Biology subjects

Hoyt, D. W.

Publications and source records attributed to Hoyt, D. W..

11 recordsLinked to original sources

bioRxiv2025

Dissolved inorganic carbon supports robust anabolism and methanogenesis in actively serpentinizing rocks

Serpentinites, hydrated ultramafic rocks that produce [hyper]alkaline, reducing, H2-rich groundwaters, host subsurface microbial ecosystems. Though in the presence of enormous reducing power, life in serpentinizing systems is limited by oxidant and carbon availability. The forms of carbon that support the serpentinite-hosted microbiome, and their rates of biological assimilation, remain poorly understood. In this work, we quantify the habitability of subsurface environments shaped by serpentinization and examine the forms of carbon that support their microbial constituents, focusing specifically on dissolved inorganic carbon, acetate, and formate. We access reacted groundwater from Earths largest terrestrial serpentinizing body and measure carbon assimilation at the single-cell level. Across all conditions, we consistently observe robust assimilation of dissolved inorganic carbon into microbial biomass. Notably, we find that dissolved inorganic carbon supports the majority of methanogenic activity in the system, even at hyperalkaline conditions (pH > 11). Inferred bioenergetic fluxes suggest that rates of biological hydrogen-consumption and methanogenesis are relevant at the landscape scale. We identify a strong potential for the microbiome to be stimulated by increases in H2 and CO2, a finding with implications for the search for life on other planetary bodies and for the growing deployment of fluid injection technologies in ultramafic rocks, such as geological hydrogen production or carbon mineralization. Significance StatementWhen iron-rich rocks interact with water, they undergo a "serpentinization" reaction that results in the production of H2 and [hyper]alkaline fluids. This abiotic process does not operate alone but rather supports and interacts with microbial life. However, it remains unknown to what extent the stressors of subsurface life under [hyper]alkaline conditions may limit microbial activity. In this work, we quantify the rates at which microorganisms transform different carbon sources across a range of serpentinizing conditions. We find that serpentinizing rocks host a remarkably robust microbiome, a finding that motivates the targeting of serpentinizing systems for life detection efforts in our solar system, as well as further analysis of efforts to leverage serpentinites for industrial-scale geological H2 and carbon drawdown projects.

microbiology↗

bioRxiv2024

Coordinated organic and inorganic nitrogen transformations fuel soil microbial blooms and increase nitrogen retention during snowmelt

Snowmelt in high-elevation watersheds triggers a microbial bloom and crash that affects nitrogen (N) export. Predicting watershed N dynamics as snowpack declines is a challenge because the mechanisms that underlie this microbial bloom and crash are uncertain. Using a multi-omic approach, we show that the dynamic molecular properties of dissolved organic N, plus high gene expression for peptidases that recycle microbial biomass, suggested that microbial turnover provided N for biosynthesis during the microbial bloom. Amino acid fermentation by Bradyrhizobia produced organic acids that also fueled denitrification and dissimilatory nitrate reduction to ammonia (DNRA) during snowmelt. Nitrification in spring was driven by Spring-Adapted Nitrososphaerales, which utilized ammonium derived from osmolyte degradation by Winter-Adapted Solirubrobacteraceae. High DNRA gene expression after snowmelt suggested significant nitrate retention, increasing watershed N retention potential. However, declining snowfall may compromise microbial regulation of soil N retention, with implications for watershed N export.

microbiology↗

bioRxiv2024

Polyphenol rewiring of the microbiome reduces methane emissions

Methane mitigation is regarded as a critical strategy to combat the scale of global warming. Currently, about 40% of methane emissions originate from microbial sources, which is causing strategies to suppress methanogens--either through direct toxic effects or by diverting their substrates and energy--to gain traction. Problematically, current microbial methane mitigation knowledge derives from rumen studies and lacks detailed microbiome-centered insights, limiting translation across ecosystems. Here we utilize genome-resolved metatranscriptomes and metabolomes to assess the impact of a proposed methane inhibitor, catechin, on greenhouse gas emissions for high-methane- emitting peatlands. In microcosms, catechin drastically reduced methane emissions by 72-84% compared to controls. Longitudinal sampling allowed for reconstruction of a novel catechin degradation pathway involving Actinomycetota and Clostridium, which break down catechin into smaller phenolic compounds within the first 21 days, followed by degradation of phenolic compounds by Pseudomonas_E from days 21 to 35. These genomes also co-expressed hydrogen-uptake genes, suggesting that hydrogenases may act as a hydrogen sink during catechin degradation, depriving methanogens of substrates. This was supported by decreased gene expression in hydrogenotrophic and hydrogen-dependent methylotrophic methanogens under catechin treatment. We also saw reduced gene expression from genomes inferred to be functioning syntrophically with hydrogen-utilizing methanogens. We propose that catechin metabolic redirection effectively starves hydrogen-utilizing methanogens, offering a potent avenue for curbing methane emissions across diverse environments including ruminants, landfills, and constructed or managed wetlands.

