Publications

2012
Beinart RA, Sanders JG, Faure B, Sylva SP, Lee RW, Becker EL, Gartman A, Luther GW, Seewald JS, Fisher CR, et al. Evidence for the role of endosymbionts in regional-scale habitat partitioning by hydrothermal vent symbioses. Proceedings of the National Academy of Sciences of the United States of America. 2012;109 :E3241-E3250.Abstract

Deep-sea hydrothermal vents are populated by dense communities of animals that form symbiotic associations with chemolithoautotrophic bacteria. To date, our understanding of which factors govern the distribution of host/symbiont associations (or holobionts) in nature is limited, although host physiology often is invoked. In general, the role that symbionts play in habitat utilization by vent holobionts has not been thoroughly addressed. Here we present evidence for symbiont-influenced, regional-scale niche partitioning among symbiotic gastropods (genus Alviniconcha) in the Lau Basin. We extensively surveyed Alviniconcha holobionts from four vent fields using quantitative molecular approaches, coupled to characterization of high-temperature and diffuse vent-fluid composition using gastight samplers and in situ electrochemical analyses, respectively. Phylogenetic analyses exposed cryptic host and symbiont diversity, revealing three distinct host types and three different symbiont phylotypes (one epsilon-proteobacteria and two gamma-proteobacteria) that formed specific associations with one another. Strikingly, we observed that holobionts with epsilon-proteobacterial symbionts were dominant at the northern fields, whereas holobionts with gamma-proteobacterial symbionts were dominant in the southern fields. This pattern of distribution corresponds to differences in the vent geochemistry that result from deep subsurface geological and geothermal processes. We posit that the symbionts, likely through differences in chemolithoautotrophic metabolism, influence niche utilization among these holobionts. The data presented here represent evidence linking symbiont type to habitat partitioning among the chemosynthetic symbioses at hydrothermal vents and illustrate the coupling between subsurface geothermal processes and niche availability.

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Dilly GF, Young CR, Lane WS, Pangilinan J, Girguis PR. Exploring the limit of metazoan thermal tolerance via comparative proteomics: thermally induced changes in protein abundance by two hydrothermal vent polychaetes. Proceedings of the Royal Society B-Biological Sciences. 2012;279 :3347-3356.Abstract

Temperatures around hydrothermal vents are highly variable, ranging from near freezing up to 300 degrees C. Nevertheless, animals thrive around vents, some of which live near the known limits of animal thermotolerance. Paralvinella sulfincola, an extremely thermotolerant vent polychaete, and Paralvinella palmiformis, a cooler-adapted congener, are found along the Juan de Fuca Ridge in the northwestern Pacific. We conducted shipboard high-pressure thermotolerance experiments on both species to characterize the physiological adaptations underlying P. sulfincola's pronounced thermotolerance. Quantitative proteomics, expressed sequence tag (EST) libraries and glutathione assays revealed that P. sulfincola (i) exhibited an upregulation in the synthesis and recycling of glutathione with increasing temperature, (ii) downregulated nicotinamide adenine dinucleotide (NADH) and succinate dehydrogenases (key enzymes in oxidative phosphorylation) with increasing temperature, and (iii) maintained elevated levels of heat shock proteins (HSPs) across all treatments. In contrast, P. palmiformis exhibited more typical responses to increasing temperatures (e. g. increasing HSPs at higher temperatures). These data reveal differences in how a mesotolerant and extremely thermotolerant eukaryote respond to thermal stress, and suggest that P. sulfincola's capacity to mitigate oxidative stress via increased synthesis of antioxidants and decreased flux through the mitochondrial electron transport chain enable pronounced thermotolerance. Ultimately, oxidative stress may be the key factor in limiting all metazoan thermotolerance.

