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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition

ABSTRACT Understanding the organizational principles of microbial communities is essential for interpreting ecosystem stability. Previous studies have investigated the formation of bacterial communities under nutrient-poor conditions or obligate relationships to observe cooperative interactions among different species. How microorganisms form stabilized communities in nutrient-rich environments, without obligate metabolic interdependency for growth, is still not fully disclosed. In this study, three bacterial strains isolated from the Populus deltoides rhizosphere were co-cultured in complex medium, and their growth behavior was tracked. These strains co-exist in mixed culture over serial transfer for multiple growth-dilution cycles. Competition is proposed as an emergent interaction relationship among the three bacteria based on their significantly decreased growth levels. The effects of different initial inoculum ratios, up to three orders of magnitude, on community structure were investigated, and the final compositions of the mixed communities with various starting composition indicate that community structure is not dependent on the initial inoculum ratio. Furthermore, the competitive relationships within the community were not altered by different initial inoculum ratios. The community structure was simulated by generalized Lotka-Volterra and dynamic flux balance analysis to provide mechanistic predictions into emergence of community structure under a nutrient-rich environment. Metaproteomic analyses provide support for the metabolite exchanges predicted by computational modeling and for highly altered physiologies when microbes are grown in co-culture. These findings broaden our understanding of bacterial community dynamics and metabolic diversity in higher-order interactions and could be significant in the management of rhizospheric bacterial communities. IMPORTANCE Bacteria naturally co-exist in multispecies consortia, and the ability to engineer such systems can be useful in biotechnology. Despite this, few studies have been performed to understand how bacteria form a stable community and interact with each other under nutrient-rich conditions. In this study, we investigated the effects of initial inoculum ratios on bacterial community structure using a complex medium and found that the initial inoculum ratio has no significant impact on resultant community structure or on interaction patterns between community members. The microbial population profiles were simulated using computational tools in order to understand intermicrobial relationships and to identify potential metabolic exchanges that occur during stabilization of the bacterial community. Studying microbial community assembly processes is essential for understanding fundamental ecological principles in microbial ecosystems and can be critical in predicting microbial community structure and function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Divergent Responses of Forest Soil Microbial Communities under Elevated CO 2 in Different Depths of Upper Soil Layers

Numerous studies have shown that the continuous increase of atmosphere CO 2 concentrations may have profound effects on the forest ecosystem and its functions. However, little is known about the response of belowground soil microbial communities under elevated atmospheric CO 2 (eCO 2 ) at different soil depth profiles in forest ecosystems. In this paper, we examined soil microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) after a 10-year eCO 2 exposure using a high-throughput functional gene microarray (GeoChip). The results showed that eCO 2 significantly shifted the compositions, including phylogenetic and functional gene structures, of soil microbial communities at both soil depths. Key functional genes, including those involved in carbon degradation and fixation, methane metabolism, denitrification, ammonification, and nitrogen fixation, were stimulated under eCO 2 at both soil depths, although the stimulation effect of eCO 2 on these functional markers was greater at the soil depth of 0 to 5 cm than of 5 to 15 cm. Moreover, a canonical correspondence analysis suggested that NO 3 -N, total nitrogen (TN), total carbon (TC), and leaf litter were significantly correlated with the composition of the whole microbial community. This study revealed a positive feedback of eCO 2 in forest soil microbial communities, which may provide new insight for a further understanding of forest ecosystem responses to global CO 2 increases. The concentration of atmospheric carbon dioxide (CO 2 ) has continuously been increasing since the industrial revolution. Understanding the response of soil microbial communities to elevated atmospheric CO 2 (eCO 2 ) is important for predicting the contribution of the forest ecosystem to global atmospheric change. This study analyzed the effect of eCO 2 on microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) in a forest ecosystem. Our findings suggest that the compositional and functional structures of microbial communities shifted under eCO 2 at both soil depths. Finally, more functional genes involved in carbon, nitrogen, and phosphorus cycling were stimulated under eCO 2 at the soil depth of 0 to 5 cm than at the depth of 5 to 15 cm.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Impacts of chemical gradients on microbial community structure

