Environment-guided bioprospecting of plant growth-promoting bacteria in tropical and subtropical ecosystems

Identifying efficient plant growth-promoting bacteria (PGPB) is essential for advancing sustainable agriculture in tropical and subtropical ecosystems. We conducted a literature review to determine how ecological factors influence the discovery of elite PGPB. We hypothesized that (i) natural ecosystems harbor bacteria with broader functional diversity and greater stress tolerance due to environmental filtering, and (ii) isolates from agricultural systems are more effective due to prior selection through plant–microbe interactions. Data on PGPB functional traits and plant responses to inoculation were compiled from studies published between 2015 and 2025, including isolates from native and agricultural systems. Analyses based on Z-score standardization and principal component analysis revealed substantial variability among genera and indicated that PGPB traits are shaped by ecological constraints associated with the environment of origin. Meta-analyses of plant growth response ratios showed that isolates from agricultural systems were, on average, more effective than those from native ecosystems; plant growth promotion followed the gradient endophytic > rhizosphere > bulk soil; and isolates applied to their original host outperformed those applied to different hosts. Overall, these findings highlight the role of the environment as an ecological filter shaping microbial functional traits. This study provides a predictive framework for strain selection, supporting ecologically guided bioprospecting strategies for the development of more efficient PGPB inoculants.