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Nyholm SV, Song PF, Dang JN, Bunce C, Girguis PR. Expression and Putative Function of Innate Immunity Genes under in situ Conditions in the Symbiotic Hydrothermal Vent Tubeworm Ridgeia piscesae. Plos One. 2012;7 (6).Abstract

The relationships between hydrothermal vent tubeworms and sulfide-oxidizing bacteria have served as model associations for understanding chemoautotrophy and endosymbiosis. Numerous studies have focused on the physiological and biochemical adaptations that enable these symbioses to sustain some of the highest recorded carbon fixation rates ever measured. However, far fewer studies have explored the molecular mechanisms underlying the regulation of host and symbiont interactions, specifically those mediated by the innate immune system of the host. To that end, we conducted a series of studies where we maintained the tubeworm, Ridgeia piscesae, in high-pressure aquaria and examined global and quantitative changes in gene expression via high-throughput transcriptomics and quantitative real-time PCR (qPCR). We analyzed over 32,000 full-length expressed sequence tags as well as 26 Mb of transcript sequences from the trophosome (the organ that houses the endosymbiotic bacteria) and the plume (the gas exchange organ in contact with the free-living microbial community). R. piscesae maintained under conditions that promote chemoautotrophy expressed a number of putative cell signaling and innate immunity genes, including pattern recognition receptors (PRRs), often associated with recognizing microbe-associated molecular patterns (MAMPs). Eighteen genes involved with innate immunity, cell signaling, cell stress and metabolite exchange were further analyzed using qPCR. PRRs, including five peptidoglycan recognition proteins and a Toll-like receptor, were expressed significantly higher in the trophosome compared to the plume. Although PRRs are often associated with mediating host responses to infection by pathogens, the differences in expression between the plume and trophosome also implicate similar mechanisms of microbial recognition in interactions between the host and symbiont. We posit that regulation of this association involves a molecular "dialogue'' between the partners that includes interactions between the host's innate immune system and the symbiont.

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Perner M, Gonnella G, Hourdez S, Bohnke S, Kurtz S, Girguis P. In situ chemistry and microbial community compositions in five deep-sea hydrothermal fluid samples from Irina II in the Logatchev field. Environmental Microbiology. 2012;15 :1551-60.Abstract

We present data on the co-registered geochemistry (in situ mass spectrometry) and microbiology (pyrosequencing of 16S rRNA genes; V1, V2, V3 regions) in five fluid samples from Irina II in the Logatchev hydrothermal field. Two samples were collected over 24 min from the same spot and further three samples were from spatially distinct locations (20 cm, 3 m and the overlaying plume). Four low-temperature hydrothermal fluids from the Irina II are composed of the same core bacterial community, namely specific Gammaproteobacteria and Epsilonproteobacteria, which, however, differs in the relative abundance. The microbial composition of the fifth sample (plume) is considerably different. Although a significant correlation between sulfide enrichment and proportions of Sulfurovum (Epsilonproteobacteria) was found, no other significant linkages between abiotic factors, i.e. temperature, hydrogen, methane, sulfide and oxygen, and bacterial lineages were evident. Intriguingly, bacterial community compositions of some time series samples from the same spot were significantly more similar to a sample collected 20 cm away than to each other. Although this finding is based on three single samples only, it provides first hints that single hydrothermal fluid samples collected on a small spatial scale may also reflect unrecognized temporal variability. However, further studies are required to support this hypothesis.

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Tivey MK, Becker E, Beinart R, Fisher CR, Girguis PR, Langmuir CH, Michael PJ, Reysenbach AL. Links from Mantle to Microbe at the Lau Integrated Study Site: Insights from a Back-Arc Spreading Center. Oceanography. 2012;25 (1) :62-77.Abstract

The Lau Integrated Study Site (ISS) has provided unique opportunities for study of ridge processes because of its back-arc setting in the southwestern Pacific. Its location allows study of a biogeographical province distinct from those of eastern Pacific and mid-Atlantic ridges, and crustal compositions along the ridge lie outside the range of mid-ocean ridge crustal compositions. The Lau ISS is located above a subduction zone, at an oblique angle. The underlying mantle receives water and other elements derived from the downgoing lithospheric slab, with an increase in slab influence from north to south. Water lowers the mantle melting temperature and leads to greater melt production where the water flux is greater, and to distinctive regional-scale gradients along the ridge. There are deeper faulted axial valleys with basaltic volcanism in the north and inflated axial highs with andesites in the south. Differences in igneous rock composition and release of magmatic volatiles affect compositions of vent fluids and deposits. Differences in vent fluid compositions and small-scale diffuse-flow regimes correlate with regional-scale patterns in microbial and megafaunal distributions. The interdisciplinary research effort at the Lau ISS has successfully identified linkages between subsurface processes and deep-sea biological communities, from mantle to microbe to megafauna.

