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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Toward Linking Aboveground Vegetation Properties and Soil Microbial Communities Using Remote Sensing

Despite their vital role in terrestrial ecosystem function, the distributions and dynamics of soil microbial communities (SMCs) are poorly understood. Vegetation and soil properties are the primary factors that influence SMCs. This paper discusses the potential effectiveness of remote sensing science and technologies for mapping SMC biogeography by characterizing surface biophysical properties (e.g., plant traits and community composition) strongly correlated with SMCs. Using remotely sensed biophysical properties to predict SMC distributions is extremely challenging because of the intricate interactions between biotic and abiotic factors and between above- and belowground ecosystems. However, the integration of biophysical and soil remote sensing with geospatial information about the e nvironment holds great promise for mapping SMC biogeography. Additional research needs invol ve microbial taxonomic definition, soil environmental complexity, and scaling strategies. The collaborative effort of experts from diverse disciplines is essential to linking terrestrial surface biosphere observations with subsurface microbial community distributions using remote sensing.

Hamada, Yuki↗
DOE OSTI2012

Measurements of Microbial Community Activities in Individual Soil Macroaggregates

The functional potential of single soil aggregates may provide insights into the localized distribution of microbial activities better than traditional assays conducted on bulk quantities of soil. Thus, we scaled down enzyme assays for {beta}-glucosidase, N-acetyl-{beta}-D-glucosaminidase, lipase, and leucine aminopeptidase to measure of the enzyme potential of individual aggregates (250-1000 {mu}m diameter). Across all enzymes, the smallest aggregates had the greatest activity and the range of enzyme activities observed in all aggregates supports the hypothesis that functional potential in soil may be distributed in a patchy fashion. Paired analyses of ATP as a surrogate for active microbial biomass and {beta}-glucosidase on the same aggregates suggest the presence of both extracellular {beta}-glucosidase functioning in aggregates with no detectable ATP and also of relatively active microbial communities (high ATP) that have low {beta}-glucosidase potentials. Studying function at a scale more consistent with microbial habitat presents greater opportunity to link microbial community structure to microbial community function.

09 BIOMASS FUELS↗
DOE OSTI2015

Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers

Many microbial communities are characterized by high genetic diversity. 16S ribosomal RNA sequencing can determine community members, and metagenomics can determine the functional diversity, but resolving the functional role of individual cells in high throughput remains an unsolved challenge. Here, we describe epicPCR (Emulsion, Paired Isolation and Concatenation PCR), a new technique that links functional genes and phylogenetic markers in uncultured single cells, providing a throughput of hundreds of thousands of cells with costs comparable to one genomic library preparation. We demonstrate the utility of our technique in a natural environment by profiling a sulfate-reducing community in a freshwater lake, revealing both known sulfate reducers and discovering new putative sulfate reducers. Our method is adaptable to any conserved genetic trait and translates genetic associations from diverse microbial samples into a sequencing library that answers targeted ecological questions. Potential applications include identifying functional community members, tracing horizontal gene transfer networks and mapping ecological interactions between microbial cells.

Environmental Sciences & Ecology↗
DOE OSTI2024

Sea cucumber ( Holothuria glaberrima ) intestinal microbiome dataset from Puerto Rico, generated by shotgun sequencing

