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Miyajima Y, Aoyagi T, Yoshioka H, Hori T, Takahashi HA, Tanaka M, Tsukasaki A, Goto S, Suzumura M. Impact of Concurrent aerobic-anaerobic Methanotrophy on Methane Emission from Marine Sediments in Gas Hydrate Area. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4979-4988. [PMID: 38445630 PMCID: PMC10956523 DOI: 10.1021/acs.est.3c09484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 03/07/2024]
Abstract
Microbial methane oxidation has a significant impact on the methane flux from marine gas hydrate areas. However, the environmental fate of methane remains poorly constrained. We quantified the relative contributions of aerobic and anaerobic methanotrophs to methane consumption in sediments of the gas hydrate-bearing Sakata Knoll, Japan, by in situ geochemical and microbiological analyses coupled with 13C-tracer incubation experiments. The anaerobic ANME-1 and ANME-2 species contributed to the oxidation of 33.2 and 1.4% methane fluxes at 0-10 and 10-22 cm below the seafloor (bsf), respectively. Although the aerobic Methylococcaceae species consumed only 0.9% methane flux in the oxygen depleted 0.0-0.5 cmbsf zone, their metabolic activity was sustained down to 6 cmbsf (based on rRNA and lipid biosyntheses), increasing their contribution to 10.3%. Our study emphasizes that the co-occurrence of aerobic and anaerobic methanotrophy at the redox transition zone is an important determinant of methane flux.
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Affiliation(s)
- Yusuke Miyajima
- Research
Institute for Geo-Resources and Environment, Geological Survey of
Japan, National Institute of Advanced Industrial
Science and Technology (AIST), Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Tomo Aoyagi
- Environmental
Management Research Institute, National
Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Hideyoshi Yoshioka
- Research
Institute for Geo-Resources and Environment, Geological Survey of
Japan, National Institute of Advanced Industrial
Science and Technology (AIST), Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Tomoyuki Hori
- Environmental
Management Research Institute, National
Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Hiroshi A. Takahashi
- Research
Institute of Earthquake and Volcano Geology, Geological Survey of
Japan, National Institute of Advanced Industrial
Science and Technology (AIST), Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Minako Tanaka
- KANSO
TECHNOS Co., Ltd., 14 Kanda Higashimatsushita-cho, Chiyoda-ku, Tokyo 101-0042, Japan
| | - Ayumi Tsukasaki
- Environmental
Management Research Institute, National
Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Shusaku Goto
- Research
Institute for Geo-Resources and Environment, Geological Survey of
Japan, National Institute of Advanced Industrial
Science and Technology (AIST), Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Masahiro Suzumura
- Environmental
Management Research Institute, National
Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
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Rontani JF, Bonin P. Cellular Damage of Bacteria Attached to Senescent Phytoplankton Cells as a Result of the Transfer of Photochemically Produced Singlet Oxygen: A Review. Microorganisms 2023; 11:1565. [PMID: 37375067 DOI: 10.3390/microorganisms11061565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Several studies set out to explain the presence of high proportions of photooxidation products of cis-vaccenic acid (generally considered to be of bacterial origin) in marine environments. These studies show that these oxidation products result from the transfer of singlet oxygen from senescent phytoplankton cells to the bacteria attached to them in response to irradiation by sunlight. This paper summarizes and reviews the key findings of these studies, i.e., the demonstration of the process at work and the effect of different parameters (intensity of solar irradiance, presence of bacterial carotenoids, and presence of polar matrices such as silica, carbonate, and exopolymeric substances around phytoplankton cells) on this transfer. A large part of this review looks at how this type of alteration of bacteria can affect the preservation of algal material in the marine environment, especially in polar regions where conditions drive increased transfer of singlet oxygen from sympagic algae to bacteria.
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Affiliation(s)
- Jean-François Rontani
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Patricia Bonin
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
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3
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Kurth JM, Smit NT, Berger S, Schouten S, Jetten MSM, Welte CU. Anaerobic methanotrophic archaea of the ANME-2d clade feature lipid composition that differs from other ANME archaea. FEMS Microbiol Ecol 2020; 95:5509572. [PMID: 31150548 PMCID: PMC6581649 DOI: 10.1093/femsec/fiz082] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/29/2019] [Indexed: 11/30/2022] Open
Abstract
The anaerobic oxidation of methane (AOM) is a microbial process present in marine and freshwater environments. AOM is important for reducing the emission of the second most important greenhouse gas methane. In marine environments anaerobic methanotrophic archaea (ANME) are involved in sulfate-reducing AOM. In contrast, Ca. Methanoperedens of the ANME-2d cluster carries out nitrate AOM in freshwater ecosystems. Despite the importance of those organisms for AOM in non-marine environments little is known about their lipid composition or carbon sources. To close this gap, we analysed the lipid composition of ANME-2d archaea and found that they mainly synthesise archaeol and hydroxyarchaeol as well as different (hydroxy-) glycerol dialkyl glycerol tetraethers, albeit in much lower amounts. Abundant lipid headgroups were dihexose, monomethyl-phosphatidyl ethanolamine and phosphatidyl hexose. Moreover, a monopentose was detected as a lipid headgroup that is rare among microorganisms. Batch incubations with 13C labelled bicarbonate and methane showed that methane is the main carbon source of ANME-2d archaea varying from ANME-1 archaea that primarily assimilate dissolved inorganic carbon (DIC). ANME-2d archaea also assimilate DIC, but to a lower extent than methane. The lipid characterisation and analysis of the carbon source of Ca. Methanoperedens facilitates distinction between ANME-2d and other ANMEs.
