European Journal of Sustainable Agroecosystems

Background: The rhizosphere microbiome has an essential function in some processes such as nutrient cycling, plant protection in terms of diseases and stress tolerance, and it is increasingly acknowledged as an important component of sustainable agricultural ecosystems. Integrated application of microbial bio-fertilizers with organic fertilizers (composts, vermicompost’s, manure and biochar), though still not fully studied, is considered as one of the main alternatives to chemical fertilizers. The goal of this paper is to summarize metagenomic studies of changes in the rhizosphere microbiome occurring in response to the use of bio-fertilizer-organic fertilizer integrated systems by comparing the taxonomic, functional and diversity parameters of the agricultural systems used.
Literature sources: To carry out the review, a structured search was performed in Scopus, Web of Science, PubMed and Google Scholar (2015-2025) with the goal of recognizing peer-reviewed studies and reports related to shotgun and amplicon (16S rRNA/ITS) metagenomics. A total of 67 studies were downloaded based on the methodology of literature review.
Study results: The results demonstrate that integrated systems have similar effects on increasing the alpha diversity, the abundance of Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, as well as the proliferation of functional genes responsible for nitrogen, phosphorus and carbon cycle of the crops. Bio-organic amendments are known to cause disease suppressive community restructuring although the taxa level responses are different depending on the combinations of soil type, amendment sources, and crop species as well as the experimental duration.
Research gaps: There are still several major research gaps in this field, including short study durations, lack of evidence of fungi, archaea and viruses, inconsistent metadata reporting, non-use of multi-omics approach, and little evidence of relations between the changes in microbiome and agricultural yield/production metrics.
Conclusion: Generally, the systems based on integrated biofertilizers and organic amendments lead to the formation of rhizosphere microbiomes which have a higher level of diversity and functional richness as compared to chemical fertilizers-based systems; however, further long-term experiments in laboratory conditions, including different locations, are still needed.