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Jaussi M, Jørgensen BB, Kjeldsen KU, Lomstein BA, Pearce C, Seidenkantz MS, Røy H. Cell-specific rates of sulfate reduction and fermentation in the sub-seafloor biosphere. Front Microbiol 2023; 14:1198664. [PMID: 37555068 PMCID: PMC10405931 DOI: 10.3389/fmicb.2023.1198664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 07/05/2023] [Indexed: 08/10/2023] Open
Abstract
Microorganisms in subsurface sediments live from recalcitrant organic matter deposited thousands or millions of years ago. Their catabolic activities are low, but the deep biosphere is of global importance due to its volume. The stability of deeply buried sediments provides a natural laboratory where prokaryotic communities that live in steady state with their environments can be studied over long time scales. We tested if a balance is established between the flow of energy, the microbial community size, and the basal power requirement needed to maintain cells in sediments buried meters below the sea floor. We measured rates of carbon oxidation by sulfate reduction and counted the microbial cells throughout ten carefully selected sediment cores with ages from years to millions of years. The rates of carbon oxidation were converted to power (J s-1 i.e., Watt) using the Gibbs free energy of the anaerobic oxidation of complex organic carbon. We separated energy dissipation by fermentation from sulfate reduction. Similarly, we separated the community into sulfate reducers and non-sulfate reducers based on the dsrB gene, so that sulfate reduction could be related to sulfate reducers. We found that the per-cell sulfate reduction rate was stable near 10-2 fmol C cell-1 day-1 right below the zone of bioturbation and did not decrease with increasing depth and sediment age. The corresponding power dissipation rate was 10-17 W sulfate-reducing cell-1. The cell-specific power dissipation of sulfate reducers in old sediments was similar to the slowest growing anaerobic cultures. The energy from mineralization of organic matter that was not dissipated by sulfate reduction was distributed evenly to all cells that did not possess the dsrB gene, i.e., cells operationally defined as fermenting. In contrast to sulfate reducers, the fermenting cells had decreasing catabolism as the sediment aged. A vast difference in power requirement between fermenters and sulfate reducers caused the microbial community in old sediments to consist of a minute fraction of sulfate reducers and a vast majority of fermenters.
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Affiliation(s)
- Marion Jaussi
- Department of Biology, Aarhus University, Aarhus, Denmark
| | | | | | | | - Christof Pearce
- Department of Geoscience, Aarhus University, Aarhus, Denmark
| | | | - Hans Røy
- Department of Biology, Aarhus University, Aarhus, Denmark
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2
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Pellerin A, Lotem N, Walter Anthony K, Eliani Russak E, Hasson N, Røy H, Chanton JP, Sivan O. Methane production controls in a young thermokarst lake formed by abrupt permafrost thaw. Glob Chang Biol 2022; 28:3206-3221. [PMID: 35243729 PMCID: PMC9310722 DOI: 10.1111/gcb.16151] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/21/2021] [Accepted: 02/11/2022] [Indexed: 06/01/2023]
Abstract
Methane (CH4 ) release to the atmosphere from thawing permafrost contributes significantly to global CH4 emissions. However, constraining the effects of thaw that control the production and emission of CH4 is needed to anticipate future Arctic emissions. Here are presented robust rate measurements of CH4 production and cycling in a region of rapidly degrading permafrost. Big Trail Lake, located in central Alaska, is a young, actively expanding thermokarst lake. The lake was investigated by taking two 1 m cores of sediment from different regions. Two independent methods of measuring microbial CH4 production, long term (CH4 accumulation) and short term (14 C tracer), produced similar average rates of 11 ± 3.5 and 9 ± 3.6 nmol cm-3 d-1 , respectively. The rates had small variations between the different lithological units, indicating homogeneous CH4 production despite heterogeneous lithology in the surface ~1 m of sediment. To estimate the total CH4 production, the CH4 production rates were multiplied through the 10-15 m deep talik (thaw bulb). This estimate suggests that CH4 production is higher than emission by a maximum factor of ~2, which is less than previous estimates. Stable and radioactive carbon isotope measurements showed that 50% of dissolved CH4 in the first meter was produced further below. Interestingly, labeled 14 C incubations with 2-14 C acetate and 14 C CO2 indicate that variations in the pathway used by microbes to produce CH4 depends on the age and type of organic matter in the sediment, but did not appear to influence the rates at which CH4 was produced. This study demonstrates that at least half of the CH4 produced by microbial breakdown of organic matter in actively expanding thermokarst is emitted to the atmosphere, and that the majority of this CH4 is produced in the deep sediment.
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Affiliation(s)
- André Pellerin
- Department of Earth and Environmental SciencesBen Gurion University of the NegevBeershevaIsrael
| | - Noam Lotem
- Department of Earth and Environmental SciencesBen Gurion University of the NegevBeershevaIsrael
| | - Katey Walter Anthony
- Water and Environmental Research CenterUniversity of Alaska FairbanksFairbanksAlaskaUSA
- International Arctic Research CenterFairbanksAlaskaUSA
| | - Efrat Eliani Russak
- Department of Earth and Environmental SciencesBen Gurion University of the NegevBeershevaIsrael
| | - Nicholas Hasson
- Water and Environmental Research CenterUniversity of Alaska FairbanksFairbanksAlaskaUSA
| | - Hans Røy
- Department of BiologyAarhus UniversityAarhusDenmark
| | - Jeffrey P. Chanton
- Department of Earth Ocean and Atmospheric ScienceFlorida State UniversityTallahasseeFloridaUSA
| | - Orit Sivan
- Department of Earth and Environmental SciencesBen Gurion University of the NegevBeershevaIsrael
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3
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Laufer-Meiser K, Michaud AB, Maisch M, Byrne JM, Kappler A, Patterson MO, Røy H, Jørgensen BB. Potentially bioavailable iron produced through benthic cycling in glaciated Arctic fjords of Svalbard. Nat Commun 2021; 12:1349. [PMID: 33649339 PMCID: PMC7921405 DOI: 10.1038/s41467-021-21558-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/28/2021] [Indexed: 01/31/2023] Open
Abstract
The Arctic has the highest warming rates on Earth. Glaciated fjord ecosystems, which are hotspots of carbon cycling and burial, are extremely sensitive to this warming. Glaciers are important for the transport of iron from land to sea and supply this essential nutrient to phytoplankton in high-latitude marine ecosystems. However, up to 95% of the glacially-sourced iron settles to sediments close to the glacial source. Our data show that while 0.6-12% of the total glacially-sourced iron is potentially bioavailable, biogeochemical cycling in Arctic fjord sediments converts the glacially-derived iron into more labile phases, generating up to a 9-fold increase in the amount of potentially bioavailable iron. Arctic fjord sediments are thus an important source of potentially bioavailable iron. However, our data suggests that as glaciers retreat onto land the flux of iron to the sediment-water interface may be reduced. Glacial retreat therefore likely impacts iron cycling in coastal marine ecosystems.
