Bacterial Community Composition of South China Sea Sediments through Pyrosequencing-Based Analysis of 16S rRNA Genes

PLoS ONE

Volumn 8, Issue 10, 2013, Pages

  Zhu, Daochen ^a,b   Tanabe, Shoko Hosoi ^c   Yang, Chong ^d   Zhang, Weimin ^b   Sun, Jianzhong ^a  

^a JIANGSU UNIVERSITY   (China)

^b GUANGDONG INSTITUTE OF MICROBIOLOGY   (China)

^c UNIVERSITY OF SHIGA PREFECTURE   (Japan)

^d Department of RandD   (China)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; BACTERIAL DNA;

ACTINOBACTERIA; AMPLICON; ARTICLE; BACTERIUM IDENTIFICATION; CHINA; CHLOROFLEXI; FIRMICUTES; GAMMAPROTEOBACTERIA; GENETIC ANALYSIS; MICROBIAL COMMUNITY; NONHUMAN; PHYLUM; PLANCTOMYCETES; POPULATION ABUNDANCE; PROTEOBACTERIA; PYROSEQUENCING; RNA ANALYSIS; SEA LEVEL; SEDIMENT; SEQUENCE ANALYSIS; SPECIES COMPOSITION; SPECIES DIVERSITY; TAXONOMY; BACTERIA; BIODIVERSITY; DNA SEQUENCE; ECOSYSTEM; GENETICS; MICROBIOLOGY; PHYLOGENY; PROCEDURES; RNA GENE; SEA;

BACTERIA; BIODIVERSITY; CHINA; DNA, BACTERIAL; ECOSYSTEM; GENES, RRNA; GEOLOGIC SEDIMENTS; OCEANS AND SEAS; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 84886907419     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0078501     Document Type: Article

References (39)

