@article {Jungbluth2016,
	title = {{Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt}},
	journal = {ISME Journal},
	volume = {10},
	year = {2016},
	pages = {2033{\textendash}2047},
	abstract = {Although little is known regarding microbial life within our planet{\textquoteright}s rock-hosted deep subseafloor biosphere, boreholes drilled through deep ocean sediment and into the underlying basaltic crust provide invaluable windows of access that have been used previously to document the presence of microorganisms within fluids percolating through the deep ocean crust. In this study, the analysis of 1.7 million small subunit ribosomal RNA genes amplified and sequenced from marine sediment, bottom seawater and basalt-hosted deep subseafloor fluids that span multiple years and locations on the Juan de Fuca Ridge flank was used to quantitatively delineate a subseafloor microbiome comprised of distinct bacteria and archaea. Hot, anoxic crustal fluids tapped by newly installed seafloor sampling observatories at boreholes U1362A and U1362B contained abundant bacterial lineages of phylogenetically unique Nitrospirae, Aminicenantes, Calescamantes and Chloroflexi. Although less abundant, the domain Archaea was dominated by unique, uncultivated lineages of marine benthic group E, the Terrestrial Hot Spring Crenarchaeotic Group, the Bathyarchaeota and relatives of cultivated, sulfate-reducing Archaeoglobi. Consistent with recent geochemical measurements and bioenergetic predictions, the potential importance of methane cycling and sulfate reduction were imprinted within the basalt-hosted deep subseafloor crustal fluid microbial community. This unique window of access to the deep ocean subsurface basement reveals a microbial landscape that exhibits previously undetected spatial heterogeneity.},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	doi = {10.1038/ismej.2015.248},
	author = {Jungbluth, S P and Bowers, R M and Lin, H-T and Cowen, J P and Rappe, M S}
}
@article {Lin2015,
	title = {{Dissolved amino acids in oceanic basaltic basement fluids}},
	journal = {Geochimica et Cosmochimica Acta},
	volume = {164},
	year = {2015},
	pages = {175{\textendash}190},
	abstract = {The oceanic basaltic basement contains the largest aquifer on Earth and potentially plays an important role in the global carbon cycle as a net sink for dissolved organic carbon (DOC). However, few details of the organic matter cycling in the subsurface are known because great water depths and thick sediments typically hinder direct access to this environment. In an effort to examine the role of water{\textendash}rock{\textendash}microorganism interaction on organic matter cycling in the oceanic basaltic crust, basement fluid samples collected from three borehole observatories installed on the eastern flank of the Juan de Fuca Ridge were analyzed for dissolved amino acids. Our data show that dissolved free amino acids (1{\textendash}13 nM) and dissolved hydrolyzable amino acids (43{\textendash}89 nM) are present in the basement. The amino acid concentrations in the ridge-flank basement fluids are at the low end of all submarine hydrothermal fluids reported in the literature and are similar to those in deep seawater. Amino acids in recharging deep seawater, in situ amino acid production, and diffusional input from overlying sediments are potential sources of amino acids in the basement fluids. Thermodynamic modeling shows that amino acid synthesis in the basement can be sustained by energy supplied from inorganic substrates via chemolithotrophic metabolisms. Furthermore, an analysis of amino acid concentrations and compositions in basement fluids support the notion that heterotrophic activity is ongoing. Similarly, the enrichment of acidic amino acids and depletion of hydrophobic ones relative to sedimentary particulate organic matter suggests that surface sorption and desorption also alters amino acids in the basaltic basement. In summary, although the oceanic basement aquifer is a net sink for deep seawater DOC, similar amino acid concentrations in basement aquifer and deep seawater suggest that DOC is preferentially removed in the basement over dissolved amino acids. Our data also suggest that organic carbon cycling occurs in the oceanic basaltic basement, where an active subsurface biosphere is likely responsible for amino acid synthesis and degradation.},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	doi = {10.1016/j.gca.2015.04.044},
	author = {Lin, H-T and Amend, J P and LaRowe, D E and Bingham, J-P and Cowen, J P}
}
@article {Cowen2012,
	title = {{Advanced instrument system for real-time and time-series microbial geochemical sampling of the deep (basaltic) crustal biosphere}},
	journal = {Deep-Sea Research. Part I: Oceanographic Research Papers},
	volume = {61},
	year = {2012},
	pages = {43{\textendash}56},
	abstract = {Integrated Ocean Drilling Program borehole CORK (Circulation Obviation Retrofit Kit) observatories provide long-term access to hydrothermal fluids circulating within the basaltic crust (basement), providing invaluable opportunities to study the deep biosphere. We describe the design and application parameters of the GeoMICROBE instrumented sled, an autonomous sensor and fluid sampling system. The GeoMICROBE system couples with CORK fluid delivery lines to draw large volumes of fluids from crustal aquifers to the seafloor. These fluids pass a series of in-line sensors and an in situ filtration and collection system. GeoMICROBE{\textquoteright}s major components include a primary valve manifold system, a positive displacement primary pump, sensors (e.g., fluid flow rate, temperature, dissolved O2, electrochemistry-voltammetry analyzer), a 48-port in situ filtration and fluid collection system, computerized controller, seven 24~V{\textendash}40~A batteries and wet-mateable (ODI) communications with submersibles. This constantly evolving system has been successfully connected to IODP Hole 1301A on the eastern flank of the Juan de Fuca Ridge. Also described here is a mobile pumping system (MPS), which possesses many of the same components as the GeoMICROBE (e.g., pump, sensors, controller), but is directly powered and controlled in real time via submersible operations; the MPS has been employed repeatedly to collect pristine basement fluids for a variety of geochemical and microbial studies.},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	issn = {0967-0637},
