Biology subjects

Shade, A.

Publications and source records attributed to Shade, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Biotic versus environmental controls on microbial degradation of permafrost organic matter

Permafrost thaw exposes ancient organic matter to microbial degradation, which is predicted to release globally significant quantities of greenhouse gases into the atmosphere. Though microorganisms drive these processes, the relative importance of biotic (taxonomic and functional community composition) versus environmental (e.g., soil physicochemistry) drivers and their interactions are unknown. Using a novel in situ thaw experiment conducted at the Cold Regions Research and Engineering Laboratorys Permafrost Tunnel near Fairbanks, Alaska, we experimentally separated the effects of soil physicochemistry and microbial communities under "real-world" thaw conditions. To simulate thaw, active layer soil, Holocene permafrost (2 kya), and Pleistocene permafrost (40 kya) were sterilized, inoculated with microbial communities from the different soils, enclosed in 0.22 {micro}m membrane bags to prevent immigration, and buried in the active layer. We retrieved the bags after two weeks and two months of thaw and characterized microbial community structure (16S rRNA and ITS2 amplicon sequencing), functional potential (metagenome sequencing), and soil organic matter (OM) composition at the molecular level (FT-ICR MS). Soil had a stronger effect on bacterial community and gene assemblages than inoculum, and the effects of inoculum were stronger and longer-lasting on community structure than functional potential. Pleistocene permafrost initially contained approximately eleven times more dissolved organic carbon than the other soils, and was enriched in OM derived from microbial necromass and low molecular weight organic acids. This carbon was rapidly depleted during thaw and OM compositional characteristics became increasingly similar to active layer and Holocene permafrost, paralleling shifts in Pleistocene permafrost functional gene profiles and bacterial community structure towards those of other soils. Overall, this work provides new insights into the susceptibility of OM to microbial degradation in compositionally distinct permafrost soils, and ways in which Pleistocene Yedoma permafrost carbon is likely to be particularly vulnerable to permafrost thaw.

microbiology↗

bioRxiv2026

MATRIX: Rapid Quantification of Total and Active Microbial Cells with Single Cell Phenotypes for Environmental Microbiomes

Quantifying the abundance and activity of bacteria within populations and communities is fundamental to systems microbiology and microbiome research. Yet direct microscopic cell counting remains low-throughput, labor-intensive, and prone to user variability, leading many researchers to rely on indirect proxies such as optical density or multicopy marker-gene quantification. These indirect approaches do not distinguish between active and inactive cells and can obscure ecological interpretation. Here, we introduce MATRIX (Microbial Activity and Total cell quantification via Rapid Imaging and eXtraction), an efficient workflow that integrates sample extraction, fluorescence staining, automated microscopy and image analysis, and Bayesian statistical inference to quantify total and redox-active cells and derive single-cell measurements for environmental microbial populations and communities. We demonstrate its reproducibility and versatility using both cultured isolates and high-diversity soil communities. The resulting quantitative, phenotypic datasets provide rapid, direct measurements of population of community size and activity, enabling well-powered analyses that strengthen mechanistic insight into microbial responses and improve the ecological grounding of microbiome studies. ImportanceMicrobiome studies commonly rely on relative abundance data, which cannot distinguish whether compositional shifts reflect true population growth, declines in total community size, or both. Without explicit measurements of population and community sizes, mechanistic interpretation of microbiome dynamics remains incomplete. Here we present a rapid, throughput workflow, MATRIX, that quantifies both total and redox-active bacterial cells from environmental samples. By integrating single-cell phenotypes with community-level metrics, this approach anchors microbiome datasets in direct ecological accounting rather than proxies. These measurements can clarify whether observed changes in community structure represent shifts in abundance, activity, or both, improving inference about microbial responses to stress or environmental change. MATRIX therefore offers an efficient way to incorporate quantitative ecology into systems-microbiology and microbiome studies and to strengthen the link between microbial cellular physiology, community dynamics, and eco-system function. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=125 SRC="FIGDIR/small/712149v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@1db1d8aorg.highwire.dtl.DTLVardef@708551org.highwire.dtl.DTLVardef@140a1aforg.highwire.dtl.DTLVardef@36fe58_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Disturbance increases soil microbiome functional redundancy but decreases capacity for insurance via winnowed environmental responsiveness

