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Booker AE, D'Angelo T, Adams-Beyea A, Brown JM, Nigro O, Rappé MS, Stepanauskas R, Orcutt BN. Life strategies for Aminicenantia in subseafloor oceanic crust. THE ISME JOURNAL 2023; 17:1406-1415. [PMID: 37328571 PMCID: PMC10432499 DOI: 10.1038/s41396-023-01454-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 04/11/2023] [Accepted: 04/17/2023] [Indexed: 06/18/2023]
Abstract
After decades studying the microbial "deep biosphere" in subseafloor oceanic crust, the growth and life strategies in this anoxic, low energy habitat remain poorly described. Using both single cell genomics and metagenomics, we reveal the life strategies of two distinct lineages of uncultivated Aminicenantia bacteria from the basaltic subseafloor oceanic crust of the eastern flank of the Juan de Fuca Ridge. Both lineages appear adapted to scavenge organic carbon, as each have genetic potential to catabolize amino acids and fatty acids, aligning with previous Aminicenantia reports. Given the organic carbon limitation in this habitat, seawater recharge and necromass may be important carbon sources for heterotrophic microorganisms inhabiting the ocean crust. Both lineages generate ATP via several mechanisms including substrate-level phosphorylation, anaerobic respiration, and electron bifurcation driving an Rnf ion translocation membrane complex. Genomic comparisons suggest these Aminicenantia transfer electrons extracellularly, perhaps to iron or sulfur oxides consistent with mineralogy of this site. One lineage, called JdFR-78, has small genomes that are basal to the Aminicenantia class and potentially use "primordial" siroheme biosynthetic intermediates for heme synthesis, suggesting this lineage retain characteristics of early evolved life. Lineage JdFR-78 contains CRISPR-Cas defenses to evade viruses, while other lineages contain prophage that may help prevent super-infection or no detectable viral defenses. Overall, genomic evidence points to Aminicenantia being well adapted to oceanic crust environments by taking advantage of simple organic molecules and extracellular electron transport.
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Affiliation(s)
- Anne E Booker
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | | | - Annabelle Adams-Beyea
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
- Eugene Lang College of Liberal Arts at The New School, New York City, NY, USA
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Olivia Nigro
- Department of Natural Science, Hawai'i Pacific University, Honolulu, HI, USA
| | - Michael S Rappé
- Hawai'i Institute of Marine Biology, SOEST, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | | | - Beth N Orcutt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA.
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Microbial Abundance and Diversity in Subsurface Lower Oceanic Crust at Atlantis Bank, Southwest Indian Ridge. Appl Environ Microbiol 2021; 87:e0151921. [PMID: 34469194 DOI: 10.1128/aem.01519-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
International Ocean Discovery Program Expedition 360 drilled Hole U1473A at Atlantis Bank, an oceanic core complex on the Southwest Indian Ridge, with the aim of recovering representative samples of the lower oceanic crust. Recovered cores were primarily gabbro and olivine gabbro. These mineralogies may host serpentinization reactions that have the potential to support microbial life within the recovered rocks or at greater depths beneath Atlantis Bank. We quantified prokaryotic cells and analyzed microbial community composition for rock samples obtained from Hole U1473A and conducted nutrient addition experiments to assess if nutrient supply influences the composition of microbial communities. Microbial abundance was low (≤104 cells cm-3) but positively correlated with the presence of veins in rocks within some depth ranges. Due to the heterogeneous nature of the rocks downhole (alternating stretches of relatively unaltered gabbros and more significantly altered and fractured rocks), the strength of the positive correlations between rock characteristics and microbial abundances was weaker when all depths were considered. Microbial community diversity varied at each depth analyzed. Surprisingly, addition of simple organic acids, ammonium, phosphate, or ammonium plus phosphate in nutrient addition experiments did not affect microbial diversity or methane production in nutrient addition incubation cultures over 60 weeks. The work presented here from Site U1473A, which is representative of basement rock samples at ultraslow spreading ridges and the usually inaccessible lower oceanic crust, increases our understanding of microbial life present in this rarely studied environment and provides an analog for basement below ocean world systems such as Enceladus. IMPORTANCE The lower oceanic crust below the seafloor is one of the most poorly explored habitats on Earth. The rocks from the Southwest Indian Ridge (SWIR) are similar to rock environments on other ocean-bearing planets and moons. Studying this environment helps us increase our understanding of life in other subsurface rocky environments in our solar system that we do not yet have the capability to access. During an expedition to the SWIR, we drilled 780 m into lower oceanic crust and collected over 50 rock samples to count the number of resident microbes and determine who they are. We also selected some of these rocks for an experiment where we provided them with different nutrients to explore energy and carbon sources preferred for growth. We found that the number of resident microbes and community structure varied with depth. Additionally, added nutrients did not shape the microbial diversity in a predictable manner.
