Bacterial diversity of South African soils
The soil is an essential part of the environment as it provides support for life which comprises microorganisms, plants, animals and humanity. Ecosystem services such as nutrient cycling, food production and temperature regulation are important in maintaining life, all of which can be attributed to the soil; it is therefore of importance that the soil is properly managed. The soil-dwelling organisms contribute immensely to the general functioning of the soil. Bacteria are numerically abundant and diverse microorganisms present in the soil, are important potential markers of soil health and quality. The abundance, diversity, and richness of bacteria is largely dependent on the organic matter content of the soil. Several studies carried out show that soils rich and abundant in bacteria are good for agricultural purposes as they release important nutrients necessary for plant growth. South Africa is faced with an increase in land degradation which affects agricultural productivity. Some studies have shown that land degradation affects bacterial diversity, richness and abundance. Soil samples were obtained from specific locations (Mpumalanga indigenous forests, Limpopo agricultural soil and North West agricultural soil), to determine the bacterial diversity in soils possibly undergoing degradation, their causes and indicators of soils currently undergoing degradation. Samples were assessed using High-throughput sequencing. The bacterial DNA from the soil were extracted using the PowerSoil DNA isolation kit (Mo Bio labs, USA), following the manufacturer's instructions. Data analysis was carried out on the microbiome analyst and the PAST platform. The bacteria class found to be most abundant in agricultural and forest soils was Proteobacteria, with a relative abundance value of 47.3% and 35.5% respectively. The richness of bacterial phyla was higher in the forest (natural/undisturbed) soil than in the Limpopo and North West agricultural soils with richness values of 1969, 1710 and 1663 respectively. The Limpopo agricultural site had the highest bacterial diversity with a value of 6.6, while the North West agricultural soil and Mpumalanga forest soil had a bacterial diversity of 6.5 and 6.4 respectively. Principal component analysis showed that the class of bacteria that brought about significant differences amongst the soil of Limpopo, the North West and Mpumalanga sites were Actinobacteria, Nitrospirae, Proteobacteria and Verrucomicrobia. It was observed that the most abundant phyla in both indigenous and commercial forest sites were Proteobacteria, Acidobacteria, Verrucomicrobia, Chloroflexi and Actinobacteria, while the most abundant classes in both the indigenous and commercial forest sites were Verrucomicrobia, Alphaproteobacteria, Holophagae, Betaproteobacteria, Acidobacteria, Ktedonobacteria and Actinobacteria. There were notable significant differences (p=0.03 using ANOVA) observed in the phyla Acidobacteria, Actinobacteria, Proteobacteria and Verrucomicrobia and the class Alphaproteobacteria, Betaproteobacteria, Holophagae and Verrucomicrobia in the indigenous and commercial forest sites. The soil organic carbon (SOC), nitrate, total carbon (TC), pH, calcium, magnesium, potassium and sodium content showed significant changes (p<0.05) from the indigenous sites to the commercial sites, having higher values in the indigenous sites than the forest sites. Intensive and continuous tillage should be discouraged for best agricultural productivity as this tends to reduce the bacterial abundance, richness, and diversity, all of which are important for healthy plant growth. Bacterial abundance, richness and diversity also help the plants build resistance against sudden environmental changes. The use of cover cropping in agriculture is advised as this help increase the organic matter content of the soil, which is necessary for increased bacterial abundance, richness and diversity. The effect of the commercialization of natural lands (forests) has not been researched fully. It may have a negative effect on the bacterial composition of the soil which inadvertently affects ecosystem services. Comparing the bacterial composition of indigenous and commercial forests showed that there is a significant difference in the phyla and class composition of bacteria. From this research the physical and chemical properties had no effect on the bacterial diversity using CCA.