Phylogenetic diversity of planktonic archaea in the estuarine region of East China Sea

Microbiological Research

Volumn 162, Issue 1, 2007, Pages 26-36

  Zeng, Yonghui ^a   Li, Heyang ^a   Jiao, Nianzhi ^a  

^a XIAMEN UNIVERSITY   (China)

Author keywords

16S rDNA analysis; East China Sea; Phylogenetic diversity; Planktonic archaea; RFLP

Indexed keywords

BIODIVERSITY; CLONING; ECOSYSTEMS; ESTUARIES; GENETIC ENGINEERING; MARINE BIOLOGY;

PHYLOGENETIC DIVERSITY; PLANKTONIC ARCHAEA; POLYMORPHISM; RDNA ANALYSIS;

PLANTS (BOTANY);

COMMUNITY STRUCTURE; DOMINANCE; ESTUARINE ECOSYSTEM; FUNCTIONAL ROLE; GENETIC ANALYSIS; MICROBIAL COMMUNITY; PHYLOGENETICS; PLANKTON; POLYMERASE CHAIN REACTION; PROKARYOTE; RELATEDNESS; RNA; SPECIES DIVERSITY;

ASIA; CHINA; EAST CHINA SEA; EURASIA; FAR EAST; PACIFIC OCEAN; YANGTZE ESTUARY;

ARCHAEA; CANDIDATUS NITROSOPUMILUS MARITIMUS; CRENARCHAEOTA; EURYARCHAEOTA; MARINE GROUP II;

EID: 33846053229     PISSN: 09445013     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.micres.2006.03.007     Document Type: Article

References (36)

1. Achenbach L., and Woese C.R. 16S and 23S rRNA-like primers. In: Sower K.R., and Schreier H.J. (Eds). Archaea-A Laboratory Manual (1995), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York 521-523
2. Amann R.I., Ludwig W., and Schleifer H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59 (1995) 143-169
3. Barns S.M., Delwiche C.F., Palmer J.D., and Pace N.R. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc. Natl. Acad. Sci. USA 93 (1996) 9188-9193
4. DeLong E.F. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89 (1992) 5685-5689
5. DeLong E.F. Everything in moderation: archaea as 'non-extremophiles'. Curr. Opin. Genet. Dev. 8 (1998) 649-654
6. DeLong E.F. Oceans of archaea. ASM News 69 (2003) 503-511
7. DeLong E.F., Wu K.Y., Prezelin B.B., and Jovine R.V. High abundance of archaea in Antarctic marine picoplankton. Nature 371 (1994) 695-697
8. Eder W., Schmidt M., Koch M., Garbe-Schonberg D., and Huber R. Prokaryotic phylogenetic diversity and corresponding geochemical data of the brine-seawater interface of the Shaban Deep, Red Sea. Environ. Microbiol. 4 (2002) 758-763
9. Fuhrman J.A., and Davis A.A. Widespread archaea and novel bacteria from the deep sea as shown by 16s rRNA gene sequences. Mar. Ecol. Progr. Ser. 150 (1997) 275-285
10. Fuhrman J.A., McCallum K., and Davis A.A. Novel major archaebacterial group from marine plankton. Nature 356 (1992) 148-149
11. Fuhrman J.A., McCallum K., and Davis A.A. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl. Environ. Microbiol. 59 (1993) 1294-1302
12. Gordon D.A., and Giovannoni S.J. Detection of stratified microbial populations related to Chlorobium and Fibrobacter species in the Atlantic and Pacific oceans. Appl. Environ. Microbiol. 62 (1996) 1171-1177
13. JGOFS, 1996. Protocols for the Joint Global Ocean Flux studies (JGOFS) core measurements. Report No. 19. JGOFS International Project Office Center for Studies of Environment and Resources, Bergen, Norway, pp. 119-122.
14. Jiao N.Z., Yang Y.H., Koshigawa H., and Watanabe M. Influence of hydrographic conditions on picoplankton distribution in the East China Sea, a marginal sea of the Northwest Pacific. Aquat. Microb. Ecol. 30 (2002) 37-48
15. Jiao N.Z., Yang Y.H., Hong N., Ma Y., Harada S., Koshikawaa H., and Watanabe M. Dynamics of autotrophic picoplankton and heterotrophic bacteria in the East China Sea. Cont. Shelf Res. 25 (2005) 1265-1279
16. Karner M., DeLong E.F., and Karl D.M. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409 (2001) 507-510
17. Kelly K.M., and Chistoserdov A.Y. Phylogenetic analysis of the succession of bacterial communities in the Great South Bay (Long Island). FEMS Microbiol. Ecol. 35 (2001) 85-95
18. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16 (1980) 111-120
19. Konneke M., Bernhard A.E., Torre J.R., Walker C.B., Waterbury J.B., and Stahl D.A. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437 (2005) 543-546
20. Massana R., Murray A.E., Preston C.M., and DeLong E.F. Vertical distribution and phylogenetic characterization of marine planktonic archaea in the Santa Barbara Channel. Appl. Environ. Microbiol. 63 (1997) 50-56
21. Massana R., DeLong E.F., and Pedrós-Alió C. A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Appl. Environ. Microbiol. 66 (2000) 1777-1787
22. Moyer C.L., Dobbs F.C., and Karl D.M. Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Appl. Environ. Microbiol. 60 (1994) 871-879
23. Mullins T.D., Britschgi T.B., Krest R.L., and Giovannoni S.J. Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol. Oceanogr. 40 (1995) 148-158
24. Porter K.G., and Feig Y.C. The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr. 25 (1980) 943-948
25. Saitou N., and Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4 (1987) 406-425
26. Schallenberg M., Kalff J., and Rasmussen J.B. Solutions to problems in enumerating sediment bacteria by direct counts. Appl. Environ. Microbiol. 55 (1989) 1214-1219
27. Schloss P.D., and Handelsman J. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71 (2005) 1501-1506
28. Shao P., Chen Y.Q., Zhou H., Qu L.H., Ma Y., Li H.Y., and Jiao N.Z. Phylogenetic diversity of archaea in prawn farm sediment. Mar. Biol. 146 (2005) 133-142
29. Takai K., and Sako Y. A molecular view of archaeal diversity in marine and terrestrial hot water environments. FEMS Microbiol. Ecol. 28 (1999) 177-188
30. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res. 24 (1997) 4876-4882
31. Urakawa H., Kita-Tsukamoto K., and Ohwada K. Reassessment of the taxonomic position of Vibrio iliopiscarius (Onarheim et al. 1994) and proposal for Photobacterium iliopiscarium comb. nov. Int. J. Syst. Bacteriol. 49 (1999) 257-260
32. Urakawa H., Kita-Tsukamoto K., and Ohwada K. Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis. Microbiology 145 (1999) 3305-3315
33. Wang P., Wang F.P., Xu M.X., and Xiao X. Molecular phylogeny of methylotrophs in a deep-sea sediment from a tropical west Pacific warm pool. FEMS Microbiol. Ecol. 47 (2004) 77-84
34. Woese C.R. Bacterial evolution. Microbiol. Rev. 51 (1987) 221-271
35. Woese C.R., Kandler O., and Wheelis M.L. Towards a natural system of organisms: proposal for the domains archaea, bacteria and eucarya. Proc. Natl. Acad. Sci. USA 87 (1990) 4576-4579
36. Xu M.X., Wang F.P., and Xiao X. Analysis of archaeal 16S rDNA in the deep sea sediments. Progr. Nat. Sci. 13 (2003) 598-603