Diversity of 16S rRNA genes from bacteria of sugarcane rhizosphere soil

Brazilian Journal of Medical and Biological Research

Volumn 44, Issue 12, 2011, Pages 1215-1221

  Pisa, G ^a   Magnani, G S ^a   Weber, H ^a   Souza, E M ^a   Faoro, H ^a   Monteiro, R A ^a   Daros, E ^a   Baura, V ^a   Bespalhok, J P ^a   Pedrosa, F O ^a   Cruz, L M ^a  

^a FEDERAL UNIVERSITY OF PARANÁ   (Brazil)

Author keywords

16S rRNA; Bacteria; Biodiversity; Nitrogen fixation; Soil; Sugarcane

Indexed keywords

NITROGEN; RNA 16S;

ACIDOBACTERIA; ACTINOBACTERIA; ARTICLE; AZOSPIRILLUM; BACILLUS; BACTERIAL GENE; BACTERIUM; BACTERIUM CULTURE; BACTEROIDETES; BRADYRHIZOBIUM; BRAZIL; BURKHOLDERIA; FERTILIZATION; FIRMICUTES; GENETIC VARIABILITY; MESORHIZOBIUM; MICROBIAL COMMUNITY; NITROGEN AVAILABILITY; NONHUMAN; PHYLUM; PLANT GROWTH; PLANT ROOT; PROTEOBACTERIA; RHIZOBIUM; RHIZOSPHERE; SOIL; SUGARCANE; TAXONOMY; VERRUCOMICROBIA;

EID: 82355184031     PISSN: 0100879X     EISSN: 1414431X     Source Type: Journal    
DOI: 10.1590/S0100-879X2011007500148     Document Type: Article

References (32)

1. Fierer N, Jackson RB. The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci U S A 2006; 103: 626-631.
2. Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AK, Kent AD, et al. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 2007; 1: 283-290.
3. Stocker R, Seymour JR, Samadani A, Hunt DE, Polz MF. Rapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches. Proc Natl Acad Sci U S A 2008; 105: 4209-4214.
4. Toro M, Azcon R, Barea J. Improvement of arbuscular mycorrhiza development by inoculation of soil with phos-phate-solubilizing rhizobacteria to improve rock phosphate bioavailability ((sup32)P) and nutrient cycling. Appl Environ Microbiol 1997; 63: 4408-4412.
5. Boyle SA, Yarwood RR, Bottomley PJ, Myrold DD. Bacterial and fungal contributions to soil nitrogen cycling under Douglas fr and red alder at two sites in Oregon. Soil Biol Biochem 2008; 40: 443-451.
6. Gray EJ, Smith DL. Intracellular and extracellular PGPR: commonalities and distinctions in the plant-bacterium signaling processes. Soil Biol Biochem 2005; 37: 395-412.
7. Qiu H, Huang J, Yang J, Rozelle S, Zhang Y, Zhang Y. Bio-ethanol development in China and the potential impacts on its agricultural economy. Appl Energ 2010; 87: 76-83.
8. Walter A, Rosillo-Calle F, Dolzan P, Piacente E, Borges da Cunha K. Perspectives on fuel ethanol consumption and trade. Biomass Bioenerg 2008; 32: 730-748.
9. Borneman J, Skroch PW, O'Sullivan KM, Palus JA, Rum-janek NG, Jansen JL, et al. Molecular microbial diversity of an agricultural soil in Wisconsin. Appl Environ Microbiol 1996; 62: 1935-1943.
10. Janssen PH. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 2006; 72: 1719-1728.
11. Lane DJ. 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (Editors), Nucleic acid techniques in bacterial sys-tematics. New York: John Wiley and Sons; 1991. p 115-175.
12. Rosch C, Mergel A, Bothe H. Biodiversity of denitrifying and dinitrogen-fxing bacteria in an acid forest soil. Appl Environ Microbiol 2002; 68: 3818-3829.
13. Sambrook J, Fritsch EF, Maniatis T. Molecular cloning: A laboratory manual. 2nd edn. New York: Cold Spring Harbor Laboratory Press; 1989.
14. Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998; 8: 175-185.
15. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 2009; 37: D141-D145.
16. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifer for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007; 73: 5261-5267.
17. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 2009; 75: 7537-7541.
18. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007; 35: 7188-7196.
19. Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.6. http://evolution.genetics.washington.edu/phylip. html.
20. Jukes T, Cantor C. Evolution of protein molecules. In: Munro HN (Editor), Mammalian protein metabolism. New York: Academic Press; 1969. p 21-132.
21. Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R, Schaffer AA. Database indexing for production Mega-BLAST searches. Bioinformatics 2008; 24: 1757-1764.
22. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res 2010; 38: D46-D51.
23. Osborne CA, Galic M, Sangwan P, Janssen PH. PCR-generated artefact from 16S rRNA gene-specifc primers. FEMS Microbiol Lett 2005; 248: 183-187.
24. Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, Hiom SJ, et al. Design and evaluation of useful bacterium-specifc PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 1998; 64: 795-799.
25. Hongoh Y, Yuzawa H, Ohkuma M, Kudo T. Evaluation of primers and PCR conditions for the analysis of 16S rRNA genes from a natural environment. FEMS Microbiol Lett 2003; 221: 299-304.
26. Spain AM, Krumholz LR, Elshahed MS. Abundance, composition, diversity and novelty of soil Proteobacteria. ISME J 2009; 3: 992-1000.
27. Fulthorpe RR, Roesch LF, Riva A, Triplett EW. Distantly sampled soils carry few species in common. ISME J 2008; 2: 901-910.
28. Rousk J, Baath E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, et al. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J 2010; 4: 1340-1351.
29. Upchurch R, Chiu C-Y, Everett K, Dyszynski G, Coleman DC, Whitman WB. Differences in the composition and diversity of bacterial communities from agricultural and forest soils. Soil Biol Biochem 2008; 40: 1294-1305.
30. Roesch LFW, Camargo FAO, Bento FM, Triplett EW. Biodiversity of diazotrophic bacteria within the soil, root and stem of feld-grown maize. Plant Soil 2007; 302: 91-104.
31. Magnani GS, Didonet CM, Cruz LM, Picheth CF, Pedrosa FO, Souza EM. Diversity of endophytic bacteria in Brazilian sugarcane. Genet Mol Res 2010; 9: 250-258.
32. Suman A, Shasany AK, Singh M, Shahi HN, Gaur A, Khanuja SPS. Molecular assessment of diversity among endophytic diazotrophs isolated from subtropical Indian sugarcane. World J Microb Biot 2001; 17: 39-45.