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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Diazotrophs Show Signs of Restoration in Amazon Rain Forest Soils with Ecosystem Rehabilitation

Biological nitrogen fixation can be an important source of nitrogen in tropical forests that serve as a major CO 2 sink. Extensive deforestation of the Amazon is known to influence microbial communities and the biogeochemical cycles they mediate. However, it is unknown how diazotrophs (nitrogen-fixing microorganisms) respond to deforestation and subsequent ecosystem conversion to agriculture, as well as whether they can recover in secondary forests that are established after agriculture is abandoned. To address these knowledge gaps, here we combined a spatially explicit sampling approach with high-throughput sequencing of nifH genes. The main objectives were to assess the functional distance decay relationship of the diazotrophic bacterial community in a tropical forest ecosystem and to quantify the roles of various factors that drive the observed changes in the diazotrophic community structure. We observed an increase in local diazotrophic diversity (α-diversity) with a decrease in community turnover (β-diversity), associated with a shift in diazotrophic community structure as a result of the forest-to-pasture conversion. Both diazotrophic community turnover and structure showed signs of recovery in secondary forests. Changes in the diazotrophic community were primarily driven by the change in land use rather than differences in geochemical characteristics or geographic distances. The diazotroph communities in secondary forests resembled those in primary forests, suggesting that at least partial recovery of diazotrophs is possible following agricultural abandonment. IMPORTANCE The Amazon region is a major tropical forest region that is being deforested at an alarming rate to create space for cattle ranching and agriculture. Diazotrophs (nitrogen-fixing microorganisms) play an important role in supplying soil N for plant growth in tropical forests. It is unknown how diazotrophs respond to deforestation and whether they can recover in secondary forests that establish after agriculture is abandoned. Using high-throughput sequencing of nifH genes, we characterized the response of diazotrophs’ β-diversity and identified major drivers of changes in diazotrophs from forest-to-pasture and pasture-to-secondary-forest conversions. Studying the impact of land use change on diazotrophs is important for a better understanding of the impact of deforestation on tropical forest ecosystem functioning, and our results on the potential recovery of diazotrophs in secondary forests imply the possible restoration of ecosystem functions in secondary forests.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Snowmelt Periods as Hot Moments for Soil N Dynamics: a Case Study in Maine, USA

We examined patterns of soil N availability during the vernal transition and how warming winter and ecosystem N status (N-enriched vs. N-limited) altered these patterns. Soils were sampled at the Bear Brook Watershed in Maine during 2015 and 2016. 2016 was a warmer winter with less snowfall than 2015, and therefore had earlier snowmelt and a longer vernal transition. Across both years, thaw periods consistently showed signs of being transition periods, especially evident in the N-enriched watershed — ammonium concentrations were highest during this period due to microbial community turnover and cell lysis, whereas nitrate concentrations were lowest due to flushing by meltwater. The N-enriched soils had 4–5-times more ammonium than the N-limited soils overall, although this difference was magnified during melt periods (10–14-fold). This indicates that the altered microbial community in the chronically N-manipulated soils might be more susceptible to community turnover and lysis during snowmelt. Our results indicate that ecosystem N status influences the response of forest soil N dynamics to a changing vernal transition in a time of accelerating climate change.

vernal transition, forest soils, nitrogen, N-enric↗
DOE OSTI2025

Time-series RNA metabarcoding of the active Populus tremuloides root microbiome reveals hidden temporal dynamics and dormant core members

The rhizosphere is a critical interface between plant roots and soil, harboring diverse microbial communities that are essential to plant and ecosystem health. Although these communities exhibit stark temporal dynamics, their dormancy/activity transitions remain poorly understood. Such transitions may enable microbes to rapidly adjust functional contributions faster than community turnover alone would allow. Here, we used RNA metabarcoding to characterize the active fraction of microbial communities on the roots of quaking aspen (Populus tremuloides) in a time-series study across a natural environmental gradient. We explore cryptic temporal microbial community dynamics of rhizosphere communities at the ecosystem scale. The active rhizosphere bacterial and fungal communities were more temporally dynamic than total communities, while total communities exhibited a stronger response to site-specific conditions. Notably, some core microbiome members were often inactive, yielding a smaller “active core” subset. The fungal endophyte Hyaloscypha finlandica was the only microbe that was both present and active in all plots across all timepoints. Soil temperature strongly influenced both total and active community composition, with the fungal class Eurotiomycetes showing a temperature-dependent seasonal decline in abundance. Together, these results reveal that modulation of microbial activity levels is a key mechanism by which the plant root holobiont responds to environmental variation, and that even dominant symbionts may frequently persist in dormancy within the rhizosphere.

