OCE-PRF Biological methane sinks in the deep ocean: Linking genomic diversity and ecophysiology in syntrophic methane-oxidizing consortia

California Institute Of Technology, Pasadena CA

Investigators

Abstract

This award is funded in whole or in part under the American Rescue Plan Act of 2021 (Public Law 117-2). Microbes are the workhorses behind every biogeochemical cycle, where they control the availability of different nutrients and other compounds. Methane seeps in the deep sea are one such system, where methane and other gases seep out from marine sediments, and they account for a significant fraction of the global methane budget. At these seeps, diverse microbial communities thrive and can metabolize the methane released from the seafloor. However, little is known about the specific forces and processes controlling the distribution of these microbes and their ability to perform their important metabolisms. This project investigates the links between microbial diversity and the environment in a methane-degrading system, focusing on consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). The results will clarify the fundamental determinants of microbial community composition and improve understanding of marine methane dynamics. The proposed work will engage the broader public in several ways. Undergraduate students from backgrounds underrepresented in STEM will be mentored over a summer research project through the Caltech WAVE program. The researcher will also partner with local elementary, high school, and undergraduate-serving programs through the Caltech CTL&O office and the Center for Environmental Microbial Interactions (CEMI) to encourage student participation in research opportunities related to the proposed work. Through existing collaborations between the ANSEP program and the Orphan lab, the researcher will participate in the ANSEP middle school Career Exploration in Marine Science program. This project aims to identify 1) how the genomic diversity of ANME/SRB partners is structured across scales ranging from individual consortia to environmental gradients and 2) the genes and ecological factors determining ecological outcomes for each partner. Samples containing ANME/SRB consortia have been previously obtained from methane seep sediments with a range of biogeochemical parameters. Individual consortia will be sorted and sequenced to produce high-quality metagenome-assembled genomes (MAGs) for comparative analysis to reveal the strain-level composition of individual consortia and the proportion of each strain across different sediment samples to different methane seeps. Functional profiling of MAGs will then allow comparative genomic approaches to identify the genes most likely to be critical to each population’s success in each environment. Predictions will be experimentally tested by a range of laboratory experiments including nanoscale secondary ion mass spectroscopy (NanoSIMS), bioorthogonal non-canonical amino acid tagging (BONCAT), and fluorescence in situ hybridization (FISH). The genes and associated ecophysiology identified here will result in greater understanding of the factors controlling methane at seep- and basin-scales, and more broadly, the generalizable principles of how microbes adapt to heterogeneous environments. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.