Illumina MiSeq based assessment of bacterial community structure and diversity along the heavy metal concentration gradient in Sukinda chromite mine area soils, India

Abstract

Abstract Using Illumina Miseq based 16S rRNA amplicon sequencing approach, the present study evaluated the influence of chromite mining on soil bacterial diversity and community structure in two in situ mine sites along with one chromite mine overburden soil and a forest soil adjacent to Sukinda chromite mines area of Odisha, India exhibiting different heavy metals (Cr, Pb, Mn etc.) concentration gradient. The soil bacterial communities at four study sites harbour a distinct set of phyla types which varies among the sites in relation to soil physico-chemical properties. Among the four locations, the overburden site (medium level of contamination) was distributed with higher bacterial operational taxonomic units (OTUs) abundance clustered at 97% sequence identity, whereas nearby forest soil sample with least contamination was reported with lesser number of bacterial OTUs. Principal component analysis plot indicated that in situ sites were distributed with closely related or most common species than other two samples. The dataset comprises more than 20000 OTUs that are affiliated to seven major bacterial phyla: Actinobacteria and Proteobacteria followed by Firmicutes, Acidobacteria, Chloriflexi, Bacteroidetes and unclassified phylum in all four samples. There is a shift in phylum level bacterial population (Actinobacteria, Proteobacteria and Acidobacteria) from contaminated sites to control sites and suggests that these bacterial groups may be the most metal tolerant organisms found in the contaminated sites. At species level, in situ sites were enriched with most common abundant microbes such as Shigella sp., Bacteroides sp., Propionibacterium acnes, Pantoea sp., Aciditerrimonas sp., Reyranella sp., Alphaproteobacterium sp., Burkholderiaceae sp. Soil pH and concentration of heavy metal such as chromium play a key role in affecting the structure and diversity of microbial communities in this study. This work demonstrates first-ever study in revealing bacterial diversity and presents background information of bacterial communities of Sukinda chromite mine area and shed light on possible bioremediation promoted by bacterial communities.