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Affiliation(s)
- Julia M Kurth
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
| | - Nadine T Smit
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry and Utrecht University, P.O. Box 59, 1790 AB Den Burg (Texel), The Netherlands.,Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
| | - Stefanie Berger
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Stefan Schouten
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry and Utrecht University, P.O. Box 59, 1790 AB Den Burg (Texel), The Netherlands.,Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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4
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Bhattarai S, Cassarini C, Lens PNL. Physiology and Distribution of Archaeal Methanotrophs That Couple Anaerobic Oxidation of Methane with Sulfate Reduction. Microbiol Mol Biol Rev 2019; 83:e00074-18. [PMID: 31366606 PMCID: PMC6710461 DOI: 10.1128/mmbr.00074-18] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In marine anaerobic environments, methane is oxidized where sulfate-rich seawater meets biogenic or thermogenic methane. In those niches, a few phylogenetically distinct microbial types, i.e., anaerobic methanotrophs (ANME), are able to grow through anaerobic oxidation of methane (AOM). Due to the relevance of methane in the global carbon cycle, ANME have drawn the attention of a broad scientific community for 4 decades. This review presents and discusses the microbiology and physiology of ANME up to the recent discoveries, revealing novel physiological types of anaerobic methane oxidizers which challenge the view of obligate syntrophy for AOM. An overview of the drivers shaping the distribution of ANME in different marine habitats, from cold seep sediments to hydrothermal vents, is given. Multivariate analyses of the abundance of ANME in various habitats identify a distribution of distinct ANME types driven by the mode of methane transport. Intriguingly, ANME have not yet been cultivated in pure culture, despite intense attempts. Further advances in understanding this microbial process are hampered by insufficient amounts of enriched cultures. This review discusses the advantages, limitations, and potential improvements for ANME laboratory-based cultivation systems.
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Affiliation(s)
- S Bhattarai
- UNESCO-IHE, Institute for Water Education, Delft, The Netherlands
| | - C Cassarini
- UNESCO-IHE, Institute for Water Education, Delft, The Netherlands
- National University of Ireland Galway, Galway, Ireland
| | - P N L Lens
- UNESCO-IHE, Institute for Water Education, Delft, The Netherlands
- National University of Ireland Galway, Galway, Ireland
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5
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Wang J, Cai C, Li Y, Hua M, Wang J, Yang H, Zheng P, Hu B. Denitrifying Anaerobic Methane Oxidation: A Previously Overlooked Methane Sink in Intertidal Zone. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:203-212. [PMID: 30457852 DOI: 10.1021/acs.est.8b05742] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The intertidal zone is an open ecosystem rich in organic matter and plays an important role in global biogeochemical cycles. It was previously considered that methane was mainly removed by sulfate-dependent anaerobic methane oxidation (sulfate-AOM) process in marine ecosystems while other anaerobic methane oxidation processes were ignored. Recent researches have demonstrated that denitrifying anaerobic methane oxidation (DAMO), consisting of nitrite-dependent anaerobic methane oxidation (nitrite-AOM) and nitrate-dependent anaerobic methane oxidation (nitrate-AOM), can also oxidize methane. In this work, the community structure, quantity and potential methane oxidizing rate of DAMO archaea and bacteria in the intertidal zone were studied by high-throughput sequencing, qPCR and stable isotope tracing method. The results showed that nitrate-AOM and nitrite-AOM were both active in the intertidal zone and showed approximate methane oxidation rates. The copy number of 16S rRNA gene of DAMO archaea and DAMO bacteria were 104 ∼ 105 copies g-1 (dry sediment), whereas NC10 bacteria were slightly higher. The contribution rate of DAMO process to total anaerobic methane removal in the intertidal zone reached 65.6% ∼ 100%, which indicates that DAMO process is an important methane sink in intertidal ecosystem. Laboratory incubations also indicated that DAMO archaea were more sensitive to oxygen and preferred a more anoxic environment. These results help us draw a more complete picture of methane and nitrogen cycles in natural habitats.
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Affiliation(s)
- Jiaqi Wang
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
| | - Chaoyang Cai
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
| | - Yufen Li
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
| | - Miaolian Hua
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
| | - Junren Wang
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
| | - Hongrui Yang
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
| | - Ping Zheng
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
| | - Baolan Hu
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety , Hangzhou , China
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6
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Martinez-Cruz K, Leewis MC, Herriott IC, Sepulveda-Jauregui A, Anthony KW, Thalasso F, Leigh MB. Anaerobic oxidation of methane by aerobic methanotrophs in sub-Arctic lake sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 607-608:23-31. [PMID: 28686892 DOI: 10.1016/j.scitotenv.2017.06.187] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 06/20/2017] [Accepted: 06/22/2017] [Indexed: 05/25/2023]
Abstract
Anaerobic oxidation of methane (AOM) is a biological process that plays an important role in reducing the CH4 emissions from a wide range of ecosystems. Arctic and sub-Arctic lakes are recognized as significant contributors to global methane (CH4) emission, since CH4 production is increasing as permafrost thaws and provides fuels for methanogenesis. Methanotrophy, including AOM, is critical to reducing CH4 emissions. The identity, activity, and metabolic processes of anaerobic methane oxidizers are poorly understood, yet this information is critical to understanding CH4 cycling and ultimately to predicting future CH4 emissions. This study sought to identify the microorganisms involved in AOM in sub-Arctic lake sediments using DNA- and phospholipid-fatty acid (PLFA)- based stable isotope probing. Results indicated that aerobic methanotrophs belonging to the genus Methylobacter assimilate carbon from CH4, either directly or indirectly. Other organisms that were found, in minor proportions, to assimilate CH4-derived carbon were methylotrophs and iron reducers, which might indicate the flow of CH4-derived carbon from anaerobic methanotrophs into the broader microbial community. While various other taxa have been reported in the literature to anaerobically oxidize methane in various environments (e.g. ANME-type archaea and Methylomirabilis Oxyfera), this report directly suggest that Methylobacter can perform this function, expanding our understanding of CH4 oxidation in anaerobic lake sediments.
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Affiliation(s)
- Karla Martinez-Cruz
- Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, 306 Tanana Loop, 99775 Fairbanks, AK, USA; Biotechnology and Bioengineering Department, Cinvestav, 2508 IPN Av, 07360, Mexico City, Mexico.
| | - Mary-Cathrine Leewis
- Institute of Arctic Biology, University of Alaska Fairbanks, 930 N Koyukuk Dr, 99775Fairbanks, AK, USA.
| | - Ian Charold Herriott
- Institute of Arctic Biology, University of Alaska Fairbanks, 930 N Koyukuk Dr, 99775Fairbanks, AK, USA.
| | - Armando Sepulveda-Jauregui
- Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, 306 Tanana Loop, 99775 Fairbanks, AK, USA.
| | - Katey Walter Anthony
- Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, 306 Tanana Loop, 99775 Fairbanks, AK, USA.
| | - Frederic Thalasso
- Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, 306 Tanana Loop, 99775 Fairbanks, AK, USA; Biotechnology and Bioengineering Department, Cinvestav, 2508 IPN Av, 07360, Mexico City, Mexico.
| | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, 930 N Koyukuk Dr, 99775Fairbanks, AK, USA.
