Abstract
This study evaluated diazotrophic bacterial diversity of soils from four different sites in South and North America. Approximately one hundred and thirty-nine thousand partial sequences of the small subunit of the bacterial ribosomal RNA gene generated for a previous study were used for this work. Sequences that presented at least 90% similarity with known diazotrophic organisms were pulled from the original dataset and a new library containing 14,842 sequences from nitrogen-fixing bacteria were analysed. The number of sequences and the abundance of identifiable/cultivable diazotrophic genera were used for the calculation of the Shannon–Weaver diversity index and Evenness. All soils exhibited similar diazotrophic diversity, illustrating the great amount of similarity found between randomly chosen soils. Out of 81 diazotrophic genera, 45 were found in common in the four soils tested irrespective of the localization or cultivation. The degree of dominance of these common genera within their communties differed widely between soils. Sixteen types were found in only one sample.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Altschul S, Madden T, Schaeffer A, Zhang J, Zhang Z, Miller W, Lipman D (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
Chelius MK, Triplett EW (2001) The diversity of archaea and bacteria in association with the roots of Zea mays L. Microb Ecol 41:252–263
Curtis TP, Sloan WT, Scannell JW (2002) Estimating prokaryotic diversity and its limits. PNAS 99:10494–10499
DeSantis TZ Jr, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM et al (2006) NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Research 34(Web Server issue):W394–W399
Hsu S, Buckley DH (2009) Evidence for the functional significance of diazotroph community structure in soil. ISME J 3:124–136
Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJM (2001) Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 67:4399–4406
Kennedy IR, Choudhury ATMA, Kecskes ML (2004) Non- symbiotic bacterial diazotrophs in crop-farming systems: can their potential for plant growth promotion be better exploited? Soil Biol Biochem 36:1229–1244
Mullins TD, Britschgi TB, Krest RL, Giovannoni SJ (1995) Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol Oceanogr 40:148–158
Pace NR, Stahl DA, Lane DJ, Olsen GJ (1997) The analysis of natural microbial-populations by ribosomal-RNA sequences. Adv Microbiol Ecol 9:1–55
Roesch LFW, Fulthorpe R, Riva A, Casellas G, Hadwin AKM, Kent AD, Daroub SH, Camargo FAO, Farmerie W, Triplett E (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283–290
Roesch LFW, Camargo FAO, Bento FM, Triplett EW (2008) Biodiversity of diazotrophic bacteria within the soil, root and stem of field-grown maize. Plant Soil 302:91–104
Rösch C, Mergel A, Bothe H (2002) Biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil. Appl Environ Microbiol 68:3818–3829
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541
Sturz AV, Nowak J (2000) Endophytic communities of rhizobacteria and the strategies required to create yield enhancing associations with crops. Appl Soil Ecol 15:183–190
Widmer F, Shaffer BT, Porteous LA, Seidler RJ (1999) Analysis of nifH gene pool complexity in soil and litter at a Douglas fir forest site in the Oregon Cascade Mountain Range. Appl Environ Microbiol 65:374–380
Young JPW (1992) Phylogenetic classification of nitrogen-fixing organisms. In: Stacy G, Burris RH, Evans HJ (eds) New horizons in nitrogen fixation. Chapman and Hall, New York, pp 43–86
Zehr JP, McReynolds LA (1989) Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium thiebautii. Appl Environ Microbiol 55:2522–2526
Acknowledgments
This work was financially supported by Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (FAPERGS) process number: 0901855. L. F. W. Roesch acknowledges the research fellowship from CNPq process number 503370/2009-6.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Roesch, L.F.W., Fulthorpe, R.R., Jaccques, R.J.S. et al. Biogeography of diazotrophic bacteria in soils. World J Microbiol Biotechnol 26, 1503–1508 (2010). https://doi.org/10.1007/s11274-010-0326-6
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11274-010-0326-6