Microbial diversity and metabolic potential in long-term Cr(VI) polluted soil during in situ biostimulation: a pilot effective assay

Excess industrial Cr(VI) waste and its improper disposal have resulted in the contamination of diverse environments, including soils and aquifers. To contend with high concentration of Cr(VI), a dangerous mutagen and oxidizing agent, diverse bacteria have developed a broad spectrum of metabolic strategies, mainly through chromate efflux pumps and reduction of Cr(VI) to Cr(III), which is less toxic and unable to cross biological membranes. In this study, we performed an in situ biostimulation assay in a highly alkaline and saline soil from a long-term contaminated site in Guanajuato, México. Four percent molasses was an effective treatment in promoting the Cr(VI) reduction by indigenous microorganisms. Initial Cr(VI) concentration was 5.6 to 12.4 g per kg of soil; After biostimulation assay (20 days), Cr(VI) was reduced from 0.75 to 3.02 g per kg of soil. DNA and RNA extraction from biostimulated samples was performed to carry out metagenomic and metatranscriptomic studies. Furthermore, 16S rDNA V3 and V4 amplicons were sequenced using illumina MiSeq technology complementing the study. The results showed an enrichment at Class level of Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, Nitriliruptoria and Bacilli. The enrichment of Halomonas spp. during the biostimulation assay was remarkable, reaching 92% of the population and becoming the most dominant genus. On the other hand, comparative metagenomic and metatranscriptomic analysis was carried out in order to know the whole microbial population and the genes expressed during the reduction of Cr(VI) to Cr(III). We identified reductase genes associated with various bacterial groups. Interestingly, all the expressed reductase genes were exclusively from the genus Halomonas, which are related with our taxonomic assignment analysis. This study improves our understanding of the response of bacterial communities to high exposure to chromate and offers an alternative to the restoration of environments severely contaminated with this powerful toxic agent.