Redundancy is the capacity of coexisting populations to perform similar functions, supporting stable outputs under disturbance. The insurance hypothesis proposes that diverse communities are more resilient because they can respond to varied environmental stressors. Both redundancy and insurance likely shape resilience, but their relative contributions and potential interactions remain unclear. Here, we examined functional redundancy and potential for insurance in soil microbial communities disturbed by an ongoing underground fire in Centralia, Pennsylvania, USA, using seven years of deep metagenome sequencing from heated and reference sites. Analyses of taxonomic and functional diversity showed that functional redundancy increased with disturbance intensity, driven by declines in both diversity and average genome size. Biogeochemistry-relevant metabolisms, such as carbohydrate and nitrogen pathways, showed greater per-genome investment with disturbance intensity, indicating enhanced redundancy. However, transcription factor evenness - linked to community environmental responsiveness- was lower in heated soils. Thus, prolonged disturbance that imposes a strong selection can increase redundancy and near-term stability while simultaneously diminishing insurance potential against future stress, revealing tradeoffs between these mechanisms in microbial community resilience.

ecology↗

bioRxiv2025

Evaluating the legacy of drought exposure on root and rhizosphere bacterial microbiomes over two plant generations

Drought is a critical risk in developing countries for staple crops like common bean (Phaseolus vulgaris L.). We conducted an experiment to understand the legacy effects of repeated drought exposure across plant generations on the root and rhizosphere microbiome of the common bean, hypothesizing that a legacy of exposure improves overall plant microbiome resilience. We profiled the bacterial microbiome using marker gene amplicon sequencing over two plant generations in a complete factorial design for two common bean genotypes, Red Hawk and Flavert. We performed parallel experiments for Red Hawk in two different countries using soils of Pays de la Loire, France, and Michigan, USA. Despite the clear and relatively consistent drought effects on the plant phenotypes, there was neither response of the Red Hawk microbiomes to drought, nor a notable legacy of drought exposure. For Flavert, there was a minor legacy drought effect for the second generation in the rhizosphere microbiome beta diversity. This study demonstrates that rhizosphere microbiomes can be resistant to drought stress and that cross-generational legacy depends on soil origin and host genotype. Such parallel experiments across countries, while difficult to implement, are useful to inform generalities and build theory towards prediction on microbiome responses to global change.

microbiology↗

bioRxiv2025

Activation dynamics and assembly of root zone soil bacterial communities in response to stress-associated phytohormones

Plants can "cry for help" to recruit supportive microbiome members during stressful conditions. We evaluated the activation dynamics of root zone soil bacteria in response to phytohormones produced when plants are stressed, hypothesizing that the activated taxa support plant resilience. We conducted a 2-week laboratory experiment using mesocosms of root zone soil collected from two different crops: the annual legume common bean (Phaseolus vulgaris L.) and the perennial grass switchgrass (Panicum virgatum). We inactivated the microbiome by drying and then treated the soils with either abscisic acid, salicylic acid, a carrier control (methanol), or water, and then quantified the reactivation dynamics of bacterial populations over time, at one, 7, and 14 days after phytohormone addition, using amplicon sequencing of 16S rRNA and rDNA. There were several Actinobacterial taxa that switched from an average population-inactive to a population-active state after exposure to abscisic acid and salicylic acid, with Microbispora lineages switching especially noted. Some taxa were activated only in one crops soil, and some were activated in both crops soils in response to the same phytohormone. This work suggests that different bacteria have different specificities to phytohormones as plant stress signals and provides insights into understanding the mechanisms by which stressed plants may "cry for help" to recruit bacteria from the root zone to the rhizosphere. ImportanceGlobal food security is an urgent societal challenge that has been intensified by climate change and other anthropogenic stressors placed on the environment. Microbial bioinoculants are a promising solution to improve crop health and resilience, but ensuring their persistence and activation in the field remains a challenge. This study examined how dormant root-zone associated bacteria reactivate after exposure to the plant stress hormones abscisic acid and salicylic acid. The experiment revealed that certain bacteria taxa could reactivate in response to these plant stress signals and persist for at least two weeks. This work advances understanding of the potential cues for reactivation of beneficial plant-associated microbes and supports goals toward developing microbial solutions for sustainable agriculture.

