Application of a nifH oligonucleotide microarray for profiling diversity of N2-fixing microorganisms in marine microbial mats

Environmental Microbiology

Volumn 8, Issue 10, 2006, Pages 1721-1735

  Moisander, Pia H ^a   Shiue, Lily ^b   Steward, Grieg F ^c   Jenkins, Bethany D ^d   Bebout, Brad M ^e   Zehr, Jonathan P ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of California Santa Cruz   (United States)

^c UNIVERSITY OF HAWAII   (United States)

^d UNIVERSITY OF RHODE ISLAND   (United States)

^e NASA AMES RESEARCH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; NITROGENASE REDUCTASE; OXIDOREDUCTASE;

ARTICLE; BACTERIUM; CHEMISTRY; CLUSTER ANALYSIS; DNA MICROARRAY; DNA SEQUENCE; ENZYMOLOGY; GENETIC VARIABILITY; GENETICS; METHODOLOGY; MEXICO; MICROBIOLOGY; MOLECULAR GENETICS; NITROGEN FIXATION; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION;

BACTERIA; BASE SEQUENCE; CLUSTER ANALYSIS; DNA, BACTERIAL; MEXICO; MOLECULAR SEQUENCE DATA; NITROGEN FIXATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OXIDOREDUCTASES; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS); WATER MICROBIOLOGY;

EID: 33748304118     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2006.01108.x     Document Type: Article

References (33)