The sea cucumber (H. glaberrima) is a species found in the shallow waters near coral reefs and seagrass beds in Puerto Rico. To characterize the microbial taxonomic composition and functional profiles present in the sea cucumber, total DNA was obtained from their intestinal system, fosmid libraries constructed, and subsequent sequencing was performed. The diversity profile displayed that the most predominant domain was Bacteria (76.56 %), followed by Viruses (23.24 %) and Archaea (0.04 %). Within the 11 phyla identified, the most abundant was Proteobacteria (73.16 %), followed by Terrabacteria group (3.20 %) and Fibrobacterota, Chlorobiota, Bacteroidota (FCB) superphylum (1.02 %). The most abundant species were Porvidencia rettgeri (21.77 %), Pseudomonas stutzeri (14.78 %), and Alcaligenes faecalis (5.00 %). The functional profile revealed that the most abundant functions are related to transporters, MISC (miscellaneous information systems), organic nitrogen, energy, and carbon utilization. The data collected in this project on the diversity and functional profiles of the intestinal system of the H. glaberrima provided a detailed view of its microbial ecology. These findings may motivate comparative studies aimed at understanding the role of the microbiome in intestinal regeneration.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Structure, function, and inhibition of drug reactivating human gut microbial β-glucuronidases

Bacterial β-glucuronidase (GUS) enzymes cause drug toxicity by reversing Phase II glucuronidation in the gastrointestinal tract. While many human gut microbial GUS enzymes have been examined with model glucuronide substrates like p-nitrophenol-β-D-glucuronide (pNPG), the GUS orthologs that are most efficient at processing drug-glucuronides remain unclear. Here we present the crystal structures of GUS enzymes from human gut commensals Lactobacillus rhamnosus, Ruminococcus gnavus , and Faecalibacterium prausnitzii that possess an active site loop (Loop 1; L1) analogous to that found in E. coli GUS, which processes drug substrates. We also resolve the structure of the No Loop GUS from Bacteroides dorei. We then compare the pNPG and diclofenac glucuronide processing abilities of a panel of twelve structurally diverse GUS proteins, and find that the new L1 GUS enzymes presented here process small glucuronide substrates inefficiently compared to previously characterized L1 GUS enzymes like E. coli GUS. We further demonstrate that our GUS inhibitors, which are effective against some L1 enzymes, are not potent towards all. Our findings pinpoint active site structural features necessary for the processing of drug-glucuronide substrates and the inhibition of such processing.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Subsurface microbial community structure shifts along the geological features of the Central American Volcanic Arc

Subduction of the Cocos and Nazca oceanic plates beneath the Caribbean plate drives the upward movement of deep fluids enriched in carbon, nitrogen, sulfur, and iron along the Central American Volcanic Arc (CAVA). These compounds fuel diverse subsurface microbial communities that in turn alter the distribution, redox state, and isotopic composition of these compounds. Microbial community structure and functions vary according to deep fluid delivery across the arc, but less is known about how microbial communities differ along the axis of a convergent margin as geological features (e.g., extent of volcanism and subduction geometry) shift. Here, we investigate changes in bacterial 16S rRNA gene amplicons and geochemical analysis of deeply-sourced seeps along the southern CAVA, where subduction of the Cocos Ridge alters the geological setting. We find shifts in community composition along the convergent margin, with communities in similar geological settings clustering together independently of the proximity of sample sites. Microbial community composition correlates with geological variables such as host rock type, maturity of hydrothermal fluid and slab depth along different segments of the CAVA. This reveals tight coupling between deep Earth processes and subsurface microbial activity, controlling community distribution, structure and composition along a convergent margin.

Science & Technology - Other Topics↗
DOE OSTI2020

Prevalent root-derived phenolics drive shifts in microbial community composition and prime decomposition in forest soil

