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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

The deep sea, the largest ocean’s compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H 2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Dynamics in microbial communities: Unraveling mechanisms to identify principles

Diversity begets higher order properties such as functional stability and robustness in microbial communities, but principles that inform conceptual (and eventually predictive) models of community dynamics are lacking. Recent work has shown that selection as well as dispersal and drift shape communities, but the mechanistic bases for assembly of communities and the forces that maintain their function in the face of environmental perturbation are not well understood. Conceptually, some interactions among community members could generate endogenous dynamics in composition, even in the absence of environmental changes. These endogenous dynamics are further perturbed by exogenous forcing factors to produce a richer network of community interactions, and it is this “system” that is the basis for higher order community properties. Elucidation of principles that follow from this conceptual model requires identifying the mechanisms that (a) optimize diversity within a community and (b) impart community stability. The network of interactions between organisms can be an important element by providing a buffer against disturbance beyond the effect of functional redundancy, as alternative pathways with different combinations of microbes can be recruited to fulfill specific functions.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2021

Microbial Community Shifts Reflect Losses of Native Soil Carbon with Pyrogenic and Fresh Organic Matter Additions and Are Greatest in Low-Carbon Soils

ABSTRACT Soil organic carbon (SOC) plays an important role in regulating global climate change, carbon and nutrient cycling in soils, and soil moisture. Organic matter (OM) additions to soils can affect the rate at which SOC is mineralized by microbes, with potentially important effects on SOC stocks. Understanding how pyrogenic organic matter (PyOM) affects the cycling of native SOC (nSOC) and the soil microbes responsible for these effects is important for fire-affected ecosystems as well as for biochar-amended systems. We used an incubation trial with five different soils from National Ecological Observatory Network sites across the United States and 13 C-labeled 350°C corn stover PyOM and fresh corn stover OM to trace nSOC-derived CO 2 emissions with and without PyOM and OM amendments. We used high-throughput sequencing of rRNA genes to characterize bacterial, archaeal, and fungal communities and their responses to PyOM and OM in soils that were previously stored at −80°C. We found that the effects of amendments on nSOC-derived CO 2 reflected the unamended soil C status, where relative increases in C mineralization were greatest in low-C soils. OM additions produced much greater effects on nSOC-CO 2 emissions than PyOM additions. Furthermore, the magnitude of the microbial community composition change mirrored the magnitude of increases in nSOC-CO 2 , indicating that a specific subset of microbes was likely responsible for the observed changes in nSOC mineralization. However, PyOM responders differed across soils and did not necessarily reflect a common “charosphere.” Overall, this study suggests that soils that already have low SOC may be particularly vulnerable to short-term increases in SOC loss with OM or PyOM additions. IMPORTANCE Soil organic matter (SOM) has an important role in global climate change, carbon and nutrient cycling in soils, and soil moisture dynamics. Understanding the processes that affect SOM stocks is important for managing these functions. Recently, understanding how fire-affected organic matter (or “pyrogenic” organic matter [PyOM]) affects existing SOM stocks has become increasingly important, due to both changing fire regimes and interest in “biochar,” pyrogenic organic matter that is produced intentionally for carbon management or as an agricultural soil amendment. We found that soils with less SOM were more prone to increased losses with PyOM (and fresh organic matter) additions and that soil microbial communities changed more in soils that also had greater SOM losses with PyOM additions. This suggests that soils that already have low SOM content may be particularly vulnerable to short-term increases in SOM loss and that a subset of the soil microbial community is likely responsible for these effects.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Microbial community composition controls carbon flux across litter types in early phase of litter decomposition

Leaf litter decomposition is a major carbon input to soil, making it a target for increasing soil carbon storage through microbiome engineering. We expand upon previous findings to show with multiple leaf litter types that microbial composition can drive variation in carbon flow from litter decomposition and specific microbial community features are associated with synonymous patterns of carbon flow among litter types. Although plant litter type selects for different decomposer communities, within a litter type, microbial composition drives variation in the quantity of dissolved organic carbon (DOC) measured at the end of the decomposition period. Bacterial richness was negatively correlated with DOC quantity, supporting our hypothesis that across multiple litter types there are common microbial traits linked to carbon flow patterns. Variation in DOC abundance (i.e. high versus low DOC) driven by microbial composition is tentatively due to differences in bacterial metabolism of labile compounds, rather than catabolism of non-labile substrates such as lignin. The temporal asynchrony of metabolic processes across litter types may be a substantial impediment to discovering more microbial features common to synonymous patterns of carbon flow among litters. Overall, our findings support the concept that carbon flow may be programmed by manipulating microbial community composition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Microbial community assembly and metabolic function during mammalian corpse decomposition

