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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Predation by a ciliate community mediates temperature and nutrient effects on a peatland prey prokaryotic community

Temperature significantly impacts microbial communities’ composition and function, which plays a vital role in the global carbon cycle that determines climate change. Nutrient influxes often accompany rising temperatures due to human activity. While ecological interactions between different microorganisms could shape their response to environmental change, we do not understand how predation may influence these responses in a warmer and increasingly nutrient-rich world. Here, we assess whether predation by a ciliate community of bacterial consumers influences changes in the diversity, biomass, and function of a freshwater prokaryotic community under different temperature and nutrient conditions. We found that predator presence mediates the effects of temperature and nutrients on the total prokaryotic community biomass and composition through various mechanisms, including direct and indirect effects. However, the total community function was resilient. Our study supports previous findings that temperature and nutrients are essential drivers of microbial community composition and function but also demonstrates how predation can mediate these effects, indicating that the biotic context is as important as the abiotic context to understanding microbial responses to novel climates.

ciliates↗
DOE OSTI2022

Degradation Reduces Microbial Richness and Alters Microbial Functions in an Australian Peatland

Abstract Peatland ecosystems cover only 3% of the world’s land area; however, they store one-third of the global soil carbon (C). Microbial communities are the main drivers of C decomposition in peatlands, yet we have limited knowledge of their structure and function. While the microbial communities in the Northern Hemisphere peatlands are well documented, we have limited understanding of microbial community composition and function in the Southern Hemisphere peatlands, especially in Australia. We investigated the vertical stratification of prokaryote and fungal communities from Wellington Plains peatland in the Australian Alps. Within the peatland complex, bog peat was sampled from the intact peatland and dried peat from the degraded peatland along a vertical soil depth gradient (i.e., acrotelm, mesotelm, and catotelm). We analyzed the prokaryote and fungal community structure, predicted functional profiles of prokaryotes using PICRUSt, and assigned soil fungal guilds using FUNGuild. We found that the structure and function of prokaryotes were vertically stratified in the intact bog. Soil carbon, manganese, nitrogen, lead, and sodium content best explained the prokaryote composition. Prokaryote richness was significantly higher in the intact bog acrotelm compared to degraded bog acrotelm. Fungal composition remained similar across the soil depth gradient; however, there was a considerable increase in saprotroph abundance and decrease in endophyte abundance along the vertical soil depth gradient. The abundance of saprotrophs and plant pathogens was two-fold higher in the degraded bog acrotelm. Soil manganese and nitrogen content, electrical conductivity, and water table level (cm) best explained the fungal composition. Our results demonstrate that both fungal and prokaryote communities are shaped by soil abiotic factors and that peatland degradation reduces microbial richness and alters microbial functions. Thus, current and future changes to the environmental conditions in these peatlands may lead to altered microbial community structures and associated functions which may have implications for broader ecosystem function changes in peatlands.

Environmental Sciences & Ecology↗
DOE OSTI2024

Microbial abundances and carbon use under ambient temperature or experimental warming in a southern boreal peatland

Abstract Organic peat soils occupy relatively little of the global land surface area but store vast amounts of soil carbon in northern latitudes where climate is warming at a rapid pace. Warming may result in strong positive feedbacks of carbon loss and global climate change driven by microbial processes if warming alters the balance between primary productivity and decomposition. To elucidate effects of warming on the microbial communities mediating peat carbon dynamics, we explored the abundance of broad microbial groups and their source of carbon (i.e. old carbon versus more recently fixed photosynthate) using microbial lipid analysis (δ 13 C PLFA) of peat samples under ambient temperatures and before/after initiation of experimental peat warming (+ 2.25, + 4.5, + 6.75, and + 9 °C). This analysis occurred over a profile to 2 m depth in an undrained, ombrotrophic peat bog in northern Minnesota. We found that the total microbial biomass and individual indicator lipid abundances were stratified by depth and strongly correlated to temperature under ambient conditions. However, under experimental warming, statistically significant effects of temperature on the microbial community were sporadic and inconsistent. For example, 3 months after experimental warming the relative abundance of Gram-negative bacterial indicators across depth combined and > 50 cm depth and Gram-positive bacterial indicators at 20–50 cm depth showed significant positive relationships to temperature. At that same timepoint, however, the relative abundance of Actinobacterial indicators across depth showed a significant negative relationship to temperature. After 10 months of experimental warming, the relative abundance of fungal biomarkers was positively related to temperature in all depths combined, and the absolute abundance of anaerobic bacteria declined with increasing temperature in the 20–50 cm depth interval. The lack of observed response in the broader microbial community may suggest that at least initially, microbial community structure with peat depth in these peatlands is driven more by bulk density and soil water content than temperature. Alternatively, the lack of broad microbial community response may simply represent a lag period, with more change to come in the future. The long-term trajectory of microbial response to warming in this ecosystem then could either be direct, after this initial lag time, or indirect through other physical or biogeochemical changes in the peat profile. These initial results provide an important baseline against which to measure long-term microbial community and carbon-cycling responses to warming and elevated CO 2 .

