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  1. Abstract

    Cycloalkanes are abundant and toxic compounds in subsurface petroleum reservoirs and their fate is important to ecosystems impacted by natural oil seeps and spills. This study focuses on the microbial metabolism of methylcyclohexane (MCH) and methylcyclopentane (MCP) in the deep Gulf of Mexico. MCH and MCP are often abundant cycloalkanes observed in petroleum and will dissolve into the water column when introduced at the seafloor via a spill or natural seep. We conducted incubations with deep Gulf of Mexico (GOM) seawater amended with MCH and MCP at four stations. Within incubations with active respiration of MCH and MCP, we found that a novel genus of bacteria belonging to thePorticoccaceaefamily (Candidatus Reddybacter) dominated the microbial community. Using metagenome‐assembled genomes, we reconstructed the central metabolism ofCandidatus Reddybacter, identifying a novel clade of the particulate hydrocarbon monooxygenase (pmo) that may play a central role in MCH and MCP metabolism. Through comparative analysis of 174 genomes, we parsed the taxonomy of thePorticoccaceaefamily and found evidence suggesting the acquisition ofpmoand other genes related to the degradation of cyclic and branched hydrophobic compounds were likely key events in the ecology and evolution of this group of organisms.

     
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  2. Abstract

    Geological sources of methane (CH4), such as hydrocarbon seeps, are significant yet poorly constrained sources of CH4to seawater and the overlying atmosphere.We investigate the radiocarbon content (14C) and concentrations of dissolved CH4in surface waters from the Coal Oil Point seep field to test the hypothesis that geological sources can dominate the regional background signal of CH4. We find that surface waters with elevated CH4concentration were populated with seep‐CH4and that lower concentrations of CH4were well explained by mixing with the regional background of nongeological CH4. Substantial differences in concentration and14C‐CH4were observed over distances <5 km, demonstrating that surface currents mix background‐CH4into the seep field. These results indicate that even a prolific seep region like the Santa Barbara Basin exerts limited influence on the regional background of CH4in the surface layer but is a significant driver of patchiness in oceanic CH4biogeochemistry.

     
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  3. Abstract

    Microbial aerobic oxidation is known to be a significant sink of marine methane (CH4), contributing to the relatively minor atmospheric release of this greenhouse gas over vast stretches of the ocean. However, the chemical kinetics of aerobic CH4oxidation are not well established, making it difficult to predict and assess the extent that CH4is oxidized in seawater following seafloor release. Here we investigate the kinetics of aerobic CH4oxidation 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 CH4sink. The goals of this investigation were to determine the response or lag time following CH4release until more rapid oxidation begins, the reaction order, and the stoichiometry of reactants utilized (i.e., CH4, oxygen, nitrate, phosphate, trace metals) during CH4oxidation. The results for both Hudson Canyon and MC118 environments show that CH4oxidation rates sharply increased within less than one month following the CH4inoculation of seawater. However, the exact temporal characteristics of this more rapid CH4oxidation 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 CH4oxidation begins.

     
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  4. Abstract

    During aerobic oxidation of methane (CH4) in seawater, a process which mitigates atmospheric emissions, the12C‐isotopologue reacts with a slightly greater rate constant than the13C‐isotopologue, leaving the residual CH4isotopically fractionated. Prior studies have attempted to exploit this systematic isotopic fractionation from methane oxidation to quantify the extent that a CH4pool has been oxidized in seawater. However, cultivation‐based studies have suggested that isotopic fractionation fundamentally changes as a microbial population blooms in response to an influx of reactive substrates. Using a systematic mesocosm incubation study with recently collected seawater, here we investigate the fundamental isotopic kinetics of aerobic CH4oxidation during a microbial bloom. As detailed in a companion paper, seawater samples were collected from seep fields in Hudson Canyon, U.S. Atlantic Margin, and atop Woolsey Mound (also known as Sleeping Dragon) which is part of lease block MC118 in the northern Gulf of Mexico, and used in these investigations. The results from both Hudson Canyon and MC118 show that in these natural environments isotopic fraction for CH4oxidation follows a first‐order kinetic process. The results also show that the isotopic fractionation factor remains constant during this methanotrophic bloom once rapid CH4oxidation begins and that the magnitude of the fractionation factor appears correlated with the first‐order reaction rate constant. These findings greatly simplify the use of natural stable isotope changes in CH4to assess the extent that CH4is oxidized in seawater following seafloor release.

     
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    Fungi in terrestrial environments are known to play a key role in carbon and nitrogen biogeochemistry and exhibit high diversity. In contrast, the diversity and function of fungi in the ocean has remained underexplored and largely neglected. In the eastern tropical North Pacific oxygen minimum zone, we examined the fungal diversity by sequencing the internal transcribed spacer region 2 (ITS2) and mining a metagenome dataset collected from the same region. Additionally, we coupled 15N-tracer experiments with a selective inhibition method to determine the potential contribution of marine fungi to nitrous oxide (N2O) production. Fungal communities evaluated by ITS2 sequencing were dominated by the phyla Basidiomycota and Ascomycota at most depths. However, the metagenome dataset showed that about one third of the fungal community belong to early-diverging phyla. Fungal N2O production rates peaked at the oxic–anoxic interface of the water column, and when integrated from the oxycline to the top of the anoxic depths, fungi accounted for 18–22% of total N2O production. Our findings highlight the limitation of ITS-based methods typically used to investigate terrestrial fungal diversity and indicate that fungi may play an active role in marine nitrogen cycling. 
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  8. Book Chapter in © Springer Nature Switzerland AG 2019 T. J. McGenity (ed.), Microbial Communities Utilizing Hydrocarbons and Lipids: Members, Metagenomics and Ecophysiology, Handbook of Hydrocarbon and Lipid Microbiology, https://doi.org/10.1007/978-3-030-14785-3_12 
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