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

Metcalf, J. L.↗
DOE OSTI2020

Peatland Microbial Community Composition Is Driven by a Natural Climate Gradient

Peatlands are important players in climate change–biosphere feedbacks via long-term net carbon (C) accumulation in soil organic matter and as potential net C sources including the potent greenhouse gas methane (CH 4 ). Interactions of climate, site-hydrology, plant community, and groundwater chemical factors influence peatland development and functioning, including C dioxide (CO 2 ) and CH 4 fluxes, but the role of microbial community composition is not well understood. To assess microbial functional and taxonomic dissimilarities, we used high throughput sequencing of the small subunit ribosomal DNA (SSU rDNA) to determine bacterial and archaeal community composition in soils from twenty North American peatlands. Targeted DNA metabarcoding showed that although Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla on average, intermediate and rich fens hosted greater diversity and taxonomic richness, as well as an array of candidate phyla when compared with acidic and nutrient-poor poor fens and bogs. Moreover, pH was revealed to be the strongest predictor of microbial community structure across sites. Predictive metagenome content (PICRUSt) showed increases in specific genes, such as purine/pyrimidine and amino-acid metabolism in mid-latitude peatlands from 38 to 45° N, suggesting a shift toward utilization of microbial biomass over utilization of initial plant biomass in these microbial communities. Overall, there appears to be noticeable differences in community structure between peatland classes, as well as differences in microbial metabolic activity between latitudes. Finally, these findings are in line with a predicted increase in the decomposition and accelerated C turnover, and suggest that peatlands north of 37° latitude may be particularly vulnerable to climate change.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

In Situ Correlated Molecular Imaging of Chemically Communicating Microbial Communities

This document constitutes the final technical report for DE-SC0006642, In Situ Correlated Molecular Imaging of Chemically Communicating Microbial Communities, a project carried out collaboratively by investigators at Notre Dame and UIUC. The work carried out under DOE support in this project produced advances in two areas: development of new highly sophisticated correlated imaging approaches and the application of these new tools to the growth and differentiation of microbial communities under a variety of environmental conditions. A significant effort involved the creation of technical enhancements and sampling approaches to allow us to advance heterocorrelated mass spectrometry imaging (MSI) and correlated Raman microscopy (CRM) from bacterial cultures and biofilms. We then exploited these measurement advances in heterocorrelated MS/CRM imaging to determine relationship of signaling molecules and excreted signaling molecules produced by P. aeruginosa to conditions relevant to the rhizosphere. In particular, we: (1) developed a laboratory testbed mimic for the rhizosphere to enable microbial growth on slides under controlled conditions; (2) integrated specific measurements of (a) rhamnolipids, (b) quinolone/quinolones, and (c) phenazines specific to P. aeruginosa; and (3) utilized the imaging tools to probe how messenger secretion, quorum sensing and swarming behavior are correlated with behavior.

09 BIOMASS FUELS↗
NASA NTRS2010

Utilization of Alternate Chirality Enantiomers in Microbial Communities

Our previous study of chirality led to interesting findings for some anaerobic extremophiles: the ability to metabolize substrates with alternate chirality enantiomers of amino acids and sugars. We have subsequently found that not just separate microbial species or strains but entire microbial communities have this ability. The functional division within a microbial community on proteo- and sugarlytic links was also reflected in a microbial diet with L-sugars and D-amino acids. Several questions are addressed in this paper. Why and when was this feature developed in a microbial world? Was it a secondary de novo adaptation in a bacterial world? Or is this a piece of genetic information that has been left in modern genomes as an atavism? Is it limited exclusively to prokaryotes, or does this ability also occur in eukaryotes? In this article, we have used a broader approach to study this phenomenon using anaerobic extremophilic strains from our laboratory collection. A series of experiments were performed on physiologically different groups of extremophilic anaerobes (pure and enrichment cultures). The following characteristics were studied: 1) the ability to grow on alternate chirality enantiomers -- L-sugars and D- amino acids; 2) Growth-inhibitory effect of alternate chirality enantiomers; 3) Stickland reaction with alternate chirality amino acids. The results of this research are presented in this paper.