Community Structure and Diversity↗
DOE OSTI2022

Geological activity shapes the microbiome in deep-subsurface aquifers by advection

Subsurface environments host diverse microorganisms in fluid-filled fractures; however, little is known about how geological and hydrological processes shape the subterranean biosphere. Here, we sampled three flowing boreholes weekly for 10 mo in a 1478-m-deep fractured rock aquifer to study the role of fracture activity (defined as seismically or aseismically induced fracture aperture change) and advection on fluid-associated microbial community composition. We found that despite a largely stable deep-subsurface fluid microbiome, drastic community-level shifts occurred after events signifying physical changes in the permeable fracture network. The community-level shifts include the emergence of microbial families from undetected to over 50% relative abundance, as well as the replacement of the community in one borehole by the earlier community from a different borehole. Null-model analysis indicates that the observed spatial and temporal community turnover was primarily driven by stochastic processes (as opposed to deterministic processes). We, therefore, conclude that the observed community-level shifts resulted from the physical transport of distinct microbial communities from other fracture(s) that outpaced environmental selection. Given that geological activity is a major cause of fracture activity and that geological activity is ubiquitous across space and time on Earth, our findings suggest that advection induced by geological activity is a general mechanism shaping the microbial biogeography and diversity in deep-subsurface habitats across the globe.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Nutrient limitation shapes functional traits of mycorrhizal fungi and phosphorus-cycling bacteria across an elevation gradient

In nutrient-limited high-elevation ecosystems, plants rely on arbuscular mycorrhizal (AM) fungi to provide mineral phosphorus (P) in the form of phosphate (PO43-). AM fungi gather these nutrients from phosphorus-cycling bacteria (PCBs) that can mineralize PO43- from organic matter and solubilize mineral-bound P. How climate, soil factors, and nutrient limitation influence AM fungi and PCB assembly remains unclear. We collected soil from montane meadows across a 1,000-m elevation gradient on three replicate mountainsides and analyzed AM fungal marker genes, P-cycling genes from shotgun metagenomes, and edaphic measurements. High-elevation soils had nearly 50-fold less soil PO₄³⁻ and 60% more AM fungal hyphae than low-elevation soils. AM fungal turnover was linked to changes in pH, organic carbon, and PO₄³-. The composition of 198 P-cycling genes was influenced by the AM fungal community structure. Drivers of individual PCB functional genes, including pH and organic carbon, varied with gene phylogeny. We found a trade-off in P-cycling strategies across elevation: P-rich, low-elevation soils supported root-colonizing AM fungi and organic P-mineralizing bacteria. P-poor, high-elevation soils were dominated by stress-tolerant AM fungi and mineral P-solubilizing bacteria. Our results suggest that AM fungi and PCB community turnover across elevation are both shaped by pH, organic carbon, and P availability. With continued climate warming, the structure and function of mountaintop ecosystems might shift to resemble lower elevations, disrupting long-established and specialized microbial assemblages, with consequences for P-cycling dynamics and the total P available to plant communities.IMPORTANCEPhosphorus (P) limits plant productivity in high-elevation ecosystems, yet the microbial networks that mobilize P, including arbuscular mycorrhizal (AM) fungi and phosphorus-cycling bacteria (PCBs), remain under-characterized in these nutrient-poor soils. We show that across a 10,00-m elevation gradient, AM fungi and P-cycling gene assemblages shift predictably with pH, organic carbon, and phosphate availability. Higher elevations, with less available P, select for stress-tolerant AM fungal taxa and PCB strategies geared toward mineral solubilization, while low-elevation sites favor root colonization by AM fungi and organic P mineralization. These results suggest that nutrient limitation can constrain microbial community assembly in consistent ways across landscapes. High mountain soils are low in P and rely on a network of underground AM fungi and PCB to deliver nutrients to plants. This study shows how those underground relationships reorganize with elevation and how climate change could collapse long-standing microbial strategies by pushing high-elevation ecosystems toward lowland conditions. As soils warm and dry, the microbial scaffolding that supports alpine plant life may become increasingly unstable.

