associated with summer months of high and rapid microbial activity, and the latter to winter months of limited and slow host growth. Taken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. Moving forward, while as our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry.

microbiology↗

bioRxiv2023

Influence of root cortical aerenchyma on the rhizosphere microbiome of field-grown maize

The root anatomical phenotype root cortical aerenchyma (RCA) decreases the metabolic cost of soil exploration and improves plant growth under drought and low soil fertility. RCA may also change the microenvironment of rhizosphere microorganisms by increasing oxygen availability or by reducing carbon rhizodeposition. We tested the hypothesis that plants with contrasting expression of RCA have different rhizosphere prokaryotic communities. Maize inbreds were grown in two field sites, Limpopo Province, South Africa and Pennsylvania, USA, and their rhizosphere soil sampled at flowering. High- and low-nitrogen fertilization was imposed as separate treatments in the experiment in South Africa. The rhizosphere microbial composition of plants with contrasting RCA was characterized by metabarcoding of the 16S rRNA genes. Geographic location was the most important factor related to the composition of rhizosphere microbial communities. In the site in South Africa, RCA explained greater percent of variance (9%) in the composition of microbial communities than genotype (7%). Although other root anatomical and architectural phenotypes were studied as possible cofactors affecting the microbial composition, RCA was among the best significant explanatory variables for the South African site although it was neutral in the Pennsylvania site. High-RCA rhizospheres significantly enriched OTUs of the families Burkholderiaceae (in South Africa) and Bacillaceae (in USA), compared to low-RCA plants, and OTUs of the families Beijerinckiaceae and Sphingomonadaceae were enriched at the two nitrogen levels in high RCA plants in South Africa. Our results are consistent with the hypothesis that RCA is an important factor for rhizosphere microbial communities, especially under suboptimal nitrogen conditions.

plant biology↗

bioRxiv2022

Life history strategies and niches of soil bacteria emerge from interacting thermodynamic, biophysical, and metabolic traits

Efficient biochemical transformation of belowground carbon by microorganisms plays a critical role in determining the long-term fate of soil carbon. As plants assimilate carbon from the atmosphere, up to 50% is exuded into the area surrounding growing roots, where it may be transformed into microbial biomass and subsequently stabilized through mineral associations. However, due to a hierarchy of interacting microbial traits, it remains elusive how emergent life-history strategies of microorganisms influence the processing of root exudate carbon. Here, by combining theory-based predictions of substrate uptake kinetics for soil bacteria and a new genome-informed trait-based dynamic energy budget model, we predicted life history traits and trade-offs of a broad range of soil bacteria growing on 82 root exudate metabolites. The model captured resource-dependent trade-offs between growth rate (power) and growth efficiency (yield) that are fundamental to microbial fitness in communities. During early phases of plant development, growth rates of bacteria were largely constrained by maximum growth potential, highlighting the predictive power of genomic traits during nutrient-replete soil conditions. In contrast, selection for efficiency was important later in the plant growing season, where the model successfully predicted microbial substrate preferences for aromatic organic acids and plant hormones. The predicted carbon-use efficiencies for growth on organics acids were much higher than typical values observed in soil. These predictions provide mechanistic underpinning for the apparent efficiency of the microbial route to mineral stabilization in the rhizosphere and add an additional layer of complexity to rhizosphere microbial community assembly.

ecology↗

bioRxiv2022

Metabolic traits and the niche of bulk soil bacteria in a Mediterranean grassland

Soil microorganisms have adapted to compete and exploit different metabolic niches in their physically and chemically diverse environment via evolution and acquisition of distinct physiological and biochemical traits. As the interface for most carbon and nutrient exchange between plants and microorganisms, the rhizosphere has received substantial attention. By comparison, what is commonly termed bulk-soil (soil free of living roots) represents a far greater volume and surface area throughout the season, and substantially higher taxonomic and phylogenetic diversity; the traits and activity of its inhabitants may also have a significant impact on overall soil function. We used a combination of comparative genomics and exoproteomics to identify metabolic traits of bacteria adapted to life in bulk soil and compared these with traits of bacteria living in the rhizosphere of wild oat, Avena barbata. In bulk soil bacteria, we observed: (i) greater investment in extracellular polymer-degrading enzyme production; (ii) greater potential for secretion (presence of signal peptides) of polymer-degrading enzymes; (iii) production of accessory proteins (carbohydrate binding modules) fused with glycoside hydrolases that enhance substrate affinity, stabilize, and increase reaction rates of polymer degrading enzymes; and (iv) organization of polymer degradation machinery within gene clusters that facilitate co-transcription of enzymes, transcription factors and transporters for polymer depolymerization products. Together, these findings suggest that unlike rhizosphere-adapted bacteria--which specialize on small molecules released primarily as root exudates--bulk soil-adapted bacteria have evolved to exploit plant polymers. This biochemically costly strategy may be mitigated by protein-level adaptations that enhance the efficiency of extracellular enzyme-mediated substrate acquisition. IMPORTANCEPlant-soil-microbe interactions are dynamic and complex, with significant implications for ecosystem functioning. Microbial traits, such as nutrient acquisition and growth yield, combined with soil and climate parameters, impact major biogeochemical processes and can define the future fate of soil carbon. Diverse soil microorganisms occupy different physical habitats within soil and exploit distinct niches by expressing different metabolic traits. Identifying and quantifying traits that underlie their fitness and function is key for understanding and predicting how soil carbon transformation and stabilization will change in the future or can be managed through intervention.