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7
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Paul BG, Ding H, Bagby SC, Kellermann MY, Redmond MC, Andersen GL, Valentine DL. Methane-Oxidizing Bacteria Shunt Carbon to Microbial Mats at a Marine Hydrocarbon Seep. Front Microbiol 2017; 8:186. [PMID: 28289403 PMCID: PMC5326789 DOI: 10.3389/fmicb.2017.00186] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/25/2017] [Indexed: 01/11/2023] Open
Abstract
The marine subsurface is a reservoir of the greenhouse gas methane. While microorganisms living in water column and seafloor ecosystems are known to be a major sink limiting net methane transport from the marine subsurface to the atmosphere, few studies have assessed the flow of methane-derived carbon through the benthic mat communities that line the seafloor on the continental shelf where methane is emitted. We analyzed the abundance and isotope composition of fatty acids in microbial mats grown in the shallow Coal Oil Point seep field off Santa Barbara, CA, USA, where seep gas is a mixture of methane and CO2. We further used stable isotope probing (SIP) to track methane incorporation into mat biomass. We found evidence that multiple allochthonous substrates supported the rich growth of these mats, with notable contributions from bacterial methanotrophs and sulfur-oxidizers as well as eukaryotic phototrophs. Fatty acids characteristic of methanotrophs were shown to be abundant and 13C-enriched in SIP samples, and DNA-SIP identified members of the methanotrophic family Methylococcaceae as major 13CH4 consumers. Members of Sulfuricurvaceae, Sulfurospirillaceae, and Sulfurovumaceae are implicated in fixation of seep CO2. The mats’ autotrophs support a diverse assemblage of co-occurring bacteria and protozoa, with Methylophaga as key consumers of methane-derived organic matter. This study identifies the taxa contributing to the flow of seep-derived carbon through microbial mat biomass, revealing the bacterial and eukaryotic diversity of these remarkable ecosystems.
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Affiliation(s)
- Blair G Paul
- Department of Earth Science, University of California, Santa Barbara, Santa BarbaraCA, USA; Marine Science Institute, University of California, Santa Barbara, Santa BarbaraCA, USA
| | - Haibing Ding
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China Qingdao, China
| | - Sarah C Bagby
- Department of Earth Science, University of California, Santa Barbara, Santa BarbaraCA, USA; Marine Science Institute, University of California, Santa Barbara, Santa BarbaraCA, USA
| | - Matthias Y Kellermann
- Department of Earth Science, University of California, Santa Barbara, Santa BarbaraCA, USA; Marine Science Institute, University of California, Santa Barbara, Santa BarbaraCA, USA
| | - Molly C Redmond
- Department of Earth Science, University of California, Santa Barbara, Santa BarbaraCA, USA; Marine Science Institute, University of California, Santa Barbara, Santa BarbaraCA, USA
| | - Gary L Andersen
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley CA, USA
| | - David L Valentine
- Department of Earth Science, University of California, Santa Barbara, Santa BarbaraCA, USA; Marine Science Institute, University of California, Santa Barbara, Santa BarbaraCA, USA
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8
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Wegener G, Kellermann MY, Elvert M. Tracking activity and function of microorganisms by stable isotope probing of membrane lipids. Curr Opin Biotechnol 2016; 41:43-52. [PMID: 27179643 DOI: 10.1016/j.copbio.2016.04.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 04/27/2016] [Accepted: 04/27/2016] [Indexed: 12/17/2022]
Abstract
Microorganisms in soils and sediments are highly abundant and phylogenetically diverse, but their specific metabolic activity and function in the environment is often not well constrained. To address this critical aspect in environmental biogeochemistry, different methods involving stable isotope probing (SIP) and detection of the isotope label in a variety of molecular compounds have been developed. Here we review recent progress in lipid-SIP, a technique that combines the assimilation of specific 13C-labeled metabolic substrates such as inorganic carbon, methane, glucose and amino acids into diagnostic membrane lipid compounds. Using the structural characteristics of certain lipid types in combination with genetic molecular techniques, the SIP approach reveals the activity and function of distinct microbial groups in the environment. More recently, deuterium labeling in the form of deuterated water (D2O) extended the lipid-SIP portfolio. Since lipid biosynthetic pathways involve hydrogen (H+) uptake from water, lipid production can be inferred from the detection of D-assimilation into these compounds. Furthermore, by combining D2O and 13C-inorganic carbon (IC) labeling in a dual-SIP approach, rates of auto- and heterotrophic carbon fixation can be estimated. We discuss the design, analytical prerequisites, data processing and interpretation of single and dual-SIP experiments and highlight a case study on anaerobic methanotrophic communities inhabiting hydrothermally heated marine sediments.
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Affiliation(s)
- Gunter Wegener
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany; MARUM Center for Marine Environmental Sciences, Leobener Straße, 28359 Bremen, Germany.
| | - Matthias Y Kellermann
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA
| | - Marcus Elvert
- MARUM Center for Marine Environmental Sciences, Leobener Straße, 28359 Bremen, Germany
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9
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Wegener G, Krukenberg V, Ruff SE, Kellermann MY, Knittel K. Metabolic Capabilities of Microorganisms Involved in and Associated with the Anaerobic Oxidation of Methane. Front Microbiol 2016; 7:46. [PMID: 26870011 PMCID: PMC4736303 DOI: 10.3389/fmicb.2016.00046] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 01/11/2016] [Indexed: 11/16/2022] Open
Abstract
In marine sediments the anaerobic oxidation of methane with sulfate as electron acceptor (AOM) is responsible for the removal of a major part of the greenhouse gas methane. AOM is performed by consortia of anaerobic methane-oxidizing archaea (ANME) and their specific partner bacteria. The physiology of these organisms is poorly understood, which is due to their slow growth with doubling times in the order of months and the phylogenetic diversity in natural and in vitro AOM enrichments. Here we study sediment-free long-term AOM enrichments that were cultivated from seep sediments sampled off the Italian Island Elba (20°C; hereon called E20) and from hot vents of the Guaymas Basin, Gulf of California, cultivated at 37°C (G37) or at 50°C (G50). These enrichments were dominated by consortia of ANME-2 archaea and Seep-SRB2 partner bacteria (E20) or by ANME-1, forming consortia with Seep-SRB2 bacteria (G37) or with bacteria of the HotSeep-1 cluster (G50). We investigate lipid membrane compositions as possible factors for the different temperature affinities of the different ANME clades and show autotrophy as characteristic feature for both ANME clades and their partner bacteria. Although in the absence of additional substrates methane formation was not observed, methanogenesis from methylated substrates (methanol and methylamine) could be quickly stimulated in the E20 and the G37 enrichment. Responsible for methanogenesis are archaea from the genus Methanohalophilus and Methanococcoides, which are minor community members during AOM (1–7‰ of archaeal 16S rRNA gene amplicons). In the same two cultures also sulfur disproportionation could be quickly stimulated by addition of zero-valent colloidal sulfur. The isolated partner bacteria are likewise minor community members (1–9‰ of bacterial 16S rRNA gene amplicons), whereas the dominant partner bacteria (Seep-SRB1a, Seep-SRB2, or HotSeep-1) did not grow on elemental sulfur. Our results support a functioning of AOM as syntrophic interaction of obligate methanotrophic archaea that transfer non-molecular reducing equivalents (i.e., via direct interspecies electron transfer) to obligate sulfate-reducing partner bacteria. Additional katabolic processes in these enrichments but also in sulfate methane interfaces are likely performed by minor community members.