Felice, Mark↗
DOE OSTI2020

Avocado_Bark_Diversity

Bark is a permanent surface for microbial colonization at the interface of trees and the surrounding air. However, little is known about the microbial communities harbored on these tissues. Studies on bark microbial ecology show a dominance of bacteria from a few phyla. Bark microbial communities of avocado (Persea americana) could have implications for tree health, as a first barrier for defense against certain pests and diseases in this economically important species. We used shotgun metagenomic sequencing to analyze the bark microbial communities of avocado trees from two orchards, and compared one of them to rhizospheric soil. Our results show that the microbial communities of avocado bark have a well-defined taxonomic structure, with consistent patterns of abundance of bacteria, fungi and archaea, even in trees from two different locations. Bacteria in avocado bark were dominated by Proteobacteria (particularly Alphaproteobacteria), Actinobacteria and Bacteroidetes, consistently with bark communities in other trees. Fungal members were dominated by Ascomycota and Basidiomycota, while most Archaea in bark were Euryarchaeota. We can conclude that avocado bark is a well-defined environment, providing niches for specific taxonomic groups. The present in-depth characterization of bark microbial communities can form a basis for their future manipulation for agronomical purposes.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1984

Succession in a microbial mat community - A Gaian perspective

The contribution of prokaryotes to Gaian control systems is discussed. The survival of the Microcoleus-dominated stratified microbial community at Laguna Figueroa, after heavy rains flooded the evaporite flat with up to 3 m of water and deposited 5-10 cm of allocthonous sediment, demonstrates the resiliency of these communities to short-term perturbations while the microbial fossil record attests to their persistence over geologic time. It is shown that the great diversity of microbial species and their short generation time make them uniquely suited for Gaian mechanisms.

Stolz, J. F.↗
DOE OSTI2026

Shrub and sedge rhizosphere communities display distinct affinities toward exudates and soil organic matter degradation: a quantitative stable isotope probing analysis

Warming temperatures are accelerating permafrost thaw and changing tundra vegetation, where woody shrubs are displacing sedges. Shrubs, such as Betula nana, and sedges, such as Eriophorum vaginatum, exhibit distinct life strategies including unique root-associated, or rhizosphere microbial communities. As permafrost thaws it unlocks previously unavailable carbon and nutrient sources resulting in deeper roots and a translocation of rhizosphere communities. Because permafrost microbial communities contain lower diversity and biomass than rhizosphere communities, the coalescence of rhizosphere and permafrost microbial communities could alter soil organic matter (SOM) degradation rates and increase greenhouse gas emissions. To identify metabolic strategies across distinct rhizosphere and permafrost microbial communities we conducted an isotope tracing incubation experiment. We inoculated thawed permafrost with shrub and sedge rhizosphere communities while adding exudates or water daily and compared this to an uninoculated control. After 46 days, we spiked samples with 18O enriched water or 13C enriched exudates and measured isotope incorporation into microbial DNA with quantitative stable isotope probing (qSIP). Our results indicate that exudate additions had little effect on uninoculated permafrost communities but the addition of exudates and rhizosphere inoculants had a compounding effect on respiration rates. We found that soils inoculated with shrub rhizosphere communities contained a mixture of exudate and SOM degraders while soils inoculated with sedge rhizosphere communities contained mainly SOM degraders. Finally, we found that individual microbial taxa exhibited maximum growth rates under specific combinations of microbial inoculant communities and exudate addition treatments. Our results reveal that microbial niches are strongly influenced by substrate preferences and community context, and suggest that a reduction in sedges and an expansion of shrubs may provide a mechanism by which permafrost carbon losses are mitigated through corresponding shifts in microbial communities and their substrate preferences.

