Biology subjects

Rich, V. I.

Publications and source records attributed to Rich, V. I..

11 recordsLinked to original sources

bioRxiv2025

Mobile genetic elements that shape microbial diversity and functions inthawing permafrost soils

The worlds ecosystems are shaped by microbiota. Their niches and their impacts depend on functional profiles influenced by gene gains and losses. While culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate gene flux, quantitative field data on the rates and impacts of MGE activity remains scarce. Here we leverage large-scale soil meta-omic data to develop and apply analytics for studying MGEs in complex natural systems. In our model permafrost-thaw ecosystem, Stordalen Mire, we identify [~]2.1 million MGE recombinases across 89 microbial phyla to assess ecological distributions, affected functions, past mobility, and current activity. This revealed MGEs shaping natural genetic diversity via differential impacts on major phyla; affecting a wide range of functions, including diverse regulatory and metabolic genes affecting carbon flux and nutrient cycling; and moving at rates that should significantly influence the realized functional profiles of natural microbiomes. These findings and this systematic meta-omic framework open new avenues to better investigate MGE diversity, activity, mobility, and impacts in nature.

microbiology↗

bioRxiv2025

From Archaea to the atmosphere: remotely sensing Arctic methane

Global atmospheric methane concentrations are rapidly rising and becoming isotopically more depleted, implying an unresolved microbial contribution. Rising Arctic temperatures are variably altering soil methane cycling, causing consequential uncertainty in the atmospheric methane budget. We demonstrated in an Arctic wetland that below-ground microbiota and methane-cycling features parallelled above-ground plant communities. To upscale emissions, we applied machine learning to remote sensing data to identify habitats, which were assigned average emissions. To upscale dynamically, we incorporated climate data, remotely-sensed water table variation, and habitat classes into a temporally-resolved biogeochemical model, to predict methane flux and isotope dynamics. This accurately estimated more depleted 13C-methane than previously used for Arctic habitats in global source partitioning. Remote-sensing of these rapidly changing inaccessible landscapes can thus help constrain the role of the Arctic in ongoing changes in global methane emissions.

microbiology↗

bioRxiv2025

Stable states in an unstable landscape: microbial resistance at the front line of climate change

Microbiome responses to warming may amplify or ameliorate terrestrial carbon loss and thus are a critical unknown in predicting climate outcomes. Because the rapid thaw of permafrost peatlands makes a very large store of soil carbon available to microbial metabolism, understanding microbiome dynamics in these systems is particularly urgent. We quantified microbial warming response over seven years across three habitats in a thawing permafrost peatland, using large-scale multi-omics data. We integrated analyses of organisms (via taxonomy), functions (via metabolic pathways and proteins), and community organization (via network structure and ecological assembly) to deeply characterize response mechanisms. We consistently found a pattern of within-habitat microbiome stability, with virtually no signal of gradual change in the warming period studied. The resistance to change appeared bolstered by habitat-specific dispersal processes and community-level functional redundancy, particularly via versatile carbon generalists. Our findings also reveal key genome-inferred metabolic processes that underlie microbiome stability. Together, our results highlight the importance of understanding the limits of these stabilizing processes and suggest that future research should reorient towards critical habitat transitions.

microbiology↗

bioRxiv2024

Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands

Current estimates of wetland contributions to the global methane budget carry high uncertainty, particularly in accurately predicting emissions from high methane-emitting wetlands. Microorganisms mediate methane cycling, yet knowledge of their conservation across wetlands remains scarce. To address this, we integrated 1,118 16S rRNA amplicon datasets (116 new), 305 metagenomes (20 new) that yielded 4,745 medium and high-quality metagenome assembled genomes (MAGs; 617 new), 133 metatranscriptomes, and annual methane flux data across 9 wetlands to create the Multi-Omics for Understanding Climate Change (MUCC) v2.0.0 database. This new resource was leveraged to link microbiome compositional profiles to encoded functions and emissions, with specific focus on methane-cycling populations and the microbial carbon decomposition networks that fuel them. We identified eight methane-cycling genera that were conserved across wetlands, and deciphered wetland specific metabolic interactions across marshes, revealing low methanogen-methanotroph connectivity in high-emitting wetlands. Methanoregula emerged as a hub methanogen across networks and was a strong predictor of methane flux, demonstrating the potential broad relevance of methylotrophic methanogenesis in these ecosystems. Collectively, our findings illuminate trends between microbial decomposition networks and methane flux and provide an extensive publicly available database to advance future wetland research.