microbiology↗

bioRxiv2021

A gut commensal niche regulates stable association of a multispecies microbiota

The intestines of animals are typically colonized by a complex, relatively stable microbiota that influences health and fitness, but the underlying mechanisms of colonization remain poorly understood. As a typical animal, the fruit fly, Drosophila melanogaster, is associated with a consistent set of commensal bacterial species, yet the reason for this consistency is unknown. Here, we use gnotobiotic flies, microscopy, and microbial pulse-chase protocols to show that a commensal niche exists within the proventriculus region of the Drosophila foregut that selectively binds bacteria with exquisite strain-level specificity. Primary colonizers saturate the niche and exclude secondary colonizers of the same strain, but initial colonization by Lactobacillus physically remodels the niche to favor secondary colonization by Acetobacter. Our results provide a mechanistic framework for understanding the establishment and stability of an intestinal microbiome. One-Sentence SummaryA strain-specific set of bacteria inhabits a defined spatial region of the Drosophila gut that forms a commensal niche.

microbiology↗

bioRxiv2021

Kinetic Properties of Microbial Exoenzymes Vary with Soil Depth but Have Similar Temperature Sensitivities Through the Soil Profile

Current knowledge of the mechanisms and responses of soil organic matter (SOM) turnover to warming is mainly limited to surface soils, although over 50% of global soil carbon is contained in subsoils. Deep soils have different physicochemical properties, nutrient inputs and microbiomes, which may harbor distinct functional traits and lead to different SOM dynamics and temperature responses. We hypothesized that kinetic and thermal properties of microbial exoenzymes, which mediate SOM depolymerization, vary with soil depth, reflecting microbial adaptation to distinct substrate and temperature regimes. We determined the Michaelis-Menten (MM) kinetics of three ubiquitous enzymes involved in carbon (C), nitrogen (N) and phosphorus (P) acquisition at six soil depths down to 90 cm at a temperate coniferous forest, and their temperature sensitivity based on Arrhenius and Macromolecular Rate Theory (MMRT) models over six temperatures between 4-50{degrees}C. Maximal enzyme velocity (Vmax) decreased strongly with depth for all enzymes, both on a dry soil mass and a microbial biomass C basis, whereas their affinities increased, indicating adaptation to lower substrate availability. Surprisingly, microbial biomass-specific catalytic efficiencies also decreased with depth, except for the P-acquiring enzyme, indicating distinct nutrient demands at depth relative to microbial abundance. These results indicated that deep soil microbiomes encode enzymes with intrinsically lower turnover and/or produce less enzymes per cell, likely reflecting distinct life strategies. The relative kinetics between different enzymes also varied with depth, suggesting an increase in relative P demand with depth, or that phosphatases may be involved in C acquisition. Warming consistently led to increased Vmax and catalytic efficiency of all enzymes, and thus to overall higher SOM-decomposition potential, but enzyme temperature sensitivity was similar through the soil profile based on both Arrhenius/Q10 and MMRT models. Nevertheless, temperature directly affected the kinetic properties of different enzyme types in a depth-dependent manner, and thus the relative depolymerization potential of different compounds. Our results indicate that kinetic and thermal properties of exoenzymes are intrinsic traits of soil microbiomes adapted to distinct physicochemical conditions associated with different soil depths, and improve our conceptual understanding of critical mechanisms underlying SOM dynamics and responses to warming through the soil profile.

microbiology↗

bioRxiv2021

Measurement of Volatile Compounds for Real-time Analysis of Soil Microbial Metabolic Response to Simulated Snowmelt

