Seasonal dynamics of marine microbial community in the South Sea of Korea

PLoS ONE

Volumn 10, Issue 6, 2015, Pages

  Suh, Sung Suk ^a   Park, Mirye ^a,b   Hwang, Jinik ^a,b   Kil, Eui Joon ^c   Jung, Seung Won ^a   Lee, Sukchan ^c   Lee, Taek Kyun ^a,b  

^a Korea Research Institute of Ships and Ocean Engineering   (South Korea)

^b University of Science and Technology (UST)   (South Korea)

^c Sungkyunkwan University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

CHLOROPHYLL A; NITRATE; PHOSPHATE; RNA 16S; SILICON DIOXIDE; SEA WATER;

ACTINOBACTERIA; ALPHAPROTEOBACTERIA; ARCOBACTER; ARTICLE; COMMUNITY STRUCTURE; CONTROLLED STUDY; ENVIRONMENTAL FACTOR; EPSILONPROTEOBACTERIA; FLAVOBACTERIA; GAMMAPROTEOBACTERIA; GLACIECOLA; KOREA; MICROBIAL COMMUNITY; NONHUMAN; PELAGIBACTER; PSEDOALTEROMONADACEAE; PYROSEQUENCING; SEASONAL VARIATION; VIBRIONACEAE; BACTERIUM; BIODIVERSITY; CLASSIFICATION; CLUSTER ANALYSIS; GENETICS; MICROBIOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; SEASON; SOUTH KOREA;

ACTINOBACTERIA; ALPHAPROTEOBACTERIA; ARCOBACTER; BACTERIA (MICROORGANISMS); CANDIDATUS PELAGIBACTER; EPSILONPROTEOBACTERIA; FLAVOBACTERIA; GAMMAPROTEOBACTERIA; GLACIECOLA; OTUS; VIBRIONACEAE;

BACTERIA; BIODIVERSITY; CLUSTER ANALYSIS; EVOLUTION, MOLECULAR; PHYLOGENY; REPUBLIC OF KOREA; RNA, RIBOSOMAL, 16S; SEASONS; SEAWATER; WATER MICROBIOLOGY;

EID: 84938703534     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0131633     Document Type: Article

References (47)

