From soil to yield: unraveling the role of microbiome diagnostics in enhancing biofertilizer efficiency

Summary in the original language of the document

Introduction: Excess use of mineral fertilizers can lead to eutrophication of rivers and lakes and biodiversity loss. Alternatives include the use of biofertilizers such as arbuscular mycorrhizal fungi (AMF). AMF form a symbiosis with most plant species, where they contribute to plant growth by providing essential nutrients such as phosphorus. However, the success of AMF inoculation is context dependent. To tackle this variability, we propose the development of microbiome diagnostics to predict successful inoculation with biofertilizer.
Materials, methods: We conducted 54 field trials in Northern Switzerland where maize was inoculated with Rhizoglomus irregulare SAF22. We calculated the mycorrhizal growth response (MGR) which is the percent change in biomass of inoculated plots compared to control plot. Soil properties were analyzed using classical chemical and physical parameters. The soil fungal community was characterized by long-read sequencing. AMF root colonization was assessed by microscopy. The root AMF community was sequenced with primers amplifying preferentially mycorrhiza. We used various statistical methods to predict the MGR based on the soil parameters and the soil microbiome.
Results and Discussion: In one quarter of the fields, inoculation with AMF increased yield significantly (Figure). Surprisingly, the degree of mycorrhizal growth response did not depend on mycorrhizal root colonization, whether assessed by either classical microscopy approach or by sequencing of the root microbiome. Soil parameters alone proved insufficient in explaining the response variability. However, integrating soil parameters with the soil microbiome resulted in a model that could explain up most of the variation in plant growth response. Furthermore, our investigation of the root microbiome unveiled intriguing dynamics. In most fields, the inoculated AMF led to a reduction in the abundance of native AMF. Moreover, in fields with high mycorrhizal growth response, the introduced strain decreased the abundance of several pathogenic strains, suggesting a possible mechanism whereby the introduced AMF effectively outcompetes root-associated plant pathogens, leading to enhanced maize plant growth. Overall, our study underscores the utility of soil fungal indicators as strong predictors of inoculation success.