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower’. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobic and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input

The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.

desert soil↗
DOE OSTI2016

Impact of CO 2 on the Evolution of Microbial Communities Exposed to Carbon Storage Conditions, Enhanced Oil Recovery, and CO 2 Leakage

Geologic carbon storage (GCS) is a crucial part of a proposed mitigation strategy to reduce the anthropogenic carbon dioxide (CO 2 ) emissions to the atmosphere. During this process, CO 2 is injected as super critical carbon dioxide (SC-CO 2 ) in confined deep subsurface storage units, such as saline aquifers and depleted oil reservoirs. The deposition of vast amounts of CO 2 in subsurface geologic formations could unintentionally lead to CO 2 leakage into overlying freshwater aquifers. Introduction of CO 2 into these subsurface environments will greatly increase the CO 2 2 concentration and will create CO 2 concentration gradients that drive changes in the microbial communities present. While it is expected that altered microbial communities will impact the biogeochemistry of the subsurface, there is no information available on how CO 2 gradients will impact these communities. The overarching goal of this project is to understand how CO 2 exposure will impact subsurface microbial communities at temperatures and pressures that are relevant to GCS and CO 2 leakage scenarios. To meet this goal, unfiltered, aqueous samples from a deep saline aquifer, a depleted oil reservoir, and a fresh water aquifer were exposed to varied concentrations of CO 2 at reservoir pressure and temperature. The microbial ecology of the samples was examined using molecular, DNA-based techniques. The results from these studies were also compared across the sites to determine any existing trends. Results reveal that increasing CO 2 leads to decreased DNA concentrations regardless of the site, suggesting that microbial processes will be significantly hindered or absent nearest the CO 2 injection/leakage plume where CO 2 concentrations are highest. At CO 2 exposures expected downgradient from the CO 2 plume, selected microorganisms emerged as dominant in the CO 2 exposed conditions. Results suggest that the altered microbial community was site specific and highly dependent on pH. The site-dependent results suggest a limited ability to predict the emerging dominant species for other CO 2 exposed environments. This study improves the understanding of how a subsurface microbial community may respond to conditions expected from GCS and CO 2 leakage. This is the first step for understanding how a CO 2 -altered microbial community may impact injectivity, permanence of stored CO 2 , and subsurface water quality. Future work with microbial communities from new subsurface sites would increase the current understanding of this project. Additionally, incorporation of metagenomic methods would increase understanding of potential microbial processes that may be prevalent in CO 2 exposed environments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Impact of CO 2 on the Evolution of Microbial Communities Exposed to Carbon Storage Conditions, Enhanced Oil Recovery, and CO 2 Leakage

Geologic carbon storage (GCS) is a crucial part of a proposed mitigation strategy to reduce the anthropogenic carbon dioxide (CO 2 ) emissions to the atmosphere. During this process, CO 2 is injected as super critical carbon dioxide (SC-CO 2 ) in confined deep subsurface storage units, such as saline aquifers and depleted oil reservoirs. The deposition of vast amounts of CO 2 in subsurface geologic formations could unintentionally lead to CO 2 leakage into overlying freshwater aquifers. Introduction of CO 2 into these subsurface environments will greatly increase the CO 2 concentration and will create CO 2 concentration gradients that drive changes in the microbial communities present. While it is expected that altered microbial communities will impact the biogeochemistry of the subsurface, there is no information available on how CO 2 gradients will impact these communities. The overarching goal of this project is to understand how CO 2 exposure will impact subsurface microbial communities at temperatures and pressures that are relevant to GCS and CO 2 leakage scenarios. To meet this goal, unfiltered, aqueous samples from a deep saline aquifer, a depleted oil reservoir, and a fresh water aquifer were exposed to varied concentrations of CO 2 at reservoir pressure and temperature. The microbial ecology of the samples was examined using molecular, DNA-based techniques. The results from these studies were also compared across the sites to determine any existing trends. Results reveal that increasing CO 2 leads to decreased DNA concentrations regardless of the site, suggesting that microbial processes will be significantly hindered or absent nearest the CO 2 injection/leakage plume where CO 2 concentrations are highest. At CO 2 exposures expected downgradient from the CO 2 plume, selected microorganisms emerged as dominant in the CO 2 exposed conditions. Results suggest that the altered microbial community was site specific and highly dependent on pH. The site-dependent results suggest a limited ability to predict the emerging dominant species for other CO 2 -exposed environments. This study improves the understanding of how a subsurface microbial community may respond to conditions expected from GCS and CO 2 leakage. This is the first step for understanding how a CO 2 -altered microbial community may impact injectivity, permanence of stored CO 2 , and subsurface water quality. Future work with microbial communities from new subsurface sites would increase the current understanding of this project. Additionally, incorporation of metagenomic methods would increase understanding of potential microbial processes that may be prevalent in CO 2 exposed environments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Tundra microbial community taxa and traits predict decomposition parameters of stable, old soil organic carbon

