Environmental Factors Affect Acidobacterial Communities below the Subgroup Level in Grassland and Forest Soils

Abstract

In soil, Acidobacteria constitute on average 20% of all bacteria, are highly diverse, and are physiologically active in situ. However, their individual functions and interactions with higher taxa in soil are still unknown. Here, potential effects of land use, soil properties, plant diversity, and soil nanofauna on acidobacterial community composition were studied by cultivation-independent methods in grassland and forest soils from three different regions in Germany. The analysis of 16S rRNA gene clone libraries representing all studied soils revealed that grassland soils were dominated by subgroup Gp6 and forest soils by subgroup Gp1 Acidobacteria. The analysis of a large number of sites (n ‫؍‬ 57) by 16S rRNA gene fingerprinting methods (terminal restriction fragment length polymorphism [T-RFLP] and denaturing gradient gel electrophoresis [DGGE]) showed that Acidobacteria diversities differed between grassland and forest soils but also among the three different regions. Edaphic properties, such as pH, organic carbon, total nitrogen, C/N ratio, phosphorus, nitrate, ammonium, soil moisture, soil temperature, and soil respiration, had an impact on community composition as assessed by fingerprinting. However, interrelations with environmental parameters among subgroup terminal restriction fragments (T-RFs) differed significantly, e.g., different Gp1 T-RFs correlated positively or negatively with nitrogen content. Novel significant correlations of Acidobacteria subpopulations (i.e., individual populations within subgroups) with soil nanofauna and vascular plant diversity were revealed only by analysis of clone sequences. Thus, for detecting novel interrelations of environmental parameters with Acidobacteria, individual populations within subgroups have to be considered.

Response of soil microorganisms to radioactive oil waste: results from a leaching experiment

“…Bacteria from the genus Burkholderia are typical soil inhabitants, and certain Burkholderia strains are resistant to hydrocarbons and are used in the bioremediation of oil-polluted sites (Bacosa et al, 2012;Weisskopf et al, 2011;Hamamura et al, 2008;Adetutu et al, 2013). Band 3 (KF926426-KF926429), which is sensitive to oily and radioactive components in the waste samples (not seen in contaminated H -and R-samples), was genetically similar to Hydrogenobacter hydrogenophilus (Z30242) uncultured Acidobacteria isolated from unpolluted grassland and forest soils (HQ598830, HQ599021; Naether et al, 2012) and an uncultured Chlorobiales bacterium found in a uranium mining waste pile (AJ295649, AJ536877; Selenska-Pobell, 2002). Band 4 (KF926430-KF926433), which dominated in H -columns, was related to an uncultured bacterium from mineral soils of the Atacama desert (JX098489, JX098426; Lynch et al, 2012) and actinomycetes from the genus Catenulispora (CP001700, AJ865857; Busti et al, 2006) as well as strains isolated from gasoline-polluted sites (or able to degrade hydrocarbons; JQ919514; Hilyard et al, 2008), including a Parvibaculum strain that catabolizes linear alkylbenzene sulfonate (AY387398; Schleheck et al, 2004).…”

The first representative of the globally widespread subdivision 6 Acidobacteria, Vicinamibacter silvestris gen. nov., sp. nov., isolated from subtropical savannah soil

“…In particular, no isolate of sd6 is available, although the latter represents the dominant subdivision in many soils (Barns et al, 1999;Foesel et al, 2014;Jones et al, 2009). 16S rRNA sequence analyses revealed that members of sd6 dominate in soils with a neutral or (slightly) basic pH, together with bacteria of sd4, whereas members of sd 1 and 3 prevail in soils which are (slightly) acidic Jones et al, 2009;Naether et al, 2012). About half of the soils on earth have a neutral or (slightly) basic pH (www.fao.org/soils-portal/soil-survey/soil-properties/chemical-properties/en/).…”

Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress

“…According to molecular studies, members of the Acidobacteria are among the most abundant bacteria in soil (35) and may represent up to 20% of the total bacteria in soil communities (36). Recent genome sequencing projects targeting bacteria belonging to this group promoted insights into their lifestyle and revealed them to be best suited to low-nutrient conditions (37)(38)(39).…”