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Characterization of Soil Bacterial Assemblies in Brazilian Savanna-Like Vegetation Reveals Acidobacteria Dominance

  • Soil Microbiology
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Abstract

The Brazilian Cerrado is the second largest biome in Brazil and is considered a biodiversity hotspot. In this work, we compared the bacterial communities in Cerrado soil associated with four types of native vegetation (Cerrado Denso, Cerrado sensu stricto, Campo Sujo, and Mata de Galeria) by ribosomal RNA intergenic spacer analysis, terminal fragment restriction length polymorphism and pyrosequencing. The fingerprinting results were very similar. The bacterial communities of Cerrado Denso and Cerrado sensu stricto grouped together and were distinct from those in Campo Sujo and Mata de Galeria. Pyrosequencing generated approximately 40,000 16S rRNA gene sequences per sample and allowed the identification of 17 phyla in soil samples under Cerrado vegetation. Acidobacteria were dominant in all areas studied with a relative frequency of 40–47 %, followed closely by Proteobacteria accounting for 34–40 % of the sequences. Results from all molecular techniques used suggested that the bacterial communities of Cerrado sensu stricto and Cerrado Denso are very similar to each other, while Campo Sujo forms a separate group, and Mata de Galeria is the most distinct with higher species richness. This is the first extensive study of native Cerrado soil microbiota, an important but endangered biome.

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Acknowledgments

This work was supported by grants from FAPDF/CNPq. JFA acknowledges a fellowship from Ouro Fino Agronegócio. APC acknowledges a fellowship from CAPES. We acknowledge Dr. Ashley Shade for critical reading of the manuscript.

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Authors and Affiliations

  1. Genomic Sciences and Biotechnology Program, Universidade Católica de Brasília, Brasilia, Federal District, Brazil

    Janaina F. Araujo & Betania F. Quirino

  2. Instituto de Ciências Biológicas, Universidade de Brasília, UnB, Brasilia, Brazil

    Alinne P. de Castro, Mercedes M. C. Bustamante & Ricardo H. Krüger

  3. Centro Nacional de Pesquisa de Recursos Genéticos e Biotecnologia, Bioinformatics Laboratory, Empresa Brasileira de Pesquisa Agropecuária, Brasilia, Federal District, Brazil

    Marcos M. C. Costa, Roberto C. Togawa & Georgios J. Pappas Júnior

  4. Department of Plant Pathology, University of Wisconsin–Madison, Madison, WI, USA

    Lynn Williamson

  5. Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA

    Jo Handelsman

  6. Embrapa-Agrienergy, Brasilia, Brazil

    Betania F. Quirino

  7. Instituto Central de Ciências Sul—Dept. de Biologia Celular, Laboratório de Enzimologia, Universidade de Brasília (UnB), Cep. 700910-900, Brasilia, Federal District, Brazil

    Ricardo H. Krüger

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  1. Janaina F. Araujo
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  2. Alinne P. de Castro
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Correspondence to Ricardo H. Krüger.

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Table S1

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Figure S 1

Structure of Cerrado vegetation physiognomies. a Pictures of areas. b Illustration of vegetation cover and topography of study areas (PDF 600 kb)

Figure S 2

Principal component analysis of soil physicochemical proprieties of Cerrado vegetation physiognomies. (CS1 Campo Sujo “1 to 5,” CS2 Campo Sujo “6 to 10,” CD1 Cerrado Denso “1 to 5,” CD2 Cerrado Denso “6 to 10,” SS1 Cerrado sensu stricto “1 to 5,” SS2 Cerrado sensu stricto “6 to 10,” MG1 Mata de Galeria “1 to 5,” and MG2 Mata de Galeria “6 to 10”) (JPEG 1905 kb)

Figure S3

Relative frequency of Acidobacteria subdivisions in the soil of different Cerrado vegetation physiognomies based on pyrosequencing data. The classifier of Ribosomal Database Project was used to assign sequences to the different subdivisions. Each Cerrado type was assigned a different color, and the replicate samples are indicated by different shades of the same color. The length of each color segment represents the percentage of that particular Acidobacteria subdivision found in each Cerrado type. Above each column, the total number of sequences identified for each Acidobacteria subdivision is shown (n) (JPEG 2033 kb)

Figure S4

Significant differences between the relative frequencies of bacterial orders of a comparison of each vegetation physiognomy by STAMP software. a Mata de Galeria and Campo Sujo. b Mata de Galeria and Cerrado sensu stricto. c Mata de Galeria and Cerrado Denso. d Campo Sujo and Cerrado sensu stricto. e Campo Sujo and Cerrado Denso. f Cerrado sensu stricto and Cerrado Denso (PDF 1477 kb)

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Araujo, J.F., de Castro, A.P., Costa, M.M.C. et al. Characterization of Soil Bacterial Assemblies in Brazilian Savanna-Like Vegetation Reveals Acidobacteria Dominance. Microb Ecol 64, 760–770 (2012). https://doi.org/10.1007/s00248-012-0057-3

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