Exploring the rhizospheric and endophytic bacterial communities of Acer pseudoplatanus growing on a TNT-contaminated soil: towards the development of a rhizocompetent TNT-detoxifying plant growth promoting consortium

Abstract

Background and aims Numerous microorganisms have been isolated from trinitrotoluene (TNT)-contaminated soils, however TNT tends to persist, indicating that the microbial biomass or activity is insufficient for degradation. Deep-rooting trees at military sites have been found to take-up contaminants from groundwater, and the extensive root and endosphere provide ideal niches for microbial TNT-transformations. Methods We characterised the rhizosphere, root endosphere and endo-phyllosphere bacteria of Acer pseudoplatanus growing at a historically TNT-contaminated location, using 16S rRNA gene fingerprinting, bacteria isolation, oxidoreductase gene-cloning, in planta growth-promotion (PGP) tests, inoculation, plant physiology measurements and microscopy. Results Based on terminal-restriction-fragment-length-polymorphism analysis, bulk soil and rhizosphere samples were highly clustered. Proteo-and Actinobacteria dominated the rhizosphere and root endosphere, whereas Alphaproteobacteria were more abundant in shoots and Actinobacteria in leaves. We isolated multiple PGP-bacteria and cloned 5 flavin-oxidoreductases belonging to the Old Yellow Enzyme family involved in TNT-reduction from 3 Pseudomonas spp., the leaf symbiont Stenotrophomonas chelatiphaga and the root endophyte Variovorax ginsengisola. Conclusions The inoculation with a selection of these strains, consortium CAP9, which combines efficient TNT-transformation capabilities with beneficial PGP-properties, has the ability to detoxify TNT in the bent grass (Agrostis capillaris) rhizosphere, stimulate plant growth and improve plant health under TNT stress.