남극 해양에서 생물막 생성 초기 단계의 세균 군집 구조 변화 Succession of bacterial community structure during the early stage of biofilm development in the Antarctic marine environment원문보기
부유 세균의 군집과 구별되는 생물막내 세균 군집은 다양한 수생태계에서 중요한 생태학적 역할을 수행한다. 자연계에서 생물막이 생태학적으로 중요함에도 불구하고, 남극 해양 환경에서 생물막 형성 과정 동안의 세균 군집 구조와 그들의 변화에 대한 연구는 수행되지 않았다. 본 연구에서, 남극 해양 환경에서 생물막 형성 초기 단계에서의 세균 군집 구조 변화를 16S rRNA 유전자의 pyrosequencing을 통해 수행하였다. 생물막내 전반적인 세균 군집은 주변의 해수의 군집과 매우 달랐다. 전체 세균 군집의 78.8%에서 88.3%를 차지한 Gammaproteobacteria와 Bacteroidetes의 상대적 풍부도는 생물막의 형성에 따라 급격하게 변하였다. Gammaproteobacteria는 생물막 형성 진행에 따라 증가하다가 (4일째에 75.7%), 7일째에 46.1%로 감소하였다. 반면, Bacteroidetes는 초기에서 중기로 갈수록 감소하다가 다시 증가하는 양상을 보이며, Gammaproteobacteria와 반대의 변화 양상을 나타내었다. 생물막 형성의 초기 과정에 우점 하는 OTU (>1%)들의 변화 양상은 시기에 따라 뚜렷한 차이를 보였다. Gammaproteobacteria에 속하는 종의 경우, 4일째까지 증가한 반면, 첫째날 가장 우점 하였던 문인 Bacteroidetes에 속하는 종은 4일째까지 감소한 후, 다시 증가하는 양상을 보였다. 흥미롭게, Pseudoalteromonas prydzensis가 67.4%를 차지하며 우점 하였는데, 이는 생물막 형성에 이 종이 중요한 역할을 수행함을 시사하는 것으로 보인다.
부유 세균의 군집과 구별되는 생물막내 세균 군집은 다양한 수생태계에서 중요한 생태학적 역할을 수행한다. 자연계에서 생물막이 생태학적으로 중요함에도 불구하고, 남극 해양 환경에서 생물막 형성 과정 동안의 세균 군집 구조와 그들의 변화에 대한 연구는 수행되지 않았다. 본 연구에서, 남극 해양 환경에서 생물막 형성 초기 단계에서의 세균 군집 구조 변화를 16S rRNA 유전자의 pyrosequencing을 통해 수행하였다. 생물막내 전반적인 세균 군집은 주변의 해수의 군집과 매우 달랐다. 전체 세균 군집의 78.8%에서 88.3%를 차지한 Gammaproteobacteria와 Bacteroidetes의 상대적 풍부도는 생물막의 형성에 따라 급격하게 변하였다. Gammaproteobacteria는 생물막 형성 진행에 따라 증가하다가 (4일째에 75.7%), 7일째에 46.1%로 감소하였다. 반면, Bacteroidetes는 초기에서 중기로 갈수록 감소하다가 다시 증가하는 양상을 보이며, Gammaproteobacteria와 반대의 변화 양상을 나타내었다. 생물막 형성의 초기 과정에 우점 하는 OTU (>1%)들의 변화 양상은 시기에 따라 뚜렷한 차이를 보였다. Gammaproteobacteria에 속하는 종의 경우, 4일째까지 증가한 반면, 첫째날 가장 우점 하였던 문인 Bacteroidetes에 속하는 종은 4일째까지 감소한 후, 다시 증가하는 양상을 보였다. 흥미롭게, Pseudoalteromonas prydzensis가 67.4%를 차지하며 우점 하였는데, 이는 생물막 형성에 이 종이 중요한 역할을 수행함을 시사하는 것으로 보인다.
Compared to planktonic bacterial populations, biofilms have distinct bacterial community structures and play important ecological roles in various aquatic environments. Despite their ecological importance in nature, bacterial community structure and its succession during biofilm development in the A...