microbiology↗

bioRxiv2024

Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils

Viruses are important components of the soil microbiome, influencing microbial population dynamics and the functions of their hosts. However, the relationships and feedbacks between virus dynamics, microbial host dynamics, and environmental disturbance is not understood. Centralia, PA, USA, is the site of an underground coal seam fire that has been burning for over 60 years. As the fire moves along the coal seam, previously heated soils cool to ambient temperature, creating a gradient of heat disturbance intensity and recovery. We examined annual soil viral population dynamics over seven consecutive years in Centralia using untargeted metagenome sequencing. Viral communities changed over time and were distinct between fire-affected and reference sites. Dissimilarity in viral communities was greater across sites (space) than within a site across years (time), and cumulative viral diversity more rapidly stabilized within a site across years than within a year across sites. There also were changes in CRISPR investment as soils cooled, corresponding to shifts in viral diversity. Finally, there were also differences in viral-encoded auxiliary metabolic genes between fire-affected and reference sites. These results indicate that despite high site-to-site soil viral diversity, there was surprising viral community consistency within a site over the years and shifting host-viral interactions in soils recovering from disturbance. Together, these results provide insights into how viral and host communities collectively respond to unpredicted environmental disturbance. HighlightsO_LIIn a seven-year annual study of temperate soils affected by an underground fire, viral communities displayed greater variability across sites (spatial) than over time (temporal). C_LIO_LIViral communities were distinct between heated and unheated soils throughout sampling. C_LIO_LISoil bacterial community composition correlated to viral community composition, though this relationship weakened when accounting for edaphic properties of soil temperature and pH. C_LIO_LISoil viral communities may be less resilient to press disturbance than their host bacterial communities. C_LIO_LIViral-host interactions may shift during soil recovery from long-term heating. C_LI

microbiology↗

bioRxiv2024

Stable, multigenerational transmission of the bean seed microbiome despite abiotic stress

Seed microbiomes initiate plant microbiome assembly, but the consequences of environmental conditions of the parent plant for seed microbiome assembly and transmission are unknown. We tracked endophytic seed bacterial communities of common bean lines exposed to drought or excess nutrients, and discovered stable transmission of 22 bacterial members regardless of parental plant treatment. This study provides insights into the maintenance of plant microbiomes across generations, even under challenging environmental stress.

microbiology↗

bioRxiv2023

Disentangling plant- and environment-mediated drivers of active rhizosphere bacterial community dynamics during short-term drought

BackgroundMitigating the effects of climate stress on crops is important for global food security. The microbiome associated with plant roots, henceforth, the rhizobiome, can harbor beneficial microbes that alleviate stress impacts. However, the factors influencing the recruitment of the rhizobiome during stress are unclear. We conducted an experiment to understand bacterial rhizobiome responses to short-term drought for two crop species: switchgrass and common bean. We used 16S rRNA and 16S rRNA gene sequencing to investigate the impact of drought severity on the recruitment of active bacterial rhizobiome members. We included planted and unplanted conditions to distinguish the environment-versus plant-mediated drivers of the active rhizobiome. ResultsThough each crop had a distinct rhizobiome, there were differences in the active microbiome structure between drought and watered and between planted and unplanted treatments. Despite their different community structures, the drought rhizobiome dynamics were similar across the two crops. However, the presence of a plant more strongly explained the rhizobiome variation in bean (17%) than in switchgrass (3%), with a small effect of plant mediation during drought only observed for the bean rhizobiome. The switchgrass rhizobiome was stable despite differences in the rhizosphere metabolite profiles between planted and unplanted treatments. Specifically, steroidal saponins and diterpennoids were enriched in drought, planted switchgrass soils. ConclusionsWe conclude that rhizobiome benefits to resist short-term drought are crop-specific, with the possibility of decoupling of plant exudation and rhizobiome responses, as we observed in switchgrass. We propose bacterial taxa uniquely associated with common bean plants during the short-term drought, which could be further evaluated to determine any plant benefit during drought.