Abstract The susceptibility of soil organic carbon (SOC) in tundra to microbial decomposition under warmer climate scenarios potentially threatens a massive positive feedback to climate change, but the underlying mechanisms of stable SOC decomposition remain elusive. Herein, Alaskan tundra soils from three depths (a fibric O horizon with litter and course roots, an O horizon with decomposing litter and roots, and a mineral-organic mix, laying just above the permafrost) were incubated. Resulting respiration data were assimilated into a 3-pool model to derive decomposition kinetic parameters for fast, slow, and passive SOC pools. Bacterial, archaeal, and fungal taxa and microbial functional genes were profiled throughout the 3-year incubation. Correlation analyses and a Random Forest approach revealed associations between model parameters and microbial community profiles, taxa, and traits. There were more associations between the microbial community data and the SOC decomposition parameters of slow and passive SOC pools than those of the fast SOC pool. Also, microbial community profiles were better predictors of model parameters in deeper soils, which had higher mineral contents and relatively greater quantities of old SOC than in surface soils. Overall, our analyses revealed the functional potential of microbial communities to decompose tundra SOC through a suite of specialized genes and taxa. These results portray divergent strategies by which microbial communities access SOC pools across varying depths, lending mechanistic insights into the vulnerability of what is considered stable SOC in tundra regions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

An integrated insight into the response of sedimentary microbial communities to heavy metal contamination

Response of biological communities to environmental stresses is a critical issue in ecology, but how microbial communities shift across heavy metal gradients remain unclear. To explore the microbial response to heavy metal contamination (e.g., Cr, Mn, Zn), the composition, structure and functional potential of sedimentary microbial community were investigated by sequencing of 16S rRNA gene amplicons and a functional gene microarray. Analysis of 16S rRNA sequences revealed that the composition and structure of sedimentary microbial communities changed significantly across a gradient of heavy metal contamination and the relative abundances were higher for Firmicutes, Chloroflexi and Crenarchaeota, but lower for Proteobacteria and Actinobacteria in highly contaminated samples. Also, molecular ecological network analysis of sequencing data indicated that their possible interactions might be enhanced in highly contaminated communities. Correspondently, key functional genes involved in metal homeostasis (e.g., chrR, metC, merB), carbon metabolism and organic remediation showed a higher abundance in highly contaminated samples, indicating that bacterial communities in contaminated areas may modulate their energy consumption and organic remediation ability. This study indicated that the sedimentary indigenous microbial community may shift the composition and structure as well as function priority and interaction network to increase their adaptability and/or resistance to environmental contamination.

