Dynamics of the bacterial and archaeal communities in the Northern South China Sea revealed by 454 pyrosequencing of the 16S rRNA gene

Deep-Sea Research Part II: Topical Studies in Oceanography

Volumn 117, Issue , 2015, Pages 97-107

  Xia, Xiaomin ^a   Guo, Wang ^a   Liu, Hongbin ^a  

^a HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

Author keywords

454 Pyrosequencing; Archaeal community; Bacterial community; South China Sea

Indexed keywords

DISCHARGE (FLUID MECHANICS); ESTUARIES; GENES; RNA;

454-PYROSEQUENCING; ARCHAEAL; BACTERIAL COMMUNITY; COMMUNITY COMPOSITION; FLOW-CYTOMETRIC ANALYSIS; NORTHERN SOUTH CHINA SEA; SOUTH CHINA SEA; SPATIO-TEMPORAL VARIATION;

BACTERIA;

ABUNDANCE; BACTERIUM; COASTAL WATER; COMMUNITY COMPOSITION; COMMUNITY DYNAMICS; CONCENTRATION (COMPOSITION); ESTUARINE ENVIRONMENT; MICROBIAL COMMUNITY; NUCLEIC ACID ANALYSIS; OPEN OCEAN; PREFERENCE BEHAVIOR; PROKARYOTE; RIVER DISCHARGE; RNA; SEASONAL VARIATION; SPATIAL DISTRIBUTION; SPATIOTEMPORAL ANALYSIS;

PACIFIC OCEAN; SOUTH CHINA SEA;

ARCHAEA; BACTERIA (MICROORGANISMS); MARINE GROUP II; PROCHLOROCOCCUS; PROKARYOTA; SYNECHOCOCCUS;

EID: 84930928982     PISSN: 09670645     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dsr2.2015.05.016     Document Type: Article

References (74)