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Shalev N, Bontognali TRR, Wheat CG, Vance D. New isotope constraints on the Mg oceanic budget point to cryptic modern dolomite formation. Nat Commun 2019; 10:5646. [PMID: 31827091 PMCID: PMC6906300 DOI: 10.1038/s41467-019-13514-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/11/2019] [Indexed: 11/09/2022] Open
Abstract
The oceanic magnesium budget is important to our understanding of Earth’s carbon cycle, because similar processes control both (e.g., weathering, volcanism, and carbonate precipitation). However, dolomite sedimentation and low-temperature hydrothermal circulation remain enigmatic oceanic Mg sinks. In recent years, magnesium isotopes (δ26Mg) have provided new constraints on the Mg cycle, but the lack of data for the low-temperature hydrothermal isotope fractionation has hindered this approach. Here we present new δ26Mg data for low-temperature hydrothermal fluids, demonstrating preferential 26Mg incorporation into the oceanic crust, on average by εsolid-fluid ≈ 1.6‰. These new data, along with the constant seawater δ26Mg over the past ~20 Myr, require a significant dolomitic sink (estimated to be 1.5–2.9 Tmol yr−1; 40–60% of the oceanic Mg outputs). This estimate argues strongly against the conventional view that dolomite formation has been negligible in the Neogene and points to the existence of significant hidden dolomite formation. Earth’s carbon cycle and oceanic magnesium cycle are controlled by processes such as weathering, volcanism and precipitation of carbonates, such as dolomite. Here, the authors contradict the view that modern dolomite formation is rare and suggest instead that dolomite accounts for ~40–60% of the global oceanic Mg output in the last 20 Ma.
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Affiliation(s)
- Netta Shalev
- Department of Earth Sciences, Institute of Geochemistry and Petrology, ETH Zürich, Clausiusstrasse 25, 8092, Zürich, Switzerland.
| | - Tomaso R R Bontognali
- Department of Earth Sciences, Institute of Geochemistry and Petrology, ETH Zürich, Clausiusstrasse 25, 8092, Zürich, Switzerland.,Space Exploration Institute, Fbg de l'Hopital 68, 2002, Neuchâtel, Switzerland.,Department of Environmental Sciences, University of Basel, Klingelbergstrasse 27, Basel, Switzerland
| | - C Geoffrey Wheat
- University of Alaska Fairbanks, PO Box 475, Moss Landing, California, 95039, USA
| | - Derek Vance
- Department of Earth Sciences, Institute of Geochemistry and Petrology, ETH Zürich, Clausiusstrasse 25, 8092, Zürich, Switzerland
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Geological storage of CO2 in sub-seafloor basalt: the CarbonSAFE pre-feasibility study offshore Washington State and British Columbia. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.egypro.2018.07.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Jungbluth SP, Bowers RM, Lin HT, Cowen JP, Rappé MS. Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt. ISME JOURNAL 2016; 10:2033-47. [PMID: 26872042 PMCID: PMC5029167 DOI: 10.1038/ismej.2015.248] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 11/20/2015] [Accepted: 11/25/2015] [Indexed: 11/16/2022]
Abstract
Although little is known regarding microbial life within our planet'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.
