WANG Liping, ZHENG Binghui, LEI Kun. Diversity and distribution of bacterial community in the coastal sediments of Bohai Bay, China[J]. Acta Oceanologica Sinica, 2015, 34(10): 122-131. doi: 10.1007/s13131-015-0719-3
Citation: WANG Liping, ZHENG Binghui, LEI Kun. Diversity and distribution of bacterial community in the coastal sediments of Bohai Bay, China[J]. Acta Oceanologica Sinica, 2015, 34(10): 122-131. doi: 10.1007/s13131-015-0719-3

Diversity and distribution of bacterial community in the coastal sediments of Bohai Bay, China

doi: 10.1007/s13131-015-0719-3
  • Received Date: 2014-06-17
  • Rev Recd Date: 2014-09-25
  • In order to understand the diversity and distribution of the bacterial community in the coastal sediment of the Bohai Bay, China, high-throughput barcoded pyrosequencing of the 16S rRNA gene was used. Metagenomic DNA was extracted from the sediment samples, and was sequenced using a 454 GS FLX Titanium system. At 97% similarity, the sequences were assigned to 22 884 operational taxonomic units (OTUs) which belonged to 41 phyla, 84 classes, 268 genera and 789 species. At the different taxonomic levels, both the dominants and their distribution varied significantly among the six coastal sediments. Proteobacteria was the first dominant phylum across all the six coastal sediments, representing 57.52%, 60.66%, 45.10%, 60.92%, 56.63% and 56.59%, respectively. Bacteroidetes was the second dominant phylum at Stas S1, S2 and S4, while Chloroflexi was the second dominant phylum at Stas S3, S5 and S6. At class level, γ-Proteobacteria was the first dominant class at Stas S1, S2, S4 and S6, while δ-Proteobacteria became the first dominant class at Stas S3 and S5. In addition, a large proportion of unclassified representatives have distributed at the different taxonomic levels. Canonical correspondence analysis (CCA) results indicated that the sediment texture, water depth (D), dissolved oxygen (DO), total nitrogen (TN) and nine EPA priority control polycyclic aromatic hydrocarbons (PAHs) including naphthalene, acenaphthylene, acenaphthene, fluorine, phenanthrene, fluoranthene, pyrene, benzo[a]anthracene and indeno[1,2,3-cd]pyrene were the important factors in regulating the bacterial community composition. Those results are very important to further understand the roles of bacterial community in the coastal biogeochemical cycles.
  • loading
  • Ager D, Evans S, Li Hong, et al. 2010. Anthropogenic disturbance af-fects the structure of bacterial communities. Environmental Microbiology, 12(3): 670-678
    Andreoni V, Cavalca L, Rao M A, et al. 2004. Bacterial communities and enzyme activities of PAHs polluted soils. Chemosphere, 57(5): 401-412
    Baker G C, Smith J J, Cowan D A. 2003. Review and re-analysis of do-main-specific 16S primers. Journal of Microbiological Methods, 55(3): 541-555
    Barbier E B, Hacker S D, Kennedy C, et al. 2011. The value of estuar-ine and coastal ecosystem services. Ecological Monographs, 81(2): 169-193
    Böer S I, Hedtkamp S I C, van Beusekom J E E, et al. 2009. Time-and sediment depth-related variations in bacterial diversity and community structure in subtidal sands. The ISME Journal, 3(7): 780-791
    Cabello P, Roldán M D, Moreno-Vivián C. 2004. Nitrate reduction and the nitrogen cycle in archaea. Microbiology, 150(11): 3527-3546
    Crump B C, Hopkinson C S, Sogin M L, et al. 2004. Microbial biogeo-graphy along an estuarine salinity gradient: combined influ-ences of bacterial growth and residence time. Applied and En-vironmental Microbiology, 70(3): 1494-1505
    Dowd S E, Sun Yan, Secor P R, et al. 2008. Survey of bacterial di-versity in chronic wounds using pyrosequencing, DGGE, and full ribosome shotgun sequencing. BMC Microbiology, 8: 43
