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Danovaro R, Dell’Anno A, Corinaldesi C, Rastelli E, Cavicchioli R, Krupovic M, Noble RT, Nunoura T, Prangishvili D. Virus-mediated archaeal hecatomb in the deep seafloor. SCIENCE ADVANCES 2016; 2:e1600492. [PMID: 27757416 PMCID: PMC5061471 DOI: 10.1126/sciadv.1600492] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 09/11/2016] [Indexed: 05/12/2023]
Abstract
Viruses are the most abundant biological entities in the world's oceans, and they play a crucial role in global biogeochemical cycles. In deep-sea ecosystems, archaea and bacteria drive major nutrient cycles, and viruses are largely responsible for their mortality, thereby exerting important controls on microbial dynamics. However, the relative impact of viruses on archaea compared to bacteria is unknown, limiting our understanding of the factors controlling the functioning of marine systems at a global scale. We evaluate the selectivity of viral infections by using several independent approaches, including an innovative molecular method based on the quantification of archaeal versus bacterial genes released by viral lysis. We provide evidence that, in all oceanic surface sediments (from 1000- to 10,000-m water depth), the impact of viral infection is higher on archaea than on bacteria. We also found that, within deep-sea benthic archaea, the impact of viruses was mainly directed at members of specific clades of Marine Group I Thaumarchaeota. Although archaea represent, on average, ~12% of the total cell abundance in the top 50 cm of sediment, virus-induced lysis of archaea accounts for up to one-third of the total microbial biomass killed, resulting in the release of ~0.3 to 0.5 gigatons of carbon per year globally. Our results indicate that viral infection represents a key mechanism controlling the turnover of archaea in surface deep-sea sediments. We conclude that interactions between archaea and their viruses might play a profound, previously underestimated role in the functioning of deep-sea ecosystems and in global biogeochemical cycles.
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Affiliation(s)
- Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona 60131, Italy
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
- Corresponding author.
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona 60131, Italy
| | - Cinzia Corinaldesi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona 60131, Italy
- Department of Sciences and Engineering of Materials, Environment and Urbanistics, Polytechnic University of Marche, Ancona 60131, Italy
| | - Eugenio Rastelli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona 60131, Italy
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mart Krupovic
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris 75015, France
| | - Rachel T. Noble
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, Morehead City, NC 28557, USA
| | - Takuro Nunoura
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, Natsushima-cho, Yokosuka 237-0061, Japan
| | - David Prangishvili
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris 75015, France
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202
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Xiong L, Jian H, Zhang Y, Xiao X. The Two Sets of DMSO Respiratory Systems of Shewanella piezotolerans WP3 Are Involved in Deep Sea Environmental Adaptation. Front Microbiol 2016; 7:1418. [PMID: 27656177 PMCID: PMC5013071 DOI: 10.3389/fmicb.2016.01418] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/26/2016] [Indexed: 12/04/2022] Open
Abstract
Dimethyl sulfoxide (DMSO) is an abundant methylated sulfur compound in deep sea ecosystems. However, the mechanism underlying DMSO-induced reduction in benthic microorganisms is unknown. Shewanella piezotolerans WP3, which was isolated from a west Pacific deep sea sediment, can utilize DMSO as the terminal electron acceptor. In this study, two putative dms gene clusters [type I (dmsEFA1B1G1H1) and type II (dmsA2B2G2H2)] were identified in the WP3 genome. Genetic and physiological analyses demonstrated that both dms gene clusters were functional and the transcription of both gene clusters was affected by changes in pressure and temperature. Notably, the type I system is essential for WP3 to thrive under in situ conditions (4°C/20 MPa), whereas the type II system is more important under high pressure or low temperature conditions (20°C/20 MPa, 4°C/0.1 MPa). Additionally, DMSO-dependent growth conferred by the presence of both dms gene clusters was higher than growth conferred by either of the dms gene clusters alone. These data collectively suggest that the possession of two sets of DMSO respiratory systems is an adaptive strategy for WP3 survival in deep sea environments. We propose, for the first time, that deep sea microorganisms might be involved in global DMSO/DMS cycling.
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Affiliation(s)
- Lei Xiong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Yuxia Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China; State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong UniversityShanghai, China
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203
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Adel M, Elbehery AHA, Aziz SK, Aziz RK, Grossart HP, Siam R. Viruses-to-mobile genetic elements skew in the deep Atlantis II brine pool sediments. Sci Rep 2016; 6:32704. [PMID: 27596223 PMCID: PMC5011723 DOI: 10.1038/srep32704] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 07/25/2016] [Indexed: 11/24/2022] Open
Abstract
The central rift of the Red Sea has 25 brine pools with different physical and geochemical characteristics. Atlantis II (ATIID), Discovery Deeps (DD) and Chain Deep (CD) are characterized by high salinity, temperature and metal content. Several studies reported microbial communities in these brine pools, but few studies addressed the brine pool sediments. Therefore, sediment cores were collected from ATIID, DD, CD brine pools and an adjacent brine-influenced site. Sixteen different lithologic sediment sections were subjected to shotgun DNA pyrosequencing to generate 1.47 billion base pairs (1.47 × 109 bp). We generated sediment-specific reads and attempted to annotate all reads. We report the phylogenetic and biochemical uniqueness of the deepest ATIID sulfur-rich brine pool sediments. In contrary to all other sediment sections, bacteria dominate the deepest ATIID sulfur-rich brine pool sediments. This decrease in virus-to-bacteria ratio in selected sections and depth coincided with an overrepresentation of mobile genetic elements. Skewing in the composition of viruses-to-mobile genetic elements may uniquely contribute to the distinct microbial consortium in sediments in proximity to hydrothermally active vents of the Red Sea and possibly in their surroundings, through differential horizontal gene transfer.
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Affiliation(s)
- Mustafa Adel
- Biology Department, Biotechnology Graduate Program and YJ-Science and Technology Research Center, American University in Cairo, Egypt
| | - Ali H A Elbehery
- Biology Department, Biotechnology Graduate Program and YJ-Science and Technology Research Center, American University in Cairo, Egypt
| | - Sherry K Aziz
- Biology Department, Biotechnology Graduate Program and YJ-Science and Technology Research Center, American University in Cairo, Egypt
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Egypt
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775 Stechlin, Germany.,Institute of Biochemistry and Biology, University of Potsdam, Am Neuen Palais 10, 14469 Potsdam, Germany
| | - Rania Siam
- Biology Department, Biotechnology Graduate Program and YJ-Science and Technology Research Center, American University in Cairo, Egypt
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204
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Rastelli E, Corinaldesi C, Petani B, Dell'Anno A, Ciglenečki I, Danovaro R. Enhanced viral activity and dark CO2
fixation rates under oxygen depletion: the case study of the marine Lake Rogoznica. Environ Microbiol 2016; 18:4511-4522. [DOI: 10.1111/1462-2920.13484] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/02/2016] [Accepted: 08/04/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Eugenio Rastelli
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
- Stazione Zoologica Anton Dohrn, Villa Comunale; Naples 80121 Italy
| | - Cinzia Corinaldesi
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Bruna Petani
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Irena Ciglenečki
- Division for Marine and Environmental Research, Bijenicka 54; Rudjer Bošković Institute; Zagreb 10001 Croatia
| | - Roberto Danovaro
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
- Stazione Zoologica Anton Dohrn, Villa Comunale; Naples 80121 Italy
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205
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Wang Y, Gao ZM, Li JT, Bougouffa S, Tian RM, Bajic VB, Qian PY. Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments. Sci Bull (Beijing) 2016. [DOI: 10.1007/s11434-016-1135-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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206
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Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments. Appl Environ Microbiol 2016; 82:4232-43. [PMID: 27208118 PMCID: PMC4959193 DOI: 10.1128/aem.01023-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 04/29/2016] [Indexed: 11/24/2022] Open
Abstract
The South Pacific Gyre (SPG) possesses the lowest rates of sedimentation, surface chlorophyll concentration, and primary productivity in the global oceans. As a direct result, deep-sea sediments are thin and contain small amounts of labile organic carbon. It was recently shown that the entire SPG sediment column is oxygenated and may be representative of up to a third of the global marine environment. To understand the microbial processes that contribute to the removal of the labile organic matter at the water-sediment interface, a sediment sample was collected and subjected to metagenomic sequencing and analyses. Analysis of nine partially reconstructed environmental genomes, which represent approximately one-third of the microbial community, revealed that the members of the SPG surface sediment microbial community are phylogenetically distinct from surface/upper-ocean organisms. These genomes represent a wide distribution of novel organisms, including deep-branching Alphaproteobacteria, two novel organisms within the Proteobacteria, and new members of the Nitrospirae, Nitrospinae, and candidate phylum NC10. These genomes contain evidence for microbially mediated metal (iron/manganese) oxidation and carbon fixation linked to nitrification. Additionally, despite hypothesized energy limitation, members of the SPG microbial community had motility and chemotaxis genes and possessed mechanisms for the degradation of high-molecular-weight organic matter. This study contributes to our understanding of the metabolic potential of microorganisms in deep-sea oligotrophic sediments and their impact on local carbon geochemistry. IMPORTANCE This research provides insight into the microbial metabolic potential of organisms inhabiting oxygenated deep-sea marine sediments. Current estimates suggest that these environments account for up to a third of the global marine sediment habitat. Nine novel deep-sea microbial genomes were reconstructed from a metagenomic data set and expand the limited number of environmental genomes from deep-sea sediment environments. This research provides phylogeny-linked insight into critical metabolisms, including carbon fixation associated with nitrification, which is assignable to members of the marine group 1 Thaumarchaeota, Nitrospinae, and Nitrospirae and neutrophilic metal (iron/manganese) oxidation assignable to a novel proteobacterium.
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207
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Dong C, Sheng H, Wang W, Zhou H, Shao Z. Bacterial distribution pattern in the surface sediments distinctive among shelf, slope and basin across the western Arctic Ocean. Polar Biol 2016. [DOI: 10.1007/s00300-016-1970-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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208
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Forster D, Dunthorn M, Mahé F, Dolan JR, Audic S, Bass D, Bittner L, Boutte C, Christen R, Claverie JM, Decelle J, Edvardsen B, Egge E, Eikrem W, Gobet A, Kooistra WHCF, Logares R, Massana R, Montresor M, Not F, Ogata H, Pawlowski J, Pernice MC, Romac S, Shalchian-Tabrizi K, Simon N, Richards TA, Santini S, Sarno D, Siano R, Vaulot D, Wincker P, Zingone A, de Vargas C, Stoeck T. Benthic protists: the under-charted majority. FEMS Microbiol Ecol 2016; 92:fiw120. [PMID: 27267932 DOI: 10.1093/femsec/fiw120] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2016] [Indexed: 11/13/2022] Open
Abstract
Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbor greater diversity than planktonic environments. We tested this by analyzing sequences of the hypervariable V4 18S rRNA from benthic and planktonic protist communities sampled in European coastal regions. Despite a similar number of OTUs in both realms, richness estimations indicated that we recovered at least 70% of the diversity in planktonic protist communities, but only 33% in benthic communities. There was also little overlap of OTUs between planktonic and benthic communities, as well as between separate benthic communities. We argue that these patterns reflect the heterogeneity and diversity of benthic habitats. A comparison of all OTUs against the Protist Ribosomal Reference database showed that a higher proportion of benthic than planktonic protist diversity is missing from public databases; similar results were obtained by comparing all OTUs against environmental references from NCBI's Short Read Archive. We suggest that the benthic realm may therefore be the world's largest reservoir of marine protist diversity, with most taxa at present undescribed.