microbiology↗

bioRxiv2023

Accounting for active populations provides a new perspective on the degree and mechanisms of soil microbiome resilience

Long-term (press) disturbances like the climate crisis and other anthropogenic pressures are fundamentally altering ecosystems and their functions. Many critical ecosystem functions, such as biogeochemical cycling, are facilitated by microbial communities. Understanding the functional consequences of microbiome responses to press disturbances requires ongoing observations of the active populations that contribute functions. This study leverages a 7-year time series of a 60-year-old coal seam fire (Centralia, Pennsylvania, USA) to examine the resilience of soil bacterial microbiomes to a press disturbance. Using 16S rRNA and 16S rRNA gene amplicon sequencing, we assessed the interannual dynamics of the active subset and the "whole" bacterial community. Contrary to our hypothesis, the whole communities demonstrated greater resilience than active subsets, suggesting that inactive members contributed to overall resilience. Thus, in addition to selection mechanisms of active populations, perceived microbiome resilience is also supported by mechanisms of dispersal, persistence, and revival from the local dormant pool.

microbiology↗

bioRxiv2022

Phyllosphere exudates select for distinct microbiome members in sorghum epicuticular wax and aerial root mucilage

Phyllosphere exudates create specialized microhabitats that shape microbial community diversity. Here, we explore the microbiome associated with two sorghum phyllosphere exudates, the epicuticular wax and aerial root mucilage. We hypothesized that these exudates selectively enrich for microbiome members that support host resilience to stress. Thus, we assessed the microbiome associated with the epicuticular wax from sorghum plants under non-limiting and limiting water conditions, and the aerial root mucilage from nitrogen-fertilized and non-fertilized plants. In parallel, we isolated and characterized hundreds of bacteria from wax and mucilage, and integrated data from cultivation-independent and -dependent approaches to gain deeper insights into phyllosphere functions and phenotypes. We found that Sphingomonadaceae and Rhizobiaceae families were the major taxa in the wax regardless of water availability to plants and that plant development only modestly affected wax bacterial community structure. The mucilage-associated bacterial microbiome contained several described diazotrophic species, and its structure was strongly influenced by sorghum development but only modestly influenced by fertilization. In contrast, the fungal community structure of mucilage was strongly affected by the year of sampling but not by fertilization or plant developmental stage, suggesting a decoupling of fungal-bacterial dynamics in the mucilage. Our bacterial isolate collection from wax and mucilage increased phylogenetic diversity of non-rhizosphere, plant-associated bacteria by ~20% from previous work, and several isolates matched 100% to detected amplicon sequence variants. This work expands our understanding of the microbiome of phyllosphere exudates and advances our long-term goal of translating microbiome research to support sorghum cultivation for biofuel production.

microbiology↗

bioRxiv2022

A coevolution experiment reveals parallel mutations in the AcrA-AcrB-TolC efflux pump that contributes to bacterial antibiotic resistance

