Spatial Variations in Microbial Community Composition in Surface Seawater from the Ultra-Oligotrophic Center to Rim of the South Pacific Gyre

PLoS ONE

Volumn 8, Issue 2, 2013, Pages

  Yin, Qi ^a   Fu, Bingbing ^a   Li, Bingyu ^a   Shi, Xiaochong ^a   Inagaki, Fumio ^b   Zhang, Xiao Hua ^a  

^a OCEAN UNIVERSITY OF CHINA   (China)

^b JAPAN AGENCY FOR MARINE EARTH SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; SEA WATER;

ARTICLE; BACTERIUM CULTURE; BACTERIUM DETECTION; BACTERIUM ISOLATE; BIOGEOGRAPHY; COMMUNITY STRUCTURE; CONTROLLED STUDY; CRENARCHAEOTA; CYANOBACTERIUM; ENVIRONMENTAL FACTOR; EURYARCHAEOTA; GENE LIBRARY; GENE SEQUENCE; MICROBIAL COMMUNITY; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PACIFIC OCEAN; PROTEOBACTERIA; REAL TIME POLYMERASE CHAIN REACTION; RNA GENE; SEA SURFACE WATERS; SPECIES DISTRIBUTION; SPECIES DIVERSITY; SPECIES DOMINANCE; SPECIES RICHNESS; UNINDEXED SEQUENCE; WATER SAMPLING; ARCHAEON; BACTERIA; BIOTA; ECOSYSTEM; GENETICS; MICROBIOLOGY; PHYLOGENY; PROCEDURES;

ARCHAEA; BACTERIA; BIOTA; ECOSYSTEM; PACIFIC OCEAN; PHYLOGENY; REAL-TIME POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEAWATER;

EID: 84873533296     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0055148     Document Type: Article

References (56)

