| dc.description.abstract | Microbial diversity and function in agro-ecosystems is influenced by various aspects
linked to soil and agronomic practices for example, tillage, irrigation, crop rotation and
application of organic and inorganic inputs. Farming systems practices may affect the
dynamic interactions existing between soil, plant and microorganisms in different
agricultural biomes. Due to limitations associated with conventional microbial cultivation
strategies, only a fractional number of cultivable species has been extensively studied.
This study explored the effects of conventional versus organic farming systems on
microbial communities. Soil samples were collected from an ongoing long-term farming
system comparison trials established in 2007 at Chuka and Thika in Kenya. Illumina
sequencing technology and analysis of 16S rDNA, 16S rRNA cDNA amplicons, fungal
ITS and mRNA transcripts were used to determine the diversity, structure and function of
bacteria, archaea and fungal communities within conventional and organic farming
systems. Grouping of sequences into operational taxonomic units at 97% similarity was
done using QIIME2 pipeline and taxonomy assigned via BLASTn against SILVA 128
and UNITE ITS database, and a curated database extracted from GreenGenes, RDPII and
NCBI. Transcriptomes were analysed using Parkinson lab pipeline
(https://github.com/ParkinsonLab/Metatranscriptome-Workshop). Statistical analysis was
done using R programming language version 3.1.5 and Vegan Community Ecology
Package version 2.5.2. R. The total number of OTUs obtained per dataset included 4,916
OTUs (16S rDNA), 530 OTUs (16S rRNA cDNA) and 1,128 OTUs (fungal ITS) at 97%
genetic distance datasets, respectively. The most notable bacterial phyla within farming
systems were Proteobacteria, Actinobacteria, Firmicutes Acidobacteria, Bacteroidetes,
Chloroflexi, Cyanobacteria, Deinococcus-Thermus, Fusobacteria, Gemmatimonadetes,
Planctomycetes and Verrucomicrobia. Farming systems in both sites were dominated by
unassigned fungal phyla. The known fungal phyla revealed included Ascomycota,
Basidiomycota, Chytridiomycota, Glomeromycota, Calcarisporiellomycota,
Kickxellomycota and Mortierellomycota. Ascomycota was most abundant in organic
farming systems while Chytridiomycota was dominant in conventional farming systems
in both sites. Conventional farming systems had a higher species richness and diversity
when compared with organic farming systems. Factors such as pH, C, N, Zn, Fe, Al, B
and micro-aggregates were found to be the major drivers of microbial diversity within
farming systems in both sites. Major metabolic pathways within the farming systems in
both sites comprised of carbohydrates and energy metabolism, biodegradation and
metabolism of xenobiotics and secondary metabolites biosynthesis. This shows that
microbes in the farming systems utilize diverse carbon sources for survival, as revealed
by metabolic processes and genes responsible for specific pathways. These findings
indicate integration of organic and inorganic inputs, not only affect the soil chemistry but
also the microbial population dynamics and their functional roles. | en_US |