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Affiliation(s)
- Gunter Wegener
- Max Planck Institute for Marine MicrobiologyBremen, Germany; MARUM, Center for Marine Environmental SciencesBremen, Germany
| | | | - S Emil Ruff
- Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Matthias Y Kellermann
- MARUM, Center for Marine Environmental SciencesBremen, Germany; Department of Earth Science and Marine Science Institute, University of California, Santa BarbaraSanta Barbara, CA, USA
| | - Katrin Knittel
- Max Planck Institute for Marine Microbiology Bremen, Germany
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10
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Méhay S, Früh-Green GL, Lang SQ, Bernasconi SM, Brazelton WJ, Schrenk MO, Schaeffer P, Adam P. Record of archaeal activity at the serpentinite-hosted Lost City Hydrothermal Field. GEOBIOLOGY 2013; 11:570-92. [PMID: 24118888 DOI: 10.1111/gbi.12062] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 09/06/2013] [Indexed: 05/22/2023]
Abstract
Samples of young, outer surfaces of brucite-carbonate deposits from the ultramafic-hosted Lost City hydrothermal field were analyzed for DNA and lipid biomarker distributions and for carbon and hydrogen stable isotope compositions of the lipids. Methane-cycling archaeal communities, notably the Lost City Methanosarcinales (LCMS) phylotype, are specifically addressed. Lost City is unlike all other hydrothermal systems known to date and is characterized by metal- and CO2 -poor, high pH fluids with high H2 and CH4 contents resulting from serpentinization processes at depth. The archaeal fraction of the microbial community varies widely within the Lost City chimneys, from 1-81% and covaries with concentrations of hydrogen within the fluids. Archaeal lipids include isoprenoid glycerol di- and tetraethers and C25 and C30 isoprenoid hydrocarbons (pentamethylicosane derivatives - PMIs - and squalenoids). In particular, unsaturated PMIs and squalenoids, attributed to the LCMS archaea, were identified for the first time in the carbonate deposits at Lost City and probably record processes exclusively occurring at the surface of the chimneys. The carbon isotope compositions of PMIs and squalenoids are remarkably heterogeneous across samples and show highly (13) C-enriched signatures reaching δ(13) C values of up to +24.6‰. Unlike other environments in which similar structural and isotopic lipid heterogeneity has been observed and attributed to diversity in the archaeal assemblage, the lipids here appear to be synthesized solely by the LCMS. Some of the variations in lipid isotope signatures may, in part, be due to unusual isotopic fractionation during biosynthesis under extreme conditions. However, we argue that the diversity in archaeal abundances, lipid structure and carbon isotope composition rather reflects the ability of the LCMS archaeal biofilms to adapt to chemical gradients in the hydrothermal chimneys and possibly to perform either methanotrophy or methanogenesis using dissolved inorganic carbon, methane or formate as a function of the prevailing environmental conditions.
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MESH Headings
- Archaea/classification
- Archaea/genetics
- Archaea/metabolism
- Bacteria/classification
- Bacteria/genetics
- Bacteria/metabolism
- Biota
- Carbon/analysis
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Genes, rRNA
- Hot Springs/microbiology
- Hydrogen/analysis
- Lipids/analysis
- RNA, Archaeal/genetics
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- S Méhay
- Department of Earth Sciences, ETH Zurich, Zurich, Switzerland
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11
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Bertram S, Blumenberg M, Michaelis W, Siegert M, Krüger M, Seifert R. Methanogenic capabilities of ANME-archaea deduced from13C-labelling approaches. Environ Microbiol 2013; 15:2384-93. [DOI: 10.1111/1462-2920.12112] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 12/20/2012] [Accepted: 02/16/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Sebastian Bertram
- Institute for Biogeochemistry and Marine Chemistry; University of Hamburg; Bundesstr. 55; 20146; Hamburg; Germany
| | - Martin Blumenberg
- Geobiology Group, Geoscience Centre; Georg-August-University Göttingen; Goldschmidtstr. 3; 37077; Göttingen; Germany
| | - Walter Michaelis
- Institute for Biogeochemistry and Marine Chemistry; University of Hamburg; Bundesstr. 55; 20146; Hamburg; Germany
| | - Michael Siegert
- Pennsylvania State University; 127 Sackett Building; University Park; PA; 16802; USA
| | - Martin Krüger
- Federal Institute for Geosciences and Natural Resources; Section Geomicrobiology; Stilleweg 2; 30655; Hannover; Germany
| | - Richard Seifert
- Institute for Biogeochemistry and Marine Chemistry; University of Hamburg; Bundesstr. 55; 20146; Hamburg; Germany
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12
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Autotrophy as a predominant mode of carbon fixation in anaerobic methane-oxidizing microbial communities. Proc Natl Acad Sci U S A 2012; 109:19321-6. [PMID: 23129626 DOI: 10.1073/pnas.1208795109] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The methane-rich, hydrothermally heated sediments of the Guaymas Basin are inhabited by thermophilic microorganisms, including anaerobic methane-oxidizing archaea (mainly ANME-1) and sulfate-reducing bacteria (e.g., HotSeep-1 cluster). We studied the microbial carbon flow in ANME-1/ HotSeep-1 enrichments in stable-isotope-probing experiments with and without methane. The relative incorporation of (13)C from either dissolved inorganic carbon or methane into lipids revealed that methane-oxidizing archaea assimilated primarily inorganic carbon. This assimilation is strongly accelerated in the presence of methane. Experiments with simultaneous amendments of both (13)C-labeled dissolved inorganic carbon and deuterated water provided further insights into production rates of individual lipids derived from members of the methane-oxidizing community as well as their carbon sources used for lipid biosynthesis. In the presence of methane, all prominent lipids carried a dual isotopic signal indicative of their origin from primarily autotrophic microbes. In the absence of methane, archaeal lipid production ceased and bacterial lipid production dropped by 90%; the lipids produced by the residual fraction of the metabolically active bacterial community predominantly carried a heterotrophic signal. Collectively our results strongly suggest that the studied ANME-1 archaea oxidize methane but assimilate inorganic carbon and should thus be classified as methane-oxidizing chemoorganoautotrophs.