microbiology↗

bioRxiv2023

Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost

While wetlands are major sources of biogenic methane (CH4), our understanding of resident microbial metabolisms is incomplete, which compromises prediction of CH4 emissions under ongoing climate change. Here, we employed genome-resolved multi-omics to expand our understanding of methanogenesis in the thawing permafrost peatland of Stordalen Mire, in arctic Sweden. In quadrupling the genomic representation of the sites methanogens and examining their encoded metabolisms, we revealed that nearly 20% (72) of the metagenome-assembled genomes (MAGs) encoded potential for methylotrophic methanogenesis. Further, 27% of the transcriptionally active methanogens expressed methylotrophic genes; for Methanosarcinales and Methanobacteriales MAGs, these data indicated use of methylated oxygen compounds (e.g., methanol), while for Methanomassiliicoccales, they primarily implicated methyl sulfides and methylamines. In addition to methanogenic methylotrophy, >1700 bacterial MAGs across 19 phyla encoded anaerobic methylotrophic potential, with expression across 12 phyla. Metabolomic analyses revealed the presence of diverse methylated compounds in the Mire, including some known methylotrophic substrates. Active methylotrophy was observed across all stages of a permafrost thaw gradient in Stordalen, with the most frozen non-methanogenic palsa found to host bacterial methylotrophy, and the partially thawed bog and fully thawed fen seen to house both methanogenic and bacterial methylotrophic activity. Methanogenesis across increasing permafrost thaw is thus revised from sole dominance of hydrogenotrophic production, and the appearance of acetoclastic at full thaw, to consider co-occurrence of methylotrophy throughout. Collectively, these findings indicate that methanogenic and bacterial methylotrophy may be an important and previously underappreciated component of carbon cycling and emissions in these rapidly changing wetland habitats.

microbiology↗

bioRxiv2023

Population ecology and potential biogeochemical impacts of ssDNA and dsDNA soil viruses along a permafrost thaw gradient

Climate change is disproportionately warming northern peatlands, which may release large carbon stores via increased microbial activity. While there are many unknowns about such microbial responses, virus roles are especially poorly characterized with studies to date largely restricted to "bycatch" from bulk metagenomes. Here, we used optimized viral particle purification techniques on 20 samples along a highly contextualized peatland permafrost thaw gradient, extracted and sequenced viral particle DNA using two library kits to capture single-stranded (ssDNA) and double-stranded (dsDNA) virus genomes (40 total viromes), and explored their diversity and potential ecosystem impacts. Both kits recovered similar dsDNA virus numbers, but only one also captured thousands of ssDNA viruses. Combining these data, we explored population-level ecology using genomic representation from 9,560 viral operational taxonomic units (vOTUs); nearly a 4-fold expansion from permafrost-associated soils, and 97% of which were novel when compared against large datasets from soils, oceans, and the human gut. In silico predictions identified putative hosts for 44% (4,149 dsDNA + 17 ssDNA) of the identified vOTUs spanning 2 eukaryotic, 12 archaeal, and 30 bacterial phyla. The recovered vOTUs encoded 1,684 putative auxiliary metabolic genes (AMGs) and other metabolic genes carried by [~]10% of detected vOTUs, of which 46% were related to carbon processing and 644 were novel. These AMGs grouped into five functional categories and 11 subcategories, and nearly half (47%) of the AMGs were involved in carbon utilization. Of these, 112 vOTUs encoded 123 glycoside hydrolases spanning 15 types involved in the degradation of polysaccharides (e.g., cellulose) to monosaccharides (e.g., galactose), or further monosaccharide degradation, which suggests virus involvement in myriad metabolisms including fermentation and central carbon metabolism. These findings expand the scope of viral roles in microbial carbon processing and suggest viruses may be critical for understanding the fate of soil organic carbon in peatlands.

microbiology↗

bioRxiv2020

Ecology and molecular targets of hypermutation in the global microbiome.

