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At least 325 records · Page 18

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DOE OSTI2020

Increased replication of dissimilatory nitrate-reducing bacteria leads to decreased anammox bioreactor performance

Background: Anaerobic ammonium oxidation (anammox) is a biological process employed to remove reactive nitrogen from wastewater. While a substantial body of literature describes the performance of anammox bioreactors under various operational conditions and perturbations, few studies have resolved the metabolic roles of their core microbial community members. Results: Here, we used metagenomics to study the microbial community of a laboratory-scale anammox bioreactor from inoculation, through a performance destabilization event, to robust steady-state performance. Metabolic analyses revealed that nutrient acquisition from the environment is selected for in the anammox community. Dissimilatory nitrate reduction to ammonium (DNRA) was the primary nitrogen removal pathway that competed with anammox. Increased replication of bacteria capable of DNRA led to the out-competition of anammox bacteria, and the loss of the bioreactor's nitrogen removal capacity. These bacteria were highly associated with the anammox bacterium and considered part of the core microbial community. Conclusions: Our findings highlight the importance of metabolic interdependencies related to nitrogen- and carbon-cycling within anammox bioreactors and the potentially detrimental effects of bacteria that are otherwise considered core microbial community members.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Genomic insights into redox-driven microbial processes for carbon decomposition in thawing Arctic soils and permafrost

Climate change is rapidly transforming Arctic landscapes where increasing soil temperatures speed up permafrost thaw. This exposes large carbon stocks to microbial decomposition, possibly worsening climate change by releasing more greenhouse gases. Understanding how microbes break down soil carbon, especially under the anaerobic conditions of thawing permafrost, is important to determine future changes. Here, we studied the microbial community dynamics and soil carbon decomposition potential in permafrost and active layer soils under anaerobic laboratory conditions that simulated an Arctic summer thaw. The microbial and viral compositions in the samples were analyzed based on metagenomes, metagenome-assembled genomes, and metagenomic viral contigs (mVCs). Following the thawing of permafrost, there was a notable shift in microbial community structure, with fermentative Firmicutes and Bacteroidota taking over from Actinobacteria and Proteobacteria over the 60-day incubation period. The increase in iron and sulfate-reducing microbes had a significant role in limiting methane production from thawed permafrost, underscoring the competition within microbial communities. We explored the growth strategies of microbial communities and found that slow growth was the major strategy in both the active layer and permafrost. Our findings challenge the assumption that fast-growing microbes mainly respond to environmental changes like permafrost thaw. Instead, they indicate a common strategy of slow growth among microbial communities, likely due to the thermodynamic constraints of soil substrates and electron acceptors, and the need for microbes to adjust to post-thaw conditions. The mVCs harbored a wide range of auxiliary metabolic genes that may support cell protection from ice formation in virus-infected cells.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Inferring microbial interactions with their environment from genomic and metagenomic data

Microbial communities assemble through a complex set of interactions between microbes and their environment, and the resulting metabolic impact on the host ecosystem can be profound. Microbial activity is known to impact human health, plant growth, water quality, and soil carbon storage which has lead to the development of many approaches and products meant to manipulate the microbiome. In order to understand, predict, and improve microbial community engineering, genome-scale modeling techniques have been developed to translate genomic data into inferred microbial dynamics. However, these techniques rely heavily on simulation to draw conclusions which may vary with unknown parameters or initial conditions, rather than more robust qualitative analysis. To better understand microbial community dynamics using genome-scale modeling, we provide a tool to investigate the network of interactions between microbes and environmental metabolites over time. Using our previously developed algorithm for simulating microbial communities from genome-scale metabolic models (GSMs), we infer the set of microbe-metabolite interactions within a microbial community in a particular environment. Because these interactions depend on the available environmental metabolites, we refer to the networks that we infer as metabolically contextualized , and so name our tool MetConSIN: Met abolically Con textualized S pecies I nteraction N etworks.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Regional biogeography versus intra-annual dynamics of the root and soil microbiome

