Isolation and identification of cultivable bacteria isolated from deep-sea sediment samples of the Indian Ocean

Jiang Zhao; Zhang Weihua

doi:10.12284/hyxb2022070

Volume 44 Issue 4

Apr. 2022

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Jiang Zhao，Zhang Weihua. Isolation and identification of cultivable bacteria isolated from deep-sea sediment samples of the Indian Ocean[J]. Haiyang Xuebao，2022, 44(4)：104–113 doi: 10.12284/hyxb2022070

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Isolation and identification of cultivable bacteria isolated from deep-sea sediment samples of the Indian Ocean

doi: 10.12284/hyxb2022070

Jiang Zhao^{1, 2
,},
Zhang Weihua^{1, 2
,
,}

1.
Engineering Research Center of Tibetan Medicine Detection Technology, Ministry of Education, Xizang Minzu University, Xianyang 712082, China
2.
Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Xizang Minzu University, Xianyang 712082, China

Received Date: 2021-08-16
Rev Recd Date: 2021-11-25
Publish Date: 2022-04-14

Abstract

Abstract

In order to explore the diversity of pure cultured bacteria in the deep-sea sedimentary environment of the Indian Ocean, bacteria were isolated and identified from 12 sediment samples collected from the Indian Ocean. A total of 343 strains of bacteria were obtained by pure culture isolation method and 16S rRNA gene sequence analysis showed that these isolates belonged to Firmicutes, Proteobacteria, Actinobacteria, Bacteroidete and were divided into 5 classes, 13 orders, 26 families and 121 species under 39 genera. The dominant taxa were Streptomyces (separation rate is 16.53%) and Bacillus (separation rate is 8.26%), among which there were 12 potential new taxa. The results show that the deep-sea sedimentary environment of the Indian Ocean is rich in culturable bacteria and contains many new species; secondly, the isolation and culture methods are directly related to the bacterial species diversity obtained from marine sediments.
- Indian Ocean,
- sedimentary environment,
- bacteria,
- isolation and identification

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References(27)

