Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Microbial Community Analysis of a Methane-Oxidizing Biofilm Using Ribosomal Tag Pyrosequencing

  • Kim, Tae-Gwan (Department of Environmental Science and Engineering, Ewha Womans University) ;
  • Lee, Eun-Hee (Department of Environmental Science and Engineering, Ewha Womans University) ;
  • Cho, Kyung-Suk (Department of Environmental Science and Engineering, Ewha Womans University)
  • Received : 2011.09.21
  • Accepted : 2011.11.04
  • Published : 2012.03.28
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Abstract

Current ecological knowledge of methanotrophic biofilms is incomplete, although they have been broadly studied in biotechnological processes. Four individual DNA samples were prepared from a methanotrophic biofilm, and a multiplex 16S rDNA pyrosequencing was performed. A complete library (before being de-multiplexed) contained 33,639 sequences (average length, 415 nt). Interestingly, methanotrophs were not dominant, only making up 23% of the community. Methylosinus, Methylomonas, and Methylosarcina were the dominant methanotrophs. Type II methanotrophs were more abundant than type I (56 vs. 44%), but less richer and diverse. Dominant non-methanotrophic genera included Hydrogenophaga, Flavobacterium, and Hyphomicrobium. The library was de-multiplexed into four libraries, with different sequencing efforts (3,915 - 20,133 sequences). Sorrenson abundance similarity results showed that the four libraries were almost identical (indices > 0.97), and phylogenetic comparisons using UniFrac test and P-test revealed the same results. It was demonstrated that the pyrosequencing was highly reproducible. These survey results can provide an insight into the management and/or manipulation of methanotrophic biofilms.

