Characteristics of aerobic methane-oxidising bacterial community at the sea-floor surface of the Nankai Trough
Noriko Okita A B D , Toshihiro Hoaki A E , Shinya Suzuki C and Masashi Hatamoto
B F
+ Author Affiliations
- Author Affiliations
A Technology Center, Taisei Corporation, 344-1 Nase-cho, Totsuka-ku, Yokohama 245-0051, Japan.
B Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka-machi, Nagaoka 940-0846, Japan.
C Marine Biological Research Institute of Japan, 4-3-16 Yutaka-chou, Shinagawa-ku, Tokyo 142-0042, Japan.
D Present address: Technology Support Center, Taisei-Yuraku Real Estate, 344-1 Nase-cho, Totsuka-ku, Yokohama 245-0051, Japan.
E Present address: Department of Civil and Environmental Engineering, National Institute of Technology, Oita College, 1666 Maki, Oita City, 870-0152, Japan.
F Corresponding author. Email: hatamoto@vos.nagaokaut.ac.jp
Marine and Freshwater Research 71(10) 1252-1258 https://doi.org/10.1071/MF19317
Submitted: 1 October 2019 Accepted: 5 February 2020 Published: 18 March 2020
Abstract
Methane hydrate is one of the new energy sources, but methane leakage could cause environmental issues such as marine ecosystem changes and global warming. The methane-oxidising bacterial (MOB) community could reflect the methane concentration, thus it may be an indicator of methane leakage. We obtained two sea-floor surface samples from a methane seep area and 12 samples from other general sea-floor areas of the Nankai Trough for the detection and phylogenetic analysis of the particulate methane monooxygenase (pmoA) gene. Using quantitative polymerase chain reaction analysis, the methane seep samples were found to have 106 copies of the pmoA gene per gram of sediment, whereas the general sea-floor area samples of the Nankai Trough contained 103–104 copies of the gene per gram of sediment. Phylogenetic analysis of the pmoA gene sequences showed that the sequences detected in the general and methane seep area samples differed significantly. Specifically, the pmof1–pmor primer pair could detect pmoA genes for the methane seep area, whereas pmoA gene from the general seafloor samples could be detected only using the A189–mb661 primer pair. The results of this study may facilitate the detection of unintended leakage of methane at methane hydrate production sites by monitoring MOB communities using pmoA-targeted phylogenetic analysis and quantification.
Additional keywords: anaerobic oxidation of methane, methanotrophs, qPCR, quantitative polymerase chain reaction.
References
Boulart, C., Connelly, D. P., and Mowlem, M. C. (2010). Sensors and technologies for in situ dissolved methane measurements and their evaluation using technology readiness levels. Trends in Analytical Chemistry 29, 186–195.| Sensors and technologies for in situ dissolved methane measurements and their evaluation using technology readiness levels.Crossref | GoogleScholarGoogle Scholar |
Cheng, Y. S., Halsey, J. L., Fode, K. A., Remsen, C. C., and Collins, M. L. P. (1999). Detection of methanotrophs in groundwater by PCR. Applied and Environmental Microbiology 65, 648–651.
| Detection of methanotrophs in groundwater by PCR.Crossref | GoogleScholarGoogle Scholar | 9925595PubMed |
Colwell, F., Matsumoto, R., and Reed, D. (2004). A review of the gas hydrates, geology, and biology of the Nankai Trough. Chemical Geology 205, 391–404.
| A review of the gas hydrates, geology, and biology of the Nankai Trough.Crossref | GoogleScholarGoogle Scholar |
Costello, A. M., and Lidstrom, M. E. (1999). Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments. Applied and Environmental Microbiology 65, 5066–5074.
| Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments.Crossref | GoogleScholarGoogle Scholar | 10543824PubMed |
Du, M., Yvon-Lewis, S., Garcia-Tigreros, F., Valentine, D. L., Mendes, S. D., and Kessler, J. D. (2014). High resolution measurements of methane and carbon dioxide in surface waters over a natural seep reveal dynamics of dissolved phase air–sea flux. Environmental Science & Technology 48, 10165–10173.
| High resolution measurements of methane and carbon dioxide in surface waters over a natural seep reveal dynamics of dissolved phase air–sea flux.Crossref | GoogleScholarGoogle Scholar |
Fukuba, T., Miyaji, A., Okamoto, T., Yamamoto, T., Kaneda, S., and Fujii, T. (2011). Integrated in situ genetic analyzer for microbiology in extreme environments. RSC Advances 1, 1567–1573.