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Affiliation(s)
- Dominik Forster
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Str. 14, D-67663 Kaiserslautern, Germany
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Str. 14, D-67663 Kaiserslautern, Germany
| | - Fréderic Mahé
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Str. 14, D-67663 Kaiserslautern, Germany
| | - John R Dolan
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR CNRS UMR 7093 and Laboratoire d'Océanographie de Villefranche-sur-Mer, Université Paris 06, F-06230 Villefranche-sur-Mer, France
| | - Stéphane Audic
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | - David Bass
- Department of Life Sciences, the Natural History Museum London, Cromwell Road, London SW7 5BD, UK Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, the Nothe, Weymouth, Dorset DT4 8UB, UK
| | - Lucie Bittner
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Str. 14, D-67663 Kaiserslautern, Germany Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France Sorbonne Universités, UPMC, CNRS, Institut de Biologie Paris-Seine (IBPS), Evolution Paris Seine, F-75005 Paris, France
| | - Christophe Boutte
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | - Richard Christen
- CNRS, UMR 7138 & Université de Nice-Sophia Antipolis, F-06103 Nice cedex 2, France Université de Nice-Sophia Antipolis & CNRS, UMR 7138 F-06103 Nice cedex 2, France
| | | | - Johan Decelle
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | - Bente Edvardsen
- Department of BioSciences, University of Oslo, Blindern, 0316 N-Oslo, Norway
| | - Elianne Egge
- Department of BioSciences, University of Oslo, Blindern, 0316 N-Oslo, Norway
| | - Wenche Eikrem
- Department of BioSciences, University of Oslo, Blindern, 0316 N-Oslo, Norway
| | - Angélique Gobet
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France CNRS, UMR 8227 & UPMC Université Paris 06, Station Biologique de Roscoff, F-29682 Roscoff, France
| | | | - Ramiro Logares
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain
| | - Ramon Massana
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain
| | - Marina Montresor
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, I-80121, Naples, Italy
| | - Fabrice Not
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | - Hiroyuki Ogata
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR CNRS UMR 7093 and Laboratoire d'Océanographie de Villefranche-sur-Mer, Université Paris 06, F-06230 Villefranche-sur-Mer, France Institute for Chemical Research, Kyoto University, Uji, 611-0011, Japan
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, 4, Boulevard d'Yvoy, CH-1211 Geneva, Switzerland
| | - Massimo C Pernice
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain
| | - Sarah Romac
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | | | - Nathalie Simon
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | | | - Sébastien Santini
- CNRS, Aix-Marseille Université, IGS UMR7256, F-13288 Marseille, France
| | - Diana Sarno
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, I-80121, Naples, Italy
| | - Raffaele Siano
- Ifremer, Centre de Brest DYNECO/Pelagos Technopôle Brest Iroise, BP 7029280 Plouzané, France
| | - Daniel Vaulot
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | | | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, I-80121, Naples, Italy
| | - Colomban de Vargas
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Str. 14, D-67663 Kaiserslautern, Germany
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209
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LaRowe DE, Amend JP. The energetics of anabolism in natural settings. THE ISME JOURNAL 2016; 10:1285-95. [PMID: 26859771 PMCID: PMC5029197 DOI: 10.1038/ismej.2015.227] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/29/2015] [Accepted: 11/02/2015] [Indexed: 11/09/2022]
Abstract
The environmental conditions that describe an ecosystem define the amount of energy available to the resident organisms and the amount of energy required to build biomass. Here, we quantify the amount of energy required to make biomass as a function of temperature, pressure, redox state, the sources of C, N and S, cell mass and the time that an organism requires to double or replace its biomass. Specifically, these energetics are calculated from 0 to 125 °C, 0.1 to 500 MPa and -0.38 to +0.86 V using CO2, acetate or CH4 for C, NO3(-) or NH4(+) for N and SO4(2-) or HS(-) for S. The amounts of energy associated with synthesizing the biomolecules that make up a cell, which varies over 39 kJ (g cell)(-1), are then used to compute energy-based yield coefficients for a vast range of environmental conditions. Taken together, environmental variables and the range of cell sizes leads to a ~4 orders of magnitude difference between the number of microbial cells that can be made from a Joule of Gibbs energy under the most (5.06 × 10(11) cells J(-1)) and least (5.21 × 10(7) cells J(-1)) ideal conditions. When doubling/replacement time is taken into account, the range of anabolism energies can expand even further.
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Affiliation(s)
- Douglas E LaRowe
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Jan P Amend
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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210
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Jørgensen SL, Zhao R. Microbial Inventory of Deeply Buried Oceanic Crust from a Young Ridge Flank. Front Microbiol 2016; 7:820. [PMID: 27303398 PMCID: PMC4882963 DOI: 10.3389/fmicb.2016.00820] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 05/13/2016] [Indexed: 11/13/2022] Open
Abstract
The deep marine biosphere has over the past decades been exposed as an immense habitat for microorganisms with wide-reaching implications for our understanding of life on Earth. Recent advances in knowledge concerning this biosphere have been achieved mainly through extensive microbial and geochemical studies of deep marine sediments. However, the oceanic crust buried beneath the sediments, is still largely unexplored with respect to even the most fundamental questions related to microbial life. Here, we present quantitative and qualitative data related to the microbial inventory from 33 deeply buried basaltic rocks collected at two different locations, penetrating 300 vertical meters into the upper oceanic crust on the west flank of the Mid-Atlantic spreading ridge. We use quantitative PCR and sequencing of 16S rRNA gene amplicons to estimate cell abundances and to profile the community structure. Our data suggest that the number of cells is relatively stable at ~104 per gram of rock irrespectively of sampling site and depth. Further, we show that Proteobacteria, especially Gammaproteobacteria dominate the microbial assemblage across all investigated samples, with Archaea, in general, represented by < 1% of the community. In addition, we show that the communities within the crust are distinct from the overlying sediment. However, many of their respective microbial inhabitants are shared between the two biomes, but with markedly different relative distributions. Our study provides fundamental information with respect to abundance, distribution, and identity of microorganisms in the upper oceanic crust.
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Affiliation(s)
- Steffen L Jørgensen
- Department of Biology, Centre for Geobiology, University of Bergen Bergen, Norway
| | - Rui Zhao
- Department of Biology, Centre for Geobiology, University of Bergen Bergen, Norway
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211
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Jangir Y, French S, Momper LM, Moser DP, Amend JP, El-Naggar MY. Isolation and Characterization of Electrochemically Active Subsurface Delftia and Azonexus Species. Front Microbiol 2016; 7:756. [PMID: 27242768 PMCID: PMC4876122 DOI: 10.3389/fmicb.2016.00756] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 05/05/2016] [Indexed: 11/29/2022] Open
Abstract
Continental subsurface environments can present significant energetic challenges to the resident microorganisms. While these environments are geologically diverse, potentially allowing energy harvesting by microorganisms that catalyze redox reactions, many of the abundant electron donors and acceptors are insoluble and therefore not directly bioavailable. Extracellular electron transfer (EET) is a metabolic strategy that microorganisms can deploy to meet the challenges of interacting with redox-active surfaces. Though mechanistically characterized in a few metal-reducing bacteria, the role, extent, and diversity of EET in subsurface ecosystems remains unclear. Since this process can be mimicked on electrode surfaces, it opens the door to electrochemical techniques to enrich for and quantify the activities of environmental microorganisms in situ. Here, we report the electrochemical enrichment of microorganisms from a deep fractured-rock aquifer in Death Valley, CA, USA. In experiments performed in mesocosms containing a synthetic medium based on aquifer chemistry, four working electrodes (WEs) were poised at different redox potentials (272, 373, 472, 572 mV vs. SHE) to serve as electron acceptors, resulting in anodic currents coupled to the oxidation of acetate during enrichment. The anodes were dominated by Betaproteobacteria from the families Comamonadaceae and Rhodocyclaceae. A representative of each dominant family was subsequently isolated from electrode-associated biomass. The EET abilities of the isolated Delftia strain (designated WE1-13) and Azonexus strain (designated WE2-4) were confirmed in electrochemical reactors using WEs poised at 522 mV vs. SHE. The rise in anodic current upon inoculation was correlated with a modest increase in total protein content. Both genera have been previously observed in mixed communities of microbial fuel cell enrichments, but this is the first direct measurement of their electrochemical activity. While alternate metabolisms (e.g., nitrate reduction) by these organisms were previously known, our observations suggest that additional ‘hidden’ interactions with external electron acceptors are also possible. Electrochemical approaches are well positioned to dissect such extracellular interactions that may be prevalent in the subsurface.
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Affiliation(s)
- Yamini Jangir
- Department of Physics and Astronomy, University of Southern California, Los Angeles CA, USA
| | - Sarah French
- Department of Physics and Astronomy, University of Southern California, Los Angeles CA, USA
| | - Lily M Momper
- Department of Biological Sciences, University of Southern California, Los Angeles CA, USA
| | - Duane P Moser
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Las Vegas NV, USA
| | - Jan P Amend
- Department of Biological Sciences, University of Southern California, Los AngelesCA, USA; Department of Earth Sciences, University of Southern California, Los AngelesCA, USA
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los AngelesCA, USA; Department of Biological Sciences, University of Southern California, Los AngelesCA, USA; Department of Chemistry, University of Southern California, Los AngelesCA, USA
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212
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Ivarsson M, Schnürer A, Bengtson S, Neubeck A. Anaerobic Fungi: A Potential Source of Biological H2 in the Oceanic Crust. Front Microbiol 2016; 7:674. [PMID: 27433154 PMCID: PMC4922220 DOI: 10.3389/fmicb.2016.00674] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/25/2016] [Indexed: 11/23/2022] Open
Abstract
The recent recognition of fungi in the oceanic igneous crust challenges the understanding of this environment as being exclusively prokaryotic and forces reconsiderations of the ecology of the deep biosphere. Anoxic provinces in the igneous crust are abundant and increase with age and depth of the crust. The presence of anaerobic fungi in deep-sea sediments and on the seafloor introduces a type of organism with attributes of geobiological significance not previously accounted for. Anaerobic fungi are best known from the rumen of herbivores where they produce molecular hydrogen, which in turn stimulates the growth of methanogens. The symbiotic cooperation between anaerobic fungi and methanogens in the rumen enhance the metabolic rate and growth of both. Methanogens and other hydrogen-consuming anaerobic archaea are known from subseafloor basalt; however, the abiotic production of hydrogen is questioned to be sufficient to support such communities. Alternatively, biologically produced hydrogen could serve as a continuous source. Here, we propose anaerobic fungi as a source of bioavailable hydrogen in the oceanic crust, and a close interplay between anaerobic fungi and hydrogen-driven prokaryotes.