Abstract Background Root and soil microbial communities constitute the below-ground plant microbiome, are drivers of nutrient cycling, and affect plant productivity. However, our understanding of their spatiotemporal patterns is confounded by exogenous factors that covary spatially, such as changes in host plant species, climate, and edaphic factors. These spatiotemporal patterns likely differ across microbiome domains (bacteria and fungi) and niches (root vs. soil). Results To capture spatial patterns at a regional scale, we sampled the below-ground microbiome of switchgrass monocultures of five sites spanning > 3 degrees of latitude within the Great Lakes region. To capture temporal patterns, we sampled the below-ground microbiome across the growing season within a single site. We compared the strength of spatiotemporal factors to nitrogen addition determining the major drivers in our perennial cropping system. All microbial communities were most strongly structured by sampling site, though collection date also had strong effects; in contrast, nitrogen addition had little to no effect on communities. Though all microbial communities were found to have significant spatiotemporal patterns, sampling site and collection date better explained bacterial than fungal community structure, which appeared more defined by stochastic processes. Root communities, especially bacterial, were more temporally structured than soil communities which were more spatially structured, both across and within sampling sites. Finally, we characterized a core set of taxa in the switchgrass microbiome that persists across space and time. These core taxa represented < 6% of total species richness but > 27% of relative abundance, with potential nitrogen fixing bacteria and fungal mutualists dominating the root community and saprotrophs dominating the soil community. Conclusions Our results highlight the dynamic variability of plant microbiome composition and assembly across space and time, even within a single variety of a plant species. Root and soil fungal community compositions appeared spatiotemporally paired, while root and soil bacterial communities showed a temporal lag in compositional similarity suggesting active recruitment of soil bacteria into the root niche throughout the growing season. A better understanding of the drivers of these differential responses to space and time may improve our ability to predict microbial community structure and function under novel conditions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology

Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Metabolic capabilities mute positive response to direct and indirect impacts of warming throughout the soil profile

Increasing global temperatures are predicted to stimulate soil microbial respiration. The direct and indirect impacts of warming on soil microbes, nevertheless, remain unclear. This is particularly true for understudied subsoil microbes. Here, we show that 4.5 years of whole-profile soil warming in a temperate mixed forest results in altered microbial community composition and metabolism in surface soils, partly due to carbon limitation. However, microbial communities in the subsoil responded differently to warming than in the surface. Throughout the soil profile—but to a greater extent in the subsoil—physiologic and genomic measurements show that phylogenetically different microbes could utilize complex organic compounds, dampening the effect of altered resource availability induced by warming. We find subsoil microbes had 20% lower carbon use efficiencies and 47% lower growth rates compared to surface soils, which constrain microbial communities. Collectively, our results show that unlike in surface soils, elevated microbial respiration in subsoils may continue without microbial community change in the near-term.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Mixed and membrane-separated culturing of synthetic cyanobacteria-yeast consortia reveals metabolic cross-talk mimicking natural cyanolichens

Metabolite exchange mediates crucial interactions in microbial communities, significantly impacting global carbon and nitrogen cycling. Understanding these chemically-mediated interactions is essential for elucidating natural community functions and developing engineered synthetic communities. This study investigated membrane-separated bioreactors (mBRs) as a novel tool to identify transient metabolites and their producers/consumers in mixed microbial communities. We compared three co-culture methods (direct mixed, 2-chamber mBR, and 3-chamber mBR) to grow a synthetic binary community of the cyanobacterium Synechococcus elongatus PCC 7942 and the fungus Rhodotorula toruloides NBRC 0880, as well as axenic S. elongatus. Despite not being natural lichen constituents, these organisms exhibited interactions resembling those in cyanolichens. S. elongatus fixed CO 2 into sugars as the primary shared metabolite, while R. toruloides secreted various biochemicals, predominantly sugar alcohols, mirroring the metabolite exchange observed in natural lichens. The mBR systems successfully captured metabolite gradients and revealed rapidly consumed compounds, including TCA cycle intermediates and amino acids. Our approach demonstrated that the 2-chamber mBR optimally balanced metabolite exchange and growth dynamics. This study provides insights into cross-species metabolic interactions and presents a valuable tool for investigating and engineering synthetic microbial communities with potential applications in biotechnology and environmental science.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Regional Differences in the Structure of Juglans nigra Phytobiome Reflect Geographical Differences in Thousand Cankers Disease Severity