arbuscular mycorrhizal fungi↗
DOE OSTI2023

Seasonality regulates the structure and biogeochemical impact of ectomycorrhizal fungal communities across environmentally divergent neotropical dry forests

Abstract Ectomycorrhizal (ECM) symbioses support forest functioning globally, yet both the structure and function of ECM fungal communities in seasonally dry neotropical forests (SDTFs), known for extreme heterogeneity in vegetation and edaphic properties, remain under characterized. Here, we evaluated the relative influences of seasonal versus spatial variation in ECM fungal community structure in soils from four environmentally divergent SDTFs. We also assessed the importance of biotic and abiotic drivers of SDTF ECM fungal community structure at regional scales, as well as ECM impacts on soil carbon (C) and nitrogen (N) cycling. ECM fungal frequency, relative abundance and richness all increased in the wet season, but spatial rather than seasonal effects explained more variation in community composition. Across the four SDTFs investigated, differences in tree communities drove ECM fungal community turnover more than geographic distances, site abiotic conditions or soil chemistry. Although soil moisture and ECM tree basal area were stronger predictors of soil biogeochemistry, incorporating ECM fungal community composition and relative abundance added explanatory power to models of soil C and N cycling in the wet season. Synthesis : Our results highlight the importance of seasonality and plant community composition in shaping different aspects of SDTF ECM fungal community structure and diversity as well as the potential for both the plant and fungal components of ECM symbioses to impact soil functioning across heterogenous SDTFs. Furthermore, our findings suggest that alterations in SDTF plant community composition due to climate or land‐use change will have important consequences for ECM fungal diversity and associated effects on soil biogeochemical cycling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Ant handling changes myrmecochore seed coat microbiomes and alters diversity of seed-borne plant pathogenic fungi

1. The putative benefits to seeds in myrmecochory (ant- mediated seed dispersal) are often cast in a reward context. However, microbes have been mostly overlooked as seed mortality agents in myrmecochory, as have potential treatments provided by ant-handling. 2. We investigated the effects of ant handling on the diversity of seed coat fungal communities of three myrmecochorous plant species. 3. Ant-handling altered measures of both alpha and beta diversity of fungal communities. Ant-handled seeds harboured different overall fungal communities and plant pathogen communities than non-ant-handled seeds. The myrmecochore pathogenic fungal community showed high dissimilarity (high pairwise community turnover) between ant-handled and control seeds, while beta diversity measures for ant- handled seeds and seeds with manually removed elaiosomes were less dissimilar. 4. Ant handling may offer an additional benefit to myrmecochorous seeds via the reduction in the seed coat pathogenic community, which may be driven by elaiosome removal or as a by-product of ant cleaning behaviours and chemical secretions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Habitat specialization and edge effects of soil microbial communities in a fragmented landscape