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Girguis PR, Holden JF. On the Potential for Bioenergy and Biofuels from Hydrothermal Vent Microbes. Oceanography. 2012;25 (1) :213-217. (pdf)
2011
Gong YM, Radachowsky SE, Wolf M, Nielsen ME, Girguis PR, Reimers CE. Benthic Microbial Fuel Cell as Direct Power Source for an Acoustic Modem and Seawater Oxygen/Temperature Sensor System. Environmental Science & Technology. 2011;45 :5047-5053.Abstract

Supported by the natural potential difference between anoxic sediment and oxic seawater, benthic microbial fuel cells (BMFCs) promise to be ideal power sources for certain low-power marine sensors and communication devices. In this study a chambered BMFC with a 0.25 m(2) footprint was used to power an acoustic modem interfaced with an oceanographic sensor that measures dissolved oxygen and temperature. The experiment was conducted in Yaquina Bay, Oregon over 50 days. Several improvements were made in the BMFC design and power management system based on lessons learned from earlier prototypes. The energy was harvested by a dynamic gain charge pump circuit that maintains a desired point on the BMFC's power curve and stores the energy in a 200 F supercapacitor. The system also used an ultralow power microcontroller and quartz clock to read the oxygen/temperature sensor hourly, store data with a time stamp, and perform daily polarizations. Data records were transmitted to the surface by the acoustic modem every 1-5 days after receiving an acoustic prompt from a surface hydrophone. After jump-starting energy production with supplemental macroalgae placed in the BMFC's anode chamber, the average power density of the BMFC adjusted to 44 mW/m(2) of seafloor area which is better than past demonstrations at this site. The highest power density was 158 mW/m(2), and the useful energy produced and stored was >= 1.7 times the energy required to operate the system.

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Petersen JM, Zielinski FU, Pape T, Seifert R, Moraru C, Amann R, Hourdez S, Girguis PR, Wankel SD, Barbe V, et al. Hydrogen is an energy source for hydrothermal vent symbioses. Nature. 2011;476 :176-180.Abstract

The discovery of deep-sea hydrothermal vents in 1977 revolutionized our understanding of the energy sources that fuel primary productivity on Earth. Hydrothermal vent ecosystems are dominated by animals that live in symbiosis with chemosynthetic bacteria. So far, only two energy sources have been shown to power chemosynthetic symbioses: reduced sulphur compounds and methane. Using metagenome sequencing, single-gene fluorescence in situ hybridization, immunohistochemistry, shipboard incubations and in situ mass spectrometry, we show here that the symbionts of the hydrothermal vent mussel Bathymodiolus from the Mid-Atlantic Ridge use hydrogen to power primary production. In addition, we show that the symbionts of Bathymodiolus mussels from Pacific vents have hupL, the key gene for hydrogen oxidation. Furthermore, the symbionts of other vent animals such as the tubeworm Riftia pachyptila and the shrimp Rimicaris exoculata also have hupL. We propose that the ability to use hydrogen as an energy source is widespread in hydrothermal vent symbioses, particularly at sites where hydrogen is abundant.

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Wankel SD, Germanovich LN, Lilley MD, Genc G, DiPerna CJ, Bradley AS, Olson EJ, Girguis PR. Influence of subsurface biosphere on geochemical fluxes from diffuse hydrothermal fluids. Nature Geoscience. 2011;4 :461-468.Abstract

Hydrothermal vents along mid-ocean systems host unique, highly productive biological communities, based on microbial chemoautotrophy, that thrive on the sulphur, metals, nitrogen and carbon emitted from the vents into the deep ocean. Geochemical studies of vents have centred on analyses of high-temperature, focused hydrothermal vents, which exhibit very high flow rates and are generally considered too hot for microbial life. Geochemical fluxes and metabolic activity associated with habitable, lower temperature diffuse fluids remain poorly constrained. As a result, little is known about the extent to which microbial communities, particularly in the subsurface, influence geochemical flux from more diffuse flows. Here, we estimate the net flux of methane, carbon dioxide and hydrogen from diffuse and focused hydrothermal vents along the Juan de Fuca ridge, using an in situ mass spectrometer and flowmeter. We show that geochemical flux from diffuse vents can equal or exceed that emanating from hot, focused vents. Notably, hydrogen concentrations in fluids emerging from diffuse vents are 50% to 80% lower than predicted. We attribute the loss of hydrogen in diffuse vent fluids to microbial consumption in the subsurface, and suggest that subsurface microbial communities can significantly influence hydrothermal geochemical fluxes to the deep ocean.