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Affiliation(s)
- Magnus Ivarsson
- Department of Palaeobiology and Nordic Center for Earth Evolution, Swedish Museum of Natural History Stockholm, Sweden
| | - Anna Schnürer
- Department of Microbiology, Uppsala BioCenter, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Stefan Bengtson
- Department of Palaeobiology and Nordic Center for Earth Evolution, Swedish Museum of Natural History Stockholm, Sweden
| | - Anna Neubeck
- Department of Geological Sciences, Stockholm University Stockholm, Sweden
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213
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Bukin SV, Pavlova ON, Manakov AY, Kostyreva EA, Chernitsyna SM, Mamaeva EV, Pogodaeva TV, Zemskaya TI. The Ability of Microbial Community of Lake Baikal Bottom Sediments Associated with Gas Discharge to Carry Out the Transformation of Organic Matter under Thermobaric Conditions. Front Microbiol 2016; 7:690. [PMID: 27242716 PMCID: PMC4861714 DOI: 10.3389/fmicb.2016.00690] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 04/26/2016] [Indexed: 11/21/2022] Open
Abstract
The ability to compare the composition and metabolic potential of microbial communities inhabiting the subsurface sediment in geographically distinct locations is one of the keys to understanding the evolution and function of the subsurface biosphere. Prospective areas for study of the subsurface biosphere are the sites of hydrocarbon discharges on the bottom of the Lake Baikal rift, where ascending fluxes of gas-saturated fluids and oil from deep layers of bottom sediments seep into near-surface sediment. The samples of surface sediments collected in the area of the Posolskaya Bank methane seep were cultured for 17 months under thermobaric conditions (80°C, 5 MPa) with the addition of complementary organic substrate, and a different composition for the gas phase. After incubation, the presence of intact cells of microorganisms, organic matter transformation and the formation of oil biomarkers was confirmed in the samples, with the addition of Baikal diatom alga Synedra acus detritus, and gas mixture CH4:H2:CO2. Taxonomic assignment of the 16S rRNA sequence data indicates that the predominant sequences in the enrichment were Sphingomonas (55.3%), Solirubrobacter (27.5%) and Arthrobacter (16.6%). At the same time, in heat-killed sediment and in sediment without any additional substrates, which were cultivated in a CH4 atmosphere, no geochemical changes were detected, nor the presence of intact cells and 16S rRNA sequences of Bacteria and Archaea. This data may suggest that the decomposition of organic matter under culturing conditions could be performed by microorganisms from low-temperature sediment layers. One possible explanation of this phenomenon is migration of the representatives of the deep thermophilic community through fault zones in the near surface sediment layers, together with gas-bearing fluids.
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Affiliation(s)
- Sergei V Bukin
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Russian Academy of Science Irkutsk, Russia
| | - Olga N Pavlova
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Russian Academy of Science Irkutsk, Russia
| | - Andrei Y Manakov
- Laboratory of Clathrate Compounds, Nikolaev Institute of Inorganic Chemistry, Russian Academy of Science Novosibirsk, Russia
| | - Elena A Kostyreva
- Laboratory of Petroleum Geochemistry, Trofimuk Institute of Petroleum Geology and Geophysics, Russian Academy of Science Novosibirsk, Russia
| | - Svetlana M Chernitsyna
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Russian Academy of Science Irkutsk, Russia
| | - Elena V Mamaeva
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Russian Academy of Science Irkutsk, Russia
| | - Tatyana V Pogodaeva
- Laboratory of Hydrochemistry and Atmosphere Chemistry, Limnological Institute, Russian Academy of Science Irkutsk, Russia
| | - Tamara I Zemskaya
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Russian Academy of Science Irkutsk, Russia
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214
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Meier DV, Bach W, Girguis PR, Gruber-Vodicka HR, Reeves EP, Richter M, Vidoudez C, Amann R, Meyerdierks A. HeterotrophicProteobacteriain the vicinity of diffuse hydrothermal venting. Environ Microbiol 2016; 18:4348-4368. [DOI: 10.1111/1462-2920.13304] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/13/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Dimitri V. Meier
- Max Planck Institute for Marine Microbiology; Celsiusstrasse 1 D-28359 Bremen Germany
| | - Wolfgang Bach
- University of Bremen, MARUM - Center for Marine Environmental Sciences, Petrology of the Ocean Crust group; Leobener Str. D-28359 Bremen Germany
| | - Peter R. Girguis
- Harvard University, Department of Organismic & Evolutionary Biology; 16 Divinity Avenue Cambridge MA 02138-2020 USA
| | | | - Eoghan P. Reeves
- University of Bremen, MARUM - Center for Marine Environmental Sciences, Petrology of the Ocean Crust group; Leobener Str. D-28359 Bremen Germany
- University of Bergen, Department of Earth Science and Centre for Geobiology; Postboks 7803 N-5020 Bergen Norway
| | - Michael Richter
- Max Planck Institute for Marine Microbiology; Celsiusstrasse 1 D-28359 Bremen Germany
| | - Charles Vidoudez
- Harvard University, Department of Organismic & Evolutionary Biology; 16 Divinity Avenue Cambridge MA 02138-2020 USA
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology; Celsiusstrasse 1 D-28359 Bremen Germany
| | - Anke Meyerdierks
- Max Planck Institute for Marine Microbiology; Celsiusstrasse 1 D-28359 Bremen Germany
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215
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Robador A, LaRowe DE, Jungbluth SP, Lin HT, Rappé MS, Nealson KH, Amend JP. Nanocalorimetric Characterization of Microbial Activity in Deep Subsurface Oceanic Crustal Fluids. Front Microbiol 2016; 7:454. [PMID: 27092118 PMCID: PMC4820435 DOI: 10.3389/fmicb.2016.00454] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/21/2016] [Indexed: 11/30/2022] Open
Abstract
Although fluids within the upper oceanic basaltic crust harbor a substantial fraction of the total prokaryotic cells on Earth, the energy needs of this microbial population are unknown. In this study, a nanocalorimeter (sensitivity down to 1.2 nW ml(-1)) was used to measure the enthalpy of microbially catalyzed reactions as a function of temperature in samples from two distinct crustal fluid aquifers. Microorganisms in unamended, warm (63°C) and geochemically altered anoxic fluids taken from 292 meters sub-basement (msb) near the Juan de Fuca Ridge produced 267.3 mJ of heat over the course of 97 h during a step-wise isothermal scan from 35.5 to 85.0°C. Most of this heat signal likely stems from the germination of thermophilic endospores (6.66 × 10(4) cells ml(-1) FLUID) and their subsequent metabolic activity at temperatures greater than 50°C. The average cellular energy consumption (5.68 pW cell(-1)) reveals the high metabolic potential of a dormant community transported by fluids circulating through the ocean crust. By contrast, samples taken from 293 msb from cooler (3.8°C), relatively unaltered oxic fluids, produced 12.8 mJ of heat over the course of 14 h as temperature ramped from 34.8 to 43.0°C. Corresponding cell-specific energy turnover rates (0.18 pW cell(-1)) were converted to oxygen uptake rates of 24.5 nmol O2 ml(-1) FLUID d(-1), validating previous model predictions of microbial activity in this environment. Given that the investigated fluids are characteristic of expansive areas of the upper oceanic crust, the measured metabolic heat rates can be used to constrain boundaries of habitability and microbial activity in the oceanic crust.
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Affiliation(s)
- Alberto Robador
- Center for Dark Energy Biosphere Investigations, NASA Astrobiology Institute, University of Southern California, Los AngelesCA, USA
| | - Douglas E. LaRowe
- Department of Earth Sciences, University of Southern California, Los AngelesCA, USA
| | - Sean P. Jungbluth
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, HonoluluHI, USA
- Hawaii Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, KaneoheHI, USA
| | - Huei-Ting Lin
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, HonoluluHI, USA
| | - Michael S. Rappé
- Hawaii Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, KaneoheHI, USA
| | - Kenneth H. Nealson
- Department of Earth Sciences, University of Southern California, Los AngelesCA, USA
- Department of Biological Sciences, University of Southern California, Los AngelesCA, USA
| | - Jan P. Amend
- Department of Earth Sciences, University of Southern California, Los AngelesCA, USA
- Department of Biological Sciences, University of Southern California, Los AngelesCA, USA
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216
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The Histone-Like Nucleoid Structuring Protein (H-NS) Is a Negative Regulator of the Lateral Flagellar System in the Deep-Sea Bacterium Shewanella piezotolerans WP3. Appl Environ Microbiol 2016; 82:2388-2398. [PMID: 26873312 DOI: 10.1128/aem.00297-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 02/05/2016] [Indexed: 11/20/2022] Open
Abstract
Although the histone-like nucleoid structuring protein (H-NS) is well known for its involvement in the adaptation of mesophilic bacteria, such as Escherichia coli, to cold environments and high-pressure stress, an understanding of the role of H-NS in the cold-adapted benthic microorganisms that live in the deep-sea ecosystem, which covers approximately 60% of the earth's surface, is still lacking. In this study, we characterized the function of H-NS in Shewanella piezotolerans WP3, which was isolated from West Pacific sediment at a depth of 1,914 m. Anhns gene deletion mutant (WP3Δhns) was constructed, and comparative whole-genome microarray analysis was performed. H-NS had a significant influence (fold change, >2) on the expression of a variety of WP3 genes (274 and 280 genes were upregulated and downregulated, respectively), particularly genes related to energy production and conversion. Notably, WP3Δhnsexhibited higher expression levels of lateral flagellar genes than WP3 and showed enhanced swarming motility and lateral flagellar production compared to those of WP3. The DNA gel mobility shift experiment showed that H-NS bound specifically to the promoter of lateral flagellar genes. Moreover, the high-affinity binding sequences of H-NS were identified by DNase I protection footprinting, and the results support the "binding and spreading" model for H-NS functioning. To our knowledge, this is the first attempt to characterize the function of the universal regulator H-NS in a deep-sea bacterium. Our data revealed that H-NS has a novel function as a repressor of the expression of genes related to the energy-consuming secondary flagellar system and to swarming motility.
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217
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Danovaro R, Molari M, Corinaldesi C, Dell’Anno A. Macroecological drivers of archaea and bacteria in benthic deep-sea ecosystems. SCIENCE ADVANCES 2016; 2:e1500961. [PMID: 27386507 PMCID: PMC4928989 DOI: 10.1126/sciadv.1500961] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 03/31/2016] [Indexed: 05/06/2023]
Abstract
Bacteria and archaea dominate the biomass of benthic deep-sea ecosystems at all latitudes, playing a crucial role in global biogeochemical cycles, but their macroscale patterns and macroecological drivers are still largely unknown. We show the results of the most extensive field study conducted so far to investigate patterns and drivers of the distribution and structure of benthic prokaryote assemblages from 228 samples collected at latitudes comprising 34°N to 79°N, and from ca. 400- to 5570-m depth. We provide evidence that, in deep-sea ecosystems, benthic bacterial and archaeal abundances significantly increase from middle to high latitudes, with patterns more pronounced for archaea, and particularly for Marine Group I Thaumarchaeota. Our results also reveal that different microbial components show varying sensitivities to changes in temperature conditions and food supply. We conclude that climate change will primarily affect deep-sea benthic archaea, with important consequences on global biogeochemical cycles, particularly at high latitudes.