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Affiliation(s)
- Sean P Jungbluth
- Hawaii Institute of Marine Biology, SOEST, University of Hawaii, Kaneohe, HI, USA.,Department of Oceanography, SOEST, University of Hawaii, Honolulu, HI, USA
| | - Robert M Bowers
- NASA Astrobiology Institute, IfA, University of Hawaii, Honolulu, HI, USA
| | - Huei-Ting Lin
- Department of Oceanography, SOEST, University of Hawaii, Honolulu, HI, USA
| | - James P Cowen
- Department of Oceanography, SOEST, University of Hawaii, Honolulu, HI, USA
| | - Michael S Rappé
- Hawaii Institute of Marine Biology, SOEST, University of Hawaii, Kaneohe, HI, USA
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Winslow DM, Fisher AT. Sustainability and dynamics of outcrop-to-outcrop hydrothermal circulation. Nat Commun 2015; 6:7567. [PMID: 26113260 PMCID: PMC4491839 DOI: 10.1038/ncomms8567] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 05/19/2015] [Indexed: 11/15/2022] Open
Abstract
Most seafloor hydrothermal circulation occurs far from the magmatic influence of mid-ocean ridges, driving large flows of water, heat and solutes through volcanic rock outcrops on ridge flanks. Here we create three-dimensional simulations of ridge–flank hydrothermal circulation, flowing between and through seamounts, to determine what controls hydrogeological sustainability, flow rate and preferred flow direction in these systems. We find that sustaining flow between outcrops that penetrate less-permeable sediment depends on a contrast in transmittance (the product of outcrop permeability and the area of outcrop exposure) between recharging and discharging sites, with discharge favoured through less-transmissive outcrops. Many simulations include local discharge through outcrops at the recharge end of an outcrop-to-outcrop system. Both of these characteristics are observed in the field. In addition, smaller discharging outcrops sustain higher flow rates than larger outcrops, which may help to explain how so much lithospheric heat is extracted globally by this process. Much hydrothermal circulation occurs away from the mid-ocean ridges and out on ridge flanks, affecting lithospheric heat deficit, solute fluxes, and influencing the biosphere. Here, the authors use 3D simulations to look at what controls the circulation and flow rate between and through seamounts.
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Affiliation(s)
- Dustin M Winslow
- Earth and Planetary Sciences Department, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Andrew T Fisher
- 1] Earth and Planetary Sciences Department, University of California Santa Cruz, Santa Cruz, California 95064, USA [2] Institute for Geophysics and Planetary Physics, University of California Santa Cruz, Santa Cruz, California 95064, USA
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The Deep Biosphere of the Subseafloor Igneous Crust. THE HANDBOOK OF ENVIRONMENTAL CHEMISTRY 2015. [DOI: 10.1007/698_2015_5014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Microbial community stratification controlled by the subseafloor fluid flow and geothermal gradient at the Iheya North hydrothermal field in the Mid-Okinawa Trough (Integrated Ocean Drilling Program Expedition 331). Appl Environ Microbiol 2014; 80:6126-35. [PMID: 25063666 DOI: 10.1128/aem.01741-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The impacts of lithologic structure and geothermal gradient on subseafloor microbial communities were investigated at a marginal site of the Iheya North hydrothermal field in the Mid-Okinawa Trough. Subsurface marine sediments composed of hemipelagic muds and volcaniclastic deposits were recovered through a depth of 151 m below the seafloor at site C0017 during Integrated Ocean Drilling Program Expedition 331. Microbial communities inferred from 16S rRNA gene clone sequencing in low-temperature hemipelagic sediments were mainly composed of members of the Chloroflexi and deep-sea archaeal group. In contrast, 16S rRNA gene sequences of marine group I Thaumarchaeota dominated the microbial phylotype communities in the coarse-grained pumiceous gravels interbedded between the hemipelagic sediments. Based on the physical properties of sediments such as temperature and permeability, the porewater chemistry, and the microbial phylotype compositions, the shift in the physical properties of the sediments is suggested to induce a potential subseafloor recharging flow of oxygenated seawater in the permeable zone, leading to the generation of variable chemical environments and microbial communities in the subseafloor habitats. In addition, the deepest section of sediments under high-temperature conditions (∼90°C) harbored the sequences of an uncultivated archaeal lineage of hot water crenarchaeotic group IV that may be associated with the high-temperature hydrothermal fluid flow. These results indicate that the subseafloor microbial community compositions and functions at the marginal site of the hydrothermal field are highly affected by the complex fluid flow structure, such as recharging seawater and underlying hydrothermal fluids, coupled with the lithologic transition of sediments.
