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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

Background Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling. Results We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric “MW-score” (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut. Conclusion METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 at https://github.com/AnantharamanLab/METABOLIC.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Considering Soil Biota and Symbioses in Forest Management and Ecosystem Restoration

At the 16th Biennial Conference of Science & Management on the Colorado Plateau & Southwest Region on 12–15 September 2022, the authors hosted a symposium on the topic of “Considering host-microbial interactions in ecosystem restoration”. The goal of this symposium was to showcase studies that demonstrate how soil biota and symbioses can be used to promote forest restoration. Two key principles emerging from the symposium and research on this topic include the following: (1) diverse, native mixes of appropriate soil biota can meaningfully shift forests and plantings towards more successful and ecologically appropriate conditions; (2) context is important to consider in determining the appropriateness of plant and microbial pairings, including the similarity of source material and work sites across a variety of factors. To summarize the literature and discussion on this topic, we offer a graphical depiction of several of the factors to consider.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Magnetically responsive nanocultures for direct microbial assessment in soil environments

Cultivating microorganisms in native-like conditions is vital for bioprospecting and accessing now unculturable species. However, there remains a gap in scalable tools that can both mimic native microenvironments and enable targeted recovery of microbes from complex settings. Such approaches are essential to advance our understanding of microbial ecology, predict community functions, and discover previously unidentified biotherapeutics. We present magnetic nanocultures—a high-throughput microsystem for isolating and growing environmental microbes under near-native conditions. These nanoliter-scale bioreactors are encapsulated in semipermeable membranes that form magnetic polymeric microcapsules using iron oxide nanoparticles within polydimethylsiloxane-based shells. This design offers mechanical stability and magnetic actuation, enabling efficient retrieval from soil-like environments. The nanocultures are optimized for optical and biological properties to support microbial encapsulation, growth, and sorting. Our study demonstrates the feasibility of using magnetically responsive microenvironments to cultivate elusive microbes, offering a promising platform for bioprospecting previously uncultured or unknown microbial species.

Usman, Huda [Department of Chemical Engineering, C↗
DOE OSTI2021

Active virus-host interactions at sub-freezing temperatures in Arctic peat soil

Abstract Background Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures). Results We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H 2 18 O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO 2 ) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up 18 O in soil and respired CO 2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients. Conclusions Overall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Eco-evolutionary strategies for relieving carbon limitation under salt stress differ across microbial clades

With the continuous expansion of saline soils under climate change, understanding the eco-evolutionary tradeoff between the microbial mitigation of carbon limitation and the maintenance of functional traits in saline soils represents a significant knowledge gap in predicting future soil health and ecological function. Through shotgun metagenomic sequencing of coastal soils along a salinity gradient, we show contrasting eco-evolutionary directions of soil bacteria and archaea that manifest in changes to genome size and the functional potential of the soil microbiome. In salt environments with high carbon requirements, bacteria exhibit reduced genome sizes associated with a depletion of metabolic genes, while archaea display larger genomes and enrichment of salt-resistance, metabolic, and carbon-acquisition genes. This suggests that bacteria conserve energy through genome streamlining when facing salt stress, while archaea invest in carbon-acquisition pathways to broaden their resource usage. These findings suggest divergent directions in eco-evolutionary adaptations to soil saline stress amongst microbial clades and serve as a foundation for understanding the response of soil microbiomes to escalating climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Extracellular DNA Alters Detection of Subtle Bacterial Responses to Soil Rewetting