microbiology↗

bioRxiv2024

Spatial evidence of cryptic methane cycling and methylotrophic metabolisms along a land-ocean transect in a California coastal wetland

Methylotrophic methanogenesis in the sulfate reduction zone of coastal and marine sediments couples with anaerobic methane oxidation (AOM), forming the cryptic methane cycle. This study provides evidence of cryptic methane cycling in the sulfate-reducing zone across a land-ocean transect of four stations--two brackish, one marine, and one hypersaline--within the Carpinteria Salt Marsh Reserve (CSMR), Southern California, USA. The top 20 cm of sediment from the transect underwent geochemical and molecular (16S rRNA) analyses, in-vitro methanogenesis incubations, and radiotracer incubations using 35S-SO4, 14C-mono-methylamine, and 14C-CH4. Sediment methane concentrations were consistently low (3 to 28 {micro}M) except at the marine station, where they increased with depth (max 665 {micro}M). Methanogenesis from mono-methylamine was detected throughout the sediment at all stations with estimated rates ranging between 0.14 and 3.8 nmol cm-3 d-1. 16S rRNA analysis identified methanogenic archaea capable of producing methane from methylamines in sediment where methanogenesis was found to be active. Metabolomic analysis of porewater showed mono-methylamine was mostly undetectable (<3 {micro}M) or present in trace amounts (<10 {micro}M) suggesting rapid metabolic turnover. In-vitro methanogenesis incubations showed no linear methane buildup, suggesting a process limiting methane emissions. AOM activity, measured with 14C-CH4, overlapped with methanogenesis from mono-methylamine activity at all stations, with rates ranging from 0.03 to 19.4 nmol cm-3 d-1. Porewater geochemical analysis showed the CSMR sediments are rich in sulfate and iron. Porewater sulfate concentrations (9-91 mM) were non-limiting across the transect, which support members of sulfate-reducing bacteria and likely responsible for sulfate reduction activity (1.5-2,506 nmol cm-3 d-1) at all stations in the CSMR. Porewater sulfide and iron (II) profiles indicated that the sediment transitioned from a predominantly iron-reducing environment at the two brackish stations to a predominantly sulfate-reducing environment at the marine and hypersaline station. AOM activity was likely coupled to sulfate and possibly iron reduction, coinciding with the presence of anaerobic methanotrophs and bacteria involved in these reductions. 16S rRNA analysis identified anaerobic methanotrophs at the marine and hypersaline stations, where they coexisted with putative methanogens, suggesting both groups, or methanogens alone, may be involved in cryptic methane cycling, preventing significant methane buildup in the sulfate-reducing zone. Differences in rate constants from 14C radiotracer incubations suggest a non-methanogenic process oxidizing mono-methylamine to inorganic carbon, likely mediated by sulfate-reducing bacteria. Understanding the potential competition of sulfate reducers with methanogens for mono-methylamine needs further investigation as it might be another important process responsible for low methane emissions in salt marshes.

microbiology↗

bioRxiv2024

Rendering the metabolic wiring powering wetland soil methane production

Accounting for only 8% of Earths land coverage, freshwater wetlands remain the foremost contributor to global methane emissions. Yet the microorganisms and processes underlying methane emissions from wetland soils remain poorly understood. Over a five-year period, we surveyed the microbial membership and in situ methane measurements from over 700 samples in one of the most prolific methane-emitting wetlands in the United States. We constructed a catalog of 2,502 metagenome-assembled genomes (MAGs), with more than half of the 70 bacterial and archaeal phyla sampled containing novel lineages. Integration of these data with 133 soil metatranscriptomes provided a genome-resolved view of the biogeochemical specialization and versatility expressed over wetland soil spatial and temporal gradients. Centimeter-scale depth differences best explained patterns of microbial community structure and transcribed functionalities, even more so than land coverage or temporal information. Moreover, while extended flooding restructured soil redox, this perturbation failed to reconfigure the transcriptional profiles of methane cycling microorganisms, contrasting with theoretical expected responses to hydrological perturbations. Co-expression analyses coupled to depth resolved methane measurements exposed the metabolisms and trophic structures most predictive of methane hotspots. Mapping the spatiotemporal transcriptional patterns on this compendium of biogeochemically classified soil derived genomes begins to untangle the microbial carbon, energy, and nutrient processing contributing to wetland methane production. ImportanceSoil microbial ecology is increasingly recognized as essential to climate mitigation, but realizing its full potential requires shifting from static genome inventories to dynamic assessments of microbial activity. This study shows that methane-cycling microbes exhibit stable, depth-stratified expression patterns, even in response to major redox and flooding shifts, undermining assumptions that water-table manipulations common in wetland management can alone reduce methanogenesis. Instead, methane cycling is shaped by spatially organized, transcriptionally active networks involving not only methanogens but also methanotrophs, fermenters, and iron reducers. These findings expose the limitations of genome-only models and highlight the need for soil diagnostics that capture in situ activity. Together, we provide a foundation for developing activity-based microbiome tools, embedding microbial functions into Earth system models, and designing interventions that move beyond "single lever" strategies and instead work with the structure and dynamics of microbial communities as complex, layered systems.