1. Alonso-Sáez L., Andersson A., Heinrich F., Bertilsson S. High archaeal diversity in Antarctic circumpolar deep waters. Environ. Microbiol. Rep. 2011, 3:689-697.
2. Azam F. Microbial control of oceanic carbon flux: the plot thickens. Science 1998, 280:694-695.
3. Bano N., Ruffin S., Ransom B., Hollibaugh J.T. Phylogenetic composition of Arctic Ocean archaeal assemblages and comparison with Antarctic assemblages. Appl. Environ. Microbiol. 2004, 70:781-789.
4. Campbell B.J., Kirchman D.L. Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient. ISME J. 2012, 7:210-220.
5. Campbell B.J., Yu L., Heidelberg J.F., Kirchman D.L. Activity of abundant and rare bacteria in a coastal ocean. Proc. Natl. Acad. Sci. 2011, 108:12776-12781.
6. Chen B., Wang L., Song S., Huang B., Sun J., Liu H. Comparisons of picophytoplankton abundance, size, and fluorescence between summer and winter in Northern South China Sea. Cont. Shelf Res. 2011, 31:1527-1540.
7. Chen B., Liu H., Huang B. Environmental controlling mechanisms on bacterial abundance in the South China Sea inferred from generalized additive models (GAMs). J. Sea Res. 2012, 72:69-76.
8. Crump B.C., Armbrust E.V., Baross J.A. Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia River, its estuary, and the adjacent coastal ocean. Appl. Environ. Microbiol. 1999, 65:3192-3204.
9. Curtis T.P., Sloan W.T., Scannell J.W. Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. 2002, 99:10494-10499.
10. DeLong E.F. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. 1992, 89:5685-5689.
11. DeLong E.F. Oceans of archaea. ASM News - Am. Soc. Microbiol. 2003, 69:503.
12. DeLong E.F., Pace N.R. Environmental diversity of bacteria and archaea. Syst. Biol. 2001, 50:470-478.
13. DeLong E.F., Wu K.Y., Prézelin B.B., Jovine R.V. High abundance of archaea in Antarctic marine picoplankton. Nature 1994, 371:695-697.
14. Dillon J.G., McMath L.M., Trout A.L. Seasonal changes in bacterial diversity in the Salton Sea. Hydrobiologia 2009, 632:49-64.
15. Dong L., Su J., Ah Wong L., Cao Z., Chen J.-C. Seasonal variation and dynamics of the Pearl River plume. Cont. Shelf Res. 2004, 24:1761-1777.
16. Du J., Xiao K., Li L., Ding X., Liu H., Lu Y., Zhou S. Temporal and spatial diversity of bacterial communities in coastal waters of the South China Sea. PloS One 2013, 8:e66968.
17. Eilers H., Pernthaler J., Peplies J., Glöckner F.O., Gerdts G., Amann R. Isolation of novel pelagic bacteria from the German Bight and their seasonal contributions to surface picoplankton. Appl. Environ. Microbiol. 2001, 67:5134-5142.
18. Flombaum P., Gallegos J.L., Gordillo R.A., Rincón J., Zabala L.L., Jiao N., Karl D.M., Li W.K., Lomas M.W., Veneziano D. Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus. Proc. Natl. Acad. Sci. 2013, 110:9824-9829.
19. Fortunato C.S., Eiler A., Herfort L., Needoba J.A., Peterson T.D., Crump B.C. Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin. ISME J. 2013, 7:1899-1911.
20. Fortunato C.S., Herfort L., Zuber P., Baptista A.M., Crump B.C. Spatial variability overwhelms seasonal patterns in bacterioplankton communities across a river to ocean gradient. ISME J. 2012, 6:554-563.
21. Fuhrman J. Bacterioplankton roles in cycling of organic matter: the microbial food web. Primary Productivity and Biogeochemical Cycles in the Sea 1992, 361-383. Springer, New York. P.G. Falkowski, A.D. Woodhead, K. Vivirito (Eds.).
22. Galand P.E., Casamayor E.O., Kirchman D.L., Potvin M., Lovejoy C. Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing. ISME J. 2009, 3:860-869.
23. Gantner S., Andersson A.F., Alonso-Sáez L., Bertilsson S. Novel primers for 16S rRNA-based archaeal community analyses in environmental samples. J. Microbiol. Methods 2011, 84:12-18.
24. Gao Z., Johnson Z.I., Wang G. Molecular characterization of the spatial diversity and novel lineages of mycoplankton in Hawaiian coastal waters. ISME J. 2010, 4:111-120.
25. Gilbert J.A., Field D., Swift P., Newbold L., Oliver A., Smyth T., Somerfield P.J., Huse S., Joint I. The seasonal structure of microbial communities in the Western English Channel. Environ. Microbiol. 2009, 11:3132-3139.
26. Gilbert J.A., Steele J.A., Caporaso J.G., Steinbrück L., Reeder J., Temperton B., Huse S., McHardy A.C., Knight R., Joint I. Defining seasonal marine microbial community dynamics. ISME J. 2011, 6:298-308.
27. Giovannoni S.J., Hayakawa D.H., Tripp H.J., Stingl U., Givan S.A., Cho J.C., Oh H.M., Kitner J.B., Vergin K.L., Rappé M.S. The small genome of an abundant coastal ocean methylotroph. Environ. Microbiol. 2008, 10:1771-1782.