References

[1]	Arrigo K R. Marine microorganisms and global nutrient cycles[J]. Nature, 2005, 437(7057): 349−355. doi: 10.1038/nature04159
[2]	Bowler C, Karl D M, Colwell R R. Microbial oceanography in a sea of opportunity[J]. Nature, 2009, 459(7244): 180−184. doi: 10.1038/nature08056
[3]	张偲, 等. 中国海洋微生物多样性[M]. 1版. 北京: 科学出版社, 2013. Zhang Si, et al. Diversities of Marine Microbes in China[M]. 1st ed. Beijing: Science Press, 2013.
[4]	Rochelle P A, Cragg B A, Fry J C, et al. Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rRNA gene sequence analysis[J]. FEMS Microbiology Ecology, 1994, 15(1/2): 215−225.
[5]	Wellsbury P, Mather I, Parkes R J. Geomicrobiology of deep, low organic carbon sediments in the Woodlark Basin, Pacific Ocean[J]. FEMS Microbiology Ecology, 2002, 42(1): 59−70. doi: 10.1111/j.1574-6941.2002.tb00995.x
[6]	Newberry C J, Webster G, Cragg B A, et al. Diversity of prokaryotes and Methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190[J]. Environmental Microbiology, 2004, 6(3): 274−287. doi: 10.1111/j.1462-2920.2004.00568.x
[7]	Inagaki F, Nunoura T, Nakagawa S, et al. Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean margin[J]. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103(8): 2815−2820. doi: 10.1073/pnas.0511033103
[8]	Bidle K A, Kastner M, Bartlett D H. A phylogenetic analysis of microbial communities associated with methane hydrate containing marine fluids and sediments in the Cascadia margin (ODP site 892B)[J]. FEMS Microbiology Letters, 1999, 177(1): 101−108. doi: 10.1111/j.1574-6968.1999.tb13719.x
[9]	Inagaki F, Suzuki M, Takai K, et al. Microbial communities associated with geological horizons in coastal subseafloor sediments from the sea of Okhotsk[J]. Applied and Environmental Microbiology, 2003, 69(12): 7224−7235. doi: 10.1128/AEM.69.12.7224-7235.2003
[10]	Heijs S K, Haese R R, Van Der Wielen P W J J, et al. Use of 16S rRNA gene based clone libraries to assess microbial communities potentially involved in anaerobic methane oxidation in a Mediterranean cold seep[J]. Microbial Ecology, 2007, 53(3): 384−398. doi: 10.1007/s00248-006-9172-3
[11]	徐丽华, 娄恺, 张华, 等. 微生物资源学[M]. 2版. 北京: 科学出版社, 2010: 90. Xu Lihua, Lou Kai, Zhang Hua, et al. Microbial Resources[M]. 2nd ed. Beijing: Science Press, 2010: 90.
[12]	Arrieta J M, Arnaud-haond S, Duarte C M. What lies underneath: Conserving the oceans’ genetic resources[J]. Proceedings of the National Academy of Sciences of the United States of America, 2010, 107(43): 18318−18324. doi: 10.1073/pnas.0911897107
[13]	Schut F, De Vries E J, Gottschal J C, et al. Isolation of typical marine bacteria by dilution culture: growth, maintenance, and characteristics of isolates under laboratory conditions[J]. Applied Environmental Microbiology, 1993, 59(7): 150−161.
[14]	王宏梅, 赵心清. 可培养海洋放线菌生物多样性的研究进展[J]. 微生物学通报, 2007, 34(5): 996−1000. doi: 10.3969/j.issn.0253-2654.2007.05.040 Wang Hongmei, Zhao Xinqing. Progress in the bio-diversity studies of culturable marine actinobacteria[J]. Microbiology China, 2007, 34(5): 996−1000. doi: 10.3969/j.issn.0253-2654.2007.05.040
[15]	Mincer T J, Jensen P R, Kauffman C A, et al. Widespread and persistent populations of a major new marine actinomycete taxon in ocean sediments[J]. Applied and Environmental Microbiology, 2002, 68(10): 5005−5011. doi: 10.1128/AEM.68.10.5005-5011.2002
[16]	Terahara T, Kobayashi T, Imada C. An effective method based on wet-heat treatment for the selective isolation of micromonospora from estuarine sediments[J]. World Journal of Microbiology and Biotechnology, 2013, 29(9): 1677−1684. doi: 10.1007/s11274-013-1330-4
[17]	Li Wenjun, Xu Ping, Schumann P, et al. Georgenia ruanii sp. nov. , a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia[J]. International Journal of Systematic and Evolutionary Microbiology, 2007, 57(Pt7): 1424−1428.
[18]	Messick J B, Berent L M, Cooper S K. Development and evaluation of a PCR-based assay for detection of Haemobartonella felis in cats and differentiation of H. felis from related bacteria by restriction fragment length polymorphism analysis[J]. Journal of Clinical Microbiology, 1998, 36(2): 462−466. doi: 10.1128/JCM.36.2.462-466.1998
[19]	Kim O S, Cho Y J, Lee K, et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species[J]. International Journal of Systematic and Evolutionary Microbiology, 2012, 62(3): 716−721.
[20]	Thompson J D, Gibson T J, Plewniak F, et al. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools[J]. Nucleic Acids Research, 1997, 25(24): 4876−4882. doi: 10.1093/nar/25.24.4876
[21]	Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets[J]. Molecular Biology and Evolution, 2016, 33(7): 1870−1874. doi: 10.1093/molbev/msw054
[22]	Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees[J]. Molecular Biology and Evolution, 1987, 4(4): 406−425.
[23]	Wayne L G, Brenner D J, Colwell R R, et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics[J]. International Journal of Systematic Bacteriology, 1987, 37(4): 463−464.
[24]	Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards[J]. Microbiology Today, 2006, 8(4): 6−9.
[25]	Goodfellow M, Fiedler H P. A guide to successful bioprospecting: informed by actinobacterial systematics[J]. Antonie van Leeuwenhoek, 2010, 98(2): 119−142. doi: 10.1007/s10482-010-9460-2
[26]	徐盈. 南海沉积环境细菌分离方法及多样性研究[D]. 昆明: 云南大学, 2012. Xu Ying. Study on isolation methods and bacterial diversity in sediment environments from South China Sea[D]. Kunming: Yunnan University, 2012.
[27]	张偲, 张长生, 田新朋, 等. 中国海洋微生物多样性研究[J]. 中国科学院院刊, 2010, 25(6): 651−658. doi: 10.3969/j.issn.1000-3045.2010.06.011 Zhang Si, Zhang Changsheng, Tian Xinpeng, et al. The study of diversities of marine microbes in China[J]. Bulletin of the Chinese Academy of Sciences, 2010, 25(6): 651−658. doi: 10.3969/j.issn.1000-3045.2010.06.011