Green Manure Effects on Soil Microbiota Depend on Seasonal Cropping Cycle, Manure Species, and Kohlrabi Cultivar

Introduction Green manure application is widely used to improve soil fertility, but its effects on soil microbial communities are context‐dependent. This study examined how green manure species and seasonal cropping cycle influence root‐zone soil microbiomes, soil chemistry, and kohlrabi growth. Materials and Methods A randomised block field experiment tested three green manure species and two kohlrabi cultivars across two seasonal cropping cycles: October sowing and March incorporation followed by kohlrabi cultivation from April to June, and April sowing and June incorporation followed by cultivation from July to September. Bacterial and fungal communities were characterised using 16S rRNA gene and ITS amplicon sequencing and qPCR, alongside soil chemistry and plant‐growth measurements. Results Plant responses were generally modest but more favourable in the second cycle, particularly following Phacelia tanacetifolia . Cropping cycle was the main source of microbial variation, while green manure significantly affected community composition. Bacterial responses differed between cultivars, whereas fungal responses differed between cropping cycles. Treatment effects were driven mainly by compositional turnover rather than increased diversity, with distinct changes in taxon relative abundance. Raphanus sativus and Ph. tanacetifolia altered bacterial composition in cultivar Luna, while all three green manures altered fungal composition in both cycles. Rhizobiales taxa frequently showed higher relative abundance following Pisum sativum , whereas Ph. tanacetifolia was associated with the largest number differentially abundant bacterial taxa. Several detected taxa belonged to groups previously linked to plant–soil processes, although these patterns do not demonstrate microbial function. Soil chemistry differed primarily between cropping cycles and showed only a limited number of associations with microbial composition or diversity and none with qPCR‐based microbial abundance. Conclusions Green manure effects on root‐zone soil microbiomes depend strongly on species, cropping cycle and crop cultivar. Integrating these context‐dependent responses with direct functional analyses may help optimise green manure‐based cropping systems for sustainable agriculture.