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Affiliation(s)
- Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
- Corresponding author.
| | - Massimiliano Molari
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- HGF MPG Joint Research for Deep-Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Cinzia Corinaldesi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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218
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219
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Ino K, Konno U, Kouduka M, Hirota A, Togo YS, Fukuda A, Komatsu D, Tsunogai U, Tanabe AS, Yamamoto S, Iwatsuki T, Mizuno T, Ito K, Suzuki Y. Deep microbial life in high-quality granitic groundwater from geochemically and geographically distinct underground boreholes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:285-294. [PMID: 26743638 DOI: 10.1111/1758-2229.12379] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 12/30/2015] [Accepted: 12/30/2015] [Indexed: 06/05/2023]
Abstract
Deep granitic aquifer is one of the largest, but least understood, microbial habitats. To avoid contamination from the surface biosphere, underground drilling was conducted for 300 m deep granitic rocks at the Mizunami underground research laboratory (URL), Japan. Slightly alkaline groundwater was characterized by low concentrations of dissolved organic matter and sulfate and the presence of > 100 nM H2 . The initial biomass was the highest (∼10(5) cells ml(-1) ) with the dominance of Hydrogenophaga spp., whereas the phylum Nitrospirae became predominant after 3 years with decreasing biomass (∼10(4) cells ml(-1) ). One week incubation of groundwater microbes after 3 years with (13) C-labelled bicarbonate and 1% H2 and subsequent single-cell imaging with nanometer-scale secondary ion mass spectrometry demonstrated that microbial cells were metabolically active. Pyrosequencing of microbial communities in groundwater retrieved at 3-4 years after drilling at the Mizunami URL and at 14 and 25 years after the drilling at the Grimsel Test Site, Switzerland, revealed the occurrence of common Nitrospirae lineages at the geographically distinct sites. As the close relatives of the Nitrospirae lineages were exclusively detected from deep groundwaters and terrestrial hot springs, it suggests that these bacteria are indigenous and potentially adapted to the deep terrestrial subsurface.
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Affiliation(s)
- Kohei Ino
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Uta Konno
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8567, Japan
| | - Mariko Kouduka
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Akinari Hirota
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8567, Japan
| | - Yoko S Togo
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8567, Japan
| | - Akari Fukuda
- Japan Atomic Energy Agency, 1-64 Yamanouchi, Akiyo-cho, Mizunami, Gifu, 509-6132, Japan
| | - Daisuke Komatsu
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Urumu Tsunogai
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Akihumi S Tanabe
- Graduate School of Global Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Satoshi Yamamoto
- Graduate School of Global Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Teruki Iwatsuki
- Japan Atomic Energy Agency, 1-64 Yamanouchi, Akiyo-cho, Mizunami, Gifu, 509-6132, Japan
| | - Takashi Mizuno
- Japan Atomic Energy Agency, 1-64 Yamanouchi, Akiyo-cho, Mizunami, Gifu, 509-6132, Japan
| | - Kazumasa Ito
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8567, Japan
| | - Yohey Suzuki
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Bunkyo-ku, Tokyo, 113-0033, Japan
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220
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Stewart LC, Llewellyn JG, Butterfield DA, Lilley MD, Holden JF. Hydrogen and thiosulfate limits for growth of a thermophilic, autotrophic Desulfurobacterium species from a deep-sea hydrothermal vent. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:196-200. [PMID: 26696328 PMCID: PMC6092745 DOI: 10.1111/1758-2229.12368] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 12/01/2015] [Indexed: 06/05/2023]
Abstract
Hydrothermal fluids (341°C and 19°C) were collected < 1 m apart from a black smoker chimney and a tubeworm mound on the Boardwalk edifice at the Endeavour Segment in the northeastern Pacific Ocean to study anaerobic microbial growth in hydrothermal mineral deposits. Geochemical modelling of mixed vent fluid and seawater suggests the mixture was anoxic above 55°C and that low H2 concentrations (79 μmol kg(-1) in end-member hydrothermal fluid) limit anaerobic hydrogenotrophic growth above this temperature. A thermophilic, hydrogenotrophic sulfur reducer, Desulfurobacterium strain HR11, was isolated from the 19°C fluid raising questions about its H2 -dependent growth kinetics. Strain HR11 grew at 40-77°C (Topt 72-75°C), pH 5-8.5 (pHopt 6-7) and 1-5% (wt vol(-1) ) NaCl (NaClopt 3-4%). The highest growth rates occurred when S2 O3 (2-) and S° were reduced to H2 S. Modest growth occurred by NO3 (-) reduction. Monod constants for its growth were Ks of 30 μM for H2 and Ks of 20 μM for S2 O3 (2-) with a μmax of 2.0 h(-1) . The minimum H2 and S2 O3 (2-) concentrations for growth were 3 μM and 5 μM respectively. Possible sources of S2 O3 (2-) and S° are from abiotic dissolved sulfide and pyrite oxidation by O2 .
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Affiliation(s)
- Lucy C. Stewart
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - James G. Llewellyn
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - David A. Butterfield
- Joint Institute for the Study of the Atmosphere and Ocean, University of Washington, Seattle, WA 98195, USA
| | - Marvin D. Lilley
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - James F. Holden
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
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221
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Baquiran JPM, Ramírez GA, Haddad AG, Toner BM, Hulme S, Wheat CG, Edwards KJ, Orcutt BN. Temperature and Redox Effect on Mineral Colonization in Juan de Fuca Ridge Flank Subsurface Crustal Fluids. Front Microbiol 2016; 7:396. [PMID: 27064928 PMCID: PMC4815438 DOI: 10.3389/fmicb.2016.00396] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 03/14/2016] [Indexed: 02/01/2023] Open
Abstract
To examine microbe-mineral interactions in subsurface oceanic crust, we evaluated microbial colonization on crustal minerals that were incubated in borehole fluids for 1 year at the seafloor wellhead of a crustal borehole observatory (IODP Hole U1301A, Juan de Fuca Ridge flank) as compared to an experiment that was not exposed to subsurface crustal fluids (at nearby IODP Hole U1301B). In comparison to previous studies at these same sites, this approach allowed assessment of the effects of temperature, fluid chemistry, and/or mineralogy on colonization patterns of different mineral substrates, and an opportunity to verify the approach of deploying colonization experiments at an observatory wellhead at the seafloor instead of within the borehole. The Hole U1301B deployment did not have biofilm growth, based on microscopy and DNA extraction, thereby confirming the integrity of the colonization design against bottom seawater intrusion. In contrast, the Hole U1301A deployment supported biofilms dominated by Epsilonproteobacteria (43.5% of 370 16S rRNA gene clone sequences) and Gammaproteobacteria (29.3%). Sequence analysis revealed overlap in microbial communities between different minerals incubated at the Hole U1301A wellhead, indicating that mineralogy did not separate biofilm structure within the 1-year colonization experiment. Differences in the Hole U1301A wellhead biofilm community composition relative to previous studies from within the borehole using similar mineral substrates suggest that temperature and the diffusion of dissolved oxygen through plastic components influenced the mineral colonization experiments positioned at the wellhead. This highlights the capacity of low abundance crustal fluid taxa to rapidly establish communities on diverse mineral substrates under changing environmental conditions such as from temperature and oxygen.
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Affiliation(s)
- Jean-Paul M Baquiran
- Department of Biological Sciences, University of Southern California Los Angeles, CA, USA
| | - Gustavo A Ramírez
- Department of Biological Sciences, University of Southern California Los Angeles, CA, USA
| | - Amanda G Haddad
- Department of Earth Sciences, University of Southern California Los Angeles, CA, USA
| | - Brandy M Toner
- Department of Soil, Water and Climate, University of Minnesota St. Paul, MN, USA
| | - Samuel Hulme
- Moss Landing Marine Laboratories Moss Landing, CA, USA
| | - Charles G Wheat
- School of Fisheries and Ocean Sciences, University of Alaska Fairbanks Fairbanks, AK, USA
| | - Katrina J Edwards
- Department of Biological Sciences, University of Southern CaliforniaLos Angeles, CA, USA; Department of Earth Sciences, University of Southern CaliforniaLos Angeles, CA, USA
| | - Beth N Orcutt
- Bigelow Laboratory for Ocean Sciences East Boothbay, ME, USA
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222
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Zhang X, Feng X, Wang F. Diversity and Metabolic Potentials of Subsurface Crustal Microorganisms from the Western Flank of the Mid-Atlantic Ridge. Front Microbiol 2016; 7:363. [PMID: 27047476 PMCID: PMC4797314 DOI: 10.3389/fmicb.2016.00363] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 03/07/2016] [Indexed: 02/01/2023] Open
Abstract
Deep-sea oceanic crust constitutes the largest region of the earth’s surface. Accumulating evidence suggests that unique microbial communities are supported by iron cycling processes, particularly in the young (<10 million-year old), cool (<25°C) subsurface oceanic crust. To test this hypothesis, we investigated the microbial abundance, diversity, and metabolic potentials in the sediment-buried crust from “North Pond” on western flank of the Mid-Atlantic Ridge. Three lithologic units along basement Hole U1383C were found, which typically hosted ∼104 cells cm-3 of basaltic rock, with higher cell densities occurring between 115 and 145 m below seafloor. Similar bacterial community structures, which are dominated by Gammaproteobacterial and Sphingobacterial species closely related to iron oxidizers, were detected regardless of variations in sampling depth. The metabolic potentials of the crust microbiota were assayed by metagenomic analysis of two basalt enrichments which showed similar bacterial structure with the original sample. Genes coding for energy metabolism involved in hydrocarbon degradation, dissimilatory nitrate reduction to ammonium, denitrification and hydrogen oxidation were identified. Compared with other marine environments, the metagenomes from the basalt-hosted environments were enriched in pathways for Fe3+ uptake, siderophore synthesis and uptake, and Fe transport, suggesting that iron metabolism is an important energy production and conservation mechanism in this system. Overall, we provide evidence that the North Pond crustal biosphere is dominated by unique bacterial groups with the potential for iron-related biogeochemical cycles.
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Affiliation(s)
- Xinxu Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China; State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong UniversityShanghai, China
| | - Xiaoyuan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China; State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong UniversityShanghai, China
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223
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Meyer JL, Jaekel U, Tully BJ, Glazer BT, Wheat CG, Lin HT, Hsieh CC, Cowen JP, Hulme SM, Girguis PR, Huber JA. A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge. Sci Rep 2016; 6:22541. [PMID: 26935537 PMCID: PMC4776111 DOI: 10.1038/srep22541] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/15/2016] [Indexed: 11/23/2022] Open
Abstract
The rock-hosted, oceanic crustal aquifer is one of the largest ecosystems on Earth, yet little is known about its indigenous microorganisms. Here we provide the first phylogenetic and functional description of an active microbial community residing in the cold oxic crustal aquifer. Using subseafloor observatories, we recovered crustal fluids and found that the geochemical composition is similar to bottom seawater, as are cell abundances. However, based on relative abundances and functional potential of key bacterial groups, the crustal fluid microbial community is heterogeneous and markedly distinct from seawater. Potential rates of autotrophy and heterotrophy in the crust exceeded those of seawater, especially at elevated temperatures (25 °C) and deeper in the crust. Together, these results reveal an active, distinct, and diverse bacterial community engaged in both heterotrophy and autotrophy in the oxygenated crustal aquifer, providing key insight into the role of microbial communities in the ubiquitous cold dark subseafloor biosphere.