Microbial communities are often characterized using DNA-based sequencing, but these approaches also capture extracellular DNA (exDNA) released from dead cells, potentially altering inference about microbial responses to environmental change. This may be especially important during pulse disturbances, such as soil drying–rewetting, which can increase microbial mortality and transient necromass pools. We assessed whether exDNA altered inference about bacterial responses to drying–rewetting (an 80 mm simulated rainfall event following a 28-day drought) in conventionally tilled corn and perennial switchgrass soils. We quantified bacterial abundance (16 S rRNA gene copies), alpha diversity, and community composition in paired soil samples with exDNA included (+ exDNA) and in samples treated with propidium monoazide (PMAxx) to reduce amplification of exDNA (− exDNA). At our level of replication (n = 4), PMAxx treatment did not significantly alter overall temporal response patterns (i.e., no significant main effect of DNA treatment or DNA × time interaction). However, PMAxx treatment increased sensitivity to detect some pairwise temporal changes in bacterial abundance and community composition in corn soils following rewetting. exDNA pools were proportionally highest immediately after rewetting in corn soils, suggesting transient extracellular DNA may contribute to masking during disturbance recovery. In contrast, PMAxx treatment had comparatively small effects in switchgrass soils, which exhibited weaker temporal responses overall. Inclusion of exDNA also changed which taxa appeared most responsive to rewetting. Together, our results suggest that exDNA does not uniformly bias soil microbial inference, but may reduce detectability of subtle disturbance-driven shifts in certain soils. Future studies should advance knowledge of microbial turnover and necromass dynamics, particularly using multiple complementary methods, to help predict when exDNA is most likely to influence ecological inference.

drying-rewetting↗
NASA NTRS1981

Microbial ecology of extreme environments: Antarctic dry valley yeasts and growth in substrate limited habitats

The multiple stresses temperature, moisture, and for chemoheterotrophs, sources of carbon and energy of the Dry Valley Antarctica soils allow at best depauperate communities, low in species diversity and population density. The nature of community structure, the operation of biogeochemical cycles, the evolution and mechanisms of adaptation to this habitat are of interest in informing speculations upon life on other planets as well as in modeling the limits of gene life. Yeasts of the Cryptococcus vishniacil complex (Basidiobiastomycetes) are investigated, as the only known indigenes of the most hostile, lichen free, parts of the Dry Valleys. Methods were developed for isolating these yeasts (methods which do not exclude the recovery of other microbiota). The definition of the complex was refined and the importance of nitrogen sources was established as well as substrate competition in fitness to the Dry Valley habitats.

Vishniac, H. S.↗
DOE OSTI2023

Plant–soil feedback under drought: does history shape the future?

Plant–soil feedback (PSF) is widely recognised as a driver of plant community composition, but understanding of its response to drought remains in its infancy. Here, we provide a conceptual framework for the role of drought in PSF, considering plant traits, drought severity, and historical precipitation over ecological and evolutionary timescales. Comparing experimental studies where plants and microbes do or do not share a drought history (through co-sourcing or conditioning), we hypothesise that plants and microbes with a shared drought history experience more positive PSF under subsequent drought. To reflect real-world responses to drought, future studies need to explicitly include plant–microbial co-occurrence and potential co-adaptation and consider the precipitation history experienced by both plants and microbes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Microbial Drivers of Plant Performance during Drought Depend upon Community Composition and the Greater Soil Environment

The increasing occurrence of drought is a global challenge that threatens food security through direct impacts to both plants and their interacting soil microorganisms. Plant growth promoting microbes are increasingly being harnessed to improve plant performance under stress. However, the magnitude of microbiome impacts on both structural and physiological plant traits under water limited and water replete conditions are not well-characterized. Using two microbiomes sourced from a ponderosa pine forest and an agricultural field, we performed a greenhouse experiment that used a crossed design to test the individual and combined effects of the water availability and the soil microbiome composition on plant performance. Specifically, we studied the structural and leaf functional traits of maize that are relevant to drought tolerance. We further examined how microbial relationships with plant phenotypes varied under different combinations of microbial composition and water availability. We found that water availability and microbial composition affected plant structural traits. Surprisingly, they did not alter leaf function. Maize grown in the forest-soil microbiome produced larger plants under well-watered and water-limited conditions, compared to an agricultural soil community. Although leaf functional traits were not significantly different between the watering and microbiome treatments, the bacterial composition and abundance explained significant variability in both plant structure and leaf function within individual treatments, especially water-limited plants. Our results suggest that bacteria-plant interactions that promote plant performance under stress depend upon the greater community composition and the abiotic environment.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1992

