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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Direct evidence for the role of microbial community composition in the formation of soil organic matter composition and persistence

The largest terrestrial carbon sink on earth is soil carbon stocks. As the climate changes, the rate at which the Earth’s climate warms depends in part on the persistence of soil organic carbon. Microbial turnover forms the backbone of soil organic matter (SOM) formation and it has been recently proposed that SOM molecular complexity is a key driver of stability. Despite this, the links between microbial diversity, chemical complexity and biogeochemical nature of SOM remain missing. Here we tested the hypotheses that distinct microbial communities shape the composition of SOM, and microbial-derived SOM has distinct decomposition potential depending on its community of origin. We inoculated microbial communities of varying diversities into a model soil matrix amended with simple carbon (cellobiose) and measured the thermal stability of the resultant SOM. Using a Rock-Eval ® ramped thermal analysis, we found that microbial community composition drives the chemical fingerprint of soil carbon. While diversity was not a driver of SOM composition, bacteria-only communities lead to more thermally labile soil C pools than communities with bacteria and fungi. Our results provide direct evidence for a link between microbial community structure, SOM composition, and thermal stability. This evidence demonstrates the relevance of soil microorganisms in building persistent SOM stocks.

Domeignoz-Horta, Luiz A. (ORCID:0000000346186253)↗
DOE OSTI2024

Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12

Abstract Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests that corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids showed distinct shifts in bacterial community composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community- and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.

58 GEOSCIENCES↗
DOE OSTI2025

The overlooked interaction of emerging contaminants and microbial communities: a threat to ecosystems and public health

Abstract Context and aims Emerging contaminants (ECs) and microbial communities should not be viewed in isolation, but through the One Health perspective. Both ECs and microorganisms lie at the core of this interconnected framework, as they directly influence the health of humans, animals, and the environment. The interactions between ECs and microbial communities can have profound implications for public health, affecting all three domains. However, these ECs-microorganism interactions remain underexplored, potentially leaving significant public health and ecological risks unrecognized. Therefore, this article seeks to alert the scientific community to the overlooked interactions between ECs and microbial communities, emphasizing the pivotal role these interactions may play in the management of ‘One Health.’ Results The most extensively studied interaction between ECs and microbial communities is biodegradation. However, other more complex and concerning interactions demand attention, such as the impact of ECs on microbial ecology (disruptions in ecosystem balance affecting nutrient and energy cycles) and the rise and spread of antimicrobial resistance (a growing global health crisis). Although these ECs-microbial interactions had not been extensively studied, there are scientific evidence that ECs impact on microbial communities may be concerning for public health and ecosystem balance. Conclusions So, this perspective summarizes the impact of ECs through a One Health lens and underscores the urgent need to understand their influence on microbial communities, while highlighting the key challenges researchers must overcome. Tackling these challenges is vital to mitigate potential long-term consequences for both ecosystems and public health.

Gomes, Inês B. (ORCID:0000000207313662)↗
DOE OSTI2021

An evolutionary algorithm for designing microbial communities via environmental modification

Despite a growing understanding of how environmental composition affects microbial communities, it remains difficult to apply this knowledge to the rational design of synthetic multispecies consortia. This is because natural microbial communities can harbour thousands of different organisms and environmental substrates, making up a vast combinatorial space that precludes exhaustive experimental testing and computational prediction. Here, we present a method based on the combination of machine learning and metabolic modelling that selects optimal environmental compositions to produce target community phenotypes. In this framework, dynamic flux balance analysis is used to model the growth of a community in candidate environments. A genetic algorithm is then used to evaluate the behaviour of the community relative to a target phenotype, and subsequently adjust the environment to allow the organisms to approach this target. We apply this iterative process to thousands of in silico communities of varying sizes, showing how it can rapidly identify environments that yield desired taxonomic compositions and patterns of metabolic exchange. Moreover, this combination of approaches produces testable predictions for the assembly of experimental microbial communities with specific properties and can facilitate rational environmental design processes for complex microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Community detection robustness of graph neural networks