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13
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Lin YS, Lipp JS, Elvert M, Holler T, Hinrichs KU. Assessing production of the ubiquitous archaeal diglycosyl tetraether lipids in marine subsurface sediment using intramolecular stable isotope probing. Environ Microbiol 2012; 15:1634-46. [DOI: 10.1111/j.1462-2920.2012.02888.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 08/30/2012] [Indexed: 11/27/2022]
Affiliation(s)
- Yu-Shih Lin
- Organic Geochemistry Group; Department of Geosciences and MARUM Center for Marine Environmental Sciences; University of Bremen; PO Box 330 440; D-28359; Bremen; Germany
| | - Julius S. Lipp
- Organic Geochemistry Group; Department of Geosciences and MARUM Center for Marine Environmental Sciences; University of Bremen; PO Box 330 440; D-28359; Bremen; Germany
| | - Marcus Elvert
- Organic Geochemistry Group; Department of Geosciences and MARUM Center for Marine Environmental Sciences; University of Bremen; PO Box 330 440; D-28359; Bremen; Germany
| | - Thomas Holler
- Max Planck Institute for Marine Microbiology; Bremen; Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group; Department of Geosciences and MARUM Center for Marine Environmental Sciences; University of Bremen; PO Box 330 440; D-28359; Bremen; Germany
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14
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House CH, Beal EJ, Orphan VJ. The Apparent Involvement of ANMEs in Mineral Dependent Methane Oxidation, as an Analog for Possible Martian Methanotrophy. Life (Basel) 2011; 1:19-33. [PMID: 25382054 PMCID: PMC4187123 DOI: 10.3390/life1010019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 09/14/2011] [Accepted: 11/11/2011] [Indexed: 11/17/2022] Open
Abstract
On Earth, marine anaerobic methane oxidation (AOM) can be driven by the microbial reduction of sulfate, iron, and manganese. Here, we have further characterized marine sediment incubations to determine if the mineral dependent methane oxidation involves similar microorganisms to those found for sulfate-dependent methane oxidation. Through FISH and FISH-SIMS analyses using 13C and 15N labeled substrates, we find that the most active cells during manganese dependent AOM are primarily mixed and mixed-cluster aggregates of archaea and bacteria. Overall, our control experiment using sulfate showed two active bacterial clusters, two active shell aggregates, one active mixed aggregate, and an active archaeal sarcina, the last of which appeared to take up methane in the absence of a closely-associated bacterial partner. A single example of a shell aggregate appeared to be active in the manganese incubation, along with three mixed aggregates and an archaeal sarcina. These results suggest that the microorganisms (e.g., ANME-2) found active in the manganese-dependent incubations are likely capable of sulfate-dependent AOM. Similar metabolic flexibility for Martian methanotrophs would mean that the same microbial groups could inhabit a diverse set of Martian mineralogical crustal environments. The recently discovered seasonal Martian plumes of methane outgassing could be coupled to the reduction of abundant surface sulfates and extensive metal oxides, providing a feasible metabolism for present and past Mars. In an optimistic scenario Martian methanotrophy consumes much of the periodic methane released supporting on the order of 10,000 microbial cells per cm2 of Martian surface. Alternatively, most of the methane released each year could be oxidized through an abiotic process requiring biological methane oxidation to be more limited. If under this scenario, 1% of this methane flux were oxidized by biology in surface soils or in subsurface aquifers (prior to release), a total of about 1020 microbial cells could be supported through methanotrophy with the cells concentrated in regions of methane release.
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Affiliation(s)
- Christopher H House
- Department of Geosciences and Penn State Astrobiology Research Center, The Pennsylvania State University, 220 Deike Building, University Park, PA 16802, USA.
| | - Emily J Beal
- Department of Geosciences and Penn State Astrobiology Research Center, The Pennsylvania State University, 220 Deike Building, University Park, PA 16802, USA.
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA.
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15
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Abstract
Methane is the most abundant hydrocarbon in the atmosphere, and it is an important greenhouse gas, which has so far contributed an estimated 20% of postindustrial global warming. A great deal of biogeochemical research has focused on the causes and effects of the variation in global fluxes of methane throughout earth's history, but the underlying microbial processes and their key agents remain poorly understood. This is a disturbing knowledge gap because 85% of the annual global methane production and about 60% of its consumption are based on microbial processes. Only three key functional groups of microorganisms of limited diversity regulate the fluxes of methane on earth, namely the aerobic methanotrophic bacteria, the methanogenic archaea, and their close relatives, the anaerobic methanotrophic archaea (ANME). The ANME represent special lines of descent within the Euryarchaeota and appear to gain energy exclusively from the anaerobic oxidation of methane (AOM), with sulfate as the final electron acceptor according to the net reaction: CH(4) + SO(42-) ---> HCO(3-) + HS(-) + H(2)O. This review summarizes what is known and unknown about AOM on earth and its key catalysts, the ANME clades and their bacterial partners.
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Affiliation(s)
- Katrin Knittel
- Max Planck Institute for Marine Microbiology, Bremen 28359, Germany.