Thousand cankers disease threatens Juglans nigra (Eastern Black Walnut) in urban and natural landscapes. Incidence and severity of thousand cankers disease is higher in the host’s introduced range in the western United States. We hypothesized that these differences are driven partly by geographical variation in the host phytobiome due to its roles in host stress tolerance, nutrient acquisition, and defense. To evaluate the role of the phytobiome in mediating thousand cankers disease, we characterized the J. nigra phytobiome of diseased and healthy trees in portions of its native (Indiana and Tennessee) and introduced (Washington) ranges. Grafted clones present in each state and open-pollinated populations were sampled. DNA was extracted from soil and branch (caulosphere) tissues and internal transcribed spacer and 16s regions were sequenced for characterization of fungal and bacterial communities. We found that microbial communities in the caulosphere and soil differ between native and introduced ranges of J. nigra and harbor different mutualistic and pathogenic microorganisms. Additionally, caulosphere microbial communities were more species rich and diverse in the native range of J. nigra, suggesting greater levels of functional redundancy and multifunctionality in the native-range phytobiome compared with the introduced range. We also found higher network complexity in the caulosphere of trees in the introduced range and evidence for two alternative stable community states associated with diseased and healthy trees. Our results provide support for the hypothesis that geographical variation in thousand cankers disease incidence and severity is partially driven by differences in the phytobiome of J. nigra in its introduced and native ranges.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Assessing residential activity in a home plumbing system simulator: monitoring the occurrence and relationship of major opportunistic pathogens and phagocytic amoebas

Opportunistic premise plumbing pathogens (OPPPs) have been detected in buildings’ plumbing systems causing waterborne disease outbreaks in the United States. In this study, we monitored the occurrence of OPPPs along with free-living amoeba (FLA) and investigated the effects of residential activities in a simulated home plumbing system (HPS). Water samples were collected from various locations in the HPS and analyzed for three major OPPPs: Legionella pneumophila, nontuberculous mycobacterial species (e.g., Mycobacterium avium, M. intracellulare, and M. abscessus), and Pseudomonas aeruginosa along with two groups of amoebas (Acanthamoeba and Vermamoeba vermiformis). A metagenomic approach was also used to further characterize the microbial communities. Results show that the microbial community is highly diverse with evidence of spatial and temporal structuring influenced by environmental conditions. L. pneumophila was the most prevalent pathogen (86% of samples), followed by M. intracellulare (66%) and P. aeruginosa (21%). Interestingly, M. avium and M. abscessus were not detected in any samples. The data revealed a relatively low prevalence of Acanthamoeba spp. (4%), while V. vermiformis was widely detected (81%) across all the sampling locations within the HPS. Locations with a high concentration of L. pneumophila and M. intracellulare coincided with the highest detection of V. vermiformis, suggesting the potential growth of both populations within FLA and additional protection in drinking water. After a period of stagnation lasting at least 2-weeks, the concentrations of OPPPs and amoeba immediately increased and then decreased gradually back to the baseline. Furthermore, monitoring the microbial population after drainage of the hot water tank and partial drainage of the entire HPS demonstrated no significant mitigation of the selected OPPPs. This study demonstrates that these organisms can adjust to their environment during such events and may survive in biofilms and/or grow within FLA, protecting them from stressors in the supplied water.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Seeding Advanced Treated Wastewater for Purposes of Direct Potable Reuse

Direct potable reuse (DPR) is a promising solution to address water scarcity. However, a better understanding of how introducing advanced treated water (ATW) affects microbial communities present in distribution systems is needed. Here, in this study, we measured changes to the microbial water quality in simulated distribution systems that were conditioned using treated, unimpaired surface water (SW) and then transitioned to ATW. In addition, we investigated whether adding a biological filtration step would seed the microbial community of the ATW and whether the influence would persist in the simulated distribution systems. We found that the bulk water in the ATW-fed distribution systems had lower cell counts and ATP concentrations and a distinct microbial community (based on 16S amplicon sequencing) compared to the SW-fed or the seeded ATW-fed systems. However, biofilm community composition and biomass remained consistent regardless of the feedwater. Increased microbial biomass and diversity were present in the seeded ATW, with several amplicon sequence variants identified as being introduced by the biological filter. Our results suggest that directly introducing ATW to distribution systems could disturb the existing microbial community. Preparing ATW for distribution via biological filtration may deliver more predictable and stable microbial water quality than introducing unseeded ATW.