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

Oligosaccharide production and signaling correlate with delayed flowering in an Arabidopsis genotype grown and selected in high

Since industrialization began, atmospheric CO2 ([CO2]) has increased from 270 to 415 ppm and is projected to reach 800-1000 ppm this century. Some Arabidopsis ecotypes delayed flowering in elevated [CO2] relative to current [CO2], while others showed no change or accelerations. To predict genotype-specific flowering behaviors, we must understand the mechanisms driving flowering response to rising [CO2]. [CO2] changes alter photosynthesis and carbohydrates in C3 plants. Plants sense carbohydrate levels and exogenous carbohydrate application influences flowering time and flowering transcript levels. We asked how organismal changes in carbohydrates and transcription correlate with changes in flowering time under elevated [CO2]. We used a genotype (SG) of Arabidopsis that was selected for high fitness at elevated [CO2] (700 ppm). SG delays flowering under elevated [CO2] (700 ppm) relative to current [CO2] (400 ppm). We compared SG to a closely related control genotype (CG) that shows no [CO2]- induced flowering change. We compared metabolomic and transcriptomic profiles in these genotypes at current and elevated [CO2] to assess correlations with flowering in these conditions. While both genotypes altered carbohydrates in response to elevated [CO2], SG had higher levels of sucrose than CG and showed a stronger increase in glucose and fructose in elevated [CO2]. Both genotypes demonstrated transcriptional changes, with CG increasing genes related to fructose 1,6-bisphosphate breakdown, amino acid synthesis, and secondary metabolites; and SG decreasing genes related to starch and sugar metabolism, but increasing genes involved in oligosaccharide production and sugar modifications. Genes associated with flowering regulation within the photoperiod, vernalization, and meristem identity pathways were altered in these genotypes. Elevated [CO2] may act through carbohydrate changes to influence transcription in both genotypes and delayed flowering in SG. Changes in the oligosaccharide pool may contribute to delayed flowering in SG. This work extends the literature exploring genotypic-specific flowering responses to elevated [CO2].

plant biology↗

bioRxiv2022

Targeted curation of the gut microbial gene content modulating human cardiovascular disease

Despite the promise of the gut microbiome to forecast human health, few studies expose the microbial functions underpinning such predictions. To comprehensively inventory gut microorganisms and their gene content that control trimethylamine induced cardiovascular disease, we mined over 200,000 gut-derived genomes from cultivated and uncultivated microbial lineages. Creating MAGICdb (Methylated Amine Gene Inventory of Catabolism database), we designated an atherosclerotic profile for 6,341 microbial genomes that encoded metabolisms associated with heart disease. We used MAGICdb to evaluate diverse human fecal metatranscriptome and metaproteome datasets, demonstrating how this resource eases the recovery of methylated amine gene content previously obscured in microbiome datasets. From the feces of healthy and diseased subjects, we show MAGICdb gene markers predicted cardiovascular disease as effectively as traditional blood diagnostics. This functional microbiome catalog is a public, exploitable resource, enabling a new era of microbiota-based therapeutics.

genomics↗

bioRxiv2022

Genome-resolved metaproteomics decodes the microbial and viral contributions to coupled carbon and nitrogen cycling in river sediments