1. Abed, R.M.M., and Garcia-Pichel, F. (2001) Long-term compositional changes after transplant in a microbial mat cyanobacterial community revealed using a polyphasic approach. Environ Microbiol 3: 53-62.
2. Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S.R., et al. (2002) The Pfam protein families database. Nucl Acids Res 30: 276-280.
3. Bebout, B.M., Carpenter, S.P., Des Marais, D.J., Discipulo, M., Embaye, T., Garcia-Pichel, F., et al. (2002) Long-term manipulations of intact microbial mat communities in a greenhouse collaboratory: simulating Earth's present and past field environments. Astrobiology 2: 383-402.
4. Bodrossy, L., Stralis-Pavese, N., Murrell, J.C., Radajewski, S., Weilharter, A., and Sessitsch, A. (2003) Development and validation of a diagnostic microbial microarray for methanotrophs. Environ Microbiol 5: 566-582.
5. Chien, Y.-T., and Zinder, S.H. (1994) Cloning, DNA sequencing, and characterization of a nifD-homologous gene grom the archaeon Methanosarcina barkeri 227 which resembles nifD1 from the eubacterium Clostridium pasteurianum. J Bacteriol 176: 6590-6598.
6. Des Marais, D.J., and Walter, M.R. (1999) Astrobiology: exploring the origins, evolution, and distribution of life in the universe. Ann Rev Syst 30: 397-420.
7. El Fantroussi, S., Urakawa, H., Berhard, A.E., Kelly, J.J., Noble, P.A., Smidt, H., et al. (2003) Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays. Appl Environ Microbiol 69: 2377-2382.
8. Guschin, D.Y., Mobarry, B.K., Proudnikov, D., Stahl, D.A., Rittman, B.E., and Mirzabekov, A.D. (1997) Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl Environ Microbiol 63: 2397-2402.
9. Hoehler, T.M., Bebout, B.M., and Des Marais, D.J. (2001) The role of microbial mats in the production of reduced gases on the early Earth. Nature 6844: 324-327.
10. Hughes, J.B., Hellmann, J.J., Ricketts, T.R., and Bohannan, B.J.M. (2001) Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 67: 4399-4406.
11. Jenkins, B.D., Steward, G.F., Short, S.M., Ward, B.B., and Zehr, J.P. (2004) Fingerprinting diazotroph communities in the Chesapeake Bay by using a DNA macroarray. Appl Environ Microbiol 70: 1767-1776.
12. Kemp, P.F., and Aller, J.Y. (2004) Estimating prokaryotic diversity: when are 16S rDNA libraries large enough? Limnol Oceanogr: Methods 2: 114-125.
13. Mitterer, G., Huber, M., Leidinger, E., Kirisits, C., Lubitz, W., Mueller, M.W., and Schmidt, W.M. (2004) Microarray-based identification of bacteria in clinical samples by solid-phase PCR amplification of 23S ribosomal DNA sequences. J Clin Microbiol 42: 1048-1057.
14. Nicolaisen, M., Justesen, A.F., Thrane, U., Skouboe, P., and Holmstrøm, K. (2005) An oligonucleotide microarray for the identification and differentiation of trichothecene producing and non-producing Fusarium species occurring on cereal grain. J Microbiol Meth 62: 57-69.
15. Nübel, U., Garcia-Pichel, F., Kühl, M., and Muyzer, G. (1999) Quantifying microbial diversity: morphotypes, 16S rRNA genes, and carotenoids of oxygenic phototrophs in microbial mats. Appl Environ Microbiol 65: 422-430.
16. Omoregie, E.O., Crumbliss, L.L., Bebout, B.M., and Zehr, J.P. (2004a) Comparison of diazotroph community structure in Lyngbya sp. & Microcoleus chthonoplastes dominated microbial mats from Guerrero Negro, Baja, Mexico. FEMS Microbiol Ecol 47: 305-318.
17. Omoregie, E.O., Crumbliss, L.L., Bebout, B.M., and Zehr, J.P. (2004b) Determination of nitrogen-fixing phylotypes in Lyngbya sp. & Microcoleus chthonoplastes cyanobacterial mats from Guerrero Negro, Baja, Mexico. Appl Environ Microbiol 70: 2119-2128.
18. Panicker, G., Call, D.R., Krug, M.J., and Bej, A.K. (2004) Detection of pathogenic Vibrio spp. in shellfish by using multiplex PCR and DNA microarrays. Appl Environ Microbiol 70: 7436-7444.
19. Postgate, J.R. (1987) Nitrogen Fixation. London, UK: Edward Arnold.
20. Rhee, S.-K., Liy, X., Chong, S.C., Wan, X., and Zhou, J. (2004) Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl Environ Microbiol 70: 4303-4317.
21. Risatti, J.B., Capman, W.C., and Stahl, D.A. (1994) Community structure of a microbial mat: the phylogenetic dimension. Proc Natl Acad Sci 91: 10173-10177.
22. Small, J., Call, D.R., Brockman, F.J., Straub, T.M., and Chandler, D.P. (2001) Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl Environ Microbiol 67: 4708-4716.
23. Steppe, T.F., and Paerl, H.W. (2002) Potential N-2 fixation by sulfate reducing bacteria in a marine intertidal microbial mat. Aquat Microb Ecol 28: 1-12.
24. Steward, G.F., Jenkins, B.D., Ward, B.B., and Zehr, J.P. (2004) Development and testing of a DNA macroarray to assess nitrogenase (nifH) gene diversity. Appl Environ Microbiol 70: 1455-1465.
25. Taroncher-Oldenburg, G., Griner, E.M., Francis, C.A., and Ward, B.B. (2003) Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl Environ Microbiol 69: 1159-1171.
26. Tillett, D., and Neilan, B.A. (2000) Xanthogenate nucleic acid isolation from cultured and environmental cyanobacteria. J Phycol 36: 251-258.
27. Wang, R.-F., Beggs, M.L., Robertson, L.H., and Cerniglia, C.E. (2002) Design and evaluation of oligonucleotide-microarray method for the detection of human intestinal bacteria in fecal samples. FEMS Microbiol Lett 213: 175-182.
28. Wilson, K.H., Wilson, W.J., Radosevich, J.L., DeSantis, T.Z., Viswanathan, V.S., Kuczmarski, T.A., and Andersen, G.L. (2002) High-density microarray of small-subunit ribosomal DNA probes. Appl Environ Microbiol 68: 2535-2541.
29. Wu, L., Thompson, D.K., Li, G., Hurt, R.A., Tiedje, J.M., and Zhou, J. (2001) Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl Environ Microbiol 67: 5780-5790.
30. Zehr, J.P., Mellon, M., Braun, S., Litaker, W., Steppe, T., and Paerl, H.W. (1995) Diversity of heterotrophic nitrogen fixation genes in a marine cyanobacterial mat. Appl Environ Microbiol 61: 2527-2532.
31. Zehr, J.P., and Turner, P.J. (2001) Nitrogen fixation: nitrogenase genes and gene expression. Meth Microbiology 30: 271-286.
32. Zehr, J.P., Jenkins, B.D., Short, S.M., and Steward, G.F. (2003) Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environ Microbiol 5: 539-554.
33. Zehr, J.P., Church, M.J., and Moisander, P.H. (2006) Diversity, distribution and biogeochemical significance of nitrogen-fixing microorganisms in anoxic and suboxic ocean environments. In Past and Present Water Column Anoxia. NATO Science Series IV. Earth and Environmental Sciences, Vol. 64. Neritin, L.N. (ed.). Dordrecht, The Netherlands: Springer, pp. 337-371.