Phenolic compounds perform various functions in soil ranging from microbial substrate to toxin and form the basis of several plant-mediated processes. The aim of this study was to investigate how phenolics commonly exuded by tree roots influence soil organic matter (SOM) decomposition and interact with other labile forms of carbon (C) abundant in root exudates. Therefore, we performed a 38-day incubation experiment and assessed whether phenolic compounds (benzoic acid, caffeic acid and catechin) facilitated or inhibited SOM decomposition in a glucose-amended forest soil. Changes in decomposition, substrate use, fungal and bacterial community composition, and microbial abundance and activity were measured over time using 13 C-stable-isotope tracing, DNA-based molecular methods and enzyme assays. Our findings showed that phenolics inhibited microbial activity and abundance to varying degrees. Yet, benzoic acid was the only compound producing a substantial priming effect leading to a 21% increase in SOM decomposition, which was amplified in glucose-amended soils. This stimulation in microbial activity was associated with an increase in β-1,4-glucosidase activity and the bacterial genera Paraburkholderia and Caballeronia of the Burkholderiaceae family. Phenolics drove microbial community shifts in glucose-amended soils with negligible interactive effects. In conclusion, phenolic priming of SOM decomposition is associated with microbial community shifts and amplified in the presence of glucose. This evidence emphasizes the need for considering phenolics and interactions among root exudates as priming mechanisms in the rhizosphere and other soil environments where aromatics and phenolic compounds are abundant.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem

In this study, we show how invasive plant species drive rapid shifts in the soil environment from surrounding native communities. Each of the three plant invaders had different but consistent effects on soils. Thus, there does not appear to be a one-size-fits-all strategy for how plant invaders alter grassland soil environments. This work represents a crucial step toward understanding how invaders might be able to prevent or impair native reestablishment by changing soil biotic and abiotic properties. Plant invasions often reduce native plant diversity and increase net primary productivity. Invaded soils appear to differ from surrounding soils in ways that impede restoration of diverse native plant communities. We hypothesize that invader-mediated shifts in edaphic properties reproducibly alter soil microbial community structure and function. Here, we take a holistic approach, characterizing plant, prokaryotic, and fungal communities and soil physicochemical properties in field sites, invasion gradients, and experimental plots for three invasive plant species that cooccur in the Rocky Mountain West. Each invader had a unique impact on soil physicochemical properties. We found that invasions drove shifts in the abundances of specific microbial taxa, while overall belowground community structure and functional potential were fairly constant. Forb invaders were generally enriched in copiotrophic bacteria with higher 16S rRNA gene copy numbers and showed greater microbial carbohydrate and nitrogen metabolic potential. Older invasions had stronger effects on abiotic soil properties, indicative of multiyear successions. Overall, we show that plant invasions are idiosyncratic in their impact on soils and are directly responsible for driving reproducible shifts in the soil environment over multiyear time scales. IMPORTANCE In this study, we show how invasive plant species drive rapid shifts in the soil environment from surrounding native communities. Each of the three plant invaders had different but consistent effects on soils. Thus, there does not appear to be a one-size-fits-all strategy for how plant invaders alter grassland soil environments. This work represents a crucial step toward understanding how invaders might be able to prevent or impair native reestablishment by changing soil biotic and abiotic properties.

Microbiology↗
DOE OSTI2022

Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation

Background: Microbial colonization of subsurface shales following hydraulic fracturing offers the opportunity to study coupled biotic and abiotic factors that impact microbial persistence in engineered deep subsurface ecosystems. Shale formations underly much of the continental USA and display geographically distinct gradients in temperature and salinity. Complementing studies performed in eastern USA shales that contain brine-like fluids, here we coupled metagenomic and metabolomic approaches to develop the first genome-level insights into ecosystem colonization and microbial community interactions in a lower-salinity, but high-temperature western USA shale formation. Results: We collected materials used during the hydraulic fracturing process (i.e., chemicals, drill muds) paired with temporal sampling of water produced from three different hydraulically fractured wells in the STACK (Sooner Trend Anadarko Basin, Canadian and Kingfisher) shale play in OK, USA. Relative to other shale formations, our metagenomic and metabolomic analyses revealed an expanded taxonomic and metabolic diversity of microorganisms that colonize and persist in fractured shales. Importantly, temporal sampling across all three hydraulic fracturing wells traced the degradation of complex polymers from the hydraulic fracturing process to the production and consumption of organic acids that support sulfate- and thiosulfate-reducing bacteria. Furthermore, we identified 5587 viral genomes and linked many of these to the dominant, colonizing microorganisms, demonstrating the key role that viral predation plays in community dynamics within this closed, engineered system. Lastly, top-side audit sampling of different source materials enabled genome-resolved source tracking, revealing the likely sources of many key colonizing and persisting taxa in these ecosystems. Conclusions: These findings highlight the importance of resource utilization and resistance to viral predation as key traits that enable specific microbial taxa to persist across fractured shale ecosystems. We also demonstrate the importance of materials used in the hydraulic fracturing process as both a source of persisting shale microorganisms and organic substrates that likely aid in sustaining the microbial community. Moreover, we showed that different physicochemical conditions (i.e., salinity, temperature) can influence the composition and functional potential of persisting microbial communities in shale ecosystems. Together, these results expand our knowledge of microbial life in deep subsurface shales and have important ramifications for management and treatment of microbial biomass in hydraulically fractured wells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Differentiation strategies of soil rare and abundant microbial taxa in response to changing climatic regimes