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16
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Jagersma GC, Meulepas RJW, Heikamp-de Jong I, Gieteling J, Klimiuk A, Schouten S, Damsté JSS, Lens PNL, Stams AJM. Microbial diversity and community structure of a highly active anaerobic methane-oxidizing sulfate-reducing enrichment. Environ Microbiol 2009; 11:3223-32. [PMID: 19703218 DOI: 10.1111/j.1462-2920.2009.02036.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Anaerobic oxidation of methane (AOM) is an important methane sink in the ocean but the microbes responsible for AOM are as yet resilient to cultivation. Here we describe the microbial analysis of an enrichment obtained in a novel submerged-membrane bioreactor system and capable of high-rate AOM (286 mumol g(dry weight)(-1) day(-1)) coupled to sulfate reduction. By constructing a clone library with subsequent sequencing and fluorescent in situ hybridization, we showed that the responsible methanotrophs belong to the ANME-2a subgroup of anaerobic methanotrophic archaea, and that sulfate reduction is most likely performed by sulfate-reducing bacteria commonly found in association with other ANME-related archaea in marine sediments. Another relevant portion of the bacterial sequences can be clustered within the order of Flavobacteriales but their role remains to be elucidated. Fluorescent in situ hybridization analyses showed that the ANME-2a cells occur as single cells without close contact to the bacterial syntrophic partner. Incubation with (13)C-labelled methane showed substantial incorporation of (13)C label in the bacterial C(16) fatty acids (bacterial; 20%, 44% and 49%) and in archaeal lipids, archaeol and hydroxyl-archaeol (21% and 20% respectively). The obtained data confirm that both archaea and bacteria are responsible for the anaerobic methane oxidation in a bioreactor enrichment inoculated with Eckernförde bay sediment.
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Affiliation(s)
- G Christian Jagersma
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
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17
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Orphan VJ, Turk KA, Green AM, House CH. Patterns of 15N assimilation and growth of methanotrophic ANME-2 archaea and sulfate-reducing bacteria within structured syntrophic consortia revealed by FISH-SIMS. Environ Microbiol 2009; 11:1777-91. [PMID: 19383036 DOI: 10.1111/j.1462-2920.2009.01903.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methane release from the oceans is controlled in large part by syntrophic interactions between anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (DSS), frequently found as organized consortia. An understanding of the specifics of this symbiotic relationship and the metabolic heterogeneity existing between and within individual methane-oxidizing aggregates is currently lacking. Here, we use the microanalytical method FISH-SIMS (fluorescence in situ hybridization-secondary ion mass spectrometry) to describe the physiological traits and anabolic activity of individual methanotrophic consortia, specifically tracking (15)N-labelled protein synthesis to examine the effects of organization and size on the metabolic activity of the syntrophic partners. Patterns of (15)N distribution within individual aggregates showed enhanced (15)N assimilation in ANME-2 cells relative to the co-associated DSS revealing a decoupling in anabolic activity between the partners. Protein synthesis in ANME-2 cells was sustained throughout the core of individual ANME-2/DSS consortia ranging in size range from 4 to 20 μm. This indicates that metabolic activity of the methane-oxidizing archaea is not limited to, or noticeably enhanced at the ANME-2/DSS boundary. Overall, the metabolic activity of both syntrophic partners within consortia was greater than activity measured in representatives of the ANME-2 and DSS observed alone, with smaller ANME-2/DSS aggregates displaying a tendency for greater (15)N uptake and doubling times ranging from 3 to 5 months. The combination of (15)N-labelling and FISH-SIMS provides an important perspective on the extent of heterogeneity within methanotrophic aggregates and may aid in constraining predictive models of activity and growth by these syntrophic consortia.
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Affiliation(s)
- Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA.
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18
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Wegener G, Niemann H, Elvert M, Hinrichs KU, Boetius A. Assimilation of methane and inorganic carbon by microbial communities mediating the anaerobic oxidation of methane. Environ Microbiol 2008; 10:2287-98. [PMID: 18498367 DOI: 10.1111/j.1462-2920.2008.01653.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The anaerobic oxidation of methane (AOM) is a major sink for methane on Earth and is performed by consortia of methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). Here we present a comparative study using in vitro stable isotope probing to examine methane and carbon dioxide assimilation into microbial biomass. Three sediment types comprising different methane-oxidizing communities (ANME-1 and -2 mixture from the Black Sea, ANME-2a from Hydrate Ridge and ANME-2c from the Gullfaks oil field) were incubated in replicate flow-through systems with methane-enriched anaerobic seawater medium for 5-6 months amended with either (13)CH(4) or H(13)CO(3)(-). In all three sediment types methane was anaerobically oxidized in a 1:1 stoichiometric ratio compared with sulfate reduction. Similar amounts of (13)CH(4) or (13)CO(2) were assimilated into characteristic archaeal lipids, indicating a direct assimilation of both carbon sources into ANME biomass. Specific bacterial fatty acids assigned to the partner SRB were almost exclusively labelled by (13)CO(2), but only in the presence of methane as energy source and not during control incubations without methane. This indicates an autotrophic growth of the ANME-associated SRB and supports previous hypotheses of an electron shuttle between the consortium partners. Carbon assimilation efficiencies of the methanotrophic consortia were low, with only 0.25-1.3 mol% of the methane oxidized.
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Affiliation(s)
- Gunter Wegener
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359 Bremen, Germany.
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19
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Factors controlling the distribution of archaeal tetraethers in terrestrial hot springs. Appl Environ Microbiol 2008; 74:3523-32. [PMID: 18390673 DOI: 10.1128/aem.02450-07] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glycerol dialkyl glycerol tetraethers (GDGTs) found in hot springs reflect the abundance and community structure of Archaea in these extreme environments. The relationships between GDGTs, archaeal communities, and physical or geochemical variables are underexamined to date and when reported often result in conflicting interpretations. Here, we examined profiles of GDGTs from pure cultures of Crenarchaeota and from terrestrial geothermal springs representing a wide distribution of locations, including Yellowstone National Park (United States), the Great Basin of Nevada and California (United States), Kamchatka (Russia), Tengchong thermal field (China), and Thailand. These samples had temperatures of 36.5 to 87 degrees C and pH values of 3.0 to 9.2. GDGT abundances also were determined for three soil samples adjacent to some of the hot springs. Principal component analysis identified four factors that accounted for most of the variance among nine individual GDGTs, temperature, and pH. Significant correlations were observed between pH and the GDGTs crenarchaeol and GDGT-4 (four cyclopentane rings, m/z 1,294); pH correlated positively with crenarchaeol and inversely with GDGT-4. Weaker correlations were observed between temperature and the four factors. Three of the four GDGTs used in the marine TEX(86) paleotemperature index (GDGT-1 to -3, but not crenarchaeol isomer) were associated with a single factor. No correlation was observed for GDGT-0 (acyclic caldarchaeol): it is effectively its own variable. The biosynthetic mechanisms and exact archaeal community structures leading to these relationships remain unknown. However, the data in general show promise for the continued development of GDGT lipid-based physiochemical proxies for archaeal evolution and for paleo-ecology or paleoclimate studies.