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Affiliation(s)
- Julie L Meyer
- Josephine Bay Paul Center, Marine Biological Laboratory, 7 MBL St., Woods Hole, MA 02543
| | - Ulrike Jaekel
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA 02138
| | - Benjamin J Tully
- Center for Dark Energy Biosphere Investigations, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089
| | - Brian T Glazer
- Department of Oceanography, University of Hawai'i at Mānoa, 1000 Pope Rd., Honolulu, HI 96822
| | - C Geoffrey Wheat
- Global Undersea Research Unit, University of Alaska Fairbanks, P.O. Box 475, Moss Landing, CA 95039
| | - Huei-Ting Lin
- Department of Oceanography, University of Hawai'i at Mānoa, 1000 Pope Rd., Honolulu, HI 96822
| | - Chih-Chiang Hsieh
- Department of Oceanography, University of Hawai'i at Mānoa, 1000 Pope Rd., Honolulu, HI 96822
| | - James P Cowen
- Department of Oceanography, University of Hawai'i at Mānoa, 1000 Pope Rd., Honolulu, HI 96822
| | - Samuel M Hulme
- Moss Landing Marine Laboratory, 8272 Moss Landing Road, Moss Landing, CA 95039
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA 02138
| | - Julie A Huber
- Josephine Bay Paul Center, Marine Biological Laboratory, 7 MBL St., Woods Hole, MA 02543
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Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent. ISME JOURNAL 2016; 10:1925-38. [PMID: 26872039 PMCID: PMC5029171 DOI: 10.1038/ismej.2015.258] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 12/07/2015] [Accepted: 12/10/2015] [Indexed: 01/13/2023]
Abstract
The chemolithoautotrophic microbial community of the rocky subseafloor potentially provides a large amount of organic carbon to the deep ocean, yet our understanding of the activity and metabolic complexity of subseafloor organisms remains poorly described. A combination of metagenomic, metatranscriptomic, and RNA stable isotope probing (RNA-SIP) analyses were used to identify the metabolic potential, expression patterns, and active autotrophic bacteria and archaea and their pathways present in low-temperature hydrothermal fluids from Axial Seamount, an active submarine volcano. Metagenomic and metatranscriptomic results showed the presence of genes and transcripts for sulfur, hydrogen, and ammonium oxidation, oxygen respiration, denitrification, and methanogenesis, as well as multiple carbon fixation pathways. In RNA-SIP experiments across a range of temperatures under reducing conditions, the enriched 13C fractions showed differences in taxonomic and functional diversity. At 30 °C and 55 °C, Epsilonproteobacteria were dominant, oxidizing hydrogen and primarily reducing nitrate. Methanogenic archaea were also present at 55 °C, and were the only autotrophs present at 80 °C. Correspondingly, the predominant CO2 fixation pathways changed from the reductive tricarboxylic acid (rTCA) cycle to the reductive acetyl-CoA pathway with increasing temperature. By coupling RNA-SIP with meta-omics, this study demonstrates the presence and activity of distinct chemolithoautotrophic communities across a thermal gradient of a deep-sea hydrothermal vent.
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225
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Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments. ISME JOURNAL 2016; 10:1939-53. [PMID: 26872043 DOI: 10.1038/ismej.2015.257] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/27/2015] [Accepted: 12/01/2015] [Indexed: 01/10/2023]
Abstract
Marine sediments are the largest carbon sink on earth. Nearly half of dark carbon fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with (14)C-carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70-86% of dark carbon fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark carbon fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with (14)C-bicarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter, JTB255 and SSr clades) that made up >50% of dark carbon fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and carbon fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria. The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine carbon and sulfur cycles.
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226
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Bach W. Some Compositional and Kinetic Controls on the Bioenergetic Landscapes in Oceanic Basement. Front Microbiol 2016; 7:107. [PMID: 26903986 PMCID: PMC4746428 DOI: 10.3389/fmicb.2016.00107] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/20/2016] [Indexed: 11/13/2022] Open
Abstract
This contribution assesses the availability of catabolic energy for microbial life during water-rock reactions in the flanks of mid-ocean ridges, where basaltic and ultramafic rocks interact with circulating seawater. In addition to equilibrium thermodynamic computations, results for kinetic reaction paths are presented. In these calculations, it is assumed that dissolution of olivine and basalt glass control the rates of hydrogen forming reactions in ultramafic and basaltic rocks, respectively. The results suggest that all ocean crust basement rocks release enough hydrogen (H2,aq) to support hydrogenotrophic life at low water-to-rock ratios. Olivine dissolution rate control imposes a stronger effect on hydrogen production than phase equilibrium controls, indicating that magnetite formation is not a requirement for production of large amounts of hydrogen in ultramafic rocks. The formation of non-tronite and celadonite are primarily responsible for the formation of the moderate amounts of hydrogen (H2,aq) expected in basaltic ridge flanks. Under conditions of large seawater fluxes required to account for the great global convective heat flow in ridge flanks, however, hydrogen production in basaltic ridge flanks is insufficient for supporting hydrogenotrophic life. It is hence proposed that the role of Fe oxidation in basaltic ridge flanks is greater than previously suggested. A standing stock of 2.4(∗)10(28) cells may be supported by Fe oxidation in basaltic ridge flanks, equivalent of about 10% of the sedimentary deep biosphere. The size of a hydrogenotrophic biomass within the ocean crust is more difficult to estimate because the rates and processes of hydrogen release are insufficiently constrained. In any case, hydrogenotrophy in the ocean crust should be of key importance only in olivine-rich basement rocks and in sedimented ridge flanks with low time-integrated seawater fluxes.
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Affiliation(s)
- Wolfgang Bach
- MARUM and Geoscience Department, University of BremenBremen, Germany; Centre of Excellence in Geobiology and Department of Earth Sciences, University of BergenBergen, Norway
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227
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Bienhold C, Zinger L, Boetius A, Ramette A. Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria. PLoS One 2016; 11:e0148016. [PMID: 26814838 PMCID: PMC4731391 DOI: 10.1371/journal.pone.0148016] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 01/12/2016] [Indexed: 11/19/2022] Open
Abstract
The deep ocean floor covers more than 60% of the Earth's surface, and hosts diverse bacterial communities with important functions in carbon and nutrient cycles. The identification of key bacterial members remains a challenge and their patterns of distribution in seafloor sediment yet remain poorly described. Previous studies were either regionally restricted or included few deep-sea sediments, and did not specifically test biogeographic patterns across the vast oligotrophic bathyal and abyssal seafloor. Here we define the composition of this deep seafloor microbiome by describing those bacterial operational taxonomic units (OTU) that are specifically associated with deep-sea surface sediments at water depths ranging from 1000-5300 m. We show that the microbiome of the surface seafloor is distinct from the subsurface seafloor. The cosmopolitan bacterial OTU were affiliated with the clades JTB255 (class Gammaproteobacteria, order Xanthomonadales) and OM1 (Actinobacteria, order Acidimicrobiales), comprising 21% and 7% of their respective clades, and about 1% of all sequences in the study. Overall, few sequence-abundant bacterial types were globally dispersed and displayed positive range-abundance relationships. Most bacterial populations were rare and exhibited a high degree of endemism, explaining the substantial differences in community composition observed over large spatial scales. Despite the relative physicochemical uniformity of deep-sea sediments, we identified indicators of productivity regimes, especially sediment organic matter content, as factors significantly associated with changes in bacterial community structure across the globe.
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Affiliation(s)
- Christina Bienhold
- HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany, and Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Lucie Zinger
- HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany, and Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Antje Boetius
- HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany, and Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Alban Ramette
- HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany, and Max Planck Institute for Marine Microbiology, Bremen, Germany
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228
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Henri PA, Rommevaux-Jestin C, Lesongeur F, Mumford A, Emerson D, Godfroy A, Ménez B. Structural Iron (II) of Basaltic Glass as an Energy Source for Zetaproteobacteria in an Abyssal Plain Environment, Off the Mid Atlantic Ridge. Front Microbiol 2016; 6:1518. [PMID: 26834704 PMCID: PMC4720738 DOI: 10.3389/fmicb.2015.01518] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/17/2015] [Indexed: 12/27/2022] Open
Abstract
To explore the capability of basaltic glass to support the growth of chemosynthetic microorganisms, complementary in situ and in vitro colonization experiments were performed. Microbial colonizers containing synthetic tholeitic basaltic glasses, either enriched in reduced or oxidized iron, were deployed off-axis from the Mid Atlantic Ridge on surface sediments of the abyssal plain (35°N; 29°W). In situ microbial colonization was assessed by sequencing of the 16S rRNA gene and basaltic glass alteration was characterized using Scanning Electron Microscopy, micro-X-ray Absorption Near Edge Structure at the Fe-K-edge and Raman microspectroscopy. The colonized surface of the reduced basaltic glass was covered by a rind of alteration made of iron-oxides trapped in a palagonite-like structure with thicknesses up to 150 μm. The relative abundance of the associated microbial community was dominated (39% of all reads) by a single operational taxonomic unit (OTU) that shared 92% identity with the iron-oxidizer Mariprofundus ferrooxydans PV-1. Conversely, the oxidized basaltic glass showed the absence of iron-oxides enriched surface deposits and correspondingly there was a lack of known iron-oxidizing bacteria in the inventoried diversity. In vitro, a similar reduced basaltic glass was incubated in artificial seawater with a pure culture of the iron-oxidizing M. ferrooxydans DIS-1 for 2 weeks, without any additional nutrients or minerals. Confocal Laser Scanning Microscopy revealed that the glass surface was covered by twisted stalks characteristic of this iron-oxidizing Zetaproteobacteria. This result supported findings of the in situ experiments indicating that the Fe(II) present in the basalt was the energy source for the growth of representatives of Zetaproteobacteria in both the abyssal plain and the in vitro experiment. In accordance, the surface alteration rind observed on the reduced basaltic glass incubated in situ could at least partly result from their activity.
