Abstract
Trace metals are required in many cellular processes in bacteria but also induce toxic effects to cells when present in excess. As such, various forms of adaptive responses towards extracellular trace metal ions are essential for the survival and fitness of bacteria in their environment. A soil Pseudomonas putida, strain S13.1.2 has been isolated from French vineyard soil samples, and shown to confer resistance to copper ions. Further investigation revealed a high capacity to tolerate elevated concentrations of various heavy metals including nickel, cobalt, cadmium, zinc and arsenic. The complete genome analysis was conducted using single-molecule real-time (SMRT) sequencing and the genome consisted in a single chromosome at the size of 6.6 Mb. Presence of operons and gene clusters such as cop, cus, czc, nik, and asc systems were detected and accounted for the observed resistance phenotypes. The unique features in terms of specificity and arrangements of some genetic determinants were also highlighted in the study. Our findings has provided insights into the adaptation of this strain to accumulation and persistence of copper and other heavy metals in vineyard soil environment.Electronic supplementary materialThe online version of this article (doi:10.1186/s13568-016-0269-x) contains supplementary material, which is available to authorized users.
Highlights
Natural or anthropogenic accumulation of heavy metals in the environment could be tenacious and exhibit toxicity towards living organisms
Isolation and characterization of strain S13.1.2 Sequence comparison with GenBank databases using the BLASTN followed by phylogenetic analysis revealed the closest identified relative to P. putida NBRC 14164 sharing 99 % of sequence identity
Copper resistance and other heavy metal resistance traits of strain S13.1.2 Growth of P. putida S13.1.2 in the presence of various CuSO4 concentrations in LB medium was observed in media supplemented with up to 3.5 mM of the copper salt
Summary
Natural or anthropogenic accumulation of heavy metals in the environment could be tenacious and exhibit toxicity towards living organisms. This phenomenon is exemplified by the CzcCBA system that mediates an efflux of Co2+, Zn2+ and Cd2+ ions (Nies 2000) Another family of heavy metal transport protein, namely P-type ATPases, are involved in both import of inorganic cations to cytoplasm from periplasm or outside of the cell, and export of these ions from/to cytoplasm in a reversed manner. Reduction of the pentavalent arsenate [As(V)] ion to its trivalent arsenite [As(III)] counterpart by the arsenate reductase ArsC enables the detoxification and efflux of As(III) through the membrane pump protein ArsB (Cai et al 1998; Carlin et al 1995) These systems are often regulated in response to the presence of metal ions that in turn activates transcription of subsequent resistance determinants. Examples include the regulator ArsR that induces the expression of the ars arsenite/antimonite resistance operon upon exposure to these ions (Sato and Kobayashi 1998), or CzcD, a cation diffusion facilitator protein that partially regulates the expression of the CzcCBA system (Nies 1992)
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