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Affiliation(s)
- Katja Laufer-Meiser
- grid.7048.b0000 0001 1956 2722Center for Geomicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark ,grid.15649.3f0000 0000 9056 9663Present Address: GEOMAR, Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Alexander B. Michaud
- grid.7048.b0000 0001 1956 2722Center for Geomicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark ,grid.296275.d0000 0000 9516 4913Present Address: Bigelow Laboratory for Ocean Sciences, Maine, USA
| | - Markus Maisch
- grid.10392.390000 0001 2190 1447Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - James M. Byrne
- grid.10392.390000 0001 2190 1447Center for Applied Geosciences, University of Tübingen, Tübingen, Germany ,grid.5337.20000 0004 1936 7603Present Address: School of Earth Sciences, University of Bristol, Wills Memorial Building, Bristol, UK
| | - Andreas Kappler
- grid.10392.390000 0001 2190 1447Center for Applied Geosciences, University of Tübingen, Tübingen, Germany ,grid.15649.3f0000 0000 9056 9663Present Address: GEOMAR, Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Molly O. Patterson
- grid.264260.40000 0001 2164 4508Department of Geological Sciences and Environmental Studies, Binghamton University, New York, USA
| | - Hans Røy
- grid.7048.b0000 0001 1956 2722Center for Geomicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Bo Barker Jørgensen
- grid.7048.b0000 0001 1956 2722Center for Geomicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark
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4
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Nielsen SD, Paegle I, Borisov SM, Kjeldsen KU, Røy H, Skibsted J, Koren K. Optical Sensing of pH and O 2 in the Evaluation of Bioactive Self-Healing Cement. ACS Omega 2019; 4:20237-20243. [PMID: 31815225 PMCID: PMC6893957 DOI: 10.1021/acsomega.9b02541] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/31/2019] [Indexed: 05/08/2023]
Abstract
Leakage from cementitious structures with a retaining function can have devastating environmental consequences. Leaks can originate from cracks within the hardened cementitious material that is supposed to seal the structure off from the surrounding environment. Bioactive self-healing concretes containing bacteria capable of microbially inducing CaCO3 precipitation have been suggested to mitigate the healing of such cracks before leaking occurs. An important parameter determining the biocompatibility of concretes and cements is the pH environment. Therefore, a novel ratiometric pH optode imaging system based on an inexpensive single-lens reflex (SLR) camera was used to characterize the pH of porewater within cracks of submerged hydrated oil and gas well cement. This enabled the imaging of pH with a spatial distribution in high resolution (50 μm per pixel) and a gradient of 1.4 pH units per 1 mm. The effect of fly ash substitution and hydration time on the pH of the cement surface was evaluated by this approach. The results show that pH is significantly reduced from pH >11 to below 10 with increasing fly ash content as well as hydration time. The assessment of bioactivity in the cement was evaluated by introducing superabsorbent polymers with encapsulated Bacillus alkalinitrilicus endospores into the cracks. The bacterial activity was measured using oxygen optodes, which showed the highest bacterial activity with increasing amounts of fly ash substitution in the cement, correlating with the decrease in the pH. Overall, our results demonstrate that the pH of well cements can be reliably measured and modified to sustain the microbial activity.
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Affiliation(s)
- Søren Dollerup Nielsen
- Center
for Geomicrobiology, Aarhus University Centre for Water Technology,
Section for Microbiology, Department of Bioscience, and Department of Chemistry and Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
- E-mail: (S.D.N.)
| | - Ieva Paegle
- Department
of Civil Engineering, Technical University
of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Sergey M. Borisov
- Institute
of Analytical Chemistry and Food Chemistry, Graz University of Technology, 8010 Graz, Austria
| | - Kasper Urup Kjeldsen
- Center
for Geomicrobiology, Aarhus University Centre for Water Technology,
Section for Microbiology, Department of Bioscience, and Department of Chemistry and Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
| | - Hans Røy
- Center
for Geomicrobiology, Aarhus University Centre for Water Technology,
Section for Microbiology, Department of Bioscience, and Department of Chemistry and Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
| | - Jørgen Skibsted
- Center
for Geomicrobiology, Aarhus University Centre for Water Technology,
Section for Microbiology, Department of Bioscience, and Department of Chemistry and Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
| | - Klaus Koren
- Center
for Geomicrobiology, Aarhus University Centre for Water Technology,
Section for Microbiology, Department of Bioscience, and Department of Chemistry and Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
- E-mail: (K.K.)
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5
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Pelikan C, Jaussi M, Wasmund K, Seidenkrantz MS, Pearce C, Kuzyk ZZA, Herbold CW, Røy H, Kjeldsen KU, Loy A. Glacial Runoff Promotes Deep Burial of Sulfur Cycling-Associated Microorganisms in Marine Sediments. Front Microbiol 2019; 10:2558. [PMID: 31787951 PMCID: PMC6853847 DOI: 10.3389/fmicb.2019.02558] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/23/2019] [Indexed: 12/22/2022] Open
Abstract
Marine fjords with active glacier outlets are hot spots for organic matter burial in the sediments and subsequent microbial mineralization. Here, we investigated controls on microbial community assembly in sub-arctic glacier-influenced (GI) and non-glacier-influenced (NGI) marine sediments in the Godthåbsfjord region, south-western Greenland. We used a correlative approach integrating 16S rRNA gene and dissimilatory sulfite reductase (dsrB) amplicon sequence data over six meters of depth with biogeochemistry, sulfur-cycling activities, and sediment ages. GI sediments were characterized by comparably high sedimentation rates and had "young" sediment ages of <500 years even at 6 m sediment depth. In contrast, NGI stations reached ages of approximately 10,000 years at these depths. Sediment age-depth relationships, sulfate reduction rates (SRR), and C/N ratios were strongly correlated with differences in microbial community composition between GI and NGI sediments, indicating that age and diagenetic state were key drivers of microbial community assembly in subsurface sediments. Similar bacterial and archaeal communities were present in the surface sediments of all stations, whereas only in GI sediments were many surface taxa also abundant through the whole sediment core. The relative abundance of these taxa, including diverse Desulfobacteraceae members, correlated positively with SRRs, indicating their active contributions to sulfur-cycling processes. In contrast, other surface community members, such as Desulfatiglans, Atribacteria, and Chloroflexi, survived the slow sediment burial at NGI stations and dominated in the deepest sediment layers. These taxa are typical for the energy-limited marine deep biosphere and their relative abundances correlated positively with sediment age. In conclusion, our data suggests that high rates of sediment accumulation caused by glacier runoff and associated changes in biogeochemistry, promote persistence of sulfur-cycling activity and burial of a larger fraction of the surface microbial community into the deep subsurface.