Graph neural networks (GNNs) are increasingly widely used for community detection in attributed networks. They combine structural topology with node attributes through message passing and pooling. However, their robustness or lack thereof with respect to different perturbations and targeted attacks in conjunction with community detection tasks is not well understood. To shed light on latent mechanisms behind GNN sensitivity on community detection tasks, we conduct a systematic computational evaluation of six widely adopted GNN architectures graph convolutional network, graph attention network, graph sample and aggregate (GraphSAGE), differentiable pooling (DiffPool), minimum cut pooling (MinCUT), and deep modularity networks (DMoN). The analysis covers three perturbation categories: node attribute manipulations, edge topology distortions, and adversarial attacks. We use element-centric similarity as the evaluation metric on synthetic benchmarks and real-world citation networks. Our findings indicate that supervised GNNs tend to achieve higher baseline accuracy, while unsupervised methods, particularly DMoN, maintain stronger resilience under targeted and adversarial perturbations. Furthermore, robustness appears to be strongly influenced by community strength, with well-defined communities reducing performance loss. Across all models, node attribute perturbations associated with targeted edge deletions and shifts in attribute distributions tend to cause the largest degradation in community recovery. These findings highlight important trade-offs between accuracy and robustness in GNN-based community detection and offer insights into selecting architectures resilient to noise and adversarial attacks.

Goel, Jaidev [Virginia Polytechnic Inst. and State↗
DOE OSTI2024

The direct and indirect drivers shaping RNA viral communities in grassland soils

ABSTRACT Recent studies have revealed diverse RNA viral communities in soils. Yet, how environmental factors influence soil RNA viruses remains largely unknown. Here, we recovered RNA viral communities from bulk metatranscriptomes sequenced from grassland soils managed for 5 years under multiple environmental conditions including water content, plant presence, cultivar type, and soil depth. More than half of the unique RNA viral contigs (64.6%) were assigned with putative hosts. About 74.7% of these classified RNA viral contigs are known as eukaryotic RNA viruses suggesting eukaryotic RNA viruses may outnumber prokaryotic RNA viruses by nearly three times in this grassland. Of the identified eukaryotic RNA viruses and the associated eukaryotic species, the most dominant taxa were Mitoviridae with an average relative abundance of 72.4%, and their natural hosts, Fungi with an average relative abundance of 56.6%. Network analysis and structural equation modeling support that soil water content, plant presence, and type of cultivar individually demonstrate a significant positive impact on eukaryotic RNA viral richness directly as well as indirectly on eukaryotic RNA viral abundance via influencing the co-existing eukaryotic members. A significant negative influence of soil depth on soil eukaryotic richness and abundance indirectly impacts soil eukaryotic RNA viral communities. These results provide new insights into the collective influence of multiple environmental and community factors that shape soil RNA viral communities and offer a structured perspective of how RNA virus diversity and ecology respond to environmental changes. IMPORTANCE Climate change has been reshaping the soil environment as well as the residing microbiome. This study provides field-relevant information on how environmental and community factors collectively shape soil RNA communities and contribute to ecological understanding of RNA viral survival under various environmental conditions and virus-host interactions in soil. This knowledge is critical for predicting the viral responses to climate change and the potential emergence of biothreats.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Bacterial community dynamics as a result of growth-yield trade-off and multispecies metabolic interactions toward understanding the gut biofilm niche

