Succession of bacterial community structure during the early stage of biofilm development in the Antarctic marine environment |
Lee, Yung Mi
(Division of Polar Life Sciences, Korea Polar Research Institute)
Cho, Kyung Hee (Division of Polar Life Sciences, Korea Polar Research Institute) Hwang, Kyuin (Division of Polar Life Sciences, Korea Polar Research Institute) Kim, Eun Hye (Division of Polar Life Sciences, Korea Polar Research Institute) Kim, Mincheol (Arctic Research Center, Korea Polar Research Institute) Hong, Soon Gyu (Division of Polar Life Sciences, Korea Polar Research Institute) Lee, Hong Kum (Division of Polar Life Sciences, Korea Polar Research Institute) |
1 | Costerton, J.W., Stewart, P.S., and Greenberg, E.P. 1999. Bacterial biofilms: a common cause of persistent infections. Science 284, 1318-1322. DOI |
2 | Dang, H. and Lovell, C.R. 2000. Bacterial primary colonization and early succession on surfaces in marine waters as determined by amplified rRNA gene restriction analysis and sequence analysis of 16S rRNA genes. Appl. Environ. Microbiol. 66, 467-475. DOI |
3 | Decho, A. 2000. Exopolymer microdomains as a structuring agent for heterogeneity within microbial biofilms, pp. 9-15. In Riding, R. and Awramik, S. (eds.), Microbial sediments. Springer Berlin Heidelberg. |
4 | Delille, D. 1996. Biodiversity and function of bacteria in the southern ocean. Biodivers. Conserv. 5, 1505-1523. DOI |
5 | Donlan, R.M. 2002. Biofilms: Microbial life on surfaces. Emerg. Infect. Dis. 8, 881-890. DOI |
6 | Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C., and Knight, R. 2011. Uchime improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194-2200. DOI |
7 | Egan, S., Thomas, T., and Kjelleberg, S. 2008. Unlocking the diversity and biotechnological potential of marine surface associated microbial communities. Curr. Opin. Microbiol. 11, 219-225. DOI |
8 | Field, K.G., Gordon, D., Wright, T., Rappe, M., Urback, E., Vergin, K., and Giovannoni, S.J. 1997. Diversity and depth-specific distribution of sar11 cluster rRNA genes from marine planktonic bacteria. Appl. Environ. Microbiol. 63, 63-70. |
9 | Flemming, H.C. 2002. Biofouling in water systems - cases, causes and countermeasures. Appl. Microbiol. Biotechnol. 59, 629-640. DOI |
10 | Gaylarde, C.C. and Morton, L.H.G. 1999. Deteriogenic biofilms on buildings and their control: a review. Biofouling 14, 59-74. DOI |
11 | Gillan, D.C., Speksnijder, A.G.C.L., Zwart, G., and De Ridder, C. 1998. Genetic diversity of the biofilm covering Montacuta ferruginosa (Mollusca, Bivalvia) as evaluated by denaturing gradient gel electrophoresis analysis and cloning of PCR-amplified gene fragments coding for 16S rRNA. Appl. Environ. Microbiol. 64, 3464-3472. |
12 | Hamady, M., Lozupone, C., and Knight, R. 2009. Fast unifrac: Facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and phylochip data. ISME J. 4, 17-27. |
13 | Holmström, C. and Kjelleberg, S. 1999. Marine Pseudoalteromonas species are associated with higher organisms and produce biologically active extracellular agents. FEMS Microbiol. Ecol. 30, 285-293. DOI |
14 | Hong, P.Y., Hwang, C., Ling, F., Andersen, G.L., LeChevallier, M.W., and Liu, W.T. 2010. Pyrosequencing analysis of bacterial biofilm communities in water meters of a drinking water distribution system. Appl. Environ. Microbiol. 76, 5631-5635. DOI |