Despite the important roles of soil microbes, especially the most diverse rare taxa in maintaining community diversity and multifunctionality, how different climate regimes alter the stability and functions of the rare microbial biosphere remains unknown. We reciprocally transplanted field soils across a latitudinal gradient to simulate climate change and sampled the soils annually after harvesting the maize over the following 6 years (from 2005 to 2011). By sequencing microbial 16S ribosomal RNA gene amplicons, we found that changing climate regimes significantly altered the composition and dynamics of soil microbial communities. A continuous succession of the rare and abundant communities was observed. Rare microbial communities were more stable under changing climatic regimes, with lower variations in temporal dynamics, and higher stability and constancy of diversity. More nitrogen cycling genes were detected in the rare members than in the abundant members, including amoA, napA, nifH, nirK, nirS, norB and nrfA. Random forest analysis and receiver operating characteristics analysis showed that rare taxa may act as potential contributors to maize yield under changing climatics. The study indicates that the taxonomically and functionally diverse rare biosphere has the potential to increase functional redundancy and enhance the ability of soil communities to counteract environmental disturbances. With ongoing global climate change, exploring the succession process and functional changes of rare taxa may be important in elucidating the ecosystem stability and multifunctionality that are mediated by microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Final Report for Project "A high-throughput pipeline for mapping inter-species interactions and metabolic synergy relevant to next-generation biofuel production"

The goal of our project was to implement a pipeline for the systematic, computationally-driven study and optimization of microbial interactions and their effect on lignocellulose degradation and biofuel production. We specifically sought to design and construct artificial microbial consortia that could collectively degrade lignocellulose from plant biomass, and produce precursors of energy-rich biofuels. This project fits into the bigger picture goal of helping identify a sustainable strategy for the production of energy-rich biofuels that would satisfy the existing energy constraints and demand of our society. Based on the observation that complex natural microbial communities tend to be metabolically efficient and ecologically robust, we pursued the study of a microbial system in which the desired engineering function is achieved through division of labor across multiple microbial species. Our approach was aimed at bypassing the complexity of natural communities by establishing a rational approach to design small synthetic microbial consortia. Towards this goal, we combined multiple approaches, including computer modeling of ecosystem-level microbial metabolism, mass spectrometry of metabolites, genetic engineering, and experimental evolution. The microbial production of biofuels from lignocellulose is a complex, multi-step process. Microbial consortia are an ideal approach to consolidated bioprocessing: a community of microorganisms performs a wide variety of functions more efficiently and is more resilient to environmental perturbations than a microbial monoculture. Each organism we chose for this project addresses a specific challenge: lignin degradation (Pseudomonas putida); (hemi)cellulose degradation (Cellulomonas fimi); lignin degradation product demethoxylation (Methylobacterium spp); generation of biofuel lipid precursors (Yarrowia lipolytica). These organisms are genetically tractable, aerobic, and have been used in biotechnological applications. Throughout the project, we have used mass spectrometry to characterize and measure the metabolic inputs and outputs of each of these consortium members, providing valuable information for model refinement, and enabling the establishment of metabolism-mediated interactions. In addition to lignocellulose degradation, we have started addressing the challenge of removing metabolites (e.g. formaldehyde) produced by the demethoxylation of lignin monomers, which can otherwise inhibit microbial growth due to their toxicity. On the computational side, we have implemented genome-scale models for all consortium members, based on KBase reconstructions and literature curation, and we studied small consortia and their properties. Overall, our project has identified a complex landscape of interactions types and metabolic processes relevant to community-level functions, illustrating the challenges and opportunities of microbial community engineering for the transformation of biomass into bioproducts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Year-Round Shotgun Metagenomes Reveal Stable Microbial Communities in Agricultural Soils and Novel Ammonia Oxidizers Responding to Fertilization