Abstract Bacterial communities are ubiquitous, found in natural ecosystems, such as soil, and within living organisms, like the human microbiome. The dynamics of these communities in diverse environments depend on factors such as spatial features of the microbial niche, biochemical kinetics, and interactions among bacteria. Moreover, in many systems, bacterial communities are influenced by multiple physical mechanisms, such as mass transport and detachment forces. One example is gut mucosal communities, where dense, closely packed communities develop under the concurrent influence of nutrient transport from the lumen and fluid-mediated detachment of bacteria. In this study, we model a mucosal niche through a coupled agent-based and finite-volume modeling approach. This methodology enables us to model bacterial interactions affected by nutrient release from various sources while adjusting individual bacterial kinetics. We explored how the dispersion and abundance of bacteria are influenced by biochemical kinetics in different types of metabolic interactions, with a particular focus on the trade-off between growth rate and yield. Our findings demonstrate that in competitive scenarios, higher growth rates result in a larger share of the niche space. In contrast, growth yield plays a critical role in neutralism, commensalism, and mutualism interactions. When bacteria are introduced sequentially, they cause distinct spatiotemporal effects, such as deeper niche colonization in commensalism and mutualism scenarios driven by species intermixing effects, which are enhanced by high growth yields. Moreover, sub-ecosystem interactions dictate the dynamics of three-species communities, sometimes yielding unexpected outcomes. Competitive, fast-growing bacteria demonstrate robust colonization abilities, yet they face challenges in displacing established mutualistic systems. Bacteria that develop a cooperative relationship with existing species typically obtain niche residence, regardless of their growth rates, although higher growth yields significantly enhance their abundance. Our results underscore the importance of bacterial niche dynamics in shaping community properties and succession, highlighting a new approach to manipulating microbial systems.

Microbiology↗
DOE OSTI2024

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

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

Science & Technology - Other Topics↗
DOE OSTI2021

Remote Alaska Communities Energy Efficiency Competition: Energy Efficiency for the Gem of the Yukon (Final Report)

Over the past decade, the City of Ruby has been proactive in working to reduce cost and energy use in the community. Ruby (Tl’aa’ologhe) is a remote city in Alaska located on the south bank of the Yukon River near the Kilbuck-Kuskokwim Mountains, about 50 air miles east of Galena and 230 air miles west of Fairbanks. As of 2019, the community has a population of over 150 people and most of Ruby’s residents are Koyukon Athabascan. Ruby has a long history of promoting local efficiency and clean energy in an effort to become more sustainable. Between 2007-2010, the community hosted Alaska’s first demonstration of an in-river hydrokinetic test project, sponsored by the Yukon River Inter-Tribal Watershed Council. In 2011, a 5kW solar photo-voltaic (PV) array was installed by the Interior Regional Housing Authority. In 2012, the community had a new power plant constructed by the Alaska Energy Authority that supplies waste heat to the washeteria, clinic and public safety garage, saving the community more than 4,000 gallons of heating fuel per year. The clinic, constructed by the Tanana Chiefs Conference, is one of the most energy efficient buildings in the interior and utilizes new building efficiency standards that were passed by the tribes. It has a 5kW solar PV array that provides energy into the local electric grid and offsets approximately 20% of the annual energy use. Building on this legacy, the City of Ruby entered into Department of Energy’s (DOE’s) Remote Alaska Communities Energy Efficiency Competition (RACEE) in 2016, pledging to reduce per-capita energy use 15% by 2020. During the second phase of the competition, 13 communities including Ruby were provided funding for tailored technical assistance to measure energy use and create energy efficiency plans.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2024

A Program Design Combining Community Solar and Weatherization for Manufactured Homes in Michigan

The Michigan Department of Environment, Great Lakes, and Energy (EGLE) is interested in combining community solar with weatherization programs for manufactured homes. To collect program strategies, EGLE made a request for technical assistance from the US Department of Energy’s National Community Solar Partnership (NCSP). Lawrence Berkeley National Lab developed this study in response. It briefly reviews issues relevant to the question, attempts to lay out a methodology for more in-depth analysis, and provides some recommendations for program design and implementation. While the research is specific to Michigan, the recommendations and methodologies could serve as an example for other states and regions. The paper first provides an overview of manufactured home communities in Michigan, with a discussion of demographics and energy issues they face. It then discusses weatherization opportunities for manufactured homes, opportunities for community solar, and opportunities for combining the two. The methodology proposed is intended to help EGLE: -Identify priority locations, -Set eligibility criteria for communities and households, and -Make the most of federal and other funding sources The paper concludes with recommendations for a program that combines community solar with efficient electrification of manufactured homes to reduce the burden of the largest source of energy expenditure in Michigan, winter heating bills. Specifically, it envisions community solar subscriptions for occupants of manufactured homes that have been converted to high-efficiency cold weather heat pumps. The combination can be managed to alleviate seasonal variations in both solar and heating bills, such as through an annualized “budget billing” program.