Abstract Soil microorganisms play outsized roles in nutrient cycling, plant health, and climate regulation. Despite their importance, we have a limited understanding of how soil microbes are affected by habitat fragmentation, including their responses to conditions at fragment edges, or “edge effects.” To understand the responses of soil communities to edge effects, we analyzed the distributions of soil bacteria, archaea, and fungi in an experimentally fragmented system of open patches embedded within a forest matrix. In addition, we identified taxa that consistently differed among patch, edge, or matrix habitats (“specialists”) and taxa that showed no habitat preference (“nonspecialists”). We hypothesized that microbial community turnover would be most pronounced at the edge between habitats. We also hypothesized that specialist fungi would be more likely to be mycorrhizal than nonspecialist fungi because mycorrhizae should be affected more by different plant hosts among habitats, whereas specialist prokaryotes would have smaller genomes (indicating reduced metabolic versatility) and be less likely to be able to sporulate than nonspecialist prokaryotes. Across all replicate sites, the matrix and patch soils harbored distinct microbial communities. However, sites where the contrasts in vegetation and pH between the patch and matrix were most pronounced exhibited larger differences between patch and matrix communities and tended to have edge communities that differed from those in the patch and forest. There were similar numbers of patch and matrix specialists, but very few edge specialist taxa. Acidobacteria and ectomycorrhizae were more likely to be forest specialists, while Chloroflexi, Ascomycota, and Glomeromycota (i.e., arbuscular mycorrhizae) were more likely to be patch specialists. Contrary to our hypotheses, nonspecialist bacteria were not more likely than specialist bacteria to have larger genomes or to be spore‐formers. We found partial support for our mycorrhizal hypothesis: arbuscular mycorrhizae, but not ectomycorrhizae, were more likely to be specialists. Overall, our results indicate that soil microbial communities are sensitive to edges, but not all taxa are equally affected, with arbuscular mycorrhizae in particular showing a strong response to habitat edges. In the context of increasing habitat fragmentation worldwide, our results can help inform efforts to maintain the structure and functioning of the soil microbiome.

Winfrey, Claire C. [Department of Ecology and Evol↗
DOE OSTI2025

Ecological acclimation: A framework to integrate fast and slow responses to climate change

Ecological responses to climate change occur across vastly different time-scales, from minutes for physiological plasticity to decades or centuries for community turnover and evolutionary adaptation. Accurately predicting the range of ecosystem trajectories will require models that incorporate both fast processes that may keep pace with climate change and slower ones likely to lag behind and generate disequilibrium dynamics. However, the knowledge necessary for this integration is currently fragmented across disciplines. We develop ‘ecological acclimation’ as a unifying framework to emphasize the similarity of dynamics driven by processes operating on dramatically different time-scales and levels of biological organization. The framework focuses on ecoclimate sensitivities, measured as the change in an ecological response variable per unit of climate change. Acclimation processes acting at different time-scales cause these sensitivities to shift in magnitude and even direction over time. We highlight shifting ecoclimate sensitivities in case studies from diverse ecosystems, including terrestrial plant communities, coral reefs and soil microbiomes. Models predicting future ecosystem states inevitably make assumptions about acclimation processes; these assumptions must be explicit for users to evaluate whether a model is appropriate for a given forecast horizon. Similarly, decision frameworks that clearly account for multiple acclimation processes and their distinct time-scales will help natural resource managers plan for ecological impacts of climate change from years to many decades into the future. We outline a synthetic research programme focused on the time-scales of ecological acclimation to reduce uncertainty in ecological forecasts.

climate adaptation↗
DOE OSTI2023

Geology and elevation shape bacterial assembly in Antarctic endolithic communities

Ice free areas of continental Antarctica are among the coldest and driest environments on Earth, and yet, they support surprisingly diverse and highly adapted microbial communities. Endolithic growth is one of the key adaptations to such extreme environments and often represents the dominant life-form. Despite growing scientific interest, little is known of the mechanisms that influence the assembly of endolithic microbiomes across these harsh environments. Here, we used metagenomics to examine the diversity and assembly of endolithic bacterial communities across Antarctica within different rock types and over a large elevation range. While granite supported richer and more heterogeneous communities than sandstone, elevation had no apparent effect on taxonomic richness, regardless of rock type. Conversely, elevation was clearly associated with turnover in community composition, with the deterministic process of variable selection driving microbial assembly along the elevation gradient. The turnover associated with elevation was modulated by geology, whereby for a given elevation difference, turnover was consistently larger between communities inhabiting different rock types. Overall, selection imposed by elevation and geology appeared stronger than turnover related to other spatially-structured environmental drivers. Our findings indicate that at the cold-arid limit of life on Earth, geology and elevation are key determinants of endolithic bacterial heterogeneity. This also suggests that warming temperatures may threaten the persistence of such extreme-adapted organisms.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Viral but not bacterial community successional patterns reflect extreme turnover shortly after rewetting dry soils

