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

Abstract

The large-scale use of the herbicide glyphosate leads to growing ecotoxicological and human health concerns. Microbe-assisted phytoremediation arises as a good option to remove, contain, or degrade glyphosate from soils and waterbodies, and thus avoid further spreading to non-target areas. To achieve this, availability of plant-colonizing, glyphosate-tolerant and -degrading strains is required and at the same time, it must be linked to plant-microorganism interaction studies focusing on a substantive ability to colonize the roots and degrade or transform the herbicide. In this work, we isolated bacteria from a chronically glyphosate-exposed site in Argentina, evaluated their glyphosate tolerance using the minimum inhibitory concentration assay, their <i>in vitro</i> degradation potential, their plant growth-promotion traits, and performed whole genome sequencing to gain insight into the application of a phytoremediation strategy to remediate glyphosate contaminated agronomic soils. Twenty-four soil and root-associated bacterial strains were isolated. Sixteen could grow using glyphosate as the sole source of phosphorous. As shown in MIC assay, some strains tolerated up to 10000 mg kg^-1 of glyphosate. Most of them also demonstrated a diverse spectrum of <i>in vitro</i> plant growth-promotion traits, confirmed in their genome sequences. Two representative isolates were studied for their root colonization. An isolate of <i>Ochrobactrum haematophilum</i> exhibited different colonization patterns in the rhizoplane compared to an isolate of <i>Rhizobium</i> sp. Both strains were able to metabolize almost 50% of the original glyphosate concentration of 50 mg l^-1 in 9 days. In a microcosms experiment with <i>Lotus corniculatus</i> L, <i>O. haematophilum</i> performed better than <i>Rhizobium</i>, with 97% of glyphosate transformed after 20 days. The results suggest that <i>L. corniculatus</i> in combination with to <i>O. haematophilum</i> can be adopted for phytoremediation of glyphosate on agricultural soils. An effective strategy is presented of linking the experimental data from the isolation of tolerant bacteria with performing plant-bacteria interaction tests to demonstrate positive effects on the removal of glyphosate from soils.