15 | Hwang, K., Oh, J., Kim, T.K., Kim, B.K., Yu, D.S., Hou, B.K., Caetano-Anolles, G., Hong, S.G., and Kim, K.M. 2013. Clustom: A novel method for clustering 16S rRNA next generation sequences by overlap minimization. PLoS One 8, e62623. DOI |
16 | Jones, P., Cottrell, M., Kirchman, D., and Dexter, S. 2007. Bacterial community structure of biofilms on artificial surfaces in an estuary. Microb. Ecol. 53, 153-162. DOI |
17 | Jukes, T.H. and Cantor, C.R. 1969. Evolution of protein molecules, pp. 21-32. In Munro, H.N. Mammalian Protein Metabolism, Academic Press, New York, NY, USA. |
18 | Lane, D.J. 1991. 16S/23S rRNA sequencing, pp. 115-175. In Stackebrandt, E. and Goodfellow, M. (eds.), Nucleic Acid Techniques in Bacterial Systematics. John Wiley & Sons Press, New York, NY, USA. |
19 | Kim, O.S., Cho, Y.J., Lee, K., Yoon, S.H., Kim, M., Na, H., Park, S.C., Jeon, Y.S., Lee, J.H., Yi, H., et al. 2012. Introducing eztaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int. J. Syst. Evol. Microbiol. 62, 716-721. DOI |
20 | Kwon, K.K., Lee, S.J., Park, J.H., Ahn, T.Y., and Lee, H.K. 2006. Psychroserpens mesophilus sp. nov., a mesophilic marine bacterium belonging to the family Flavobacteriaceae isolated from a young biofilm. Int. J. Syst. Evol. Microbiol. 56, 1055-1058. DOI |
21 | Lau, S.C.K., Tsoi, M.M.Y., Li, X., Plakhotnikova, I., Dobretsov, S., Wu, M., Wong, P.K., Pawlik, J.R., and Qian, P.Y. 2006. Stenothermobacter spongiae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a marine sponge in the Bahamas, and emended description of Nonlabens tegetincola. Int. J. Syst. Evol. Microbiol. 56, 181-185. DOI |
22 | Lee, O.O., Lau, S.C.K., Tsoi, M.M. Y., Li, X., Plakhotnikova, I., Dobretsov, S., Wu, M.C.S., Wong, P.K., and Qian, P.Y. 2006. Gillisia myxillae sp. nov., a novel member of the family Flavobacteriaceae, isolated from the marine sponge Myxilla incrustans. Int. J. Syst. Evol. Microbiol. 56, 1795-1799. DOI |
23 | Lee, J.W., Nam, J.H., Kim, Y.H., Lee, K.H., and Lee, D.H. 2008. Bacterial communities in the initial stage of marine biofilm formation on artificial surfaces. J. Microbiol. 46, 174-182. DOI |
24 | Lyautey, E., Jackson, C., Cayrou, J., Rols, J.L., and Garabetian, F. 2005. Bacterial community succession in natural river biofilm assemblages. Microb. Ecol. 50, 589-601. DOI |
25 | Nedashkovskaya, O.I., Vancanneyt, M., Kim, S.B., and Zhukova, N.V. 2009. Winogradskyella echinorum sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius. Int. J. Syst. Evol. Microbiol. 59, 1465-1468. DOI |
26 | Maki, J.S., Little, B.J., Wagner, P., and Mitchell, R. 1990. Biofilm formation on metal surfaces in Antarctic waters. Biofouling 2, 27-38. DOI |
27 | Molin, S. and Tolker-Nielsen, T. 2003. Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure. Curr. Opin. Biotechnol. 14, 255-261. DOI |
28 | Moss, J.A., Nocker, A., Lepo, J.E., and Snyder, R.A. 2006. Stability and change in estuarine biofilm bacterial community diversity. Appl. Environ. Microbiol. 72, 5679-5688. DOI |
29 | Nichols, C.M., Bowman, J.P., and Guezennec, J. 2005. Olleya marilimosa gen. nov., sp. nov., an exopolysaccharide-producing marine bacterium from the family Flavobacteriaceae, isolated from the southern ocean. Int. J. Syst. Evol. Microbiol. 55, 1557-1561. DOI |
30 | Oh, J., Kim, B.K., Cho, W.S., Hong, S.G., and Kim, K.M. 2012. Pyrotrimmer: A software with gui for pre-processing 454 amplicon sequences. J. Microbiol. 50, 766-769. DOI |