Schaefer, Sean R [Natural Resources and Earth Syst↗
DOE OSTI2020

Microbial functional genes commonly respond to elevated carbon dioxide

Atmospheric CO 2 concentration is increasing, largely due to anthropogenic activities. Previous studies of individual free-air CO 2 enrichment (FACE) experimental sites have shown significant impacts of elevated CO 2 (eCO 2 ) on soil microbial communities; however, no common microbial response patterns have yet emerged, challenging our ability to predict ecosystem functioning and sustainability in the future eCO 2 environment. Here we analyzed 66 soil microbial communities from five FACE sites, and showed common microbial response patterns to eCO 2 , especially for key functional genes involved in carbon and nitrogen fixation (e.g., pcc/acc for carbon fixation, nifH for nitrogen fixation), carbon decomposition (e.g., amyA and pulA for labile carbon decomposition, mnp and lcc for recalcitrant carbon decomposition), and greenhouse gas emissions (e.g., mcrA for methane production, norB for nitrous oxide production) across five FACE sites. Also, the relative abundance of those key genes was generally increased and directionally associated with increased biomass, soil carbon decomposition, and soil moisture. In addition, a further literature survey of more disparate FACE experimental sites indicated increased biomass, soil carbon decay, nitrogen fixation, methane and nitrous oxide emissions, plant and soil carbon and nitrogen under eCO 2 . A conceptual framework was developed to link commonly responsive functional genes with ecosystem processes, such as pcc/acc vs. soil carbon storage, amyA/pulA/mnp/lcc vs. soil carbon decomposition, and nifH vs. nitrogen availability, suggesting that such common responses of microbial functional genes may have the potential to predict ecosystem functioning and sustainability in the future eCO 2 environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are emerging as a valuable avenue for predicting, understanding and designing microbial communities. Computation of microbial ecosystems in time and space (COMETS) extends dynamic flux balance analysis to generate simulations of multiple microbial species in molecularly complex and spatially structured environments. Here we describe how to best use and apply the most recent version of COMETS, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, evolutionary dynamics and extracellular enzyme activity modules. In addition to a command-line option, COMETS includes user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, as well as comprehensive documentation and tutorials. Overall, this protocol provides a detailed guideline for installing, testing and applying COMETS to different scenarios, generating simulations that take from a few minutes to several days to run, with broad applicability to microbial communities across biomes and scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Seasonality and longer-term development generate temporal dynamics in the Populus microbiome

ABSTRACT Temporal variation in community composition is central to our understanding of the assembly and functioning of microbial communities, yet the controls over temporal dynamics for microbiomes of long-lived plants, such as trees, remain unclear. Temporal variation in tree microbiomes could arise primarily from seasonal (i.e., intra-annual) fluctuations in community composition or from longer-term changes across years as host plants age. To test these alternatives, we experimentally isolated temporal variation in plant microbiome composition using a common garden and clonally propagated plants, and we used amplicon sequencing to characterize bacterial/archaeal and fungal communities in the leaf endosphere, root endosphere, and rhizosphere of two Populus spp. over four seasons across two consecutive years. Microbial community composition differed among seasons and years (which accounted for up to 21% of the variation in microbial community composition) and was correlated with seasonal dissimilarity in climatic conditions. However, microbial community dissimilarity was also positively correlated with time, reflecting longer-term compositional shifts as host trees aged. Together, our findings demonstrate that temporal patterns in tree microbiomes arise from both seasonal fluctuations and longer-term changes, which interact to generate unique seasonal patterns each year. In addition to shedding light on two important controls over the assembly of plant microbiomes, our results also suggest future studies of tree microbiomes should account for background temporal dynamics when testing the drivers of spatial patterns in microbial community composition and temporal responses of plant microbiomes to environmental change. IMPORTANCE Microbiomes are integral to the health of host plants, but we have a limited understanding of the factors that control how the composition of plant microbiomes changes over time. Especially little is known about the microbiome of long-lived trees, relative to annual and non-woody plants. We tested how tree microbiomes changed between seasons and years in poplar (genus Populus ), which are widespread and ecologically important tree species that also serve as important biofuel feedstocks. We found the composition of bacterial, archaeal, and fungal communities differed among seasons, but these seasonal differences depended on year. This dependence was driven by longer-term changes in microbial composition as host trees developed across consecutive years. Our findings suggest that temporal variation in tree microbiomes is driven by both seasonal fluctuations and longer-term (i.e., multiyear) development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Altering plant carbon allocation to stems has distinct effects on rhizosphere soil microbiome assembly, interactions, and potential functions in sorghum

