Metagenomic and culture-dependent characterization of between-field variation in phosphorus-cycling microbial communities and functional potential across tobacco–safflower rotation fields
- 1Lijiang Branch of Yunnan Provincial Tobacco Company
- 2Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences
Abstract
Introduction: 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.
Methods: 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.
Results: 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.
Conclusion: 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.
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BibTeX
@article{luo2026metagenomic,
title = {{Metagenomic and culture-dependent characterization of between-field variation in phosphorus-cycling microbial communities and functional potential across tobacco–safflower rotation fields}},
author = {You Luo and Yu Wang and Zhufeng Shi and Zilin Li and Te Pu and Yanni Wang and Ming Ni and Xun He and Jing Li and Chenying Li and Xuewei Li and Peiwen Yang},
journal = {Frontiers in Microbiology},
year = {2026},
month = oct,
doi = {10.3389/fmicb.2026.1983930},
url = {https://www.frontiersin.org/articles/10.3389/fmicb.2026.1983930/full},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Metagenomic and culture-dependent characterization of between-field variation in phosphorus-cycling microbial communities and functional potential across tobacco–safflower rotation fields
AU - You Luo
AU - Yu Wang
AU - Zhufeng Shi
AU - Zilin Li
AU - Te Pu
AU - Yanni Wang
AU - Ming Ni
AU - Xun He
AU - Jing Li
AU - Chenying Li
AU - Xuewei Li
AU - Peiwen Yang
PY - 2026
DA - 2026/10/08
JO - Frontiers in Microbiology
DO - 10.3389/fmicb.2026.1983930
UR - https://www.frontiersin.org/articles/10.3389/fmicb.2026.1983930/full
AB - Introduction: 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. Methods: 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. Results: 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. Conclusion: 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.
SN - 1664-302X
ER -