As central members of soil trophic networks, viruses have the potential to drive substantial microbial mortality and nutrient turnover. Pinpointing viral contributions to terrestrial ecosystem processes remains a challenge, as temporal dynamics are difficult to unravel in the spatially and physicochemically heterogeneous soil environment. In Mediterranean grasslands, the first rainfall after seasonal drought provides an ecosystem reset, triggering microbial activity during a tractable window for capturing short-term dynamics. In this report we simulated precipitation in microcosms from four distinct dry grassland soils and generated 144 viromes, 84 metagenomes and 84 16S ribosomal RNA gene amplicon datasets to characterize viral, prokaryotic and relic DNA dynamics over 10 days. Vastly different viral communities in each soil followed remarkably similar successional trajectories. Wet-up triggered a significant increase in viral richness, followed by extensive compositional turnover. Temporal succession in prokaryotic communities was much less pronounced, perhaps suggesting differences in the scales of activity captured by viromes (representing recently produced, ephemeral viral particles) and total DNA. Still, differences in the relative abundances of Actinobacteria (enriched in dry soils) and Proteobacteria (enriched in wetted soils) matched those of their predicted phages, indicating viral predation of dominant bacterial taxa. Rewetting also rapidly depleted relic DNA, which subsequently reaccumulated, indicating substantial new microbial mortality in the days after wet-up, particularly of the taxa putatively under phage predation. Production of abundant, diverse viral particles via microbial host cell lysis appears to be a conserved feature of the early response to soil rewetting, and results suggest the potential for ‘Cull-the-Winner’ dynamics, whereby viruses infect and cull but do not decimate dominant host populations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Microbially mediated mechanisms underlie soil carbon accrual by conservation agriculture under decade-long warming

Increasing soil organic carbon (SOC) in croplands by switching from conventional to conservation management may be hampered by stimulated microbial decomposition under warming. Here, we test the interactive effects of agricultural management and warming on SOC persistence and underlying microbial mechanisms in a decade-long controlled experiment on a wheat-maize cropping system. Warming increased SOC content and accelerated fungal community temporal turnover under conservation agriculture (no tillage, chopped crop residue), but not under conventional agriculture (annual tillage, crop residue removed). Microbial carbon use efficiency (CUE) and growth increased linearly over time, with stronger positive warming effects after 5 years under conservation agriculture. According to structural equation models, these increases arose from greater carbon inputs from the crops, which indirectly controlled microbial CUE via changes in fungal communities. As a result, fungal necromass increased from 28 to 53%, emerging as the strongest predictor of SOC content. Collectively, our results demonstrate how management and climatic factors can interact to alter microbial community composition, physiology and functions and, in turn, SOC formation and accrual in croplands.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Linking Community‐Climate Disequilibrium to Ecosystem Function

Turnover in species composition often lags behind the pace of climate change, resulting in mismatches between climate and communities. However, the impact of these community‐climate disequilibria on ecosystem functions is rarely considered, and current methods for measuring disequilibria assume that species ranges were, until recently, in equilibrium with climate. Here, in this work, we develop a simple theoretical model to address both of these problems by linking community‐climate disequilibrium with ecosystem functioning. We show how disequilibrium can impair functioning in the near‐term even when climate change is expected to enhance functioning in the long‐term. Responses are most likely to change over time in communities where turnover is slow, the impact of disequilibrium counteracts the direct effects of climate on ecosystem function, and pre‐existing disequilibrium is large. These findings emphasise the importance of precise and unbiased estimates of community‐climate disequilibria for improving ecological forecasts. By fitting our model to time series of both climate and ecosystem function from a metacommunity simulation, we show the potential for community‐climate disequilibrium to be inferred without direct knowledge about species' distributions or climatic tolerances. We end by outlining a research agenda to apply dynamic disequilibrium concepts and test novel hypotheses across diverse ecosystems.

climate change↗
DOE OSTI2023

The persistence and conversion of coastal foredune and swale vegetation community distributions 63 years later

