Genomic and functional characterization of compost-derived bacteria identifies a candidate bioinoculant that influences tomato physiology and leaf metabolism

Soil biodiversity is increasingly threatened by anthropogenic activities, with intensive agriculture having a particularly detrimental impact on soil microbial communities and potentially disrupting plant-microbe interactions that contribute to plant growth and resilience to environmental stresses. Biofertilizers based on Plant Growth-Promoting Rhizobacteria (PGPR) and organic amendments represent promising strategies to restore microbial diversity and promote crop health. Although compost is widely used as an organic fertilizer, its potential as a reservoir of culturable beneficial bacteria for the development of bioinoculants remains largely unexplored. In this work, we isolated and identified six bacterial strains from commercial compost derived from municipal organic waste and screened them for plant growth-promoting traits. Two representative isolates, Kocuria rhizophila and Glutamicibacter arilaitensis, were subjected to whole-genome sequencing and comparative analyses to investigate their taxonomy, functional potential, rhizosphere competence, secondary metabolism, plastic degradation associated features, and predicted human pathogenicity. K. rhizophila was subsequently tested as an inoculant on tomato plants grown in soil, compost-amended soil, or sterile compost-amended soil. Five of the six isolates exhibited many of the plant growth-promoting traits tested. Genomic analyses of the two strains supported several of the observed phenotypes and revealed functions potentially associated with nutrient metabolism, plant-root interactions, environmental adaptation, and degradation of plastic polymers. Neither strain was predicted to be pathogenic to humans, indicating a potentially low safety risk for their application as bioinoculants. Upon inoculation with K. rhizophila, plant responses were influenced primarily by substrate type, although the bacterium produced specific, substrate-dependent effects at 33 days post inoculation. Inoculation resulted in a trend towards increased dry biomass in plants grown in sterile compost and influenced leaf metabolic profiles at 33 days. These results support the potential of K. rhizophila as a compost-derived bioinoculant and indicate that enriching compost with beneficial strains isolated from the same matrix could be a useful approach to complement its effects on plant growth.