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Biogeochemical Consequences of the Sedimentary Subseafloor Biosphere. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/b978-0-444-62617-2.00009-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Kastner M, Solomon EA, Harris RN, Torres ME. Fluid Origins, Thermal Regimes, and Fluid and Solute Fluxes in the Forearc of Subduction Zones. EARTH AND LIFE PROCESSES DISCOVERED FROM SUBSEAFLOOR ENVIRONMENTS - A DECADE OF SCIENCE ACHIEVED BY THE INTEGRATED OCEAN DRILLING PROGRAM (IODP) 2014. [DOI: 10.1016/b978-0-444-62617-2.00022-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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12
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Modeling the Impact of Diffuse Vent Microorganisms Along Mid-Ocean Ridges and Flanks. ACTA ACUST UNITED AC 2013. [DOI: 10.1029/178gm11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
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Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank. ISME JOURNAL 2012; 7:161-72. [PMID: 22791235 DOI: 10.1038/ismej.2012.73] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Despite its immense size, logistical and methodological constraints have largely limited microbiological investigations of the subseafloor basement biosphere. In this study, a unique sampling system was used to collect fluids from the subseafloor basaltic crust via a Circulation Obviation Retrofit Kit (CORK) observatory at Integrated Ocean Drilling Program borehole 1301A, located at a depth of 2667 m in the Pacific Ocean on the eastern flank of the Juan de Fuca Ridge. Here, a fluid delivery line directly accesses a 3.5 million years old basalt-hosted basement aquifer, overlaid by 262 m of sediment, which serves as a barrier to direct exchange with bottom seawater. At an average of 1.2 × 10(4) cells ml(-1), microorganisms in borehole fluids were nearly an order of magnitude less abundant than in surrounding bottom seawater. Ribosomal RNA genes were characterized from basement fluids, providing the first snapshots of microbial community structure using a high-integrity fluid delivery line. Interestingly, microbial communities retrieved from different CORKs (1026B and 1301A) nearly a decade apart shared major community members, consistent with hydrogeological connectivity. However, over three sampling years, the dominant gene clone lineage changed from relatives of Candidatus Desulforudis audaxviator within the bacterial phylum Firmicutes in 2008 to the Miscellaneous Crenarchaeotic Group in 2009 and a lineage within the JTB35 group of Gammaproteobacteria in 2010, and statistically significant variation in microbial community structure was observed. The enumeration of different phylogenetic groups of cells within borehole 1301A fluids supported our observation that the deep subsurface microbial community was temporally dynamic.