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Robidart JC, Roque A, Song P, Girguis PR. Linking Hydrothermal Geochemistry to Organismal Physiology: Physiological Versatility in Riftia pachyptila from Sedimented and Basalt-hosted Vents. Plos One. 2011;6 (7) :e21692, 1-12.Abstract

Much of what is known regarding Riftia pachyptila physiology is based on the wealth of studies of tubeworms living at diffuse flows along the fast-spreading, basalt-hosted East Pacific Rise (EPR). These studies have collectively suggested that Riftia pachyptila and its chemoautotrophic symbionts are physiologically specialized, highly productive associations relying on hydrogen sulfide and oxygen to generate energy for carbon fixation, and the symbiont's nitrate reduction to ammonia for energy and biosynthesis. However, Riftia also flourish in sediment-hosted vents, which are markedly different in geochemistry than basalt-hosted systems. Here we present data from shipboard physiological studies and global quantitative proteomic analyses of Riftia pachyptila trophosome tissue recovered from tubeworms residing in the EPR and the Guaymas basin, a sedimented, hydrothermal vent field. We observed marked differences in symbiont nitrogen metabolism in both the respirometric and proteomic data. The proteomic data further suggest that Riftia associations in Guaymas may utilize different sulfur compounds for energy generation, may have an increased capacity for energy storage, and may play a role in degrading exogenous organic carbon. Together these data reveal that Riftia symbionts are far more physiologically plastic than previously considered, and that -contrary to previous assertions- Riftia do assimilate reduced nitrogen in some habitats. These observations raise new hypotheses regarding adaptations to the geochemical diversity of habitats occupied by Riftia, and the degree to which the environment influences symbiont physiology and evolution.

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Scott KM, Fox G, Girguis PR. Measuring Isotope Fractionation by Autotrophic Microorganisms and Enzymes. Methods in Enzymology: Methods in Methane Metabolism, Pt A. 2011;494 :281-299.Abstract

Physical, chemical, and biological processes commonly discriminate among stable isotopes. Therefore, the stable isotope compositions of biomass, growth substrates, and products often carry the isotopic fingerprints of the processes that shape them. Therefore, measuring isotope fractionation by enzymes and cultures of autotrophic microorganisms can provide insights at many levels, from metabolism to ecosystem function. Discussed here are considerations relevant to measuring isotope discrimination by enzymes as well at, intact cells, with an emphasis on stable one-carbon isotopes and autotrophic microorganisms.

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Rabaey K, Girguis P, Nielsen LK. Metabolic and practical considerations on microbial electrosynthesis. Current Opinion in Biotechnology. 2011;22 :371-7.Abstract

The production of biofuels and biochemicals is highly electron intensive. To divert fermentative and respiratory pathways to the product of interest, additional electrons (i.e. reducing power) are often needed. Meanwhile, the past decade has seen the breakthrough of sustainable electricity sources such as solar and wind. Microbial electrosynthesis (MES) is at the nexus of both, as it uses electrical energy as source of reducing power for microorganisms. This review addresses the key opportunities and challenges for MES. While exciting as a concept, MES needs to overcome many biological, electrochemical, logistical and economic challenges. Particularly the latter is critical, as on a 'per electron basis' MES does not yet appear to deliver a substantial benefit relative to existing approaches.