Abstract Altering plant carbon allocation from leaves to stems is key to improve biomass for forage, fuel, and renewable chemicals. The sorghum dry stalk ( D ) locus controls a quantitative trait for sugar accumulation, with enhanced carbon allocation in the stems of juicy green ( dd ) sorghum but reduced carbon allocation in that of dry white ( DD ) sorghum. However, it remains unclear whether altering sorghum sugar accumulation in stem affects below‐ground microbiome. Here we investigated sorghum rhizosphere soil microbiome in near isogenic lines with different magnitude of carbon allocations and accumulation in the stems. Results showed that enhanced carbon accumulation in stems of juicy green sorghum results in stronger selection in rhizosphere microbiome assembly. The rhizosphere soil microbial communities selected in juicy green sorghum tended to be fast‐growing microbial taxa which possessed potential functions that would promote higher potential capacity to use chemically labile carbon sources and potentially result in higher potential decomposition rates. We found the rhizosphere microbes selected by juicy green sorghum form weaker interactions than dry white sorghum. This is the first comprehensive study revealing how the different magnitude of carbon allocations to stems regulates microbial community assembly, microbial interaction, and microbial functions. This study indicates that future plant modification for bioenergy crops should also consider the impacts on belowground microbial community without compromising the sustainability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Microbial and Geochemical Dynamics of an Aquifer Stimulated for Microbial Induced Calcite Precipitation (MICP)

Microbially induced calcite precipitation (MICP) is an alternative to existing soil stabilization techniques for construction and erosion. As with any biologically induced process in soils or aquifers, it is important to track changes in the microbial communities that occur as a result of the treatment. Our research assessed how native microbial communities developed in response to injections of reactants (dilute molasses as a carbon source; urea as a source of nitrogen and alkalinity) that promoted MICP in a shallow aquifer. Microbial community composition (16S rRNA gene) and ureolytic potential (ureC gene copy numbers) were also measured in groundwater and artificial sediment. Aquifer geochemistry showed evidence of sulfate reduction, nitrification, denitrification, ureolysis, and iron reduction during the treatment. The observed changes in geochemistry corresponded to microbial community succession in the groundwater and this matched parallel geophysical and mineralogical evidence of calcite precipitation in the aquifer. We detected an increase in the number of ureC genes in the microbial communities at the end of the injection period, suggesting an increase in the abundance of microbes possessing this gene as needed to hydrolyze urea and stimulate MICP. We identify geochemical and biological markers that highlight the microbial community response that can be used along with geophysical and geotechnical evidence to assess progress of MICP.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Biogeochemistry of the Antrim Shale Natural Gas Reservoir

The Antrim Shale, located in the Michigan Basin, United States (U.S.), is a major U.S. shale play having produced over 2.5 Trillion Cubic Feet (Tcf) of unconventional shale natural gas as of 2010. The shallow nature of this formation sets it apart from other, more characterized unconventional shale gas plays. The depth of gas production of the Antrim ranges from approximately 150 to 600 m and it is typically vertically drilled, contrary to deeper, horizontally drilled shales. A thorough understanding of the biogeochemistry and microbiology of this complex system will be advantageous for improving well performance, produced water management, and potential biocidal treatment as microbial community composition can vary substantially even among closely spaced wells. In this study, we analyzed produced water collected from nine different wells in the Antrim Shale by investigating the geochemical and microbial community composition of the produced water to gain greater insight into the overall biogeochemistry of this unique shale system. The majority of the wells from this study had high total dissolved solids (TDS) primarily composed of chloride and sodium, averaging 86,804 mg/L with a maximum 116,223 mg/L; however, three of the wells sampled along the northern margin of the basin exhibited significantly lower TDS ranging from 4932 to 6496 mg/L. Overall, our microbial community analysis revealed relatively low abundance within our samples and high variability of the microbial community among the sampled wells. The majority of bacterial sequences were identified within Proteobacteria, Firmicutes, and Actinobacteria phyla and metagenomic sequencing revealed the low presence of Methanobacteriaceae within each sample. We also investigated potential microbial community drivers and found that TDS, sodium, chloride, iodide, bromide, ammonium, potassium, and strontium were significantly correlated with the observed microbial community. The varying geochemical conditions between wells demonstrate different subsurface environmental niches, potentially driving the heterogeneous microbial communities we observed from well to well. This analysis suggests an important relationship between both well location and geochemistry and the observed microbial community that can persist in the reservoir. Continued studies of the Antrim Shale will improve our understanding of the complex interdependencies of this ecosystem.