    Edgar R C, Haas B J, Clemente J C, et al. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27(16): 2194-2200
    Ellis R J, Neish B, Trett M W, et al. 2001. Comparison of microbial and meiofaunal community analyses for determining impact of heavy metal contamination. Journal of Microbiological Meth-ods, 45(3): 171-185
    Freitag T E, Klenke T, Krumbein W E, et al. 2003. Effect of anoxia and high sulphide concentrations on heterotrophic microbial com-munities in reduced surface sediments (Black Spots) in sandy intertidal flats of the German Wadden Sea. FEMS Microbiology Ecology, 44(3): 291-301
    Gallego J L R, García-Martínez M J, Llamas J F, et al. 2007. Biodegrad-ation of oil tank bottom sludge using microbial consortia. Bio-degradation, 18(3): 269-281
    Gillan D C, Danis B, Pernet P, et al. 2005. Structure of sediment-asso-ciated microbial communities along a heavy-metal contamina-tion gradient in the marine environment. Applied and Environ-mental Microbiology, 71(2): 679-690
    Girvan M S, Bullimore J, Pretty J N, et al. 2003. Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Applied and Environmental Mi-crobiology, 69(3): 1800-1809
    Gomes N C M, Cleary D F R, Calado R, et al. 2011. Mangrove bacteri-al richness. Communicative & Integrative Biology, 4(4): 419-423
    Guo Feng, Zhang Tong. 2012. Profiling bulking and foaming bacteria in activated sludge by high throughput sequencing. Water Re- search, 46(8): 2772-2782
    Haritash A K, Kaushik C P. 2009. Biodegradation aspects of Polycyc-lic Aromatic Hydrocarbons (PAHs): A review. Journal of Haz-ardous Materials, 169(1): 1-15
    Kim B S, Kim B K, Lee J H, et al. 2008. Rapid phylogenetic dissection of prokaryotic community structure in tidal flat using pyrosequencing. The Journal of Microbiology, 46(4): 357-363
    Kolukirik M, Ince O, Cetecioglu Z, et al. 2011. Spatial and temporal changes in microbial diversity of the Marmara Sea sediments. Marine Pollution Bulletin, 62(11): 2384-2394
    Köster M, Meyer-Reil L-A. 2001. Characterization of carbon and mi-crobial biomass pools in shallow water coastal sediments of the southern Baltic Sea (Nordrügensche Bodden). Marine Ecology Progress Series, 214: 25-41
    Kwon S, Moon E, Kim T-S, et al. 2011. Pyrosequencing demonstrated complex microbial communities in a membrane filtration sys-tem for a drinking water treatment plant. Microbes and Envir-onments, 26(2): 149-155
    Lauber C L, Hamady M, Knight R, et al. 2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial com-munity structure at the continental scale. Applied and Environ-mental Microbiology, 75(15): 5111-5120
    Lemos L N, Fulthorpe R R, Triplett E W, et al. 2011. Rethinking micro-bial diversity analysis in the high throughput sequencing era. Journal of Microbiological Methods, 86(1): 42-51
    Lim Y W, Kim B K, Kim C, et al. 2010. Assessment of soil fungal com-munities using pyrosequencing. The Journal of Microbiology, 48(3): 284-289
    Magalhães C M, Machado A, Matos P, et al. 2011. Impact of copper on the diversity, abundance and transcription of nitrite and ni-trous oxide reductase genes in an urban European estuary. FEMS Microbiology Ecology, 77(2): 274-284
    McLellan S L, Huse S M, Mueller-Spitz S R, et al. 2010. Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent. Environmental Microbio-logy, 12(2): 378-392
    Pinto A J, Xi Chuanwu, Raskin L. 2012. Bacterial community struc-ture in the drinking water microbiome is governed by filtration processes. Environmental Science & Technology, 46(16): 8851-8859
    Qian Peiyuan, Wang Yong, Lee O O, et al. 2011. Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing. The ISME Journal, 5(3): 507-518
