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Results for “Metagenomic Assembly”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily

Abstract Hydrothermal vents have been key to our understanding of the limits of life, and the metabolic and phylogenetic diversity of thermophilic organisms. Here we used environmental metagenomics combined with analysis of physicochemical data and 16S rRNA gene amplicons to characterize the sediment-hosted microorganisms at the recently discovered Auka vents in the Gulf of California. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 30% of those currently known, showing the microbial community in Auka hydrothermal sediments is highly diverse. 16S rRNA gene amplicon screening of 224 sediment samples across the vent field indicates that the MAGs retrieved from a single site are representative of the microbial community in the vent field sediments. Metabolic reconstruction of a vent-specific, deeply branching clade within the Desulfobacterota suggests these organisms metabolize sulfur using novel octaheme cytochrome-c proteins related to hydroxylamine oxidoreductase. Community-wide comparison between Auka MAGs and MAGs from Guaymas Basin revealed a remarkable 20% species-level overlap, suggestive of long-distance species transfer over 400 km and subsequent sediment colonization. Optimal growth temperature prediction on the Auka MAGs, and thousands of reference genomes, shows that thermophily is a trait that has evolved frequently. Taken together, our Auka vent field results offer new perspectives on our understanding of hydrothermal vent microbiology.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Pangenomics reveals alternative environmental lifestyles among chlamydiae

Chlamydiae are highly successful strictly intracellular bacteria associated with diverse eukaryotic hosts. Here we analyzed metagenome-assembled genomes of the “Genomes from Earth’s Microbiomes” initiative from diverse environmental samples, which almost double the known phylogenetic diversity of the phylum and facilitate a highly resolved view at the chlamydial pangenome. Chlamydiae are defined by a relatively large core genome indicative of an intracellular lifestyle, and a highly dynamic accessory genome of environmental lineages. We observe chlamydial lineages that encode enzymes of the reductive tricarboxylic acid cycle and for light-driven ATP synthesis. We show a widespread potential for anaerobic energy generation through pyruvate fermentation or the arginine deiminase pathway, and we add lineages capable of molecular hydrogen production. Genome-informed analysis of environmental distribution revealed lineage-specific niches and a high abundance of chlamydiae in some habitats. Together, our data provide an extended perspective of the variability of chlamydial biology and the ecology of this phylum of intracellular microbes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea

Trace metals have been an important ingredient for life throughout Earth’s history. Here, we describe the genome-guided cultivation of a member of the elusive archaeal lineage Caldarchaeales (syn. Aigarchaeota), Wolframiiraptor gerlachensis, and its growth dependence on tungsten. A metagenome-assembled genome (MAG) of W. gerlachensis encodes putative tungsten membrane transport systems, as well as pathways for anaerobic oxidation of sugars probably mediated by tungsten-dependent ferredoxin oxidoreductases that are expressed during growth. Catalyzed reporter deposition-fluorescence in-situ hybridization (CARD-FISH) and nanoscale secondary ion mass spectrometry (nanoSIMS) show that W. gerlachensis preferentially assimilates xylose. Phylogenetic analyses of 78 high-quality Wolframiiraptoraceae MAGs from terrestrial and marine hydrothermal systems suggest that tungsten-associated enzymes were present in the last common ancestor of extant Wolframiiraptoraceae. Our observations imply a crucial role for tungsten-dependent metabolism in the origin and evolution of this lineage, and hint at a relic metabolic dependence on this trace metal in early anaerobic thermophiles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Multiple sources of aerobic methane production in aquatic ecosystems include bacterial photosynthesis

Aquatic ecosystems are globally significant sources of the greenhouse gas methane to the atmosphere. Until recently, methane production was thought to be a strictly anaerobic process confined primarily to anoxic sediments. However, supersaturation of methane in oxygenated waters has been consistently observed in lakes and the ocean (termed the ‘methane paradox’), indicating that methane can be produced under oxic conditions through unclear mechanisms. Here we show aerobic methane production from multiple sources in freshwater incubation experiments under different treatments and based on biogeochemical, metagenomic, and metatranscriptomic data. We find that aerobic methane production appears to be associated with (bacterio)chlorophyll metabolism and photosynthesis, as well as with Proteobacterial degradation of methylphosphonate. Genes encoding pathways for putative photosynthetic- and methylphosphonate-based methane production also co-occur in Proteobacterial metagenome-assembled genomes. Our findings provide insight into known mechanisms of aerobic methane production, and suggest a potential co-occurring mechanism associated with bacterial photosynthesis in aquatic ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater

Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant. By creating a co-occurrence network with thousands of time-resolved microbial populations from over 100 samples spanning four operating configurations, known and novel microbial consortia with potential to drive methane production were identified. Interactions between these populations were further resolved in relation to specific process configurations by mapping metagenome assembled genomes and cognate gene expression data onto the network. Prominent interactions included transcriptionally active Methanolinea methanogens and syntrophic benzoate oxidizing Syntrophorhabdus , as well as a Methanoregulaceae population and putative syntrophic acetate oxidizing bacteria affiliated with Bateroidetes (Tenuifilaceae) expressing the glycine cleavage bypass of the Wood–Ljungdahl pathway.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Genome-resolved biogeography of Phaeocystales, cosmopolitan bloom-forming algae

Phaeocystales, comprising the genus Phaeocystis and an uncharacterized sister lineage, are nanoplanktonic haptophytes widespread in the global ocean. Several species form mucilaginous colonies and influence key biogeochemical cycles, yet their underlying diversity and ecological strategies remain underexplored. Here, we present new genomic data from 13 strains, including three high-quality reference genomes (N50 > 30 kbp), and integrate previous metagenome-assembled genomes to resolve a robust phylogeny. Divergence timing of P. antarctica aligns with Miocene cooling and Southern Ocean isolation. Genomic traits reveal metabolic flexibility, including mixotrophic nitrogen acquisition in temperate waters and gene expansions linked to polar nutrient adaptation. Concordantly, transcriptomic comparisons between temperate and polar Phaeocystis suggest Southern Ocean populations experience iron and B12 limitation. We also identify signatures of horizontal gene transfer and endogenous giant virus/virophage insertions. Together, these findings highlight Phaeocystales as an ecologically versatile and geographically widespread lineage shaped by evolutionary innovation and adaptation to contrasting environmental stressors.

Füssy, Zoltán↗
DOE OSTI2025

Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient

Anthropogenic-driven climate change is accelerating permafrost thaw, threatening to release vast carbon stores through increased microbial activity. While microbial roles are increasingly studied, the contributions of viruses remain largely unexplored, in part due to soil-associated technical challenges that have hindered their detection and characterization. Here, we applied an optimized virion enrichment workflow along a permafrost thaw gradient, identifying 9,963 viral populations (vOTUs), including single- and double-stranded DNA viruses, with 99.9% novelty compared to other soils. Hosts were predicted for 38% of vOTUs, spanning nine archaeal, and 36 bacterial phyla, 22% of which were linked to metagenome-assembled genomes, including key carbon-cycling taxa. Genomic analyses revealed 811 putative auxiliary metabolic genes (AMGs) from 658 vOTUs, nearly half involved in carbon processing. These included 59 glycoside hydrolases (GH) across nine GH families, 45 for monosaccharide degradation, and seven involved in short-chain fatty acid and C1 metabolism, linking viruses to both early and late stages of carbon turnover. Additionally, six vOTUs carried racD, which may stabilize microbial necromass and promote long-term carbon storage. Viral and AMG functional diversity increased with thaw stage, indicating that viruses might participate in a broadening range of microbial metabolic processes as permafrost thaws. These findings expand our understanding of virus contributions in microbial carbon processing and suggest their important role in deciphering soil carbon fate under changing climate conditions.

Biological and medical sciences↗
DOE OSTI2021

Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems

Abstract Candidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that are often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity and host association of CPR bacteria and DPANN archaea has not been studied. Here, we performed genome-resolved metagenomic analysis of one agricultural and seven pristine groundwater microbial communities and recovered 746 CPR and DPANN genomes in total. The pristine sites, which serve as local sources of drinking water, contained up to 31% CPR bacteria and 4% DPANN archaea. We observed little species-level overlap of metagenome-assembled genomes (MAGs) across the groundwater sites, indicating that CPR and DPANN communities may be differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy imaging and genomic analyses enabled us to identify CPR and DPANN lineages that reproducibly attach to host cells and showed that the growth of CPR bacteria seems to be stimulated by attachment to host-cell surfaces. Our analysis reveals site-specific diversity of CPR bacteria and DPANN archaea that coexist with diverse hosts in groundwater aquifers. Given that CPR and DPANN organisms have been identified in human microbiomes and their presence is correlated with diseases such as periodontitis, our findings are relevant to considerations of drinking water quality and human health.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A genomic catalog of Earth’s microbiomes

