Metagenomic and culture-dependent characterization of between-field variation in phosphorus-cycling microbial communities and functional potential across tobacco–safflower rotation fields

Abstract

Rhizosphere microorganisms contribute to soil phosphorus (P) transformation and plant P acquisition, but P-cycling microbial communities and functional associations across tobacco–safflower rotation fields remain poorly characterized. Twenty-one safflower rhizosphere soil samples were collected from seven tobacco–safflower rotation fields in Lijiang, China. Soil physicochemical properties were measured, and shotgun metagenomics was used to characterize P-cycling bacterial communities and genes associated with P solubilization, mineralization, regulation, and transport. Culturable phosphate-solubilizing bacteria were isolated, preliminarily assigned taxonomically using 16S rRNA gene sequences, and evaluated by plate and liquid-culture assays. Soil properties and P-cycling bacterial communities showed pronounced between-field variation. Metagenomic screening identified 6,019 non-redundant gene sequences assigned to 38 predefined P-cycling KO terms, with 460 genus-level bacterial taxa. Among 124 taxa shared across all fields, Nocardioides, Arthrobacter, Streptomyces, Gaiella , and Marmoricola were major dominant genera. PCoA and PERMANOVA showed significant field differences at the phylum ( R 2 = 0.983, p = 0.001) and genus ( R 2 = 0.964, p = 0.001) levels. Soil pH was associated with all four P-cycling functional modules. Exploratory random-forest analysis identified Sphingomonas, Streptomyces, Nocardioides , and Arthrobacter as candidate indicator taxa associated with variation in soil available P. Eighty-six culturable phosphate-solubilizing isolates representing 45 putative species-level taxa were obtained, with Streptomyces the most abundant genus (22.1%). Streptomyces isolates had solubilization index values of 1.10–1.89. The isolate with the highest SI, Streptomyces sp. LG-4, provisionally affiliated with S. endophyticus , reached a maximum net phosphate solubilization of 354.60 ± 7.22 mg L −1 on day 3. Soil physicochemical heterogeneity, particularly pH, was associated with between-field differences in P-cycling microbial communities and metagenomically inferred functional potential. Because no non-rotation or monoculture controls were included, these patterns should be interpreted as field-associated variation rather than effects of the rotation system itself. Both metagenomic and culture-dependent analyses highlighted Streptomyces as a candidate group of interest, while Streptomyces sp. LG-4 showed phosphate-solubilizing capacity under laboratory conditions and requires further taxonomic and functional validation.