Science & Technology - Other Topics↗
DOE OSTI2025

Quorum sensing modulates microbial community structure through regulation of secondary metabolites

Bacteria are recognized for their diverse metabolic capabilities, yet the impact of microbe-microbe interactions on multispecies community structure and dynamics is poorly understood. Cell-to-cell signaling in the form of quorum sensing (QS) often regulates secondary metabolite production and microbial interactions. Here, we examine how acylhomoserine lactone (AHL)-mediated QS impacts microbial community structure in a 10-member synthetic community of isolates from Populus deltoides . To explore the role of QS in microbial community structure and dynamics, we disrupted AHL signaling by exogenous addition of AiiA-lactonase, an enzyme that cleaves the lactone ring. Microbial community structure resulting from signal inactivation, as measured by 16S rRNA amplicon sequencing and secondary metabolite production, was assessed after successive passaging of the community. Further, we investigated the impact of quorum quenching on specific microbe-microbe interactions using pairwise inhibition assays. Our results indicate that AHL inactivation alters the relative abundance of dominant community members at later passages but does not impact the overall membership in the community. Quorum quenching significantly alters the metabolic profile in lactonase-treated communities. This metabolic alteration impacts microbe-microbe interactions through decreased inhibition of other community members. Together, these results indicate that QS impacts microbial community structure through the regulation of secondary metabolites in dominant members and that the membership of microbial communities can be relatively stable despite changes in metabolic profiles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities

Although elevated CO 2 (eCO 2 ) significantly affects the -diversity, composition, function, interaction and dynamics of soil microbial communities at the local scale, little is known about eCO 2 impacts on the geographic distribution of micro-organisms regionally or globally. Here, we examined the -diversity of 110 soil microbial communities across six free air CO 2 enrichment (FACE) experimental sites using a high-throughput functional gene array. The -diversity of soil microbial communities was significantly (P<0.05) correlated with geographic distance under both CO 2 conditions, but declined significantly (P<0.05) faster at eCO 2 with a slope of -0.0250 than at ambient CO 2 (aCO 2 ) with a slope of -0.0231 although it varied within each individual site, indicating that the spatial turnover rate of soil microbial communities was accelerated under eCO 2 at a larger geographic scale (e.g. regionally). Both distance and soil properties significantly (P<0.05) contributed to the observed microbial -diversity. Furthermore, this study provides new hypotheses for further understanding their assembly mechanisms that may be especially important as global CO 2 continues to increase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Spatial gradients in the characteristics of soil-carbon fractions are associated with abiotic features but not microbial communities

Coastal terrestrial-aquatic interfaces (TAIs) are dynamic zones of carbon biogeochemical cycling influenced by landscape-scale salinity gradients. However, there is significant cross-system heterogeneity in salinity influences over TAI soil biogeochemical function, such as gas fluxes and dissolved organic carbon concentrations. One potential explanation for the lack of consistency is unrecognized variation in soil organic carbon chemistry and microbial communities. To provide a foundation for understanding the role of C chemistry and microbial communities on biogeochemical cycling in coastal soils, we evaluated associations among a landscape scale soil salinity gradient, molecular-level soil carbon chemistry, and microbial community assembly processes. Based on observations in related systems we hypothesized systematic shifts along the salinity gradient in organic carbon thermodynamics, biochemical transformation profiles, and heteroatom content. While the thermodynamic favorability of water soluble organic compounds in shallow soils did decrease with increasing salinity (R2=0.78, p<0.00001), this was opposite the expected direction. The number of inferred biochemical transformations and total heteroatom content also decreased with increasing salinity. These patterns indicate lower microbial activity at higher salinity that is potentially constrained by less favorable organic carbon. Furthermore, organic compound classes appeared to be primarily marine/algal derived in the floodplains with greater terrestrial signatures in upland soil. Based on a recent simulation-based study we further hypothesized a relationship between microbial community assembly processes and carbon chemistry. Null modelling revealed particularly strong influences of dispersal limitation over microbial composition, which may be due limited hydrologic connectivity within the clay-rich soils. Signatures of dispersal limitation indicate stochastically assembled microbial communities, which was further reflected in the lack of an association between community assembly processes and carbon chemistry. This suggests a disconnect between microbial composition and carbon biogeochemistry, thereby indicating that the salinity-associated gradient in carbon chemistry was driven by a combination of spatially-structured inputs and salinity-associated metabolic responses of microbial communities that are independent of community composition. Our results collectively indicate that soil carbon chemistry varies systematically with salinity at the landscape scale. This variation has not been accounted for in studies examining impacts of salinity to biogeochemical rates and pools. We propose that impacts of salinity in coastal soil biogeochemistry need to be understood in context of carbon chemistry and microbial physiology, while microbial composition may have less influence.