16S↗

DOE OSTI2022

Long-term compost amendment modulates wheat genotype differences in belowground carbon allocation, microbial rhizosphere recruitment and nitrogen acquisition

The implementation of soil health-promoting practices, such as cover cropping and compost application, has important implications for nutrient cycling and management in agroecosystems. At the same time, plant belowground carbon (C) allocation patterns can influence nutrient cycling and availability in soil through changes to the microbial community, but the effects may depend on the crop genotype and management practices in place. We evaluated belowground C allocation patterns using 13 C labeling and root architecture in two genotypes of winter wheat (Triticum aestivum) with different levels of exudation and belowground allocation strategies in soils with contrasting compost amendment legacy (108.7 Mg ha -1 every 2 years over 10 years vs. no compost). We also measured microbial community structure and function in the rhizosphere and quantified uptake of residue-derived N from 15 N-labelled cover crop residues. We found an interactive effect between soil management and genotype, where in the no-compost soil, the high-exudation genotype (Snowmass) increased exudation by over 4-fold, while the low-exudate genotype (Byrd) increased only 2-fold. While we did not observe genotype differences in rhizosphere enzyme activity or dissolved N pools, residue N uptake was 1.8 times greater for Snowmass in the compost-amended soil. There were more rhizosphere microbial taxa associated with the high-exudate genotype (Snowmass); nine bacterial and seven fungal families were indicative of Snowmass, versus one bacterial and four fungal families for Byrd. Our results suggest that the high-exudation strategy can influence the rhizosphere microbial community, and lead to greater short-term residue N uptake in high SOM soil. By directly linking root architecture, exudation, microbial communities, and N mineralization and uptake dynamics, this work demonstrates that plasticity in root C allocation is genotype-specific and influences microbial communities and nutrient cycling depending on the soil health context.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity

Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth’s environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Metatranscriptomic analysis reveals dissimilarity in viral community activity between an ice-free and ice-covered winter in Lake Erie

Winter is a relatively under-studied season in freshwater ecology. The paucity of wintertime surveys has led to a lack of knowledge regarding microbial community activity during the winter in Lake Erie, a North American Great Lake. Viruses shape microbial communities and regulate biogeochemical cycles by acting as top-down controls, yet very few efforts have been made to examine active virus populations during the winter in Lake Erie. Furthermore, climate change-driven declines in seasonal ice cover have been shown to influence microbial community structure, but no studies have compared viral community activity between different ice cover conditions. We surveyed surface water metatranscriptomes for viral hallmark genes as a proxy for active virus populations and compared activity metrics between ice-covered and ice-free conditions from two sampled winters. Transcriptionally active viral communities were detected in both winters, spanning diverse phylogenetic clades of putative bacteriophage (Caudoviricetes), giant viruses (Nucleocytoviricota, or NCLDV), and RNA viruses (Orthornavirae). However, viral community activity metrics revealed pronounced differences between the ice-covered and ice-free winters. Viral community composition was distinct between winters and viral hallmark gene richness was reduced in the ice-covered relative to the ice-free conditions. In addition, the observed differences in viral communities correlated with microbial community activity metrics. Overall, these findings contribute to our understanding of the viral populations that are active during the winter in Lake Erie and suggest that viral community activity may be associated with ice cover extent.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Plant-microbe interactions: from genes to ecosystems using Populus as a model system

Plant-microbe symbioses span a continuum from pathogenic to mutualistic with functional consequences for both organisms in the symbiosis. In order to increase sustainable food and fuel production in the future, it is imperative that we harness these symbioses. The tree genus Populus is an excellent model system for studies examining plant-microbe interactions due to the wealth of genomic information available and the molecular tools that have been developed to manipulate Populus-microbe symbioses. In this review, we highlight how Populus can serve as a model system to explore plant-microbe interactions. Specifically, highlighting research linking Populus-microbe interactions from the gene to the ecosystem level. We explore why Populus is an excellent model for perennial plant systems, the molecular underpinnings of Populus-microbe interactions, how host genetics influence microbial community composition, and how microbial communities vary at fine spatial scales and between Populus species. Further, we explore how the patterns of the microbiome may affect ecosystem level functions in managed and natural ecosystems. Understanding and manipulating these interactions in Populus has the potential to improve plant health and impact ecosystem sustainability and processes as Populus trees function as foundational species in many natural ecosystems and are also deployed in managed ecosystems for various agroforestry applications.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

