Strain-specific strategies underlie convergent phosphate solubilization in Bacillus

The stability of ecosystem functions under changing environmental conditions is often attributed to convergent functioning, where different mechanisms lead to similar outcomes. In soil systems, microbial activity is a major driver of nutrient cycling, yet it remains unclear whether the presence of the same genes across taxa reliably translates into redundant outcomes. We addressed this in microbial phosphate solubilization, critical when applying alternative phosphorus (P) fertilizers such as BCplus, a biochar-based fertilizer from pyrolyzed animal bones coated with sulfur. Using multi-omics analyses, we compared two soil isolates—Bacillus licheniformis COM1 and Psychrobacillus psychrodurans INOP01—alongside the reference strain B. velezensis DSM 23117. P. psychrodurans was excluded due to poor growth under P limitation. Despite similar growth and P mobilization, B. licheniformis and B. velezensis relied on distinct strategies, indicating that mechanistically diverse regulatory programs can yield convergent phosphate-solubilizing outcomes. Transcriptional changes extended beyond P metabolism, with both strains inducing nitrate reduction and adjusting sulfur metabolism, underscoring tight coupling of P, nitrogen, and sulfur cycling. B. velezensis responded rapidly by inducing Pho genes, organic acid production, nitrate respiration, and plant growth–promoting traits including indole-3-acetic acid biosynthesis. B. licheniformis instead showed a slower adaptation marked by malate-driven acidification, dissimilatory nitrate reduction to ammonium, and late riboflavin activation. While both strains solubilized phosphate, their mechanisms differed, illustrating that convergence at the functional outcome does not imply similarity in regulation or metabolism. These results highlight the need to account for strain-specific pathways when developing microbial inoculants to optimize nutrient turnover in low-input systems.