First high-quality draft genome of Ochrobactrum haematophilum P6BS-III, a highly glyphosate-tolerant strain isolated from agricultural soil in Argentina

Abstract

We report here on a high-quality draft genome sequence of Ochrobactrum haematophilum strain P6BS-III (DSM 106071), a Gram negative, non-sporulating bacterium isolated from a pastureland (Buenos Aires province, Argentina) which had been chronically exposed to the herbicide glyphosate. The genome of 5.25 Mb with a DNA G+C content of 56.63% size was estimated to contain 5,291 protein coding genes and 57 RNA genes. Genome analysis revealed the presence of the phn operon, which is involved in the phosphonate degradation pathway, and a class II 5-enolpyruvylshikimate-3-phosphate synthase (EPSP) that confers tolerance to glyphosate. Genes related to plant growth promotion traits are also present, and include genes for phosphorus metabolism, calcium phosphate and phytate solubilization, siderophore production, organic acid biosynthesis and indole acetic acid (IAA) production.

Indirect Effects of the Herbicide Glyphosate on Plant, Animal and Human Health Through its Effects on Microbial Communities

“…Intensive and long-term glyphosate use has led to the selection of bacterial and fungal strains with low sensitivity to glyphosate through various resistance mechanisms, ranging from low permeability of the cell wall, active removal from the cell, to changes in the EPSPS binding site (Liu et al, 2013;Massot et al, 2019;Priestman et al, 2005;Rainio et al, 2021;Staub et al, 2012;van Bruggen et al, 2018). Some glyphosate-resistant E. coli and Pseudomonas strains contain a gene coding for an ABC transporter that enhances the efflux of glyphosate from the cell (Staub et al, 2012).…”

“…Overall, pathogenic bacteria are less sensitive than nonpathogenic bacteria irrespective of the method used to assess growth. MIC values also depend on the year of isolation of the cultures studied relative to the time since glyphosate introduction into the environment (Bote et al, 2019a;Grube et al, 2019;Massot et al, 2019). Recent isolates are less sensitive to glyphosate and GBH than older isolates.…”

Isolation, Biochemical and Genomic Characterization of Glyphosate Tolerant Bacteria to Perform Microbe-Assisted Phytoremediation

“…A phylogenetic analysis of a total of 599 EPSPS protein sequences including the 10 obtained in this work, and the Ochrobactrum haematophilum P6BS-III single sequence ( Massot et al, 2019 ) was carried out. The results grouped the sequences in two clusters, one of them including the sequence of the CP4, and the other one including sequences of the Rhizobium genus and at a significant distance of the typically sensitive EPSPS Class I of E. coli , with less than approximately 40% of amino acid identity ( Figure 1B ).…”

“…Ochrobactrum sp. P6BS-III, recently reported as Ochrobactrum haematophilum P6BS-III ( Massot et al, 2019 ), showed various in vitro plant growth promotion abilities, such as production of IAA, phosphorus solubilization, and siderophores production. The Ochrobactrum genus was previously reported with the ability of degrading different organic compounds ( Kiliç, 2009 ; Abraham and Silambarasan, 2016 ; Chudasama and Thaker, 2017 ).…”