Vegetation shifts can directly alter habitat dynamics and indirectly impact habitat stability relative to disturbance response. Barrier island dune habitats exhibit spatiotemporally dynamic topography that is affected by vegetation. However, vegetation distribution data can be rare and vegetation persistence is largely unknown such that species turnover over in communities can occur unnoticed. This is true despite concerns and documented cases of woody encroachment related to climate change in these ecogeomorphic habitats where physical stability to resist storm erosion varies with vegetation distribution and density. In 1956 and 1957, the vegetation of Island Beach State Park, NJ, was mapped as a permanent record for subsequent ecological study. In June 2020, we remapped the vegetation of 5.4 of 17 km north to south, seaward of the thicket community boundary. We maintained the same classification system as the historic record, physically mapping vegetation patches via GPS. We quantified changes in thicket, heather, and grass community distribution between the two time periods. Habitat persistence and conversion varied in the 63 years. Heath communities saw 80%–97% habitat loss in conversion to woody thicket. Conversely, thicket community distribution drastically increased, replacing heath where it was previously prevalent. This represents the first known documented instances of woody encroachment for Morella pensylvanica. When they did not expand, thicket communities receded landward or underwent turnover to an invasive species. Woody species of interest for dune stabilization occupied areas of similar habitat characteristics. Dune vegetation distribution persistence from 1957 to 2020 was relatively consistent and stable with the exception of heath habitat conversion. Barrier island stability is directly related to vegetation stability such that understanding where community shifts might occur over time can aid in managing and modeling efforts surrounding these dynamic ecogeomorphic habitats.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Climate warming causes photobiont degradation and carbon starvation in a boreal climate sentinel lichen

The long-term potential for acclimation by lichens to changing climates is poorly known, despite their prominent roles in forested ecosystems. Although often considered “extremophiles,” lichens may not readily acclimate to novel climates well beyond historical norms. In a previous study, Evernia mesomorpha transplants in a whole-ecosystem climate change experiment showed drastic mass loss after 1 yr of warming and drying; however, the causes of this mass loss were not addressed. We examined the causes of this warming-induced mass loss by measuring physiological, functional, and reproductive attributes of lichen transplants. Severe loss of mass and physiological function occurred above +2°C of experimental warming. Loss of algal symbionts (“bleaching”) and turnover in algal community compositions increased with temperature and were the clearest impacts of experimental warming. Enhanced CO 2 had no significant physiological or symbiont composition effects. The functional loss of algal photobionts led to significant loss of mass and specific thallus mass (STM), which in turn reduced water-holding capacity (WHC). Although algal genotypes remained detectable in thalli exposed to higher stress, within-thallus photobiont communities shifted in composition toward greater diversity. The strong negative impacts of warming and/or lower humidity on Evernia mesomorpha were driven by a loss of photobiont activity. Analogous to the effects of climate change on corals, the balance of symbiont carbon metabolism in lichens is central to their resilience to changing conditions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Biological Mechanisms May Contribute to Soil Carbon Saturation Patterns: Modeling Archive