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Anderson BW, Coogan LA, Gillis KM. The role of outcrop-to-outcrop fluid flow in off-axis oceanic hydrothermal systems under abyssal sedimentation conditions. ACTA ACUST UNITED AC 2012. [DOI: 10.1029/2011jb009052] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Fichtel K, Mathes F, Könneke M, Cypionka H, Engelen B. Isolation of sulfate-reducing bacteria from sediments above the deep-subseafloor aquifer. Front Microbiol 2012; 3:65. [PMID: 22363336 PMCID: PMC3282481 DOI: 10.3389/fmicb.2012.00065] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 02/06/2012] [Indexed: 11/13/2022] Open
Abstract
On a global scale, crustal fluids fuel a large part of the deep-subseafloor biosphere by providing electron acceptors for microbial respiration. In this study, we examined bacterial cultures from sediments of the Juan de Fuca Ridge, Northeast Pacific (IODP Site U1301). The sediments comprise three distinctive compartments: an upper sulfate-containing zone, formed by bottom-seawater diffusion, a sulfate-depleted zone, and a second (∼140 m thick) sulfate-containing zone influenced by fluid diffusion from the basaltic aquifer. In order to identify and characterize sulfate-reducing bacteria, enrichment cultures from different sediment layers were set up, analyzed by molecular screening, and used for isolating pure cultures. The initial enrichments harbored specific communities of heterotrophic microorganisms. Strains affiliated to Desulfosporosinus lacus, Desulfotomaculum sp., and Desulfovibrio aespoeensis were isolated only from the top layers (1.3–9.1 meters below seafloor, mbsf), while several strains of Desulfovibrio indonesiensis and a relative of Desulfotignum balticum were obtained from near-basement sediments (240–262 mbsf). Physiological tests on three selected strains affiliated to Dv. aespoeensis, Dv. indonesiensis, and Desulfotignum balticum indicated that all reduce sulfate with a limited number of short-chain n-alcohols or fatty acids and were able to ferment either ethanol, pyruvate, or betaine. All three isolates shared the capacity of growing chemolithotrophically with H2 as sole electron donor. Strain P23, affiliating with Dv. indonesiensis, even grew autotrophically in the absence of any organic compounds. Thus, H2 might be an essential electron donor in the deep-subseafloor where the availability of organic substrates is limited. The isolation of non-sporeforming sulfate reducers from fluid-influenced layers indicates that they have survived the long-term burial as active populations even after the separation from the seafloor hundreds of meters above.
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Affiliation(s)
- Katja Fichtel
- Paleomicrobiology, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg Oldenburg, Germany
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Edwards KJ, Fisher AT, Wheat CG. The deep subsurface biosphere in igneous ocean crust: frontier habitats for microbiological exploration. Front Microbiol 2012; 3:8. [PMID: 22347212 PMCID: PMC3271274 DOI: 10.3389/fmicb.2012.00008] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 01/05/2012] [Indexed: 11/17/2022] Open
Abstract
We discuss ridge flank environments in the ocean crust as habitats for subseafloor microbial life. Oceanic ridge flanks, areas far from the magmatic and tectonic influence of seafloor spreading, comprise one of the largest and least explored microbial habitats on the planet. We describe the nature of selected ridge flank crustal environments, and present a framework for delineating a continuum of conditions and processes that are likely to be important for defining subseafloor microbial "provinces." The basis for this framework is three governing conditions that help to determine the nature of subseafloor biomes: crustal age, extent of fluid flow, and thermal state. We present a brief overview of subseafloor conditions, within the context of these three characteristics, for five field sites where microbial studies have been done, are underway, or have been proposed. Technical challenges remain and likely will limit progress in studies of microbial ridge flank ecosystems, which is why it is vital to select and design future studies so as to leverage as much general understanding as possible from work focused at a small number of sites. A characterization framework such that as presented in this paper, perhaps including alternative or additional physical or chemical characteristics, is essential for achieving the greatest benefit from multidisciplinary microbial investigations of oceanic ridge flanks.
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Affiliation(s)
- Katrina J. Edwards
- Department of Biological Sciences, University of Southern CaliforniaLos Angeles, CA, USA
| | - Andrew T. Fisher
- Department of Earth and Planetary Sciences, University of California Santa CruzSanta Cruz, CA, USA
| | - C. Geoffrey Wheat
- Global Undersea Research Unit, University of Alaska FairbanksFairbanks, CA, USA
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Fisher A, Cowen J, Wheat C, Clark J. Preparation and injection of fluid tracers during IODP Expedition 327, eastern flank of Juan de Fuca Ridge. ACTA ACUST UNITED AC 2011. [DOI: 10.2204/iodp.proc.327.108.2011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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Coggon RM, Teagle DA. Hydrothermal calcium-carbonate veins reveal past ocean chemistry. Trends Analyt Chem 2011. [DOI: 10.1016/j.trac.2011.02.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Orcutt BN, Sylvan JB, Knab NJ, Edwards KJ. Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol Mol Biol Rev 2011; 75:361-422. [PMID: 21646433 PMCID: PMC3122624 DOI: 10.1128/mmbr.00039-10] [Citation(s) in RCA: 320] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The majority of life on Earth--notably, microbial life--occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean-the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.-has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats.
