An in-depth analysis of actinobacterial communities shows their high diversity in grassland soils along a gradient of mixed heavy metal contamination

Abstract

Several previous studies indicated that Actinobacteria may be enriched in soils with elevated content of heavy metals. In this study, we have developed a method for the in-depth analysis of actinobacterial communities in soil through phylum-targeted high-throughput sequencing and used it to address this question and examine the community composition in grassland soils along a gradient of heavy metal contamination (Cu, Zn, Cd, Pb). The use of the 16Sact111r primer specific for Actinobacteria resulted in a dataset obtained by pyrosequencing where over 98 % of the sequences belonged to Actinobacteria. The diversity within the Actinobacterial community was not affected by the heavy metals, but the contamination was the most important factor affecting community composition. The most significant changes in community composition were due to the content of Cu and Pb, while the effects of Zn and Cd were relatively minor. For the most abundant actinobacterial taxa, the abundance of taxa identified as members of the genera Acidothermus, Streptomyces, Pseudonocardia, Janibacter and Microlunatus increased with increasing metal content, while those belonging to Jatrophihabitans and Actinoallomurus decreased. The genus Ilumatobacter contained operational taxonomic units (OTUs) that responded to heavy metals both positively and negatively. This study also confirmed that Actinobacteria appear to be less affected by heavy metals than other bacteria. Because several Actinobacteria were also identified in playing a significant role in cellulose and lignocellulose decomposition in soil, they potentially represent important decomposers of organic matter in such environments.