The dynamics of individual microbial populations and their gene functions in agricultural soils, especially after major activities such as nitrogen (N) fertilization, remain elusive but are important for a better understanding of nutrient cycling. In this paper, we analyzed 20 short-read metagenomes collected at four time points during 1 year from two depths (0 to 5 and 20 to 30 cm) in two Midwestern agricultural sites representing contrasting soil textures (sandy versus silty loam) with similar cropping histories. Although the microbial community taxonomic and functional compositions differed between the two locations and depths, they were more stable within a depth/site throughout the year than communities in natural aquatic ecosystems. For example, among the 69 population genomes assembled from the metagenomes, 75% showed a less than 2-fold change in abundance between any two sampling points. Interestingly, six deep-branching Thaumarchaeota and three complete ammonia oxidizer (comammox) Nitrospira populations increased up to 5-fold in abundance upon the addition of N fertilizer. These results indicated that indigenous archaeal ammonia oxidizers may respond faster (are more copiotrophic) to N fertilization than previously thought. None of 29 recovered putative denitrifier genomes encoded the complete denitrification pathway, suggesting that denitrification is carried out by a collection of different populations. Altogether, our study identified novel microbial populations and genes responding to seasonal and human-induced perturbations in agricultural soils that should facilitate future monitoring efforts and N-related studies. Even though the impact of agricultural management on the microbial community structure has been recognized, an understanding of the dynamics of individual microbial populations and what functions each population carries are limited. Yet, this information is important for a better understanding of nutrient cycling, with potentially important implications for preserving nitrogen in soils and sustainability. Finally, here, we show that reconstructed metagenome-assembled genomes (MAGs) are relatively stable in their abundance and functional gene content year round, and seasonal nitrogen fertilization has selected for novel Thaumarchaeota and comammox Nitrospira nitrifiers that are potentially less oligotrophic than their marine counterparts previously studied.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2020

Shedding Light on Microbial Dark Matter with A Universal Language of Life

The majority of microbial genomes have yet to be cultured, and most proteins predicted from microbial genomes or sequenced from the environment cannot be functionally annotated. As a result, current computational approaches to describe microbial systems rely on incomplete reference databases that cannot adequately capture the full functional diversity of the microbial tree of life, limiting our ability to model high-level features of biological sequences. The scientific community needs a means to capture the functionally and evolutionarily relevant features underlying biology, independent of our incomplete reference databases. Such a model can form the basis for transfer learning tasks, enabling downstream applications in environmental microbiology, medicine, and bioengineering. Here we present LookingGlass, a deep learning model capturing a “universal language of life”. LookingGlass encodes contextually-aware, functionally and evolutionarily relevant representations of short DNA reads, distinguishing reads of disparate function, homology, and environmental origin. We demonstrate the ability of LookingGlass to be fine-tuned to perform a range of diverse tasks: to identify novel oxidoreductases, to predict enzyme optimal temperature, and to recognize the reading frames of DNA sequence fragments. LookingGlass is the first contextually-aware, general purpose pre-trained “biological language” representation model for short-read DNA sequences. LookingGlass enables functionally relevant representations of otherwise unknown and unannotated sequences, shedding light on the microbial dark matter that dominates life on Earth.