Abstract The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2024

Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to thermophilic hosts

Geothermal springs house unicellular red algae in the class Cyanidiophyceae that dominate the microbial biomass at these sites. Little is known about host-virus interactions in these environments. We analyzed the virus community associated with red algal mats in three neighboring habitats (creek, endolithic, soil) at Lemonade Creek, Yellowstone National Park (YNP), USA. We find that despite proximity, each habitat houses a unique collection of viruses, with the giant viruses, Megaviricetes, dominant in all three. The early branching phylogenetic position of genes encoded on metagenome assembled virus genomes (vMAGs) suggests that the YNP lineages are of ancient origin and not due to multiple invasions from mesophilic habitats. The existence of genomic footprints of adaptation to thermophily in the vMAGs is consistent with this idea. The Cyanidiophyceae at geothermal sites originated ca. 1.5 Bya and are therefore relevant to understanding biotic interactions on the early Earth.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Morphine and high-fat diet differentially alter the gut microbiota composition and metabolic function in lean versus obese mice

There are known associations between opioids, obesity, and the gut microbiome, but the molecular connection/mediation of these relationships is not understood. To better clarify the interplay of physiological, genetic, and microbial factors, this study investigated the microbiome and host inflammatory responses to chronic opioid administration in genetically obese, diet-induced obese, and lean mice. Samples of feces, urine, colon tissue, and plasma were analyzed using targeted LC-MS/MS quantification of metabolites, immunoassays of inflammatory cytokine levels, genome-resolved metagenomics, and metaproteomics. Genetic obesity, diet-induced obesity, and morphine treatment in lean mice each showed increases in distinct inflammatory cytokines. Metagenomic assembly and binning uncovered over 400 novel gut bacterial genomes and species. Morphine administration impacted the microbiome’s composition and function, with the strongest effect observed in lean mice. This microbiome effect was less pronounced than either diet or genetically driven obesity. Based on inferred microbial physiology from the metaproteome datasets, a high-fat diet transitioned constituent microbes away from harvesting diet-derived nutrients and towards nutrients present in the host mucosal layer. Considered together, these results identified novel host-dependent phenotypes, differentiated the effects of genetic obesity versus diet induced obesity on gut microbiome composition and function, and showed that chronic morphine administration altered the gut microbiome.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Distinct and rich assemblages of giant viruses in Arctic and Antarctic lakes

Giant viruses (GVs) are key players in ecosystem functioning, biogeochemistry, and eukaryotic genome evolution. GV diversity and abundance in aquatic systems can exceed that of prokaryotes, but their diversity and ecology in lakes, especially polar ones, remain poorly understood. We conducted a comprehensive survey and meta-analysis of GV diversity across 20 lakes, spanning polar to temperate regions, combining our extensive lake metagenome database from the Canadian Arctic and subarctic with publicly available datasets. Leveraging a novel GV genome identification tool, we identified 3304 GV metagenome-assembled genomes, revealing lakes as untapped GV reservoirs. Phylogenomic analysis highlighted their dispersion across all Nucleocytoviricota orders. Strong GV population endemism emerged between lakes from similar regions and biomes (Antarctic and Arctic), but a polar/temperate barrier in lacustrine GV populations and differences in their gene content could be observed. Our study establishes a robust genomic reference for future investigations into lacustrine GV ecology in fast changing polar environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Wildfire impact on soil microbiome life history traits and roles in ecosystem carbon cycling

Abstract Wildfires, which are increasing in frequency and severity with climate change, reduce soil microbial biomass and alter microbial community composition and function. The soil microbiome plays a vital role in carbon (C) and nitrogen (N) cycling, but its complexity makes it challenging to predict post-wildfire soil microbial dynamics and resulting impacts on ecosystem biogeochemistry. The application of biogeochemically relevant conceptual trait-based frameworks to the soil microbiome can distill this complexity, enabling enhanced predictability of soil microbiome recovery following wildfire and subsequent impacts to biogeochemical cycles. Conceptual frameworks that have direct links to soil C and N cycling have been developed for the soil microbiome; the Y-A-S framework overviews soil microbiome life history strategies that have tradeoffs with one another and others have proposed frameworks specific to wildfire. Here, we aimed to delineate post-wildfire changes of bacterial traits in western US coniferous forests to inform how severe wildfire influences soil microbiome recovery and resultant biogeochemical cycling. We utilized a comprehensive metagenome-assembled genome catalog from post-wildfire soils representing 1 to 11 years following low- and high-severity burning to identify traits that enable the persistence of microbial taxa in burned soils and influence ecosystem C and N cycling. We found that high-severity wildfire initially selects for fast growers and, up to a decade post-fire, taxa that invest in genes for acquiring diverse resources from the external environment, which in combination could increase soil C losses. This work begins to disentangle how climate change–induced shifts in wildfire behavior might alter microbially mediated soil biogeochemical cycling.