    Qiao Min, Wang Chunxia, Huang Shengbiao, et al. 2006. Composi-tion, sources, and potential toxicological significance of PAHs in the surface sediments of the Meiliang Bay, Taihu Lake, China. Environment International, 32: 28-33
    Raghukumar C, Vipparty V, David J, et al. 2001. Degradation of crude oil by marine cyanobacteria. Applied Microbiology and Bio-technology, 57(3): 433-436
    Roane T M, Kellogg S T. 1996. Characterization of bacterial com-munities in heavy metal contaminated soils. Canadian Journal of Microbiology, 42(6): 593-603
    Roesch L F, Fulthorpe R R, Riva A, et al. 2007. Pyrosequencing enu-merates and contrasts soil microbial diversity. The ISME Journ-al, 1(4): 283-290
    Roh S W, Kim K-H, Nam Y-D, et al. 2010. Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing. The ISME Journal, 4(1): 1-16
    Röling W F M, Milner M G, Jones D M, et al. 2002. Robust hydrocar-bon degradation and dynamics of bacterial communities dur-ing nutrient-enhanced oil spill bioremediation. Applied and Environmental Microbiology, 68(11): 5537-5548
    Schlesinger W H. 1997. Biogeochemistry: An Analysis of Global Change. San Diego: Academic Press, 588
    Schloss P D, Westcott S L, Ryabin T, et al. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology, 75(23): 7537-7541
    Shepard F P. 1954. Nomenclature based on sand-silt-clay ratios. Journal of Sedimentary Petrology, 24(3): 151-158
    Sorkhoh N, Al-Hasan R, Radwan S, et al. 1992. Self-cleaning of the Gulf. Nature, 359(6391): 109
    Surridge A K J, Wehner F C, Cloete T E. 2009. Bioremediation of pol-luted soil. In: Singh A, Kuhad R C, Ward O P, et al., eds. Ad-vances in Applied Bioremediation. Berlin: Springer, 103-121
    Teira E, Hernando-Morales V, Martínez-García S, et al. 2013. Re-sponse of bacterial community structure and function to exper-imental rainwater additions in a coastal eutrophic embayment. Estuarine, Coastal and Shelf Science, 119: 44-53
    Tripathi B M, Kim M, Singh D, et al. 2012. Tropical soil bacterial com-munities in Malaysia: pH dominates in the equatorial tropics too. Microbial Ecology, 64(2): 474-484
    Wang Liping, Liu Lusan, Zheng Binghui, et al. 2013. Analysis of the bacterial community in the two typical intertidal sediments of Bohai Bay, China by pyrosequencing. Marine Pollution Bullet-in, 72(1): 181-187
    Wobus A, Bleul C, Massen S, et al. 2003. Microbial diversity and func-tional characterization of sediments from reservoirs of differ-ent trophic state. FEMS Microbiology Ecology, 46(3): 331-347
    Yakimov M M, Giuliano L, Gentile G, et al. 2003. Oleispira antarctica gen. nov., sp. nov., a novel hydrocarbonoclastic marine bacteri-um isolated from Antarctic coastal sea water. International Journal of Systematic and Evolutionary Microbiology, 53(3): 779-785
    Yakimov M M, Golyshin P N, Lang S, et al. 1998. Alcanivorax borku-mensis gen. nov., sp. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium. International Journal of Systematic and Evolutionary Microbiology, 48(2): 339-348
    Zeng Yinxin, Yu Yong, Li Huirong, et al. 2013. Phylogenetic diversity of planktonic bacteria in the Chukchi Borderland region in summer. Acta Oceanologica Sinica, 32(6): 66-74
    Zhang Tong, Shao Mingfei, Ye Lin. 2012. 454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treat-ment plants. The ISME Journal, 6(6): 1137-1147
    Zhang Xiaojun, Yue Siqing, Zhong Huihui, et al. 2011. A diverse bac-terial community in an anoxic quinoline-degrading bioreactor determined by using pyrosequencing and clone library analys-is. Applied Microbiology and Biotechnology, 91(2): 425-434
  • 加载中

Catalog

    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Article Metrics

    Article views (1088) PDF downloads(1295) Cited by()
    Proportional views
    Related

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return