Impacts of the Three Gorges Dam on microbial structure and potential function

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Yan, Qingyun ^a,b   Bi, Yonghong ^a   Deng, Ye ^b,e   He, Zhili ^b   Wu, Liyou ^b   Van Nostrand, Joy D ^b   Shi, Zhou ^b   Li, Jinjin ^a,f   Wang, Xi ^a,f   Hu, Zhengyu ^a   Yu, Yuhe ^a   Zhou, Jizhong ^b,c,d  

^a INSTITUTE OF HYDROBIOLOGY   (China)

^b UNIVERSITY OF OKLAHOMA   (United States)

^c TSINGHUA UNIVERSITY   (China)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^e RESEARCH CENTER FOR ECO ENVIRONMENTAL SCIENCES   (China)

^f UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENE; BIODIVERSITY; CHINA; DNA SEQUENCE; GENETIC VARIABILITY; MICROBIOLOGY; PHYSIOLOGY; PHYTOPLANKTON; PROTEOBACTERIA; RIVER; WATER QUALITY;

BIODIVERSITY; CHINA; GENES, BACTERIAL; GENETIC VARIATION; PHYTOPLANKTON; PROTEOBACTERIA; RIVERS; SEQUENCE ANALYSIS, DNA; WATER MICROBIOLOGY; WATER QUALITY;

EID: 84923827605     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep08605     Document Type: Article

References (58)

