Phosphite as an engineered niche for Pseudomonas veronii in a synthetic soil bacterial community

ABSTRACT Bioaugmentation, the process of soil restoration by introducing microorganisms capable of degrading pollutants, is a promising and cost-effective strategy for environmental remediation. Aromatic hydrocarbons, such as benzene, toluene, ethylbenzene, and p-xylene (BTEX), are highly toxic environmental contaminants that could be transformed to less harmful products through the inoculation of certain organisms capable of BTEX degradation. However, a barrier to successful bioaugmentation is the inoculant’s failure to establish within the resident microbial community. In an effort to improve inoculant proliferation, we have investigated phosphite as a phosphorus source for selective nutrient supply. Phosphite is an inaccessible form of phosphorus to organisms that lack the capacity for phosphite oxidation to phosphate. We introduced a phosphite dehydrogenase-coding gene (ptxD) into the genome of the toluene-degrading bacterium Pseudomonas veronii 1YdBTEX2 to couple phosphite metabolism and aromatic hydrocarbon clearance. When inoculated in either soil matrix or liquid soil extract, P. veronii proliferates in a phosphite- and toluene-dependent manner in both growing and stable synthetic soil microbial communities, although the selective effects of phosphite and toluene were not additive in a carbon-limited context. Once toluene is metabolized, P. veronii abundance decays, and the microbial community recovers diversity and abundance resembling the uninoculated controls. Additional members of the microbial community were also enriched in the presence of phosphite, and genomic analysis suggests that these microorganisms utilize an alkaline phosphatase, phoV, for phosphite assimilation. IMPORTANCE Bioaugmentation is a promising solution to soil contamination, but its practical application is limited due to poor inoculant establishment in the native soil community. This can often be attributed to low nutrient availability and resource competition with native microorganisms. We proposed the use of phosphite as a selective nutrient source to support the growth of a toluene-degrading bacterium, Pseudomonas veronii, in a model soil system. We engineered a strain of this organism that was capable of using phosphite as a phosphorus source and saw that phosphite application enhanced the abundance of the inoculant sixfold within a synthetic soil community. In this study, we present the first investigation of a phosphite selection system in the soil microbiome and characterize the environmental conditions in which it is effective. By demonstrating the potential of formulated nutritional niches in soil microbiome interventions, we provide significant insights into the field of microbiome engineering. Bioaugmentation is a promising solution to soil contamination, but its practical application is limited due to poor inoculant establishment in the native soil community. This can often be attributed to low nutrient availability and resource competition with native microorganisms. We proposed the use of phosphite as a selective nutrient source to support the growth of a toluene-degrading bacterium, Pseudomonas veronii, in a model soil system. We engineered a strain of this organism that was capable of using phosphite as a phosphorus source and saw that phosphite application enhanced the abundance of the inoculant sixfold within a synthetic soil community. In this study, we present the first investigation of a phosphite selection system in the soil microbiome and characterize the environmental conditions in which it is effective. By demonstrating the potential of formulated nutritional niches in soil microbiome interventions, we provide significant insights into the field of microbiome engineering.