Soil Acidobacterial 16S rRNA Gene Sequences Reveal Subgroup Level Differences between Savanna-Like Cerrado and Atlantic Forest Brazilian Biomes

Hindawi Publishing Corporation International Journal of Microbiology Volume 2014, Article ID 156341, 12 pages http://dx.doi.org/10.1155/2014/156341 Research Article Soil Acidobacterial 16S rRNA Gene Sequences Reveal Subgroup Level Differences between Savanna-Like Cerrado and Atlantic Forest Brazilian Biomes Elisa C. P. Catão,1 Fabyano A. C. Lopes,1 Janaína F. Araújo,1 Alinne P. de Castro,1 Cristine C. Barreto,2 Mercedes M. C. Bustamante,3 Betania F. Quirino,2,4 and Ricardo H. Krüger1,2 1 Cellular Biology Department, Instituto Central de Ciências Sul, Universidade de Brası́lia (UnB), 700910-900 Brası́lia, DF, Brazil Genomic Sciences and Biotechnology, Universidade Católica de Brası́lia, 70790-160 Brası́lia, DF, Brazil 3 Ecology Department, Universidade de Brası́lia (UnB), 700910-900 Brası́lia, DF, Brazil 4 Genetics and Biotechnology Laboratory, Embrapa-Agroenergy, 70770-901 Brası́lia, DF, Brazil 2 Correspondence should be addressed to Ricardo H. Krüger; Received 16 June 2014; Revised 18 August 2014; Accepted 31 August 2014; Published 15 September 2014 Academic Editor: Akira Hiraishi Copyright © 2014 Elisa C. P. Catão et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 16S rRNA sequences from the phylum Acidobacteria have been commonly reported from soil microbial communities, including those from the Brazilian Savanna (Cerrado) and the Atlantic Forest biomes, two biomes that present contrasting characteristics of soil and vegetation. Using 16S rRNA sequences, the present work aimed to study acidobacterial diversity and distribution in soils of Cerrado savanna and two Atlantic forest sites. PCA and phylogenetic reconstruction showed that the acidobacterial communities found in “Mata de galeria” forest soil samples from the Cerrado biome have a tendency to separate from the other Cerrado vegetation microbial communities in the direction of those found in the Atlantic Forest, which is correlated with a high abundance of Acidobacteria subgroup 2 (GP2). Environmental conditions seem to promote a negative correlation between GP2 and subgroup 1 (GP1) abundance. Also GP2 is negatively correlated to pH, but positively correlated to high Al3+ concentrations. The Cerrado soil showed the lowest Acidobacteria richness and diversity indexes of OTUs at the species and subgroups levels when compared to Atlantic Forest soils. These results suggest specificity of acidobacterial subgroups to soils of different biomes and are a starting point to understand their ecological roles, a topic that needs to be further explored. 1. Introduction Acidobacteria are one of the most abundant phyla in the soil habitats [1]. More than 30% or even 50% of the sequences obtained in 16S rRNA gene clone libraries from soil belong to the phylum Acidobacteria [2] and a great part (4 to 16% transcripts of 16S rRNA from 9 to 31% 16S rRNA genes of Acidobacteria) of these are also physiologically active [3]. Currently, there are 26 acidobacterial subgroups [4], but not all subgroups have cultured representatives. The ubiquitous and abundant presence of Acidobacteria in soils suggests that these microorganisms have an important role in biogeochemical cycles. Acidobacteria may be, for example, essential for maintenance of soil fertility and to enhance vegetation growth, since microorganisms are related to organic matter decomposition and nutrient cycling. However, the answer to these questions still depends on culturing Acidobacteria under laboratory conditions. Although the number of cultivated Acidobacteria is constantly increasing, only few species have been isolated from soils and marine environments. Currently, there are only 14 described genera, eight belonging to Acidobacteria subgroup 1 (GP1): Acidobacterium [5], Terriglobus [6, 7], Edaphobacter [8], Granulicella [9, 10], “Acidiphila” [11], Telmatobacter [12], Acidicapsa [13], and Bryocella [14]. Subgroup 8 is the Class Holophagae and comprises the genera Holophaga [15], Geothrix [16], and Acanthopleuribacter [17]. There is only one genus in culture belonging to subgroup 3 (GP3): Bryobacter 2 International Journal of Microbiology [18], and recently, two genera from subgroup 4 (GP4) were described: Blastocatella [19] and its close relative Aridibacter [20]. The genus Thermotomaculum is the only cultured representative of subgroup 10 [21]. Although these isolates were obtained from distinct environments ranging from acidic environments [5, 13, 18] to marine hydrothermal vents [21], to the tundra soil [9], they are usually considered to be slow-growing organisms that thrive in oligotrophic habitats. The analysis of 16S rRNA gene clone libraries and pyrosequencing demonstrated that the abundance of Acidobacteria is usually correlated with low values of soil pH [22] and that subgroups GP1, GP4, and GP6 are predominant in soil [1, 23]. These works consider mostly soils from the northern hemisphere and Acidobacteria from Brazilian biomes have not been compared yet. Brazil comprises six biomes: the Atlantic Forest, the Amazon Forest, the Cerrado (the Brazilian Savanna), the Caatinga, the Pampa, and the Pantanal (see Figure S1 in Supplementary Material available online at http://dx.doi.org/10.1155/2014/ 156341). The Cerrado and the Atlantic Forest are on the list of the world’s priorities for conservation efforts because they are biodiversity hotspots [24]. Both of these Brazilian biomes are rapidly being converted to pastures and agricultural fields. The Cerrado is a Savanna-like biome that occurs mostly in the center-west region of country. It is the second largest biome of Brazil, corresponding to 24% of the Brazilian territory (http://www.ibama.gov.br/). In contrast to the inland Cerrado, the Atlantic Forest is a biome that occurs mainly in the Brazilian coast, from the state of Rio Grande do Norte to Rio Grande do Sul. Aiming to compare the diversity and structure of acidobacterial communities in contrasting Brazilian ecosystems, here we present the analysis of 16S rRNA gene sequences from three works that describe soil acidobacterial communities from the Cerrado (present work, also described in [25]) and the Atlantic Forest [26, 27]. The analysis of soil parameters that may influence the diversity and distribution of Acidobacteria subgroups is also presented. The ecological roles of Acidobacteria in soils are not well understood. In this work, we begin to address this topic by correlating specific Acidobacteria subgroups to the soil environment found in the Brazilian biomes Cerrado and Atlantic Forest. Kit (MOBIO Laboratories, Inc.) according to manufacturer’s instructions. 16S rDNA PCR using metagenomic DNA from soil as a template was amplified with the bacterial-specific primers 27F (5󸀠 AGAGTTTGA TCMTGGCTCAG 3󸀠 ) and 1492R (5󸀠 GGYTACCTTGTTACGACTT 3󸀠 ). The amplified bands were (...truncated)