The effect of environmental parameters and fertilization practices on yield and soil microbial diversity in a Kenyan paddy rice field

Rice is gaining importance for nutrition in sub-Saharan Africa, but domestic production can only cover a fraction of the actual needs. Suboptimal fertilization limits production and affordable solutions are needed. It is, however, of utmost importance to minimize negative impacts on the environment and on soil health, which is largely determined by microbial processes. An agronomic field trial was conducted at the KALRO Mwea research site (Central Kenya) to compare mineral and organic fertilization effects on rice plant parameters and on soil microbial abundance and diversity. Abundance of fungi and bacteria was quantified by ddPCR and the community composition was determined by amplicon sequencing of the ITS2- and 16S-regions, respectively. Mineral fertilizer had a strong positive effect on panicle number, spikelet number, grain yield and straw dry weight, but fertilizer type did not significantly influence soil microbial community abundance or composition. The rice development stage shaped fungal communities with differences between the vegetative and the reproductive stages, whereas the bacterial communities were mainly influenced by soil depth in a range from 0 to 30 cm. Additionally, spatial effects between rows of the experimental field were observed, resulting in row-specific differences in soil organic carbon, total nitrogen and certain fungal taxa, notwithstanding that the field was manually ploughed to a depth of 30 cm before the experiment. This study is the first census of soil fungal and bacterial communities in an African paddy rice field and provides insights into similarities and differences to paddy rice fields in other regions. To increase local African rice production, manure application alone might not be sufficient due to the poor nutrient status of traditional farm-yard manure, yet it can be part of a sustainable and more efficient fertilization strategy.