Arable agriculture changes soil microbial communities in the South African Grassland Biome

Gilbert Kamgan Nkuekam,Don A Cowan,Angel Valverde

doi:10.17159/sajs.2018/20170288

Abstract

Many studies, mostly in temperate regions of the northern hemisphere, have demonstrated that agricultural practices affect the composition and diversity of soil microbial communities. However, very little is known about the impact of agriculture on the microbial communities in other regions of the world, most particularly on the African continent. In this study, we used MiSeq amplicon sequencing of bacterial 16S rRNA genes and fungal ITS regions to characterise microbial communities in agricultural and natural grassland soils located in the Mpumalanga Province of South Africa. Nine soil chemical parameters were also measured to evaluate the effects of edaphic factors on microbial community diversity. Bacterial and fungal communities were significantly richer and more diverse in natural grassland than in agricultural soils. Microbial taxonomic composition was also significantly different between the two habitat types. The phylum Acidobacteria was significantly more abundant in natural grassland than in agricultural soils, while Actinobacteria and the family Nectriaceae showed the opposite pattern. Soil pH and phosphorus significantly influenced bacterial communities, whereas phosphorus and calcium influenced fungal communities. These findings may be interpreted as a negative impact of land-use change on soil microbial diversity and composition. Significance:   This report is the first of the effect of land-use changes on the diversity of the soil microbial communities in African grassland soils. Land-use changes influence the diversity and structure of soil microbial communities in the Grassland Biome of South Africa. This study serves as a baseline for future studies on South African soil microbial diversity

Highlights

Soils represent a reservoir for a wide diversity of microorganisms such as bacteria, fungi and viruses.[1]
We evaluated and compared the compositions of the bacterial and fungal communities in agricultural and natural grassland soils from 15 sites in the Mpumalanga Province in the Grassland Biome of South Africa using deep amplicon sequencing
The relative numbers of bacterial versus fungal taxa cannot be quantified from our data, our results suggest that natural grassland soils are richer in bacterial taxa than in fungal taxa, which is in agreement with previous studies showing that soil microbial biomass in natural grasslands is usually strongly dominated by bacteria.[32,33]

Summary

Introduction

Soils represent a reservoir for a wide diversity of microorganisms such as bacteria, fungi and viruses.[1]. Soil microbial communities are important drivers of ecosystem functioning and climate change mitigation through the fixation, immobilisation and cycling of greenhouse gases.[4] Plants synthesise organic matter via photosynthetic activities and provide energy to soil microbes through root exudates.[5,6] In return, soil microorganisms provide the plants with critical ‘services’, including decomposition of organic matter, mineral cycling and biocontrol of soilborne pathogens.[4,7] Land use, such as the modification of a natural ecosystem for agriculture purposes, has been proven to have significant effects on soil microbial communities by changing the physical and chemical properties of the soil. Inventories of the composition and differences in the bacterial and fungal communities in Mpumalanga’s agricultural and natural grassland soils will contribute to the body of knowledge, and can provide a description of the core soil microbial communities in the unmodified grassland

Materials and methods

Results and discussion

G6 A14 A1 A13 G7 G4 G13 G15 A3 G14 G9 G8 A4 A9 A15 G2 G11 G5 G12