Combined microbial inoculation and reduced inorganic fertilization enhances diversity and functionality in potato rhizosphere microbiome at field scale

Abstract

Background

Intensive potato farming heavily relies on mineral fertilizers which can be detrimental to the environment. Microbial inoculants emerge as a sustainable alternative to such fertilizers due to their potential to improve nutrient availability and plant health. Nevertheless, their effect on potato rhizosphere and tuberosphere require further elucidation.

Methods

A field experiment was conducted in Southeast Spain on potato using a randomized block design involving four fertilization treatments: conventional mineral fertilization (F100); 50% fertilization reduction (F50); and F50 combined with two distinct microbial inoculants (F50 + BA, containing Azospirillum, Bacillus, and Pseudomonas; and F50 + BAFU, containing Azotobacter, Bacillus, and non-mycorrhizal fungi). Soil samples from the bulk, rhizosphere, and tuberosphere were collected at four key growth stages: pre-planting, pre-inoculation, post-inoculation, and at harvest. Microbial community composition and diversity were assessed using sequencing data and estimated absolute abundance. The functional potential of the soil microbiome was evaluated by quantifying key genes involved in carbon and nitrogen biogeochemical cycles via quantitative PCR.

Results

In the post-inoculation stage, the estimated absolute abundance of potential pathogenic fungi such as Neocosmospora, Botryotrichum, and Gibellulopsis was significantly decreased in the F50 + BAFU and F50 + BA treatments compared to the F50 treatment, which showed the highest estimated absolute abundance values (1.48 × 10⁵, 1.20 × 10⁶, and 6.87 × 10⁵ copies g⁻¹ soil, respectively) (p-value < 0.05). Shannon diversity significantly varied across plant growth stages and soil compartments (p-value < 0.001), with the tuberosphere generally exhibiting the highest richness. Notably, during the post-inoculation period, diversity was significantly higher in the F50 + BA treatment than in F100 (p-value < 0.05), indicating a positive effect of microbial inoculation under reduced fertilization. By normalizing functional gene abundance to total microbial biomass (gene/16S rRNA ratio) during the post-inoculation period, we observed not only a quantitative increase but also evidence of a treatment-driven functional enrichment, as in the F50 + BAFU and F50 + BA treatments, that significantly increased the abundances of key nitrogen cycling genes, such as nifH (0.09 and 0.06 copies g^‒1 soil in April, respectively) and nirK (0.008 and 0.011 copies g^‒1 soil in April, respectively), as well as gene GH7 (0.012 copies g^‒1 soil in May), compared to the F100 and F50 treatments (p-value < 0.05).

Conclusion

Microbial inoculants offer a promising strategy for reducing chemical fertilizer inputs in semi-arid potato cultivation by enhancing beneficial soil functions, temporarily promoting beneficial microbes, improving nitrogen cycling, and suppressing pathogens, thereby supporting a resilient crop microbiome.

Graphical Abstract