Agricultural practices affect the bacterial community structure in soil. It was hypothesized that agricultural practices would also affect the bacteria involved in the degradation of crop residue. Soil was sampled from four different agricultural practices, i.e. conventional agriculture on the flat or on beds, or conservation agriculture on the flat or on beds. Cultivating crops on the flat is done traditionally, but cultivating crops on beds was introduced so as to avoid water logging during the rainy season and its potential negative effect on yields. Soil from these four treatments was amended in the laboratory with maize residue (Zea mays L.) or its neutral detergent fibre (NDF) fraction, mostly consisting of (hemi) cellulose, and incubated aerobically for 14 days. Maize residue was applied to soil as it is left in the field in conservation agriculture and NDF was added to study which bacteria were favoured by application of (hemi) cellulose. Soil was incubated aerobically while the carbon mineralization and the bacterial population were monitored. On the one hand, the relative abundance of phylotypes belonging to bacterial groups that preferred low nutrient environments was higher in soil with conservation agriculture (e.g. Acidobacteria 17.6%, Planctomycetes 1.7% and Verrucomicrobia 1.5%) compared to conventional practices (Acidobacteria 11.8%, Planctomycetes 0.9% and Verrucomicrobia 0.4%). On the other hand, the relative abundance of phylotypes belonging to bacterial groups that preferred nutrient rich environments, such as Actinobacteria, showed an opposite trend. It was 11.9% in conservation agriculture and 16.2% in conventional practices. The relative abundance of Arthrobacter (Actinobacteria) and Bacillales more than doubled when maize residue was applied to soil compared to the unamended soil and that of Actinomycetales when maize or NDF was applied. Application of organic material reduced the relative abundance of a wide range of bacterial groups, e.g. Acidobacteria, Bacteroidetes, Planctomycetes and Verrucomicrobia. It was found that application of organic material favoured the same bacterial groups that were more abundant in the soil cultivated conventionally while it reduced those that were favoured in conservation agriculture.