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20
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Krüger M, Wolters H, Gehre M, Joye SB, Richnow HH. Tracing the slow growth of anaerobic methane-oxidizing communities by 15N-labelling techniques. FEMS Microbiol Ecol 2008; 63:401-11. [DOI: 10.1111/j.1574-6941.2007.00431.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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21
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Abstract
Methane has long been known to be used as a carbon and energy source by some aerobic alpha- and delta-proteobacteria. In these organisms the metabolism of methane starts with its oxidation with O(2) to methanol, a reaction catalyzed by a monooxygenase and therefore restricted to the aerobic world. Methane has recently been shown to also fuel the growth of anaerobic microorganisms. The oxidation of methane with sulfate and with nitrate have been reported, but the mechanisms of anaerobic methane oxidation still remains elusive. Sulfate-dependent methane oxidation is catalyzed by methanotrophic archaea, which are related to the Methanosarcinales and which grow in close association with sulfate-reducing delta-proteobacteria. There is evidence that anaerobic methane oxidation with sulfate proceeds at least in part via reversed methanogenesis involving the nickel enzyme methyl-coenzyme M reductase for methane activation, which under standard conditions is an endergonic reaction, and thus inherently slow. Methane oxidation coupled to denitrification is mediated by bacteria belonging to a novel phylum and does not involve methyl-coenzyme M reductase. The first step in methane oxidation is most likely the exergonic formation of 2-methylsuccinate from fumarate and methane catalyzed by a glycine-radical enzyme.
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Affiliation(s)
- Rudolf K Thauer
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany.
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22
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Moran JJ, Beal EJ, Vrentas JM, Orphan VJ, Freeman KH, House CH. Methyl sulfides as intermediates in the anaerobic oxidation of methane. Environ Microbiol 2007; 10:162-73. [PMID: 17903217 DOI: 10.1111/j.1462-2920.2007.01441.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While it is clear that microbial consortia containing Archaea and sulfate-reducing bacteria (SRB) can mediate the anaerobic oxidation of methane (AOM), the interplay between these microorganisms remains unknown. The leading explanation of the AOM metabolism is 'reverse methanogenesis' by which a methanogenesis substrate is produced and transferred between species. Conceptually, the reversal of methanogenesis requires low H(2) concentrations for energetic favourability. We used (13)C-labelled CH(4) as a tracer to test the effects of elevated H(2) pressures on incubations of active AOM sediments from both the Eel River basin and Hydrate Ridge. In the presence of H(2), we observed a minimal reduction in the rate of CH(4) oxidation, and conclude H(2) does not play an interspecies role in AOM. Based on these results, as well as previous work, we propose a new model for substrate transfer in AOM. In this model, methyl sulfides produced by the Archaea from both CH(4) oxidation and CO(2) reduction are transferred to the SRB. Metabolically, CH(4) oxidation provides electrons for the energy-yielding reduction of CO(2) to a methyl group ('methylogenesis'). Methylogenesis is a dominantly reductive pathway utilizing most methanogenesis enzymes in their forward direction. Incubations of seep sediments demonstrate, as would be expected from this model, that methanethiol inhibits AOM and that CO can be substituted for CH(4) as the electron donor for methylogenesis.
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Affiliation(s)
- James J Moran
- Department of Geosciences, The Penn State Astrobiology Research Center, The Pennsylvania State University, University Park, PA 16802, USA.
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23
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Lösekann T, Knittel K, Nadalig T, Fuchs B, Niemann H, Boetius A, Amann R. Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby Mud Volcano, Barents Sea. Appl Environ Microbiol 2007; 73:3348-62. [PMID: 17369343 PMCID: PMC1907091 DOI: 10.1128/aem.00016-07] [Citation(s) in RCA: 301] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Submarine mud volcanoes are formed by expulsions of mud, fluids, and gases from deeply buried subsurface sources. They are highly reduced benthic habitats and often associated with intensive methane seepage. In this study, the microbial diversity and community structure in methane-rich sediments of the Haakon Mosby Mud Volcano (HMMV) were investigated by comparative sequence analysis of 16S rRNA genes and fluorescence in situ hybridization. In the active volcano center, which has a diameter of about 500 m, the main methane-consuming process was bacterial aerobic oxidation. In this zone, aerobic methanotrophs belonging to three bacterial clades closely affiliated with Methylobacter and Methylophaga species accounted for 56%+/-8% of total cells. In sediments below Beggiatoa mats encircling the center of the HMMV, methanotrophic archaea of the ANME-3 clade dominated the zone of anaerobic methane oxidation. ANME-3 archaea form cell aggregates mostly associated with sulfate-reducing bacteria of the Desulfobulbus (DBB) branch. These ANME-3/DBB aggregates were highly abundant and accounted for up to 94%+/-2% of total microbial biomass at 2 to 3 cm below the surface. ANME-3/DBB aggregates could be further enriched by flow cytometry to identify their phylogenetic relationships. At the outer rim of the mud volcano, the seafloor was colonized by tubeworms (Siboglinidae, formerly known as Pogonophora). Here, both aerobic and anaerobic methane oxidizers were found, however, in lower abundances. The level of microbial diversity at this site was higher than that at the central and Beggiatoa species-covered part of the HMMV. Analysis of methyl-coenzyme M-reductase alpha subunit (mcrA) genes showed a strong dominance of a novel lineage, mcrA group f, which could be assigned to ANME-3 archaea. Our results further support the hypothesis of Niemann et al. (54), that high methane availability and different fluid flow regimens at the HMMV provide distinct niches for aerobic and anaerobic methanotrophs.