Changes in the sequence of an organisms genome, i.e. mutations, are the raw material of evolution1. The frequency and location of mutations can be constrained by specific molecular mechanisms, such as Diversity-generating retroelements (DGRs)2-4. DGRs introduce mutations in specific target genes, and were characterized from several cultivated bacteria and bacteriophages2. Whilst a larger diversity of DGR loci has been identified in genomic data from environmental samples, i.e. metagenomes, the ecological role of these DGRs and their associated evolutionary drivers remain poorly understood5-7. Here we built and analyzed an extensive dataset of >30,000 metagenome-derived DGRs, and determine that DGRs have a single evolutionary origin and a universal bias towards adenine mutations. We further identified six major lineages of DGRs, each associated with a specific ecological niche defined as a genome type, i.e. whether the DGR is encoded on a viral or cellular genome, a limited set of taxa and environments, and a distinct type of target. Finally, we leverage read mapping and metagenomic time series to demonstrate that DGRs are consistently and broadly active, and responsible for >10% of all amino acid changes in some organisms at a conservative estimate. Overall, these results highlight the strong constraints under which DGRs diversify and expand, and elucidate several distinct roles these elements play in natural communities and in shaping microbial community structure and function in our environment.

microbiology↗

bioRxiv2020

Diverse Arctic lake sediment microbiota shape methane emission temperature sensitivity

Northern post-glacial lakes are a significant and increasing source of atmospheric carbon (C), largely through ebullition (bubbling) of microbially-produced methane (CH4) from the sediments1. Ebullitive CH4 flux correlates strongly with temperature, suggesting that solar radiation is the primary driver of these CH4 emissions2. However, here we show that the slope of the temperature-CH4 flux relationship differs spatially, both within and among lakes. Hypothesizing that differences in microbiota could explain this heterogeneity, we compared site-specific CH4 emissions with underlying sediment microbial (metagenomic and amplicon), isotopic, and geochemical data across two post-glacial lakes in Northern Sweden. The temperature-associated increase in CH4 emissions was greater in lake middles--where methanogens were more abundant--than edges, and sediment microbial communities were distinct between lake edges and middles. Although CH4 emissions projections are typically driven by abiotic factors1, regression modeling revealed that microbial abundances, including those of CH4-cycling microorganisms and syntrophs that generate H2 for methanogenesis, can be useful predictors of porewater CH4 concentrations. Our results suggest that deeper lake regions, which currently emit less CH4 than shallower edges, could add substantially to overall CH4 emissions in a warmer Arctic with longer ice-free seasons and that future CH4 emission predictions from northern lakes may be improved by accounting for spatial variations in sediment microbiota.