A Hoarfrost↗
DOE OSTI2015

Development of a Fluorescence-Activated Cell Sorting Method Coupled with Whole Genome Amplification To Analyze Minority and Trace Dehalococcoides Genomes in Microbial Communities

Dehalococcoides mccartyi are functionally important bacteria that catalyze the reductive dechlorination of chlorinated ethenes. However, these anaerobic bacteria are fastidious to isolate, making downstream genomic characterization challenging. In order to facilitate genomic analysis, a fluorescence-activated cell sorting (FACS) method was developed in this study to separate D. mccartyi cells from a microbial community, and the DNA of the isolated cells was processed by whole genome amplification (WGA) and hybridized onto a D. mccartyi microarray for comparative genomics against four sequenced strains. First, FACS was successfully applied to a D. mccartyi isolate as positive control, and then microarray results verified that WGA from 10 6 cells or ∼1 ng of genomic DNA yielded high-quality coverage detecting nearly all genes across the genome. As expected, some inter- and intrasample variability in WGA was observed, but these biases were minimized by performing multiple parallel amplifications. Subsequent application of the FACS and WGA protocols to two enrichment cultures containing ∼10% and ∼1% D. mccartyi cells successfully enabled genomic analysis. As proof of concept, this study demonstrates that coupling FACS with WGA and microarrays is a promising tool to expedite genomic characterization of target strains in environmental communities where the relative concentrations are low.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Documenting the function of non-cultivated microorganisms in terrestrial ecosystems

The terrestrial biosphere contains a large fraction of global carbon and nearly 70% of the organic carbon in these systems is found in soils. Global changes in atmospheric CO 2 , temperature, precipitation, and ecosystem N inputs, are expected to impact primary production and carbon inputs to soils, but it remains difficult to predict the response of soil processes to anthropogenic change. Models that predict soil C-cycling as a function of ecosystem properties do not explain well variation in soil processes. Our difficulty in predicting the response of soil processes to environmental change suggests a need for a greater understanding of the biotic mechanisms that govern the soil C-cycle. Changes in microbial community structure and function have been proposed to impact soil C-cycling. However, our ability to predict the impacts of these changes on terrestrial ecosystems is constrained by our limited understanding of mechanisms that drive microbial processes in soil systems. We have applied a newly developed approach of Microbial Food Web Mapping to chart the carbon assimilation dynamics of microbial taxa in soils. This method made it possible to track different classes of 13C-labeled substrates into the DNA of nearly every member of the soil community simultaneously over time. Microbial Food Web Mapping was used to identify and characterize microbial taxa that fill key roles in the soil carbon cycle. We mapped the assimilation of carbon into thousands of discrete soil microorganisms as a function of soil carbon content and pH. In so doing we characterized assimilatory carbon metabolism, an essential component of soil C-cycling, for a vast array of uncultivated soil microorganisms. Further, we characterized the spatial and temporal dynamics of these microorganisms across a series of sites representing variation in soil characteristics. This project revealed fundamental aspects of soil C-cycling and provided ecological and metabolic insights on diverse uncultivated soil organisms that are widespread and play major roles in the global C-cycle. The genetic capacity of microbial communities can be studied through ‘omic approaches but it remains difficult to make direct links between the genetic capacity of microorganisms and their function in the soil C-cycle. Microbial Food Web Mapping makes it possible to link gene sequences to soil C-cycle processes as they occur in soil. This approach allows us to characterize the activity of non-cultivated microorganisms in a range of terrestrial systems. This data will be used to build a base of information about the role of non-cultivated organisms in critical C-cycle processes in terrestrial ecosystems and will provide insight on the manner in which soil communities metabolize soil organic matter. The results generated by this project will improve our ability to examine the impacts of management decisions, soil history, and environmental change on the behavior of microbial communities in terrestrial ecosystems, revealing the ecological mechanisms by which microbes regulate both C mineralization and carbon retention in soils, and improving our ability to predict changes in terrestrial ecosystem processes in the face of accelerating global change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2010