Compared to planktonic bacterial populations, biofilms have distinct bacterial community structures and play important ecological roles in various aquatic environments. Despite their ecological importance in nature, bacterial community structure and its succession during biofilm development in the Antarctic marine environment have not been elucidated. In this study, the succession of bacterial community, particularly during the early stage of biofilm development, in the Antarctic marine environment was investigated by pyrosequencing of the 16S rRNA gene. Overall bacterial distribution in biofilms differed considerably from surrounding seawater. Relative abundance of Gammaproteobacteria and Bacteroidetes which accounted for 78.9-88.3% of bacterial community changed drastically during biofilm succession. Gammaproteobacteria became more abundant with proceeding succession (75.7% on day 4) and decreased to 46.1% on day 7. The relative abundance of Bacteroidetes showed opposite trend to Gammaproteobacteria, decreasing from the early days to the intermediate days and becoming more abundant in the later days. There were striking differences in the composition of major OTUs (${\geq}1%$) among samples during the early stages of biofilm formation. Gammaproteobacterial species increased until day 4, while members of Bacteroidetes, the most dominant group on day 1, decreased until day 4 and then increased again. Interestingly, Pseudoalteromonas prydzensis was predominant, accounting for up to 67.4% of the biofilm bacterial community and indicating its important roles in the biofilm development.
Compared to planktonic bacterial populations, biofilms have distinct bacterial community structures and play important ecological roles in various aquatic environments. Despite their ecological importance in nature, bacterial community structure and its succession during biofilm development in the Antarctic marine environment have not been elucidated. In this study, the succession of bacterial community, particularly during the early stage of biofilm development, in the Antarctic marine environment was investigated by pyrosequencing of the 16S rRNA gene. Overall bacterial distribution in biofilms differed considerably from surrounding seawater. Relative abundance of Gammaproteobacteria and Bacteroidetes which accounted for 78.9-88.3% of bacterial community changed drastically during biofilm succession. Gammaproteobacteria became more abundant with proceeding succession (75.7% on day 4) and decreased to 46.1% on day 7. The relative abundance of Bacteroidetes showed opposite trend to Gammaproteobacteria, decreasing from the early days to the intermediate days and becoming more abundant in the later days. There were striking differences in the composition of major OTUs (${\geq}1%$) among samples during the early stages of biofilm formation. Gammaproteobacterial species increased until day 4, while members of Bacteroidetes, the most dominant group on day 1, decreased until day 4 and then increased again. Interestingly, Pseudoalteromonas prydzensis was predominant, accounting for up to 67.4% of the biofilm bacterial community and indicating its important roles in the biofilm development.
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문제 정의
Pioneer species were different from those of temperate marine environments and they did not remain high in abundance over time. These findings support the views that bacterial community composition of biofilm is niche-specific and influenced by interactions with the surrounding environment. Pseudoalteromonas prydzensis played a significant role in the maturation of biofilm and this may result from its known characteristics of EPS production and ability to compete for nutrients and space.
제안 방법
자연계에서 생물막이 생태학적으로 중요함에도 불구하고, 남극 해양 환경에서 생물막 형성 과정 동안의 세균 군집 구조와 그들의 변화에 대한 연구는 수행되지 않았다. 본 연구에서, 남극 해양 환경에서 생물막 형성 초기 단계에서의 세균 군집 구조 변화를 16S rRNA 유전자의 pyrosequencing을 통해 수행하였다. 생물막 내 전반적인 세균 군집은 주변의 해수의 군집과 매우 달랐다.
대상 데이터
We thank Ji Young Jung (Korea Polar Research Institute) for statistical analysis using the R software package. This work was supported by Grants PE07050 and PE15020 from the Korea Polar Research Institute.
collection and processing Acryl plates (200 mm × 300 mm × 3 mm) were cleaned with dish-cleaner, washed with sterilized water, and then submerged in seawater at a depth of approximately 30–60 cm vertically in the coastal area near King Sejong Station, King George Island, Antarctica (62°13'20.67''S, 58°47'11.32''W) from January 15–21, 2007.
데이터처리
Correlation between abundance of major OTUs and sampling time was analyzed by Pearson correlation analysis. Negative values indicate that the OTUs are early colonizers and positive values indicate that they are late colonizer during biofilm development.
이론/모형
Sequences with ambiguous nucleotides or shorter than 180 bp were discarded. Chimeric reads were detected and discarded using the de novo chimera detection algorithm UCHIME (Edgar et al., 2011). Sequence clustering was performed by CLUSTOM (Hwang et al.
Phylogenetic tree for fast UniFrac analysis was prepared by aligning sequences against pre-aligned SILVA reference sequences in MOTHUR and phylogenetic tree reconstruction using a neighbor-joining algorithm with Jukes & Cantor model (Jukes and Cantor, 1969) in the MEGA 6 program (Tamura et al., 2013).
, 2009). Relatedness among samples was assessed by principal coordinates analysis (PCoA) using the weighted algorithm of Fast UniFrac (Hamady et al., 2009). Phylogenetic tree for fast UniFrac analysis was prepared by aligning sequences against pre-aligned SILVA reference sequences in MOTHUR and phylogenetic tree reconstruction using a neighbor-joining algorithm with Jukes & Cantor model (Jukes and Cantor, 1969) in the MEGA 6 program (Tamura et al.
