Microbial Ecology

, Volume 60, Issue 4, pp 840–849

Bacterial Community Diversity in the Brazilian Atlantic Forest Soils

  • Thiago Bruce
  • Ivana B. Martinez
  • Oswaldo Maia Neto
  • Ana Carolina P. Vicente
  • Ricardo H. Kruger
  • Fabiano L. Thompson
Soil Microbiology

Abstract

The aim of this study was to characterize the bacterial community diversity of the Brazilian Atlantic forest soil by means of both cultivation and 16S rRNA clone libraries. A collection of 86 representative isolates, obtained from six samples of Atlantic forest soils from the National Park of Serra dos Órgãos (PARNASO), belonged to the genera Arthrobacter, Bacillus, Burkholderia, Leifsonia, Paenibacillus, Pseudomonas, Ralstonia, Serratia, and Streptomyces according to the 16S rRNA sequences. Representative isolates from the different genera degraded cellulose and lignin. The culture-independent analysis based on 894 partial 16S rRNA gene sequences revealed that the most frequently retrieved groups belonged to the phyla Acidobacteria (29–54%), Proteobacteria (16–38%), and Verrucomicrobia (0.6–14%). The majority of the sequences (82.6%) were unidentified singletons and doubletons, indicating a high diversity of rare unique sequences. Chao1 estimator disclosed a high number of phyla (41–152) and species (263–446). This is the first survey on the Atlantic Forest soils using a combination of cultivation and culture-independent approaches. We conclude that the Brazilian Atlantic Forest soil represents a vast source of novel bacteria.

Supplementary material

248_2010_9750_MOESM1_ESM.pdf (27 kb)
Table 1SCharacteristics of Brazilian Atlantic Forest soil samples and position of the sites. OM organic matter. mEq/cm3 milliequivalent/cm3. (PDF 26 kb)
248_2010_9750_MOESM2_ESM.pdf (30 kb)
Table 2SQuantification of culturable bacteria and morphotypes obtained by different culture media. No. types, number of morphotypes. (PDF 30 kb)
248_2010_9750_MOESM3_ESM.pdf (20 kb)
Table 3SDistribution of 16S rRNA clone library sequences of frequent groups in the different locations. (PDF 19 kb)
248_2010_9750_MOESM4_ESM.pdf (201 kb)
Figure 1SMap and pictures of the sampling sites showing details of the vegetation. a Map of the sampling site; b Bonfim Amarelo; c Bonfim Vermelho; d Ajax (traço preto arenoso); e Torto (Vale das Antas), and f Campo Úmido. (PDF 201 kb)
248_2010_9750_MOESM5_ESM.pdf (611 kb)
Figure 2SRarefaction curves (a, b, and c) and collectors curve (d, e, and f) of the 16S rRNA clone libraries based on the furthest neighbor algorithm using the cut-off levels of 0.03, 0.10, and 0.20. (PDF 610 kb)
248_2010_9750_MOESM6_ESM.pdf (44 kb)
Figure 3SRelationship between Shannon diversity index values and pH of different types of soils from Brazilian Atlantic Forest. (PDF 43 kb)
248_2010_9750_MOESM7_ESM.pdf (40 kb)
Figure 4SRelated Alphaproteobacteria 16S rRNA found in both fractions (isolates and clones). Phylogenetic tree based on partial 16S rRNA sequences and the neighbor-joining method. (PDF 40 kb)
248_2010_9750_MOESM8_ESM.pdf (294 kb)
Figure 5SRelated Actinobacteria 16S rRNA sequences found in both fractions (isolates and clones). Phylogenetic tree based on partial 16S rRNA sequences and the neighbor-joining method. (PDF 294 kb)
248_2010_9750_MOESM9_ESM.pdf (254 kb)
Figure 6SRelated Firmicutes 16S rRNA sequence found in both fractions (isolates and clones). Phylogenetic tree based on partial 16S rRNA sequences and the neighbor-joining method. (PDF 254 kb)

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Thiago Bruce
    • 1
  • Ivana B. Martinez
    • 1
    • 2
  • Oswaldo Maia Neto
    • 1
  • Ana Carolina P. Vicente
    • 3
  • Ricardo H. Kruger
    • 4
  • Fabiano L. Thompson
    • 1
    • 5
  1. 1.Department of Genetics, Institute of BiologyFederal University of Rio de Janeiro (UFRJ)Rio de JaneiroBrazil
  2. 2.Program in Applied Microbiology and Parasitology (MIP), Department of Microbiology and ParasitologyFederal Fluminense University (UFF)Rio de JaneiroBrazil
  3. 3.Department of GeneticsIOC-FIOCRUZRio de JaneiroBrazil
  4. 4.Department of EnzymologyUniversity of BrasiliaBrasiliaBrazil
  5. 5.Centro de Ciências da Saúde, Laboratory of MicrobiologyFederal University of Rio de Janeiro (UFRJ)Rio de JaneiroBrazil

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