Low impact of organic soil amendments on the banana microbiome (Gammaproteobacteria) in smallholder agro-ecosystems of Uganda. Banana microbiome

Organic matter inputs affect both soil physicochemical properties and biotic factors related to the soil microbiota, e.g., microbial biomass, diversity and community structure. The response of microbial colonization of the East African highland banana cultivar ‘Mpologoma’ (AAA genome) under different mulch and manure treatments was investigated on smallholder farms in Uganda. Different combinations of mulch and manure were applied on plots on fifty four farms from which plots on three farms were sampled to study in detail shifts within the dominant gammaproteobacterial microbiome. Significant differences (P<0.05) in the plant-associated above- and belowground microbial community composition and diversity were found among individual sampled farms, independent of added soil inputs. Across farms, banana fruit harbored a richer and more balanced gammaproteobacterial community than the rhizo- and endospheres. In general, the gammaproteobacterial microbiome appeared stable with no significant response to organic matter inputs after 24 months of treatment. While two farms showed a generally higher diversity in rhizo- and endosphere, no major impact on the alpha diversity was observed for treatments. Gammaproteobacterial beta diversity was shaped by microenvironment (44%) as well as sampling site (4%). Global effects of treatments in the rhizosphere analyzed using LEfSe showed significantly enriched genera, such as Enterobacter, under manure and mulch treatments. While bunch size and total yield were increased with manure and mulch, our results highlight general short-term microbial stability of Ugandan banana cropping systems with increases in the gammaproteobacterial community.