Manure source distance and soil depth: a natural screening system for nutrient-solubilizing bacteria

To develop and validate an ecology-driven strategy that leverages natural manure proximity and soil depth gradients as a screening system for the targeted isolation of nutrient-solubilizing bacteria (NSB) with high biofertilizer potential..

A full-factorial sampling design was implemented across gradients of distance-from-manure (5 points, 8-m intervals) and soil depth (0-20, 20-40, 40-60 cm) in a coconut plantation. Culturable bacteria were isolated using a culture-dependent approach on a nutrient-rich medium, identified via 16S rRNA gene sequencing, and functionally screened in vitro for nitrogen fixation, phosphate solubilization (PS), and potassium solubilization (KS) capabilities.

Manure input and soil depth interacted to form a heterogeneous soil nutrient landscape, with available phosphorus (AP) identified as the most influential environmental factor shaping the bacterial community. Phosphate-solubilizing bacteria (PSB) were significantly enriched in low-P habitats, verifying the niche-based selection of functional bacteria. This gradient-based screening strategy enabled the targeted recovery of multifunctional NSB strains (e.g. Klebsiella and Enterobacter) with concurrent nitrogen fixation, phosphate and potassium solubilization capacities, which were isolated from specific microhabitats, including deep, nutrient-depleted soil layers.

This study demonstrates that intersecting manure- and soil-depth gradients form a powerful, predictable natural screening system for the targeted isolation of beneficial bacteria. This ecology-driven strategy effectively links microbial ecology to bioprospecting. It provides a curated library of isolates with defined ecological origins and a predictive framework for developing customized biofertilizers, thereby enhancing microbial resource mining efficiency and contributing to sustainable agriculture.