The Rhizosphere Microbiome as a Mediator of Crop Responses to Fertilization Strategies
This narrative review synthesizes evidence that different fertilization strategies alter rhizosphere microbiome structure and function, with organic and biological fertilizers tending to favor microbial diversity and beneficial functions compared to exclusive and excessive use of mineral fertilizers.
| Population | Cultivated plants (multiple species including wheat, maize, and watermelon) in agricultural soils subject to long-term fertilization |
|---|---|
| Intervention | Mineral fertilizers (especially nitrogen), organic and biological fertilizers (PGPR, AMF), alone or combined |
| Comparator | Comparisons between fertilizer types, doses, and combinations; no fertilization in some cited studies |
| Outcome | Rhizosphere microbial diversity (Shannon index and species richness); nifH gene copy number (diazotrophs); Functional gene profile for carbon and nitrogen cycling; Disease index in continuous cropping (watermelon); Plant growth promotion by PGPR and synthetic communities (SynComs); Wheat rhizosphere microbial community structure under inorganic nitrogen; Ecosystem multifunctionality correlated with microbiome functional potential |
Summary of findings
| Outcome | Effect | 95% CI | Certainty | Clinical relevance | Notes |
|---|---|---|---|---|---|
| Rhizosphere microbial diversity (Shannon index and species richness) | Excessive N fertilizer (N300 vs lower doses): significant decrease in Shannon index and species richness of diazotrophs; in the pooled effect size or 95% CI reported | — | Low | — | |
| nifH gene copy number (diazotrophs) | N300 (300 kg N ha-1): significant decrease in nifH copy number vs lower N doses; in the quantified effect size or 95% CI reported | — | Low | — | |
| Functional gene profile for carbon and nitrogen cycling | Organic fertilizer: enrichment of carbon fixation and nitrate reduction genes; mineral fertilizer: enrichment of nitrification and anammox genes; direction diverges by fertilizer type; in the effect size or 95% CI reported | — | Low | — | |
| Disease index in continuous cropping (watermelon) | Introduction of healthy soil: reduction in plant disease index via increased microbial network stability and complexity; positive cohesion negatively correlated with disease index; in the quantified effect size or 95% CI reported | — | Low | — | |
| Plant growth promotion by PGPR and synthetic communities (SynComs) | SynComs with moderately related strains: enhanced plant growth, root colonization, IAA production, and siderophore production vs single strains; in the pooled effect size or 95% CI reported | — | Low | — | |
| Wheat rhizosphere microbial community structure under inorganic nitrogen | Inorganic N application: significant alteration of taxonomic and predicted functional structure of wheat rhizosphere microbiome; in the quantified effect size or 95% CI reported | — | Low | — | |
| Ecosystem multifunctionality correlated with microbiome functional potential | Significant positive correlation between rhizosphere microbiome functional potential (carbon degradation, nitrification, organic P mineralization taxa) and ecosystem multifunctionality; in the effect size or 95% CI reported | — | Low | — |
Context
The rhizosphere hosts microbial communities regulating nutrient cycling, pathogen suppression, and stress resistance. Excessive inorganic nitrogen fertilization is associated with soil acidification and microbial dysbiosis. Understanding how each fertilization strategy modulates this microbiome is essential for reducing inputs without yield loss.
What the study showed
Excessive nitrogen fertilizer dose (N300, 300 kg N ha⁻¹) significantly reduced nifH gene copy number, species richness, and Shannon index of diazotrophs in black soil maize. Organic fertilizers enriched carbon fixation and nitrate reduction genes, while mineral fertilizers promoted nitrification and anammox genes. Introduction of healthy soil in continuous watermelon cropping reduced the disease index by increasing microbial network stability and complexity. Absolute numbers and 95% CIs for most outcomes were not reported by the review.
How it was done
Non-systematic narrative review published in 2026 in Plants (Basel). No PRISMA or PROSPERO protocol registered. Synthesizes heterogeneous primary studies (field experiments, metagenomics, synthetic community assays) without quantitative meta-analysis. No explicit search strategy, inclusion/exclusion criteria, or risk of bias assessment of included studies.
Effect magnitude
No pooled effect size with 95% CI is reported; cited studies present isolated effects without quantitative synthesis, precluding estimation of overall magnitude.
Risk of bias
Narrative review without systematic methodology (AMSTAR-2 not applicable due to lack of protocol). No formal risk of bias assessment of primary studies (RoB 2 or ROBINS-I not applied). Heterogeneity of crops, soils, climates, and fertilizer doses across primary studies prevents generalization. Predominantly metagenomics and observational data; causal relationships not established.
What this study does NOT prove
This narrative review does not prove causality between any fertilization strategy and microbial health or productivity outcomes. It is not generalizable to ecosystems, crops, or climates not represented in the cited studies.
In clinical practice
This article generates no direct clinical recommendation. Agronomy professionals should interpret the data as hypotheses to be tested locally. Partial replacement of mineral fertilizers with organic or biological alternatives may be considered in management protocols but requires validation in controlled trials specific to each crop and soil.
Limitations
Narrative review without systematic methodology (AMSTAR-2 not applicable due to lack of protocol). No formal risk of bias assessment of primary studies (RoB 2 or ROBINS-I not applied). Heterogeneity of crops, soils, climates, and fertilizer doses across primary studies prevents generalization. Predominantly metagenomics and observational data; causal relationships not established.
What is still missing
Long-term randomized field trials with simultaneously measured productivity and microbial health outcomes are needed. Meta-analyses with primary data harmonized by soil type, crop, and fertilizer dose are absent.
Technical appendix
Version history
- 1.0 · 2026-10-26 — Auto-generated under Evidence Standard v1.0