Determining the flux of methane into Hudson Canyon at the edge of methane clathrate hydrate stability

Author Posting. © American Geophysical Union, 2016. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry, Geophysics, Geosystems 17 (2016): 3882–3892, doi:10.1002/2016GC006421.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 km2 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 CO2 is expected to have minimal influences on seawater pH.National Science Foundation Grant Number: OCE-1318102; U.S. Department of Energy award Grant Numbers: DE-FE0013999 and NSF OCE-1352301, DOE-USGS, DE-FE0002911 and DE-FE00058062017-04-1

Investigations of Aerobic Methane Oxidation in Two Marine Seep Environments: Part 1—Chemical Kinetics

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 CH4 oxidation are not well established, making it difficult to predict and assess the extent that CH4 is oxidized in seawater following seafloor release. Here we investigate the kinetics of aerobic CH4 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 CH4 sink. The goals of this investigation were to determine the response or lag time following CH4 release until more rapid oxidation begins, the reaction order, and the stoichiometry of reactants utilized (i.e., CH4, oxygen, nitrate, phosphate, trace metals) during CH4 oxidation. The results for both Hudson Canyon and MC118 environments show that CH4 oxidation rates sharply increased within less than one month following the CH4 inoculation of seawater. However, the exact temporal characteristics of this more rapid CH4 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 CH4 oxidation begins

Investigations of Aerobic Methane Oxidation in Two Marine Seep Environments: Part 2—Isotopic Kinetics

During aerobic oxidation of methane (CH4) in seawater, a process which mitigates atmospheric emissions, the 12C‐isotopologue reacts with a slightly greater rate constant than the 13C‐isotopologue, leaving the residual CH4 isotopically fractionated. Prior studies have attempted to exploit this systematic isotopic fractionation from methane oxidation to quantify the extent that a CH4 pool 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 CH4 oxidation 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 CH4 oxidation follows a first‐order kinetic process. The results also show that the isotopic fractionation factor remains constant during this methanotrophic bloom once rapid CH4 oxidation 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 CH4 to assess the extent that CH4 is oxidized in seawater following seafloor release

Production of two highly abundant 2-methyl-branched fatty acids by blooms of the globally significant marine cyanobacteria Trichodesmium erythraeum

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gosselin, K. M., Nelson, R. K., Spivak, A. C., Sylva, S. P., Van Mooy, B. A. S., Aeppli, C., Sharpless, C. M., O’Neil, G. W., Arrington, E. C., Reddy, C. M., & Valentine, D. L. Production of two highly abundant 2-methyl-branched fatty acids by blooms of the globally significant marine cyanobacteria Trichodesmium erythraeum. ACS Omega, 6(35), (2021): 22803–22810, https://doi.org/10.1021/acsomega.1c03196.The bloom-forming cyanobacteria Trichodesmium contribute up to 30% to the total fixed nitrogen in the global oceans and thereby drive substantial productivity. On an expedition in the Gulf of Mexico, we observed and sampled surface slicks, some of which included dense blooms of Trichodesmium erythraeum. These bloom samples contained abundant and atypical free fatty acids, identified here as 2-methyldecanoic acid and 2-methyldodecanoic acid. The high abundance and unusual branching pattern of these compounds suggest that they may play a specific role in this globally important organism.This work was funded with grants from the National Science Foundation grants OCE-1333148, OCE-1333162, and OCE-1756254 and the Woods Hole Oceanographic Institution (IR&D). GCxGC analysis made possible by WHOI’s Investment in Science Fund

Early Career Aquatic Scientists Forge New Connections at Eco-DAS XV

A sense of kuleana (personal responsibility) in caring for the land and sea. An appreciation for laulima (many hands cooperating). An understanding of aloha ’āina (love of the land). The University of Hawai’i at Manoa hosted the 2023 Ecological Dissertations in Aquatic Sciences (Eco-DAS) program, which fostered each of these intentions by bringing together a team of early career aquatic ecologists for a week of networking and collaborative, interdisciplinary project development (Fig. 1)

Genomic Insights into the Marine Microbial Response to Oil Spills: Biogeographic Priming, Cryptic Hydrocarbon Cycling, and Substrate Specialization

