Long-term farming and cropping systems with contrasting nitrogen forms and input diversity influence soil prokaryotic diversity in the central highlands of Kenya

Background: Understanding how farming systems management influences soil microbial communities is essential for advancing sustainable agriculture in tropical regions. Long-term experiments provide valuable opportunities to assess how cumulative management practices shape soil microbial diversity and community composition.

Methods: We investigated prokaryotic communities after 15 years of continuous management in the Long-Term Farming Systems Comparison Trial (SysCom-Kenya) at two contrasting sites (Chuka and Thika) in the Central Highlands of Kenya. Four systems were evaluated: conventional low-input (Conv-Low), conventional high-input (Conv-High), organic low-input (Org-Low), and organic high-input (Org-High). Soil samples were collected at key crop growth stages (vegetative, reproductive, and maturity) of maize, baby corn, and potato. Prokaryotic diversity and community composition were characterized using 16S rRNA gene amplicon sequencing, and soil chemical properties were analyzed to explore potential abiotic drivers.

Results: Prokaryotic community composition and diversity varied primarily with site and farming system, with secondary variation across crop growth stages. Across all systems, communities were dominated by members of the phyla Proteobacteria and Actinobacteria, followed by Acidobacteria, Firmicutes, and Chloroflexi. Organic systems, particularly organic high-input, tended to support higher richness and evenness than conventional systems, while low-input systems consistently exhibited lower prokaryotic richness and diversity than high-input systems. Diversity generally increased toward later crop growth stages, although phenological effects were variable. Canonical correspondence analysis identified soil pH, ammonium-N, and available phosphorus as important correlates of community structure, especially at the drier Thika site. Taxon-specific enrichment patterns differed across systems and crop stages, indicating compositional differentiation rather than functional dominance.

Conclusion: Our findings indicate that long-term management intensity and organic input diversity exert a stronger influence on soil prokaryotic communities than short-term crop phenology. Despite limitations from sample pooling, this study provides novel evidence from sub-Saharan Africa that diversified organic input management can enhance soil microbial diversity and potential resilience, supporting sustainable soil management in tropical farming systems.