soil carbon, Coastal Biogeochemistry, microbial co↗
DOE OSTI2023

Elevated temperature alters microbial communities, but not decomposition rates, during 3 years of in situ peat decomposition

ABSTRACT Peatlands are large carbon sinks with primary production outpacing decomposition of organic matter. Results from the S pruce and P eatland R esponses U nder C hanging E nvironments (SPRUCE) study show net losses of organic matter and increased greenhouse gas production from peatlands in response to whole-ecosystem warming. Here, we investigated how warming and elevated CO 2 impact peat microbial communities and peat soil decomposition rates and characterized microbial communities through amplicon sequencing and compositional changes across four depth increments. Microbial diversity and community composition were significantly impacted by soil depth, temperature, and CO 2 treatment. Bacterial/archaeal α-diversity increased significantly with increasing temperature, and fungal α-diversity was lower under elevated CO 2 treatments. Trans domain microbial networks showed higher complexity of microbial communities in decomposition ladder depths from the warmed enclosures, and the number of highly connected hub taxa within the networks was positively correlated with temperature. Methanogenic hubs were identified in the networks constructed from the warmest enclosures, indicating increased importance of methanogenesis in response to warming. Microbial community responses were not however reflected in measures of peat soil decomposition, as warming and elevated CO 2 had no significant short-term effects on soil mass loss or composition. Regardless of treatment, on average only 4.5% of the original soil mass was lost after 3 years and variation between replicates was high, potentially masking treatment effects. Previous results at the SPRUCE experiment have shown warming is accelerating organic-matter decomposition and CO 2 and CH 4 production, and our results suggest these changes may be driven by warming-induced shifts in microbial communities. IMPORTANCE Microbial community changes in response to climate change drivers have the potential to alter the trajectory of important ecosystem functions. In this paper, we show that while microbial communities in peatland systems responded to manipulations of temperature and CO 2 concentrations, these changes were not associated with similar responses in peat decomposition rates over 3 years. It is unclear however from our current studies whether this functional resiliency over 3 years will continue over the longer time scales relevant to peatland ecosystem functions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions

Wetland restoration on peat islands previously drained for agriculture has potential to reverse land subsidence and sequester atmospheric carbon dioxide as peat accretes. However, the emission of methane could potentially offset the greenhouse gas benefits of captured carbon. As microbial communities play a key role in governing wetland greenhouse gas fluxes, we are interested in how microbial community composition and functions are associated with wetland hydrology, biogeochemistry, and methane emission, which is critical to modeling the microbial component in wetland methane fluxes and to managing restoration projects for maximal carbon sequestration. Here, we couple sequence-based methods with biogeochemical and greenhouse gas measurements to interrogate microbial communities from a pilot-scale restored wetland in the Sacramento-San Joaquin Delta of California, revealing considerable spatial heterogeneity even within this relatively small site. A number of microbial populations and functions showed strong correlations with electron acceptor availability and methane production; some also showed a preference for association with plant roots. Marker gene phylogenies revealed a diversity of major methane-producing and -consuming populations and suggested novel diversity within methanotrophs. Methanogenic archaea were observed in all samples, as were nitrate-, sulfate-, and metal-reducing bacteria, indicating that no single terminal electron acceptor was preferred despite differences in energetic favorability and suggesting spatial microheterogeneity and microniches. Notably, methanogens were negatively correlated with nitrate-, sulfate-, and metal-reducing bacteria and were most abundant at sampling sites with high peat accretion and low electron acceptor availability, where methane production was highest. Wetlands are the largest nonanthropogenic source of atmospheric methane but also a key global carbon reservoir. Characterizing belowground microbial communities that mediate carbon cycling in wetlands is critical to accurately predicting their responses to changes in land management and climate. Here, we studied a restored wetland and revealed substantial spatial heterogeneity in biogeochemistry, methane production, and microbial communities, largely associated with the wetland hydraulic design. We observed patterns in microbial community composition and functions correlated with biogeochemistry and methane production, including diverse microorganisms involved in methane production and consumption. We found that methanogenesis gene abundance is inversely correlated with genes from pathways exploiting other electron acceptors, yet the ubiquitous presence of genes from all these pathways suggests that diverse electron acceptors contribute to the energetic balance of the ecosystem. These investigations represent an important step toward effective management of wetlands to reduce methane flux to the atmosphere and enhance belowground carbon storage.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community

