Organic and conventional farming systems shape soil bacterial community composition in tropical arable farming

Soils present a limited resource for agricultural production and bear a vast diversity of organisms crucial for crop health and the provision of ecosystem services. There is growing evidence that agricultural practices affect soil microbial community structure and function but currently, there is a knowledge gap when it comes to tropical arable farming systems. In this study, we investigated the long-term impact of organic and conventional production systems on bacterial communities in two field trial located on a rhodic and humic nitisol in the Central Highlands of Kenya. The field sites operate on a full factorial design, testing farming systems (organic vs conventional) and input levels (high vs low). Including four field replication we assessed soil bacterial community structure via amplicon sequencing of the 16S rRNA gene and soils capacity for nitrification and nitrous oxide reduction via qPCR of functional genes (bacterial and archaeal amoA, nosZ) after 12 years of distinct management and before the start of the 5th three-year crop rotation period in 2019. The abundances of amoA bearing nitrifiers and nosZ bearing nitrous oxide reducers were enhanced in the high input organic production system on humic but not in rhodic nitisols. For both soil types, high input organic production system resulted in distinct bacterial community structure with enhanced bacterial richness compared to conventional and low input production systems. In rhodic and humic nitisols 160 and 84 OTUs were found to be indicative for organic production system at high input levels organic. Taxa associated with this system were identified as potential primary decomposers or symbionts related to plant nitrogen fixation, suggesting organic fertilization strategies such as manure composting as major driver for changes in soil bacterial community structure. This study reveals that organic production systems at high input levels on tropical nitisols translates to distinct soil bacterial communities with increased capacity for soil processes that are crucial for crop nutrient supply. •Distinct soil bacterial communities in organic systems in humic and rhodic nitisols•Increased bacterial richness in high input organic systems in humic nitisols•High-input organic farming raises nitrification capacity in humic nitisols.•Lifestyle of indicative taxa mainly linked with organic matter decomposition