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References

  1. Blumel, S., M. Contzen, M. Lutz, A. Stolz, and H.-J. Knackmuss. 1998. Isolation of a bacterial strain with the ability to utilize the sulfonated azo compound 4-carboxy-4'-sulfoazobenzene as the sole source of carbon and energy. Appl. Environ. Microbiol. 64: 2315-2317.
  2. Bodrossy, L., N. Stralis-Pavese, J. C. Murrell, S. Radajewski, A. Weilharter, and A. Sessitsch. 2003. Development and validation of a diagnostic microbial microarray for methanotrophs. Environ. Microbiol. 5: 566-582. https://doi.org/10.1046/j.1462-2920.2003.00450.x
  3. Chao, A., R. L. Chazdon, R. K. Colwell, and T.-J. Shen. 2005. A new statistical approach for assessing similarity of species composition with incidence and abundance data. Ecol. Lett. 8: 148-159.
  4. Chao, A., R. L. Chazdon, R. K. Colwell, and T.-J. Shen. 2006. Abundance-based similarity indices and their estimation when there are unseen species in samples. Biometrics 62: 361-371. https://doi.org/10.1111/j.1541-0420.2005.00489.x
  5. Chun, J., J.-H. Lee, Y. Jung, M. Kim, S. Kim, B. K. Kim, and Y.-W. Lim. 2007. EzTaxon: A Web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int. J. Syst. Evol. Microbiol. 57: 2259-2261. https://doi.org/10.1099/ijs.0.64915-0
  6. Clapp, L. W., J. M. Regan, F. Ali, J. D. Newman, J. K. Park, and D. R. Noguera. 1999. Activity, structure, and stratification of membrane attached methanotrophic biofilms cometabolically degrading trichloroethylene. Water Sci. Technol. 39: 153-161.
  7. Cole, J. R., Q. Wang, E. Cardenas, J. Fish, B. Chai, R. J. Farris, et al. 2009. The ribosomal database project: Improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37: D141-D145. https://doi.org/10.1093/nar/gkn879
  8. Costello, A. M., A. J. Auman, J. L. Macalady, K. M. Scow, and M. E. Lidstrom. 2002. Estimation of methanotroph abundance in a freshwater lake sediment. Environ. Microbiol. 4: 443-450. https://doi.org/10.1046/j.1462-2920.2002.00318.x
  9. Droege, M. and B. Hill. 2008. The Genome Sequencer FLXTM System - Longer reads, more applications, straight forward bioinformatics and more complete data sets. J. Biotechnol. 136: 3-10. https://doi.org/10.1016/j.jbiotec.2008.03.021
  10. Gaidos, E., A. Rusch, and M. Ilardo. 2011. Ribosomal tag pyrosequencing of DNA and RNA from benthic coral reef microbiota: Community spatial structure, rare members and nitrogen-cycling guilds. Environ. Microbiol. 13: 1138-1152. https://doi.org/10.1111/j.1462-2920.2010.02392.x
  11. Gebert, J., A. Grongroft, M. Schloter, and A. Gattinger. 2004. Community structure in a methanotroph biofilter as revealed by phospholipid fatty acid analysis. FEMS Microbiol. Lett. 240: 61-68. https://doi.org/10.1016/j.femsle.2004.09.013
  12. Gebert, J., N. Stralis-Pavese, M. Alawi, and L. Bodrossy. 2008. Analysis of methanotrophic communities in landfill biofilters using diagnostic microarray. Environ. Microbiol. 10: 1175-1188. https://doi.org/10.1111/j.1462-2920.2007.01534.x
  13. Hery, M., A. C. Singer, D. Kumaresan, L. Bodrossy, N. Stralis-Pavese, J. I. Prosser, et al. 2008. Effect of earthworms on the community structure of active methanotrophic bacteria in a landfill cover soil. ISME J. 2: 92-104. https://doi.org/10.1038/ismej.2007.66
  14. Hall-Stoodley, L., J. W. Costerton, and P. Stoodley. 2004. Bacterial biofilms: From the natural environment to infectious diseases. Nat. Rev. Microbiol. 2: 95-108. https://doi.org/10.1038/nrmicro821
  15. Hanson, R. and T. Hanson. 1996. Methanotrophic bacteria. Microbiol. Rev. 60: 439-471.
  16. Henckel, T., P. Roslev, and R. Conrad. 2000. Effects of $O_2$ and $CH_4$ on presence and activity of the indigenous methanotrophic community in rice field soil. Environ. Microbiol. 2: 666-679. https://doi.org/10.1046/j.1462-2920.2000.00149.x
  17. Huson, D. H., A. F. Auch, J. Qi, and S. C. Schuster. 2007. MEGAN analysis of metagenomic data. Genome Res. 17: 377-386. https://doi.org/10.1101/gr.5969107
  18. Iguchi, H., H. Yurimoto, and Y. Sakai. 2011. Methylovulum miyakonense gen. nov., sp. nov., a type I methanotroph isolated from forest soil. Int. J. Syst. Evol. Microbiol. 61: 810-815. https://doi.org/10.1099/ijs.0.019604-0
  19. Kolb, S., C. Knief, S. Stubner, and R. Conrad. 2003. Quantitative detection of methanotrophs in soil by novel pmoA-targeted realtime PCR assays. Appl. Environ. Microbiol. 69: 2423-2429. https://doi.org/10.1128/AEM.69.5.2423-2429.2003
  20. Lambo, A. J. and T. R. Patel. 2007. Biodegradation of polychlorinated biphenyls in Aroclor 1232 and production of metabolites from 2,4,4'-trichlorobiphenyl at low temperature by psychrotolerant Hydrogenophaga sp. strain IA3-A. J. Appl. Microbiol. 102: 1318-1329. https://doi.org/10.1111/j.1365-2672.2006.03268.x
  21. Larkin, M. A., G. Blackshields, N. P. Brown, R. Chenna, P. A. McGettigan, H. McWilliam, et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948. https://doi.org/10.1093/bioinformatics/btm404
  22. Lee, E.-H., H. Park, and K.-S. Cho. 2010. Characterization of methane, benzene and toluene-oxidizing consortia enriched from landfill and riparian wetland soils. J. Hazard. Mater. 184: 313-320. https://doi.org/10.1016/j.jhazmat.2010.08.038
  23. Lee, M.-L. T., F. C. Kuo, G. A. Whitmore, and J. Sklar. 2000. Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations. Proc. Natl. Acad. Sci. USA 97: 9834-9839. https://doi.org/10.1073/pnas.97.18.9834