ABSTRACT Unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive. To delineate the importance of LGT in mediating the response of a groundwater microbial community to heavy metal contamination, representative Rhodanobacter reference genomes were sequenced and compared to shotgun metagenome sequences. 16S rRNA gene-based amplicon sequence analysis indicated that Rhodanobacter populations were highly abundant in contaminated wells with low pHs and high levels of nitrate and heavy metals but remained rare in the uncontaminated wells. Sequence comparisons revealed that multiple geochemically important genes, including genes encoding Fe 2+ /Pb 2+ permeases, most denitrification enzymes, and cytochrome c 553 , were native to Rhodanobacter and not subjected to LGT. In contrast, the Rhodanobacter pangenome contained a recombinational hot spot in which numerous metal resistance genes were subjected to LGT and/or duplication. In particular, Co 2+ /Zn 2+ /Cd 2+ efflux and mercuric resistance operon genes appeared to be highly mobile within Rhodanobacter populations. Evidence of multiple duplications of a mercuric resistance operon common to most Rhodanobacter strains was also observed. Collectively, our analyses indicated the importance of LGT during the evolution of groundwater microbial communities in response to heavy metal contamination, and a conceptual model was developed to display such adaptive evolutionary processes for explaining the extreme dominance of Rhodanobacter populations in the contaminated groundwater microbiome. IMPORTANCE Lateral gene transfer (LGT), along with positive selection and gene duplication, are the three main mechanisms that drive adaptive evolution of microbial genomes and communities, but their relative importance is unclear. Some recent studies suggested that LGT is a major adaptive mechanism for microbial populations in response to changing environments, and hence, it could also be critical in shaping microbial community structure. However, direct evidence of LGT and its rates in extant natural microbial communities in response to changing environments is still lacking. Our results presented in this study provide explicit evidence that LGT played a crucial role in driving the evolution of a groundwater microbial community in response to extreme heavy metal contamination. It appears that acquisition of genes critical for survival, growth, and reproduction via LGT is the most rapid and effective way to enable microorganisms and associated microbial communities to quickly adapt to abrupt harsh environmental stresses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

The unique chemistry of Eastern Mediterranean water masses selects for distinct microbial communities by depth

The waters of the Eastern Mediterranean are characterized by unique physical and chemical properties within separate water masses occupying different depths. Distinct water masses are present throughout the oceans, which drive thermohaline circulation. These water masses may contain specific microbial assemblages. The goal of this study was to examine the effect of physical and geological phenomena on the microbial community of the Eastern Mediterranean water column. Chemical measurements were combined with phospholipid fatty acid (PLFA) analysis and high-throughput 16S rRNA sequencing to characterize the microbial community in the water column at five sites. We demonstrate that the chemistry and microbial community of the water column were stratified into three distinct water masses. The salinity and nutrient concentrations vary between these water masses. Nutrient concentrations increased with depth, and salinity was highest in the intermediate water mass. Our PLFA analysis indicated different lipid classes were abundant in each water mass, suggesting that distinct groups of microbes inhabit these water masses. 16S rRNA gene sequencing confirmed the presence of distinct microbial communities in each water mass. Taxa involved in autotrophic nitrogen cycling were enriched in the intermediate water mass suggesting that microbes in this water mass may be important to the nitrogen cycle of the Eastern Mediterranean. The Eastern Mediterranean also contains numerous active hydrocarbon seeps. We sampled above the North Alex Mud Volcano, in order to test the effect of these geological features on the microbial community in the adjacent water column. The community in the waters overlaying the mud volcano was distinct from other communities collected at similar depths and was enriched in known hydrocarbon degrading taxa. Furthermore, our results demonstrate that physical phenomena such stratification as well as geological phenomena such as mud volcanoes strongly affect microbial community structure in the Eastern Mediterranean water column.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Amplicon Sequencing Assessment to Measure Microbial Community Response from Heavy Metal Contaminated Soils in Savannah River site, Tims Branch watershed