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Affiliation(s)
- Beth N. Orcutt
- Center for Geomicrobiology, Aarhus University, 8000 Aarhus, Denmark
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Jason B. Sylvan
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Nina J. Knab
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Katrina J. Edwards
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
- Department of Earth Sciences, University of Southern California, Los Angeles, California 90089
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Coggon RM, Teagle DAH, Smith-Duque CE, Alt JC, Cooper MJ. Reconstructing Past Seawater Mg/Ca and Sr/Ca from Mid-Ocean Ridge Flank Calcium Carbonate Veins. Science 2010; 327:1114-7. [PMID: 20133522 DOI: 10.1126/science.1182252] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Rosalind M Coggon
- Department of Earth Science and Engineering, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
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Fisher AT, Davis EE, Becker K. Borehole-to-borehole hydrologic response across 2.4 km in the upper oceanic crust: Implications for crustal-scale properties. ACTA ACUST UNITED AC 2008. [DOI: 10.1029/2007jb005447] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
Developing a method for secure sequestration of anthropogenic carbon dioxide in geological formations is one of our most pressing global scientific problems. Injection into deep-sea basalt formations provides unique and significant advantages over other potential geological storage options, including (i) vast reservoir capacities sufficient to accommodate centuries-long U.S. production of fossil fuel CO2 at locations within pipeline distances to populated areas and CO2 sources along the U.S. west coast; (ii) sufficiently closed water-rock circulation pathways for the chemical reaction of CO2 with basalt to produce stable and nontoxic (Ca(2+), Mg(2+), Fe(2+))CO(3) infilling minerals, and (iii) significant risk reduction for post-injection leakage by geological, gravitational, and hydrate-trapping mechanisms. CO2 sequestration in established sediment-covered basalt aquifers on the Juan de Fuca plate offer promising locations to securely accommodate more than a century of future U.S. emissions, warranting energized scientific research, technological assessment, and economic evaluation to establish a viable pilot injection program in the future.
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Hutnak M, Fisher AT. Influence of sedimentation, local and regional hydrothermal circulation, and thermal rebound on measurements of seafloor heat flux. ACTA ACUST UNITED AC 2007. [DOI: 10.1029/2007jb005022] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
To determine the microbial community diversity within old oceanic crust, a novel sampling strategy was used to collect crustal fluids at Baby Bare Seamount, a 3.5 Ma old outcrop located in the north-east Pacific Ocean on the eastern flank of the Juan de Fuca Ridge. Stainless steel probes were driven directly into the igneous ocean crust to obtain samples of ridge flank crustal fluids. Genetic signatures and enrichment cultures of microorganisms demonstrate that these crustal fluids host a microbial community composed of species indigenous to the subseafloor, including anaerobic thermophiles, and species from other deep-sea habitats, such as seawater and sediments. Evidence using molecular techniques indicates the presence of a relatively small but active microbial population, dominated by bacteria. The microbial community diversity found in the crustal fluids may indicate habitat variability in old oceanic crust, with inputs of nutrients from seawater, sediment pore-water fluids and possibly hydrothermal sources. This report further supports the presence of an indigenous microbial community in ridge flank crustal fluids and advances our understanding of the potential physiological and phylogenetic diversity of this community.
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Affiliation(s)
- Julie A Huber
- University of Washington, School of Oceanography, Center for Astrobiology and Early Evolution, Box 357940 Seattle, 98195, USA.