1. Chapin FS III, Zavaleta ES, Eviner VT, Naylor RL, Vitousek PM, Reynolds HL, et al. Consequences of changing biodiversity. Nature. 2000; 405(6783):234-42. doi: 10.1038/35012 241 PMID: 10821284
2. Suh S-S, Park M, Hwang J, Lee S, Chung Y, Lee T-K. Distinct patterns of marine bacterial communities in the South and North Pacific Oceans. Journal of Microbiology. 2014; 52(10):834-41. doi: 10.1007/s12275-014-4287-6
3. Nemergut DR, Costello EK, Hamady M, Lozupone C, Jiang L, Schmidt SK, et al. Global patterns in the biogeography of bacterial taxa. Environmental microbiology. 2011; 13(1):135-44. doi: 10.1111/j.1462- 2920.2010.02315.x PMID: 21199253
4. Sterner R, Elser J. Ecological stoichiometry: the biology of elements from molecules to the biosphere The University of Chicago Press Princeton. New Jersey. 2002.
5. Caron DA. New accomplishments and approaches for assessing protistan diversity and ecology in natural ecosystems. Bioscience. 2009; 59(4):287-99. doi: 10.1525/bio.2009.5 9.4.7
6. Fuhrman JA. Microbial community structure and its functional implications. Nature. 2009; 459(7244):193-9. doi: 10.1038/nature08058 PMID: 19444205
7. Aravindraja C, Viszwapriya D, Pandian SK. Ultradeep 16S rRNA sequencing analysis of geographically similar but diverse unexplored marine samples reveal varied bacterial community composition. 2013. doi: 10.1371/journal.pone.0076724
8. Yang C, Li Y, Zhou B, Zhou Y, Zheng W, Tian Y, et al. Illumina sequencing-based analysis of free-living bacterial community dynamics during an Akashiwo sanguine bloom in Xiamen sea, China. Scientific reports. 2015; 5. doi: 10.1038/srep08476
9. Emami K, Askari V, Ullrich M, Mohinudeen K, Anil AC, Khandeparker L, et al. Characterization of bacteria in ballast water using MALDI-TOF mass spectrometry. PloS one. 2012; 7(6):e38515. doi: 10.1371/journal.pone.0038515 PMID: 22685576
10. Ganesh S, Parris DJ, DeLong EF, Stewart FJ. Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone. The ISME journal. 2014; 8(1):187-211. doi: 10.1038/ismej.2013.144 PMID: 24030599
11. Ladau J, Sharpton TJ, Finucane MM, Jospin G, Kembel SW, O'Dwyer J, et al. Global marine bacterial diversity peaks at high latitudes in winter. The ISME journal. 2013; 7(9):16 69-77. doi: 10.1038/ismej.2013.37
12. Lee OO, Wang Y, Yang J, Lafi FF, Al-Suwailem A, Qian P-Y. Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea. The ISME journal. 2011; 5(4):650-64. doi: 10.1038/ismej.2010.165 PMID: 21085196
13. Fierer N, Jackson RB. The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences of the United States of America. 200 6; 103(3):626-31. doi: 10.1073/pnas.0507535103 PMID: 16407148
14. Rusch D, Halpern A, Sutton G, Heidelberg K, Williamson S. The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern. 2007. doi: 10.1371/journa l.pbio.0050077
15. Rocap G, Distel DL, Waterbury JB, Chisholm SW. Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences. Applied and Environmental Microbiology. 2002; 68(3):1180-91. doi: 10.1128/AEM.68.3.1180-1191.2002 PMID: 11872466
16. Selje N, Simon M, Brinkhoff T. A newly discovered Roseobacter cluster in temperate and polar oceans. Nature. 2004; 427(6973):445-8. doi: 10.1038/nature02272 PMID: 14749832
17. Chow C-ET, Sachdeva R, Cram JA, Steele JA, Needham DM, Patel A, et al. Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight. The ISME journal. 2013; 7(12):2259-73. doi: 10.1038/ismej.2013.122 PMID: 23864126
18. Fuhrman JA, Hewson I, Schwalbach MS, Steele JA, Brown MV, Naeem S. Annually reoccurring bacterial communities are predictable from ocean conditions. Proceedings of the National Academy of Sciences. 2006; 103(35):13104-9. doi: 10.1073/pnas.0602399103
19. Morris RM, Vergin KL, Cho J-C, Rappé MS, Carlson CA, Giovannoni SJ. Temporal and spatial response of bacterioplankton lineages to annual convective overturn at the Bermuda Atlantic Time-Series Study Site. Limnology and Oceanography. 2005; 50(5):1687-96. doi: 10.4319/lo.2005.50.5.1687
20. Gilbert JA, Field D, Swift P, Newbold L, Oliver A, Smyth T, et al. The seasonal structure of microbial communities in the Western English Channel. Environmental microbiology. 2009; 11(12):3132-9. doi: 10.1111/j.1462-2920.2009.02017.x PMID: 19659500
21. Nedwell D, Rutter M. Influence of temperature on growth rate and competition between two psychrotolerant Antarctic bacteria: low temperature diminishes affinity for substrate uptake. Applied and Environmental Microbiology. 1994; 60(6):1984-92. doi: 0099-2240/94$01.00+0. PMID: 8031092
22. Church MJ. Resource control of bacterial dynamics in the sea. Microbial Ecology of the Oceans, Second Edition. 2008:335-82. doi: 10.1002/9780470281840.ch10
23. Fuhrman JA, Steele JA, Hewson I, Schwalbach MS, Brown MV, Green JL, et al. A latitudinal diversity gradient in planktonic marine bacteria. Proceedings of the National Academy of Sciences. 2008; 105(22):7774-8. doi: 10.1073/pnas.0803070105
24. Chong C, Pearce D, Convey P, Tan I. The identification of environmental parameters which could influence soil bacterial community composition on the Antarctic Peninsula-a statistical approach. Antarctic Science. 2012; 24(03):249-58. doi: 10.1017/S0954102012000 028