03 NATURAL GAS↗
DOE OSTI2021

The Impact of Stand Age and Fertilization on the Soil Microbiome of Miscanthus × giganteus

Yield of the perennial grass Miscanthus × giganteus has shown an inconsistent and unpredictable response to nitrogen (N) fertilizer, yet fertilization underpins the crop’s environmental and economic sustainability. The interactions among soil microbial communities, N availability, and Miscanthus × giganteus and management may explain changes in plant productivity. In this study, soil samples from different stand ages of Miscanthus × giganteus in a replicated chronosequence field trial were used to investigate the effects of stand age and N fertilizer rates on microbial community structure. We hypothesized that there is a definable Miscanthus × giganteus soil microbiome and that this community varies significantly with stand age and fertilization. Our results showed that the main phyla in soil microbial communities, regardless of plant age, are similar but microbial community structures are significantly different. The variation in observed microbial communities generally decreases with older stand ages. The amount of N fertilizer applied also affected the microbial community structure associated with different aged Miscanthus × giganteus. Specifically, the relative abundance of Proteobacteria (Alphaproteobacteria and Gammaproteobacteria) and Acidobacteria (subgroup Gp1) increased shortly after fertilization and was more associated with younger Miscanthus × giganteus. Furthermore, our results show a significant relationship between bacterial α diversity and fertilization rates and that this response is also affected by stand age. Overall, our results emphasize linkages between microbial community structure, plant age, and fertilization in Miscanthus × giganteus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization

The liquid residue resulting from various agroindustrial processes is both rich in organic material and an attractive source to produce a variety of chemicals. Using microbial communities to produce chemicals from these liquid residues is an active area of research, but it is unclear how to deploy microbial communities to produce specific products from the different agroindustrial residues. To address this, we fed anaerobic bioreactors one of several agroindustrial residues (carbohydrate-rich lignocellulosic fermentation conversion residue, xylose, dairy manure hydrolysate, ultra-filtered milk permeate, and thin stillage from a starch bioethanol plant) and inoculated them with a microbial community from an acid-phase digester operated at the wastewater treatment plant in Madison, WI, United States. The bioreactors were monitored over a period of months and sampled to assess microbial community composition and extracellular fermentation products. We obtained metagenome assembled genomes (MAGs) from the microbial communities in each bioreactor and performed comparative genomic analyses to identify common microorganisms, as well as any community members that were unique to each reactor. Collectively, we obtained a dataset of 217 non-redundant MAGs from these bioreactors. This metagenome assembled genome dataset was used to evaluate whether a specific microbial ecology model in which medium chain fatty acids (MCFAs) are simultaneously produced from intermediate products (e.g., lactic acid) and carbohydrates could be applicable to all fermentation systems, regardless of the feedstock. MAGs were classified using a multiclass classification machine learning algorithm into three groups, organisms fermenting the carbohydrates to intermediate products, organisms utilizing the intermediate products to produce MCFAs, and organisms producing MCFAs directly from carbohydrates. This analysis revealed common biological functions among the microbial communities in different bioreactors, and although different microorganisms were enriched depending on the agroindustrial residue tested, the results supported the conclusion that the microbial ecology model tested was appropriate to explain the MCFA production potential from all agricultural residues.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2002

The Biogeochemistry of Benthic Photosynthetic Communities

Microbial mats are our earliest, and most pervasive evidence of life on Earth. In addition to their importance as the crucible of microbial evolution on Earth, microbial mats may be important in our search for life outside of our solar system. This lecture will introduce various types of microbial mats, and their fossilized counterparts, stromatolites by presenting examples of these communities. Biogeochemical cycles important in microbial mats will be introduced and discussed.

