Metagenome of microorganisms associated with the toxic Cyanobacteria Microcystis aeruginosa analyzed using the 454 sequencing platform

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• 作者：Nan Li (1) (2) (3)
  Lei Zhang (1) (2) (4)
  Fuchao Li (2)
  Yuezhu Wang (5)
  Yongqiang Zhu (5)
  Hui Kang (5)
  Shengyue Wang (5)
  Song Qin (1)
  
• 关键词：Microcystis aeruginosa ; ectosymbiosis ; diversity ; COGs ; algal bloom ; metagenome
• 刊名：Chinese Journal of Oceanology and Limnology
• 出版年：2011
• 出版时间：May 2011
• 年：2011
• 卷：29
• 期：3
• 页码：505-513
• 全文大小：355KB
• 参考文献：1. Aleya L, Michard M, Khattabi H, Devaux J. 2006. Coupling of the biochemical composition and calorific ocntent of zooplankters with the / Microcystis aeruginosa proliferation in a highly eutrophic reservoir. / Environ. Technol., 27(11): 1 181- 190. CrossRef
  2. Baptista M S, Vasconcelos M T. 2006. Cyanobacteria metal interactions: requirements, toxicity, and ecological implications. / Crit. Rev. Microbiol., 32(3): 127-37. CrossRef
  3. Berg K A, Lyra C, Sivonen K, Paulin L, Suomalainen S, Tuomi P, Rapala J. 2009. High diversity of cultivable heterotrophic bacteria in association with cyanobacterial water blooms. / Isme Journal, 3(3): 314-25. CrossRef
  4. Bourne D G, Riddles P, Jones G J, Smith W, Blakeley R L. 2001. Characterisation of a gene cluster involved in bacterial degradation of the cyanobacterial toxin microcystin LR. / Environ. Toxicol., 16(6): 523-34. CrossRef
  5. Eiler A, Bertilsson S. 2004. Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes. / Environmental Microbiology, 6(12): 1 228- 243. CrossRef
  6. Ewing B, Green P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. / Genome Res., 8(3): 186-94.
  7. Fuhrman J A. 1999. Marine viruses and their biogeochemical and ecological effects. / Nature, 399(6 736): 541-48. CrossRef
  8. Gordon D, Abajian C, Green P. 1998. Consed: a graphical tool for sequence finishing. / Genome Res., 8(3): 195-02.
  9. Harada K, Imanishi S, Kato H, Mizuno M, Ito E, Tsuji K. 2004. Isolation of Adda from microcystin-LR by microbial degradation. / Toxicon., 44(1): 107-09. CrossRef
  10. Ho L, Hoefel D, Saint C P, Newcombe G. 2007. Isolation and identification of a novel microcystin-degrading bacterium from a biological sand filter. / Water Res., 41(1): 4 685- 695.
  11. Huber H, Hohn M J, Rachel R, Fuchs T, Wimmer V C, Stetter K O. 2002. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. / Nature, 417(6 884): 63-7. CrossRef
  12. Ishii H, Nishijima M, Abe T. 2004. Characterization of degradation process of cyanobacterial hepatotoxins by a gram-negative aerobic bacterium. / Water Res., 38(11): 2 667- 676. CrossRef
  13. Ishii K. Fukui M. 2001. Optimization of annealing temperature to reduce bias caused by a primer mismatch in multitemplate PCR. / Applied and Environmental Microbiology, 67(8): 3 753- 755. CrossRef
  14. Jiang L J, Yang L Y, Xiao L, Shi X L, Gao G, Qin B. 2007. Quantitative studies on phosphorus transference occuring between Microcystis aeruginosa and its attached bacterium ( / Pseudomonas sp.). / Hydrobiologia, 581: 161-65. CrossRef
  15. Juliana C R, Renan B D, Luis F D B C, Eduardo V C, Edmar C S, Andrea M A N. 2009. Molecular identification and dynamics of microbial communities in reactor treating organic household waste. / Appl. Microbiol. Biotechnol., 84(4): 777-89. CrossRef
  16. Kroes I, Lepp P W, Relman D A. 1999. Bacterial diversity within the human subgingival crevice. Proceedings of the National Academy of Sciences of the United States of America, 96(25): 14 547-4 552. CrossRef
  17. Mackenzie C, Eraso J M, Choudhary M, Roh J H, Zeng X H, Bruscella P, Puskas A, Kaplan S. 2007. Postgenomic adventures with Rhodobacter sphaeroides. / Annual Review of Microbiology, 61: 283-07. CrossRef
  18. Maruyama T, Kato K, Yokoyama A, Tanaka T, Hiraishi A, Park H D. 2003. Dynamics of microcystin-degrading bacteria in mucilage of Microcystis. / Microbial Ecology, 46: 279-88. CrossRef
  19. Paerl H. 2008. Nutrient and other environmental controls of harmful cyanobacterial blooms along the freshwater-marine continuum. / Adv. Exp. Med. Biol., 619: 217-37. CrossRef
  20. Petrie L, North N N, Dollhopf S L, Balkwill D L, Kostka J E. 2003. Enumeration and characterization of iron(III)-reducing microbial communities from acidic subsurface sediments contaminated with uranium(VI). / Applied and Environmental Microbiology, 69(12): 7 467- 479. CrossRef
  21. Pope P B, Patel B K. 2008. Metagenomic analysis of a freshwater toxic cyanobacteria bloom. / FEMS Microbiol. Ecol., 64(1): 9-7. CrossRef
  22. Saito T, Okano K, Park H D, Itayama T, Inamori Y, Neilan B A, Burns B P, Sugiura N. 2003. Detection and sequencing of the microcystin LR-degrading gene, mlrA, from new bacteria isolated from Japanese lakes. / FEMS Microbiol. Lett., 229(2): 271-76. CrossRef
  23. Sedmak B, Elersek T. 2005. Microcystins induce morphological and physiological changes in selected representative phytoplanktons. / Microb. Ecol., 50(4): 298-05. CrossRef
  24. Valeria A M, Ricardo E J, Stephan P, Alberto W D. 2006. Degradation of Microcystin-RR by / Sphingomonas sp. CBA4 isolated from San Roque reservoir (Cordoba -Argentina). / Biodegradation, 17(5): 447-55. CrossRef
  25. Wang G C Y, Wang Y. 1997. Frequency of formation of chimeric molecules is a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes. / Applied and Environmental Microbiology, 63(12): 4 645- 650.
  26. Webster N S, Wilson K J, Blackall L L, Hill R T. 2001. Phylogenetic diversity of bacteria associated with the marine sponge Rhopaloeides odorabile. / Applied and Environmental Microbiology, 67(1): 434-44. CrossRef
  27. Weng L, Rubin E M, Bristow J. 2006. Application of sequence-based methods in human microbial ecology. / Genome Research, 16: 316-22. CrossRef
  28. Yoshida T, Takashima Y, Tomaru Y, Shirai Y, Takao Y, Hiroishi S, Nagasaki K. 2006. Isolation and characterization of a cyanophage infecting the toxic cyanobacterium Microcystis aeruginosa. / Applied and Environmental Microbiology, 72(2): 1 239- 247.
  29. Zhang X, Hu H Y, Men Y J, Yang J, Christoffersen K. 2009. Feeding characteristics of a golden alga ( / Poterioochromonas sp.) grazing on toxic cyanobacterium Microcystis aeruginosa. / Water Res., 43(12): 2 953- 960. CrossRef
  30. Zurawell R W, Chen H R, Burke J M, Prepas E E. 2005. Hepatotoxic cyanobacteria: A review of the biological importance of microcystins in freshwater environments. / Journal of Toxicology and Environmental Health-Part B-Critical Reviews, 8(1): 1-7. CrossRef
  
