Metabolic and genomic analysis elucidates strain-level variation in Microbacterium spp. isolated from chromate contaminated sediment

Abstract

Hexavalent chromium [Cr(VI)] is a soluble carcinogen that has caused widespread contamination of soil and water in many industrial nations. Bacteria have the potential to aid remediation as certain strains can catalyze the reduction of Cr(VI) to insoluble and less toxic Cr(III). Here, we examine Cr(VI) reducing Microbacterium spp. (Cr-K1W, Cr-K20, Cr-K29, and Cr-K32) isolated from contaminated sediment (Seymore, Indiana) and show varying chromate responses despite the isolates' phylogenetic similarity (i.e., identical 16S rRNA gene sequences). Detailed analysis identified differences based on genomic metabolic potential, growth and general metabolic capabilities, and capacity to resist and reduce Cr(VI). Taken together, the discrepancies between the isolates demonstrate the complexity inter-strain variation can have on microbial physiology and related biogeochemical processes.

Keywords: Chromium reduction; Microbacterium; Strain-level variation.

Figure 1. Comparison of the isolate’s ability to grow and reduce chromate.

Chromate reduction (gray fill) and growth curves of Microbacterium spp. in the presence (black fill) or absence (no fill) of chromate. Negative (uninoculated) controls for chromate reduction are labeled in each graph with an asterisk. (A) Cr-K1W, diamond; (B) Cr-K29, triangle; (C) Cr-K32, circle; (D) Cr-K20, square (n = 3, error bars are SD).

Figure 2. PCA of metabolic fingerprinting.

Principal component analysis plot of the four isolates based on their ability to utilize a metabolic substrate.

Figure 3. PCA of Pfam catagories.

Principal component analysis of 21 Pfam catagories from IMG annotations of the four Microbacterium sp. genomes. Top five eigenvalues were then plotted as the vectors after analysis.