Pikuta, Elena V.↗
DOE OSTI2021

Influence of shrub willow buffers strategically integrated in an Illinois corn-soybean field on soil health and microbial community composition

We report soil serves many important ecological functions and is an integral part of our existence as a society. However, concerns for soil health are growing globally, in part due to the negative impacts of agricultural management on soil resources. The production of perennial bioenergy crops on marginal land in row-crop production systems is one solution that could improve land-use efficiency and address the sustainability of cropland management. Because the relationship between crop management and the environment is complex, more research is needed to evaluate the potential benefits perennial bioenergy crop production has on soil health, as well as other ecosystem services. In this study, shrub willow buffers were strategically integrated into a corn-soybean cropping system with the main objective of reducing nitrate-N leaching from grain crop production while producing biomass for bioenergy. Two buffer systems (defined by landscape positions) were included for comparison, one on marginal land with exposure to nitrate-N leaching from upslope grain (southern plots) and one on fertile soils with less nitrate-N leaching potential (northern plots). Evaluation of soil (chemistry, bulk density, microbial community) and shrub willow vegetation properties ( fine roots, leaf litter decomposition, and nutrient uptake dynamics), showed that landscape position plays an important role in (1) the dynamics of soil chemical properties, (2) shrub willow's influence and productivity, and (3) the provision of additional ecosystem services such as reductions in nitrous oxide emissions and nitrate-N leaching. In addition, the combination of crop type and landscape position (N-grain, N-willow, S-grain, and S-willow) influenced the species composition of the soil microbial community, resulting in unique and identifiable communities. These results highlight the potential application of shrub willow buffers for ecosystem service provision and support of ecosystem processes; however, understanding the relationship between the microbial community, crop type, and landscape is important for understanding the sustainability of the design.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2013

Microbial Community Changes in Hydraulic Fracturing Fluids and Produced Water from Shale Gas Extraction

Microbial communities associated with produced water from hydraulic fracturing are not well understood, and their deleterious activity can lead to significant increases in production costs and adverse environmental impacts. In this study, we compared the microbial ecology in prefracturing fluids (fracturing source water and fracturing fluid) and produced water at multiple time points from a natural gas well in southwestern Pennsylvania using 16S rRNA gene-based clone libraries, pyrosequencing, and quantitative PCR. The majority of the bacterial community in prefracturing fluids constituted aerobic species affiliated with the class Alphaproteobacteria. However, their relative abundance decreased in produced water with an increase in halotolerant, anaerobic/facultative anaerobic species affiliated with the classes Clostridia, Bacilli, Gammaproteobacteria, Epsilonproteobacteria, Bacteroidia, and Fusobacteria. Produced water collected at the last time point (day 187) consisted almost entirely of sequences similar to Clostridia and showed a decrease in bacterial abundance by 3 orders of magnitude compared to the prefracturing fluids and produced water samplesfrom earlier time points. Geochemical analysis showed that produced water contained higher concentrations of salts and total radioactivity compared to prefracturing fluids. This study provides evidence of long-term subsurface selection of the microbial community introduced through hydraulic fracturing, which may include significant implications for disinfection as well as reuse of produced water in future fracturing operations.

03 NATURAL GAS↗
DOE OSTI2023

Tundra Soil Viruses Mediate Responses of Microbial Communities to Climate Warming

The rise of global temperature causes the degradation of the substantial reserves of carbon (C) stored in tundra soils, in which microbial processes play critical roles. Viruses are known to influence the soil C cycle by encoding auxiliary metabolic genes and infecting key microorganisms, but their regulation of microbial communities under climate warming remains unexplored. In this study, we evaluated the responses of viral communities for about 5 years of experimental warming at two depths (15 to 25 cm and 45 to 55 cm) in the Alaskan permafrost region. Our results showed that the viral community and functional gene composition and abundances (including viral functional genes related to replication, structure, infection, and lysis) were significantly influenced by environmental conditions such as total nitrogen (N), total C, and soil thawing duration. Although long-term warming did not impact the viral community composition at the two depths, some glycoside hydrolases encoded by viruses were more abundant at both depths of the warmed plots. With the continuous reduction of total C, viruses may alleviate methane release by altering infection strategies on methanogens. Importantly, viruses can adopt lysogenic and lytic lifestyles to manipulate microbial communities at different soil depths, respectively, which could be one of the major factors causing the differences in microbial responses to warming. This study provides a new ecological perspective on how viruses regulate the responses of microbes to warming at community and functional scales.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2013