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Affiliation(s)
- Claus Pelikan
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Marion Jaussi
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kenneth Wasmund
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Marit-Solveig Seidenkrantz
- Palaeoceanography and Palaeoclimate Group, Arctic Research Centre, and iClimate Interdisciplinary Centre for Climate Change, Department of Geoscience, Aarhus University, Aarhus, Denmark
| | - Christof Pearce
- Palaeoceanography and Palaeoclimate Group, Arctic Research Centre, and iClimate Interdisciplinary Centre for Climate Change, Department of Geoscience, Aarhus University, Aarhus, Denmark
| | - Zou Zou Anna Kuzyk
- Department of Geological Sciences, Centre for Earth Observation Science, University of Manitoba, Winnipeg, MB, Canada
| | - Craig W. Herbold
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Hans Røy
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper Urup Kjeldsen
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
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6
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Scoma A, Garrido-Amador P, Nielsen SD, Røy H, Kjeldsen KU. The Polyextremophilic Bacterium Clostridium paradoxum Attains Piezophilic Traits by Modulating Its Energy Metabolism and Cell Membrane Composition. Appl Environ Microbiol 2019; 85:e00802-19. [PMID: 31126939 PMCID: PMC6643245 DOI: 10.1128/aem.00802-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 05/13/2019] [Indexed: 11/20/2022] Open
Abstract
In polyextremophiles, i.e., microorganisms growing preferentially under multiple extremes, synergistic effects may allow growth when application of the same extremes alone would not. High hydrostatic pressure (HP) is rarely considered in studies of polyextremophiles, and its role in potentially enhancing tolerance to other extremes remains unclear. Here, we investigated the HP-temperature response in Clostridium paradoxum, a haloalkaliphilic moderately thermophilic endospore-forming bacterium, in the range of 50 to 70°C and 0.1 to 30 MPa. At ambient pressure, growth limits were extended from the previously reported 63°C to 70°C, defining C. paradoxum as an actual thermophile. Concomitant application of high HP and temperature compared to standard conditions (i.e., ambient pressure and 50°C) remarkably enhanced growth, with an optimum growth rate observed at 22 MPa and 60°C. HP distinctively defined C. paradoxum physiology, as at 22 MPa biomass, production increased by 75% and the release of fermentation products per cell decreased by >50% compared to ambient pressure. This metabolic modulation was apparently linked to an energy-preserving mechanism triggered by HP, involving a shift toward pyruvate as the preferred energy and carbon source. High HPs decreased cell damage, as determined by Syto9 and propidium iodide staining, despite no organic solute being accumulated intracellularly. A distinct reduction in carbon chain length of phospholipid fatty acids (PLFAs) and an increase in the amount of branched-chain PLFAs occurred at high HP. Our results describe a multifaceted, cause-and-effect relationship between HP and cell metabolism, stressing the importance of applying HP to define the boundaries for life under polyextreme conditions.IMPORTANCE Hydrostatic pressure (HP) is a fundamental parameter influencing biochemical reactions and cell physiology; however, it is less frequently applied than other factors, such as pH, temperature, and salinity, when studying polyextremophilic microorganisms. In particular, how HP affects microbial tolerance to other and multiple extremes remains unclear. Here, we show that under polyextreme conditions of high pH and temperature, Clostridium paradoxum demonstrates a moderately piezophilic nature as cultures grow to highest cell densities and most efficiently at a specific combination of temperature and HP. Our results highlight the importance of considering HP when exploring microbial physiology under extreme conditions and thus have implications for defining the limits for microbial life in nature and for optimizing industrial bioprocesses occurring under multiple extremes.
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Affiliation(s)
- Alberto Scoma
- Department of Bioscience, Section of Microbiology, Aarhus University, Aarhus, Denmark
| | - Paloma Garrido-Amador
- Department of Bioscience, Section of Microbiology, Aarhus University, Aarhus, Denmark
| | | | - Hans Røy
- Department of Bioscience, Section of Microbiology, Aarhus University, Aarhus, Denmark
| | - Kasper Urup Kjeldsen
- Department of Bioscience, Section of Microbiology, Aarhus University, Aarhus, Denmark
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7
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Petro C, Zäncker B, Starnawski P, Jochum LM, Ferdelman TG, Jørgensen BB, Røy H, Kjeldsen KU, Schramm A. Marine Deep Biosphere Microbial Communities Assemble in Near-Surface Sediments in Aarhus Bay. Front Microbiol 2019; 10:758. [PMID: 31031732 PMCID: PMC6474314 DOI: 10.3389/fmicb.2019.00758] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 03/26/2019] [Indexed: 11/30/2022] Open
Abstract
Analyses of microbial diversity in marine sediments have identified a core set of taxa unique to the marine deep biosphere. Previous studies have suggested that these specialized communities are shaped by processes in the surface seabed, in particular that their assembly is associated with the transition from the bioturbated upper zone to the nonbioturbated zone below. To test this hypothesis, we performed a fine-scale analysis of the distribution and activity of microbial populations within the upper 50 cm of sediment from Aarhus Bay (Denmark). Sequencing and qPCR were combined to determine the depth distributions of bacterial and archaeal taxa (16S rRNA genes) and sulfate-reducing microorganisms (SRM) (dsrB gene). Mapping of radionuclides throughout the sediment revealed a region of intense bioturbation at 0–6 cm depth. The transition from bioturbated sediment to the subsurface below (7 cm depth) was marked by a shift from dominant surface populations to common deep biosphere taxa (e.g., Chloroflexi and Atribacteria). Changes in community composition occurred in parallel to drops in microbial activity and abundance caused by reduced energy availability below the mixed sediment surface. These results offer direct evidence for the hypothesis that deep subsurface microbial communities present in Aarhus Bay mainly assemble already centimeters below the sediment surface, below the bioturbation zone.
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Affiliation(s)
- Caitlin Petro
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Birthe Zäncker
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Piotr Starnawski
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Lara M Jochum
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Timothy G Ferdelman
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Hans Røy
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper U Kjeldsen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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8
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Kamp A, Petro C, Røy H, Nielsen S, Carvalho P, Stief P, Schramm A. Intracellular nitrate in sediments of an oxygen-deficient marine basin is linked to pelagic diatoms. FEMS Microbiol Ecol 2018; 94:5040219. [PMID: 29931199 DOI: 10.1093/femsec/fiy122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/15/2018] [Indexed: 11/13/2022] Open
Abstract
Intracellular nitrate is an important electron acceptor in oxygen-deficient aquatic environments, either for the nitrate-storing microbes themselves, or for ambient microbial communities through nitrate leakage. This study links the spatial distribution of intracellular nitrate with the abundance and identity of nitrate-storing microbes in sediments of the Bornholm Basin, an environmental showcase for severe hypoxia. Intracellular nitrate (up to 270 nmol cm-3 sediment) was detected at all 18 stations along a 35-km transect through the basin and typically extended as deep as 1.6 cm into the sediment. Intracellular nitrate contents were particularly high at stations where chlorophyll contents suggested high settling rates of pelagic primary production. The depth distribution of intracellular nitrate matched that of the diatom-specific photopigment fucoxanthin in the upper 1.6 cm and calculations support that diatoms are the major nitrate-storing microbes in these sediments. In contrast, other known nitrate-storing microbes, such as sulfide-oxidizing bacteria and foraminifers, played only a minor role, if any. Strikingly, 18S rRNA gene sequencing revealed that the majority of the diatoms in the sediment were pelagic species. We conclude that intracellular nitrate stored by pelagic diatoms is transported to the seafloor by settling phytoplankton blooms, implying a so far overlooked 'biological nitrate pump'.
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Affiliation(s)
- Anja Kamp
- AIAS, Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark.,Center for Geomicrobiology and Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Caitlin Petro
- Center for Geomicrobiology and Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Hans Røy
- Center for Geomicrobiology and Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Susanne Nielsen
- Center for Geomicrobiology and Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Pedro Carvalho
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Peter Stief
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Andreas Schramm
- Center for Geomicrobiology and Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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9
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Ijiri A, Inagaki F, Kubo Y, Adhikari RR, Hattori S, Hoshino T, Imachi H, Kawagucci S, Morono Y, Ohtomo Y, Ono S, Sakai S, Takai K, Toki T, Wang DT, Yoshinaga MY, Arnold GL, Ashi J, Case DH, Feseker T, Hinrichs KU, Ikegawa Y, Ikehara M, Kallmeyer J, Kumagai H, Lever MA, Morita S, Nakamura KI, Nakamura Y, Nishizawa M, Orphan VJ, Røy H, Schmidt F, Tani A, Tanikawa W, Terada T, Tomaru H, Tsuji T, Tsunogai U, Yamaguchi YT, Yoshida N. Deep-biosphere methane production stimulated by geofluids in the Nankai accretionary complex. Sci Adv 2018; 4:eaao4631. [PMID: 29928689 PMCID: PMC6007163 DOI: 10.1126/sciadv.aao4631] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 05/01/2018] [Indexed: 06/08/2023]
Abstract
Microbial life inhabiting subseafloor sediments plays an important role in Earth's carbon cycle. However, the impact of geodynamic processes on the distributions and carbon-cycling activities of subseafloor life remains poorly constrained. We explore a submarine mud volcano of the Nankai accretionary complex by drilling down to 200 m below the summit. Stable isotopic compositions of water and carbon compounds, including clumped methane isotopologues, suggest that ~90% of methane is microbially produced at 16° to 30°C and 300 to 900 m below seafloor, corresponding to the basin bottom, where fluids in the accretionary prism are supplied via megasplay faults. Radiotracer experiments showed that relatively small microbial populations in deep mud volcano sediments (102 to 103 cells cm-3) include highly active hydrogenotrophic methanogens and acetogens. Our findings indicate that subduction-associated fluid migration has stimulated microbial activity in the mud reservoir and that mud volcanoes may contribute more substantially to the methane budget than previously estimated.
