Cadmium stress triggers significant metabolic reprogramming in Enterococcus faecium CX 2-6

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.