Diversity of bacterioplankton in contrasting Tibetan lakes revealed by high-density microarray and clone library analysis

FEMS Microbiology Ecology

Volumn 86, Issue 2, 2013, Pages 277-287

  Zhang, Rui ^a,b   Wu, Qinglong ^a,c   Piceno, Yvette M ^d   Desantis, Todd Z ^d   Saunders, F Michael ^a   Andersen, Gary L ^d   Liu, Wen Tso ^a,e  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b XIAMEN UNIVERSITY   (China)

^c NANJING INSTITUTE OF GEOGRAPHY AND LIMNOLOGY   (China)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^e University of Illinois at Urbana Champaign   (United States)

Author keywords

Microbial diversity; PhyloChip; Tibetan lakes

Indexed keywords

RNA 16S;

BACTERIOPLANKTON; CLONE; COMMUNITY STRUCTURE; DNA FINGERPRINTING; GENE; LAKE ECOSYSTEM; MOUNTAIN; RELATIVE ABUNDANCE; SALINE LAKE; SALINITY; SELECTION; SPECIES DIVERSITY; TAXONOMY; WATER CHEMISTRY;

ALTITUDE; ARTICLE; BACTERIUM; BIODIVERSITY; CHEMISTRY; CHINA; CLASSIFICATION; DNA MICROARRAY; ECOSYSTEM; GENE LIBRARY; GENETICS; ISOLATION AND PURIFICATION; LAKE; MICROBIAL DIVERSITY; MICROBIOLOGY; PHYLOCHIP; PHYLOGENY; PLANKTON; SALINITY; TIBETAN LAKES;

MICROBIAL DIVERSITY; PHYLOCHIP; TIBETAN LAKES;

ALTITUDE; BACTERIA; BIODIVERSITY; ECOSYSTEM; GENE LIBRARY; LAKES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; PLANKTON; RNA, RIBOSOMAL, 16S; SALINITY; TIBET;

CHINA; QINGHAI; QINGHAI LAKE;

BACTERIA (MICROORGANISMS);

EID: 84885952760     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/1574-6941.12160     Document Type: Article

References (41)