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Affiliation(s)
- Akira Ijiri
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | - Fumio Inagaki
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
- Research and Development Center for Ocean Drilling Science, JAMSTEC, Yokohama 236-0001, Japan
| | - Yusuke Kubo
- Center for Deep Earth Exploration, JAMSTEC, Yokohama 236-0001, Japan
| | - Rishi R. Adhikari
- Department of Earth and Environmental Sciences, University of Potsdam, D-14476 Potsdam-Golm, Germany
| | - Shohei Hattori
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
| | - Tatsuhiko Hoshino
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | - Hiroyuki Imachi
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka 237-0061, Japan
| | - Shinsuke Kawagucci
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka 237-0061, Japan
| | - Yuki Morono
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | - Yoko Ohtomo
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | - Shuhei Ono
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sanae Sakai
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka 237-0061, Japan
| | - Ken Takai
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka 237-0061, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo 152-8551, Japan
| | - Tomohiro Toki
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - David T. Wang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Marcos Y. Yoshinaga
- MARUM and Department of Geosciences, University of Bremen, D-28334 Bremen, Germany
| | - Gail L. Arnold
- Center for Geomicrobiology, Department of Biological Sciences, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Juichiro Ashi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-0885, Japan
| | - David H. Case
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Tomas Feseker
- MARUM and Department of Geosciences, University of Bremen, D-28334 Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM and Department of Geosciences, University of Bremen, D-28334 Bremen, Germany
| | - Yojiro Ikegawa
- Civil Engineering Research Laboratory, Central Research Institute of Electric Power Industry, Abiko, Chiba 270-1194, Japan
| | - Minoru Ikehara
- Center for Advanced Marine Core Research, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Jens Kallmeyer
- Department of Earth and Environmental Sciences, University of Potsdam, D-14476 Potsdam-Golm, Germany
| | - Hidenori Kumagai
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | - Mark A. Lever
- Center for Geomicrobiology, Department of Biological Sciences, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Sumito Morita
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8567, Japan
| | | | - Yuki Nakamura
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-0885, Japan
| | - Manabu Nishizawa
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka 237-0061, Japan
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hans Røy
- Center for Geomicrobiology, Department of Biological Sciences, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Frauke Schmidt
- MARUM and Department of Geosciences, University of Bremen, D-28334 Bremen, Germany
| | - Atsushi Tani
- Department of Earth and Space Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Wataru Tanikawa
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | | | - Hitoshi Tomaru
- Department of Earth Sciences, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
| | - Takeshi Tsuji
- Department of Earth Resources Engineering, Kyushu University, Fukuoka 819-0395, Japan
- International Institute for Carbon-Neutral Energy Research, Department of Earth Resources Engineering, Kyushu University, 744 Motooka, Fukuoka-shi, Fukuoka 819-0395, Japan
| | - Urumu Tsunogai
- Graduate School of Environmental Studies, Nagoya University, Nagoya 464-8601, Japan
| | - Yasuhiko T. Yamaguchi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-0885, Japan
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Naohiro Yoshida
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo 152-8551, Japan
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10
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Marietou A, Røy H, Jørgensen BB, Kjeldsen KU. Sulfate Transporters in Dissimilatory Sulfate Reducing Microorganisms: A Comparative Genomics Analysis. Front Microbiol 2018; 9:309. [PMID: 29551997 PMCID: PMC5840216 DOI: 10.3389/fmicb.2018.00309] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 02/09/2018] [Indexed: 12/31/2022] Open
Abstract
The first step in the sulfate reduction pathway is the transport of sulfate across the cell membrane. This uptake has a major effect on sulfate reduction rates. Much of the information available on sulfate transport was obtained by studies on assimilatory sulfate reduction, where sulfate transporters were identified among several types of protein families. Despite our growing knowledge on the physiology of dissimilatory sulfate-reducing microorganisms (SRM) there are no studies identifying the proteins involved in sulfate uptake in members of this ecologically important group of anaerobes. We surveyed the complete genomes of 44 sulfate-reducing bacteria and archaea across six phyla and identified putative sulfate transporter encoding genes from four out of the five surveyed protein families based on homology. We did not find evidence that ABC-type transporters (SulT) are involved in the uptake of sulfate in SRM. We speculate that members of the CysP sulfate transporters could play a key role in the uptake of sulfate in thermophilic SRM. Putative CysZ-type sulfate transporters were present in all genomes examined suggesting that this overlooked group of sulfate transporters might play a role in sulfate transport in dissimilatory sulfate reducers alongside SulP. Our in silico analysis highlights several targets for further molecular studies in order to understand this key step in the metabolism of SRMs.
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Affiliation(s)
- Angeliki Marietou
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Hans Røy
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Bo B Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper U Kjeldsen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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11
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Volpi M, Lomstein BA, Sichert A, Røy H, Jørgensen BB, Kjeldsen KU. Identity, Abundance, and Reactivation Kinetics of Thermophilic Fermentative Endospores in Cold Marine Sediment and Seawater. Front Microbiol 2017; 8:131. [PMID: 28220111 PMCID: PMC5292427 DOI: 10.3389/fmicb.2017.00131] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/18/2017] [Indexed: 11/23/2022] Open
Abstract
Cold marine sediments harbor endospores of fermentative and sulfate-reducing, thermophilic bacteria. These dormant populations of endospores are believed to accumulate in the seabed via passive dispersal by ocean currents followed by sedimentation from the water column. However, the magnitude of this process is poorly understood because the endospores present in seawater were so far not identified, and only the abundance of thermophilic sulfate-reducing endospores in the seabed has been quantified. We investigated the distribution of thermophilic fermentative endospores (TFEs) in water column and sediment of Aarhus Bay, Denmark, to test the role of suspended dispersal and determine the rate of endospore deposition and the endospore abundance in the sediment. We furthermore aimed to determine the time course of reactivation of the germinating TFEs. TFEs were induced to germinate and grow by incubating pasteurized sediment and water samples anaerobically at 50°C. We observed a sudden release of the endospore component dipicolinic acid immediately upon incubation suggesting fast endospore reactivation in response to heating. Volatile fatty acids (VFAs) and H2 began to accumulate exponentially after 3.5 h of incubation showing that reactivation was followed by a short phase of outgrowth before germinated cells began to divide. Thermophilic fermenters were mainly present in the sediment as endospores because the rate of VFA accumulation was identical in pasteurized and non-pasteurized samples. Germinating TFEs were identified taxonomically by reverse transcription, PCR amplification and sequencing of 16S rRNA. The water column and sediment shared the same phylotypes, thereby confirming the potential for seawater dispersal. The abundance of TFEs was estimated by most probable number enumeration, rates of VFA production, and released amounts of dipicolinic acid during germination. The surface sediment contained ∼105-106 inducible TFEs cm-3. TFEs thus outnumber thermophilic sulfate-reducing endospores by an order of magnitude. The abundance of cultivable TFEs decreased exponentially with sediment depth with a half-life of 350 years. We estimate that 6 × 109 anaerobic thermophilic endospores are deposited on the seafloor per m2 per year in Aarhus Bay, and that these thermophiles represent >10% of the total endospore community in the surface sediment.