The anaerobic fungus Neocallimastix californiae shifts metabolism and produces melanin in response to lignin-derived aromatic compounds

Biological deconstruction of lignocellulose for sustainable chemical production offers an opportunity to harness evolutionarily specialized enzymes and organisms for industrial bioprocessing. While hydrolysis of cellulose and hemicellulose by CAZymes yields fermentable sugars, ligninolysis releases a heterogeneous mix of aromatic compounds that likely play a crucial role in shaping microbial communities and microbial metabolism. Here, we interrogated the metabolomic and transcriptomic response of a lignocellulolytic anaerobic fungus, Neocallimastix californiae, to a heterogeneous mixture of aromatic compounds derived from lignin. Through exposing the fungus to both a concentration it might experience in its native environment and an elevated concentration of alkaline lignin, we observe that N. californiae transforms vanillin and that supplying alkaline lignin at 0.125 g/L, alongside cellulose, enhances the growth and polysaccharide-degrading activity of N. californiae. Altogether, our results further suggest that vanillin consumption, increased polymer-degrading activity, increased metabolic activity, and transcriptomic remodeling of amino acid synthesis genes all coincide with increased melanin production by fungal cells. These observations challenge previous notions that aromatics from lignocellulose only inhibit the growth and polymer deconstruction capabilities of the biomass-degrading anaerobic fungi (Neocallimastigomycetes). This study demonstrates that anaerobic fungi have a complex relationship with aromatic chemicals derived from lignin and hemicellulose and shift their metabolism in response to the addition of lignocellulose-derived aromatics to their growth medium. Further, as no known pathways for the biochemical transformation of aromatics were detected in these organisms despite observed transcriptome remodeling in the presence of aromatics, we suggest they might encode novel biochemical routes for scavenging amino acid building blocks from aromatic monomers derived from hemicellulose side chains and lignin.

Anaerobic fungi↗

DOE OSTI2020

Coastal Wetland Carbon Processes in a Warmer Climate (Final Report)

Coastal wetlands are global hotspots of carbon storage. Marshes, mangroves, and seagrass meadows account for about half of the total marine soil carbon budget and bury carbon at rates roughly equivalent to terrestrial forests despite occupying just 2.5% of Earth’s land area. Coastal wetlands have recently been recognized as important for storing carbon, but the future sink strength and carbon stock stability of these systems is uncertain because global change drivers such as temperature and elevated CO 2 disturb the complex ecology that drives high rates of soil carbon sequestration. The dynamics of coastal wetland carbon pools are not presently represented in earth system models. Our goals are to understand the influence of warming and elevated CO 2 on C cycling and to forecast the stability of tidal wetland soil carbon pools at the terrestrial-aquatic interface. We designed and implemented a novel field manipulation of elevated CO 2 and temperature and operated it from 2016 to 2020. We learned that plant communities and microbial communities respond differently to rising temperature, and that the net effects of these responses means that a modest amount of warming will increase tidal marsh carbon sequestration, while warming above that level will diminish the potential for additional carbon sequestration. In mathematical terms the system showed non-linear responses which are important for building forecast models.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

General Biology 2 Sugar Beet Lab - Spring 24

This module uses the Department of Energy Systems Biology Knowledgebase (KBase) platform to explore topics such as genome assembly, metagenomics, and phylogenomics. Here students will use sequences from DNA that they collected to compare the metagenomes of microbial communities from the rhizosphere of plants grown in fertilized vs. unfertilized soils. Using these data students will evaluate the impact of fertilizer on these communities and how these microbial communities influence soil health and plant growth.

Schirmer, Aaron [Northeastern Illinois University,↗

DOE OSTI2025

General Biology 2 Sugar Beet Lab - SU2025 - Final

59 BASIC BIOLOGICAL SCIENCES↗