Abstract:
Management practices such as tillage, crop rotation, irrigation, organic and inorganic inputs
application are known to influence diversity and function of soil microbial populations. In this
study, we investigated the effect of conventional versus organic farming systems at low and
high input levels on structure and diversity of prokaryotic microbial communities. Soil samples
were collected from the ongoing long-term farming system comparison trials established
in 2007 at Chuka and Thika in Kenya. Physicochemical parameters for each sample
were analyzed. Total DNA and RNA amplicons of variable region (V4—V7) of the 16S rRNA
gene were generated on an Illumina platform using the manufacturer’s instructions. Diversity
indices and statistical analysis were done using QIIME2 and R packages, respectively.
A total of 29,778,886 high quality reads were obtained and assigned to 16,176 OTUs at 97%
genetic distance across both 16S rDNA and 16S rRNA cDNA datasets. The results pointed
out a histrionic difference in OTUs based on 16S rDNA and 16S rRNA cDNA. Precisely,
while 16S rDNA clustered by site, 16S rRNA cDNA clustered by farming systems. In both
sites and systems, dominant phylotypes were affiliated to phylum Actinobacteria, Proteobacteria
and Acidobacteria. Conventional farming systems showed a higher species richness
and diversity compared to organic farming systems, whilst 16S rRNA cDNA datasets
were similar. Physiochemical factors were associated differently depending on rRNA and
rDNA. Soil pH, electrical conductivity, organic carbon, nitrogen, potassium, aluminium, zinc,
iron, boron and micro-aggregates showed a significant influence on the observed microbial
diversity. The observed higher species diversity in the conventional farming systems can be
attributed to the integration of synthetic and organic agricultural inputs. These results show
that the type of inputs used in a farming system not only affect the soil chemistry but also the
microbial population dynamics and eventually the functional roles of these microbes.