25. Tinta T, Vojvoda J, Mozetič P, Talaber I, Vodopivec M, Malfatti F, et al. Bacterial community shift is induced by dynamic environmental parameters in a changing coastal ecosystem (northern Adriatic, northeastern Mediterranean Sea)-a 2-year time-series study. Environmental microbiology. 2014. doi: 10.1111/1462-2920.12519
26. Humphrey G, Jeffrey S. Tests of accuracy of spectrophotometric equations for the simultaneous determination of chlorophylls a, b, c1 and c2. Phytoplankton Pigments in Oceanography: Guidelines to Modern Methods Monographs on Oceanographic Methodology. 1997; 10:616-21.
27. Kuehn JS, Gorden PJ, Munro D, Rong R, Dong Q, Plummer PJ, et al. Bacterial community profiling of milk samples as a means to understand culture-negative bovine clinical mastitis. 2013. doi: 10.1371/journal.pone.0061959
28. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic acids research. 2007; 35(21):7188-96. doi: 10.1093/nar/gkm864 PMID: 17947321
29. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology. 2007; 73(16):5261-7. doi: 10.1128/AEM.00062-07 PMID: 17586664
30. Hamady M, Lozupone C, Knight R. Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. The ISME journal. 2010; 4(1):17-27. doi: 10.1038/ismej.2009.97 PMID: 19710709
31. Lozupone CA, Hamady M, Kelley ST, Knight R. Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities. Applied and Environmental Microbiology. 2007; 73(5):1576-85. doi: 10.1128/AEM.01996-06 PMID: 17220268
32. Kim M, Yoon H, Kim Y, Kim Y, Kong W, Kim J. Comparative analysis of bacterial diversity and communities inhabiting the fairy ring of Tricholoma matsutake by barcoded pyrosequencing. Journal of applied microbiology. 2014; 117(3):699-710. doi: 10.1111/jam.12572 PMID: 24922184
33. Yi H, Yong D, Lee K, Cho Y-J, Chun J. Profiling bacterial community in upper respiratory tracts. BMC infectious diseases. 2014; 14(1):583. doi: 10.1186/s12879-014-0583-3
34. Harley CD, Randall Hughes A, Hultgren KM, Miner BG, Sorte CJ, Thornber CS, et al. The impacts of climate change in coastal marine systems. Ecology letters. 2006; 9(2):228-41. doi: 10.1111/j.1461-0248.2005.00871.x PMID: 16958887
35. Harvell C, Kim K, Burkholder J, Colwell R, Epstein PR, Grimes D, et al. Emerging marine diseases-climate links and anthropogenic factors. Science. 1999; 285(5433):1505-10. doi: 10.1126/science.285.5433.1505 PMID: 10498537
36. Lehtoranta J, Ekholm P, Pitkänen H. Coastal eutrophication thresholds: a matter of sediment microbial processes. AMBIO: A Journal of the Human Environment. 2009; 38(6):303-8. doi: 10.1579/09-A-656.1
37. Smith VH. Eutrophication of freshwater and coastal marine ecosystems a global problem. Environmental Science and Pollution Research. 2003; 10(2):126-39. PMID: 12729046
38. Giovannoni SJ, Vergin KL. Seasonality in ocean microbial communities. Science. 2012; 335(6069):671-6. doi: 10.1126/science.1198078 PMID: 22323811
39. Campbell BJ, Kirchman DL. Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient. The ISME journal. 2013; 7(1):210-20. doi: 10.1038/ismej.2012.93 PMID: 22895159
40. Pommier T, Canbäck B, Riemann L, Boström K, Simu K, Lundberg P, et al. Global patterns of diversity and community structure in marine bacterioplankton. Molecular ecology. 2007; 16(4):867-80. doi: 10.1111/j.1365-294X.2006.03189.x PMID: 17284217
41. Ghiglione J, Murray A. Pronounced summer to winter differences and higher wintertime richness in coastal Antarctic marine bacterioplankton. Environmental microbio logy. 2012; 14(3):617-29. doi: 10.1111/j.1462-2920.2011.02601.x
42. Barz M, Beimgraben C, Staller T, Germer F, Opitz F, Marquardt C, et al. Distribution analysis of hydrogenases in surface waters of marine and freshwater environments. 2010. doi: 10.1371/journal.pone.0013846
43. Johnson ZI, Zinser ER, Coe A, McNulty NP, Woodward EMS, Chisholm SW. Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science. 2006; 311(5768):1737-40. doi: 10.1126/science.1118052 PMID: 16556835
44. Lindström ES. Investigating influential factors on bacterioplankton community composition: results from a field study of five mesotrophic lakes. Microbial Ecology. 2001; 42(4):598-605. doi: 10.1007/s00248-001-0031-y PMID: 12024242
45. Brinkmeyer R, Knittel K, Jürgens J, Weyland H, Amann R, Helmke E. Diversity and structure of bacterial communities in Arctic versus Antarctic pack ice. Applied and Environmental Microbiology. 2003; 69(11):6610-9. doi: 10.1128/AEM.69.11.6610-6619.2003 PMID: 14602620
46. Motes M, DePaola A, Cook D, Veazey J, Hunsucker J, Garthright W, et al. Influence of Water Temperature and Salinity onVibrio vulnificus in Northern Gulf and Atlantic Coast Oysters (Crassostrea virginica). Applied and Environmental Microbiology. 1998; 64(4):1459-65. doi: 0099-2240/98/$04.0010. PMID: 9546182
47. Johnson C, Flowers A, Noriea N, Zimmerman A, Bowers J, DePaola A, et al. Relationships between environmental factors and pathogenic Vibrios in the Northern Gulf of Mexico. Applied and Environmental Microbiology. 2010; 76(21):7076-84. doi: 10.1128/AEM.00697-10 PMID: 20817802