• 作者单位：Nan Li (1) (2) (3)
  Lei Zhang (1) (2) (4)
  Fuchao Li (2)
  Yuezhu Wang (5)
  Yongqiang Zhu (5)
  Hui Kang (5)
  Shengyue Wang (5)
  Song Qin (1)
  
  1. Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
  2. Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
  3. Graduate University of Chinese Academy of Sciences, Beijing, 100049, China
  4. South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangdong, 510301, China
  5. Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China
  
• ISSN：1993-5005

文摘

In this study, the 454 pyrosequencing technology was used to analyze the DNA of the Microcystis aeruginosa symbiosis system from cyanobacterial algal blooms in Taihu Lake, China. We generated 183 228 reads with an average length of 248 bp. Running the 454 assembly algorithm over our sequences yielded 22 239 significant contigs. After excluding the M. aeruginosa sequences, we obtained 1 322 assembled contigs longer than 1 000 bp. Taxonomic analysis indicated that four kingdoms were represented in the community: Archaea (n = 9; 0.01%), Bacteria (n = 98 921; 99.6%), Eukaryota (n = 373; 3.7%), and Viruses (n = 18; 0.02%). The bacterial sequences were predominantly Alphaproteobacteria (n = 41 805; 83.3%), Betaproteobacteria (n = 5 254; 10.5%) and Gammaproteobacteria (n = 1 180; 2.4%). Gene annotations and assignment of COG (clusters of orthologous groups) functional categories indicate that a large number of the predicted genes are involved in metabolic, genetic, and environmental information processes. Our results demonstrate the extraordinary diversity of a microbial community in an ectosymbiotic system and further establish the tremendous utility of pyrosequencing.