Our seas, oceans, and coastal zones are under great stress and pollution, particularly by crude oil, which fuels the global economy. Subsurface petroleum reservoirs originate from geo-thermo-chemical reactions on biological debris over millions of years, resulting in a complex heterogeneous mixture of hydrocarbons, with major components consisting of alkanes with different chain lengths and branch points, cycloalkanes, branched cycloalkanes, mono-aromatic, and polycyclic aromatic hydrocarbons. Populations of hydrocarbon-degrading bacteria, including many species that cannot utilize other carbon sources, are present in all marine systems and play an important role in turnover and fate of these compounds. In this dissertation, the microbial response to petroleum components is probed in multiple environments to understand the role different chemical fractions play in eliciting different niches of oil consumers, and to identify factors controlling basal seed populations of hydrocarbon degraders poised to bloom to petroleum disasters. Through study in the subtropical North Atlantic Ocean, a cryptic long-chain alkane cycle has been confirmed, originating from cyanobacteria, dwarfing the quantity of other petroleum inputs to the ocean. In Chapter 1, I demonstrate waters in the mesopelagic underlying the photic zone hosted n-alkane degrading bacteria that bloomed rapidly when fed pentadecane, exhibiting exponential oxygen loss due to respiration within a week. Parallel experiments performed with sinking particles collected in situ from beneath the deep chlorophyll maximum—representing an export flux of particulate-phase pentadecane and its microbial consumers from the euphotic zone—exhibited similarly rapid bloom timing with pentadecane, but with greater oxygen decline. Notably, bloom onset timing for other petroleum compounds with no biogenic origin in the mesopelagic is an order of magnitude slower compared to biogenic alkanes. Metagenomic analyses of pentadecane blooms exposes the metabolic pathways used for pentadecane consumption. Analysis of gene abundance in unaltered seawater from oligotrophic settings reveals long-chain alkane genes are prolific in this setting and highlights the much lower prevalence of genes related to aromatic and short-chain alkane consumption. This work emphasizes the impact of phytoplankton-derived alkanes on the widespread abundance of long-chain alkane degraders in the ocean. The lack of biological hydrocarbon accumulation in the ocean points to their efficient consumption by networks of microorganisms. From analysis of sinking particles out of the photic zone, we know biogenic alkane consumption largely occurs in the sunlit ocean. To gain an understanding of which microbes consume biogenic alkanes we analyze the Tara Oceans global dataset for the presence of the alkane-1-monooxygenase gene (alkB). Stations within the North Atlantic subtropical gyre reveal alkB-related genes are abundant in the surface ocean and deep chlorophyll maximum and these genes are phylogenetically distinct from the ancestrally related delta-9 fatty acid desaturase and xylene monooxygenase. Notably, a dominant clade of alkB-like monooxygenases belongs to the globally abundant Marine Group II (MGII) archaea and is consistently present in all surface and DCM stations. This highly successful group of surface-ocean-dwelling archaea is known for a chemoorganoheterotrophic lifestyle targeting lipids, proteins and amino acids and can utilize photoheterotrophy, but a key role in biohydrocarbon cycling was unexpected as MGII archaea are not among the ~300 genera of bacteria and archaea previously identified as hydrocarbon degraders. Our further analysis of MGII genomes show alkane-1-monooxygenase genes are present in every genus of the MGII taxonomic order, and that other genes required to shunt alkane-derived carboxylic acids into central carbon metabolism are common among MGII. In the Gulf of Mexico (GOM), the biodegradation of n-pentane in the deep ocean was investigated along a gradient of natural seepage influences, illuminating the regional influence natural seeps have on priming petroleum hydrocarbon consumption. This seawater-soluble, volatile, compound is known to partition to the ocean’s interior following release from the seafloor and is abundant in petroleum reservoirs and refined products. The predominant member of the microbial community in n-pentane blooms is Cycloclasticus, and interestingly one Cycloclasticus ecotype favors the seep-ridden region of the GOM, whereas the other favors the open ocean environment far from natural seepage. Metagenomic analysis of the contrasting Cycloclasticus variants indicate the open ocean adapted variant encodes more general pathways for alkane consumption including short-chain alkanes, aromatics, and long-chain alkanes and possess pathways for dissimilatory nitrate reduction and thiosulfate oxidation, whereas the near-seep variant specializes solely on short-chain alkanes and aerobic metabolism. Metagenomic reconstruction and phylogenetic analysis of Cycloclasticus from publicly available sequence data reveals distinct strategies in hydrocarbon generalization and specialization for each major clade within the Cycloclasticus genera. Cycloalkanes are a major component of petroleum and many refined petroleum products. Methylated cycloalkane incubations using methylcyclohexane and methylcyclopentane were conducted in stations spanning a transect across the Gulf of Mexico. In three out of four stations, a single strain belonging to a novel genus within the Poricccaceae family and class Gammaproteobacteria bloomed to consume the methyl-cycloalkane provided within 18-21 days. Metagenomic reconstruction and analysis of the central carbon metabolism reveal a distinct strategy to oxidize cycloalkanes. A larger phylogenomic analysis reveals this methyl-cycloalkane consumer belongs to a monophyletic clade of genomes belonging to the same genera which originate from other environments with petroleum influence at subseafloor aquifers, hydrothermal vents, and petroleum mesocosms from a variety of marine sources. A defining feature of this clade is the presence of a divergent particulate hydrocarbon monooxygenase, which in the phylogenetic tree of the CuMMO enzyme superfamily (of ammonia and hydrocarbon monooxygenases) forms a distinct novel monophyletic clade from all other ammonia, methane, ethane, and ethylene monooxygenases

Investigations of Aerobic Methane Oxidation In Two Marine Seep Environments: Part 1 - Chemical Kinetics

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 CH4 oxidation are not well established, making it difficult to predict and assess the extent that CH4 is oxidized in seawater following seafloor release. Here we investigate the kinetics of aerobic CH4 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 CH4 sink. The goals of this investigation were to determine the response or lag time following CH4 release until more rapid oxidation begins, the reaction order, and the stoichiometry of reactants utilized (i.e., CH4, oxygen, nitrate, phosphate, trace metals) during CH4 oxidation. The results for both Hudson Canyon and MC118 environments show that CH4 oxidation rates sharply increased within less than one month following the CH4 inoculation of seawater. However, the exact temporal characteristics of this more rapid CH4 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 CH4 oxidation begins

Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria.

BackgroundCyanobacteria 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.ResultsMembers 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.ConclusionWe 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

Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria.

BackgroundCyanobacteria 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.ResultsMembers 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.ConclusionWe 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

Production of Two Highly Abundant 2-Methyl-Branched Fatty Acids by Blooms of the Globally Significant Marine Cyanobacteria Trichodesmium erythraeum.

The bloom-forming cyanobacteria Trichodesmium contribute up to 30% to the total fixed nitrogen in the global oceans and thereby drive substantial productivity. On an expedition in the Gulf of Mexico, we observed and sampled surface slicks, some of which included dense blooms of Trichodesmium erythraeum. These bloom samples contained abundant and atypical free fatty acids, identified here as 2-methyldecanoic acid and 2-methyldodecanoic acid. The high abundance and unusual branching pattern of these compounds suggest that they may play a specific role in this globally important organism