1. Claustre H, Maritorena S, (2003) The many shades of ocean blue. Science 302: 1514-1515.
2. Ras J, Claustre H, Uitz J, (2008) Spatial variability of phytoplankton pigment distributions in the subtropical South Pacific Ocean: comparison between in situ and predicted data. Biogeosciences 5: 353-369.
3. Morel A, Gentili B, Claustre H, Babin M, Bricaud A, et al. (2007) Optical properties of the "clearest" natural waters. Limnol Oceanogr 52: 217-229.
4. D'Hondt S, Spivack AJ, Pockalny R, Ferdelman TG, Fischer JP, et al. (2009) Subseafloor sedimentary life in the South Pacific Gyre. Proc Natl Acad Sci USA 106: 11651-11656.
5. Lami R, Cottrell MT, Ras J, Ulloa O, Obernosterer I, et al. (2007) High abundances of aerobic anoxygenic photosynthetic aacteria in the South Pacific Ocean. Appl Environ Microbiol 73: 4198-4205.
6. Halm H, Lam P, Ferdelman TG, Lavik G, Dittmar T, et al. (2012) Heterotrophic organisms dominate nitrogen fixation in the South Pacific Gyre. ISME J 6: 1238-1249.
7. Collins RE, Rocap G, Deming JW, (2010) Persistence of bacterial and archaeal communities in sea ice through an Arctic winter. Environ Microbiol 12: 1828-1841.
8. Lane DJ (1991) 16S/23S sequencing. In: Stackebrandt E, Goodfellow M, editors. Nucleic Acid Techniques in Bacterial Systematics. Wiley: Chichester, UK, 115-176.
9. DeLong EF, (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89: 5685-5689.
10. Thompson JR, Marcelino LA, Polz MF, (2002) Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'. Nucleic Acids Res 30: 2083-2088.
11. Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, et al. (2003) The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31: 442-443.
12. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2011) GenBank. Nucleic Acids Res 39 (Database issue): D32-D37.
13. Altschul S, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
14. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
15. 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.
16. Chao A, Lee SM, (1992) Estimating the number of classes via sample coverage. J Am Stat Assoc 87: 210-217.
17. Kemp PF, Aller JY, (2004) Bacterial diversity in aquatic and other environments: what 16S rDNA libraries can tell us. FEMS Microbiol Ecol 47: 161-177.
18. Zhang W, Ki JS, Qian PY, (2008) Microbial diversity in polluted harbor sediments I: bacterial community assessment based on four clone libraries of 16S rDNA. Estuar Coast Shelf Sci 76: 668-681.
19. Dang H, Li TG, Chen MN, Huang GQ, (2008) Cross-ocean distribution of Rhodobacterales bacteria as primary surface colonizers in temperate coastal marine waters. Appl Environ Microbiol 74: 52-60.
20. Lozupone CA, Hamady M, Kelley ST, Knight R, (2007) Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 73: 1576-1585.
21. ter Braak CJF, Šmilauer P (2002) CANOCO Reference Manualand CanoDraw for Windows User's Guide: Software for Canonical Community Ordination (version 4.5). Ithaca, NY: Microcomputer Power.
22. Kimura M, (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120.
23. Saitou N, Nei M, (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
24. Wang Q, Garrity GM, Tiedje JM, Cole JR, (2007) Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Appl Environ Microbiol 73: 5261-5267.
25. Suzuki MT, Taylor LT, Delong EF, (2000) Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5′-nuclease assays. Appl Environ Microbiol 66: 4605-4614.
26. Fierer N, Jackson JA, Vilgalys R, Jackson RB, (2005) Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Appl Environ Microbiol 71: 4117-4120.
27. Lozupone C, Knight R, (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235.
28. Montoya JP, Holl CM, Zehr JP, Hansen A, Villareal TA, et al. (2004) High rates of N2 fixation by unicellular diazotrophs in the oligotrophic Pacific Ocean. Nature 430: 1027-1031.
29. Voss M, Croot P, Lochte K, Mills M, Peeken I (2004) Patterns of nitrogen fixation along 10°N in the tropical Atlantic. Geophys Res Lett 31: doi:10.1029/2004 GL020127.
30. Labrenz M, Brettar I, Christen R, Flavier S, Bötel J, et al. (2004) Development and application of a Real-Time PCR approach for quantification of uncultured bacteria in the central Baltic Sea. Appl Environ Microbiol 70: 4971-4979.
31. Sahm K, Berninger UG, (1998) Abundance, vertical distribution, and community structure of benthic prokaryotes from permanently cold marine sediments (Svalbard, Arctic Ocean). Mar Ecol Prog Ser 165: 71-80.
32. Pei AY, Oberdorf WE, Nossa CW, Agarwal A, Chokshi P, et al. (2010) Diversity of 16S rRNA genes within individual prokaryotic genomes. Appl Environ Microbiol 76: 3886-3897.
33. Brown MV, Philip GK, Bunge JA, Smith MC, Bissett A, et al. (2009) Microbial community structure in the North Pacific ocean. ISME J 3: 1374-1386.
34. Campbell BJ, Yu L, Heidelberg JF, Kirchman DL, (2011) Activity of abundant and rare bacteria in a coastal ocean. Proc Natl Acad Sci USA 108: 12776-12781.
35. Qian PY, Wang Y, Lee OO, Lau SCK, Yang J, et al. (2011) Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing. ISME J 5: 507-518.
36. 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.
37. Kirchman DL, Dittel AI, Malmatrom RR, Cottrell MT, (2005) Biogeography of major bacterial groups in the Delaware Estuary. Limnol Oceanogr 50: 1697-1706.
38. Cottrell MT, Kirchman DL, (2000) Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization. Appl Environ Microbiol 66: 5116-5122.
39. Shaw AK, Halpern AL, Beeson K, Tran B, Venter JC, et al. (2008) It's all relative: ranking the diversity of aquatic bacterial communities. Environ Microbiol 10: 2200-2210.
40. Orcutt BN, Sylvan JB, Knab NJ, Edwards KJ, (2011) Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol Mol Biol Rev 75: 361-422.
41. Bowman JS, Rasmussen S, Blom N, Deming JW, Rysgaard S, et al. (2012) Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene. ISME J 6: 11-20.
42. Karner MB, Delong EF, Karl DM, (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409: 507-510.
43. Könneke M, Bernhard AE, Torre JR, Walker CB, Waterbury JB, et al. (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437: 543-546.
44. Kwon KK, Lee HS, Yang SH, Kim SJ, (2005) Kordiimonas gwangyangensis gen. nov., sp. nov., a marine bacterium isolated from marine sediments that forms a distinct phyletic lineage (Kordiimonadales ord. nov.) in the 'Alphaproteobacteria'. Int J Syst Evol Microbiol 55: 2033-2037.
45. Basse HJ, Auling G (2005) Genus II. Achromobacter Yabuuchi and Yano 1981, 477VP emend. Yabuuchi, Kawamura, Kosako and Ezaki 1998a, 1083. In: Garrity GM, editor. Bergey's Manual of Systamatic Bacteriology, 2nd edn. Vol. 2: The Proteobacteria. New York: Springer-Verlag. 658-662.
46. Park M, Kim C, Yang J, Lee H, Shin W, et al. (2005) Isolation and characterization of diazotrophic growth promoting bacteria from rhizosphere of agricultural crops of Korea. Microbiol Res 160: 127-133.
47. D'Hondt S, Jørgensen BB, Miller DJ, Batzke A, Blake R, et al. (2004) Distributions of microbial activities in deep subseafloor sediments. Science 306: 2216-2221.
48. D'Hondt S, Abrams LJ, Anderson R, Dorrance J, Durbin A, et al. (2011) SKNOX-02RR: drilling site survey-life in subseafloor sediments of the South Pacific Gyre. Proc IODP 329. Available: http://publications.iodp.org/proceedings/329/EXP_REPT/CHAPTERS/329_112.PDF.
49. Muyzer G, Waal EC, Uitterlinden AG, (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 695-700.
50. Overmann J, Coolen MJL, Tuschak C, (1999) Specific detection of different phylogenetic groups of chemocline bacteria based on PCR and denaturing gradient gel electrophoresis of 16S rRNA gene fragments. Arch Microbiol 172: 83-94.
51. Stach JEM, Maldonado LA, Ward AC, Goodfellow M, Bull AT, (2003) New primers for the class Actinobacteria: application to marine and terrestrial environments. Environ Microbiol 5: 828-841.
52. Manz W, Amann R, Ludwig W, Vancanneyt M, Schleifer K-H, (1996) Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment. Microbiology 142: 1097-1106.
53. Meier H, Amann R, Ludwig W, Schleifer K-H, (1999) Specific oligonucleotide probes for in situ detection of a major group of gram-positive bacteria with low DNA G+C content. Syst Appl Microbiol 22: 186-196.
54. Nubel U, Garcia-Pichel F, Muyzer G, (1997) PCR primers to amplify 16S rRNA genes from cyanobacteria. Appl Environ Microbiol 63: 3327-3332.
55. Vetriani C, Tran HV, Kerkhof LJ, (2003) Fingerprinting microbial assemblages from the oxic/anoxic chemocline of the Black Sea. Appl Environ Microbiol 69: 6481-6488.
56. Moissl C, Rudolph C, Rachel R, Koch M, Huber R, (2003) In situ growth of the novel SM1 euryarchaeon from a string-of pearls-like microbial community in its cold biotope, its physical separation and insights into its structure and physiology. Arch Microbiol 180: 211-217.