1. Karner, M. B., DeLong, E. F. & Karl, D. M. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409, 507-510 (2001).
2. Woese, C. R. There must be a prokaryote somewhere: microbiology's search for itself. Microbiol. Rev. 58, 1-9 (1994).
3. Crump, B. C. & Hobbie, J. E. Synchrony and seasonality in bacterioplankton communities of two temperate rivers. Limnol. Oceanogr. 50, 1718-1729 (2005).
4. Yu, Y. H., Yan, Q. Y. & Feng, W. S. Spatiotemporal heterogeneity of plankton communities in Lake Donghu, China, as revealed by PCR-denaturing gradient gel electrophoresis and its relation to biotic and abiotic factors. FEMS Microbiol. Ecol. 63, 328-337 (2008).
5. Comte, J. & del Giorgio, P. A. Linking the patterns of change in composition and function in bacterioplankton successions along environmental gradients. Ecology 91, 1466-1476 (2010).
6. Helland-Hansen, E., Holtedahl, T. & Liye, K. A. Hydropower Development, Vol. 3: Enviromental Effects (Norwegian Institute of Technology Press, Trondheim, 1995).
7. Dumestre, J. F., Casamayor, E. O., Massana, R. & Pedros-Alio, C. Changes in bacterial and archaeal assemblages in an equatorial river induced by the water eutrophication of Petit Saut dam reservoir (French Guiana). Aquat. Microb. Ecol. 26, 209-221 (2001).
8. Wang, S. et al.Diversity of microbial plankton across the Three Gorges Dam of the Yangtze River, China. Geosci. Front. 3, 335-349 (2012).
9. Ruiz-Gonzalez, C., Proia, L., Ferrera, I., Gasol, J. M. & Sabater, S. Effects of large river dam regulation on bacterioplankton community structure. FEMS Microbiol. Ecol. 84, 316-331 (2013).
10. Lopez-Garcia, P., Rodriguez-Valera, F., Pedros-Alio, C. & Moreira, D. Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature 409, 603-607 (2001).
11. Moon-van der Staay, S. Y., De Wachter, R. & Vaulot, D. Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature 409, 607-610 (2001).
12. Zhou, J. Z. et al. Bacterial phylogenetic diversity and a novel candidate division of two humid region, sandy surface soils. Soil Biol. Biochem. 35, 915-924 (2003).
13. Tringe, S. G. & Rubin, E. M. Metagenomics: DNA sequencing of environmental samples. Nat. Rev. Genet. 6, 805-814 (2005).
14. Tringe, S. G. et al. Comparative metagenomics of microbial communities. Science 308, 554-557 (2005).
15. Steffen, M.M. et al. Comparative metagenomics of toxic freshwater cyanobacteria bloom communities on two continents. PLoS ONE 7, e44002 (2012).
16. Burke, C., Steinberg, P., Rusch, D., Kjelleberg, S. & Thomas, T. Bacterial community assembly based on functional genes rather than species. Proc. Natl. Acad. Sci. U. S. A. 108, 14288-14293 (2011).
17. Davenport, C. F. & Tummler, B. Advances in computational analysis of metagenome sequences. Environ. Microbiol. 15, 1-5 (2013).
18. He, Z. L., Deng, Y. & Zhou, J. Z. Development of functional gene microarrays for microbial community analysis. Curr. Opin. Biotech. 23, 49-55 (2012).
19. He, Z. L., Van Nostrand, J. D. & Zhou, J. Z. Applications of functional gene microarrays for profiling microbial communities. Curr. Opin. Biotech. 23, 460-466 (2012).
20. Xie, W. et al. Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries. ISME J. 5, 414-426 (2011).
21. Oh, S. et al.Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem. Appl. Environ. Microbiol. 77, 6000-6011 (2011).
22. Ghai, R. Metagenomics of the water column in the pristine upper course of the Amazon river. PLoS ONE 6, e23785 (2011).
23. Wang, H. Y. Effects of the Three Gorges Reservoir on the water environment of the Xiangxi River with the proposal of countermeasures. Resour. Environ. Yangtze Basin. 14, 233-237 (2005).
24. Ye, L., Xu, Y. Y., Han, X. Q. & Cai, Q. H. Daily dynamics of nutrients and chlorophyll a during a spring phytoplankton bloom in Xiangxi Bay of the Three Gorges Reservoir. J. Freshwater Ecol. 21, 315-321 (2006).
25. Zhou, G. J. et al. Phytoplankton variation and its relationship with the environment in Xiangxi Bay in spring after damming of the Three-Gorges, China. Environ. Monit. Assess. 176, 125-141 (2011).
26. Bi, Y. H. et al. The effect of TGR's experimental impoundment on phytoplankton communities in Xiangxi River, China. Phycologia 48, 8-8 (2009).
27. Sekiguchi, H., Watanabe, M., Nakahara, T., Xu, B. H. & Uchiyama, H. Succession of bacterial community structure along the Changjiang River determined by denaturing gradient gel electrophoresis and clone library analysis. Appl. Environ. Microbiol. 68, 5142-5150 (2002).
28. Yan, Q. Y., Yu, Y. H., Feng, W. S., Yu, Z. G. & Chen, H. T. Plankton community composition in the Three Gorges Reservoir Region revealed by PCR-DGGE and its relationships with environmental factors. J. Environ. Sci. 20, 732-738 (2008).
29. Yang, X. et al. Decrease of NH4 1-N by bacterioplankton accelerated the removal of cyanobacterial blooms in aerated aquatic ecosystem. J. Environ. Sci. 25, 2223-2228 (2013).
30. Raup, D. M. & Crick, R. E. Measurement of faunal similarity in paleontology. J. Paleontol. 53, 1213-1227 (1979).
31. Jurgens, K. & Matz, C. Predation as a shaping force for the phenotypic and genotypic composition of planktonic bacteria. Anton. Leeuw. Int. J. G. 81, 413-434 (2002).
32. Belasky, P. Biogeography of Indo-Pacific larger foraminifera and scleractinian corals: a probabilistic approach to estimating taxonomic diversity, faunal similarity, and sampling bias. Paleogeogr. Paleoclimatol. Paleoecol. 122, 119-141 (1996).
33. Fierer, N. et al. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc. Natl. Acad. Sci. U. S. A. 109, 21390-21395 (2012).
34. Simek, K. et al. Shifts in bacterial community composition associated with different microzooplankton size fractions in a eutrophic reservoir. Limnol. Oceanogr. 44, 1634-1644 (1999).
35. Warkentin, M., Freese, H. M. & Schumann, R. Bacterial activity and bacterioplankton diversity in the eutrophic River Warnow: direct measurement of bacterial growth efficiency and its effect on carbon utilization. Microb. Ecol. 61, 190-200 (2011).
36. Diaz, S. & Cabido, M. Vive la difference: plant functional diversity matters to ecosystem processes. Trends Ecol. Evol. 16, 646-655 (2001).
37. Petchey, O. L. & Gaston, K. J. Functional diversity (FD), species richness and community composition. Ecol. Lett. 5, 402-411 (2002).
38. Green, J. L., Bohannan, B. J. M. & Whitaker, R. J. Microbial biogeography: from taxonomy to traits. Science 320, 1039-1043 (2008).
39. Raes, J., Letunic, I., Yamada, T., Jensen, L. J. & Bork, P. Toward molecular traitbased ecology through integration of biogeochemical, geographical and metagenomic data. Mol. Syst. Biol. 7, 473 (2011).
40. Frossard, A., Gerull, L., Mutz, M. & Gessner, M. O. Disconnect of microbial structure and function: enzyme activities and bacterial communities in nascent stream corridors. ISME J. 6, 680-691 (2012).
41. Wang, Y. Y. & Chen, F. Z. Decomposition and phosphorus release from four different size fractions of Microcystis spp. taken from Lake Taihu, China. J. Environ. Sci. 20, 891-896 (2008).
42. Artigas, J. et al. Phosphorus use by planktonic communities in a large regulated Mediterranean river. Sci. Total. Environ. 426, 180-187 (2012).
43. Breitbart, M. et al. Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Cienegas, Mexico. Environ. Microbiol. 11, 16-34 (2009).
44. Zeng, H., Song, L. R., Yu, Z. G. & Chen, H. T. Distribution of phytoplankton in the Three-Gorge Reservoir during rainy and dry seasons. Sci. Total. Environ. 367, 999-1009 (2006).
45. Zhou, G. J., Bi, Y. H., Zhao, X. M., Chen, L. & Hu, Z. Y. Algal growth potential and nutrient limitation in spring in three-Gorges reservoir, China. Fresen. Environ. Bull. 18, 1642-1647 (2009).
46. Steven, B., Gallegos-Graves, L., Starkenburg, S. R., Chain, P. S. & Kuske, C. R. Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study. Env. Microbiol. Rep. 4, 248-256 (2012).
47. Wang, J., Wang, B. S. & Luo, Z. Q. Dictionary of the Yangtze River (Wuhan Press, Wuhan, 1997).
48. Huang, X. F. Survey, Observation and Analysis of Lake Ecology (China Standard Press, Beijing, 2000).
49. He, Z. L. et al.Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2. Ecol. Lett. 13, 564-575 (2010).
50. Yang, Y. F. et al. Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland. Global Change Biol. 19, 637-648 (2013).
51. Bates, S. T. et al. Examining the global distribution of dominant archaeal populations in soil. ISME J. 5, 908-917 (2011).
52. Li, R. Q. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265-272 (2010).
53. Zhu, W. H., Lomsadze, A. & Borodovsky, M. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res. 38, e132 (2010).
54. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).
55. Muller, J. et al. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res. 38, D190-D195 (2010).
56. Kanehisa, M. et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36, D480-D484 (2008).
57. Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461 (2010).
58. Abubucker, S. et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comp. Biol. 8, e1002358 (2012).