One interference mechanism of bacterial competition is the production of antibiotics. Bacteria exposed to antibiotics can resist antibiotic inhibition through intrinsic and/or acquired mechanisms. Here, we performed a coevolution experiment to understand long-term consequences of antibiotic production and antibiotic resistance for two environmental bacterial strains. We grew five independent lines of the antibiotic-producing environmental strain, Burkholderia thailandensis E264, and the antibiotic-inhibited environmental strain, Flavobacterium johnsoniae UW101, together and separately on agar plates for 7.5 months (1.5 month incubations), transferring each line five times to new agar plates. We first observed that the F. johnsoniae ancestor could tolerate the B. thailandensis-produced antibiotic through efflux mechanisms. We then sequenced the genomes of clonal isolates from the coevolved and monoculture F. johnsoniae lines, and uncovered mutational ramifications to the long-term antibiotic exposure. The coevolved genomes from F. johnsoniae revealed four potential mutational signatures of antibiotic resistance that were not observed in the evolved monoculture lines. Two mutations were found in tolC: one corresponding to a 33 bp deletion and the other corresponding to a nonsynonymous mutation. A third mutation was observed as a 1 bp insertion coding for a RagB/SusD nutrient uptake protein. The last mutation was a G83R nonsynonymous mutation in acetyl-coA carboxylayse carboxyltransferase subunit alpha (AccA). Placing the tolC 33 bp deletion back into the F. johnsoniae ancestor conferred some antibiotic resistance, but not to the degree of resistance observed in coevolved lines. Furthermore, the accA mutation matched a previously described mutation conferring resistance to B. thailandensis-produced thailandamide. Analysis of B. thailandensis transposon mutants for thailandamide production revealed that thailandamide was bioactive against F. johnsoniae, but also suggested that additional B. thailandensis-produced antibiotics were involved in the inhibition of F. johnsoniae. This study reveals how long-term interspecies chemical interactions can result in a novel mutation in efflux that contribute to antibiotic resistance.

microbiology↗

bioRxiv2021

Bioactive exometabolites drive maintenance competition in simple bacterial communities

During prolonged resource limitation, bacterial cells can persist in metabolically active states of non-growth. These maintenance periods, such as those experienced in stationary phase, can include upregulation of secondary metabolism and release of exometabolites into the local environment. As resource limitation is common of many environmental microbial habitats, we hypothesized that neighboring bacterial populations employ exometabolites to compete or cooperate during maintenance, and that these exometabolite-facilitated interactions can drive community outcomes. Here, we evaluated the consequences of exometabolite interactions over stationary phase among three environmental strains: Burkholderia thailandensis E264, Chromobacterium subtsugae, and Pseudomonas syringae pv.tomato DC3000. We assembled them into synthetic communities that only permitted chemical interactions. We compared the responses (transcripts) and outputs (exometabolites) of each member with and without neighbors. We found that transcriptional dynamics were changed with different neighbors, and that some of these changes were coordinated between members. The dominant competitor B. thailandensis consistently upregulated biosynthetic gene clusters to produce bioactive exometabolites for both exploitative and interference competition. These results demonstrate that competition strategies during maintenance can contribute to community-level outcomes. It also suggests that the traditional concept of defining competitiveness by growth outcomes may be narrow, and that maintenance competition could be an additional or alternative measure.

microbiology↗

bioRxiv2021

Multi-omics profiling of Earth's biomes reveals that microbial and metabolite composition are shaped by the environment

As our understanding of the structure and diversity of the microbial world grows, interpreting its function is of critical interest for understanding and managing the many systems microbes influence. Despite advances in sequencing, lack of standardization challenges comparisons among studies that could provide insight into the structure and function of microbial communities across multiple habitats on a planetary scale. Technical variation among distinct studies without proper standardization of approaches prevents robust meta-analysis. Here, we present a multi-omics, meta-analysis of a novel, diverse set of microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry), centering our description on relationships and co-occurrences of microbially-related metabolites and microbial taxa across environments. Standardized protocols and analytical methods for characterizing microbial communities, including assessment of molecular diversity using untargeted metabolomics, facilitate identification of shared microbial and metabolite features, permitting us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of a community resource that will become more valuable with time. To provide examples of applying this database, we outline important ecological questions that can be addressed, and test the hypotheses that every microbe and metabolite is everywhere, but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment. The relative abundances of microbially-related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner, and highlight the power of certain chemistry - in particular terpenoids - in distinguishing Earths environments.

