Bacterial and archaeal communities in deep sea waters near the Ninetyeast Ridge in Indian Ocean -- Journal of Oceanology and Limnology,2021,39(2):582-597

	Cite this paper:
	Ping GAO, Lingyun QU, Guangxun DU, Qinsheng WEI, Xuelei ZHANG, Guang YANG. Bacterial and archaeal communities in deep sea waters near the Ninetyeast Ridge in Indian Ocean[J]. Journal of Oceanology and Limnology, 2021, 39(2): 582-597

Bacterial and archaeal communities in deep sea waters near the Ninetyeast Ridge in Indian Ocean

Ping GAO^1,2, Lingyun QU^1,2, Guangxun DU¹, Qinsheng WEI^1,3, Xuelei ZHANG¹, Guang YANG¹

1 Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), Qingdao 266061, China;
2 Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China;
3 Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China

Abstract:

Depth-dependent distribution patterns of bacterial and archaeal communities in deep sea water column around the Ninetyeast Ridge in the Indian Ocean were investigated using 16S rRNA gene profiling. Sampling was conducted at the northern Ninetyeast Ridge (1°59.89'N-9°59.70'S, 87°58.90'E-88°00.03'E) from September to November 2016 where samples were collected from the bathyal (1 000 m) to bathypelagic depths (>4 000 m) in four different stations. A total of 1 565 405 clean data falling into 6 712 bacterial OTUs and 1 452 727 clean data falling into 806 archaeal OTUs based on 97% similarity level were analyzed. Most of the bacterial 16S rRNA gene sequences were affiliated with Gammaproteobacteria, followed by Alphaproteobacteria and Bacteroidia. The archaeal 16S rRNA gene sequences mostly affiliated to Nitrososphaeria (Thaumarchaeota) dominated with relative abundances ranging from 52.68% to 97.2%, followed by Thermoplasmata (Euryarchaeota). Vertical partitioning of bacterial and archaeal communities among different water layers was observed. Canonical correspondence analysis (CCA) and Spearman's correlations revealed that depth (P=0.003), dissolved oxygen (P=0.019), and nitrite (P=0.033) were the main environmental factors affecting bacterial community structure at genus level in the Ninetyeast Ridge. On the other hand, the first two CCA axes accounted for 74.4% of the explained total variance, it seems that the archaeal communities at genus level were heavily influenced by the environmental variables including depth, dissolved oxygen (DO), nitrite, salinity, phosphate, ammonia, nitrate, and silicate, but none of them exhibited any significant correlation on the structuring (P>0.1).

