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

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.

Soil Microbial Biomass Across a Gradient of Preserved Native Cerrado

“…Additionally, soil chemical properties positively influenced the soil microbial biomass in CSS and CD because nutrients, such as P and K, contribute to increased microbial biomass . Araujo et al (2012) evaluated the bacterial community in a Cerrado gradient from southeastern Brazil, and found higher nutrient levels in the Cerradao. These properties influenced soil microorganisms through the input of diverse nutrient sources into the belowground system.…”

Molecular detection on culture medium of Acidobacteria from Amazon soils

“…The soil samples were collected in November 2011 from six different sampling sites located at three different municipalities in the Brazilian Amazon region: (1) Five soil cores (5 cm in diameter, 0-to 20-cm topsoil layer) were collected from each sampling site using a cylindrical soil corer aseptically and transported to the laboratory in a sealed polyethylene bag at ambient temperature and stored overnight at 4 o C. The soil samples were collected from five sampling points at each site, with one central sampling point and other four sampling points (at least 50 m away from the central point) directed toward the north, south, east, and west of the central point. An accurately weighed aliquot of soil (6 g fresh weight) from each of the five soil samples per sampling site was suspended in 100 mL sterile salt solution (3.9 g 2-[N-morpholino]ethanesulphonic acid, 0.4 mM MgSO 4 , 0.6 mM CaCl 2 , and 0.4 mM (NH 4 ) 2 HPO 4 per litre) and mixed using a Teflon-coated magnetic bar for 15 min at approximately 200 r.p.m.…”

“…The PA(1.5) colony was identified as Acidobacteria subdivision [1] (100% identity with 16S rRNA gene sequences) and the PA(2.1) colony as belonging to Acidobacteria subdivision [3] (100% identity with 16S rRNA gene sequences) (Figure 4). Based on the partial sequencing of the 16S rRNA gene (1488 bp), the acidobacterial colonies PA(2.6) and SC-2(3.2) were identified as Acidobacteria subdivision [1] (100% identity with 16S rRNA gene sequences) (Figure 4), and both were isolated and preserved by lyophilisation and mineral oil. All the four acidobacterial colonies did not grow when inoculated in liquid VL55 medium; however, PA(2.6) and SC-2(3.2) were able to grow on solid medium under atmosphere-unamended air.…”

“…The culture-independent approach based on the direct recovery of bacterial 16S rRNA from tropical soils indicated the predominance of Acidobacteria in soils from Western Amazon (Kim et al, 2007;Jesus et al, 2009), Central Amazon (Navarrete et al, 2010), Southeastern Amazon , and the Brazilian Cerrado (Araujo et al, 2012). Among the 26 acidobacterial subdivisions classified, subdivisions [1-7, 10,11,13,16-18,22, and 25] have been detected in Amazon soils using 16S rRNA gene pyrosequencing Cannavan, 2012).…”

“…Although many laboratories are attempting to obtain pure cultures of Acidobacteria from different environments worldwide, the taxonomically described diversity within this group remains very limited. More than half of the currently characterised Acidobacteria belong to subdivision [1], and only 18/141 high-quality 16S rRNA gene sequences from bacterial isolates are classified as subdivision [3] (Ribosomal Database Project (RDP) II v10.4; http://rdp.msu.edu/). Members of Acidobacteria subdivision [1] (Dedysh et al, 2006;Kulichevskaya et al, 2010).…”