ecology↗

bioRxiv2021

Endophytic microbiome variation at the level of a single plant seed

Like other plant compartments, the seed harbors a microbiome. The members of the seed microbiome are the first to colonize a germinating seedling, and they initiate the trajectory of microbiome assembly for the next plant generation. Therefore, the members of the seed microbiome are important for the dynamics of plant microbiome assembly and the vertical transmission of potentially beneficial symbionts. However, it remains challenging to assess the microbiome at the individual seed level (and, therefore, for the future individual plant) due to low endophytic microbial biomass, seed exudates that can select for particular members, and high plant and plastid contamination of resulting reads. Here, we report a protocol for extracting metagenomic DNA from an individual seed (common bean, Phaseolus vulgaris L.) with minimal disruption of host tissue, which we expect to be generalizable to other medium-and large-seed plant species. We applied this protocol to quantify the 16S rRNA V4 and ITS2 amplicon composition and variability for individual seeds harvested from replicate common bean plants grown under standard, controlled conditions to maintain health. Using metagenomic DNA extractions from individual seeds, we compared seed-to-seed, pod-to-pod, and plant-to-plant microbiomes, and found highest microbiome variability at the plant level. This suggests that several seeds from the same plant could be pooled for microbiome assessment, given experimental designs that apply treatments at the maternal plant level. This study adds protocols and insights to the growing toolkit of approaches to understand the plant-microbiome engagements that support the health of agricultural and environmental ecosystems.

microbiology↗

bioRxiv2021

Genome-centric analyses of seasonal phyllosphere microbiome activities in perennial crops

Plants and microorganisms form beneficial associations. Understanding plant-microbe interactions will inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify key leaf microbiome members on field-grown switchgrass and miscanthus, and quantify their activities for switchgrass over two growing seasons. We integrate metagenome and metatranscriptome sequencing from 192 leaf samples collected over key time points in crop phenology. We curated 40 focal metagenome-assembled-genomes (MAGs) and conservatively focus analysis on transcript recruitment to medium and high-quality MAGs that were <10% contaminated and >50% complete. Classes represented by these MAGs (Actinomycetia, Alpha- and Gamma-Proteobacteria, and Bacteroidota) were active and had seasonal dynamics in key functions, including enrichments in transcripts for of short chain dehydrogenase, molybdopterin oxioreductase, and polyketide cyclase in the late season. The majority of MAGs had activated stress-associated pathways, including trehalose metabolism, indole acetic acid degradation, betaine biosynthesis, and reactive oxygen species degradation, suggesting direct engagement with the host environment. We also detected seasonally activated biosynthetic pathways for terpenes (carotenoid and isoprenoids), and for various non-ribosomal peptide pathways that were poorly annotated. Overall, this study overcame laboratory and bioinformatic challenges associated with field-based leaf metatranscriptome analysis to inform potential key activities of these phyllosphere populations. These activities collectively support that leaf-associated bacterial populations are seasonally dynamic, responsive to host cues and interactively engage in feedbacks with the plant.

microbiology↗

bioRxiv2020

Exometabolite dynamics over stationary phase reveal strain-specific responses to nutrient limitation

Microbial exponential growth is expected to occur infrequently outside of the laboratory, in the environment. Instead, resource-limited conditions impose non-growth states for microbes. However, non-growth states are uncharacterized for the majority of environmental bacteria, especially in regard to exometabolite production. To investigate exometabolite production in response to nutrient limitation, we compared exometabolites produced over time in stationary phase across three environmental bacteria: Burkholderia thailandensis E264 (ATCC 700388), Chromobacterium violaceum ATCC 31532, and Pseudomonas syringae pathovar tomato DC3000 (ATCC BAA-871). We grew each strain in monoculture and investigated exometabolite dynamics over time from mid-exponential to stationary phase. We focused on exometabolites that were released into the media and accumulated over 45 hours, including approximately 20 hours of stationary phase. In concert, we analyzed transcripts (RNAseq) to inform interpretation of exometabolite output. We found that a majority of exometabolites released under these conditions were strain-specific. A subset of identified exometabolites were involved in both central and secondary metabolism. Transcript analysis supported that exometabolites were released from intact cells, as various transporters were either upregulated or consistently expressed. Interestingly, we found that all strains released succinate, and that each strain re-routed their metabolic pathways involved in succinate production during stationary phase. Overall, these results show that non-growth states can also be metabolically active and dynamic. Furthermore, they show that environmental bacteria have the capability to transform a resource-limited extracellular environment into a rich chemical milieu. This work has implications for understanding microbial community interactions via exometabolites, and within resource-limited environments. ImportanceNon-growth states are common for bacteria that live in resource-limited environments, and yet these states remain largely uncharacterized in cellular metabolism and metabolite output. Here, we investigated and compared stationary phase exometabolites and RNA transcripts for each of three environmental bacterial strains. We observed that diverse exometabolites were produced and that they collectively exhibited clear and directional dynamics over time. Additionally, each bacteria strain had a characteristic exometabolite profile and dynamic. This work affirms that stationary phase is not at all "stationary" for these bacteria, and sets the stage for understanding how individual metabolisms support interspecies interactions in resource-limited environments.