Snowmelt dynamics are a significant determinant of microbial metabolism in soil and regulate global biogeochemical cycles of carbon and nutrients by creating seasonal variations in soil redox and nutrient pools. With an increasing concern that climate change accelerates both snowmelt timing and rate, obtaining an accurate characterization of microbial response to snowmelt is important for understanding biogeochemical cycles intertwined with soil. However, observing microbial metabolism and its dynamics non-destructively remains a major challenge for systems such as soil. Microbial volatile compounds (mVCs) emitted from soil represent information-dense signatures and when assayed non-destructively using state-of-the-art instrumentation such as Proton Transfer Reaction-Time of Flight-Mass Spectrometry (PTR-TOF-MS) provide time resolved insights into the metabolism of active microbiomes. In this study, we used PTR-TOF-MS to investigate the metabolic trajectory of microbiomes from a subalpine forest soil, and their response to a simulated wet-up event akin to snowmelt. Using an information theory approach based on the partitioning of mutual information, we identified mVC metabolite pairs with robust interactions, including those that were non-linear and with time lags. The biological context for these mVC interactions was evaluated by projecting the connections onto the Kyoto Encyclopedia of Genes and Genomes (KEGG) network of known metabolic pathways. Simulated snowmelt resulted in a rapid increase in the production of trimethylamine (TMA) suggesting that anaerobic degradation of quaternary amine osmo/cryoprotectants, such as glycine betaine, may be important contributors to this resource pulse. Unique and synergistic connections between intermediates of methylotrophic pathways such as dimethylamine, formaldehyde and methanol were observed upon wet-up and indicate that the initial pulse of TMA was likely transformed into these intermediates by methylotrophs. Increases in ammonia oxidation signatures (transformation of hydroxylamine to nitrite) were observed in parallel, and while the relative role of nitrifiers or methylotrophs cannot be confirmed, the inferred connection to TMA oxidation suggests either a direct or indirect coupling between these processes. Overall, it appears that such mVC time-series from PTR-TOF-MS combined with causal inference represents an attractive approach to non-destructively observe soil microbial metabolism and its response to environmental perturbation.

microbiology↗

bioRxiv2021

Community RNA-Seq: Multi-kingdom responses to living versus decaying root inputs in soil

Roots are the primary source of organic carbon inputs to most soils. Decomposition is a multi-trophic process involving multiple kingdoms of microbial life, but typically microbial ecology studies focus on one or two major lineages in isolation. We used Illumina shotgun RNA sequencing to conduct PCR-independent SSU rRNA community analysis ("community RNA-Seq") to simultaneously study the bacteria, archaea, fungi, and microfauna surrounding both living and decomposing roots of the annual grass, Avena fatua. Plants were grown in 13CO2-labeled microcosms amended with 15N-root litter. We identified rhizosphere substrate preferences for 13C-exudates versus 15N-litter 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 groups more prominent role in detritus elemental cycling in the rhizosphere. Our results emphasize that decomposition is a multi-trophic process involving cross-kingdom interactions, and the trajectory of carbon through this soil food web likely impacts the fate of carbon in soil.

microbiology↗

bioRxiv2020

Enhancement of antimicrobial diversity in situ through relaxed symbiont specificity in an insect/actinomycete partnership

Some insects form symbioses in which actinomycetes provide defense against pathogens by making antimicrobials. The range of chemical strategies employed across these associations, and how these strategies relate to insect lifestyle, remains underexplored. We assessed subsocial passalid beetles of the species Odontotaenius disjunctus, and their frass (fecal material) which is an important food resource within their galleries, as a model insect/actinomycete system. Through chemical and phylogenetic analyses, we found that O. disjunctus frass collected across eastern North America harbored multiple lineages of Streptomyces and diverse antimicrobials. Metabolites detected in frass displayed synergistic and antagonistic inhibition of a fungal entomopathogen, Metarhizium anisopliae, and multiple streptomycete isolates inhibited this pathogen when co-cultivated directly in frass. These findings support a model in which the lifestyle of O. disjunctus accommodates multiple Streptomyces lineages in their frass, resulting in a rich repertoire of antimicrobials that likely insulates their galleries against pathogenic invasion.

microbiology↗

bioRxiv2019

Sympatric and allopatric differentiation delineate population structure in a free-living terrestrial bacterium