Nelson, Amelia R.↗
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 OSTI2024

Bacterial population-level trade-offs between drought tolerance and resource acquisition traits impact decomposition

Microbes drive fundamental ecosystem processes, such as decomposition. Environmental stressors are known to affect microbes, their fitness, and the ecosystem functions that they perform; yet, understanding the causal mechanisms behind this influence has been difficult. We used leaf litter on soil surface as a model in situ system to assess changes in bacterial genomic traits and decomposition rates for 18 months with drought as a stressor. We hypothesized that genome-scale trade-offs due to investment in stress tolerance traits under drought reduce the capacity for bacterial populations to carry out decomposition, and that these population-level trade-offs scale up to impact emergent community traits, thereby reducing decomposition rates. We observed drought tolerance mechanisms that were heightened in bacterial populations under drought, identified as higher gene copy numbers in metagenome-assembled genomes. A subset of populations under drought had reduced carbohydrate-active enzyme genes that suggested—as a trade-off—a decline in decomposition capabilities. These trade-offs were driven by community succession and taxonomic shifts as distinct patterns appeared in populations. We show that trait–trade-offs in bacterial populations under drought could scale up to reduce overall decomposition capabilities and litter decay rates. Using a trait-based approach to assess the population ecology of soil bacteria, we demonstrate genome-level trade-offs in response to drought with consequences for decomposition rates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Phylometagenomics of cycad coralloid roots reveals shared symbiotic signals

Cycads are known to host symbiotic cyanobacteria, includingNostocalesspecies, as well as other sympatric bacterial taxa within their specialized coralloid roots. Yet, it is unknown if these bacteria share a phylogenetic origin and/or common genomic functions that allow them to engage in facultative symbiosis with cycad roots. To address this, we obtained metagenomic sequences from 39 coralloid roots sampled from diverse cycad species and origins in Australia and Mexico. Culture-independent shotgun metagenomic sequencing was used to validate sub-community co-cultures as an efficient approach for functional and taxonomic analysis. Our metanalysis shows a host-independent microbiome core consisting of seven bacterial orders with high species diversity within the identified taxa. Moreover, we recovered 43 cyanobacterial metagenome-assembled genomes, and in addition toNostocspp., symbiotic cyanobacteria of the genusAulosirawere identified for the first time. Using this robust dataset, we used phylometagenomic analysis to reveal three monophyletic cyanobiont clades, two host-generalist and one cycad-specific that includesAulosiraspp. Although the symbiotic clades have independently arisen, they are enriched in certain functional genes, such as those related to secondary metabolism. Furthermore, the taxonomic composition of associated sympatric bacterial taxa remained constant. Our research quadruples the number of cycad cyanobiont genomes and provides a robust framework to decipher cyanobacterial symbioses, with the potential of improving our understanding of symbiotic communities. This study lays a solid foundation to harness cyanobionts for agriculture and bioprospection, and assist in conservation of critically endangered cycads.

Genetics & Heredity↗
DOE OSTI2024

Genomics and physiology of Catenibacillus, human gut bacteria capable of polyphenol C-deglycosylation and flavonoid degradation

The genusCatenibacillus(familyLachnospiraceae, phylumBacillota) includes only one cultivated species so far,Catenibacillus scindens,isolated from human faeces and capable of deglycosylating dietary polyphenols and degrading flavonoid aglycones. Another human intestinalCatenibacillusstrain not taxonomically resolved at that time was recently genome-sequenced. We analysed the genome of this novel isolate, designatedCatenibacillus decagia, and showed its ability to deglycosylateC-coupled flavone and xanthone glucosides andO-coupled flavonoid glycosides. Most of the resulting aglycones were further degraded to the corresponding phenolic acids. Including the recently sequenced genome ofC. scindensand ten faecal metagenome-assembled genomes assigned to the genusCatenibacillus, we performed a comparative genome analysis and searched for genes encoding potentialC-glycosidases and other polyphenol-converting enzymes. According to genome data and physiological characterization, the core metabolism ofCatenibacillusstrains is based on a fermentative lifestyle with butyrate production and hydrogen evolution. BothC. scindensandC. decagiaencode a flavonoidO-glycosidase, a flavone reductase, a flavanone/flavanonol-cleaving reductase and a phloretin hydrolase. Several gene clusters encode enzymes similar to those of the flavonoidC-deglycosylation system ofDoreastrain PUE (DgpBC), while separately located genes encode putative polyphenol-glucoside oxidases (DgpA) required forC-deglycosylation. The diversity ofdgpAanddgpBCgene clusters might explain the broadC-glycoside substrate spectrum ofC. scindensandC. decagia. The otherCatenibacillusgenomes encode only a few potential flavonoid-converting enzymes. Our results indicate that severalCatenibacillusspecies are well-equipped to deglycosylate and degrade dietary plant polyphenols and might inhabit a corresponding, specific niche in the gut.

Genetics & Heredity↗