Environmental Science and Engineering Seminar

Environmental sequencing allows us to observe the vast majority of microbial diversity that remains unculturable. Cohort-level analyses go further by integrating these surveys across space and time to identify groups of microbes that share environmental conditions and dispersal pathways and that function collectively through competition, cooperation, syntrophy, and genetic exchange. Here, I will discuss two examples of cohort-level analyses. First, I will discuss a high-resolution sampling effort along a South Pacific transect from Easter Island to 70°S that captured a broad gradient in ventilation age, ranging from newly formed Antarctic Bottom Water to interior waters that have circulated for more than a millennium. We found that microbial genomes cluster into six spatial cohorts that are not only delineated by depth, but also large-scale circulatory features. Distinct functional signatures also emerged across these circulation-driven zones. For example, genes for light harvesting and iron uptake dominated in surface waters, while adaptations for cold, high pressure, and anaerobic metabolism characterized deep and ancient waters. Antarctic Bottom Water communities also carried hallmarks of rapid genetic exchange, suggesting horizontal gene transfer may help microbes adapt as they sink into the deep ocean. In the second case, we collected metagenomes, metatranscriptomes, and gas flux measurements from Northern California rice paddy soils throughout a growing season to investigate the microbial underpinnings of methane emissions from rice cultivation. We found strong stratification by soil horizon, with rhizosphere and upper-soil cohorts varying with seasonal shifts in moisture and plant development, while deep soil communities remained stable over time. Most methanogenesis was hydrogenotrophic, and hydrogen appeared to be a central currency, with diverse hydrogenases encoded across soil compartments. Deep sequencing also revealed novel genomic features, such as a 200-heme multiheme cytochrome encoded by a deep soil methanotroph, and a "mini-borg" extrachromosomal element fully incorporated into a Methanoperedens nitroreducens genome. Overall, cohort-level surveys can expose the abiotic drivers of microbial activity by tracking how communities partition across space and time and contextualizing genomes within the consortia that mediate their metabolic potential.