Comprehensive genomic and phenotypic metal resistance profile of Pseudomonas putida strain S13.1.2 isolated from a vineyard soil

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.

Pea (Pisum sativum l.) Plant Shapes Its Rhizosphere Microbiome for Nutrient Uptake and Stress Amelioration in Acidic Soils of the North-East Region of India

“…The higher abundance of iron complex outer membrane receptor protein in the rhizosphere indicates the enrichment of Gram-negative bacteria, which outer membrane receptor system for siderophore-mediated Fe transportation (Ahmed and Holmström, 2014). The CzcA protein has been reported to be involved in the efflux of heavy metals ions (Nies, 2000) and was also present in metal resistance Pseudomonas putida S13.1.2 isolated from a vineyard soil (Chong et al, 2016). Rhizosphere offers a variety of abiotic stress, including temperature fluctuations, salinity, osmolarity, oxygen concentration, and nutrient concentration, to the bacteria; RNA polymerase sigma-70 factors play relevant roles in adapting to different kinds of stresses (Martínez-Salazar et al, 2009;Mishra et al, 2011).…”

Impact of Chemical and Biological Fungicides Applied to Grapevine on Grape Biofilm, Must, and Wine Microbial Diversity

“…The presence of Methylobacterium has been recently reported by Portillo et al (2016) in the grape surface of different varieties; and Ps. putida , present in grapevine soil, is very important because its capacity of resisting different metal contamination ( Chong et al, 2016 ). Furthermore, the identification of Bacillus subtilis applied from grapevine until the AF depletion should be taken into consideration in future works.…”

Comparative genome analysis of the vineyard weed endophyte Pseudomonas viridiflava CDRTc14 showing selective herbicidal activity

“…A recent study revealed that long-term association with metal-hyperaccumulator plant leads to local adaptation by Pseudomonas endophytes 50 . Copper and arsenic resistant Pseudomonas strains have been frequently isolated from the vineyard environment 51 , 52 . Indeed, vineyards have been treated with copper-containing pesticides to control plant pathogens 53 as well as with sodium arsenate till the end of the last century, which may still be present in vineyard soils 54 .…”