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Bacterial soil community in a Brazilian sugarcane field

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Abstract

The assessment of bacterial communities in soil gives insight into microbial behavior under prevailing environmental conditions. In this context, we assessed the composition of soil bacterial communities in a Brazilian sugarcane experimental field. The experimental design encompassed plots containing common sugarcane (variety SP80-1842) and its transgenic form (IMI-1 — imazapyr herbicide resistant). Plants were grown in such field plots in a completely randomized design with three treatments, which addressed the factors transgene and imazapyr herbicide application. Soil samples were taken at three developmental stages during plant growth and analyzed using 16S ribosomal RNA (rRNA)-based PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and clone libraries. PCR-DGGE fingerprints obtained for the total bacterial community and specific bacterial groups — Actinobacteria, Alphaproteobacteria and Betaproteobacteria — revealed that the structure of these assemblages did not differ over time and among treatments. Nevertheless, slight differences among 16S rRNA gene clone libraries constructed from each treatment could be observed at particular cut-off levels. Altogether, the libraries encompassed a total of eleven bacterial phyla and the candidate divisions TM7 and OP10. Clone sequences affiliated with the Proteobacteria, Actinobacteria, Firmicutes and Acidobacteria were, in this order, most abundant. Accurate phylogenetic analyses were performed for the phyla Acidobacteria and Verrucomicrobia, revealing the structures of these groups, which are still poorly understood as to their importance for soil functioning and sustainability under agricultural practices.

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References

  • Altschul SF, Madden TL, Schaäffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acid Res 25:3389–3402

    Article  CAS  PubMed  Google Scholar 

  • Andreote FD, Azevedo JL, Araújo WL (2009) Assessing the diversity of bacterial communities associated with plants. Braz J Microbiol 40:417–432

    Article  Google Scholar 

  • Andreote FD, Mendes R, Dini-Andreote F, Rossetto PB, Labate CA, Pizzirani-Kleiner AA, van Elsas JD, Azevedo JL, Araújo WL (2008) Transgenic tobacco revealing altered bacterial diversity in the rhizosphere during early plant development. Antonie Leeuwenhoek 93:415–424

    Article  CAS  PubMed  Google Scholar 

  • Baldani JI, Caruso L, Baldani VLD, Goi SR, Döbereiner J (1997) Recent advances in BNF with non-legume plants. Soil Biol Biochem 29:911–922

    Article  CAS  Google Scholar 

  • Baldani JI, Reis VM, Baldani VLD, Döbereiner J (2002) A brief story of nitrogen fixation in sugarcane — reasons for success in Brazil. Funct Plant Biol 29:417–423

    Article  Google Scholar 

  • Boddey RM, Urquiaga S, Alves BJR, Reis V (2003) Endophytic nitrogen fixation in sugarcane: present knowledge and future applications. Plant Soil 252:139–149

    Article  CAS  Google Scholar 

  • Brons JK, van Elsas JD (2008) Analysis of bacterial communities in soil by use of denaturing gradient gel electrophoresis and clone libraries, as influenced by different reverse primers. Appl Environ Microbiol 74:2717–2727

    Article  CAS  PubMed  Google Scholar 

  • Goldemberg J (2007) Ethanol for a sustainable energy future. Science 315:808–810

    Article  CAS  PubMed  Google Scholar 

  • Gomes NCM, Heuer H, Schonfeld J, Costa R, Mendonca-Hagler L, Smalla K (2001) Bacterial diversity of the rhizosphere of maize (Zea mays) grown in tropical soil studied by temperature gradient gel electrophoresis. Plant Soil 232:167–180

    Article  CAS  Google Scholar 

  • Heuer H, Krsek M, Baker P, Smalla K, Wellington EMH (1997) Analysis of Actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl Environ Microbiol 63:3233–3241

    CAS  PubMed  Google Scholar 

  • James EK (2000) Nitrogen fixation in endophytic and associative symbiosis. Field Crops Res 65:197–209

    Article  Google Scholar 

  • Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72:1719–1728

    Article  CAS  PubMed  Google Scholar 

  • Janssen PH, Yates PS, Grinton BE, Taylor PM, Sait M (2002) Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl Environ Microbiol 68:2391–2396

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Kowalchuk GA, Bruinsma M, van Veen JA (2003) Assessing responses of soil microorganisms to GM plants. Trends Ecol Evol 18:403–410

    Article  Google Scholar 

  • Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR (1985) Rapid-Determination of 16S ribosomal-RNA sequences for phylogenetic analyses. Proc Natl Acad Sci USA 82:6955–6959

    Article  CAS  PubMed  Google Scholar 

  • Letunic I, Bork P (2007) Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23:127–128