1. Schmitt S, Tsai P, Bell J, Fromont J, Ilan M, et al. (2012) Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges. ISME J 6: 564-576. doi:10.1038/ismej.2011.116. PubMed: 21993395.
2. Godoy-Vitorino F, Goldfarb KC, Karaoz U, Leal S, Garcia-Amado MA, et al. (2012) Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows. ISME J 6: 531-541. doi:10.1038/ismej.2011.131. PubMed: 21938024.
3. Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, et al. (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A 103: 12115-12120. doi:10.1073/pnas.0605127103. PubMed: 16880384.
4. Teixeira LC, Peixoto RS, Cury JC, Sul WJ, Pellizari VH, et al. (2010) Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica. ISME J 4: 989-1001. doi:10.1038/ismej.2010.35. PubMed: 20357834.
5. Fuhrman JA, (2009) Microbial community structure and its functional implications. Nature 459: 193-199. doi:10.1038/nature08058. PubMed: 19444205.
6. Graham DE, Wallenstein MD, Vishnivetskaya TA, Waldrop MP, Phelps TJ, et al. (2012) Microbes in thawing permafrost: the unknown variable in the climate change equation. ISME J 6: 709-712. doi:10.1038/ismej.2011.163. PubMed: 22094350.
7. Hollister EB, Engledow AS, Hammett AJ, Provin TL, Wilkinson HH, et al. (2010) Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments. ISME J 4: 829-838. doi:10.1038/ismej.2010.3. PubMed: 20130657.
8. Gilbert JA, Field D, Swift P, Newbold L, Oliver A, et al. (2009) The seasonal structure of microbial communities in the Western English Channel. Environ Microbiol 11: 3132-3139. doi:10.1111/j.1462-2920.2009.02017.x. PubMed: 19659500.
9. Kirchman DL, Cottrell MT, Lovejoy C, (2010) The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes. Environ Microbiol 12: 1132-1143. doi:10.1111/j.1462-2920.2010.02154.x. PubMed: 20132284.
10. Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR, et al. (2007) Microbial population structures in the deep marine biosphere. Science 318: 97-100. doi:10.1126/science.1146689. PubMed: 17916733.
11. Galand PE, Casamayor EO, Kirchman DL, Lovejoy C, (2009) Ecology of the rare microbial biosphere of the Arctic Ocean. Proc Natl Acad Sci U S A 106: 22427-22432. doi:10.1073/pnas.0908284106. PubMed: 20018741.
12. Tamburini F, Adatte T, Follmi K, Bernasconi SM, Steinmann P, (2003) Investigating the history of East Asian monsoon and climate during the last glacial-interglacial period (0-140 000 years): mineralogy and geochemistry of ODP Sites 1143 and 1144, South China Sea. Mar Geol 201: 147-168. doi:10.1016/S0025-3227(03)00214-7.
13. Barber PH, Palumbi SR, Erdmann MV, Moosa MK, (2000) Biogeography. A marine Wallace's line? Nature 406: 692-693. doi:10.1038/35021135. PubMed: 10963585.
14. Wang SH, Yan W, Magalhaes HV, Chen Z, Pinheiro ML, et al. (2012) Calcium isotope fractionation and its controlling factors over authigenic carbonates in the cold seeps of the northern South China Sea. Chin Sci Bull 57: 1325-1332. doi:10.1007/s11434-012-4990-9.
15. Schauer R, Bienhold C, Ramette A, Harder J, (2010) Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean. Isme J 4: 159-170. doi:10.1038/ismej.2009.106. PubMed: 19829317.
16. Zinger L, Amaral-Zettler LA, Fuhrman JA, Horner-Devine MC, Huse SM, et al. (2011) Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLOS ONE 6: e24570. doi:10.1371/journal.pone.0024570. PubMed: 21931760.
17. Cao HL, Hong YG, Li M, Gu JD, (2011) Diversity and abundance of ammonia-oxidizing prokaryotes in sediments from the coastal Pearl River estuary to the South China Sea. Antonie Van Leeuwenhoek Int J Gen Mol Microbiol 100: 545-556. doi:10.1007/s10482-011-9610-1. PubMed: 21717206.
18. Liao L, Xu XW, Wang CS, Zhang DS, Wu M, (2009) Bacterial and archaeal communities in the surface sediment from the northern slope of the South China Sea. J Zhejiang Univ-Sci B 10: 890-901. doi:10.1631/jzus.B0920181. PubMed: 19946953.
19. Wang GH, Dong JD, Li XA, Sun HM, (2010) The bacterial diversity in surface sediment from the South China Sea. Acta Oceanol Sin 29: 98-105. doi:10.1007/s13131-010-0028-9.
20. Moisander PH, Beinart RA, Voss M, Zehr JP, (2008) Diversity and abundance of diazotrophic microorganisms in the South China Sea during intermonsoon. Isme J 2: 954-967. doi:10.1038/ismej.2008.51. PubMed: 18528417.
21. Zhou MY, Chen XL, Zhao HL, Dang HY, Luan XW, et al. (2009) Diversity of Both the Cultivable Protease-Producing Bacteria and Their Extracellular Proteases in the Sediments of the South China Sea. Microb Ecol 58: 582-590. doi:10.1007/s00248-009-9506-z. PubMed: 19301066.
22. Zhang Y, Jiao NZ, Sun ZY, Hu AY, Zheng QA, (2011) Phylogenetic diversity of bacterial communities in South China Sea mesoscale cyclonic eddy perturbations. Res Microbiol 162: 320-329. doi:10.1016/j.resmic.2010.12.006. PubMed: 21187147.
23. Sapp M, Parker ER, Teal LR, Schratzberger M, (2010) Advancing the understanding of biogeography-diversity relationships of benthic microorganisms in the North Sea. FEMS Microbiol Ecol 74: 410-429. doi:10.1111/j.1574-6941.2010.00957.x. PubMed: 20735476.
24. Polymenakou PN, Bertilsson S, Tselepides A, Stephanou EG, (2005) Bacterial community composition in different sediments from the Eastern Mediterranean Sea: a comparison of four 16S ribosomal DNA clone libraries. Microb Ecol 50: 447-462. doi:10.1007/s00248-005-0005-6. PubMed: 16328662.
25. Kouridaki I, Polymenakou PN, Tselepides A, Mandalakis M, Smith KL Jr., (2010) Phylogenetic diversity of sediment bacteria from the deep Northeastern Pacific Ocean: a comparison with the deep Eastern Mediterranean Sea. Int Microbiol 13: 143-150. PubMed: 20890848.
26. Klotz MG, Bryant DA, Hanson TE, (2011) The microbial sulfur cycle. Front Microbiol 2: 241. PubMed: 22144979.
27. Sievert SM, Kiene R, Schulz H, (2007) The sulfur cycle. J Oceanogr 20: 117-123. doi:10.5670/oceanog.2007.55.
28. Kobayashi T, Koide O, Mori K, Shimamura S, Matsuura T, et al. (2008) Phylogenetic and enzymatic diversity of deep subseafloor aerobic microorganisms in organics- and methane-rich sediments off Shimokita Peninsula. Extremophiles 12: 519-527. doi:10.1007/s00792-008-0157-7. PubMed: 18368287.
29. Pedrós-Alió C, (2006) Marine microbial diversity: can it be determined? Trends Microbiol 14: 257-263. doi:10.1016/j.tim.2006.04.007. PubMed: 16679014.
30. Teira E, Lekunberri I, Gasol JM, Nieto-Cid M, Alvarez-Salgado XA, et al. (2007) Dynamics of the hydrocarbon-degrading Cycloclasticus bacteria during mesocosm-simulated oil spills. Environ Microbiol 9: 2551-2562. doi:10.1111/j.1462-2920.2007.01373.x. PubMed: 17803779.
31. Fuhrman JA, Hewson I, Schwalbach MS, Steele JA, Brown MV, et al. (2006) Annually reoccurring bacterial communities are predictable from ocean conditions. Proc Natl Acad Sci U S A 103: 13104-13109. doi:10.1073/pnas.0602399103. PubMed: 16938845.
32. Cottrell MT, Kirchman DL, (2003) Contribution of major bacterial groups to bacterial biomass production (thymidine and leucine incorporation) in the Delaware estuary. Limnol Oceanogr 48: 168-178. doi:10.4319/lo.2003.48.1.0168.
33. Zhang Y, Jiao NZ, Cottrell MT, Kirchman DL, (2006) Contribution of major bacterial groups to bacterial biomass production along a salinity gradient in the South China Sea. Aquat Microb Ecol 43: 233-241. doi:10.3354/ame043233.
34. Galli I, Teira G, Perlo F, Bonato P, Tisocco O, et al. (2008) Animal performance and meat quality in cull cows with early weaned calves in Argentina. Meat Sci 79: 521-528. doi:10.1016/j.meatsci.2007.10.007. PubMed: 22062912.
35. Pester M, Bittner N, Deevong P, Wagner M, Loy A, (2010) A 'rare biosphere' microorganism contributes to sulfate reduction in a peatland. ISME J 4: 1591-1602. doi:10.1038/ismej.2010.75. PubMed: 20535221.
36. Wang Y, Qian PY, (2009) Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies. PLOS ONE 4: e7401. doi:10.1371/journal.pone.0007401. PubMed: 19816594.
37. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, et al. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196. doi:10.1093/nar/gkm864. PubMed: 17947321.
38. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541. doi:10.1128/AEM.01541-09. PubMed: 19801464.
39. Schloss PD, Handelsman J, (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-1506. doi:10.1128/AEM.71.3.1501-1506.2005. PubMed: 15746353.