Stochastic assembly outweighs deterministic filtering: crop phenological stages drive bacterial-fungal divergence between bulk and rhizosphere soils in saline-alkali fields
Abstract
Soil salinization threatens crop productivity partly by disrupting rhizosphere microbiomes that support plant stress tolerance. However, most studies have focused on single growth stages or bulk soil, limiting a deeper insight into the temporal dynamics and assembly mechanisms of rhizosphere communities across the crop life cycle. We investigated bacterial and fungal communities in a long-term maize field with saline-alkali soil. Bulk and rhizosphere soils were sampled at seedling, heading, and maturity. Using 16S rRNA and ITS amplicon sequencing, iCAMP, functional prediction, and co-occurrence networks, we found that maize phenological stage significantly structured bacterial and fungal community composition, while the difference between the rhizosphere and bulk soil was not significant. Microbial diversity increased toward maturity in bulk soil, whereas rhizosphere bacterial diversity showed a seedling-stage bottleneck and fungal diversity remained higher than that in bulk soil. The rhizosphere enriched copiotrophic Proteobacteria and Actinobacteriota, whereas bulk soil favored oligotrophic Chloroflexi and Acidobacteriota. Drift (and others) represented the largest single assembly category across phenological stages in both compartments, with relative contributions exceeding 38%. Deterministic contributions to bacterial assembly remained stable across stages and compartments, whereas rhizosphere fungal assembly became more stochastic at maturity. Under the saline-alkali conditions examined here, stochastic processes remained dominant, and deterministic filtering did not become the predominant mode of community assembly. Predicted functional profiles shifted with plant development: organic phosphorus mineralization was enriched at seedling, phosphate transport and nitrogen fixation at maturity, and salt-tolerance functions shifted from compatible-solute synthesis to ion homeostasis and antioxidant defense. The rhizosphere showed reduced bacterial network connectivity but more positive fungal associations and a higher proportion of cross-kingdom associations. Together, these results characterize a “growth stage-rhizosphere effect-salinity stress” framework in saline-alkali maize field, in which environmental control shifts from salinity toward nutrient stoichiometry for bacteria and microbial biomass for fungi. These patterns may inform growth-stage-specific microbiome management in saline-alkali soil.
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BibTeX
@article{wu2026stochastic,
title = {{Stochastic assembly outweighs deterministic filtering: crop phenological stages drive bacterial-fungal divergence between bulk and rhizosphere soils in saline-alkali fields}},
author = {Dongming Wu and Shuailing Hou and Jingwen Wang and Dali Song and Zitian Wang and Jichen Wang and Yuyi Li and Fangbo Zhang and Chao Ai and Wei Zhou and Miao Gao},
journal = {Frontiers in Microbiology},
year = {2026},
month = nov,
doi = {10.3389/fmicb.2026.1992553},
url = {https://www.frontiersin.org/articles/10.3389/fmicb.2026.1992553},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Stochastic assembly outweighs deterministic filtering: crop phenological stages drive bacterial-fungal divergence between bulk and rhizosphere soils in saline-alkali fields
AU - Dongming Wu
AU - Shuailing Hou
AU - Jingwen Wang
AU - Dali Song
AU - Zitian Wang
AU - Jichen Wang
AU - Yuyi Li
AU - Fangbo Zhang
AU - Chao Ai
AU - Wei Zhou
AU - Miao Gao
PY - 2026
DA - 2026/11/05
JO - Frontiers in Microbiology
DO - 10.3389/fmicb.2026.1992553
UR - https://www.frontiersin.org/articles/10.3389/fmicb.2026.1992553
AB - Soil salinization threatens crop productivity partly by disrupting rhizosphere microbiomes that support plant stress tolerance. However, most studies have focused on single growth stages or bulk soil, limiting a deeper insight into the temporal dynamics and assembly mechanisms of rhizosphere communities across the crop life cycle. We investigated bacterial and fungal communities in a long-term maize field with saline-alkali soil. Bulk and rhizosphere soils were sampled at seedling, heading, and maturity. Using 16S rRNA and ITS amplicon sequencing, iCAMP, functional prediction, and co-occurrence networks, we found that maize phenological stage significantly structured bacterial and fungal community composition, while the difference between the rhizosphere and bulk soil was not significant. Microbial diversity increased toward maturity in bulk soil, whereas rhizosphere bacterial diversity showed a seedling-stage bottleneck and fungal diversity remained higher than that in bulk soil. The rhizosphere enriched copiotrophic Proteobacteria and Actinobacteriota, whereas bulk soil favored oligotrophic Chloroflexi and Acidobacteriota. Drift (and others) represented the largest single assembly category across phenological stages in both compartments, with relative contributions exceeding 38%. Deterministic contributions to bacterial assembly remained stable across stages and compartments, whereas rhizosphere fungal assembly became more stochastic at maturity. Under the saline-alkali conditions examined here, stochastic processes remained dominant, and deterministic filtering did not become the predominant mode of community assembly. Predicted functional profiles shifted with plant development: organic phosphorus mineralization was enriched at seedling, phosphate transport and nitrogen fixation at maturity, and salt-tolerance functions shifted from compatible-solute synthesis to ion homeostasis and antioxidant defense. The rhizosphere showed reduced bacterial network connectivity but more positive fungal associations and a higher proportion of cross-kingdom associations. Together, these results characterize a “growth stage-rhizosphere effect-salinity stress” framework in saline-alkali maize field, in which environmental control shifts from salinity toward nutrient stoichiometry for bacteria and microbial biomass for fungi. These patterns may inform growth-stage-specific microbiome management in saline-alkali soil.
SN - 1664-302X
ER -