Structure and Function of Subsurface Microbial Communities Affecting Radionuclide Transport and Bio-immobilization

The goal of this research project was to employ a multi-disciplinary team to investigate the DOE-ERSP Field Research Center at Oak Ridge, TN (ORFRC), which contains well-defined subsurface contaminant plumes with contrasting pH and redox conditions. Part of the team would pursue cultivation-independent characterization of the microbial groups catalyzing relevant biogeochemical reactions to gain an understanding of the physiological mechanisms controlling radionuclide immobilization. Other team members would focus on cultivation and physiological characterization of model microorganisms from the site using single cell sorting methods. In order to understand and predict the in situ function of microbial communities, the PIs hope to develop new strategies for cultivation and to couple phylogenetic structure with microbial community function. Specific objectives by the Rutgers group was to discern the active bacteria at the Oak Ridge Research Field Challenge Site: 1. by applying stable isotope probing techniques to enrichment cultures developed from Florida State University; 2. by fingerprinting intact rRNA from groundwater samples obtained along the various flow pathways at ORFRC; and 3. by identifying functional genes for N and S cycling along the flowpaths to aid in detection of active bacteria.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2014

Microbial community composition and diversity in Caspian Sea sediments

The Caspian Sea is heavily polluted due to industrial and agricultural effluents as well as extraction of oil and gas reserves. Microbial communities can influence the fate of contaminants and nutrients. However, insight into the microbial ecology of the Caspian Sea significantly lags behind other marine systems. Here we describe microbial biomass, diversity and composition in sediments collected from three sampling stations in the Caspian Sea. Illumina sequencing of 16S rRNA genes revealed the presence of a number of known bacterial and archaeal heterotrophs suggesting that organic carbon is a primary factor shaping microbial communities. Surface sediments collected from bottom waters with low oxygen levels were dominated by Gammaproteobacteria while surface sediments collected from bottom waters under hypoxic conditions were dominated by Deltaproteobacteria , specifically sulfate-reducing bacteria. Thaumarchaeota was dominant across all surface sediments indicating that nitrogen cycling in this system is strongly influenced by ammonia-oxidizing archaea. This study provides a baseline assessment that may serve as a point of reference as this system changes or as the efficacy of new remediation efforts are implemented.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2014

Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities

One of the major environmental concerns of the Deepwater Horizon oil spill in the Gulf of Mexico was the ecological impact of the oil that reached shorelines of the Gulf Coast. Here we investigated the impact of the oil on the microbial composition in beach samples collected in June 2010 along a heavily impacted shoreline near Grand Isle, Louisiana. Successional changes in the microbial community structure due to the oil contamination were determined by deep sequencing of 16S rRNA genes. Metatranscriptomics was used to determine expression of functional genes involved in hydrocarbon degradation processes. In addition, potential hydrocarbon-degrading Bacteria were obtained in culture. The 16S data revealed that highly contaminated samples had higher abundances of Alpha- and Gammaproteobacteria sequences. Successional changes in these classes were observed over time, during which the oil was partially degraded. The metatranscriptome data revealed that PAH, n-alkane, and toluene degradation genes were expressed in the contaminated samples, with high homology to genes from Alteromonadales, Rhodobacterales, and Pseudomonales. Notably, Marinobacter (Gammaproteobacteria) had the highest representation of expressed genes in the samples. A Marinobacter isolated from this beach was shown to have potential for transformation of hydrocarbons in incubation experiments with oil obtained from the Mississippi Canyon Block 252 (MC252) well; collected during the Deepwater Horizon spill. The combined data revealed a response of the beach microbial community to oil contaminants, including prevalence of Bacteria endowed with the functional capacity to degrade oil.