Long-term presence of heavy metal contamination in soils is correlated with changes in microbial community structures and can lead to the reduction of indigenous species. Tolerance to soil heavy metal toxicity varies among different microbial communities. It remains unclear whether long term effects caused by metal perturbations are associated with soil microbial community dysregulation in Tims Branch watershed. Research Questions: Does heavy metal contamination in Tims Branch soils decrease microbial species diversity significantly compared to non-contaminated soils? Does the species richness decrease in contaminated samples? between samples? Is diversity in low, mid and high contamination soils significantly different compared to control samples? Hypothesis: The relative abundance and diversity of species are significantly altered in soils which are contaminated with heavy metals in the Tims Branch watershed. Objectives: Use amplicon sequencing technology along with bioinformatics to compare bacterial communities between four sites in Tims Branch watershed. Evaluate the percent relative abundance and diversity across the site. Conclusions: All bacterial communities exposed to different heavy metal concentrations were dominated by four major groups (Proteobacteria, Acidobacteria, Chloroflexi and Verrucomicrobia). The dominant phyla Proteobacteria, Acidobacteria and Chloroflexi accounted for 61 % of the relative abundance. Soil bacterial α-diversity, expressed as observed species richness metric and Shannon's diversity index, was the highest in sample location four (high contamination). The lowest observed was at the control location. Species richness increased when concentrations of heavy metals were localized, inferring that the metals can alter microbial community structure. PERMANOVA analysis between contaminated groups tested significant using the Adonis (F (4,29) =1.9712; p < 0.001). There is a 20 percent variation explained between groups (R2 = 0.214). This analysis proves to be beneficial in detecting microbial communities altered by contaminated soils. Moreover, certain concentrations of heavy metals can alter microbial community structures.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2018

Exploring variation in phyllosphere microbial communities across four hemlock species

Abstract The hemlock woolly adelgid (HWA) is an insect native to Asia and likely western North America. First reported in eastern North America in 1951, it has devastated eastern hemlock ( Tsuga canadensis ) populations. Loss of hemlock will greatly affect the structure and function of eastern forests. Susceptibility to adelgid infestation varies within eastern hemlocks and across other hemlock species. Our study was conducted to determine whether eastern hemlocks share a similar stem (phyllosphere) microbial community with other co‐occurring hemlocks and whether community‐level shifts are associated within trees of the same species based on HWA infestation. Surprisingly, we found no difference in microbial community composition or diversity between trees of the same species based on the level of HWA infestation. However, microbial communities varied significantly across the four hemlock trees sampled, native T. canadensis and three non‐natives: Tsuga chinensis , Tsuga dumosa , and Tsuga sieboldii . Within these tree hosts, microbial communities from T. dumosa and T. chinensis clustered together, and microbial communities from T. canadensis and T. sieboldii clustered separately from all other tree species. Additionally, specific indicator taxa were identified for all the tree species sampled. These results indicate that Asian hemlocks might not fill the same niche in eastern forests as the native eastern hemlock. Further work should be conducted to determine how differences in hemlock species and associated microbial communities might scale up to alter organismal interactions involving hemlocks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Visualizing Microbial Community Dynamics via a Controllable Soil Environment

Visualizing microbial community dynamics within soil environments remains challenging. Here, we developed a custom-built SoilBox system that facilitates probing various changes occurring in microbial community development and molecular processes when exposed to environmental perturbations (e.g., temperature changes, drought, nutrient availability). Using confocal microscopy along with mass spectrometry imaging, we demonstrate the power of this system by correlating microbial growth and spatial metabolic information from soil communities under different moisture regimes.

59 BASIC BIOLOGICAL SCIENCES↗