A global census of nitrogenase diversity

Environmental Microbiology

Volumn 13, Issue 7, 2011, Pages 1790-1799

  Gaby, John Christian ^a   Buckley, Daniel H ^a  

^a Cornell University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NITROGENASE REDUCTASE; OXIDOREDUCTASE;

ARTICLE; CLUSTER ANALYSIS; CYANOBACTERIUM; ENVIRONMENT; ENZYMOLOGY; GAMMAPROTEOBACTERIA; GENETIC DATABASE; GENETIC VARIABILITY; GENETICS; NITROGEN FIXATION; PHYLOGENY; SOIL;

CLUSTER ANALYSIS; CYANOBACTERIA; DATABASES, GENETIC; ENVIRONMENT; GAMMAPROTEOBACTERIA; GENETIC VARIATION; NITROGEN FIXATION; OXIDOREDUCTASES; PHYLOGENY; SOIL;

CYANOBACTERIA; GAMMAPROTEOBACTERIA; OTUS;

EID: 79959816953     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2011.02488.x     Document Type: Article

References (44)

1. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and Wheeler, D. (2008) Genbank. Nucleic Acids Res 36 (database issue): D25-D30.
2. Brune, A., and Friedrich, M. (2000) Microecology of the termite gut: structure and function on a microscale. Curr Opin Microbiol 3: 263-269.
3. 2 reveals novel noncultivated diazotrophs in soil. Appl Environ Microbiol 73: 3196-3204.
4. Bürgmann, H., Widmer, F., Von Sigler, W., and Zeyer, J. (2004) New molecular screening tools for analysis of free-living diazotrophs in soil. Appl Environ Microbiol 70: 240-247.
5. Chien, Y.-T., and Zinder, S.H. (1994) Cloning, DNA-sequencing, and characterization of a nifD-homologous gene from the archaeon Methanosarcina barkeri 227 which resembles nifD1 from the eubacterium Clostridium pasteurianum. J Bacteriol 176: 6590-6598.
6. Church, M.J., Short, C.M., Jenkins, B.D., Karl, D.M., and Zehr, J.P. (2005) Temporal patterns of nitrogenase gene (nifH) expression in the oligotrophic North Pacific Ocean. Appl Environ Microbiol 71: 5362-5370.
7. Finn, R.D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J.E., etal. (2010) The Pfam protein families database. Nucleic Acids Res 38: D211-D222.
8. Hall, T.A. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 41: 95-98.
9. Hsu, S.-F., and Buckley, D.H. (2009) Evidence for the functional significance of diazotroph community structure in soil. ISME J 3: 124-136.
10. Hughes, J.B., Hellmann, J.J., Ricketts, T.H., and Bohannan, B.J.M. (2002) Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 67: 4399-4406.
11. Karl, D., Michaels, A., Bergman, B., Capone, D., Carpenter, E., Letelier, R., etal. (2002) Dinitrogen fixation in the world's oceans. Biogeochemistry 57/58: 47-98.
12. Konstantinidis, K.T., Ramette, A., and Tiedje, J.M. (2006) The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 361: 1929-1940.
13. Kulakov, L.A., McAlister, M.B., Ogden, K.L., Larkin, M.L., and O'Hanlon, J.F. (2002) Analysis of bacteria contaminating ultrapure water in industrial systems. Appl Environ Microbiol 68: 1548-1555.
14. Langlois, R.J., LaRoche, J., and Raab, P.A. (2005) Diazotrophic diversity and distribution in the Tropical and Subtropical Atlantic Ocean. Appl Environ Microbiol 71: 7910-7919.
15. Langlois, R.J., Hümmer, D., and LaRoche, J. (2008) Abundances and distributions of the dominant nifH phylotypes in the Northern Atlantic Ocean. Appl Environ Microbiol 74: 1922-1931.
16. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, etal. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
17. Lundgren, P., Söderbäck, E., Singer, A., Carpenter, E., and Bergman, B. (2001) Katagnymene: characterization of a novel marine diazotroph. J Phycol 37: 1052-1062.
18. 2 fixation. Am J Sci 305: 546-595.
19. Marusina, A.I., Boulygina, E.S., Kuznetsov, B.B., Tourova, T.P., Kravchenko, I.K., and Gal'chenko, V.F. (2001) A system of oligonucleotide primers for the amplification of nifH genes of different taxonomic groups of prokaryotes. Mikrobiologiya 70: 86-91.
20. 2 fixation domain. Science 327: 1512-1514.
21. Needoba, J.A., Foster, R.A., Sakamoto, C., Zehr, J.P., and Johnson, K.S. (2007) Nitrogen fixation by unicellular diazotrophic cyanobacteria in the temperate oligotrophic North Pacific Ocean. Limnol Oceanogr 52: 1317-1327.