Key words: deep sea water|the Ninetyeast Ridge|16S rRNA gene|bacteria|archaea

Received: 2020-01-06 Revised: 2020-01-06

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References:
Agogué H, Lamy D, Neal P R, Sogin M L, Herndl G J. 2011. Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing. Molecular Ecology, 20(2):258-274.
Bandekar M, Ramaiah N, Jain A, Meena R M. 2018. Seasonal and depth-wise variations in bacterial and archaeal groups in the Arabian Sea oxygen minimum zone. Deep Sea Research Part II:Topical Studies in Oceanography, 156:4-18.
Barlett M A, Leff L G. 2010. The effects of N:P ratio and nitrogen form on four major freshwater bacterial taxa in biofilms. Canadian Journal of Microbiology, 56(1):32-43.
Beman J M, Carolan M T. 2013. Deoxygenation alters bacterial diversity and community composition in the ocean's largest oxygen minimum zone. Nature Communications, 4:2 705.
Biddanda B, Ogdahl M, Cotner J. 2001. Dominance of bacterial metabolism in oligotrophic relative to eutrophic waters. Limnology and Oceanography, 46(3):730-739.
Bouvier T C, de Giorgio P A. 2002. Compositional changes in free-living bacterial communities along a salinity gradient in two temperate estuaries. Limnology and Oceanography, 47(2):453-470.
Brin L D, Giblin A E, Rich J J. 2014. Environmental controls of anammox and denitrification in Southern New England estuarine and shelf sediments. Limnology and Oceanography, 59(3):851-860.
Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P. 2008. Mesophilic crenarchaeota:proposal for a third archaeal phylum, the Thaumarchaeota. Nature Reviews Microbiology, 6(3):245-252.
Chao A, Ma M-C, Yang M C K. 1993. Stopping rules and estimation for recapture debugging with unequal failure rates. Biometrika, 80(1):193-201.
Chao A. 1984. Nonparametric estimation of the number of classes in a population. Scandinavian Journal of Statistics, 11(4):265-270.
Cho J C C, Giovannoni S J. 2004. Cultivation and growth characteristics of a diverse group of oligotrophic marine Gammaproteobacteria. Applied and Environmental Microbiology, 70(1):432-440.
Christner B C, Priscu J C, Achberger AM, Barbante C, Carter S P, Christianson K, Michaud A B, Mikucki J A, Mitchell A C, Skidmore M L, Vick-Majors T J, the WISSARD Science Team. 2014. A microbial ecosystem beneath the West Antarctic ice sheet. Nature, 512(7514):310-313.
Cottrell M T, Waidner L A, Yu L Y, Kirchman D L. 2005. Bacterial diversity of metagenomic and PCR libraries from the Delaware River. Environmental Microbiology, 7(12):1 883-1 895.
Cunliffe M, Upstill-Goddard R C, Murrell J C. 2011. Microbiology of aquatic surface microlayers. FEMS Microbiology Reviews, 35(2):233-246.
Dong Y, Zhao Y, Zhang W Y, Li Y, Zhou F, Liu C G, Wu Y, Liu S M, Zhang W C, Xiao T. 2014. Bacterial diversity and community structure in the East China Sea by 454 sequencing of the 16S rRNA gene. Chinese Journal of Oceanology and Limnology, 32(3):527-541.
Edgar R C, Haas B J, Clemente J C, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27(16):2 194-2 200.
Edgar R C. 2013. UPARSE:highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10(10):996-998.
Feng B W, Li X R, Wang J H, Hu Z Y, Meng H, Xiang L Y, Quan Z X. 2009. Bacterial diversity of water and sediment in the Changjiang estuary and coastal area of the East China Sea. FEMS Microbiology Ecology, 70(2):236-248.
Freedman Z, Zak D R. 2014. Atmospheric N deposition increases bacterial laccase-like multicopper oxidases:implications for organic matter decay. Applied and Environmental Microbiology, 80(14):4 460-4 468.
Guo X P, Lu D P, Niu Z S, Feng J N, Chen Y R, Tou F Y, Liu M, Yang Y. 2018. Bacterial community structure in response to environmental impacts in the intertidal sediments along the Yangtze Estuary, China. Marine Pollution Bulletin, 126:141-149.