In free-living bacteria and archaea, the equivalent of the biological species concept does not exist, creating several barriers to the study of the processes contributing to microbial diversification. As such, microorganisms are often operationally defined using conserved marker genes (i.e., 16S rRNA gene) or whole-genome measurements (i.e., ANI) to interpret intra-specific processes. However, as in eukaryotes, investigations into microbial populations must consider the potential for interacting genotypes among individuals that are subjected to similar environmental selective pressures. Therefore, we isolated 26 strains within a single bacterial ecotype (equivalent to a eukaryotic species definition) from a common habitat (leaf litter) across a regional climate gradient and asked whether the genetic diversity in a free-living soil bacterium (Curtobacterium) was consistent with patterns of allopatric or sympatric differentiation. By examining patterns of gene flow, our results indicate that microbial populations are delineated by gene flow discontinuities and exhibit evidence for population-specific adaptation. We conclude that the genetic structure within this bacterium is due to both adaptation within localized microenvironments (isolation-by-environment) as well as dispersal limitation between geographic locations (isolation-by-distance).

evolutionary biology↗

bioRxiv2019

Physiological adaptations of leaf litter microbial communities to long-term drought

Drought represents a significant stress to soil microorganisms and is known to reduce microbial activity and organic matter decomposition in Mediterranean ecosystems. However, we still lack a detailed understanding of the drought stress adaptations of microbial decomposers. We hypothesised that drought causes greater microbial allocation to stress tolerance relative to growth pathways. Here we present metatranscriptomic and metabolomic data on the physiological response of in situ microbial communities on plant leaf litter to long-term drought and pulse wetting in Californian grass and shrub ecosystems. Wetting litter after a long dry summer caused only subtle shifts in gene expression. On grass litter, communities from the decade-long ambient and reduced precipitation treatments had distinct functional profiles. The most discernable physiological adaptations to drought were production or uptake of compatible solutes to maintain cellular osmotic balance, and synthesis of capsular and extracellular polymeric substances as a mechanism to retain water. The results show a clear functional response to drought in grass litter communities with greater allocation to survival relative to growth that could affect decomposition under drought. In contrast, communities on chemically more diverse and complex shrub litter had smaller physiological differences in response to long-term drought but higher investment in resource acquisition traits across treatments, suggesting that the functional response to drought is constrained by substrate quality. Our findings suggest, for the first time in a field setting, a trade-off between microbial drought stress tolerance, resource acquisition and growth traits in leaf litter microbial communities.

microbiology↗

bioRxiv2019

Niche differentiation is spatially and temporally regulated in the rhizosphere

The rhizosphere is a hotspot for microbial C transformations, and the origin of root polysaccharides and polymeric carbohydrates that are important precursors to soil organic matter. However, the ecological mechanisms that underpin rhizosphere carbohydrate depolymerization are poorly understood. Using Avena fatua, a common annual grass, we analyzed time-resolved metatranscriptomes to compare microbial function in rhizosphere, detritusphere, and combined rhizosphere-detritusphere habitats. Population transcripts were binned with a unique reference database generated from soil isolate and single amplified genomes, metagenomes, and stable isotope probing metagenomes. While soil habitat significantly affected both community composition and overall gene expression, succession of microbial functions occurred at a faster time scale than compositional changes. Using hierarchical clustering of upregulated decomposition gene expression, we identified four distinct microbial guilds populated by taxa whose functional succession patterns suggest specialization for substrates provided by fresh growing roots, decaying root detritus, the combination of live and decaying root biomass, or aging root material. Carbohydrate depolymerization genes were consistently upregulated in the rhizosphere, and both taxonomic and functional diversity were high in the combined rhizosphere-detritusphere--suggesting coexistence of rhizosphere guilds is facilitated by niche differentiation. Metatranscriptome-defined guilds provide a framework to model rhizosphere succession and its consequences for soil carbon cycling.

ecology↗

bioRxiv2018

Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change

Microorganisms are critical in terrestrial carbon cycling because their growth, activity and interactions with the environment largely control the fate of recent plant carbon inputs, as well as the stability of assimilated carbon (Gleixner, 2013; Schimel and Schaeffer, 2012). Soil carbon stocks reflect a balance between microbial decomposition and stabilization of organic carbon. The balance can shift under altered environmental conditions (Davidson and Janssens, 2006), and new research suggests that knowledge of microbial physiology may be critical for projecting changes in soil carbon and improving the prognosis of climate change feedbacks (Allison et al., 2010; Bradford et al., 2016; Liang et al., 2017; Wieder et al., 2015). Still, predicting the ecosystem implications of microbial processes remains a challenge. Here we argue that this challenge can be m ...

ecology↗