A comparative study on the impact of fiveDesmodiumspecies on soil microbiome reveals enrichment of selected bacterial and fungal taxa

Abstract

AbstractIntroductionSeveralDesmodiumspp. are used as intercrops in push-pull pest management systems to repel insect herbivores. In addition,Desmodiumsuppresses the parasitic weedStriga, and diversifies the soil microbiome with negative impacts on fungi. We investigated the impact of a 2-year cropping of fiveDesmodiumspecies on soil microbiome populations.MethodologyTotal DNA was obtained from root zone soil samples collected from a two-years-old common garden experiment with replicated plots of fiveDesmodiumspp. at the international centre for insect physiology and ecology (ICIPE), Mbita, Kenya. Subsequently, 16S and ITS DNA sequencing were performed and the data was analysed by using QIIME2 and Calypso.ResultsOur findings show significant differences in composition and abundance of specific microbial taxa among theDesmodiumplots and the bulk soil, with a stronger shift observed for fungal community profiles than bacteria. There was, however, no significant difference in overall diversity, richness and evenness of microbial communities among theDesmodiumplots and the bulk soil. Similarly, beta diversity analysis did not reveal a significant association of variation to specificDesmodiumspp. plots.Discussion and conclusionThis is the first study to compare impact and association of whole soil microbiomes to differentDesmodiumspecies. Whereas long-termDesmodiumcropping clearly shifts whole microbiome communities, no significant difference in overall diversity and richness of microbial populations was observed among the studied plots. However, there was a divergence of individual taxa reflected on their increased abundance in association to specificDesmodiumspp., pointing towards potential impact on ecosystem services. These findings indicate that significant shifts in whole microbial populations due toDesmodiumspp. and thus potentially provision of associated ecosystem services require longer cultivation periods to solidify. Future studies should focus on techniques that monitor real-time changes in microbial populations such as RNA-seq to ascertain live and dead microbes, and thus infer ecological services.