Total genomic DNA was extracted from the seawater and biofilm samples using a modified CTAB method (Stewart and Via, 1993) as follows. A biofilm sample (0.
성능/효과
3%를 차지한 Gammaproteobacteria와 Bacteroidetes의 상대적 풍부도는 생물막의 형성에 따라 급격하게 변하였다. Gammaproteobacteria는 생물막 형 성 진행에 따라 증가하다가 (4일째에 75.7%), 7일째에 46.1%로 감소하였다. 반면, Bacteroidetes는 초기에서 중기로 갈수록 감소하다가 다시 증가하는 양상을 보이며, Gammaproteobacteria와 반대의 변화 양상을 나타내었다.
3). In terms of OTU richness, the phylum Bacteroidetes was the largest group, followed by the classes Gammaproteobacteria and Alphaproteobacteria (Fig. 3). The number of OTUs affiliated with Bacteroidetes and Gammaproteobacteria decreased until day 4, and then increased again (Fig.
2% on day 3. Maximum abundance of Pseudoalteromonas prydzensis (67.4%) was obtained on day 4, after which the abundance decreased.
Rarefaction curves and diversity indices (Chao1 and ACE) calculated from 1,357 resampled sequence reads for each sample at 97% similarity levels revealed that the biofilm samples showed a higher level of bacterial diversity than seawater (Table 1, Fig. 3, and Supplementary data Fig. S1). Bacterial OTU richness on day 1 was 703 and 710, as represented by Chao1 and ACE indices, respectively, which was almost twice of that of seawater.
Thirty-six major OTUs with 1% or higher relative abundance in at least one biofilm sample were selected to investigate the dynamics of bacterial community composition. Sequence similarities between major OTUs and their closely related type strains ranged from 83.8% to 100% (Table 2). Major OTUs were affiliated with Bacteroidetes, Cyanobacteria, Firmicutes, Gammaproteobacteria, and Alphaproteobacteria.
The most evident pioneer species were those that are related to Polaribacter filamentus (96.5% sequence similarity), Algibacter mikhailovii (92.3%), and Polaribacter butkevichii (95.7%) (Pearson correlation, r = 0.85, r = 0.86, r = 0.90, respectively and all P < 0.05) (Table 2).
The other late colonizers mostly belonged to Bacteroidetes. The most prominent result from this analysis was that one major OTU, identified as Pseudoalteromonas prydzensis, made up 67.4% of the bacterial community. It accounted for 5.
생물막 내 전반적인 세균 군집은 주변의 해수의 군집과 매우 달랐다. 전체 세균 군집의 78.8%에서 88.3%를 차지한 Gammaproteobacteria와 Bacteroidetes의 상대적 풍부도는 생물막의 형성에 따라 급격하게 변하였다. Gammaproteobacteria는 생물막 형 성 진행에 따라 증가하다가 (4일째에 75.
Gammaproteobacteria에 속하는 종의 경우, 4일째까지 증가한 반면, 첫째날 가장 우점 하였던문인 Bacteroidetes에 속하는 종은 4일째까지 감소한 후, 다시 증가하는 양상을 보였다. 흥미롭게, Pseudoalteromonas prydzensis 가 67.4%를 차지하며 우점 하였는데, 이는 생물막 형성에 이종이 중요한 역할을 수행함을 시사하는 것으로 보인다.
참고문헌 (48)
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.
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.
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.
Bowman, J.P. 1998. Pseudoalteromonas prydzensis sp. nov., a psychrotrophic, halotolerant bacterium from antarctic sea ice. Int. J. Syst. Evol. Microbiol. 48, 1037-1041.
Bowman, J.P. 2007. Bioactive compound synthetic capacity and ecological significance of marine bacterial genus Pseudoalteromonas. Mar. Drugs 5, 220-241.
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.
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.
Delille, D. 1996. Biodiversity and function of bacteria in the southern ocean. Biodivers. Conserv. 5, 1505-1523.
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.
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.
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.
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.
Holmstrom, 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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Pohlon, E., Marxsen, J., and Kusel, K. 2010. Pioneering bacterial and algal communities and potential extracellular enzyme activities of stream biofilms. FEMS Microbiol. Ecol. 71, 364-373.
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.
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.
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.
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.
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.
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.
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.
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.
Watnick, P. and Kolter, R. 2000. Biofilm, city of microbes. J. Bacteriol. 182, 2675-2679.
Webster, N.S. and Negri, A.P. 2006. Site-specific variation in antarctic marine biofilms established on artificial surfaces. Environ. Microbiol. 8, 1177-1190.
Widmer, F., Hartmann, M., Frey, B., and Kolliker, R. 2006. A novel strategy to extract specific phylogenetic sequence information from community T-RFLP. J. Microbiol. Methods 66, 512-520.
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