Rivers have a significant role in global carbon and nitrogen cycles, serving as a nexus for nutrient transport between terrestrial and marine ecosystems. Although rivers have a small global surface area, they contribute substantially to global greenhouse gas emissions through microbially mediated processes within the river hyporheic zone. Despite this importance, microbial roles in these climatically relevant systems are mostly inferred from 16S rRNA amplicon surveys, which are not sufficiently resolved to inform biogeochemical models. To survey the metabolic potential and gene expression underpinning carbon and nitrogen biogeochemical cycling in river sediments, we collected an integrated dataset of over 30 metagenomes, metaproteomes, and paired metabolomes. We reconstructed over 500 microbial metagenome assembled genomes (MAGs), which we dereplicated into 55 unique genomes spanning 12 bacterial and archaeal phyla. We also reconstructed 2482 viral genomic contigs, which were dereplicated into 111 viral MAGs >10kb in size. As a result of integrating gene expression data with geochemical and metabolite data, we created a conceptual model that uncovers new roles for microorganisms in organic matter decomposition, carbon sequestration, nitrogen mineralization, nitrification, and denitrification. Integrated through shared resource pools of ammonium, carbon dioxide, and inorganic nitrogen we show how these metabolic pathways could ultimately contribute to carbon dioxide and nitrous oxide fluxes from hyporheic sediments. Further, by linking viral genomes to these active microbial hosts, we provide some of the first insights into viral modulation of river sediment carbon and nitrogen cycling. ImportanceHere we created HUM-V (Hyporheic Uncultured Microbial and Viral), an annotated microbial and viral genome catalog that captures the strain and functional diversity encoded in river sediments. Demonstrating its utility, this genomic inventory encompasses multiple representatives of the most dominant microbial and archaeal phyla reported in river sediments and provides novel viral genomes that can putatively infect these. Furthermore, we used HUM-V to recruit gene expression data to decipher the functional activities of these genomes and reconstruct their active roles in river sediment biogeochemical cycling. We show the power of genome resolved, multi-omics to uncover the organismal interactions and chemical handoffs shaping an intertwined carbon and nitrogen metabolic network and create a framework that can be extended to other river sediments. The accessible microbial and viral genomes in HUM-V will serve as a community resource to further advance more untargeted, activity-based measurements in these and related freshwater terrestrial-aquatic ecosystems.

microbiology↗

bioRxiv2021

ORT: A workflow linking genome-scale metabolic models with reactive transport codes

MotivationNutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed. ResultsWe propose a workflow ( Omics to Reactive Transport - ORT) for utilizing metagenomic and environmental data to describe the effect of microbiological processes in macroscopic reactive transport models. This workflow utilizes and couples two open-source software packages: KBase (a software platform for systems biology) and PFLOTRAN (a reactive transport modeling code). We describe the architecture of ORT and demonstrate an implementation using metagenomic and geochemical data from a river system. Our demonstration uses microbiological drivers of nitrification and denitrification to predict nitrogen cycling patterns which agree with those provided with generalized stoichiometries. While our example uses data from a single measurement, our workflow can be applied to spatiotemporal metagenomic datasets to allow for iterative coupling between KBASE and PFLOTRAN. Availability and ImplementationInteractive models available at https://pflotranmodeling.paf.subsurfaceinsights.com/pflotran-simple-model/. Microbiological data available at NCBI via BioProject ID PRJNA576070. ORT Python code available at https://github.com/subsurfaceinsights/ort-kbase-to-pflotran. KBase narrative available at https://narrative.kbase.us/narrative/71260 or static narrative (no login required) at https://kbase.us/n/71260/258 Contactrebecca.rubinstein@subsurfaceinsights.com or roelof.versteeg@subsurfaceinsights.com Supplementary informationSupplementary data are available online.

bioinformatics↗

bioRxiv2019

Switchgrass Rhizosphere Metabolite Chemistry Driven by Nitrogen Availability

Plants and soil microorganisms interact closely in the rhizosphere where plants may exchange carbon (C) for functional benefits from the microbial community. For example, the bioenergy crop, switchgrass (Panicum virgatum) is thought to exchange root-exuded C for nitrogen (N) fixed by diazotrophs (free-living N-fixers). However, this interaction is not well characterized and it is not known how or if switchgrass responds to diazotrophs or their activity. To explore this question, we assessed rhizosphere metabolite chemistry of switchgrass grown in a hydroponic system under two N levels and under inoculated or uninoculated conditions. We found switchgrass root exudate chemistry to be more responsive to N availability than to diazotroph presence. Total metabolite concentrations were generally greater under high N versus low N and unaffected by inoculation. Examination of rhizosphere chemical fingerprints indicates metabolite chemistry was also driven strongly by N availability with a greater relative abundance of carbohydrates under high N and greater relative abundance of organic acids under low N. We also found evidence of changes in rhizosphere chemical fingerprints by inoculation treatment suggesting a potential for switchgrass to respond or even recruit diazotrophs. However, we found little evidence of N treatment and inoculation interaction effects which suggests switchgrass response to diazotroph presence is not mediated by N availability.

ecology↗