Influence of plant polymers on the distribution and cultivation of bacteria in the phylum Acidobacteria

Abstract

Members of the phylum Acidobacteria are among the most abundant bacteria in soil. Although they have been characterized as versatile heterotrophs, it is unclear if the types and availability of organic resources influence their distribution in soil. The potential for organic resources to select for different acidobacteria was assessed using molecular and cultivation-based approaches with agricultural and managed grassland soils in Michigan. The distribution of acidobacteria varied with the carbon content of soil: the proportion of subdivision 4 sequences was highest in agricultural soils (ca. 41%) that contained less carbon than grassland soils, where the proportions of subdivision 1, 3, 4, and 6 sequences were similar. Either readily oxidizable carbon or plant polymers were used as the sole carbon and energy source to isolate heterotrophic bacteria from these soils. Plant polymers increased the diversity of acidobacteria cultivated but decreased the total number of heterotrophs recovered compared to readily oxidizable carbon. Two phylogenetically novel Acidobacteria strains isolated on the plant polymer medium were characterized. Strains KBS 83 (subdivision 1) and KBS 96 (subdivision 3) are moderate acidophiles with pH optima of 5.0 and 6.0, respectively. Both strains grew slowly (μ = 0.01 h(-1)) and harbored either 1 (strain KBS 83) or 2 (strain KBS 96) copies of the 16S rRNA encoding gene-a genomic characteristic typical of oligotrophs. Strain KBS 83 is a microaerophile, growing optimally at 8% oxygen. These metabolic characteristics help delineate the niches that acidobacteria occupy in soil and are consistent with their widespread distribution and abundance.

FIG. 1.

Structure of acidobacterial communities in agricultural and managed grassland soils in MI based on acidobacterial 16S rRNA gene surveys. Average proportion (± standard deviation) of acidobacterial subdivisions in the agricultural and managed grassland soils at the KBS LTER from four field replicates.

FIG. 2.

Relationship between the average percentage of acidobacterial subdivision 4 sequences and carbon concentration for the upper 7 centimeters of soil from the agricultural and managed grassland soils. The four field replicates for each soil treatment are depicted as black boxes, whereas additional unreplicated acidobacterial libraries included in this analysis are depicted as gray boxes. These libraries were generated from other treatments at the KBS LTER. Carbon data were averaged for each treatment from historical data obtained from the KBS LTER website for carbon data collected between 1989 and 2001. Raw data and a detailed description of the treatments can be found at the KBS LTER website (http://lter.kbs.msu.edu/).

FIG. 3.

Summary of acidobacterial sequence diversity. Maximum likelihood tree based on 16S rRNA gene sequences from cultivated representatives, environmental clones, and partial acidobacterial sequences detected from cultivation experiments using readily oxidizable carbon (black box, n = 28) and plant polymers (gray box, n = 16). Subdivision nodes supported by a bootstrap value of 100% are indicated with a filled circle (•). Geothrix fermentans and Holophaga foetida of subdivision 8 were used as an outgroup (not shown). The scale bar indicates 0.10 changes per nucleotide.

FIG. 4.

Maximum likelihood tree of the acidobacterial subdivisions 1, 3, and 8 (indicated to the right of the group) based on 16S rRNA genes using sequences obtained from cultivated representatives and environmental clones. Geothrix fermentans, Holophaga foetida, and Acanthopleuribacter pedi of subdivision 8 were used as an outgroup. Strains from this study are in bold font. Internal nodes supported by a bootstrap value of >95% are indicated with a filled circle (•) and those of >70% with an open circle (○). The scale bar indicates 0.10 changes per nucleotide.

FIG. 5.

Phase-contrast and transmission electron micrograph of KBS 83 (A and B) and KBS 96 (C and D). The arrow in panel A indicates the capsular material layer produced by KBS 83. Scale bars indicate 1 μm (B and D) and 200 nm (A and C).

FIG. 6.

Summary of growth rates for strain KBS 83 under different concentrations of oxygen (vol/vol oxygen balanced with He). Each black box represents the average growth rate ± standard error at the respective oxygen concentration.