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Methane seeps were investigated in Hudson Canyon, the largest shelf-break canyon on the northern U.S. Atlantic Margin. The seeps investigated are located at or updip of the nominal limit of methane clathrate hydrate stability. The acoustic identification of bubble streams was used to guide water column sampling in a 32 km 2 region within the canyon's thalweg. By incorporating measurements of dissolved methane concentration with methane oxidation rates and current velocity into a steady state box model, the total emission of methane to the water column in this region was estimated to be 12 kmol methane per day (range: 6-24 kmol methane per day). These analyses suggest that the emitted methane is largely retained inside the canyon walls below 300 m water depth, and that it is aerobically oxidized to near completion within the larger extent of Hudson Canyon. Based on estimated methane emissions and measured oxidation rates, the oxidation of this methane to dissolved CO 2 is expected to have minimal influences on seawater pH.

Microbial aerobic oxidation is known to be a significant sink of marine methane (CH 4 ), contributing to the relatively minor atmospheric release of this greenhouse gas over vast stretches of the ocean. However, the chemical kinetics of aerobic CH 4 oxidation are not well established, making it difficult to predict and assess the extent that CH 4 is oxidized in seawater following seafloor release. Here we investigate the kinetics of aerobic CH 4 oxidation using mesocosm incubations of fresh seawater samples collected from seep fields in Hudson Canyon, U.S. Atlantic Margin and MC118, Gulf of Mexico to gain a fundamental chemical understanding of this CH 4 sink. The goals of this investigation were to determine the response or lag time following CH 4 release until more rapid oxidation begins, the reaction order, and the stoichiometry of reactants utilized (i.e., CH 4 , oxygen, nitrate, phosphate, trace metals) during CH 4 oxidation. The results for both Hudson Canyon and MC118 environments show that CH 4 oxidation rates sharply increased within less than one month following the CH 4 inoculation of seawater. However, the exact temporal characteristics of this more rapid CH 4 oxidation varied based on location, possibly dependent on the local circulation and biogeochemical conditions at the point of seawater collection. The data further suggest that methane oxidation behaves as a first-order kinetic process and that the reaction rate constant remains constant once rapid CH 4 oxidation begins. Plain Language SummaryIn and below the seafloor resides the largest global reservoir of methane, a potent greenhouse gas. Following the release of methane from the seafloor, a significant fraction dissolves in the overlying seawater and is oxidized by indigenous microorganisms, helping to prevent its atmospheric release. However, the timing and chemical requirements for this process to occur are not well established, making it difficult to predict and assess the efficiency of methane oxidation following seafloor release. This study systematically measured the chemical changes that are associated with aerobic methane oxidation in seawater using water collected from regions of active seafloor methane release along the U.S. Atlantic margin and the Gulf of Mexico. These results help to refine our understanding of how quickly and how much methane can typically be oxidized in seawater. Key Points:• Aerobic methane oxidation was investigated and showed that two moles of oxygen are not required to oxidize one mole of methane • After a lag time lasting days to weeks, methane was rapidly oxidized in a few days following first-order chemical kinetics • These results appear consistent between different oceanic environments, despite regional variabilities Supporting Information:• Supporting Information S1

Background Cyanobacteria maintain extensive repertoires of regulatory genes that are vital for adaptation to environmental stress. Some cyanobacterial genomes have been noted to encode diversity-generating retroelements (DGRs), which promote protein hypervariation through localized retrohoming and codon rewriting in target genes. Past research has shown DGRs to mainly diversify proteins involved in cell-cell attachment or viral-host attachment within viral, bacterial, and archaeal lineages. However, these elements may be critical in driving variation for proteins involved in other core cellular processes. Results Members of 31 cyanobacterial genera encode at least one DGR, and together, their retroelements form a monophyletic clade of closely-related reverse transcriptases. This class of retroelements diversifies target proteins with unique domain architectures: modular ligand-binding domains often paired with a second domain that is linked to signal response or regulation. Comparative analysis indicates recent intragenomic duplication of DGR targets as paralogs, but also apparent intergenomic exchange of DGR components. The prevalence of DGRs and the paralogs of their targets is disproportionately high among colonial and filamentous strains of cyanobacteria. Conclusion We find that colonial and filamentous cyanobacteria have recruited DGRs to optimize a ligand-binding module for apparent function in signal response or regulation. These represent a unique class of hypervariable proteins, which might offer cyanobacteria a form of plasticity to adapt to environmental stress. This analysis supports the hypothesis that DGR-driven mutation modulates signaling and regulatory networks in cyanobacteria, suggestive of a new framework for the utility of localized genetic hypervariation.