28. Giovannoni S.J., Vergin K.L. Seasonality in ocean microbial communities. Science 2012, 335:671-676.
29. Herfort L., Schouten S., Abbas B., Veldhuis M.J., Coolen M.J., Wuchter C., Boon J.P., Herndl G.J., Sinninghe Damsté J.S. Variations in spatial and temporal distribution of Archaea in the North Sea in relation to environmental variables. FEMS Microbiol. Ecol. 2007, 62:242-257.
30. Hollibaugh J.T., Gifford S.M., Moran M.A., Ross M.J., Sharma S., Tolar B.B. Seasonal variation in the metratranscriptomes of a Thaumarchaeota population from SE USA coastal waters. ISME J. 2013, 8:685-698.
31. Hu A., Jiao N., Zhang C.L. Community structure and function of planktonic Crenarchaeota: changes with depth in the South China Sea. Microb. Ecol. 2011, 62:549-563.
32. Hu A., Jiao N., Zhang R., Yang Z. Niche partitioning of marine group I Crenarchaeota in the euphotic and upper mesopelagic zones of the East China Sea. Appl. Environ. Microbiol. 2011, 77:7469-7478.
33. Jamieson R.E., Rogers A.D., Billett D.S.M., Smale D.A., Pearce D.A. Patterns of marine bacterioplankton biodiversity in the surface waters of the Scotia Arc, Southern Ocean. FEMS Microbiol. Ecol. 2012, 80:452-468.
34. Jiao N., Herndl G.J., Hansell D.A., Benner R., Kattner G., Wilhelm S.W., Kirchman D.L., Weinbauer M.G., Luo T., Chen F. Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean. Nat. Rev. Microbiol. 2010, 8:593-599.
35. Jiao N., Tang K., Cai H., Mao Y. Increasing the microbial carbon sink in the sea by reducing chemical fertilization on the land. Nat. Rev. Microbiol. 2010, 9:75.
36. Jing H., Zhang R., Pointing S.B., Liu H., Qian P. Genetic diversity and temporal variation of the marine Synechococcus community in the subtropical coastal waters of Hong Kong. Can. J. Microbiol. 2009, 55:311-318.
37. Karner M.B., DeLong E.F., Karl D.M. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 2001, 409:507-510.
38. Kirchman D.L., Dittel A.I., Malmstrom R.R., Cottrell M.T. Biogeography of major bacterial groups in the Delaware Estuary. Limnol. Oceanogr. 2005, 50:1697-1706.
39. Kirchman D.L., Keel R.G., Simon M., Welschmeyer N.A. Biomass and production of heterotrophic bacterioplankton in the oceanic subarctic Pacific. Deep Sea Res. Part I: Oceanogr. Res. Pap. 1993, 40:967-988.
40. Kong L., Jing H., Kataoka T., Sun J., Liu H. Phylogenetic diversity and spatio-temporal distribution of nitrogenase genes (nifH) in the northern South China Sea. Aquat. Microb. Ecol. 2011, 65:15-27.
41. Lee Chen Yl Spatial and seasonal variations of nitrate-based new production and primary production in the South China Sea. Deep Sea Res. Part I: Oceanogr. Res. Pap. 2005, 52:319-340.
42. Letunic I., Bork P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 2007, 23:127-128.
43. Lincoln S.A., Wai B., Eppley J.M., Church M.J., Summons R.E., DeLong E.F. Planktonic Euryarchaeota are a significant source of archaeal tetraether lipids in the ocean. Proc. Natl. Acad. Sci. 2014, 111:9858-9863.
44. Liu F., Tang S., Chen C. Impact of nonlinear mesoscale eddy on phytoplankton distribution in the northern South China Sea. J. Mar. Syst. 2013, 123:33-40.
45. Liu H., Jing H., Wong T.H., Chen B. Co-occurrence of phycocyanin-and phycoerythrin-rich Synechococcus in subtropical estuarine and coastal waters of Hong Kong. Environ. Microbiol. Rep. 2014, 6:90-99.
46. Liu K.K., Chao S.Y., Shaw P.T., Gong G.C., Chen C.C., Tang T. Monsoon-forced chlorophyll distribution and primary production in the South China Sea: observations and a numerical study. Deep Sea Res. Part I: Oceanogr. Res. Pap. 2002, 49:1387-1412.
47. Massana R., DeLong E.F., Pedrós-Alió C. A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Appl. Environ. Microbiol. 2000, 66:1777-1787.
48. Massana R., Murray A.E., Preston C.M., DeLong E.F. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Appl. Environ. Microbiol. 1997, 63:50-56.
49. Moeseneder M., Winter C., Arrieta J., Herndl G. Terminal-restriction fragment length polymorphism (T-RFLP) screening of a marine archaeal clone library to determine the different phylotypes. J. Microbiol. Methods 2001, 44:159-172.
50. Mou X., Sun S., Edwards R.A., Hodson R.E., Moran M.A. Bacterial carbon processing by generalist species in the coastal ocean. Nature 2008, 451:708-711.
51. Murray A., Preston C., Massana R., Taylor L., Blakis A., Wu K., DeLong E. Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica. Appl. Environ. Microbiol. 1998, 64:2585-2595.