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Affiliation(s)
- Marta Volpi
- Center for Geomicrobiology, Department of Bioscience, Aarhus UniversityAarhus, Denmark
| | | | | | | | | | - Kasper U. Kjeldsen
- Center for Geomicrobiology, Department of Bioscience, Aarhus UniversityAarhus, Denmark
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12
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Tarpgaard IH, Jørgensen BB, Kjeldsen KU, Røy H. The marine sulfate reducer Desulfobacterium autotrophicum HRM2 can switch between low and high apparent half-saturation constants for dissimilatory sulfate reduction. FEMS Microbiol Ecol 2017; 93:2966865. [DOI: 10.1093/femsec/fix012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 02/01/2017] [Indexed: 12/22/2022] Open
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13
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Teske A, de Beer D, McKay LJ, Tivey MK, Biddle JF, Hoer D, Lloyd KG, Lever MA, Røy H, Albert DB, Mendlovitz HP, MacGregor BJ. The Guaymas Basin Hiking Guide to Hydrothermal Mounds, Chimneys, and Microbial Mats: Complex Seafloor Expressions of Subsurface Hydrothermal Circulation. Front Microbiol 2016; 7:75. [PMID: 26925032 PMCID: PMC4757712 DOI: 10.3389/fmicb.2016.00075] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/15/2016] [Indexed: 11/13/2022] Open
Abstract
The hydrothermal mats, mounds, and chimneys of the southern Guaymas Basin are the surface expression of complex subsurface hydrothermal circulation patterns. In this overview, we document the most frequently visited features of this hydrothermal area with photographs, temperature measurements, and selected geochemical data; many of these distinct habitats await characterization of their microbial communities and activities. Microprofiler deployments on microbial mats and hydrothermal sediments show their steep geochemical and thermal gradients at millimeter-scale vertical resolution. Mapping these hydrothermal features and sampling locations within the southern Guaymas Basin suggest linkages to underlying shallow sills and heat flow gradients. Recognizing the inherent spatial limitations of much current Guaymas Basin sampling calls for comprehensive surveys of the wider spreading region.
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Affiliation(s)
- Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Dirk de Beer
- Microsensor Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Luke J McKay
- Department of Marine Sciences, University of North Carolina at Chapel HillChapel Hill, NC, USA; Center for Biofilm Engineering and Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA
| | - Margaret K Tivey
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution Woods Hole, MA, USA
| | - Jennifer F Biddle
- School of Marine Science and Policy, University of Delaware Lewes, DE, USA
| | - Daniel Hoer
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Karen G Lloyd
- Department of Marine Sciences, University of North Carolina at Chapel HillChapel Hill, NC, USA; Department of Microbiology, University of Tennessee at KnoxvilleKnoxville, TN, USA
| | - Mark A Lever
- Department of Marine Sciences, University of North Carolina at Chapel HillChapel Hill, NC, USA; Department of Environmental Sciences, Eidgenössische Technische HochschuleZurich, Switzerland
| | - Hans Røy
- Center for Geomicrobiology, Aarhus University Aarhus, Denmark
| | - Daniel B Albert
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Howard P Mendlovitz
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Barbara J MacGregor
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
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14
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Laufer K, Nordhoff M, Røy H, Schmidt C, Behrens S, Jørgensen BB, Kappler A. Coexistence of Microaerophilic, Nitrate-Reducing, and Phototrophic Fe(II) Oxidizers and Fe(III) Reducers in Coastal Marine Sediment. Appl Environ Microbiol 2015; 82:1433-1447. [PMID: 26682861 PMCID: PMC4771319 DOI: 10.1128/aem.03527-15] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 12/14/2015] [Indexed: 02/04/2023] Open
Abstract
Iron is abundant in sediments, where it can be biogeochemically cycled between its divalent and trivalent redox states. The neutrophilic microbiological Fe cycle involves Fe(III)-reducing and three different physiological groups of Fe(II)-oxidizing microorganisms, i.e., microaerophilic, anoxygenic phototrophic, and nitrate-reducing Fe(II) oxidizers. However, it is unknown whether all three groups coexist in one habitat and how they are spatially distributed in relation to gradients of O2, light, nitrate, and Fe(II). We examined two coastal marine sediments in Aarhus Bay, Denmark, by cultivation and most probable number (MPN) studies for Fe(II) oxidizers and Fe(III) reducers and by quantitative-PCR (qPCR) assays for microaerophilic Fe(II) oxidizers. Our results demonstrate the coexistence of all three metabolic types of Fe(II) oxidizers and Fe(III) reducers. In qPCR, microaerophilic Fe(II) oxidizers (Zetaproteobacteria) were present with up to 3.2 × 10(6) cells g dry sediment(-1). In MPNs, nitrate-reducing Fe(II) oxidizers, anoxygenic phototrophic Fe(II) oxidizers, and Fe(III) reducers reached cell numbers of up to 3.5 × 10(4), 3.1 × 10(2), and 4.4 × 10(4) g dry sediment(-1), respectively. O2 and light penetrated only a few millimeters, but the depth distribution of the different iron metabolizers did not correlate with the profile of O2, Fe(II), or light. Instead, abundances were homogeneous within the upper 3 cm of the sediment, probably due to wave-induced sediment reworking and bioturbation. In microaerophilic Fe(II)-oxidizing enrichment cultures, strains belonging to the Zetaproteobacteria were identified. Photoferrotrophic enrichments contained strains related to Chlorobium and Rhodobacter; the nitrate-reducing Fe(II) enrichments contained strains related to Hoeflea and Denitromonas. This study shows the coexistence of all three types of Fe(II) oxidizers in two near-shore marine environments and the potential for competition and interrelationships between them.
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Affiliation(s)
- Katja Laufer
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - Mark Nordhoff
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - Hans Røy
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Caroline Schmidt
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - Sebastian Behrens
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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15
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Gittel A, Donhauser J, Røy H, Girguis PR, Jørgensen BB, Kjeldsen KU. Ubiquitous Presence and Novel Diversity of Anaerobic Alkane Degraders in Cold Marine Sediments. Front Microbiol 2015; 6:1414. [PMID: 26733961 PMCID: PMC4681840 DOI: 10.3389/fmicb.2015.01414] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 11/27/2015] [Indexed: 01/05/2023] Open
Abstract
Alkanes are major constituents of crude oil and are released to the marine environment by natural seepage and from anthropogenic sources. Due to their chemical inertness, their removal from anoxic marine sediments is primarily controlled by the activity of anaerobic alkane-degrading microorganisms. To facilitate comprehensive cultivation-independent surveys of the diversity and distribution of anaerobic alkane degraders, we designed novel PCR primers that cover all known diversity of the 1-methylalkyl succinate synthase gene (masD/assA), which catalyzes the initial activation of alkanes. We studied masD/assA gene diversity in pristine and seepage-impacted Danish coastal sediments, as well as in sediments and alkane-degrading enrichment cultures from the Middle Valley (MV) hydrothermal vent system in the Pacific Northwest. MasD/assA genes were ubiquitously present, and the primers captured the diversity of both known and previously undiscovered masD/assA gene diversity. Seepage sediments were dominated by a single masD/assA gene cluster, which is presumably indicative of a substrate-adapted community, while pristine sediments harbored a diverse range of masD/assA phylotypes including those present in seepage sediments. This rare biosphere of anaerobic alkane degraders will likely increase in abundance in the event of seepage or accidental oil spillage. Nanomolar concentrations of short-chain alkanes (SCA) were detected in pristine and seepage sediments. Interestingly, anaerobic alkane degraders closely related to strain BuS5, the only SCA degrader in pure culture, were found in mesophilic MV enrichments, but not in cold sediments from Danish waters. We propose that the new masD/assA gene lineages in these sediments represent novel phylotypes that are either fueled by naturally occurring low levels of SCA or that metabolize medium- to long-chain alkanes. Our study highlights that masD/assA genes are a relevant diagnostic marker to identify seepage and microseepage, e.g., during prospecting for oil and gas, and may act as an indicator of anthropogenic oil spills in marine sediments.
