Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
권호 표지
DOI QR코드

DOI QR Code

The Phylogenetic Affiliation of an Uncultured Population of Ammonia-Oxidizing Bacteria Harboring Environmental Sequences of amoA Cluster-3

  • Hong, Jin-Kyung (Institute of Environmental Sciences and Department of Environmental Sciences, Hankuk University of Foreign Studies) ;
  • Cho, Jae-Chang (Institute of Environmental Sciences and Department of Environmental Sciences, Hankuk University of Foreign Studie)
  • Received : 2011.01.17
  • Accepted : 2011.03.23
  • Published : 2011.06.28
Download PDF
⟨ Previous Next ⟩

Abstract

We investigated the phylogenetic diversity of ammoniaoxidizing bacteria (AOB) in Yellow Sea continental shelf sediment by the cloning and sequencing of PCR-amplified amoA and 16S rRNA genes. Phylogenetic analysis of the amoA-related clones revealed that the diversity of AOB was extremely low at the study site. The majority (92.7%) of amoA clones obtained belonged to a single cluster, environmental amoA cluster-3, the taxonomic position of which was previously unknown. Phylogenetic analysis on AOB-specific 16S rRNA gene sequences also demonstrated a very low diversity. All of the cloned 16S rRNA gene sequences comprised a single phylotype that belonged to the members of uncultured Nitrosospira cluster-1, suggesting that AOB belonging to the uncultured Nitrosospira cluster-1 could carry amoA sequences of environmental amoA cluster-3.

