Biology subjects

Ellenbogen, J. B.

Publications and source records attributed to Ellenbogen, J. B..

6 recordsLinked to original sources

bioRxiv2026

Deciphering the microbial contributors to methane cycling in coastal wetlands

Although wetlands are increasingly recognized as important contributors to the global methane budget, the microorganisms and processes involved methane cycling are poorly characterized, particularly in coastal brackish and saline systems. Here, we investigated microbial and geochemical factors contributing to methane dynamics in three coastal wetlands with different salinities, dominant vegetation types, and soil chemical characteristics. These included a freshwater flotant marsh, a cypress swamp, and a mesohaline salt marsh. Specifically, we paired methane porewater concentrations, surface fluxes, geochemistry, and 16S rRNA gene sequencing to address how microbial community composition links to porewater concentrations and its potential effects on emissions. We found that porewater methane concentrations across sites were the highest in the swamp, followed by the salt marsh and the flotant marsh, and were explained by methanogen richness and abundance. While methane-cycling microbial communities were significantly structured by salinity, two microbial taxa (Methanosaeta and Methanomicrobiaceae) were present across all sites. Hydrogenotrophs were the most abundant methanogen functional group, with Methanomicrobiaceae and Methanobacterium discriminant among wetlands. In contrast, methanotroph functional types varied among wetlands. Type I dominated the freshwater flotant marsh, while the anaerobic methanotrophic archaea the saltwater marsh. These findings contribute to an enhanced understanding of the microbiological contributions to methane emissions from coastal wetlands. Scientific Significance Statement TopicThis study provides critical insights into the microbial and geochemical controls on methane emissions across coastal wetlands along a salinity gradient. Challenging the prevailing paradigm, methane porewater concentrations did not inversely correlate with salinity, as the swamp site with intermediate salinity exhibited the highest concentrations. Methanogen richness and abundance emerged as strong predictors of methane concentrations, while methanotroph richness had no predictive value. Two core methanogens, Methanosaeta and Methanomicrobiaceae, were consistently present across all wetland types. The findings highlight potential role of the water column as a biological methane filter, especially in saline environments. This study significantly advances the understanding of methane cycling in coastal wetlands by decoupling methane emissions from salinity gradients and emphasizing the role of microbial communities and local environmental factors. These insights are essential for refining biogeochemical models to forecast greenhouse gas emissions under sea-level rise and saltwater intrusion scenarios. Scientific Significance Statement OutletThis work integrates microbial ecology, geochemistry, and ecosystem structure to address interdisciplinary questions relevant to the limnological community. Here, we reveal how microbial community composition, rather than salinity alone, predicts methane emissions, offering a fresh perspective into carbon cycling in estuarine and coastal environments. The findings also provide critical insights for improving greenhouse gas emission models to predict climate change feedback from coastal areas.

microbiology↗

bioRxiv2025

Virus community response rewires methane-suppressed peat microcosm carbon metabolism

Human activities are accelerating permafrost thaw and subsequent methane emissions from increased microbial activity, prompting microbiome engineering efforts as an emissions mitigation strategy. We recently demonstrated that catechin amendment could drastically reduce methane emissions (>80%) in peat microcosms by enriching catechin-degrading prokaryotes that outcompeted methanogens for hydrogen. However, viral contributions to such microbiome-level responses remain unexplored and we hypothesized that viral dynamics could help shape the microbiome response as nutrient amendments may alter cellular physiology in ways that could induce lytic viral activity. Here, we performed virus ecogenomics analyses of the previously-studied time-resolved multi-omics data collected from catechin-amended peat microcosms. We conservatively identified 900 putatively lytic viral operational taxonomic units (vOTUs), with 41% predicted to infect active host genomes including the most transcriptionally active vOTUs predicted to infect key catechin-degrading genera (Clostridium and undescribed Bacillota JAGFXR01). Notably, a single JAGFXR01-targeting vOTU dominating the viral response (>40% of community viral transcription; 20-156-fold more abundant than its host), which we interpreted as induction resulting in intense lytic activity that could release catechin-degradation intermediates to other community members. Consistent with this, gene expression analysis revealed elevated catechin-intermediate degradation and hydrogenase signals in 34 additional polyphenol-degrading metagenome-assembled genomes. These findings support a model consistent with a viral shunt-like process that extends our previous prokaryote-centric model: viral lysis of fast-growing catechin degraders redistributes phenolic intermediates to diverse phenol-degrading taxa that sustain methane suppression via hydrogen consumption. Beyond carbon-cycling importance in this system, elucidating unintended virus-mediated responses to nutrient and prebiotic interventions will enable more predictable and effective microbiome engineering strategies across soil, ocean, and human ecosystems.

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

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↗

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↗