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Affiliation(s)
- Pauline A Henri
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Univ Paris Diderot, Centre National de la Recherche Scientifique Paris, France
| | - Céline Rommevaux-Jestin
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Univ Paris Diderot, Centre National de la Recherche Scientifique Paris, France
| | - Françoise Lesongeur
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS/UMR 6197 Plouzané, France
| | - Adam Mumford
- Bigelow Laboratory for Ocean Sciences East Boothbay, ME, USA
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences East Boothbay, ME, USA
| | - Anne Godfroy
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS/UMR 6197 Plouzané, France
| | - Bénédicte Ménez
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Univ Paris Diderot, Centre National de la Recherche Scientifique Paris, France
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229
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Steen IH, Dahle H, Stokke R, Roalkvam I, Daae FL, Rapp HT, Pedersen RB, Thorseth IH. Novel Barite Chimneys at the Loki's Castle Vent Field Shed Light on Key Factors Shaping Microbial Communities and Functions in Hydrothermal Systems. Front Microbiol 2016; 6:1510. [PMID: 26779165 PMCID: PMC4703759 DOI: 10.3389/fmicb.2015.01510] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/14/2015] [Indexed: 01/23/2023] Open
Abstract
In order to fully understand the cycling of elements in hydrothermal systems it is critical to understand intra-field variations in geochemical and microbiological processes in both focused, high-temperature and diffuse, low-temperature areas. To reveal important causes and effects of this variation, we performed an extensive chemical and microbiological characterization of a low-temperature venting area in the Loki's Castle Vent Field (LCVF). This area, located at the flank of the large sulfide mound, is characterized by numerous chimney-like barite (BaSO4) structures (≤ 1 m high) covered with white cotton-like microbial mats. Results from geochemical analyses, microscopy (FISH, SEM), 16S rRNA gene amplicon-sequencing and metatranscriptomics were compared to results from previous analyses of biofilms growing on black smoker chimneys at LCVF. Based on our results, we constructed a conceptual model involving the geochemistry and microbiology in the LCVF. The model suggests that CH4 and H2S are important electron donors for microorganisms in both high-temperature and low-temperature areas, whereas the utilization of H2 seems restricted to high-temperature areas. This further implies that sub-seafloor processes can affect energy-landscapes, elemental cycling, and the metabolic activity of primary producers on the seafloor. In the cotton-like microbial mats on top of the active barite chimneys, a unique network of single cells of Epsilonproteobacteria interconnected by threads of extracellular polymeric substances (EPS) was seen, differing significantly from the long filamentous Sulfurovum filaments observed in biofilms on the black smokers. This network also induced nucleation of barite crystals and is suggested to play an essential role in the formation of the microbial mats and the chimneys. Furthermore, it illustrates variations in how different genera of Epsilonproteobacteria colonize and position cells in different vent fluid mixing zones within a vent field. This may be related to niche-specific physical characteristics. Altogether, the model provides a reference for future studies and illustrates the importance of systematic comparative studies of spatially closely connected niches in order to fully understand the geomicrobiology of hydrothermal systems.
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Affiliation(s)
- Ida H Steen
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Håkon Dahle
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Runar Stokke
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Irene Roalkvam
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Frida-Lise Daae
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Hans Tore Rapp
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Rolf B Pedersen
- Centre for Geobiology, University of BergenBergen, Norway; Department of Earth Science, University of BergenBergen, Norway
| | - Ingunn H Thorseth
- Centre for Geobiology, University of BergenBergen, Norway; Department of Earth Science, University of BergenBergen, Norway
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230
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Honkalas V, Dabir A, Dhakephalkar PK. Life in the Anoxic Sub-Seafloor Environment: Linking Microbial Metabolism and Mega Reserves of Methane Hydrate. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 156:235-262. [DOI: 10.1007/10_2015_5004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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231
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Analysis of Low-Biomass Microbial Communities in the Deep Biosphere. ADVANCES IN APPLIED MICROBIOLOGY 2016; 95:149-78. [PMID: 27261783 DOI: 10.1016/bs.aambs.2016.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Over the past few decades, the subseafloor biosphere has been explored by scientific ocean drilling to depths of about 2.5km below the seafloor. Although organic-rich anaerobic sedimentary habitats in the ocean margins harbor large numbers of microbial cells, microbial populations in ultraoligotrophic aerobic sedimentary habitats in the open ocean gyres are several orders of magnitude less abundant. Despite advances in cultivation-independent molecular ecological techniques, exploring the low-biomass environment remains technologically challenging, especially in the deep subseafloor biosphere. Reviewing the historical background of deep-biosphere analytical methods, the importance of obtaining clean samples and tracing contamination, as well as methods for detecting microbial life, technological aspects of molecular microbiology, and detecting subseafloor metabolic activity will be discussed.
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232
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Abstract
Global microbial cell numbers in the seabed exceed those in the overlying water column, yet these organisms receive less than 1% of the energy fixed as organic matter in the ocean. The microorganisms of this marine deep biosphere subsist as stable and diverse communities with extremely low energy availability. Growth is exceedingly slow, possibly regulated by virus-induced mortality, and the mean generation times are tens to thousands of years. Intermediate substrates such as acetate are maintained at low micromolar concentrations, yet their turnover time may be several hundred years. Owing to slow growth, a cell community may go through only 10,000 generations from the time it is buried beneath the mixed surface layer until it reaches a depth of tens of meters several million years later. We discuss the efficiency of the energy-conserving machinery of subsurface microorganisms and how they may minimize energy consumption through necessary maintenance, repair, and growth.
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Affiliation(s)
- Bo Barker Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, 8000 Aarhus C, Denmark; ,
| | - Ian P G Marshall
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, 8000 Aarhus C, Denmark; ,
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233
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Microbial Surface Colonization and Biofilm Development in Marine Environments. Microbiol Mol Biol Rev 2015; 80:91-138. [PMID: 26700108 DOI: 10.1128/mmbr.00037-15] [Citation(s) in RCA: 462] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.
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234
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He Y, Feng X, Fang J, Zhang Y, Xiao X. Metagenome and Metatranscriptome Revealed a Highly Active and Intensive Sulfur Cycle in an Oil-Immersed Hydrothermal Chimney in Guaymas Basin. Front Microbiol 2015; 6:1236. [PMID: 26617579 PMCID: PMC4639633 DOI: 10.3389/fmicb.2015.01236] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 10/26/2015] [Indexed: 11/13/2022] Open
Abstract
The hydrothermal vent system is a typical chemosynthetic ecosystem in which microorganisms play essential roles in the geobiochemical cycling. Although it has been well-recognized that the inorganic sulfur compounds are abundant and actively converted through chemosynthetic pathways, the sulfur budget in a hydrothermal vent is poorly characterized due to the complexity of microbial sulfur cycling resulting from the numerous parties involved in the processes. In this study, we performed an integrated metagenomic and metatranscriptomic analysis on a chimney sample from Guaymas Basin to achieve a comprehensive study of each sulfur metabolic pathway and its hosting microorganisms and constructed the microbial sulfur cycle that occurs in the site. Our results clearly illustrated the stratified sulfur oxidation and sulfate reduction at the chimney wall. Besides, sulfur metabolizing is closely interacting with carbon cycles, especially the hydrocarbon degradation process in Guaymas Basin. This work supports that the internal sulfur cycling is intensive and the net sulfur budget is low in the hydrothermal ecosystem.
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Affiliation(s)
- Ying He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China ; State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University Shanghai, China
| | - Xiaoyuan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Jing Fang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Yu Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China ; State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University Shanghai, China ; Institute of Oceanology, Shanghai Jiao Tong University Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China ; State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University Shanghai, China ; Institute of Oceanology, Shanghai Jiao Tong University Shanghai, China
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235
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A Fungal-Prokaryotic Consortium at the Basalt-Zeolite Interface in Subseafloor Igneous Crust. PLoS One 2015; 10:e0140106. [PMID: 26488482 PMCID: PMC4619311 DOI: 10.1371/journal.pone.0140106] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/22/2015] [Indexed: 11/19/2022] Open
Abstract
We have after half a century of coordinated scientific drilling gained insight into Earth´s largest microbial habitat, the subseafloor igneous crust, but still lack substantial understanding regarding its abundance, diversity and ecology. Here we describe a fossilized microbial consortium of prokaryotes and fungi at the basalt-zeolite interface of fractured subseafloor basalts from a depth of 240 m below seafloor (mbsf). The microbial consortium and its relationship with the surrounding physical environment are revealed by synchrotron-based X-ray tomographic microscopy (SRXTM), environmental scanning electron microscopy (ESEM), and Raman spectroscopy. The base of the consortium is represented by microstromatolites—remains of bacterial communities that oxidized reduced iron directly from the basalt. The microstromatolites and the surrounding basalt were overlaid by fungal cells and hyphae. The consortium was overgrown by hydrothermally formed zeolites but remained alive and active during this event. After its formation, fungal hyphae bored in the zeolite, producing millimetre-long tunnels through the mineral substrate. The dissolution could either serve to extract metals like Ca, Na and K essential for fungal growth and metabolism, or be a response to environmental stress owing to the mineral overgrowth. Our results show how microbial life may be maintained in a nutrient-poor and extreme environment by close ecological interplay and reveal an effective strategy for nutrient extraction from minerals. The prokaryotic portion of the consortium served as a carbon source for the eukaryotic portion. Such an approach may be a prerequisite for prokaryotic-eukaryotic colonisation of, and persistence in, subseafloor igneous crust.
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236
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Fichtel K, Logemann J, Fichtel J, Rullkötter J, Cypionka H, Engelen B. Temperature and pressure adaptation of a sulfate reducer from the deep subsurface. Front Microbiol 2015; 6:1078. [PMID: 26500624 PMCID: PMC4594026 DOI: 10.3389/fmicb.2015.01078] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/21/2015] [Indexed: 11/13/2022] Open
Abstract
Microbial life in deep marine subsurface faces increasing temperatures and hydrostatic pressure with depth. In this study, we have examined growth characteristics and temperature-related adaptation of the Desulfovibrio indonesiensis strain P23 to the in situ pressure of 30 MPa. The strain originates from the deep subsurface of the eastern flank of the Juan de Fuca Ridge (IODP Site U1301). The organism was isolated at 20°C and atmospheric pressure from ~61°C-warm sediments approximately 5 m above the sediment-basement interface. In comparison to standard laboratory conditions (20°C and 0.1 MPa), faster growth was recorded when incubated at in situ pressure and high temperature (45°C), while cell filamentation was induced by further compression. The maximum growth temperature shifted from 48°C at atmospheric pressure to 50°C under high-pressure conditions. Complementary cellular lipid analyses revealed a two-step response of membrane viscosity to increasing temperature with an exchange of unsaturated by saturated fatty acids and subsequent change from branched to unbranched alkyl moieties. While temperature had a stronger effect on the degree of fatty acid saturation and restructuring of main phospholipids, pressure mainly affected branching and length of side chains. The simultaneous decrease of temperature and pressure to ambient laboratory conditions allowed the cultivation of our moderately thermophilic strain. This may in turn be one key to a successful isolation of microorganisms from the deep subsurface adapted to high temperature and pressure.