1. Auguet J, Barberan A & Casamayor E (2010) Global ecological patterns in uncultured Archaea. ISME J 4: 182-190.
2. Brodie EL, DeSantis TZ, Joyner DC et al. (2006) Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol 72: 6288-6298.
3. Brodie EL, DeSantis TZ, Parker JPM, Zubietta IX, Piceno YM & Andersen GL (2007) Urban aerosols harbor diverse and dynamic bacterial populations. P Natl Acad Sci USA 104: 299-304.
4. Clarke KR & Gorley RN (2001) PRIMER v5: User Manual/Tutorial. PRIMER-E Ltd, Plymouth, UK.
5. DeSantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM & Andersen GL (2007) High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol 53: 371-383.
6. García-Martínez J & Rodríguez-Valera F (2000) Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of Group I. Microb Ecol 9: 935-948.
7. Giebel HA, Brinkhoff T, Zwisler W, Selje N & Simon M (2009) Distribution of Roseobacter RCA and SAR11 lineages and distinct bacterial communities from the subtropics to the Southern Ocean. Environ Microbiol 11: 2164-2178.
8. Giovannoni SJ, Britschgi TB, Moyer CL & Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345: 60-63.
9. Greenberg AE, Clesceri LS & Eaton AD (1992) Standard Methods for the Examination of Water and Wastewater. American Public Health Association, Washington, DC.
10. Hahn MW (2006) The microbial diversity of inland waters. Curr Opin Biotechnol 17: 256-261.
11. Jiang H, Dong H, Zhang G, Yu B, Chapman LR & Fields MW (2006) Microbial diversity in water and sediment of Lake Chaka, an athalassohaline lake in Northwestern China. Appl Environ Microbiol 72: 3832-3845.
12. Jiang H, Dong H, Yu B, Liu X, Li Y, Ji S & Zhang CL (2007) Microbial response to salinity change in Lake Chaka, a hypersaline lake on Tibetan plateau. Environ Microbiol 9: 2603-2621.
13. Jiang H, Dong H, Yu B, Ye Q, Shen J, Rowe H & Zhang C (2008) Dominance of putative marine benthic Archaea in Qinghai Lake, north-western China. Environ Microbiol 10: 2355-2367.
14. Jiang H, Dong H, Deng S, Yu B, Huang Q & Wu Q (2009) Response of archaeal community structure to environmental changes in lakes on the Tibetan Plateau, northwestern China. Geomicrobiol J 26: 289-297.
15. Kan J, Evans SE, Chen F & Suzuki MT (2008) Novel estuarine bacterioplankton in rRNA operon libraries from the Chesapeake Bay. Aquat Microb Ecol 51: 55-66.
16. Liu WT, Marsh TL, Cheng H & Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63: 4516-4522.
17. Liu Y, Yao T, Zhu L, Jiao N, Liu X, Zeng Y & Jiang H (2009) Bacterial diversity of freshwater alpine Lake Puma Yumco on the Tibetan Plateau. Geomicrobiol J 26: 131-145.
18. Liu X, Yao T, Kang S, Jiao N, Zeng Y & Liu Y (2010) Bacterial community of the largest oligosaline lake, Namco on the Tibetan Plateau. Geomicrobiol J 27: 669-682.
19. Logares R, Brate J, Heinrich F, Shalchian-Tabrizi K & Bertilsson S (2010) Infrequent transitions between saline and fresh waters in one of the most abundant microbial lineages (SAR11). Mol Biol Evol 27: 347-357.
20. Lozupone CA & Knight R (2007) Global patterns in bacterial diversity. P Natl Acad Sci USA 104: 11436.
21. Morris RM, Rappé MS, Connon SA, Vergin KL, Siebold WA, Carlson CA & Giovannoni SJ (2002) SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420: 806-810.
22. Pruesse E, Peplies J & Glöckner FO (2012) SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28: 1823-1829.
23. Sagaram US, DeAngelis KM, Trivedi P, Andersen GL, Lu SE & Wang N (2009) Bacterial diversity analysis of Huanglongbing pathogen-infected citrus, using PhyloChip arrays and 16S rRNA gene clone library sequencing? Appl Environ Microbiol 75: 1566-1574.
24. Salcher MM, Pernthaler J & Posch T (2011) Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria 'that rule the waves'(LD12). ISME J 5: 1242-1252.
25. Saldanha AJ (2004) Java Treeview - extensible visualization of microarray data. Bioinformatics 20: 3246.
26. 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.
27. Stingl U, Tripp HJ & Giovannoni SJ (2007) Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site. ISME J 1: 361-371.
28. Tsiamis G, Katsaveli K, Ntougias S, Kyrpides N, Andersen G, Piceno Y & Bourtzis K (2008) Prokaryotic community profiles at different operational stages of a Greek solar saltern. Res Microbiol 159: 609-627.
29. Wang J, Soininen J, Zhang Y, Wang B, Yang X & Shen J (2011a) Contrasting patterns in elevational diversity between microorganisms and macroorganisms. J Biogeogr 38: 595-603.
30. Wang J, Yang D, Zhang Y, Shen J, van der Gast C, Hahn MW & Wu Q (2011b) Do patterns of bacterial diversity along salinity gradients differ from those observed for macroorganisms? PLoS ONE 6: e27597.
31. Warnecke F, Sommaruga R, Sekar R, Hofer JS & Pernthaler J (2005) Abundances, identity, and growth state of Actinobacteria in mountain lakes of different UV transparency. Appl Environ Microbiol 71: 5551.
32. Whitman WB, Coleman DC & Wiebe WJ (1998) Prokaryotes: the unseen majority. P Natl Acad Sci USA 95: 6578-6583.
33. Wu QL, Zwart G, Schauer M, Kamst-van Agterveld MP & Hahn MW (2006) Bacterioplankton community composition along a salinity gradient of sixteen high-mountain lakes located on the Tibetan Plateau, China. Appl Environ Microbiol 72: 5478-5485.
34. Wu QL, Chatzinotas A, Wang J & Boenigk J (2009) Genetic diversity of eukaryotic plankton assemblages in eastern Tibetan lakes differing by their salinity and altitude. Microb Ecol 58: 569-581.
35. Wu QL, Xing P & Liu WT (2010) East Tibetan lakes harbour novel clusters of picocyanobacteria as inferred from the 16S-23S rRNA internal transcribed spacer sequences. Microb Ecol 59: 614-622.
36. Xing P, Hahn MW & Wu QL (2009) Low taxon richness of bacterioplankton in high-altitude lakes of the eastern Tibetan Plateau, with a predominance of Bacteroidetes and Synechococcus spp. Appl Environ Microbiol 75: 7017-7025.
37. Yergeau E, Schoondermark-Stolk SA, Brodie EL, Déjean S, DeSantis TZ, Gonçalves O, Piceno YM, Andersen GL & Kowalchuk GA (2009) Environmental microarray analyses of Antarctic soil microbial communities. ISME J 3: 340-351.
38. Zhang R, Liu B, Lau SCK, Ki JS & Qian PY (2007) Particle-attached and free-living bacterial communities in a contrasting marine environment: Victoria Harbor, Hong Kong. FEMS Microbiol Ecol 61: 496-508.
39. Zhang R, Thiyagarajan V & Qian P-Y (2008) Evaluation of terminal-restriction fragment length polymorphism analysis in contrasting marine environments. FEMS Microbiol Ecol 65: 169-178.
40. Zheng D & Yao TD (2004) Uplifting of Tibetan Plateau with its environmental effects. Science Press, Beijing.
41. Zwart G, Crump BC, Kamst-van Agterveld MP, Hagen F & Han SK (2002) Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat Microb Ecol 28: 141-155.