microbiology↗

bioRxiv2020

Glacier ice archives fifteen-thousand-year-old viruses

While glacier ice cores provide climate information over tens to hundreds of thousands of years, study of microbes is challenged by ultra-low-biomass conditions, and virtually nothing is known about co-occurring viruses. Here we establish ultra-clean microbial and viral sampling procedures and apply them to two ice cores from the Guliya ice cap (northwestern Tibetan Plateau, China) to study these archived communities. This method reduced intentionally contaminating bacterial, viral, and free DNA to background levels in artificial-ice-core control experiments, and was then applied to two authentic ice cores to profile their microbes and viruses. The microbes differed significantly across the two ice cores, presumably representing the very different climate conditions at the time of deposition that is similar to findings in other cores. Separately, viral particle enrichment and ultra-low-input quantitative viral metagenomic sequencing from [~]520 and [~]15,000 years old ice revealed 33 viral populations (i.e., species-level designations) that represented four known genera and likely 28 novel viral genera (assessed by gene-sharing networks). In silico host predictions linked 18 of the 33 viral populations to co-occurring abundant bacteria, including Methylobacterium, Sphingomonas, and Janthinobacterium, indicating that viruses infected several abundant microbial groups. Depth-specific viral communities were observed, presumably reflecting differences in the environmental conditions among the ice samples at the time of deposition. Together, these experiments establish a clean procedure for studying microbial and viral communities in low-biomass glacier ice and provide baseline information for glacier viruses, some of which appear to be associated with the dominant microbes in these ecosystems. ImportanceThis study establishes ultra-clean microbial and viral sampling procedures for glacier ice, which complements prior in silico decontamination methods and expands, for the first time, the clean procedures to viruses. Application of these methods to glacier ice confirmed prior common microbiological findings for a new ice core climate record, and provides a first window into viral genomes and their ecology from glacier ice across two time horizons, and emphasizes their likely impact on abundant microbial groups. Together these efforts provide clean sampling approaches and foundational datasets that should enable simultaneous access to an archived virosphere in glacier ice.

ecology↗

bioRxiv2018

Soil viruses are underexplored players in ecosystem carbon processing

Rapidly thawing permafrost harbors ~30-50% of global soil carbon, and the fate of this carbon remains unknown. Microorganisms will play a central role in its fate, and their viruses could modulate that impact via induced mortality and metabolic controls. Because of the challenges of recovering viruses from soils, little is known about soil viruses or their role(s) in microbial biogeochemical cycling. Here, we describe 53 viral populations (vOTUs) recovered from seven quantitatively-derived (i.e. not multiple-displacement-amplified) viral-particle metagenomes (viromes) along a permafrost thaw gradient. Only 15% of these vOTUs had genetic similarity to publicly available viruses in the RefSeq database, and ~30% of the genes could be annotated, supporting the concept of soils as reservoirs of substantial undescribed viral genetic diversity. The vOTUs exhibited distinct ecology, with dramatically different distributions along the thaw gradient habitats, and a shift from soil-virus-like assemblages in the dry palsas to aquatic-virus-like in the inundated fen. Seventeen vOTUs were linked to microbial hosts (in silico), implicating viruses in infecting abundant microbial lineages from Acidobacteria, Verrucomicrobia, and Deltaproteoacteria, including those encoding key biogeochemical functions such as organic matter degradation. Thirty-one auxiliary metabolic genes (AMGs) were identified, and suggested viral-mediated modulation of central carbon metabolism, soil organic matter degradation, polysaccharide-binding, and regulation of sporulation. Together these findings suggest that these soil viruses have distinct ecology, impact host-mediated biogeochemistry, and likely impact ecosystem function in the rapidly changing Arctic.

microbiology↗

bioRxiv2017

Microbial Network, Phylogenetic Diversity And Community Membership In The Active Layer Across A Permafrost Thaw Gradient

Biogenic production and release of methane (CH4) from thawing permafrost has the potential to be a strong source of radiative forcing. We investigated changes in the active layer microbial community of three sites representative of distinct permafrost thaw stages at a palsa mire in northern Sweden. The palsa sites with intact permafrost, and low radiative forcing signature had a phylogenetically clustered community dominated by Acidobacteria and Proteobacteria. The bog with thawing permafrost and low radiative forcing signature was dominated by hydrogenotrophic methanogens and Acidobacteria, had lower alpha diversity, and midrange phylogenetic clustering, characteristic of ecosystem disturbance affecting habitat filtering, shifting from palsa-like to fen-like at the waterline. The fen had no underlying permafrost, and the highest alpha, beta and phylogenetic diversity, was dominated by Proteobacteria and Euryarchaeota, and was significantly enriched in methanogens. The mire microbial network was modular with module cores consisting of clusters of Acidobacteria, Euryarchaeota, or Xanthomonodales. Loss of underlying permafrost with associated hydrological shifts correlated to changes in microbial composition, alpha, beta, and phylogenetic diversity associated with a higher radiative forcing signature. These results support the complex role of microbial interactions in mediating carbon budget changes and climate feedback in response to climate forcing.

ecology↗