| Integrated in situ genetic analyzer for microbiology in extreme environments.Crossref | GoogleScholarGoogle Scholar |
Holmes, A. J., Costello, A., Lidstrom, M. E., and Murrell, J. C. (1995). Evidence that participate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiology Letters 132, 203–208.
| Evidence that participate methane monooxygenase and ammonia monooxygenase may be evolutionarily related.Crossref | GoogleScholarGoogle Scholar | 7590173PubMed |
Inagaki, F., Tsunogai, U., Suzuki, M., Kosaka, A., Machiyama, H., Takai, K., Nunoura, T., Nealson, K. H., and Horikoshi, K. (2004). Characterization of C1-metabolizing prokaryotic communities in methane seep habitats at the Kuroshima Knoll, Southern Ryukyu Arc, by analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA genes. Applied and Environmental Microbiology 70, 7445–7455.
| Characterization of C1-metabolizing prokaryotic communities in methane seep habitats at the Kuroshima Knoll, Southern Ryukyu Arc, by analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA genes.Crossref | GoogleScholarGoogle Scholar | 15574947PubMed |
Khmelenina, V. N., Kalyuzhnaya, M. G., Starostina, N. G., Suzina, N. E., and Trotsenko, Y. A. (1997). Isolation and characterization of halotolerant alkaliphilic methanotrophic bacteria from Tuva Soda Lakes. Current Microbiology 35, 257–261.
| Isolation and characterization of halotolerant alkaliphilic methanotrophic bacteria from Tuva Soda Lakes.Crossref | GoogleScholarGoogle Scholar |
Kinoshita, Y., Maruyama, S., Honza, E., Yamakado, N., Usami, T., and Handa, K. (1975). Technical notes on deep sea bottom sampling. In ‘Cruise Report No. 4. Deep Sea Mineral Resources Investigation in the Eastern Central Pacific Basin’. (Eds A. Mizuno and J. Chujo.) pp. 49–61. (Geological Survey of Japan: Tokyo, Japan.)
Knittel, K., and Boetius, A. (2009). Anaerobic oxidation of methane: progress with an unknown process. Annual Review of Microbiology 63, 311–334.
| Anaerobic oxidation of methane: progress with an unknown process.Crossref | GoogleScholarGoogle Scholar | 19575572PubMed |
Konno, Y., Fujii, T., Sato, A., Akamine, K., Naiki, M., Masuda, Y., Yamamoto, K., and Nagao, J. (2017). Key findings of the world’s first offshore methane hydrate production test off the coast of Japan: toward future commercial production. Energy & Fuels 31, 2607–2616.
| Key findings of the world’s first offshore methane hydrate production test off the coast of Japan: toward future commercial production.Crossref | GoogleScholarGoogle Scholar |
Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, , Buchner, A., Lai, T., Steppi, S., Jobb, G., Förster, W., Brettske, I., Gerber, S., Ginhart, A. W., Gross, O., Grumann, S., Hermann, S., Jost, R., König, A., Liss, T., Lüßmann, R., May, M., Nonhoff, B., Reichel, B., Strehlow, R., Stamatakis, A., Stuckmann, N., Vilbig, A., Lenke, M., Ludwig, T., Bode, A., and Schleifer, K. H. (2004). ARB: a software environment for sequence data. Nucleic Acids Research 32, 1363–1371.
| ARB: a software environment for sequence data.Crossref | GoogleScholarGoogle Scholar | 14985472PubMed |
McDonald, I. R., Bodrossy, L., Chen, Y., and Murrell, J. C. (2008). Molecular ecology techniques for the study of aerobic methanotrophs. Applied and Environmental Microbiology 74, 1305–1315.
| Molecular ecology techniques for the study of aerobic methanotrophs.Crossref | GoogleScholarGoogle Scholar | 18165358PubMed |
Niemann, H., Lösekann, T., de Beer, D., Elvert, M., Nadalig, T., Knittel, K., Amann, R., Sauter, E. J., Schlüter, M., Klages, M., Foucher, J. P., and Boetius, A. (2006). Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink. Nature 443, 854–858.
| Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink.Crossref | GoogleScholarGoogle Scholar | 17051217PubMed |
Okita, N., Hoaki, T., Suzuki, S., and Hatamoto, M. (2019). Characteristics of microbial community structure at the seafloor surface of the Nankai Trough. Journal of Pure & Applied Microbiology 13, 1917–1928.
| Characteristics of microbial community structure at the seafloor surface of the Nankai Trough.Crossref | GoogleScholarGoogle Scholar |
Reeburgh, W. S. (2007). Oceanic methane biogeochemistry. Chemical Reviews 107, 486–513.
| Oceanic methane biogeochemistry.Crossref | GoogleScholarGoogle Scholar | 17261072PubMed |
Research Consortium for Methane Hydrate Resources in Japan (2008). Japan’s methane hydrate R&D Program. Phase 1. Comprehensive report of research results. Available at http://www.mh21japan.gr.jp/english/wp/wp-content/uploads/ca434ff85adf34a4022f54b2503d86e92.pdf [Verified 18 February 2020].
