Biology subjects

McGivern, B. B.

Publications and source records attributed to McGivern, B. B..

6 recordsLinked to original sources

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

CAMPER: curated annotations for profiling microbial polyphenol metabolic potential

SummaryPolyphenols are diverse and abundant carbon sources across ecosystems-having important roles in host-associated and terrestrial systems alike. However, the microbial genes encoding polyphenol metabolic enzymes are poorly represented in commonly used annotation databases, limiting widespread surveying of this metabolism. Here we present CAMPER, a tool that combines custom annotation searches with database-derived searches to both annotate and summarize polyphenol metabolism genes for a wide audience. With CAMPER, users will identify potential polyphenol-active genes and genomes to more broadly understand microbial carbon cycling in their datasets. Availability and ImplementationCAMPER is implemented in Python and is published under the GNU General Public License Version 3. It is available as both a standalone tool and as a database in DRAM v.1.5+. The source code and full documentation is available on GitHub at https://github.com/WrightonLabCSU/CAMPER.

bioinformatics↗

bioRxiv2023

A functional microbiome catalog crowdsourced from North American rivers

Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires understanding the spatial drivers of river microbiomes. However, the unifying microbial processes governing river biogeochemistry are hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we employed a community science effort to accelerate the sampling, sequencing, and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). This resource profiled the identity, distribution, function, and expression of thousands of microbial genomes across rivers covering 90% of United States watersheds. Specifically, GROWdb encompasses 1,469 microbial species from 27 phyla, including novel lineages from 10 families and 128 genera, and defines the core river microbiome for the first time at genome level. GROWdb analyses coupled to extensive geospatial information revealed local and regional drivers of microbial community structuring, while also presenting a myriad of foundational hypotheses about ecosystem function. Building upon the previously conceived River Continuum Concept1, we layer on microbial functional trait expression, which suggests the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures2, 3 so that it can be widely accessed across disciplines for watershed predictive modeling and microbiome-based management practices.

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↗

bioRxiv2021

Variation in root exudate composition influences soil microbiome membership and function

Root exudation is one of the primary processes that mediate interactions between plant roots, microorganisms, and the soil matrix. Previous research has shown that plant root exudate profiles vary between species and genotypes which can likely support different microbial associations. Here, utilizing distinct sorghum genotypes as a model system, we characterized the chemical heterogeneity between root exudates and the effects of that variability on soil microbial membership and metabolisms. Distinct exudate chemical profiles were quantified and used to formulate synthetic root exudate treatments, a High Organic acid Treatment (HOT) and a High Sugar Treatment (HST). Root exudate treatments were added to laboratory soil reactors and 16S rRNA gene profiling illustrated distinct microbial membership in response to HST or HOT amendments. Alpha and beta diversity metrics were significantly different between treatments, (Shannons, p < 0.0001, mrpp = 0.01, respectively). Exometabolite production was highest in the HST, with increased production of key organic acids, non-proteinogenic amino acids, and three plant growth-promoting phytohormones (benzoic acid, salicylic acid, indole-3-acetic acid), suggesting plant-derived sugars fuel microbial carbon metabolism and contribute to phytohormone production. Linking the metabolic capacity of metagenome-assembled genomes in the HST to the exometabolite patterns, we identified potential plant growth-promoting microorganisms that could produce these phytohormones. Our findings emphasize the tractability of high-resolution multi-omics tools to investigate soil microbiomes, opening the possibility of manipulating native microbial communities to improve specific soil microbial functions and enhance crop production. ImportanceUnderstanding interactions between plant root exudates and the soil microbiome provides an avenue for a more comprehensive appreciation for how plant roots modulate their microbial counterparts to promote an environment favorable to plant fitness. Although these dynamics are appreciated as indispensable, mechanisms controlling specific rhizobiome membership and complexity are not fully understood. In this study, we investigate how variability in root exudation, modeled after differences observed between distinct sorghum genotypes, contributes to altered microbial membership and metabolisms. The results demonstrate how microbial diversity is influenced by root exudates of differing chemical composition and how changes in microbial membership correspond to modifications in carbon utilization and enhance production of plant-relevant metabolites. Our findings suggest carbon substrate preferences among bacteria in semi-arid climate soils and mechanisms for root exudate utilization. These findings provide new information on plant-soil environments useful for the development of efficient and precise microbiota management strategies in agricultural systems.

plant biology↗

bioRxiv2020

DRAM for distilling microbial metabolism to automate the curation of microbiome function

Microbial and viral communities transform the chemistry of Earths ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles, and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.

microbiology↗