16S rRNA gene↗
NASA NTRS1998

Sources of Hydrogen as Food for Deep Microbial Communities

To survive in deep subsurface environments autolithotrophic microbial communities require a sustainable food supply. One possible source is H2 which forms when H2O reacts with ferrous iron at rock surfaces or mineral grain boundaries to produce H2 plus ferric iron. The amount of H2 that can be supplied in this way, however, is relatively small and may not last for more than a few hundred or thousand years. A much larger reservoir of H2 exists in the rocks, inside mineral grains, arising from an as yet little-known redox conversion that affects OH- in nominally anhydrous minerals. These OH- represent small amounts of "water" that become incorporated during crystallization in H2O-laden environments. A corollary of the H2 formation from OH- is the formation of peroxy, an oxidized form of oxygen. While the peroxy become part of the mineral structure, the H2 molecules are diffusively mobile and can escape from within the mineral grains, entering the intergranular space. Assuming cautiously realistic number densities of OH- undergoing the in situ redox conversion to H2 plus peroxy, a 10 km deep rock column is expected to contain enough H2 to allow for a constant degassing rate of 50-100 nmole H2 per day per sq cm over 30 million years.

Freund, Friedemann↗
NASA NTRS2002

Hydrogen in rocks: an energy source for deep microbial communities

To survive in deep subsurface environments, lithotrophic microbial communities require a sustainable energy source such as hydrogen. Though H2 can be produced when water reacts with fresh mineral surfaces and oxidizes ferrous iron, this reaction is unreliable since it depends upon the exposure of fresh rock surfaces via the episodic opening of cracks and fissures. A more reliable and potentially more voluminous H2 source exists in nominally anhydrous minerals of igneous and metamorphic rocks. Our experimental results indicate that H2 molecules can be derived from small amounts of H2O dissolved in minerals in the form of hydroxyl, OH- or O3Si-OH, whenever such minerals crystallized in an H2O-laden environment. Two types of experiments were conducted. Single crystal fracture experiments indicated that hydroxyl pairs undergo an in situ redox conversion to H2 molecules plus peroxy links, O3Si/OO\SiO3. While the peroxy links become part of the mineral structure, the H2 molecules diffused out of the freshly fractured mineral surfaces. If such a mechanism occurred in natural settings, the entire rock column would become a volume source of H2. Crushing experiments to facilitate the outdiffusion of H2 were conducted with common crustal igneous rocks such as granite, andesite, and labradorite. At least 70 nmol of H2/g diffused out of coarsely crushed andesite, equivalent at standard pressure and temperature to 5,000 cm3 of H2/m3 of rock. In the water-saturated, biologically relevant upper portion of the rock column, the diffusion of H2 out of the minerals will be buffered by H2 saturation of the intergranular water film.

Hydrogen/analysis↗
DOE OSTI2018

Agulhas Current Properties Shape Microbial Community Diversity and Potential Functionality

Understanding the impact of oceanographic features on marine microbial ecosystems remains a major ecological endeavour. Here we assess microbial diversity, community structure and functional capacity along the Agulhas current system and the Subtropical convergence in the South Indian Ocean (SIO). Samples collected from the epipelagic, oxygen minimum and bathypelagic zones were analysed by 16S rRNA gene amplicon and metagenomic sequencing. In contrast to previous studies, we found high taxonomic richness in surface and deep water samples, but generally low richness for oxygen minimum zone communities. Beta-diversity analysis revealed significant dissimilarity between the three water depths. Most microbial communities were dominated by marine Gammaproteobacteria, with strikingly low levels of picocyanobacteria. Community composition was strongly influenced by specific environmental factors including depth, salinity, and the availability of both oxygen and light. Carbon, nitrogen and sulphur cycling capacity is the SIO was linked to several autotrophic and copiotrophic Alphaproteobacteria and Gammaproteobacteria. Taken together, our data suggest that the environmental conditions in the Agulhas current system, particularly depth-related parameters, substantially influence microbial community structure. While the capacity for biogeochemical cycling of nitrogen and sulphur is linked primarily by the dominant Gammaproteobacterial taxa, ecologically rare taxa drive carbon cycling.

59 BASIC BIOLOGICAL SCIENCES↗