14 SOLAR ENERGY↗
DOE OSTI2024

Navigating Options for Transportation Electrification and Solar Charging: Steps and Lessons Learned in Montana Communities

This document is intended to assist communities who are considering investing in electric transportation. It can assist communities engage stakeholders, prioritize community goals, assess electric transportation options, and navigate complex decisions about deploying zero emission electric transportation in their community. It covers technological, economic and environmental aspects of the transition to electric vehicles (EV), and highlights the specific considerations related to the deployment of renewable energy technologies (e.g., distributed solar) in combination with EV supply equipment (EVSE, e.g., charging stations). There are many important decisions to make and questions for communities to ask themselves as they consider electric vehicle types, charging infrastructure, and electricity generation options. This guide will help communities assess: (1) Which stage in the decision-making process they are in with respect to EV deployment; (2) Questions they can explore to guide their decisions about EV deployment; (3) How to engage key stakeholders on EV deployment options; (4) Tradeoffs and benefits of various electric transportation options and; (5) Synergies of pairing electric vehicle charging and renewable energy generation technologies. The analysis and lessons learned presented in this roadmap are intended to serve as a template and guide for similarly situated communities across the country who want to prepare for and play a role in the electrified transportation future.

14 SOLAR ENERGY↗
DOE OSTI2024

RACEE: Community of Klawock Competition Project Summary

RACEE is a US Department of Energy (DOE) competition that challenged rural Alaskan communities to commit to saving 15% energy by 2020 (baseline 2010) which aligns with the State’s Energy Efficiency goal. In January 2016, 64 communities, including eight Southeast communities, submitted pledges to become energy champions and move to the next phase of the competition. In April, DOE announced that 13 communities would be eligible to apply for up to $3.4 million in funding to implement the community energy efficiency plans they develop in Phase II of the competition. Klawock is one of those 13 communities and the only eligible community in Southeast Alaska.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2022

Snowmass '21 Community Engagement Frontier 6: Public Policy and Government Engagement: Congressional Advocacy for Areas Beyond HEP Funding

This document has been prepared as a Snowmass contributed paper by the Public Policy & Government Engagement topical group (CEF06) within the Community Engagement Frontier. The charge of CEF06 is to review all aspects of how the High Energy Physics (HEP) community engages with government at all levels and how public policy impacts members of the community and the community at large, and to assess and raise awareness within the community of direct community-driven engagement of the US federal government (\textit{i.e.} advocacy). The focus of this paper is the potential for HEP community advocacy on topics other than funding for basic research.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2025

Microbial Community Analysis & Functional Evaluation in Soils

The overall objective of this proposal was to develop technologies to alter the composition and function of important members of microbial communities. In particular, the overall objective of the microbial community editing portion of the proposal focuses on developing foundational tools and understanding required to predict, alter and design grass rhizosphere communities impacting DOE missions. Specifically, the project is centered on the Microbial Community Analysis & Functional Evaluation in Soils (m-CAFES) to manipulate microbial consortia associated with plants of interest for the bioenergy sector, under the presumption that bacterial communities can be manipulated to enhance plant health. For tasks of specific interest to us, we are focusing on developing novel Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) based technologies (primarily focusing on Aim 1) and their delivery modalities (notably subaim 1.2) to edit specific bacterial genomes of interest to enhance their functionalities, and programmably ablate specific undesirable members of bacterial communities for plant health. We are focusing on engineering bacteriophages (bacterial viruses, for subaim 1.2) to carry programmable CRISPR-Cas systems (subaim 1.1) to target (ablate) or alter (edit) genomes of interest. This will enable us to carry out microbial perturbations that will impact community composition and function and ultimately plant growth and health, to enable the next phase of the project by deploying them in situ (subaims 1.3 and 1.4).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Resource Characterization for Community Scale Tidal Instream Energy in Maine [Abstract]