Functional Molecular Ecological Networks

Biodiversity and its responses to environmental changes are central issues in ecology and for society. Almost all microbial biodiversity research focuses on “species” richness and abundance but not on their interactions. Although a network approach is powerful in describing ecological interactions among species, defining the network structure in a microbial community is a great challenge. Also, although the stimulating effects of elevated CO 2 (eCO 2 ) on plant growth and primary productivity are well established, its influences on belowground microbial communities, especially microbial interactions, are poorly understood. Here, a random matrix theory (RMT)-based conceptual framework for identifying functional molecular ecological networks was developed with the high-throughput functional gene array hybridization data of soil microbial communities in a long-term grassland FACE (free air, CO 2 enrichment) experiment. Our results indicate that RMT is powerful in identifying functional molecular ecological networks in microbial communities. Both functional molecular ecological networks under eCO 2 and ambient CO 2 (aCO 2 ) possessed the general characteristics of complex systems such as scale free, small world, modular, and hierarchical. However, the topological structures of the functional molecular ecological networks are distinctly different between eCO 2 and aCO 2 , at the levels of the entire communities, individual functional gene categories/groups, and functional genes/sequences, suggesting that eCO 2 dramatically altered the network interactions among different microbial functional genes/populations. Such a shift in network structure is also significantly correlated with soil geochemical variables. In short, elucidating network interactions in microbial communities and their responses to environmental changes is fundamentally important for research in microbial ecology, systems microbiology, and global change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Marine microbial community responses related to wetland carbon mobilization in the coastal zone

Abstract Here, we examine how marine microbial communities respond when dissolved organic matter (DOM) is mobilized from coastal wetlands. Biological transformations of this DOM may increase in the presence of reactive substrates, such as algal‐derived DOM (ADOM) in the coastal zone—a process known as priming. We performed laboratory experiments examining transformations of DOM derived from coastal wetland peat (PDOM) with and without the presence ADOM. Associated shifts in microbial community composition and functional gene abundance were measured to evaluate mechanisms of priming effects. ADOM presence stimulated CO 2 production when compared to the seawater control, which was further enhanced in the copresence of PDOM. DOM characterization showed a substantial difference in features present at the end of the incubation when PDOM was present with and without ADOM, while metagenomic sequencing indicated shifts in microbial community composition and identified 23 unique functional genes associated with pathways for the breakdown of aromatic compounds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Routes and rates of bacterial dispersal impact surface soil microbiome composition and functioning

Abstract Recent evidence suggests that, similar to larger organisms, dispersal is a key driver of microbiome assembly; however, our understanding of the rates and taxonomic composition of microbial dispersal in natural environments is limited. Here, we characterized the rate and composition of bacteria dispersing into surface soil via three dispersal routes (from the air above the vegetation, from nearby vegetation and leaf litter near the soil surface, and from the bulk soil and litter below the top layer). We then quantified the impact of those routes on microbial community composition and functioning in the topmost litter layer. The bacterial dispersal rate onto the surface layer was low (7900 cells/cm2/day) relative to the abundance of the resident community. While bacteria dispersed through all three routes at the same rate, only dispersal from above and near the soil surface impacted microbiome composition, suggesting that the composition, not rate, of dispersal influenced community assembly. Dispersal also impacted microbiome functioning. When exposed to dispersal, leaf litter decomposed faster than when dispersal was excluded, although neither decomposition rate nor litter chemistry differed by route. Overall, we conclude that the dispersal routes transport distinct bacterial communities that differentially influence the composition of the surface soil microbiome.

59 BASIC BIOLOGICAL SCIENCES↗