    Article  CAS  PubMed  Google Scholar 

  • Liu B, Zeng Q, Yan F, Xu H, Xu C (2005) Effects of transgenic plants on soil microorganisms. Plant Soil 271:1–13

    Article  CAS  Google Scholar 

  • Loiret FG, Grimm B, Hajirezaei MR, Kleiner D, Ortega E (2009) Inoculation of sugarcane with Pantoea sp. increases amino acid contents in shoot tissues; serine, alanine, glutamine and asparagine permit concomitantly ammonium excretion and nitrogenase activity of the bacterium. J Plant Physiol 166:1152–1161

    Article  CAS  PubMed  Google Scholar 

  • Ludwig W, Strunk O, Westram R et al (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371

    Article  CAS  PubMed  Google Scholar 

  • Luvizotto DM, Marcon J, Andreote FD, Dini-Andreote F, Neves AAC, Araújo WL, Pizzirani-kleiner AA (2010) Genetic diversity and plant-growth related features of Burkholderia spp. from sugarcane roots. World J Microbiol Biotechnol (in press)

  • McCourt JA, Pang SS, King-Scott J, Guddat LW, Duggleby RG (2005) Herbicide-binding sites revealed in the structure of plant acetohydroxyacid synthase. Proc Natl Acad Sci USA 103:569–573

    Article  Google Scholar 

  • Mendes R, Pizzirani-Kleiner AA, Araujo WL, Raaijmakers JM (2007) Diversity of cultivated endophytic bacteria from sugarcane: genetic and biochemical characterization of Burkholderia cepacia complex isolates. Appl Environ Microbiol 73:7259–7267

    Article  CAS  PubMed  Google Scholar 

  • Mirza MS, Ahmad W, Latif F, Haurat J, Bally R, Normand P, Malik KA (2001) Isolation, partial characterization, and the effect of plant growth-promoting bacteria (PGPB) on micro-propagated sugarcane in vitro. Plant Soil 237:47–54

    Article  CAS  Google Scholar 

  • Muthukumarasamy R, Revathi G, Vadivelu M (2000) Antagonistic potential of N2-fixing Acetobacter diazotrophicus against Colletotricum falcatum Went., a causal organism of red-rot of sugarcane. Curr Sci 78:1063–1065

    Google Scholar 

  • Nunes da Rocha U, Andreote FD, Azevedo JL, van Elsas JD, van Overbeek LS (2010) Cultivation of hitherto-uncultured bacteria belonging to the Verrucomicrobia subdivision 1 from the potato (Solanum tuberosum L.) rhizosphere. J Soils Sediments 10:326–339

    Article  Google Scholar 

  • Oliveira ALM, Stoffels M, Schmid M, Reis VM, Baldani JI, Hartmann A (2009) Colonization of sugarcane plantlets by mixed inoculations with diazotrophic bacteria. Eur J Soil Biol 45:106–113

    Article  CAS  Google Scholar 

  • Rademaker J, Louws FJ, Versalovic J, Bruijn FJ (2004) Computer-assisted analysis of molecular fingerprint profiles and database construction. In: Kowalchuk GA, Bruijn FJ, Head IM, Akkermans AD, van Elsas JD (eds) Molecular microbial ecology manual. Kluwer Academic Publishers, Dordrecht, pp 1397–1446

    Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71:1501–1506

    Article  CAS  PubMed  Google Scholar 

  • Schmalenberger A, Tebbe CC (2003) Bacterial diversity in maize rhizospheres: conclusions on the use of genetic profiles based on PCR-amplified partial small subunit rRNA genes in ecological studies. Mol Ecol 12:251–261

    Article  CAS  PubMed  Google Scholar 

  • Singleton DR, Furlong MA, Rathbun SL, Whitman WB (2001) Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl Environ Microbiol 67:4374–4376

    Article  CAS  PubMed  Google Scholar 

  • Smalla K, Oros-Sichler M, Milling A, Heuer H, Baumgarte S, Becker R, Neuber G, Kropf S, Ulrich A, Tebbe C (2007) Bacterial diversity of soils assessed by DGGE, T-RFLP and SSCP fingerprints of PCR-amplified 16S rRNA gene fragments: do the different methods provide similar results? J Microbiol Methods 69:470–479

    Article  CAS  PubMed  Google Scholar 

  • Stuart RM, Romão AS, Pizzirani-kleiner AA, Azevedo JL, Araújo WL (2010) Culturable endophytic filamentous fungi from leaves of transgenic imidazolinone-tolerant sugarcane and its non-transgenic isolines. Arch Microbiol 192:307–313