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Childress JJ, Girguis PR. The metabolic demands of endosymbiotic chemoautotrophic metabolism on host physiological capacities. Journal of Experimental Biology. 2011;214 :312-325.Abstract

While chemoautotrophic endosymbioses of hydrothermal vents and other reducing environments have been well studied, little attention has been paid to the magnitude of the metabolic demands placed upon the host by symbiont metabolism and the adaptations necessary to meet such demands. Here we make the first attempt at such an evaluation, and show that moderate to high rates of chemoautotrophic or methanotrophic metabolism impose oxygen uptake and proton equivalent elimination demands upon the hosts that are much higher than is typical for the non-symbiotic annelid, bivalve and gastropod lineages to which they are related. The properties of the hosts are described and compared to determine which properties are associated with and predictive of the highest rates. We suggest that the high oxygen demand of these symbionts is perhaps the most limiting flux for the symbioses. Among the consequences of such demands has been the widespread presence of circulating and/or tissue hemoglobins in these symbioses that are necessary to support high metabolic rates in thioautotrophic endosymbioses. We also compare photoautotrophic with chemoautotrophic and methanotrophic endosymbioses to evaluate the differences and similarities in physiologies. These analyses suggest that the high demand for oxygen by chemoautotrophic and methanotrophic symbionts is likely a major factor precluding their endosymbiosis with cnidarians.

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Gartman A, Yucel M, Madison AS, Chu DW, Ma SF, Janzen CP, Becker EL, Beinart RA, Girguis PR, Luther GW. Sulfide Oxidation across Diffuse Flow Zones of Hydrothermal Vents. Aquatic Geochemistry. 2011;17 :583-601.Abstract

The sulfide (H(2)S/HS(-)) that is emitted from hydrothermal vents begins to oxidize abiotically with oxygen upon contact with ambient bottom water, but the reaction kinetics are slow. Here, using in situ voltammetry, we report detection of the intermediate sulfur oxidation products polysulfides [S(x)(2-)] and thiosulfate [S(2)O(3)(2-)], along with contextual data on sulfide, oxygen, and temperature. At Lau Basin in 2006, thiosulfate was identified in less than one percent of approximately 10,500 scans and no polysulfides were detected. Only five percent of 11,000 voltammetric scans taken at four vent sites at Lau Basin in May 2009 show either thiosulfate or polysulfides. These in situ data indicate that abiotic sulfide oxidation does not readily occur as H(2)S contacts oxic bottom waters. Calculated abiotic potential sulfide oxidation rates are < 10(-3) mu M/min and are consistent with slow oxidation and the observed lack of sulfur oxidation intermediates. It is known that the thermodynamics for the first electron transfer step for sulfide and oxygen during sulfide oxidation in these systems are unfavorable, and that the kinetics for two electron transfers are not rapid. Here, we suggest that different metal catalyzed and/or biotic reaction pathways can readily produce sulfur oxidation intermediates. Via shipboard high-pressure incubation experiments, we show that snails with chemosynthetic endosymbionts do release polysulfides and may be responsible for our field observations of polysulfides.

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Luther GW, Findlay AJ, MacDonald DJ, Owings SM, Hanson TE, Beinart RA, Girguis PR. Thermodynamics and kinetics of sulfide oxidation by oxygen: a look at inorganically controlled reactions and biologically mediated processes in the environment. Frontiers in Microbiology. 2011;2.Abstract

The thermodynamics for the first electron transfer step for sulfide and oxygen indicates that the reaction is unfavorable as unstable superoxide and bisulfide radical ions would need to be produced. However, a two-electron transfer is favorable as stable S(0) and peroxide would be formed, but the partially filled orbitals in oxygen that accept electrons prevent rapid kinetics. Abiotic sulfide oxidation kinetics improve when reduced iron and/or manganese are oxidized by oxygen to form oxidized metals which in turn oxidize sulfide. Biological sulfur oxidation relies on enzymes that have evolved to overcome these kinetic constraints to affect rapid sulfide oxidation. Here we review the available thermodynamic and kinetic data for H2S and HS center dot as well as O-2, reactive oxygen species, nitrate, nitrite, and NOx species. We also present new kinetic data for abiotic sulfide oxidation with oxygen in trace metal clean solutions that constrain abiotic rates of sulfide oxidation in metal free solution and agree with the kinetic and thermodynamic calculations. Moreover, we present experimental data that give insight on rates of chemolithotrophic and photolithotrophic sulfide oxidation in the environment. We demonstrate that both anaerobic photolithotrophic and aerobic chemolithotrophic sulfide oxidation rates are three or more orders of magnitude higher than abiotic rates suggesting that in most environments biotic sulfide oxidation rates will far exceed abiotic rates due to the thermodynamic and kinetic constraints discussed in the first section of the paper. Such data reshape our thinking about the biotic and abiotic contributions to sulfide oxidation in the environment.