31 | Pohlon, E., Marxsen, J., and Küsel, K. 2010. Pioneering bacterial and algal communities and potential extracellular enzyme activities of stream biofilms. FEMS Microbiol. Ecol. 71, 364-373. DOI |
32 | Sakshaug, E. and Slagstad, D.A.G. 1991. Light and productivity of phytoplankton in polar marine ecosystems: a physiological view. Polar Res. 10, 69-86. DOI |
33 | Stewart, C.N. Jr and Via, L.E. 1993. A rapid ctab DNA isolation technique useful for rapd fingerprinting and other PCR applications. Biotechniques 14, 748-758. |
34 | Salta, M., Wharton, J.A., Blache, Y., Stokes, K.R., and Briand, J.F. 2013. Marine biofilms on artificial surfaces: Structure and dynamics. Environ. Microbiol. 15, 2879-2893. |
35 | Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., Lesniewski, R.A., Oakley, B.B., Parks, D.H., Robinson, C.J., et al. 2009. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537-7541. DOI |
36 | Sekar, R., Nair, K.V.K., Rao, V.N.R., and Venugopalan, V.P. 2002. Nutrient dynamics and successional changes in a lentic freshwater biofilm. Freshwater Biol. 47, 1893-1907. DOI |
37 | Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S. 2013. MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30, 2725-2729. DOI |
38 | Vandecandelaere, I., Nercessian, O., Faimali, M., Segaert, E., Mollica, A., Achouak, W., Vos, P.D., and Vandamme, P. 2010. Bacterial diversity of the cultivable fraction of a marine electroactive biofilm. Bioelectrochemistry 78, 62-66. DOI |
39 | Wang J., Liu, M., Xiao, H., Wu, W., Xie, M., Sun, M., Zhu, C., and Li, P. 2013. Bacterial community structure in cooling water and biofilm in an industrial recirculating cooling water system. J. Bacteriol. 182, 2675-2679. |
40 | Watnick, P. and Kolter, R. 2000. Biofilm, city of microbes. J. Bacteriol. 182, 2675-2679. DOI |
41 | Webster, N., Battershill, C., and Negri, A. 2006. Recruitment of antarctic marine eukaryotes onto artificial surfaces. Polar Biol. 30, 1-10. DOI |
42 | Bowman, J.P. 1998. Pseudoalteromonas prydzensis sp. nov., a psychrotrophic, halotolerant bacterium from antarctic sea ice. Int. J. Syst. Evol. Microbiol. 48, 1037-1041. |
43 | Webster, N.S. and Negri, A.P. 2006. Site-specific variation in antarctic marine biofilms established on artificial surfaces. Environ. Microbiol. 8, 1177-1190. DOI |
44 | Widmer, F., Hartmann, M., Frey, B., and Kölliker, R. 2006. A novel strategy to extract specific phylogenetic sequence information from community T-RFLP. J. Microbiol. Methods 66, 512-520. DOI |
45 | Abell, G.C.J. and Bowman, J.P. 2005. Ecological and biogeographic relationships of class Flavobacteria in the Southern Ocean. FEMS Microbiol. Ecol. 51, 265-277. DOI |
46 | Araya, R., Tani, K., Takagi, T., Yamaguchi, N., and Nasu, M. 2003. Bacterial activity and community composition in stream water and biofilm from an urban river determined by fluorescent in situ hybridization and DGGE analysis. FEMS Microbiol. Ecol. 43, 111-119. DOI |
47 | Armstrong, E., Yan, L., Boyd, K.G., Wright, P.C., and Burgess, J.G. 2001. The symbiotic role of marine microbes on living surfaces. Hydrobiologia 461, 37-40. DOI |
48 | Bowman, J.P. 2007. Bioactive compound synthetic capacity and ecological significance of marine bacterial genus Pseudoalteromonas. Mar. Drugs 5, 220-241. DOI |