Ruff, S. E., Felden, J., Gruber-Vodicka, H. R., Marcon, Y., Knittel, K., Ramette, A., and Boetius, A. (2019). In situ development of a methanotrophic microbiome in deep-sea sediments. The ISME Journal 13, 197–213.
| In situ development of a methanotrophic microbiome in deep-sea sediments.Crossref | GoogleScholarGoogle Scholar | 30154496PubMed |
Tavormina, P. L., Ussler, W., and Orphan, V. J. (2008). Planktonic and sediment-associated aerobic methanotrophs in two seep systems along the North American Margin. Applied and Environmental Microbiology 74, 3985–3995.
| Planktonic and sediment-associated aerobic methanotrophs in two seep systems along the North American Margin.Crossref | GoogleScholarGoogle Scholar | 18487407PubMed |
Tsunogai, U., Ishibashi, J., Wakita, H., and Gamo, T. (1998). Methane-rich plumes in the Suruga Trough (Japan) and their carbon isotopic characterization. Earth and Planetary Science Letters 160, 97–105.
| Methane-rich plumes in the Suruga Trough (Japan) and their carbon isotopic characterization.Crossref | GoogleScholarGoogle Scholar |
Wasmund, K., Kurtböke, D. I., Burns, K. A., and Bourne, D. G. (2009). Microbial diversity in sediments associated with a shallow methane seep in the tropical Timor Sea of Australia reveals a novel aerobic methanotroph diversity. FEMS Microbiology Ecology 68, 142–151.
| Microbial diversity in sediments associated with a shallow methane seep in the tropical Timor Sea of Australia reveals a novel aerobic methanotroph diversity.Crossref | GoogleScholarGoogle Scholar | 19573197PubMed |
Yamamoto, K., Wang, X. X., Tamaki, M., and Suzuki, K. (2019). The second offshore production of methane hydrate in the Nankai Trough and gas production behavior from a heterogeneous methane hydrate reservoir. RSC Advances 9, 25987–26013.
| The second offshore production of methane hydrate in the Nankai Trough and gas production behavior from a heterogeneous methane hydrate reservoir.Crossref | GoogleScholarGoogle Scholar |
Yan, T., Ye, Q., Zhou, J., and Zhang, C. L. (2006). Diversity of functional genes for methanotrophs in sediments associated with gas hydrates and hydrocarbon seeps in the Gulf of Mexico. FEMS Microbiology Ecology 57, 251–259.
| Diversity of functional genes for methanotrophs in sediments associated with gas hydrates and hydrocarbon seeps in the Gulf of Mexico.Crossref | GoogleScholarGoogle Scholar | 16867143PubMed |
Ye, J.-L., Qin, X.-W., Qiu, H.-J., Liang, Q.-Y., Dong, Y.-F., Wei, J.-G., Lu, H.-L., Lu, J.-A., Shi, Y.-H., Zhong, C., and Xia, Z. (2018). Preliminary results of environmental monitoring of the natural gas hydrate production test in the South China Sea. China Geology 1, 202–209.
| Preliminary results of environmental monitoring of the natural gas hydrate production test in the South China Sea.Crossref | GoogleScholarGoogle Scholar |
Zhang, Y., and Zhai, W.-D. (2015). Shallow-ocean methane leakage and degassing to the atmosphere: triggered by offshore oil-gas and methane hydrate explorations. Frontiers in Marine Science 2, art34.
| Shallow-ocean methane leakage and degassing to the atmosphere: triggered by offshore oil-gas and methane hydrate explorations.Crossref | GoogleScholarGoogle Scholar |
Zhang, Y., Zhao, H.-D., Zhai, W.-D., Zang, K.-P., and Wang, J.-Y. (2014). Enhanced methane emissions from oil and gas exploration areas to the atmosphere – the central Bohai Sea. Marine Pollution Bulletin 81, 157–165.
| Enhanced methane emissions from oil and gas exploration areas to the atmosphere – the central Bohai Sea.Crossref | GoogleScholarGoogle Scholar | 24602676PubMed |
