Determinants of Acidobacteria activity inferred from the relative abundances of 16S rRNA transcripts in German grassland and forest soils

Abstract

16S rRNA genes and transcripts of Acidobacteria were investigated in 57 grassland and forest soils of three different geographic regions. Acidobacteria contributed 9-31% of bacterial 16S rRNA genes whereas the relative abundances of the respective transcripts were 4-16%. The specific cellular 16S rRNA content (determined as molar ratio of rRNA : rRNA genes) ranged between 3 and 80, indicating a low in situ growth rate. Correlations with flagellate numbers, vascular plant diversity and soil respiration suggest that biotic interactions are important determinants of Acidobacteria 16S rRNA transcript abundances in soils. While the phylogenetic composition of Acidobacteria differed significantly between grassland and forest soils, high throughput denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism fingerprinting detected 16S rRNA transcripts of most phylotypes in situ. Partial least squares regression suggested that chemical soil conditions such as pH, total nitrogen, C : N ratio, ammonia concentrations and total phosphorus affect the composition of this active fraction of Acidobacteria. Transcript abundance for individual Acidobacteria phylotypes was found to correlate with particular physicochemical (pH, temperature, nitrogen or phosphorus) and, most notably, biological parameters (respiration rates, abundances of ciliates or amoebae, vascular plant diversity), providing culture-independent evidence for a distinct niche specialization of different Acidobacteria even from the same subdivision.

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

“…The contrasting tendencies of pH preference displayed by different classes of Acidobacteria in this site were in agreement with some recent studies (Rousk et al, 2010;George et al, 2011;Foesel et al, 2014). Unlike most other phyla, Acidobacteria seemed to be unaffected by contamination levels that suggests a role as generalists in hydrocarboncontaminated soils (Mukherjee et al, 2013).…”

Estimates of Soil Bacterial Ribosome Content and Diversity Are Significantly Affected by the Nucleic Acid Extraction Method Employed

“…Afterwards, samples were stored at Ϫ80°C. Total soil carbon, organic carbon, total nitrogen, soluble nitrate and ammonium, and bacterial cell numbers were determined as described previously (6). The three soils selected differed with respect to soil type, texture, and carbon and nutrient contents (Table 1).…”

“…While DNA sequences provide information about the total microbial community, RNA can be used to analyze the fraction of microorganisms that has the capacity to actively synthesize proteins (3)(4)(5). The ratio of bacterial 16S rRNA transcripts to 16S rRNA gene copies has been used as an indicator of the potential specific activity since it reflects the cellular ribosome content (6,7). However, nucleic acid extraction from soils is affected by insufficient cell lysis or losses during extraction, variable reproducibility, and various effects of soil pH, clay content, and organic carbon content (8)(9)(10)(11)(12)(13), and coextracted organic compounds can inhibit DNA polymerase and reverse transcriptase employed in downstream molecular analyses (14).…”

Terracidiphilus gabretensis gen. nov., sp. nov., an Abundant and Active Forest Soil Acidobacterium Important in Organic Matter Transformation

“…pH is the most important environmental variable affecting acidobacterial abundance (8). Besides pH, a negative correlation with organic carbon availability and total nitrogen concentration in soils was observed, suggesting an oligotrophic lifestyle of Acidobacteria (22,23). Oligotrophy and preferential colonization of bulk soil instead of rhizosphere (22) suggest an adaptation to metabolize non-simple carbon compounds.…”