    Google Scholar 

  • Tiedje JM, Asuming-Brempong S, Nüsslein K, Marsh TL, Flynn SJ (1999) Opening the black box of soil microbial diversity. Appl Soil Ecol 13:109–122

    Article  Google Scholar 

  • Torsvik V, Ovreas L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240–245

    Article  CAS  PubMed  Google Scholar 

  • Weinert N, Meincke R, Gottwald C, Heuer H, Gomes NCM, Schloter M, Berg G, Smalla K (2009) Rhizosphere communities of genetically modified zeaxanthin-accumulating potato plants and their parent cultivar differ less than those of different potato cultivars. Appl Environ Microbiol 75:3859–3865

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by a grant from FAPESP (Foundation for Research Assistance of São Paulo State, Brazil). We thank FAPESP for the fellowship to W.L.A. (Proc. n° 03/10527-4). We also thank Cristiane C. P. Hardoim for valuable assistance in library construction and Dr. Eugênio César Ulian for conduction and supervision of sugarcane management conditions in field.

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Authors and Affiliations

  1. Department of Genetics, Escola Superior de Agricultura “Luiz de Queiroz”, University of São Paulo, Piracicaba, SP, Brazil

    Francisco Dini-Andreote

  2. Department of Soil Science, Escola Superior de Agricultura “Luiz de Queiroz”, University of São Paulo, Piracicaba, SP, Brazil

    Fernando Dini Andreote

  3. Microbial Ecology and Evolution Research Group, Centre of Marine Sciences (CCMAR-CIMAR), University of Algarve, Gambelas, 8005-139, Faro, Portugal

    Rodrigo Costa

  4. Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil

    Rodrigo Gouvêa Taketani

  5. Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Kerklaan 30, Groningen, 9751 NN, The Netherlands

    Francisco Dini-Andreote & Jan Dirk van Elsas

  6. Center of Biotechnological Researches, University of Mogi das Cruzes, Mogi das Cruzes, SP, Brazil

    Welington Luiz Araújo

  7. Laboratory of Molecular Biology and Microbial Ecology, NIB, University of Mogi das Cruzes, 08780-911, Mogi das Cruzes, SP, Brazil

    Welington Luiz Araújo

Authors
  1. Francisco Dini-Andreote
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  2. Fernando Dini Andreote
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  3. Rodrigo Costa
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  4. Rodrigo Gouvêa Taketani
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  5. Jan Dirk van Elsas
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  6. Welington Luiz Araújo
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Correspondence to Welington Luiz Araújo.

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Responsible Editor: Timothy Richard Cavagnaro.

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Supplemental Table S1

The table shows Chao1 richness estimations, Shannon-Weaver and Simpson diversity indices for each confidence limits assigned. “Unique”, “species” (99% and 97%), “genus” (95%) and “order” (90%) confidence limits. It was considered 16S rRNA gene sequences for each sugarcane treatment in specific (CV, TC and TH) and sequences altogether (total). (PPT 95 kb)

Supplemental Figure S1

Experimental field design. See Materials and Methods for details. Red “x” represent the two cores of subsamples collected randomly in the middle of each plot. (PPT 117 kb)

Supplemental Figure S2

Cluster analysis of DGGE fingerprints using the unweighted-pair group method for (I) total bacterial community, (II) Actinobacteria, (III) Alphaproteobacteria and (IV) Betaproteobacteria. CV, TC and TH refer to different sugarcane treatments conduced in the field (see material and methods). The numbers 1, 2 and 3 refer to samples collected in three distinct periods of sugarcane cultivation (three, ten and seventeen months, respectively). (PPT 115 kb)

Supplemental Figure S3

LIBSHUFF comparison plots of evolutionary distance by homologous coverage curves (red line) compared to heterologous coverage curve (green line). The blue line indicates the value of delta C (right y axis) for the original samples at each value of evolutionary distance. Purple line indicates the 95% of delta C for the randomized samples. The ranked values (P) of the delta C from the heterologous coverage are shown. (PPT 166 kb)

Supplemental Figure S4

Rarefaction curves of operational taxonomic units (OTU) assigned at the „unique‟, “species” (99% and 97%), “genus” (95%) and “order” (90%) levels for partial bacterial 16S rRNA gene sequences retrieved from sugarcane soil. (a), (b) and (c) refer to CV, TC and TH 16S rRNA group sequence, respectively. (d) refer to altogether sequences considered in the study. The number of OTUs were determined with DOTUR for each case evaluated. (PPT 79 kb)

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Dini-Andreote, F., Andreote, F.D., Costa, R. et al. Bacterial soil community in a Brazilian sugarcane field. Plant Soil 336, 337–349 (2010). https://doi.org/10.1007/s11104-010-0486-z

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