Bebout, Brad↗
DOE OSTI2020

Soil microbial EPS resiliency is influenced by carbon source accessibility

The adaptability of soil microbial communities to prolonged periods of drought is influenced by their ability to produce extracellular polymeric substances (EPS) with sufficient water retention properties. Microbial EPSs as water reservoirs during drought have been extensively investigated, but it remains unknown how carbon substrate accessibility to soil microbial communities will affect the chemical properties of the EPS they generate, and whether this in turn will alter their water retention ability. In this work, we observed that the accessibility of carbon substrates influenced microbial community structure and, consequently, the chemical properties of EPS produced by the microbial communities. Further, our results demonstrated that an insoluble carbon substrate (i.e., chitin), stimulated microbial communities to produce EPS with better water retention properties in comparison to a soluble carbon substrate (i.e., N-acetylglucosamine; NAG). In all, this study demonstrates the importance of carbon substrate accessibility by soil microorganisms in regulating the community structure and consequently, the EPS carbon chemistry, which in turn can greatly influence the adaptability of soil microbial communities to drought.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Viral community analysis in a marine oxygen minimum zone indicates increased potential for viral manipulation of microbial physiological state

Microbial communities in oxygen minimum zones (OMZs) are known to have significant impacts on global biogeochemical cycles, but viral influence on microbial processes in these regions are much less studied. Here we provide baseline ecological patterns using microscopy and viral metagenomics from the Eastern Tropical North Pacific (ETNP) OMZ region that enhance our understanding of viruses in these climate-critical systems. While extracellular viral abundance decreased below the oxycline, viral diversity and lytic infection frequency remained high within the OMZ, demonstrating that viral influences on microbial communities were still substantial without the detectable presence of oxygen. Viral community composition was strongly related to oxygen concentration, with viral populations in low-oxygen portions of the water column being distinct from their surface layer counterparts. However, this divergence was not accompanied by the expected differences in viral-encoded auxiliary metabolic genes (AMGs) relating to nitrogen and sulfur metabolisms that are known to be performed by microbial communities in these low-oxygen and anoxic regions. Instead, several abundant AMGs were identified in the oxycline and OMZ that may modulate host responses to low-oxygen stress. We hypothesize that this is due to selection for viral-encoded genes that influence host survivability rather than modulating host metabolic reactions within the ETNP OMZ. Together, this study shows that viruses are not only diverse throughout the water column in the ETNP, including the OMZ, but their infection of microorganisms has the potential to alter host physiological state within these biogeochemically important regions of the ocean.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Differential structure and functional gene response to geochemistry associated with the suspended and attached shallow aquifer microbiomes from the Illinois Basin, IL

Despite the clear ecological significance of the microbiomes inhabiting groundwater and connected ecosystems, our current understanding of their habitats, functionality, and the ecological processes controlling their assembly have been limited. In this study, an efficient pipeline combining geochemistry, high-throughput Fluidigm TM functional gene amplification and sequencing was developed to analyze the suspended and attached microbial communities inhabiting five groundwater monitoring wells in the Illinois Basin, USA. The dominant taxa in the suspended and the attached microbial communities exhibited significantly different spatial and temporal changes in both alpha- and beta-diversity. Further analyses of representative functional genes affiliated with N 2 fixation (nifH), methane oxidation (pmoA), and sulfate reduction (dsrB, and aprA), suggested functional redundancy within the shallow aquifer microbiomes. While more diversified functional gene taxa were observed for the suspended microbial communities than the attached ones except for pmoA, different levels of changes over time and space were observed between these functional genes. Notably, deterministic and stochastic ecological processes shaped the assembly of microbial communities and functional gene reservoirs differently. While homogenous selection was the prevailing process controlling assembly of microbial communities, the neutral processes (e.g., dispersal limitation, drift and others) were more important for the functional genes. The results suggest complex and changing shallow aquifer microbiomes, whose functionality and assembly vary even between the spatially proximate habitats and fractions. As a result, this research underscored the importance to include all the interface components for a more holistic understanding of the biogeochemical processes in aquifer ecosystems, which is also instructive for practical applications.

54 ENVIRONMENTAL SCIENCES↗