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Affiliation(s)
- Katja Fichtel
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
| | - Jörn Logemann
- Organic Geochemistry Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
| | - Jörg Fichtel
- Organic Geochemistry Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
| | - Jürgen Rullkötter
- Organic Geochemistry Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
| | - Heribert Cypionka
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
| | - Bert Engelen
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
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237
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McLoughlin N, Grosch EG. A Hierarchical System for Evaluating the Biogenicity of Metavolcanic- and Ultramafic-Hosted Microalteration Textures in the Search for Extraterrestrial Life. ASTROBIOLOGY 2015; 15:901-921. [PMID: 26496528 DOI: 10.1089/ast.2014.1259] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The low-temperature alteration of submarine volcanic glasses has been argued to involve the activity of microorganisms, and analogous fluid-rock-microbial-mediated alteration has also been postulated on Mars. However, establishing the extent to which microbes are involved in volcanic glass alteration has proven to be difficult, and the reliability of resulting textural biosignatures is debated, particularly in the early rock record. We therefore propose a hierarchical scheme to evaluate the biogenicity of candidate textural biosignatures found in altered terrestrial and extraterrestrial basaltic glasses and serpentinized ultramafic rocks. The hierarchical scheme is formulated to give increasing confidence of a biogenic origin and involves (i) investigation of the textural context and syngenicity of the candidate biosignature; (ii) characterization of the morphology and size range of the microtextures; (iii) mapping of the geological and physicochemical variables controlling the occurrence and preservation of the microtextures; (iv) in situ investigation of chemical signatures that are syngenetic to the microtexture; and (v) identification of growth patterns suggestive of biological behavior and redox variations in the host minerals. The scheme results in five categories of candidate biosignature as follows: Category 1 indicates preservation of very weak evidence for biogenicity, Categories 2 through 4 indicate evidence for increasing confidence of a biogenic origin, and Category 5 indicates that biogenic origin is most likely. We apply this hierarchical approach to examine the evidence for a biogenic origin of several examples, including candidate bacterial encrustations in altered pillow lavas, granular and tubular microtextures in volcanic glass from the subseafloor and a Phanerozoic ophiolite, mineralized microtextures in Archean metavolcanic glass, and alteration textures in olivines of the martian meteorite Yamato 000593. The aim of this hierarchical approach is to provide a framework for identifying robust biosignatures of microbial life in the altered oceanic crust on Earth, and in extraterrestrial altered mafic-ultramafic rocks, particularly on Mars.
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Affiliation(s)
| | - Eugene G Grosch
- Department of Earth Sciences, University of Bergen , Bergen, Norway
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Characteristics of the cultivable bacteria from sediments associated with two deep-sea hydrothermal vents in Okinawa Trough. World J Microbiol Biotechnol 2015; 31:2025-37. [PMID: 26410427 DOI: 10.1007/s11274-015-1953-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 09/23/2015] [Indexed: 10/23/2022]
Abstract
In this study, different culture-dependent methods were used to examine the cultivable heterotrophic bacteria in the sediments associated with two deep-sea hydrothermal vents (named HV1 and HV2) located at Iheya Ridge and Iheya North in Okinawa Trough. The two vents differed in morphology, with HV1 exhibiting diffuse flows while HV2 being a black smoker with a chimney-like structure. A total of 213 isolates were identified by near full-length 16S rRNA gene sequence analysis. Of these isolates, 128 were from HV1 and 85 were from HV2. The bacterial community structures were, in large parts, similar between HV1 and HV2. Nevertheless, differences between HV1 and HV2 were observed in one phylum, one class, 4 orders, 10 families, and 20 genera. Bioactivity analysis revealed that 25 isolates belonging to 9 different genera exhibited extracellular protease activities, 21 isolates from 11 genera exhibited extracellular lipase activities, and 13 isolates of 8 genera displayed antimicrobial activities. This is the first observation of a large population of bacteria with extracellular bioactivities existing in deep-sea hydrothermal vents. Taken together, the results of this study provide new insights into the characteristics of the cultivable heterotrophic bacteria in deep-sea hydrothermal ecosystems.
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Price MT, Fullerton H, Moyer CL. Biogeography and evolution of Thermococcus isolates from hydrothermal vent systems of the Pacific. Front Microbiol 2015; 6:968. [PMID: 26441901 PMCID: PMC4585236 DOI: 10.3389/fmicb.2015.00968] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/01/2015] [Indexed: 11/13/2022] Open
Abstract
Thermococcus is a genus of hyperthermophilic archaea that is ubiquitous in marine hydrothermal environments growing in anaerobic subsurface habitats but able to survive in cold oxygenated seawater. DNA analyses of Thermococcus isolates were applied to determine the relationship between geographic distribution and relatedness focusing primarily on isolates from the Juan de Fuca Ridge and South East Pacific Rise. Amplified fragment length polymorphism (AFLP) analysis and multilocus sequence typing (MLST) were used to resolve genomic differences in 90 isolates of Thermococcus, making biogeographic patterns and evolutionary relationships apparent. Isolates were differentiated into regionally endemic populations however there was also evidence in some lineages of cosmopolitan distribution. The biodiversity identified in Thermococcus isolates and presence of distinct lineages within the same vent site suggests the utilization of varying ecological niches in this genus. In addition to resolving biogeographic patterns in Thermococcus, this study has raised new questions about the closely related Pyrococcus genus. The phylogenetic placement of Pyrococcus type strains shows the close relationship between Thermococcus and Pyrococcus and the unresolved divergence of these two genera.
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Affiliation(s)
- Mark T Price
- Department of Biology, Western Washington University Bellingham, WA, USA
| | - Heather Fullerton
- Department of Biology, Western Washington University Bellingham, WA, USA
| | - Craig L Moyer
- Department of Biology, Western Washington University Bellingham, WA, USA
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240
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Roalkvam I, Drønen K, Stokke R, Daae FL, Dahle H, Steen IH. Physiological and genomic characterization of Arcobacter anaerophilus IR-1 reveals new metabolic features in Epsilonproteobacteria. Front Microbiol 2015; 6:987. [PMID: 26441916 PMCID: PMC4584990 DOI: 10.3389/fmicb.2015.00987] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 09/04/2015] [Indexed: 01/18/2023] Open
Abstract
In this study we characterized and sequenced the genome of Arcobacter anaerophilus strain IR-1 isolated from enrichment cultures used in nitrate-amended corrosion experiments. A. anaerophilus IR-1 could grow lithoautotrophically on hydrogen and hydrogen sulfide and lithoheterothrophically on thiosulfate and elemental sulfur. In addition, the strain grew organoheterotrophically on yeast extract, peptone, and various organic acids. We show for the first time that Arcobacter could grow on the complex organic substrate tryptone and oxidize acetate with elemental sulfur as electron acceptor. Electron acceptors utilized by most Epsilonproteobacteria, such as oxygen, nitrate, and sulfur, were also used by A. anaerophilus IR-1. Strain IR-1 was also uniquely able to use iron citrate as electron acceptor. Comparative genomics of the Arcobacter strains A. butzleri RM4018, A. nitrofigilis CI and A. anaerophilus IR-1 revealed that the free-living strains had a wider metabolic range and more genes in common compared to the pathogen strain. The presence of genes for NAD(+)-reducing hydrogenase (hox) and dissimilatory iron reduction (fre) were unique for A. anaerophilus IR-1 among Epsilonproteobacteria. Finally, the new strain had an incomplete denitrification pathway where the end product was nitrite, which is different from other Arcobacter strains where the end product is ammonia. Altogether, our study shows that traditional characterization in combination with a modern genomics approach can expand our knowledge on free-living Arcobacter, and that this complementary approach could also provide invaluable knowledge about the physiology and metabolic pathways in other Epsilonproteobacteria from various environments.
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Affiliation(s)
- Irene Roalkvam
- Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway
| | - Karine Drønen
- UniResearch, Centre for Integrated Petroleum Research Bergen, Norway
| | - Runar Stokke
- Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway
| | - Frida L Daae
- Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway
| | - Håkon Dahle
- Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway
| | - Ida H Steen
- Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway
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241
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Cao H, Shao Z, Li J, Zhang W, Qian PY. Phylogenetic diversity of nitrogen-utilizing genes in hydrothermal chimneys from 3 middle ocean ridges. Extremophiles 2015; 19:1173-82. [PMID: 26369648 DOI: 10.1007/s00792-015-0788-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 08/30/2015] [Indexed: 10/23/2022]
Abstract
Nitrogen-metabolizing genes, including nitrogenase (nifH), periplasmic nitrate reductase (napA), and cytochrome cd 1-type nitrite reductase (nirS), were collected from hydrothermal chimney sulfides on 3 middle ocean ridges and compared for the first time. There was a clear phylogenetic distinction of these nifH genes between different hydrothermal ecosystems, which supported the colonization and potential adaptation by different nitrogen fixing microbes in those sulfides. In particular, in sulfides from low-temperature hydrothermal vents of the Southwest Indian Ocean Ridge, the prevalence of nifH genes appears to be attributed to sulfate-reducing bacteria, suggesting their ecological significance. Phylogenetic analysis of nitrate/nitrite reductase genes indicated that nitrate was a critical electron acceptor for sulfur- or metal-oxidizing bacteria in these hydrothermal ecosystems. Our results provided information about the compositions and diversity of the 3 important genes involved in nitrogen fixation and nitrate/nitrite reduction processes in hydrothermal ecosystems and is the first comprehensive genetic repertoire of genes related to potential nitrogen fixation and denitrification processes in various hydrothermal environments.
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Affiliation(s)
- Huiluo Cao
- Division of Life Sciences, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, The Third Institute of Oceanography, State of Oceanic Administration, Xiamen, China
| | - Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Weipeng Zhang
- Division of Life Sciences, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Pei-Yuan Qian
- Division of Life Sciences, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
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242
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Orcutt BN, Sylvan JB, Rogers DR, Delaney J, Lee RW, Girguis PR. Carbon fixation by basalt-hosted microbial communities. Front Microbiol 2015; 6:904. [PMID: 26441854 PMCID: PMC4561358 DOI: 10.3389/fmicb.2015.00904] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 08/19/2015] [Indexed: 11/13/2022] Open
Abstract
Oceanic crust is a massive potential habitat for microbial life on Earth, yet our understanding of this ecosystem is limited due to difficulty in access. In particular, measurements of rates of microbial activity are sparse. We used stable carbon isotope incubations of crustal samples, coupled with functional gene analyses, to examine the potential for carbon fixation on oceanic crust. Both seafloor-exposed and subseafloor basalts were recovered from different mid-ocean ridge and hot spot environments (i.e., the Juan de Fuca Ridge, the Mid-Atlantic Ridge, and the Loihi Seamount) and incubated with (13)C-labeled bicarbonate. Seafloor-exposed basalts revealed incorporation of (13)C-label into organic matter over time, though the degree of incorporation was heterogeneous. The incorporation of (13)C into biomass was inconclusive in subseafloor basalts. Translating these measurements into potential rates of carbon fixation indicated that 0.1-10 nmol C g(-1) rock d(-1) could be fixed by seafloor-exposed rocks. When scaled to the global production of oceanic crust, this suggests carbon fixation rates of 10(9)-10(12) g C year(-1), which matches earlier predictions based on thermodynamic calculations. Functional gene analyses indicate that the Calvin cycle is likely the dominant biochemical mechanism for carbon fixation in basalt-hosted biofilms, although the reductive acetyl-CoA pathway and reverse TCA cycle likely play some role in net carbon fixation. These results provide empirical evidence for autotrophy in oceanic crust, suggesting that basalt-hosted autotrophy could be a significant contributor of organic matter in this remote and vast environment.
