Influence of soil physico - chemical properties on indigenous soil bacteria in selected ecosystems at Palapye,Eastern Botswana

Abstract

Advancement of knowledge on soil microbial richness is a key to environmental policy and sustainable land management. In Botswana, there is a dearth of scientific reports on soil bacterial dynamics. The aim of this study is to improve our understanding of how soil physico-chemical properties influence bacterial abundance and distribution under different land-use types (ecosystems). Six ecosystems studied include saline soil, sewage sludge dump, garden, fallow land rainfed and irrigated arable farms. A combination of agar culture and metagenomic approaches via sequencing of PCR amplified 16S rDNA genes from total extracted DNA was used to identify and characterize bacteria communities. Selected soil physico-chemical properties were determined using routine laboratory procedures. The results show that sewage sludge ecosystem had the highest organic matter (59.9 %), cation exchange capacity (8.65 cmol kg-1) and clay content (17.83 %), and these three properties mainly influenced the richness and diversity of soil bacterial communities. The soils from bare land, rainfed and irrigated arable farms had the least organic matter and could not sustain enough bacterial communities to produce the required DNA quality for metagenomics analysis. The saline soil had the highest electrical conductivity (EC) (0.716 dS m-1), an index of salinity, and had relatively higher DNA concentration (25.8 ng μL-1). Total counts of culturable bacterial population ranged between 107 and 6 x107 after using mannitol salt agar and E. coli agar. Next generation sequencing (NGS) showed the order of phyla dominance as Proteobacteria > Actinobacteria > Firmicutes > Bacteroidetes > Acidobacteria. Soils in the ecosystems have promising potential to contribute considerably to global carbon and nitrogen geochemical cycling due to the preponderance of Proteobacteria. The presence of unnamed phyla identified in the ecosystems goes further to support the need for a continued build-up of a comprehensive global soil biodiversity database through extensive research.