Guo X P, Niu Z S, Lu D P, Feng J N, Chen Y R, Tou F Y, Liu M, Yang Y. 2017. Bacterial community structure in the intertidal biofilm along the Yangtze estuary, China. Marine Pollution Bulletin, 124(1):314-320.
Haas B J, Gevers D, Earl A M, Feldgarden M, Ward D V, Giannoukos G, Ciulla D, Tabbaa D, Highlander S K, Sodergren E, Methé B, DeSantis T Z, Human Microbiome Consortium, Petrosino J F, Knight R, Birren B W. 2011. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Research, 21(3):494-504.
Haggerty J M, Dinsdale E A. 2017. Distinct biogeographical patterns of marine bacterial taxonomy and functional genes. Global Ecology and Biogeography, 26(2):177-190.
Han D, Ha H K, Hwang C Y, Lee B Y, Hur H G, Lee Y K. 2015. Bacterial communities along stratified water columns at the Chukchi Borderland in the western Arctic Ocean. Deep Sea Research Part II:Topical Studies in Oceanography, 120:52-60.
Hugoni M, Domaizon I, Taib N, Biderre-Petit C, Agogué H, Galand P E, Debroas D, Mary I. 2015. Temporal dynamics of active Archaea in oxygen-depleted zones of two deep lakes. Environmental Microbiology Reports, 7(2):321-329.
Jamieson R E, Heywood J L, Rogers A D, Billett D S M, Pearce D A. 2013. Bacterial biodiversity in deep-sea sediments from two regions of contrasting surface water productivity near the Crozet Islands, Southern Ocean. Deep Sea Research Part I:Oceanographic Research Papers, 75:67-77.
Kirchman D L. 2016. Growth rates of microbes in the oceans. Annual Review of Marine Science, 8:285-309.
Könneke M, Bernhard A E, de la Torre J R, Walker C B, Waterbury J B, Stahl D A. 2005. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature, 437(7058):543-546.
Könneke M, Lipp S J, Hinrichs K U. 2012. Carbon isotope fractionation by the marine ammonia-oxidizing archaeon Nitrosopumilus maritimus. Organic Geochemistry, 48(7):21-24.
Krishna K S, Rao D G, Raju L V S, Chaubey A K, Shcherbakov V S, Pilipenko A I, Murthy I V R. 1999. Paleocene onspreading-axis hotspot volcanism along the Ninetyeast Ridge:an interaction between the Kerguelen hotspot and the Wharton spreading center. Proceedings of the Indian Academy of Sciences-Earth and Planetary Sciences, 108(4):255-267.
Kruskal J B. 1964. Nonmetric multidimensional scaling:A numerical method. Psychometrika, 29(2):115-129.
Kumar R, Mishra A, Jha B. 2019. Bacterial community structure and functional diversity in subsurface seawater from the western coastal ecosystem of the Arabian Sea, India. Gene, 701:55-64.
Kumar S P, Narvekar J, Nuncio M, Gauns M, Sardesai S. 2009. What drives the biological productivity of the northern Indian Ocean? In:Wiggert J D, Hood R R, Naqvi S W A, Brink K H, Smith S L eds. Indian Ocean Biogeochemical Processes and Ecological Variability, Volume 185. Washington:American Geophysical Union.
Li J L, Li N, Li F C, Zou T, Yu S X, Wang Y C, Qin S, Wang G Y. 2014. Spatial diversity of bacterioplankton communities in surface water of northern South China Sea. PLoS One, 9(11):e113014.
Li Y J, Xu L Y. 2007. Improvement for unweighted pair group method with arithmetic mean and its application. Journal of Beijing University of Technology, 33(12):1 333-1 339.(in Chinese with English abstract)
Lin X J, Handley K M, Gilbert J A, Kostka J E. 2015. Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat. The ISME Journal, 9(12):2 740-2 744.
Liu J W, Liu X S, Wang M, Qiao Y L, Zheng Y F, Zhang X H. 2015. Bacterial and archaeal communities in sediments of the North Chinese marginal seas. Microbial Ecology, 70(1):105-117.
Liu J W, Zheng Y F, Lin H Y, Wang X C, Li M, Liu Y, Yu M, Zhao M X, Pedentchouk N, Lea-Smith D J, Todd J D, Magill C R, Zhang W J, Zhou S, Song D L, Zhong H H, Xin Y, Yu M, Tian J W, Zhang X H. 2019. Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench. Microbiome, 7:47.
Martens-Habbena W, Berube P M, Urakawa H, de la Torre J R, Stahl D A. 2009. Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature, 461(7266):976-979.
Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. Journal, 17(1):10-12.
McArthur J V. 2013. Processes in Microbial Ecology by David L. Kirchman. Quarterly Review of Biology, 88(2):143-144.
Menezes L D, Fernandes G L, Mulla A B, Meena R M, Damare S R. 2018. Diversity of culturable sulphur-oxidising bacteria in the oxygen minimum zones of the northern Indian Ocean. Journal of Marine Systems, https://doi.org/10.1016/j.jmarsys.2018.05.007.
Michael L, Krishna K S. 2011. Dating of the 85°E Ridge(northeastern Indian Ocean) using marine magnetic anomalies. Current Science, 100(9):1 314-1 322.
Michelsen C F, Pedas P, Glaring M A, Schjoerring J K, Stougaard P. 2013. Bacterial diversity in Greenlandic soils as affected by potato cropping and inorganic versus organic fertilization. Polar Biology, 37(1):61-71.
Naqvi S W A. 2006. Oxygen deficiency in the North Indian Ocean. Gayana, 70(S1):53-58.
Offre P, Spang A, Schleper C. 2013. Archaea in biogeochemical cycles. Annual Review of Microbiology, 67:437-457.
Parsons T R, Maita Y, Lalli C M. 1984. A Manual of Chemical and Biological Methods for Seawater Analysis. Pergamon Press, Oxford, UK.
Paulmier A, Ruiz-Pino D. 2009. Oxygen minimum zones(OMZs) in the modern ocean. Progress in Oceanography, 80(3-4):113-128.
Qian G, Wang J, Kan J J, Zhang X D, Xia Z Q, Zhang X C, Miao Y Y, Sun J. 2018. Diversity and distribution of anammox bacteria in water column and sediments of the Eastern Indian Ocean. International Biodeterioration & Biodegradation, 133:52-62.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner F O. 2012. The SILVA ribosomal RNA gene database project:improved data processing and web-based tools. Nucleic Acids Research, 41(D1):D590-D596.
Rysgaard S, Glud R N, Risgaard-Petersen N, Dalsgaard T. 2004. Denitrification and anammox activity in arctic marine sediments. Limnology and Oceanography, 49(5):1 493-1 502.
Sheik C S, Mitchell T W, Rizvi F Z, Rehman Y, Faisal M, Hasnain S, McInerney M J, Krumholz L R. 2012. Exposure of soil microbial communities to chromium and arsenic alters their diversity and structure. PLoS One, 7(6):e40059.
Shulse C N, Maillot B, Smith C R, Church M J. 2017. Polymetallic nodules, sediments, and deep waters in the equatorial North Pacific exhibit highly diverse and distinct bacterial, archaeal, and microeukaryotic communities. Microbiology, 6(2):e00428.
Sogin M L, Morrison H G, Huber J A, Mark Welch D, Huse S M, Neal P R, Arrieta J M, Herndl G J. 2006. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedings of the National Academy of Sciences of the United States of America, 103(32):12 115-12 120.
Stahl D A, de la Torre J R. 2012. Physiology and diversity of ammonia-oxidizing Archaea. Annual Review of Microbiology, 66:83-101.
Terahara T, Yamada K, Nakayama J, Igarashi Y, Kobayashi T, Imada C. 2016. Bacterial community structures of deepsea water investigated by molecular biological techniques. Gene, 576(2):696-700.
Williams T J, Wilkins D, Long E, Evans F, DeMaere M Z, Raftery M J, Ricardo C. 2013. The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics. Environmental Microbiology, 15(5):1 302-1 317.
Xie L S, Xu L, He Y, Zhang Y, Wang J H, Xu J. 2017. Archaeal diversity in the euphotic seawater at a slope in the northern South China Sea. Chinese Journal of Applied & Environmental Biology, 23(1):22-27. (in Chinese with English abstract)
Zhang L K, Kang M Y, Xu J J, Xu J, Shuai Y J, Zhou X J, Yang Z H, Ma K S. 2016. Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge. Scientific Reports, 6:25 982.
Zheng Y L, Hou L J, Newell S, Liu M, Zhou J L, Zhao H, You L L, Cheng X L. 2014. Community dynamics and activity of ammonia-oxidizing prokaryotes in intertidal sediments of the Yangtze estuary. Applied and Environmental Microbiology, 80(1):408-419.