This Modeling Archive is in support of a TES-SFA publication “Biological Mechanisms May Contribute to Soil Carbon Saturation Patterns” (Craig et al., 2021). We ran and evaluated a multi-assumption soil organic carbon (SOC) model to investigate whether alternative assumptions regarding constraints on soil microbial biomass could lead to soil carbon saturation patterns. We developed this model in the Multi-Assumption Architecture and Testbed (MAAT, https://github.com/walkeranthonyp/MAAT, tag: v1.2.1_Craig2021; Walker et al. 2018). Using MAAT, we embedded three alternative hypotheses in a microbially explicit three-pool SOC model: 1) the efficiency of mineral-associated SOC formation decreases as mineral-associated SOC approaches a maximum value (“Mineral saturation”), 2) the microbial biomass turnover rate increases with increasing microbial biomass (“Density-dependent turnover”), and 3) community carbon use efficiency decreases as microbial biomass increases toward an upper limit (“Density-dependent growth”). We ran a factorial combination of these hypotheses resulting in eight models for three different classes of model (linear decay, Michaelis-Menten decay, or reverse Michaelis-Menten decay), resulting in 24 models, 12 of which are presented or discussed in the related publication. Models were parameterized using values from previous studies with similar models (Wang et al. 2013, Wieder et al. 2014, Li et al. 2014, Georgiou et al. 2017, Hassink and Whitmore 1997) and ran to an approximate steady state (200 years) at six (6) different C input rates corresponding to 0.5, 1, 2, 4, 7, and 10 times the default input value. Further model details are available in the related publication. This archive contains output from three MAAT simulations, and scripts to run these simulations and process and plot the data. Simulations are labeled “lin”, “MM_highKm”, and “RMM_highKm” reflecting factorial runs for linear, Michealis-Menten, and reverse Michaelis-Menten models, respectively. This archive contains: • 3 R scripts prepended with “init_MAAT_” to initialize runs (1 for each simulation), • 1 csv file containing years over which to run simulations (“met_year.csv”), • 1 bash script (.bs) to run MAAT, • 6 XML files that are output from MAAT describing a run (2 for each simulation), • 3 model output csv files prepended by “out_” (1 for each simulation), and • 1 analysis R script for reproducing figures 3 and 4 in Craig et al. 2021. See included user guide (Craig_2021_modeling_archive_20210315.pdf) for file organization details.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Temporal variation in skin microbiota of cohabitating amphibians

Temporal changes and transmission patterns in host-associated microbial communities have important implications for host health. The diversity of amphibian skin microbial communities is associated with disease outcome in amphibians exposed to the fungal pathogen Batrachochytrium dendrobatidis (Bd). To successfully develop conservation strategies against Bd, we need a comprehensive understanding of how skin microbes are maintained and transmitted over time within populations. Here we used 16S rRNA sequence analysis to compare Epipedobates anthonyi frogs housed with one conspecific to frogs housed singly at four time points over the course of 1 year. We found that both α and β diversity of frog skin bacterial communities changed significantly over the course of the experiment. Specifically, we found that bacterial communities of cohabitating frogs became more similar over time. We also observed that some bacterial taxa were differentially abundant between frogs housed singly and frogs housed with a conspecific. These results suggest that conspecific contact may play a role in mediating amphibian skin microbial diversity and that turnover of skin microbial communities can occur across time. Our findings provide rationale for future studies exploring horizontal transmission as a potential mechanism of host-associated microbial maintenance in amphibians.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot

The substrates of the Brazilian campos rupestres, a grassland ecosystem, have extremely low concentrations of phosphorus and nitrogen, imposing restrictions to plant growth. Despite that, this ecosystem harbors almost 15% of the Brazilian plant diversity, raising the question of how plants acquire nutrients in such a harsh environment. Here, we set out to uncover the taxonomic profile, the compositional and functional differences and similarities, and the nutrient turnover potential of microbial communities associated with two plant species of the campos rupestres-dominant family Velloziaceae that grow over distinct substrates (soil and rock). Using amplicon sequencing data, we show that, despite the pronounced composition differentiation, the plant-associated soil and rock communities share a core of highly efficient colonizers that tend to be highly abundant and is enriched in 21 bacterial families. Functional investigation of metagenomes and 522 metagenome-assembled genomes revealed that the microorganisms found associated to plant roots are enriched in genes involved in organic compound intake, and phosphorus and nitrogen turnover. We show that potential for phosphorus transport, mineralization, and solubilization are mostly found within bacterial families of the shared microbiome, such as Xanthobacteraceae and Bryobacteraceae. We also detected the full repertoire of nitrogen cycle-related genes and discovered a lineage of Isosphaeraceae that acquired nitrogen-fixing potential via horizontal gene transfer and might be also involved in nitrification via a metabolic handoff association with Binataceae. We highlight that plant-associated microbial populations in the campos rupestres harbor a genetic repertoire with potential to increase nutrient availability and that the microbiomes of biodiversity hotspots can reveal novel mechanisms of nutrient turnover.

59 BASIC BIOLOGICAL SCIENCES↗