  24. Loy, A., W. Beisker, and H. Meier. 2005. Diversity of bacteria growing in natural mineral water after bottling. Appl. Environ. Microbiol. 71: 3624-3632. https://doi.org/10.1128/AEM.71.7.3624-3632.2005
  25. Lozupone, C., M. Hamady, and R. Knight. 2006. UniFrac - an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7: 371. https://doi.org/10.1186/1471-2105-7-371
  26. Martineau, C., L. G. Whyte, and C. W. Greer. 2010. Stable isotope probing analysis of the diversity and activity of methanotrophic bacteria in soils from the Canadian high arctic. Appl. Environ. Microbiol. 76: 5773-5784. https://doi.org/10.1128/AEM.03094-09
  27. McDonald, I. R., M. Upton, G. Hall, R. W. Pickup, C. Edwards, J. R. Saunders, et al. 1999. Molecular ecological analysis of methanogens and methanotrophs in blanket bog peat. Microb. Ecol. 38: 225-233. https://doi.org/10.1007/s002489900172
  28. Modin, O., K. Fukushi, F. Nakajima, and K. Yamamoto. 2010. Nitrate removal and biofilm characteristics in methanotrophic membrane biofilm reactors with various gas supply regimes. Water Res. 44: 85-96. https://doi.org/10.1016/j.watres.2009.09.009
  29. Pan, Y., L. Bodrossy, P. Frenzel, A.-G. Hestnes, S. Krause, C. Luke, et al. 2010. Assessing the impact of inter- as well as intra laboratory variation on reproducibility of microbial community analyses. Appl. Environ. Microbiol. 76: 7451-7458. https://doi.org/10.1128/AEM.01595-10
  30. Pettersson, E., J. Lundeberg, and A. Ahmadian. 2009. Generations of sequencing technologies. Genomics 93: 105-111. https://doi.org/10.1016/j.ygeno.2008.10.003
  31. Prosser, J. I. 2010. Replicate or lie. Environ. Microbiol. 12: 1806-1810. https://doi.org/10.1111/j.1462-2920.2010.02201.x
  32. Rainey, F. A., N. L. Ward-Rainey, P. H. Janssen, H. Hippe, and E. Stackebrandt. 1996. Clostridium paradoxum DSM 7308T contains multiple 16S rRNA genes with heterogeneous intervening sequences. Microbiology 142: 2087-2095. https://doi.org/10.1099/13500872-142-8-2087
  33. Ramos-Padron, E., S. Bordenave, S. Lin, I. M. Bhaskar, X. Dong, C. W. Sensen, et al. 2011. Carbon and sulfur cycling by microbial communities in a gypsum-treated oil sands tailings pond. Environ. Sci. Technol. 45: 439-446. https://doi.org/10.1021/es1028487
  34. Rittmann, B. E. 2006. Microbial ecology to manage processes in environmental biotechnology. Trends Biotechnol. 24: 261-266. https://doi.org/10.1016/j.tibtech.2006.04.003
  35. Semrau, J. D., A. A. DiSpirito, and S. Yoon. 2010. Methanotrophs and copper. FEMS Microbiol. Rev. 34: 1-36. https://doi.org/10.1111/j.1574-6976.2009.00197.x
  36. Stralis-Pavese, N., A. Sessitsch, A. Weilharter, T. Reichenauer, J. Riesing, J. Csontos, et al. 2004. Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers. Environ. Microbiol. 6: 347-363. https://doi.org/10.1111/j.1462-2920.2004.00582.x
  37. Thierry, S., H. Macarie, T. Iizuka, W. Geissdorfer, E. A. Assih, M. Spanevello, et al. 2004. Pseudoxanthomonas mexicana sp. nov. and Pseudoxanthomonas japonensis sp. nov., isolated from diverse environments, and emended descriptions of the genus Pseudoxanthomonas Finkmann et al. 2000 and of its type species. Int. J. Syst. Evol. Microbiol. 54: 2245-2255. https://doi.org/10.1099/ijs.0.02810-0
  38. Tolker-Nielsen, T. and S. Molin. 2000. Spatial organization of microbial biofilm communities. Microb. Ecol. 40: 75-84.
  39. Unno, T., J. Jang, D. Han, J. H. Kim, M. J. Sadowsky, O.-S. Kim, et al. 2010. Use of barcoded pyrosequencing and shared OTUs to determine sources of fecal bacteria in watersheds. Environ. Sci. Technol. 44: 7777-7782. https://doi.org/10.1021/es101500z
  40. Wang, Q., G. M. Garrity, J. M. Tiedje, and J. R. Cole. 2007. Naïve bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73: 5261-5267. https://doi.org/10.1128/AEM.00062-07
  41. Will, C., A. Thurmer, A. Wollherr, H. Nacke, N. Herold, M. Schrumpf, et al. 2010. Horizon-specific bacterial community composition of German grassland soils, as revealed by pyrosequencing-based analysis of 16S rRNA genes. Appl. Environ. Microbiol. 76: 6751-6759. https://doi.org/10.1128/AEM.01063-10
  42. Willems, A., J. Busse, M. Goor, B. Pot, E. Falsen, E. Jantzen, et al. 1989. Hydrogenophaga, a new genus of hydrogen-oxidizing bacteria that includes Hydrogenophaga flava comb. nov. (formerly Pseudomonas flava), Hydrogenophaga palleronii (formerly Pseudomonas palleronii), Hydrogenophaga pseudoflava (formerly Pseudomonas pseudoflava and "Pseudomonas carboxydoflava"), and Hydrogenophaga taeniospiralis (formerly Pseudomonas taeniospiralis). Int. J. Syst. Bacteriol. 39: 319-333. https://doi.org/10.1099/00207713-39-3-319
  43. Yoon, J.-H., S.-J. Kang, S. H. Ryu, C. O. Jeon, and T.-K. Oh. 2008. Hydrogenophaga bisanensis sp. nov., isolated from wastewater of a textile dye works. Int. J. Syst. Evol. Microbiol. 58: 393-397. https://doi.org/10.1099/ijs.0.65271-0
  44. Yoon, S., J. Carey, and J. Semrau. 2009. Feasibility of atmospheric methane removal using methanotrophic biotrickling filters. Appl. Microbiol. Biotechnol. 83: 949-956. https://doi.org/10.1007/s00253-009-1977-9
  45. Zhang, H., M. Ziv-El, B. E. Rittmann, and R. Krajmalnik-Brown. 2010. Effect of dechlorination and sulfate reduction on the microbial community structure in denitrifying membranebiofilm reactors. Environ. Sci. Technol. 44: 5159-5164. https://doi.org/10.1021/es100695n

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