Keywords

References

  1. Ashelford, K. E., N. A. Chuzhanova, J. C. Fry, A. J. Jones, and A. J. Weightman. 2006. New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl. Environ. Microbiol. 72: 5734-5741. https://doi.org/10.1128/AEM.00556-06
  2. Bano, N. and J. T. Hollibaugh. 2000. Diversity and distribution of DNA sequences with affinity to ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in the Arctic Ocean. Appl. Environ. Microbiol. 66: 1960-1969. https://doi.org/10.1128/AEM.66.5.1960-1969.2000
  3. Bayer, K., S. Schmitt, and U. Hentschel. 2008. Physiology, phylogeny and in situ evidence for bacterial and archaeal nitrifiers in the marine sponge Aplysina aerophoba. Environ. Microbiol. 10: 2942-2955. https://doi.org/10.1111/j.1462-2920.2008.01582.x
  4. Beman, J. M. and C. A. Francis. 2006. Diversity of ammoniaoxidizing archaea and bacteria in the sediments of a hypernutrified subtropical estuary: Bahia del Tobari, Mexico. Appl. Environ. Microbiol. 72: 7767-7777. https://doi.org/10.1128/AEM.00946-06
  5. Bernhard, A. E., T. Donn, A. E. Giblin, and D. A. Stahl. 2005. Loss of diversity of ammonia-oxidizing bacteria correlates with increasing salinity in an estuary system. Environ. Microbiol. 7: 1289-1297. https://doi.org/10.1111/j.1462-2920.2005.00808.x
  6. Bothe, H., G. Jost, M. Schloter, B. B. Ward, and K. Witzel. 2000. Molecular analysis of ammonia oxidation and denitrification in natural environments. FEMS Microbiol. Rev. 24: 673-690. https://doi.org/10.1111/j.1574-6976.2000.tb00566.x
  7. Boynton, W. R. and W. M. Kemp. 1985. Nutrient regeneration and oxygen consumption by sediments along an estuarine salinity gradient. Mar. Ecol. Prog. Seri. 23: 45-55.
  8. Francis, C. A., G. D. O'Mullan, and B. B. Ward. 2003. Diversity of ammonia monooxygenase (amoA) genes across environmental gradients in Chesapeake Bay sediments. Geobiology 1: 129-140. https://doi.org/10.1046/j.1472-4669.2003.00010.x
  9. Freitag, T. E., L. Chang, and J. I. Prosser. 2006. Changes in the community structure and activity of betaproteobacterial ammoniaoxidizing sediment bacteria along a freshwater-marine gradient. Environ. Microbiol. 8: 684-696. https://doi.org/10.1111/j.1462-2920.2005.00947.x
  10. Freitag, T. E. and J. I. Prosser. 2003. Community structure of ammonia-oxidizing bacteria within anoxic marine sediments. Appl. Environ. Microbiol. 69: 1359-1371. https://doi.org/10.1128/AEM.69.3.1359-1371.2003
  11. Freitag, T. E. and J. I. Prosser. 2004. Differences between betaproteobacterial ammonia-oxidizing communities in marine sediments and those in overlying water. Appl. Environ. Microbiol. 70: 3789-3793. https://doi.org/10.1128/AEM.70.6.3789-3793.2004
  12. Holmes, A. J., A. Costello, M. E. Lidstrom, and J. C. Murrell. 1995. Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiol. Lett. 132: 203-208. https://doi.org/10.1111/j.1574-6968.1995.tb07834.x
  13. Hunter, E. M., H. J. Mills, and J. E. Kostka. 2006. Microbial community diversity associated with carbon and nitrogen cycling in permeable shelf sediments. Appl. Environ. Microbiol. 72: 5689-5701. https://doi.org/10.1128/AEM.03007-05
  14. Jeong, K. S., J. H. Cho, S. R. Kim, S. Hyun, and U. Tsunogai. 2004. Geophysical and geochemical observations on actively seeping hydrocarbon gases on the south-eastern Yellow Sea continental shelf. Geo-Mar. Lett. 24: 53-62. https://doi.org/10.1007/s00367-003-0164-8
  15. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120. https://doi.org/10.1007/BF01731581
  16. Kumar, S., K. Tamura, and M. Nei. 2004. MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5: 150-163. https://doi.org/10.1093/bib/5.2.150
  17. Magalhaes, C. M., S. B. Joyeb, R. M. Moreiraa, W. J. Wiebea, and A. A. Bordaloa. 2005. Effect of salinity and inorganic nitrogen concentrations on nitrification and denitrification rates in intertidal sediments and rocky biofilms of the Douro River estuary, Portugal. Water Res. 39: 1783-1794. https://doi.org/10.1016/j.watres.2005.03.008
  18. Matulewich, V. A., P. F. Strom, and M. S. Finstein. 1975. Length of incubation for enumerating nitrifying bacteria present in various environments. Appl. Microbiol. 29: 265-268.
  19. McCaig, A. E., C. J. Phillips, J. R. Stephen, G. A. Kowalchuk, S. M. Harvey, R. A. Herbert, T. M. Embley, and J. I. Prosser. 1999. Nitrogen cycling and community structure of proteobacterial beta-subgroup ammonia-oxidizing bacteria within polluted marine fish farm sediments. Appl. Environ. Microbiol. 65: 213-220.
  20. McTavish, H., J. A. Fuchs, and A. B. Hooper. 1993. Sequence of the gene coding for ammonia monooxygenase in Nitrosomonas europaea. J. Bacteriol. 175: 2436-2444. https://doi.org/10.1128/jb.175.8.2436-2444.1993
  21. Mosier, A. C. and C. A. Francis. 2008. Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary. Environ. Microbiol. 10: 3002-3016. https://doi.org/10.1111/j.1462-2920.2008.01764.x
  22. O'Mullan, G. D. and B. B. Ward. 2005. Relationship of temporal and spatial variabilities of ammonia-oxidizing bacteria to nitrification rates in Monterey Bay, California. Appl. Environ. Microbiol. 71: 697-705. https://doi.org/10.1128/AEM.71.2.697-705.2005
  23. Purkhold, U., A. Pommerening-Roser, S. Juretschko, M. C. Schmid, H. P. Koops, and M. Wagner. 2000. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: Implications for molecular diversity surveys. Appl. Environ. Microbiol. 66: 5368-5382. https://doi.org/10.1128/AEM.66.12.5368-5382.2000
  24. Purkhold, U., M. Wagner, G. Timmermann, A. Pommerening- Roser, and H. P. Koops. 2003. 16S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: Extension of the dataset and proposal of a new lineage within the nitrosomonads. Int. J. Syst. Evol. Microbiol. 53: 1485-1494. https://doi.org/10.1099/ijs.0.02638-0
  25. Santoro, A. E., C. A. Francis, N. R. de Sieyes, and A. B. Boehm. 2008. Shifts in the relative abundance of ammoniaoxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary. Environ. Microbiol. 10: 1068-1079. https://doi.org/10.1111/j.1462-2920.2007.01547.x
  26. Schwartz, R. M. and M. O. Dayhoff. 1979. Protein and nucleic acid sequence data and phylogeny. Science 205: 1038-1039. https://doi.org/10.1126/science.205.4410.1038
  27. Stephen, J. R., A. E. McCaig, Z. Smith, J. I. Prosser, and T. M. Embley. 1996. Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia-oxidizing bacteria. Appl. Environ. Microbiol. 62: 4147-4154.
  28. Teske, A., E. Alm, J. M. Regan, S. Toze, B. E. Rittmann, and D. A. Stahl. 1994. Evolutionary relationships among ammoniaand nitrite-oxidizing bacteria. J. Bacteriol. 176: 6623-6630. https://doi.org/10.1128/jb.176.21.6623-6630.1994
  29. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positionspecific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680. https://doi.org/10.1093/nar/22.22.4673
  30. Urakawa, H., Y. Tajima, Y. Numata, and S. Tsuneda. 2008. Low temperature decreases the phylogenetic diversity of ammoniaoxidizing archaea and bacteria in aquarium biofiltration systems. Appl. Environ. Microbiol. 74: 894-900. https://doi.org/10.1128/AEM.01529-07
  31. Voytek, M. A. and B. B. Ward. 1995. Detection of ammoniumoxidizing bacteria of the beta-subclass of the class Proteobacteria in aquatic samples with the PCR. Appl. Environ. Microbiol. 61: 1444-1450.