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Affiliation(s)
- Antje Gittel
- Center for Geomicrobiology, Department of Bioscience, Aarhus University Aarhus, Denmark
| | - Johanna Donhauser
- Center for Geomicrobiology, Department of Bioscience, Aarhus University Aarhus, Denmark
| | - Hans Røy
- Center for Geomicrobiology, Department of Bioscience, Aarhus University Aarhus, Denmark
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University Cambridge, MA, USA
| | - Bo B Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University Aarhus, Denmark
| | - Kasper U Kjeldsen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University Aarhus, Denmark
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16
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Glombitza C, Jaussi M, Røy H, Seidenkrantz MS, Lomstein BA, Jørgensen BB. Formate, acetate, and propionate as substrates for sulfate reduction in sub-arctic sediments of Southwest Greenland. Front Microbiol 2015; 6:846. [PMID: 26379631 PMCID: PMC4547046 DOI: 10.3389/fmicb.2015.00846] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/03/2015] [Indexed: 11/16/2022] Open
Abstract
Volatile fatty acids (VFAs) are key intermediates in the anaerobic mineralization of organic matter in marine sediments. We studied the role of VFAs in the carbon and energy turnover in the sulfate reduction zone of sediments from the sub-arctic Godthåbsfjord (SW Greenland) and the adjacent continental shelf in the NE Labrador Sea. VFA porewater concentrations were measured by a new two-dimensional ion chromatography-mass spectrometry method that enabled the direct analysis of VFAs without sample pretreatment. VFA concentrations were low and surprisingly constant (4–6 μmol L−1 for formate and acetate, and 0.5 μmol L−1 for propionate) throughout the sulfate reduction zone. Hence, VFAs are turned over while maintaining a stable concentration that is suggested to be under a strong microbial control. Estimated mean diffusion times of acetate between neighboring cells were <1 s, whereas VFA turnover times increased from several hours at the sediment surface to several years at the bottom of the sulfate reduction zone. Thus, diffusion was not limiting the VFA turnover. Despite constant VFA concentrations, the Gibbs energies (ΔGr) of VFA-dependent sulfate reduction decreased downcore, from −28 to −16 kJ (mol formate)−1, −68 to −31 kJ (mol acetate)−1, and −124 to −65 kJ (mol propionate)−1. Thus, ΔGr is apparently not determining the in-situ VFA concentrations directly. However, at the bottom of the sulfate zone of the shelf station, acetoclastic sulfate reduction might operate at its energetic limit at ~ −30 kJ (mol acetate)−1. It is not clear what controls VFA concentrations in the porewater but cell physiological constraints such as energetic costs of VFA activation or uptake could be important. We suggest that such constraints control the substrate turnover and result in a minimum ΔGr that depends on cell physiology and is different for individual substrates.
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Affiliation(s)
- Clemens Glombitza
- Department of Bioscience, Center for Geomicrobiology, Aarhus University Aarhus, Denmark
| | - Marion Jaussi
- Department of Bioscience, Center for Geomicrobiology, Aarhus University Aarhus, Denmark
| | - Hans Røy
- Department of Bioscience, Center for Geomicrobiology, Aarhus University Aarhus, Denmark
| | - Marit-Solveig Seidenkrantz
- Department of Bioscience, Arctic Research Center, Aarhus University Aarhus, Denmark ; Department of Geoscience, Centre for Past Climate Studies, Aarhus University Aarhus, Denmark
| | - Bente A Lomstein
- Department of Bioscience, Center for Geomicrobiology, Aarhus University Aarhus, Denmark ; Section for Microbiology, Department of Bioscience, Aarhus University Aarhus, Denmark
| | - Bo B Jørgensen
- Department of Bioscience, Center for Geomicrobiology, Aarhus University Aarhus, Denmark
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17
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Lagostina L, Goldhammer T, Røy H, Evans TW, Lever MA, Jørgensen BB, Petersen DG, Schramm A, Schreiber L. Ammonia-oxidizing Bacteria of the Nitrosospira cluster 1 dominate over ammonia-oxidizing Archaea in oligotrophic surface sediments near the South Atlantic Gyre. Environ Microbiol Rep 2015; 7:404-413. [PMID: 25581373 PMCID: PMC5008181 DOI: 10.1111/1758-2229.12264] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 12/22/2014] [Accepted: 01/01/2015] [Indexed: 05/31/2023]
Abstract
Sediments across the Namibian continental margin feature a strong microbial activity gradient at their surface. This is reflected in ammonium concentrations of < 10 μM in oligotrophic abyssal plain sediments near the South Atlantic Gyre compared with ammonium concentrations of > 700 μM in upwelling areas near the coast. Here we address changes in apparent abundance and structure of ammonia-oxidizing archaeal and bacterial communities (AOA and AOB) along a transect of seven sediment stations across the Namibian shelf by analysing their respective ammonia monooxygenase genes (amoA). The relative abundance of archaeal and bacterial amoA (g(-1) DNA) decreased with increasing ammonium concentrations, and bacterial amoA frequently outnumbered archaeal amoA at the sediment-water interface [0-1 cm below seafloor (cmbsf)]. In contrast, AOA were apparently as abundant as AOB or dominated in several deeper (> 10 cmbsf), anoxic sediment layers. Phylogenetic analyses showed a change within the AOA community along the transect, from two clusters without cultured representatives at the gyre to Nitrososphaera and Nitrosopumilus clusters in the upwelling region. AOB almost exclusively belonged to the Nitrosospira cluster 1. Our results suggest that this predominantly marine AOB lineage without cultured representatives can thrive at low ammonium concentrations and is active in the marine nitrogen cycle.
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Affiliation(s)
- Lorenzo Lagostina
- Center for Geomicrobiology, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Pavia, Italy
| | - Tobias Goldhammer
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Hans Røy
- Center for Geomicrobiology, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark
| | - Thomas W Evans
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Mark A Lever
- Center for Geomicrobiology, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark
| | - Bo B Jørgensen
- Center for Geomicrobiology, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark
| | - Dorthe G Petersen
- Center for Geomicrobiology, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark
| | - Andreas Schramm
- Center for Geomicrobiology, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark
- Section for Microbiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark
| | - Lars Schreiber
- Center for Geomicrobiology, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark
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Arnold GL, Brunner B, Müller IA, Røy H. Modern applications for a total sulfur reduction distillation method - what's old is new again. Geochem Trans 2014; 15:4. [PMID: 24808759 PMCID: PMC4012173 DOI: 10.1186/1467-4866-15-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 04/10/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND The use of a boiling mixture of hydriodic acid, hypophosphorous acid, and hydrochloric acid to reduce any variety of sulfur compounds has been in use in various applications since the first appearance of this method in the literature in the 1920's. In the realm of sulfur geochemistry, this method remains a useful, but under-utilized technique. Presented here is a detailed description of the distillation set-up and procedure, as well as an overview of potential applications of this method for marine sulfur biogeochemistry/isotope studies. The presented applications include the sulfur isotope analysis of extremely low amounts of sulfate from saline water, the conversion of radiolabeled sulfate into sulfide, the extraction of refractory sulfur from marine sediments, and the use of this method to assess sulfur cycling in Aarhus Bay sediments. RESULTS The STrongly Reducing hydrIodic/hypoPhosphorous/hydrochloric acid (STRIP) reagent is capable of rapidly reducing a wide range of sulfur compounds, including the most oxidized form, sulfate, to hydrogen sulfide. Conversion of as little as approximately 5 micromole sulfate is possible, with a sulfur isotope composition reproducibility of 0.3 permil. CONCLUSIONS Although developed many decades ago, this distillation method remains relevant for many modern applications. The STRIP distillation quickly and quantitatively converts sulfur compounds to hydrogen sulfide which can be readily collected in a silver nitrate trap for further use. An application of this method to a study of sulfur cycling in Aarhus Bay demonstrates that we account for all of the sulfur compounds in pore-water, effectively closing the mass balance of sulfur cycling.