22. Orcutt, K.M., Rasmussen, U., Webb, E.A., Waterbury, J.B., Gundersen, K., and Bergman, B. (2002) Characterization of Trichodesmium spp. by genetic techniques. Appl Environ Microbiol 68: 2236-2245.
23. Paerl, H.W., and Zehr, J.P. (2000) Marine nitrogen fixation. In Microbial Ecology of the Oceans. Kirchman, D.L. (ed.). New York, USA: Wiley-Liss, pp. 387-426.
24. Poly, F., Monrozier, L.J., and Bally, R. (2001) Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil. Res Microbiol 152: 95-103.
25. Raymond, J., Siefert, J.L., Staples, C.R., and Blankenship, R.E. (2004) The natural history of nitrogen fixation. Mol Biol Evol 21: 541-554.
26. Rubio, L.M., and Ludden, P.W. (2002) The gene products of the nif regulon. In Nitrogen Fixation at the Millennium. Leigh, G.J. (ed.). Amsterdam, The Netherlands: Elsevier Science B.V., pp. 101-136.
27. Schloss, P.D., and Handelsman, J. (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-1506.
28. Sipos, R., Székely, A.J., Palatinszky, M., Révész, S., Márialigeti, K., and Nikolausz, M. (2007) Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis. FEMS Microbiol Ecol 60: 341-350.
29. Sogin, M.L., Morrison, H.G., Huber, J.A., Welch, D.M., Huse, S.M., Neal, P.R., etal. (2006) Microbial diversity in the deep sea and the underexplored 'rare biosphere'. Proc Natl Acad Sci USA 103: 12115-12120.
30. Souillard, N., Magot, M., Possot, O., and Sibold, L. (1988) Nucleotide sequence of regions homologous to nifH (nitrogenase Fe protein) from the nitrogen-fixing archaebacteria Methanococcus thermolithotrophicus and Methanobacterium ivanovii: evolutionary implications. J Mol Evol 27: 65-76.
31. Staples, C.R., Lahiri, S., Raymond, J., Von Herbulis, L., Mukhophadhyay, B., and Blankenship, R.E. (2007) Expression and association of group IV nitrogenase NifD and NifH homologs in the non-nitrogen-fixing archaeon Methanocaldococcus jannaschii. J Bacteriol 189: 7392-7398.
32. Suzuki, M.T., and Giovannoni, S.J. (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62: 625-630.
33. Tripp, H.J., Bench, S.R., Turk, K.A., Foster, R.A., Desany, B.A., Niazi, F., etal. (2010) Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacterium. Nature 464: 90-94.
34. 2-fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of nifH gene sequences. J Bacteriol 177: 1414-1417.
35. Vitousek, P.M., and Howarth, R.W. (1991) Nitrogen limitation on land and in the sea: how can it occur? Biogeochemistry 13: 87-115.
36. Young, J.P.W. (1992) Phylogenetic classification of nitrogen-fixing organisms. In Biological Nitrogen Fixation. Stacey, G., Burris, R.H., and Evans, H.J. (eds). New York, USA: Chapman and Hall, pp. 43-86.
37. Young, J.P.W. (2005) The phylogeny and evolution of nitrogenases. In Genomes and Genomics of Nitrogen-Fixing Organisms. Palacios, R., and Newton, W.E. (eds). Dordrecht, The Netherlands: Springer, pp. 221-241.
38. Zehr, J.P., and McReynolds, L.A. (1989) Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium thiebautii. Appl Environ Microbiol 55: 2522-2526.
39. Zehr, J.P., Mellon, M.T., and Zani, S. (1998) New nitrogen-fixing microorganisms detected in oligotrophic oceans by amplification of nitrogenase (nifH) genes. Appl Environ Microbiol 64: 3444-3450.
40. 2 in the subtropical North Pacific Ocean. Nature 412: 635-638.
41. Zehr, J.P., Jenkins, B.D., Short, S.M., and Steward, G.F. (2003a) Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environ Microbiol 5: 539-554.
42. Zehr, J.P., Crumbliss, L.L., Church, M.J., Omoregie, E.O., and Jenkins, B.D. (2003b) Nitrogenase genes in PCR and RT-PCR reagents: implications for studies of diversity of functional genes. Biotechniques 35: 996-1005.
43. Zehr, J.P., Montoya, J.P., Jenkins, B.D., Hewson, I., Mondragon, E., Short, C.M., etal. (2007) Experiments linking nitrogenase gene expression to nitrogen fixation in the North Pacific subtropical gyre. Limnol Oceanogr 52: 169-183.
44. 2-fixing cyanobacteria lack oxygenic photosystem II. Science 322: 1110-1112.