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25
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Mehta MP, Huber JA, Baross JA. Incidence of novel and potentially archaeal nitrogenase genes in the deep Northeast Pacific Ocean. Environ Microbiol 2005; 7:1525-34. [PMID: 16156726 DOI: 10.1111/j.1462-2920.2005.00836.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Archaea have been detected throughout the oceanic water column and are quantitatively important members of picoplankton in the deep ocean. Two common groups, group I Crenarchaeota and group II Euryarchaeota, are consistently detected in warm hydrothermal fluid and are assumed to have been drawn into the subseafloor, mixed with hydrothermal fluid and then expelled. However, because they remain resistant to cultivation, very little is known about their physiology. Here we show that cold deep-seawater from the axial valley of Endeavour Segment on the Juan de Fuca Ridge contains not only groups I and II archaea as expected, but also unique potentially archaeal nitrogenase (nifH) genes, which are required for nitrogen fixation. These nifH genes are phylogenetically distinct and have dissimilar G+C content compared with those of hydrothermal vent archaea, suggesting that they belong to non-thermophilic deep-sea archaea. Furthermore, this sample did not contain mcrA genes, which are present in methanogens, the only known archaeal nitrogen fixers. These nifH genes were not detected in upper water column samples, or in a deep-seawater sample 100 km away from the spreading axis of the Juan de Fuca Ridge. We propose that these unique nifH genes may be localized to archaea that circulate through the nitrogen-poor subseafloor at the mid-ocean ridge as part of their life cycle.
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Affiliation(s)
- Mausmi P Mehta
- University of Washington, School of Oceanography, Seattle, WA 98195, USA.
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Nanu M, Schoonman J, Goossens A. Nanocomposite three-dimensional solar cells obtained by chemical spray deposition. NANO LETTERS 2005; 5:1716-9. [PMID: 16159211 DOI: 10.1021/nl0509632] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The present study is focused on low-cost preparation of thin film TiO2/CuInS2 nanocomposite three-dimensional (3D) solar cells. With the aid of a simple spray deposition method, we have been able to obtain 3D solar cells, with a remarkable energy conversion efficiency of 5%. The new 3D solar cell design has the potential to breakdown the price barrier and to open up new production technologies for low-cost photovoltaic solar cells.
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Affiliation(s)
- Marian Nanu
- Laboratory for Inorganic Chemistry, Delft Institute for Sustainable Energy, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands.
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27
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Chapter 10 late permian double-phased mass extinction and volcanism: an oceanographic perspective. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s0920-5446(05)80010-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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28
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Cowen JP. The microbial biosphere of sediment-buried oceanic basement. Res Microbiol 2004; 155:497-506. [PMID: 15313248 DOI: 10.1016/j.resmic.2004.03.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2004] [Accepted: 03/26/2004] [Indexed: 11/25/2022]
Abstract
Low-temperature hydrothermal fluids, circulating within the vast volume of sediment-buried upper oceanic basement on the flanks of the global mid-ocean ridge system, represent a largely unexplored habitat that could potentially host a significant and unique microbial biosphere. The present state of knowledge and many remaining challenges are discussed.
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Affiliation(s)
- James P Cowen
- Department of Oceanography, School of Ocean and Earth Science and Technology, Univerisity of Hawaii, 1000 Pope Road, Honolulu, HI 96822, USA.
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29
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Embley RW, Lupton JE. Diking, event plumes, and the subsurface biosphere at mid-ocean ridges. THE SUBSEAFLOOR BIOSPHERE AT MID-OCEAN RIDGES 2004. [DOI: 10.1029/144gm06] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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30
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Baross JA, Wilcock WSD, Kelley DS, DeLong EF, Craig Cary S. The subsurface biosphere at Mid-Ocean Ridges: Issues and challenges. THE SUBSEAFLOOR BIOSPHERE AT MID-OCEAN RIDGES 2004. [DOI: 10.1029/144gm01] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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31
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