	doi = {10.1016/j.dsr.2011.11.004},
	url = {http://dx.doi.org/10.1016/j.dsr.2011.11.004},
	author = {Cowen, J P and Copson, D A and Jolly, J and Hsieh, C -C and Lin, H -T and Glazer, B T and Wheat, C G}
}
@article {Fornari2012,
	title = {{The East Pacific Rise Between 9 degrees N and 10 degrees N: Twenty-Five Years of Integrated, Multidisciplinary Oceanic Spreading Center Studies}},
	journal = {Oceanography},
	volume = {25},
	number = {1},
	year = {2012},
	month = {mar},
	pages = {18{\textendash}43},
	publisher = {OCEANOGRAPHY SOC},
	address = {ROCKVILLE; P.O. BOX 1931, ROCKVILLE, MD USA},
	abstract = {The East Pacific Rise from {\~{}}~9{\textendash}10{\textdegree}N is an archetype for a fast-spreading mid-ocean ridge. In particular, the segment near 9{\textdegree}50{\textquoteright}N has been the focus of multidisciplinary research for over two decades, making it one of the best-studied areas of the global ridge system. It is also one of only two sites along the global ridge where two historical volcanic eruptions have been observed. This volcanically active segment has thus offered unparalleled opportunities to investigate a range of complex interactions among magmatic, volcanic, hydrothermal, and biological processes associated with crustal accretion over a full magmatic cycle. At this 9{\textdegree}50{\textquoteright}N site, comprehensive physical oceanographic measurements and modeling have also shed light on linkages between hydrodynamic transport of larvae and other materials and biological dynamics influenced by magmatic processes. Integrated results of high-resolution mapping, and both in~situ and laboratory-based geophysical, oceanographic, geochemical, and biological observations and sampling, reveal how magmatic events perturb the hydrothermal system and the biological communities it hosts.},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	issn = {1042-8275},
	doi = {10.5670/oceanog.2012.02},
	author = {Fornari, D J and Von Damm, K L and Bryce, Julia G and Cowen, J P and Ferrini, Vicki and Fundis, A and Lilley, M D and Luther, G W and Mullineaux, L S and Perfit, M R and Meana-Prado, M F and Rubin, K H and Seyfried, W E and Shank, T M and Soule, S A and Tolstoy, M and White, S M}
}
@article {Lin2012,
	title = {{Inorganic chemistry, gas compositions and dissolved organic carbon in fluids from sedimented young basaltic crust on the Juan de Fuca Ridge flanks}},
	journal = {Geochimica et Cosmochimica Acta},
	volume = {85},
	year = {2012},
	pages = {213{\textendash}227},
	abstract = {The permeable upper oceanic basement serves as a plausible habitat for a variety of microbial communities. There is growing evidence suggesting a substantial subseafloor biosphere. Here new time series data are presented on key inorganic species, methane, hydrogen and dissolved organic carbon (DOC) in ridge flank fluids obtained from subseafloor observatory CORKs (Circulation Obviation Retrofit Kits) at Integrated Ocean Drilling Program (IODP) boreholes 1301A and 1026B. These data show that the new sampling methods (Cowen et al., 2012) employed at 1301A result in lower contamination than earlier studies. Furthermore, sample collection methods permitted most chemical analyses to be performed from aliquots of single large volume samples, thereby allowing more direct comparison of the data. The low phosphate concentrations (0.06{\textendash}0.2~$μ$M) suggest that relative to carbon and nitrogen, phosphorus could be a limiting nutrient in the basement biosphere. Coexisting sulfate (17{\textendash}18~mM), hydrogen sulfide (\~{}0.1~$μ$M), hydrogen (0.3{\textendash}0.7~$μ$M) and methane (1.5{\textendash}2~$μ$M) indicates that the basement aquifer at 1301A either draws fluids from multiple flow paths with different redox histories or is a complex environment that is not thermodynamically controlled and may allow co-occurring metabolic pathways including sulfate reduction and methanogenesis. The low DOC concentrations (11{\textendash}18~$μ$M) confirm that ridge flank basement is a net DOC sink and ultimately a net carbon sink. Based on the net amounts of DOC, oxygen, nitrate and sulfate removed (\~{}30~$μ$M, \~{}80~$μ$M, \~{}40~$μ$M and \~{}10~mM, respectively) from entrained bottom seawater, organic carbon may be aerobically or anaerobically oxidized in biotic and/or abiotic processes.},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	issn = {0016-7037},
	doi = {10.1016/j.gca.2012.02.017},
	url = {http://dx.doi.org/10.1016/j.gca.2012.02.017},
	author = {Lin, H -T and Cowen, J P and Olson, E J and Amend, J P and Lilley, M D}
}
@article {Johnson2000,
	title = {{Earthquake-induced changes in a hydrothermal system on the Juan de Fuca mid-ocean ridge}},
	journal = {Nature},
	volume = {407},
	number = {6801},
	year = {2000},
	pages = {174{\textendash}177},
	publisher = {Macmillian Magazines Ltd},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	issn = {0028-0836},
	doi = {10.1038/35025040},
	url = {http://dx.doi.org/10.1038/35025040},
	author = {Johnson, H P and Hutnak, M and Dziak, R P and Fox, C G and Urcuyo, I and Cowen, J P and Nabelek, J and Fisher, C R}
}