microbiology↗

bioRxiv2020

Abiotic treatment contributes to an alteration of the seed microbiome of common bean

There has been a growing interest in the seed microbiome due to its important role as an end and starting point of plant microbiome assembly that can have consequences for plant health. However, the effect of abiotic conditions on the seed microbial community remains unknown. We performed a pilot study in a controlled growth chamber to investigate how the endophytic seed microbiome of the common bean (Phaseolus vulgaris L. (var. Red Hawk)) was altered under abiotic treatments relevant for crop management with changing climate. Bean plants were subjected to one of three treatments: 66% water withholding to simulate mild drought, 50% Hoagland nutrient solution to simulate fertilization, or control with sufficient water and baseline nutrition. We performed 16S rRNA gene amplicon sequencing and ITS1 amplicon sequencing of the endophytic DNA to assess seed bacterial/archaeal and fungal community structure, respectively. We found that variability in the seed microbiome structure was high while alpha diversity was low, with tens of taxa present. Water withholding and nutrient addition altered the seed microbiome structure for bacterial/archaeal communities as compared to the control, and each treatment resulted in a distinct microbiome structure. There were no statistically supported differences in the fungal microbiome across treatments. While we discuss several limitations of this study, the promising results suggest that further investigation is needed to better understand abiotic or stress-induced changes in the seed microbiome, the mechanisms that drive those changes, and their implications for the health and stress responses of the next plant generation. ImportanceSeed microbiome members initiate the assembly of plant-associated microbial communities, but the environmental drivers of endophytic seed microbiome composition are unclear. Here, we exposed plants to short-term drought and fertilizer treatments during early vegetative growth and quantified the microbiome composition of the seeds that were ultimately produced. We found that seeds produced by plants stressed by water limitation or receiving nutrient addition had statistically different endophytic bacterial/archaeal microbiome compositions from each other and from seeds produced by control plants. This work suggests that the abiotic experience of a parental plant can influence the composition of its seed microbiome, with unknown consequences for the next plant generation.

microbiology↗

bioRxiv2020

Discovery of a spatially and temporally persistent core microbiome of the common bean rhizosphere

Plants recruit soil microbes that provide nutrients, promote growth and protect against pathogens1-3. However, the full potential of microbial communities for supporting plant health and agriculture is unrealized4-6, in part because rhizosphere members key for plant health are difficult to prioritize7. Microbes that ubiquitously associate with a plant species across large spatial scales and varied soil conditions provide a practical starting point for discovering beneficial members7. Here, we quantified the structures of bacterial/archaeal and fungal communities in the common bean rhizosphere (Phaseolus vulgaris), and assessed its core membership across space and time. To assess a spatial core, two divergent bean genotypes were grown in field conditions across five major growing regions in the United States, and then also compared to eight genotypes grown in Colombian soil. To assess a temporal core, we conducted a time course of rhizosphere and rhizoplane microbiome members over bean development in the field. Surprisingly, there were 48 persistent bacterial taxa that were detected in all samples, inclusive of U.S. and Colombian-grown beans and over plant development, suggesting cosmopolitan enrichment and time-independence. Neutral models of abundance-occupancy relationships and co-occurrence networks show that many of these core taxa are deterministically selected and likely in intimate relationships with the plant. Many of the core taxa were yet-uncultured and affiliated with Proteobacteria; these taxa are prime targets in support of translational plant-microbiome management. More generally, this work reveals that core members of the plant microbiome can have both broad ranges and temporal persistence with their host, suggesting intimate, albeit possibly opportunistic, interactions.

microbiology↗