Abstract
Heavy metal pollutions in the soils are increasingly threatening the global crop and food production. Using plant associated bacteria to remediate heavy metal contamination is a promising approach. We have isolated a cadmium (Cd) resistant Enterococcus faecium strain CX 2–6 from a heavy metal contaminated farmland. We have shown that: (i) CX 2–6 can tolerate cadmium (Cd) with a slower growth rate; (ii) The CX 2–6 complete genome is fully assembled using PacBio long reads; (iii) Differential expression analysis found 47% of CX 2–6 genes are significantly affected by Cd treatment and form three gene groups with distinct expression profiles; (iv) Differentially expressed genes (DEGs) form physically linked gene clusters in the CX 2–6 genome, and one of the gene clusters corresponds to a prophage that is unique to CX 2–6 and is strongly activated when Cd concentration is higher; (v) A majority of DEGs responding to Cd treatment are present in the core genome; and (vi) 55 noncoding RNA genes are identified and 49 of them are DEGs responding to cadmium stress. Our pan-genome analysis and comparative RNA-seq data analysis has significantly improved our understanding of the metabolic reprogramming of E. faecium CX 2–6 under Cd stress.
Highlights
Human activities and industrial developments have created tremendous stresses on the ecological environment
We have focused on two major types of ncRNAs: anti-sense RNAs that are on the opposite strand of mRNAs, and intergenic RNAs that are located in the intergenic regions of mRNAs
It is not surprising that each of the 27 anti-sense RNAs (asRNAs) has 9 identical or near identical matches in different subsets of the 18 transposases (Fig. 5A and Table S7), aside from their own genomic locations. All these findings suggest that E. faecium asRNAs play a significant role in cadmium stress response by modulating the expression of transposases
Summary
Human activities and industrial developments have created tremendous stresses on the ecological environment. As one type of abiotic stresses heavy metal pollutions in the soils are increasingly threatening the global crop and food production [1,2,3]. Consumption of foods and crops polluted by heavy metals can be a significant health risk to humans and animals [4]. For the remediation of soils contaminated with heavy metal pollutions, cheap, effective, and fast methods are in high demand and are currently being in extensive research [5,6,7]. Our recent research provided evidence that exopolysaccharides (EPS) from Lactobacillus plantarum can mediate the reduction of copper toxicity in rice seedlings, suggesting that EPS could be considered as a novel agent for effective heavy metal sequestration [9]. Others have found that two strains of Enterococcus faecium commonly used in food industry can efficiently remove cadmium
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