Introduction

Acidobacteria is a phylum of bacteria. Its members are physiologically diverse and ubiquitous, especially in soils, but are under-represented in culture. The phylum Acidobacteria is one of the most widespread and abundant on the planet, yet remarkably our knowledge of the role of these diverse organisms in the functioning of terrestrial ecosystems remains surprisingly rudimentary.

This blatant knowledge gap stems to a large degree from the difficulties associated with the cultivation of these bacteria by classical means. Given the phylogenetic breadth of the Acidobacteria, which is similar to the metabolically diverse Proteobacteria, it is clear that detailed and functional descriptions of acidobacterial assemblages are necessary. Fortunately, recent advances are providing a glimpse into the ecology of members of the phylum Acidobacteria.

Isolation methods

Changes in the traditional methods for culturing bacteria from soils have significantly improved the isolation of Acidobacteria strains in recent years. These new strategies involve the use of relatively low concentration of nutrients, non-traditional sources of carbon or complex polysaccharides longer periods of incubation, the use of gellan gum as solidifying agent, non-standard CO2 atmospheric conditions of incubation, addition of quorum-signaling molecules, catalase or cations amendments of inhibitors for undesired organisms, and amendment of environmental extracts in growth media.

It is suggested that raising the CO2 concentration may not only better mimic the CO2 concentrations typically found in soils, but may also decrease medium pH, thereby benefiting certain members of the acidobacteria, especially moderate acidophilic strains belonging to subdivision1. This combination of strategies seems to enrich not only for Acidobacteria but for many other groups of slow-growing bacteria.

Chemical factors

The chemical factors of each soil sample were determined according to Empresa Brasileira de Agropecuária-Embrapa [EMBRAPA]. Soil pH was determined in a soil/0.01 M CaCl2 1:5 suspensions. Boron was obtained by hot water extraction. Al, Ca, and Mg were extracted with 1 M potassium chloride. Ca and Mg were determined by spectrometric atomic absorption, whereas Al was determined by acid-base titration. Available P and K were extracted by ion-exchange resin and determined by colorimetry and atomic emission spectroscopy, respectively. The combined results were used to calculate the exchangeable bases sum of Ca, Mg, and K, CEC sum of Ca, Mg, K, Al and H, BS, percentage ratio between BS and CEC and potential acidity H + Al using an equation based on the Shoemaker-McLean-Pratt SMP pH-buffer method.

The strong negative correlation between the abundance of Acidobacteria and concentration of organic carbon in soil has led to the conclusion that members of this phylum may be oligotrophic bacteria. However, it was pointed out that not necessarily all members would be oligotrophic. In addition, genome sequences revealed the presence of only one or two copies of 16S rRNA genes suggesting lower growth rates, which has been previously correlated with oligotrophy. Additional evidence for interaction with soil bacteria is the fact that Edaphobacter aggregans and B. elongata were isolated from co-cultures with methanotrophic bacteria. It was demonstrated that B. elongata was unable to use CO2 and other C1 carbon compounds, which would be produced by the methanotrophic partner.

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