52. Ortega-Retuerta E., Joux F., Jeffrey W.H., Ghiglione J.-F. Spatial variability of particle-attached and free-living bacterial diversity in surface waters from the Mackenzie River to the Beaufort Sea (Canadian Arctic). Biogeosci. Discuss. 2012, 9:17401-17435.
53. Partensky F., Blanchot J., Vaulot D. Differential distribution and ecology of Prochlorococcus and Synechococcus in oceanic waters: a review. Bull. Inst. Oceanogr. Monaco 1999, 19:457-476.
54. Partensky F., Hess W., Vaulot D. Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiol. Mol. Biol. Rev. 1999, 63:106-127.
55. Pedrós-Alió C. Marine microbial diversity: can it be determined?. Trends Microbiol. 2006, 14:257-263.
56. Platt T., Rao D.S., Irwin B. Photosynthesis of picoplankton in the oligotrophic ocean. Nature 1983, 301:702-704.
57. Riemann L., Leitet C., Pommier T., Simu K., Holmfeldt K., Larsson U., Hagström Å. The native bacterioplankton community in the central Baltic Sea is influenced by freshwater bacterial species. Appl. Environ. Microbiol. 2008, 74:503-515.
58. Ruiz-González C., Lefort T., Martí G., Montserrat Sala M., Sommaruga R., Simó R., Gasol J.M. Seasonal patterns in the sunlight sensitivity of bacterioplankton from Mediterranean surface coastal waters. FEMS Microbiol. Ecol. 2011, 79:661-674.
59. Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., Lesniewski R.A., Oakley B.B., Parks D.H., Robinson C.J. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 2009, 75:7537-7541.
60. Sogin M.L., Morrison H.G., Huber J.A., Welch D.M., Huse S.M., Neal P.R., Arrieta J.M., Herndl G.J. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc. Natl. Acad. Sci. 2006, 103:12115-12120.
61. Song X., Lai Z., Ji R., Chen C., Zhang J., Huang L., Yin J., Wang Y., Lian S., Zhu X. Summertime primary production in northwest South China Sea: interaction of coastal eddy, upwelling and biological processes. Cont. Shelf Res. 2012, 48:110-121.
62. Su J. Overview of the South China Sea circulation and its influence on the coastal physical oceanography outside the Pearl River Estuary. Cont. Shelf Res. 2004, 24:1745-1760.
63. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
64. Winter C., Kerros M.E., Weinbauer M.G. Seasonal changes of bacterial and archaeal communities in the dark ocean: evidence from the Mediterranean Sea. Limnol. Oceanogr. 2009, 54:160.
65. Xie S.P., Xie Q., Wang D., Liu W.T. Summer upwelling in the South China Sea and its role in regional climate variations. J. Geophys. Res. - Ocean. (1978-2012) 2003, 108:3261.
66. Yan S., Fuchs B.M., Lenk S., Harder J., Wulf J., Jiao N.Z., Amann R. Biogeography and phylogeny of the NOR5/OM60 clade of Gammaproteobacteria. Syst. Appl. Microbiol. 2009, 32:124-139.
67. Yeo S.K., Huggett M.J., Eiler A., Rappé M.S. Coastal bacterioplankton community dynamics in response to a natural disturbance. PloS One 2013, 8:e56207.
68. Yin Q., Fu B., Li B., Shi X., Inagaki F., Zhang X.-H. Spatial variations in microbial community composition in surface seawater from the ultra-oligotrophic center to rim of the South Pacific Gyre. PloS One 2013, 8:e55148.
69. Yu Y., Lee C., Kim J., Hwang S. Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. Biotechnol. Bioeng. 2005, 89:670-679.
70. Yuan X., He L., Yin K., Pan G., Harrison P.J. Bacterial distribution and nutrient limitation in relation to different water masses in the coastal and northwestern South China Sea in late summer. Cont. Shelf Res. 2011, 31:1214-1223.
71. Yuan Y., Liao G., Yang C., Liu Z., Chen H., Wang Z.-G. Summer Kuroshio Intrusion through the Luzon Strait confirmed from observations and a diagnostic model in summer 2009. Prog. Oceanogr. 2014, 121:44-59.
72. 2 fluxes in the largest tropical marginal sea (South China Sea) based on multiple-year underway measurements. Biogeosciences 2013, 10:7775-7791.
73. Zhou W., Long A., Jiang T., Chen S., Huang L., Huang H., Cai C., Yan Y. Bacterioplankton dynamics along the gradient from highly eutrophic Pearl River Estuary to oligotrophic northern South China Sea in wet season: implication for anthropogenic inputs. Mar. Pollut. Bull. 2011, 62:726-733.
74. Zwirglmaier K., Jardillier L., Ostrowski M., Mazard S., Garczarek L., Vaulot D., Not F., Massana R., Ulloa O., Scanlan D.J. Global phylogeography of marine Synechococcus and Prochlorococcus reveals a distinct partitioning of lineages among oceanic biomes. Environ. Microbiol. 2008, 10:147-161.