Long-term lunar stations: Some ecological considerations

A major factor for long-term success of a lunar station is the ability to keep an agroecosystem functioning at a desirable, stable steady-state with ecological stability and reliability. Design for a long-lived extraterrestrial manned station must take into account interactions among its subsystems to insure that overall functionality is enhanced (or at least not compromised). Physical isolation of feed production, human living areas, recycling, and other systems may be straightforward, however, microbiological isolation will be very difficult. While it is possible to eliminate plant-associated microbiological communities by growing the plants asepticallly, it is not practical to keep plants germ-free on a large scale if humans are working with them. Ecological theory strongly suggests that some kinds of communities or organisms effectively increase the stability of ecosystems and will protect the plants from potential pathogens. A carefully designed and maintained (lunar-derived) soil can provide a variety of habitats for effective microbial buffers while adding structure to the agroecosystem. A soil can also increase ecosystem reliability through buffering otherwise large element and compound fluctuations (of nutrients, wastes, etc.) as well as buffering temperature level and atmosphere composition. We are doing experiments in ecological dynamics and attempting to extend the relevant theories.

Maguire, Bassett, Jr.↗
DOE OSTI2026

Rethinking the soil core microbiome

The concept of a core microbiome emerged from host-associated research to describe microbial members or functions conserved across clearly defined spatial, temporal, and biological boundaries. In soil- and plant-associated microbiome research, however, the term has increasingly shifted toward analytically defined subsets selected using study-specific thresholds or criteria. Synthesizing recent literature and cross-site analyses of bioenergy crop field soils, we show that the original biological meaning of the core microbiome has been blurred by dataset-specific analytical criteria. Taxa designated as ‘core’ were highly sensitive to methodological choices and often reflected explanatory value rather than conserved biological membership. Moreover, many studies that identify taxonomic ‘core’ members interpret their significance in functional terms, suggesting that functional conservation may be the biological interest. Taxonomic conservation may not be the most biologically meaningful target in highly heterogeneous soil and rhizosphere systems, where functional conservation may persist despite taxonomic turnover. Accordingly, ‘core microbiome’ should be reserved for microbial components explicitly demonstrated to be conserved across defined spatial, temporal, and environmental dimensions and linked to conserved ecological functions, while taxa selected for explanatory value are better described as ‘explanatory subsets of taxa’. Greater terminological precision will improve cross-study comparability and strengthen ecological inference in plant–soil microbiome research.

bioenergy crops↗
DOE OSTI2026

Soil physical and chemical measurements for topsoils collected during NEON campaign in East River, CO (06/14/2018-06/28/2018)

The package is part of the DOE Watershed Function Science Focus Area (SFA) project and includes soil physical and chemical measurements from topsoils collected at the East River, Colorado, in conjunction with the National Ecological Observatory Network (NEON) Airborne Observation Platform (AOP) survey conducted in June 2018. The soil measurements include soil bulk density, soil volumetric water content, soil microbial biomass C (Carbon), N (Nitrogen) and C:N (C to N ratio), soil DNA yield, soil total extractable organic C, soil total extractable N, soil extractable nitrate, soil extractable ammonium, soil dissolved inorganic N, soil dissolved organic N, soil pH, soil TOC400 (total organic carbon at 400°C), soil ROC (residual oxidizable carbon), soil TIC (total inorganic carbon), soil TOC (total organic carbon), soil TC (total carbon), soil N, soil OM (organic matter) loss on ignition. Additional associated site metadata can be found in the ESS-DIVE package 10.15485/1618130. The dataset includes (1) 2018_NEON_soil_physical_chemical_measurements.csv: soil physical and chemical measurements indexed by soil sample IGSNs; (2) samples.csv: sample metadata file used to register International Generic Sample Numbers (IGSNs); (3) flmd.csv: file level metadata file; and (4) dd.csv: data dictionary file. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

