Changes in Soil Prokaryotic Diversity in Response to Land-Use Changes in Sub-Saharan Africa

Takamitsu Ohigashi,Michael Schloter,Kabenuka Munthali,Yoshitaka Uchida,Stefanie Schulz

doi:10.3390/soilsystems5040062

Abstract

Sub-Saharan Africa is one of the most severely affected regions regarding soil degradation, a global issue with the loss of nutrients caused by inappropriate management, leading to low agricultural productivity. Here we asked the question of how soil prokaryotic communities are affected by shifts in land use management and subsequent losses in soil organic carbon. We sampled soils from three sites in Zambia which have neighboring natural and managed sites. After the measurement of soil properties, soil DNA was sequenced, targeting the 16S rRNA gene. As expected, total carbon in soil was decreased in the managed sites, with significant reductions of bacterial biomass. However, the diversity indices in the managed soils were higher than in natural soils. Particularly, the relative abundance of nitrifiers was increased in the managed soils, most likely as a result of fertilization. However also other bacteria, e.g., those which formed tight interactions with the cultivated crops including the genera Balneimonas, and Bacillus, were increased in the managed soils. In contrast bacteria belonging to the family Chloroflexi, which were high in abundance in the natural soil were outcompeted by other prokaryotes in the managed soils most likely as a result of changes in the amount of soil organic carbon. Overall, our results suggest that we need to discuss the trends of prokaryotic diversity separately from those for prokaryotic abundance. Even when bacterial abundances were decreased in the managed soils, nitrifiers’ relative abundance and diversity increased in our experiment, suggesting the possible alteration of the nitrogen cycle in managed soils in sub-Saharan Africa.

Highlights

The continuous expansion of farmlands and the increase in land-use intensity in the sub-Saharan African region, one of the fastest-developing regions in the world, is a result of the needs to fulfill the demands for food of the increasing population
According to the Venn diagrams constructed for each of the three sites, we found approximately 2000 operational taxonomic units (OTUs) unique for farm soils (Figure S2) which exceeded the number of unique OTUs present in the natural soils at all sites
In sub-Saharan African soils, the abundance of prokaryotes was decreased most likely because of losses of soil carbon and nitrogen induced by agricultural management compared to natural soils

Summary

Introduction

The continuous expansion of farmlands and the increase in land-use intensity in the sub-Saharan African region, one of the fastest-developing regions in the world, is a result of the needs to fulfill the demands for food of the increasing population. These activities caused significant soil degradation including the depletion of soil organic matter, carbon (C) and nitrogen (N), leading to the loss of agricultural productivity [1]. To establish sustainable management options, the soil microbiome and its functional traits plays a key role. Mismanagement of soils leads to a dysbiosis of the soil microbiome and a loss of soil quality including the increase of plant pathogens, affecting plant growth or microbiota which trigger the formation of greenhouse gases, turning soils from a sink for nutrients into a source for CO2, N2O and CH4 emissions [6]

Objectives

Methods

Results

Conclusion