Arbuscular mycorrhizal inoculum coupled with organic substrate induces synergistic effects for soil quality changes, and rhizosphere microbiome structure in long-term monocropped cucumber planted soil

The integrated soil biological amendments of mycorrhizal inoculation and organic substrate can be additive, synergistic, or antagonistic under plant-soil-microbe interaction. Underlying mechanisms of associated soil quality changes and microbiota structure are, however, less understood. To probe into this, consecutive greenhouse experiments (2016–2018) were conducted to study the effects of mycorrhizal inoculum (AMF: Diversispora epigaea L.) and soil organic substrate (GS: garlic stalk) were used as single and combined applications. In this study, a high-throughput sequencing approach was used to evaluate the rhizosphere microbiome structure of bacteria in the replanted substrate of 7-years of continuous cucumber cropping. From the two years of treatment, we found that co-amended GS + AMF significantly altered the soil quality changes through increasing soil organic matter, soil nutrient contents, and enzyme activities. Our 16 S rRNA amplicon revealed a distinct impact on alpha diversity and bacterial community. The observed species richness index (OTUs, Chao1, and ACE) and community diversity index (Shannon) were increased due to GS-amended soil and GS + AMF inoculation, respectively. Soil amendments also had apparent effects by altering bacterial community compositions at the phylum level, which were mostly associated with the higher abundance of Proteobacteria, Planctomycetes, Gemmatimonadetes, Actinobacteria and Bacteroidetes. Furthermore, correlation analyses revealed that the soil pH and enzyme activities emerged as the major determinants of the key microbial attributes. Our results suggest that GS + AMF treatment can directly regulate the soil environmental attributes or induce compositional shifts of microbes in the continuous cucumber cropping substrates. However, their co-inoculation impact was the shift of the key soil-microbiota consortium. Therefore, the study provides new insight into ways that can reduce the adverse effect of continuous cropping stress and eco-friendly contribute to the stable and healthy micro-ecological development in protected cultivation.