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Affiliation(s)
- Gail L Arnold
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, 8000 Aarhus, Denmark
- Department of Geological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Benjamin Brunner
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, 8000 Aarhus, Denmark
- Department of Geological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Inigo A Müller
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Hans Røy
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, 8000 Aarhus, Denmark
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Abstract
Microbial communities can subsist at depth in marine sediments without fresh supply of organic matter for millions of years. At threshold sedimentation rates of 1 millimeter per 1000 years, the low rates of microbial community metabolism in the North Pacific Gyre allow sediments to remain oxygenated tens of meters below the sea floor. We found that the oxygen respiration rates dropped from 10 micromoles of O(2) liter(-1) year(-1) near the sediment-water interface to 0.001 micromoles of O(2) liter(-1) year(-1) at 30-meter depth within 86 million-year-old sediment. The cell-specific respiration rate decreased with depth but stabilized at around 10(-3) femtomoles of O(2) cell(-1) day(-1) 10 meters below the seafloor. This result indicated that the community size is controlled by the rate of carbon oxidation and thereby by the low available energy flux.
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Affiliation(s)
- Hans Røy
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 116, 8000 Aarhus C, Denmark.
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Schauer R, Røy H, Augustin N, Gennerich HH, Peters M, Wenzhoefer F, Amann R, Meyerdierks A. Bacterial sulfur cycling shapes microbial communities in surface sediments of an ultramafic hydrothermal vent field. Environ Microbiol 2011; 13:2633-48. [PMID: 21895907 DOI: 10.1111/j.1462-2920.2011.02530.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ultramafic-hosted Logatchev hydrothermal field (LHF) is characterized by vent fluids, which are enriched in dissolved hydrogen and methane compared with fluids from basalt-hosted systems. Thick sediment layers in LHF are partly covered by characteristic white mats. In this study, these sediments were investigated in order to determine biogeochemical processes and key organisms relevant for primary production. Temperature profiling at two mat-covered sites showed a conductive heating of the sediments. Elemental sulfur was detected in the overlying mat and metal-sulfides in the upper sediment layer. Microprofiles revealed an intensive hydrogen sulfide flux from deeper sediment layers. Fluorescence in situ hybridization showed that filamentous and vibrioid, Arcobacter-related Epsilonproteobacteria dominated the overlying mats. This is in contrast to sulfidic sediments in basalt-hosted fields where mats of similar appearance are composed of large sulfur-oxidizing Gammaproteobacteria. Epsilonproteobacteria (7-21%) and Deltaproteobacteria (20-21%) were highly abundant in the surface sediment layer. The physiology of the closest cultivated relatives, revealed by comparative 16S rRNA sequence analysis, was characterized by the capability to metabolize sulfur components. High sulfate reduction rates as well as sulfide depleted in (34)S further confirmed the importance of the biogeochemical sulfur cycle. In contrast, methane was found to be of minor relevance for microbial life in mat-covered surface sediments. Our data indicate that in conductively heated surface sediments microbial sulfur cycling is the driving force for bacterial biomass production although ultramafic-hosted systems are characterized by fluids with high levels of dissolved methane and hydrogen.
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Affiliation(s)
- Regina Schauer
- Max Planck Institute for Marine Microbiology, Celsiusstr.1, D-28359 Bremen, Germany
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Jørgensen BB, Dunker R, Grünke S, Røy H. Filamentous sulfur bacteria, Beggiatoa spp., in arctic marine sediments (Svalbard, 79 degrees N). FEMS Microbiol Ecol 2010; 73:500-13. [PMID: 20608982 DOI: 10.1111/j.1574-6941.2010.00918.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Fjord sediments on the west coast of the arctic archipelago Svalbard were surveyed to understand whether large filamentous sulfur bacteria of the genus Beggiatoa thrive at seawater temperatures permanently near freezing. Two sediments had abundant populations of Beggiatoa, while at six sites, only sporadic occurrences were observed. We conclude that Beggiatoa, although previously unnoticed, are widespread in these arctic fjord sediments. Beggiatoa ranged in diameter from 2 to 52 microm and, by those tested, stored nitrate in vacuoles at up to 260 mM. The 16S rRNA gene sequence of a 20-microm-wide filament is closely associated with other large, marine, nitrate-storing Beggiatoa. The Beggiatoa mostly occurred in the upper 2-5 cm of oxidized surface sediment between oxygen and the deeper sulfidic zone. In spite of a very low or an undetectable sulfide concentration, sulfate reduction provided abundant H(2)S in this zone. The total living biomass of Beggiatoa filaments at one study site varied over 3 years between 1.13 and 3.36 g m(-2). Because of their large size, Beggiatoa accounted for up to 15% of the total prokaryotic biomass, even though the filament counts at this site were rather low, comprising <1/10,000 of the bacterial numbers on a cell basis.
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Dunker R, Røy H, Jørgensen BB. Temperature regulation of gliding motility in filamentous sulfur bacteria, Beggiatoa spp. FEMS Microbiol Ecol 2010; 73:234-42. [DOI: 10.1111/j.1574-6941.2010.00887.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Røy H, Vopel K, Huettel M, Jørgensen BB. Sulfide assimilation by ectosymbionts of the sessile ciliate, Zoothamnium niveum. Mar Biol 2009; 156:669-677. [PMID: 32921817 PMCID: PMC7477830 DOI: 10.1007/s00227-008-1117-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Accepted: 12/15/2008] [Indexed: 06/11/2023]
Abstract
We investigated the constraints on sulfide uptake by bacterial ectosymbionts on the marine peritrich ciliate Zoothamnium niveum by a combination of experimental and numerical methods. Protists with symbionts were collected on large blocks of mangrove-peat. The blocks were placed in a flow cell with flow adjusted to in situ velocity. The water motion around the colonies was then characterized by particle tracking velocimetry. This shows that the feather-shaped colony of Z. niveum generates a unidirectional flow of seawater through the colony with no recirculation. The source of the feeding current was the free-flowing water although the size of the colonies suggests that they live partly submerged in the diffusive boundary layer. We showed that the filtered volume allows Z. niveum to assimilate sufficient sulfide to sustain the symbiosis at a few micromoles per liter in ambient concentration. Numerical modeling shows that sulfide oxidizing bacteria on the surfaces of Z. niveum can sustain 100-times higher sulfide uptake than bacteria on flat surfaces, such as microbial mats. The study demonstrates that the filter feeding zooids of Z. niveum are preadapted to be prime habitats for sulfide oxidizing bacteria due to Z. niveum's habitat preference and due to the feeding current. Z. niveum is capable of exploiting low concentrations of sulfide in near norm-oxic seawater. This links its otherwise dissimilar habitats and makes it functionally similar to invertebrates with thiotrophic symbionts in filtering organs.