Coastal and island communities in Maine are seeking solutions to increase the resiliency of their electrical grid while also reducing their carbon footprint. Unfortunately, many community scale tidal resources identified on the Maine coast have not been rigorously evaluated; previous studies identified numerous hot spots but left many of them unevaluated or under evaluated (e.g., only power density was assessed in many cases). The primary objective of this TEAMER project is to evaluate selected community scale tidal instream resources to demonstrate their potential for contributing to the renewable energy needs of nearby coastal communities. The methods developed in this study will enable the total community scale tidal instream energy resource along the Maine coast to be evaluated in follow-on studies. The study will also enable turbine developers to understand how to scale and optimize their devices for deployment in turbine farms at community scale sites. Data from the study will be shared publicly through MHKDR or relevant community websites.

16 TIDAL AND WAVE POWER↗
DOE OSTI2023

A metagenome-level analysis of a microbial community fermenting ultra-filtered milk permeate

Fermentative microbial communities have the potential to serve as biocatalysts for the conversion of low-value dairy coproducts into renewable chemicals, contributing to a more sustainable global economy. To develop predictive tools for the design and operation of industrially relevant strategies that utilize fermentative microbial communities, there is a need to determine the genomic features of community members that are characteristic to the accumulation of different products. To address this knowledge gap, we performed a 282-day bioreactor experiment with a microbial community that was fed ultra-filtered milk permeate, a low-value coproduct from the dairy industry. The bioreactor was inoculated with a microbial community from an acid-phase digester. A metagenomic analysis was used to assess microbial community dynamics, construct metagenome-assembled genomes (MAGs), and evaluate the potential for lactose utilization and fermentation product synthesis of community members represented by the assembled MAGs. This analysis led us to propose that, in this reactor, members of the Actinobacteriota phylum are important in the degradation of lactose, via the Leloir pathway and the bifid shunt, and the production of acetic, lactic, and succinic acids. In addition, members of the Firmicutes phylum contribute to the chain-elongation-mediated production of butyric, hexanoic, and octanoic acids, with different microbes using either lactose, ethanol, or lactic acid as the growth substrate. We conclude that genes encoding carbohydrate utilization pathways, and genes encoding lactic acid transport into the cell, electron confurcating lactate dehydrogenase, and its associated electron transfer flavoproteins, are genomic features whose presence in Firmicutes needs to be established to infer the growth substrate used for chain elongation.

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↗
DOE OSTI2022

Protist Predation Influences the Temperature Response of Bacterial Communities

Temperature strongly influences microbial community structure and function, in turn contributing to global carbon cycling that can fuel further warming. Recent studies suggest that biotic interactions among microbes may play an important role in determining the temperature responses of these communities. However, how predation regulates these microbiomes under future climates is still poorly understood. Here, we assess whether predation by a key global bacterial consumer—protists—influences the temperature response of the community structure and function of a freshwater microbiome. To do so, we exposed microbial communities to two cosmopolitan protist species—Tetrahymena thermophila and Colpidium sp.—at two different temperatures, in a month-long microcosm experiment. While microbial biomass and respiration increased with temperature due to community shifts, these responses changed over time and in the presence of protists. Protists influenced microbial biomass and respiration rate through direct and indirect effects on bacterial community structure, and predator presence actually reduced microbial respiration at elevated temperature. Indicator species analyses showed that these predator effects were mostly determined by phylum-specific bacterial responses to protist density and cell size. Our study supports previous findings that temperature is an important driver of microbial communities but also demonstrates that the presence of a large predator can mediate these responses to warming.

59 BASIC BIOLOGICAL SCIENCES↗