2018 NEON and 2025 CHESS (Catchment Hydrology and ↗
NASA NTRS1972

Fluorescent antibody detection of microorganisms in terrestrial environments

The fluorescent antibody technique and its use in direct microscopic examination of the soil is discussed. Feasibility analyses were made to determine if the method could be used to simultaneously observe and recognize microorganisms in the soil. Some data indicate this may be possible. Data are also given on two related problems involving the interaction of soil microorganisms with plant roots to form symbiotic structures. One was concerned with the developmental ecology and biology of the root nodule of alder and the second was concerned with the ectotrophic mycorrhizal structure on forest trees, especially pines. In both, the fluorescent antibody detection of the microbial symbiont both as a free living form in soil, and as a root inhabiting form in the higher plant was emphasized. A third aspect of the research involved the detection of autotrophic ammonia oxidizing microorganisms in soil.

Schmidt, E. L.↗
DOE OSTI2024

IMAGINE BioSecurity: Mesocosm-Based Methods to Evaluate Biocontainment Strategies and Impact of Industrial Microbes Upon Native Ecosystems

Project Goals: The Integrative Modeling and Genome-scale Engineering for Biosystems Security (IMAGINE BioSecurity) SFA project seeks to establish an understanding of the behavior of engineered microbes in controlled versus environmental conditions to predictively devise new strategies for responding to biological escape. To this end, the IMAGINE Team has established a plant-soil mesocosm platform to track and quantify the fate of industrial microbes in environmental systems and assess the efficacy of biocontainment constraints upon genetically engineered microbe escape frequency and the impact of industrial microbes upon native ecological microbiomes. Abstract Text: Genetically modified industrial production microbes and their associated bioproducts have emerged as an integral component of a sustainable bioeconomy. However, the rapid development of these innovative technologies raises biosecurity concerns, namely, the risk of environmental escape. Thus, the realization of a bioeconomy hinges not only on the development and deployment of microbial production hosts, but also on the development of secure biosystems and biocontainment designs. Current laboratory-based biocontainment testing systems do not accurately reflect complexities found in natural environments, necessitating an environmentally relevant analysis pipeline that allows for the detection of rare escapees, the effect of associated bio-products, and the impact on native ecologies. To this end, we have developed an approach that utilizes soil mesocosms and integrated systems analyses to evaluate the efficacy of novel biocontainment strategies and to assess the impact of production systems upon terrestrial microbiome dynamics. We demonstrate the utility of this approach by modeling a contamination with industrial microbial chasses versus their biocontained counterparts. Here we demonstrate the broad utility of this system by highlighting findings from both strains of Saccharomyces cerevisiae that are contained with an inducible toxin anti-toxin system, and stains of Escherichia coli that are contained via genomic recoding. The resultant data demonstrate that this system has broad utility across diverse microbial chassis and biocontainment strategies, enables us to track the fate of our contaminating microbe with high sensitivity in the soil, as well as monitor broader impacts of the perturbation on the underlying soil system. The findings presented here support the use of this mesocosm-based approach to assess the environmental impact of industrial microbes and to validate biocontainment strategies.

BASIC BIOLOGICAL SCIENCES,INORGANIC, ORGANIC, PHYS↗
DOE OSTI2024

MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment

DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields—isotope, isotopolog, isotopolog label, labeling approach, and gradient position—and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.

Simpson, Abigayle↗
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 OSTI2022

KBase Narrative - Metagenome-assembled genomes from Amazonian soil microbial consortia

We report 17 metagenome-assembled genomes (MAGs) recovered from microbial consortia of forest and pasture soils, in the Brazilian Eastern Amazon. Recovered MAGs constitute novel genomes with the potential to act in important ecological processes, including the degradation of carbohydrate and sulfur and nitrogen cycling.

Mandro, Jessica Adriele↗