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Affiliation(s)
- Beth N. Orcutt
- Bigelow Laboratory for Ocean SciencesEast Boothbay, ME, USA
- University of Southern CaliforniaLos Angeles, CA, USA
| | | | - Daniel R. Rogers
- Biological Laboratories, Harvard UniversityCambridge, MA, USA
- Stonehill CollegeNorth Easton, MA, USA
| | | | - Raymond W. Lee
- School of Biological Sciences, Washington State UniversityPullman, WA, USA
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243
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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244
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Ivarsson M, Broman C, Gustafsson H, Holm NG. Biogenic Mn-Oxides in Subseafloor Basalts. PLoS One 2015; 10:e0128863. [PMID: 26107948 PMCID: PMC4479566 DOI: 10.1371/journal.pone.0128863] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 05/03/2015] [Indexed: 11/18/2022] Open
Abstract
The deep biosphere of the subseafloor basalts is recognized as a major scientific frontier in disciplines like biology, geology, and oceanography. Recently, the presence of fungi in these environments has involved a change of view regarding diversity and ecology. Here, we describe fossilized fungal communities in vugs in subseafloor basalts from a depth of 936.65 metres below seafloor at the Detroit Seamount, Pacific Ocean. These fungal communities are closely associated with botryoidal Mn oxides composed of todorokite. Analyses of the Mn oxides by Electron Paramagnetic Resonance spectroscopy (EPR) indicate a biogenic signature. We suggest, based on mineralogical, morphological and EPR data, a biological origin of the botryoidal Mn oxides. Our results show that fungi are involved in Mn cycling at great depths in the seafloor and we introduce EPR as a means to easily identify biogenic Mn oxides in these environments.
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Affiliation(s)
- Magnus Ivarsson
- Department of Palaeobiology and the Nordic Center for Earth Evolution (NordCEE), Swedish Museum of Natural History, Stockholm, Sweden
- * E-mail:
| | - Curt Broman
- Department of Geological Sciences, Stockholm University, Stockholm, Sweden
| | - Håkan Gustafsson
- Department of Biomedical Engineering (MTÖ), County Council of Östergötland, Radiation Physics, Department of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Nils G. Holm
- Department of Geological Sciences, Stockholm University, Stockholm, Sweden
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245
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Phylogeny and physiology of candidate phylum 'Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics. ISME JOURNAL 2015; 10:273-86. [PMID: 26090992 DOI: 10.1038/ismej.2015.97] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 04/09/2015] [Accepted: 05/08/2015] [Indexed: 12/31/2022]
Abstract
The 'Atribacteria' is a candidate phylum in the Bacteria recently proposed to include members of the OP9 and JS1 lineages. OP9 and JS1 are globally distributed, and in some cases abundant, in anaerobic marine sediments, geothermal environments, anaerobic digesters and reactors and petroleum reservoirs. However, the monophyly of OP9 and JS1 has been questioned and their physiology and ecology remain largely enigmatic due to a lack of cultivated representatives. Here cultivation-independent genomic approaches were used to provide a first comprehensive view of the phylogeny, conserved genomic features and metabolic potential of members of this ubiquitous candidate phylum. Previously available and heretofore unpublished OP9 and JS1 single-cell genomic data sets were used as recruitment platforms for the reconstruction of atribacterial metagenome bins from a terephthalate-degrading reactor biofilm and from the monimolimnion of meromictic Sakinaw Lake. The single-cell genomes and metagenome bins together comprise six species- to genus-level groups that represent most major lineages within OP9 and JS1. Phylogenomic analyses of these combined data sets confirmed the monophyly of the 'Atribacteria' inclusive of OP9 and JS1. Additional conserved features within the 'Atribacteria' were identified, including a gene cluster encoding putative bacterial microcompartments that may be involved in aldehyde and sugar metabolism, energy conservation and carbon storage. Comparative analysis of the metabolic potential inferred from these data sets revealed that members of the 'Atribacteria' are likely to be heterotrophic anaerobes that lack respiratory capacity, with some lineages predicted to specialize in either primary fermentation of carbohydrates or secondary fermentation of organic acids, such as propionate.
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246
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Jian H, Xiong L, He Y, Xiao X. The regulatory function of LexA is temperature-dependent in the deep-sea bacterium Shewanella piezotolerans WP3. Front Microbiol 2015; 6:627. [PMID: 26150814 PMCID: PMC4471891 DOI: 10.3389/fmicb.2015.00627] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/08/2015] [Indexed: 01/01/2023] Open
Abstract
The SOS response addresses DNA lesions and is conserved in the bacterial domain. The response is governed by the DNA binding protein LexA, which has been characterized in model microorganisms such as Escherichia coli. However, our understanding of its roles in deep-sea bacteria is limited. Here, the influence of LexA on the phenotype and gene transcription of Shewanella piezotolerans WP3 (WP3) was investigated by constructing a lexA deletion strain (WP3ΔlexA), which was compared with the wild-type strain. No growth defect was observed for WP3ΔlexA. A total of 481 and 108 genes were differentially expressed at 20 and 4°C, respectively, as demonstrated by comparative whole genome microarray analysis. Furthermore, the swarming motility and dimethylsulfoxide reduction assay demonstrated that the function of LexA was related to temperature. The transcription of the lexA gene was up-regulated during cold acclimatization and after cold shock, indicating that the higher expression level of LexA at low temperatures may be responsible for its temperature-dependent functions. The deep-sea microorganism S. piezotolerans WP3 is the only bacterial species whose SOS regulator has been demonstrated to be significantly influenced by environmental temperatures to date. Our data support the hypothesis that SOS is a formidable strategy used by bacteria against various environmental stresses.
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Affiliation(s)
- Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Lei Xiong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Ying He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China ; State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University Shanghai, China
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247
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Yang B, Zhang W, Tian R, Wang Y, Qian PY. Changing composition of microbial communities indicates seepage fluid difference of the Thuwal Seeps in the Red Sea. Antonie van Leeuwenhoek 2015; 108:461-71. [PMID: 26059861 DOI: 10.1007/s10482-015-0499-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 06/01/2015] [Indexed: 11/26/2022]
Abstract
Cold seeps are unique ecosystems that are generally characterized by high salinity and reducing solutions. Seepage fluid, the major water influx of this system, contains hypersaline water, sediment pore water, and other components. The Thuwal cold seeps were recently discovered on the continental margin of the Red Sea. Using 16S rRNA gene pyro-sequencing technology, microbial communities were investigated by comparing samples collected in 2011 and 2013. The results revealed differences in the microbial communities between the two sampling times. In particular, a significantly higher abundance of Marine Group I (MGI) Thaumarchaeota was coupled with lower salinity in 2013. In the brine pool, the dominance of Desulfobacterales in 2011 was supplanted by MGI Thaumarchaeota in 2013, perhaps due to a reduced supply of hydrogen sulfide from the seepage fluid. Collectively, this study revealed a difference in water components in this ecosystem between two sampling times. The results indicated that the seawater in this cold seep displayed a greater number of characteristics of normal seawater in 2013 than in 2011, which might represent the dominant driving force for changes in microbial community structures. This is the first study to provide a temporal comparison of the microbial biodiversity of a cold seep ecosystem in the Red Sea.
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Affiliation(s)
- Bo Yang
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong,
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248
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Polymenakou PN, Christakis CA, Mandalakis M, Oulas A. Pyrosequencing analysis of microbial communities reveals dominant cosmopolitan phylotypes in deep-sea sediments of the eastern Mediterranean Sea. Res Microbiol 2015; 166:448-457. [PMID: 25908548 DOI: 10.1016/j.resmic.2015.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/22/2015] [Accepted: 03/23/2015] [Indexed: 10/23/2022]
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249
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Algora C, Vasileiadis S, Wasmund K, Trevisan M, Krüger M, Puglisi E, Adrian L. Manganese and iron as structuring parameters of microbial communities in Arctic marine sediments from the Baffin Bay. FEMS Microbiol Ecol 2015; 91:fiv056. [PMID: 25994158 DOI: 10.1093/femsec/fiv056] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2015] [Indexed: 11/14/2022] Open
Abstract
The Arctic Baffin Bay between Canada and Greenland is sea ice-covered during the majority of the year, restricting primary production to the summer months. Sediments receive low amounts of mostly terrestrial- and less marine-derived organic matter. To study microbial communities constrained by physicochemical conditions changing with distance from land and ocean depth, we applied high-throughput 16S rRNA gene sequencing and compared sequence diversity with biogeochemical parameters in 40 different sediment samples. Samples originated from seven cores down to 470 cm below seafloor along a shelf-to-basin transect. Bacterial diversity decreased faster with depth in basin than in shelf sediments, suggesting higher organic matter content sustained diversity into greater depths. All samples were dominated by Betaproteobacteria (mostly order Burkholderiales), which were especially abundant in basin sediments with low organic carbon and high Mn and Fe pore water concentrations. Strong statistical correlations between concentrations of reduced Mn and/or Fe and the relative abundances of Betaproteobacteria suggest that this group is involved in metal reduction in Baffin Bay sediments. Dehalococcoidia (phylum Chloroflexi) were abundant in all samples, especially in shelf sediments with high organic content. This study indicates that Mn and/or Fe play important roles structuring microbial communities in Arctic sediments poor in organic matter.
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Affiliation(s)
- Camelia Algora
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Sotirios Vasileiadis
- Istituto di Chimica Agraria ed Ambientale, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Kenneth Wasmund
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Marco Trevisan
- Istituto di Chimica Agraria ed Ambientale, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Martin Krüger
- Department of Resource Geochemistry, Germany Federal Institute for Geosciences and Natural Resources (BGR), Stilleweg 2, 30655 Hannover; Germany
| | - Edoardo Puglisi
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Lorenz Adrian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
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250
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Heinzelmann SM, Villanueva L, Sinke-Schoen D, Sinninghe Damsté JS, Schouten S, van der Meer MTJ. Impact of metabolism and growth phase on the hydrogen isotopic composition of microbial fatty acids. Front Microbiol 2015; 6:408. [PMID: 26005437 PMCID: PMC4424904 DOI: 10.3389/fmicb.2015.00408] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 04/19/2015] [Indexed: 12/12/2022] Open
Abstract
Microorganisms are involved in all elemental cycles and therefore it is important to study their metabolism in the natural environment. A recent technique to investigate this is the hydrogen isotopic composition of microbial fatty acids, i.e., heterotrophic microorganisms produce fatty acids enriched in deuterium (D) while photoautotrophic and chemoautotrophic microorganisms produce fatty acids depleted in D compared to the water in the culture medium (growth water). However, the impact of factors other than metabolism have not been investigated. Here, we evaluate the impact of growth phase compared to metabolism on the hydrogen isotopic composition of fatty acids of different environmentally relevant microorganisms with heterotrophic, photoautotrophic and chemoautotrophic metabolisms. Fatty acids produced by heterotrophs are enriched in D compared to growth water with εlipid/water between 82 and 359‰ when grown on glucose or acetate, respectively. Photoautotrophs (εlipid/water between −149 and −264‰) and chemoautotrophs (εlipid/water between −217 and −275‰) produce fatty acids depleted in D. Fatty acids become, in general, enriched by between 4 and 46‰ with growth phase which is minor compared to the influence of metabolisms. Therefore, the D/H ratio of fatty acids is a promising tool to investigate community metabolisms in nature.
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Affiliation(s)
- Sandra M Heinzelmann
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands
| | - Laura Villanueva
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands
| | - Danielle Sinke-Schoen
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands ; Department of Earth Sciences, Faculty of Geosciences, Utrecht University Utrecht, Netherlands
| | - Stefan Schouten
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands ; Department of Earth Sciences, Faculty of Geosciences, Utrecht University Utrecht, Netherlands
| | - Marcel T J van der Meer
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands
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