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MESH Headings
- Aerobiosis
- Anaerobiosis
- Archaea/classification
- Archaea/genetics
- Archaea/isolation & purification
- Archaea/metabolism
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Bacteria/metabolism
- Base Sequence
- Beggiatoa/classification
- Beggiatoa/genetics
- Beggiatoa/isolation & purification
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Deltaproteobacteria/classification
- Deltaproteobacteria/genetics
- Deltaproteobacteria/isolation & purification
- Geologic Sediments/microbiology
- In Situ Hybridization, Fluorescence
- Methane/metabolism
- Methylococcaceae/classification
- Methylococcaceae/genetics
- Methylococcaceae/isolation & purification
- Microscopy, Fluorescence
- Molecular Sequence Data
- Oxidation-Reduction
- Oxidoreductases/genetics
- Phylogeny
- Piscirickettsiaceae/classification
- Piscirickettsiaceae/genetics
- Piscirickettsiaceae/isolation & purification
- Protein Subunits/genetics
- RNA, Ribosomal, 16S/genetics
- Seawater/microbiology
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Affiliation(s)
- Tina Lösekann
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359 Bremen, Germany
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24
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Affiliation(s)
- William S Reeburgh
- Department of Earth System Science, University of California, Irvine, California 92697-3100, USA.
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25
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Nauhaus K, Albrecht M, Elvert M, Boetius A, Widdel F. In vitro cell growth of marine archaeal-bacterial consortia during anaerobic oxidation of methane with sulfate. Environ Microbiol 2007; 9:187-96. [PMID: 17227423 DOI: 10.1111/j.1462-2920.2006.01127.x] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Anoxic sediment from a methane hydrate area (Hydrate Ridge, north-east Pacific; water depth 780 m) was incubated in a long-term laboratory experiment with semi-continuous supply of pressurized [1.4 MPa (14 atm)] methane and sulfate to attempt in vitro propagation of the indigenous consortia of archaea (ANME-2) and bacteria (DSS, Desulfosarcina/Desulfococcus cluster) to which anaerobic oxidation of methane (AOM) with sulfate has been attributed. During 24 months of incubation, the rate of AOM (measured as methane-dependent sulfide formation) increased from 20 to 230 micromol day(-1) (g sediment dry weight)(-1) and the number of aggregates (determined by microscopic counts) from 0.5 x 10(8) to 5.7 x 10(8) (g sediment dry weight)(-1). Fluorescence in situ hybridization targeting 16S rRNA of both partners showed that the newly grown consortia contained central archaeal clusters and peripheral bacterial layers, both with the same morphology and phylogenetic affiliation as in the original sediment. The development of the AOM rate and the total consortia biovolume over time indicated that the consortia grew with a doubling time of approximately 7 months (growth rate 0.003 day(-1)) under the given conditions. The molar growth yield of AOM was approximately 0.6 g cell dry weight (mol CH(4) oxidized)(-1); according to this, only 1% of the consumed methane is channelled into synthesis of consortia biomass. Concentrations of biomarker lipids previously attributed to ANME-2 archaea (e.g. sn-2-hydroxyarchaeol, archaeol, crocetane, pentamethylicosatriene) and Desulfosarcina-like bacteria [e.g. hexadecenoic-11 acid (16:1omega5c), 11,12-methylene-hexadecanoic acid (cy17:0omega5,6)] strongly increased over time (some of them over-proportionally to consortia biovolume), suggesting that they are useful biomarkers to detect active anaerobic methanotrophic consortia in sediments.
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Affiliation(s)
- Katja Nauhaus
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
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26
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Raghoebarsing AA, Pol A, van de Pas-Schoonen KT, Smolders AJP, Ettwig KF, Rijpstra WIC, Schouten S, Damsté JSS, Op den Camp HJM, Jetten MSM, Strous M. A microbial consortium couples anaerobic methane oxidation to denitrification. Nature 2006; 440:918-21. [PMID: 16612380 DOI: 10.1038/nature04617] [Citation(s) in RCA: 669] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Accepted: 02/02/2006] [Indexed: 11/08/2022]
Abstract
Modern agriculture has accelerated biological methane and nitrogen cycling on a global scale. Freshwater sediments often receive increased downward fluxes of nitrate from agricultural runoff and upward fluxes of methane generated by anaerobic decomposition. In theory, prokaryotes should be capable of using nitrate to oxidize methane anaerobically, but such organisms have neither been observed in nature nor isolated in the laboratory. Microbial oxidation of methane is thus believed to proceed only with oxygen or sulphate. Here we show that the direct, anaerobic oxidation of methane coupled to denitrification of nitrate is possible. A microbial consortium, enriched from anoxic sediments, oxidized methane to carbon dioxide coupled to denitrification in the complete absence of oxygen. This consortium consisted of two microorganisms, a bacterium representing a phylum without any cultured species and an archaeon distantly related to marine methanotrophic Archaea. The detection of relatives of these prokaryotes in different freshwater ecosystems worldwide indicates that the reaction presented here may make a substantial contribution to biological methane and nitrogen cycles.
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Affiliation(s)
- Ashna A Raghoebarsing
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
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27
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Evershed RP, Crossman ZM, Bull ID, Mottram H, Dungait JAJ, Maxfield PJ, Brennand EL. 13C-Labelling of lipids to investigate microbial communities in the environment. Curr Opin Biotechnol 2006; 17:72-82. [PMID: 16423522 DOI: 10.1016/j.copbio.2006.01.003] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2005] [Revised: 12/01/2005] [Accepted: 01/06/2006] [Indexed: 11/23/2022]
Abstract
The introduction of (13)C-labelled substrates to soils, sediments or cultures followed by (13)C analysis of phospholipid fatty acids (PLFAs) provides quantitative and chemotaxonomic information for the groups of microorganisms utilizing a given substrate. Gas chromatography-combustion-isotope ratio mass spectrometry has provided the high precision necessary to measure small isotopic changes (differences in the relative abundances of (13)C to (12)C expressed as delta(13)C values) for nanogram amounts of individual compounds, such as microbial PLFAs. This methodology constitutes a powerful new culture-independent method for investigating microbial communities in the environment. The information obtained is highly complementary to that obtained from gene-probe-based methods, and considerable possibilities exist to extend this methodology to include other biochemical components of microorganisms.
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Affiliation(s)
- Richard P Evershed
- Organic Geochemistry Unit, Bristol Biogeochemistry Research Centre, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
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