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Microbiological functioning, diversity, and structure of bacterial communities in ultramafic soils from a tropical savanna

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Abstract

Ultramafic soils are characterized by high levels of metals, and have been studied because of their geochemistry and its relation to their biological component. This study evaluated soil microbiological functioning (SMF), richness, diversity, and structure of bacterial communities from two ultramafic soils and from a non-ultramafic soil in the Brazilian Cerrado, a tropical savanna. SMF was represented according to simultaneous analysis of microbial biomass C (MBC) and activities of the enzymes β-glucosidase, acid phosphomonoesterase and arylsulfatase, linked to the C, P and S cycles. Bacterial community diversity and structure were studied by sequencing of 16S rRNA gene clone libraries. MBC and enzyme activities were not affected by high Ni contents. Changes in SMF were more related to the organic matter content of soils (SOM) than to their available Ni. Phylogeny-based methods detected qualitative and quantitative differences in pairwise comparisons of bacterial community structures of the three sites. However, no correlations between community structure differences and SOM or SMF were detected. We believe this work presents benchmark information on SMF, diversity, and structure of bacterial communities for a unique type of environment within the Cerrado biome.

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Acknowledgments

We thank Clodoaldo A. de Sousa, Lucas F.L.S. Rolim, Franciele Schlemmer, Leandro M. de Souza, and Milene R. Ribeiro, for their assistance during this study. We thank Fabiana de Gois Aquino for kindly providing images of the samples sites. We also thank Anglo American and their team at the Barro Alto plant for their support. This work was partially financed by, Embrapa Macroprograma 2—Grant# 02.07.01.007.00.00, Embrapa Macroprograma 3—Grant# 03.09.06.016.00.00, and the CNPq (National Council for Scientific and Technological Development) REPENSA call (562433/2010-4).

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The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Embrapa Cerrados, P.O. Box 08223, Brasília, DF, 73310-970, Brazil

    Marco Pessoa-Filho, Fábio Bueno dos Reis Junior, Rodrigo Rocha Fragoso, Ieda de Carvalho Mendes & Leide Rovênia Miranda de Andrade

  2. Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, SGAN 916, Brasília, DF, 70790-160, Brazil

    Cristine Chaves Barreto & Flávio Silva Costa

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  1. Marco Pessoa-Filho
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  2. Cristine Chaves Barreto
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Correspondence to Marco Pessoa-Filho.

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Online resource 1 (PDF 383 kb)

Images of the two ultramafic sites selected for soil sampling. (A) Site 1, with a Campo Sujo physiognomy; (B) Site 2, with a Cerrado Ralo physiognomy. (Photo credit: Fabiana de Gois Aquino)

Online resource 2 (EPS 3,059 kb)

Neighbor-joining tree based on 16S rRNA gene sequences from Site 2 clones (in boldface) and their closest hits from RDP (with their corresponding accession numbers in parenthesis). Bootstrap values above 50 are shown. The tree was rooted with Methanocaldococcus jannaschii as an outgroup

Online resource 3 (EPS 3,061 kb)

Neighbor-joining tree based on 16S rRNA gene sequences from Cerrado clones (in boldface) and their closest hits from RDP (with their corresponding accession numbers in parenthesis). Bootstrap values above 50 are shown. The tree was rooted with Methanocaldococcus jannaschii as an outgroup

Online resource 4 (EPS 3,929 kb)

Rarefaction curves from Sites 1, 2 and Cerrado. Error bars represent the 95 % CI. Curves with different symbols represent clustering of sequences into OTUs identified by different dissimilarity cutoffs shown in the legend: unique (all unique sequences), 0.03 (3 % dissimilarity), 0.1 (10 % dissimilarity), 0.2 (20 % dissimilarity)

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Pessoa-Filho, M., Barreto, C.C., dos Reis Junior, F.B. et al. Microbiological functioning, diversity, and structure of bacterial communities in ultramafic soils from a tropical savanna. Antonie van Leeuwenhoek 107, 935–949 (2015). https://doi.org/10.1007/s10482-015-0386-6

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