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2010
Nielsen ME, Girguis PR. Are hydrothermal vents natural microbial fuel cells?. Geochimica Et Cosmochimica Acta. 2010;74 :A759-A759.
Guzman JJ, Cooke KG, Gay MO, Radachowsky SE, Girguis PR, Chiu MA. Benthic Microbial Fuel Cells: Long-Term Power Sources for Wireless Marine Sensor Networks. Sensors, and Command, Control, Communications, and Intelligence (C3i) Technologies for Homeland Security and Homeland Defense Ix. 2010;7666.Abstract

Wireless marine sensor networks support an assortment of services in industries ranging from national security and defense to communications and environmental stewardship. Expansion of marine sensor networks has been inhibited by the limited availability and high cost of long-term power sources. Benthic Microbial Fuel Cells (BMFCs) are a novel form of energy harvesting for marine environments. Through research conducted in-lab and by academic collaborators, Trophos Energy has developed a series of novel BMFC architectures to improve power generation capability and overall system robustness. When integrated with Trophos' power management electronics, BMFCs offer a robust, long-term power solution for a variety of remote marine applications. The discussions provided in this paper outline the architectural evolution of BMFC technology to date, recent experimental results that will govern future BMFC designs, and the present and future applicability of BMFC systems as power sources for wireless marine sensor networks.

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Girguis PR, Nielsen ME, Reimers CE. Fundamentals of Benthic Microbial Fuel Cells: Theory, Development, and Applications. In: Bioelectrochemical systems. First edition. Springer Verlag Press ; 2010. (pdf)
Girguis PR, Nielsen ME, Figueroa I. Harnessing energy from marine productivity using bioelectrochemical systems. Current Opinion in Biotechnology. 2010;21 :252-258.Abstract

Over the past decade, studies have shown that devices called microbial fuel cells (MFCs) can harness electricity from microbially mediated degradation of organic carbon, in both lab cultures and natural environments. Other studies have shown that MFCs can harness power from coastal and deep ocean sediments, as well as from plankton, without any fuel supplementation or microbial inoculation. The fuel for these systems is organic matter resulting from oceanic primary productivity. Models suggest that MFCs may operate for decades on endogenous organic carbon. In light of their capacity to generate power in natural milieus by tapping into biogeochemical cycles, MFCs may one day provide an efficient means of generating power (or high value biofuels) directly from marine productivity.

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Wankel SD, Joye SB, Samarkin VA, Shah SR, Friederich G, Melas-Kyriazi J, Girguis PR. New constraints on methane fluxes and rates of anaerobic methane oxidation in a Gulf of Mexico brine pool via in situ mass spectrometry. Deep-Sea Research Part II -Topical Studies in Oceanography. 2010;57 :2022-2029.Abstract

Deep-sea biogeochemical cycles are, in general, poorly understood owing to the difficulties of making measurements in situ, recovering samples with minimal perturbation, and, in many cases, coping with high spatial and temporal heterogeneity. In particular, biogeochemical fluxes of volatiles such as methane remain largely unconstrained because of the difficulties with accurate quantification in situ and the patchiness of point sources such as seeps and brine pools. To better constrain biogeochemical fluxes and cycling, we have developed a deep-sea in situ mass spectrometer (ISMS) to enable high-resolution quantification of volatiles in situ. Here we report direct measurements of methane concentrations made in a Gulf of Mexico brine pool located at a depth of over 2300 m. Concentrations of up to 33 mM methane were observed within the brine pool, whereas concentrations in the water directly above were three orders of magnitude lower. These direct measurements enabled us to make the first accurate estimates of the diffusive flux from a brine pool, calculated to be 1.1 +/- 0.2 mol m(-2) yr(-1). Integrated rate measurements of aerobic methane oxidation in the water column overlying the brine pool were similar to 320 mu mol m(-2) yr(-1), accounting at most for just 0.03% of the diffusive methane flux from the brine pool. Calculated rates of anaerobic methane oxidation were 600-1200 mu M yr(-1), one to two orders of magnitude higher than previously published values of AOM in anoxic fluids. These findings suggest that brine pools are enormous point sources of methane in the deep sea, and may, in aggregate, have a pronounced impact on the global marine methane cycle. (C) 2010 Elsevier Ltd. All rights reserved.

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