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Affiliation(s)
- Hans Røy
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359 Bremen, Germany
- Present Address: Department of Biological Sciences, Center for Geomicrobiology, University of Aarhus, Ny Munkegade 1535, 8000 Aarhus C, Denmark
| | - Kay Vopel
- School of Applied Sciences, Auckland University of Technology, Mail No C43, Private Bag 92006, Auckland, 1142 New Zealand
| | - Markus Huettel
- Department of Oceanography, Florida State University, 117 N Woodward Ave., OSB 517, Tallahassee, FL 32306-4320 USA
| | - Bo Barker Jørgensen
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359 Bremen, Germany
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Kamp A, Røy H, Schulz-Vogt HN. Video-supported analysis of Beggiatoa filament growth, breakage, and movement. Microb Ecol 2008; 56:484-91. [PMID: 18335158 PMCID: PMC2755761 DOI: 10.1007/s00248-008-9367-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2007] [Revised: 12/06/2007] [Accepted: 01/27/2008] [Indexed: 05/05/2023]
Abstract
A marine Beggiatoa sp. was cultured in semi-solid agar with opposing oxygen-sulfide gradients. Growth pattern, breakage of filaments for multiplication, and movement directions of Beggiatoa filaments in the transparent agar were investigated by time-lapse video recording. The initial doubling time of cells was 15.7 +/- 1.3 h (mean +/- SD) at room temperature. Filaments grew up to an average length of 1.7 +/- 0.2 mm, but filaments of up to approximately 6 mm were also present. First breakages of filaments occurred approximately 19 h after inoculation, and time-lapse movies illustrated that a parent filament could break into several daughter filaments within a few hours. In >20% of the cases, filament breakage occurred at the tip of a former loop. As filament breakage is accomplished by the presence of sacrificial cells, loop formation and the presence of sacrificial cells must coincide. We hypothesize that sacrificial cells enhance the chance of loop formation by interrupting the communication between two parts of one filament. With communication interrupted, these two parts of one filament can randomly move toward each other forming the tip of a loop at the sacrificial cell.
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Affiliation(s)
- Anja Kamp
- Institute for Microbiology, Leibniz University of Hannover, Hannover, Germany.
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Omoregie EO, Mastalerz V, de Lange G, Straub KL, Kappler A, Røy H, Stadnitskaia A, Foucher JP, Boetius A. Biogeochemistry and community composition of iron- and sulfur-precipitating microbial mats at the Chefren mud volcano (Nile Deep Sea Fan, Eastern Mediterranean). Appl Environ Microbiol 2008; 74:3198-215. [PMID: 18378658 PMCID: PMC2394935 DOI: 10.1128/aem.01751-07] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 02/29/2008] [Indexed: 11/20/2022] Open
Abstract
In this study we determined the composition and biogeochemistry of novel, brightly colored, white and orange microbial mats at the surface of a brine seep at the outer rim of the Chefren mud volcano. These mats were interspersed with one another, but their underlying sediment biogeochemistries differed considerably. Microscopy revealed that the white mats were granules composed of elemental S filaments, similar to those produced by the sulfide-oxidizing epsilonproteobacterium "Candidatus Arcobacter sulfidicus." Fluorescence in situ hybridization indicated that microorganisms targeted by a "Ca. Arcobacter sulfidicus"-specific oligonucleotide probe constituted up to 24% of the total the cells within these mats. Several 16S rRNA gene sequences from organisms closely related to "Ca. Arcobacter sulfidicus" were identified. In contrast, the orange mat consisted mostly of bright orange flakes composed of empty Fe(III) (hydr)oxide-coated microbial sheaths, similar to those produced by the neutrophilic Fe(II)-oxidizing betaproteobacterium Leptothrix ochracea. None of the 16S rRNA gene sequences obtained from these samples were closely related to sequences of known neutrophilic aerobic Fe(II)-oxidizing bacteria. The sediments below both types of mats showed relatively high sulfate reduction rates (300 nmol x cm(-3) x day(-1)) partially fueled by the anaerobic oxidation of methane (10 to 20 nmol x cm(-3) x day(-1)). Free sulfide produced below the white mat was depleted by sulfide oxidation within the mat itself. Below the orange mat free Fe(II) reached the surface layer and was depleted in part by microbial Fe(II) oxidation. Both mats and the sediments underneath them hosted very diverse microbial communities and contained mineral precipitates, most likely due to differences in fluid flow patterns.
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MESH Headings
- Arcobacter/cytology
- Arcobacter/genetics
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Bacteria/metabolism
- Biodiversity
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Ferric Compounds/metabolism
- Ferrous Compounds/metabolism
- Genes, rRNA
- Geologic Sediments/microbiology
- Iron/metabolism
- Leptothrix/cytology
- Molecular Sequence Data
- Oxidation-Reduction
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sulfides/metabolism
- Sulfur/metabolism
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27
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Hoffmann F, Røy H, Bayer K, Hentschel U, Pfannkuchen M, Brümmer F, de Beer D. Oxygen dynamics and transport in the Mediterranean sponge Aplysina aerophoba. Mar Biol 2008; 153:1257-1264. [PMID: 24391232 PMCID: PMC3873076 DOI: 10.1007/s00227-008-0905-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Accepted: 01/03/2008] [Indexed: 05/10/2023]
Abstract
The Mediterranean sponge Aplysina aerophoba kept in aquaria or cultivation tanks can stop pumping for several hours or even days. To investigate changes in the chemical microenvironments, we measured oxygen profiles over the surface and into the tissue of pumping and non-pumping A. aerophoba specimens with Clark-type oxygen microelectrodes (tip diameters 18-30 μm). Total oxygen consumption rates of whole sponges were measured in closed chambers. These rates were used to back-calculate the oxygen distribution in a finite-element model. Combining direct measurements with calculations of diffusive flux and modeling revealed that the tissue of non-pumping sponges turns anoxic within 15 min, with the exception of a 1 mm surface layer where oxygen intrudes due to molecular diffusion over the sponge surface. Molecular diffusion is the only transport mechanism for oxygen into non-pumping sponges, which allows total oxygen consumption rates of 6-12 μmol cm-3 sponge day-1. Sponges of different sizes had similar diffusional uptake rates, which is explained by their similar surface/volume ratios. In pumping sponges, oxygen consumption rates were between 22 and 37 μmol cm-3 sponge day-1, and the entire tissue was oxygenated. Combining different approaches of direct oxygen measurement in living sponges with a dynamic model, we can show that tissue anoxia is a direct function of the pumping behavior. The sponge-microbe system of A. aerophoba thus has the possibility to switch actively between aerobic and anaerobic metabolism by stopping the water flow for more than 15 min. These periods of anoxia will greatly influence physiological variety and activity of the sponge microbes. Detailed knowledge about the varying chemical microenvironments in sponges will help to develop protocols to cultivate sponge-associated microbial lineages and improve our understanding of the sponge-microbe-system.
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Affiliation(s)
- Friederike Hoffmann
- />Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359 Bremen, Germany
| | - Hans Røy
- />Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359 Bremen, Germany
- />Center for Geomicrobiology, Department of Biological Sciences, University of Århus, Ny Munkegade 1540, 0800 Århus C, Denmark
| | - Kristina Bayer
- />Research Center for Infectious Diseases, University of Würzburg, 97070 Würzburg, Germany
| | - Ute Hentschel
- />Research Center for Infectious Diseases, University of Würzburg, 97070 Würzburg, Germany
| | - Martin Pfannkuchen
- />Biologisches Institut, Abteilung Zoologie, Universitaet Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Franz Brümmer
- />Biologisches Institut, Abteilung Zoologie, Universitaet Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Dirk de Beer
- />Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359 Bremen, Germany
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