Assessment of the biofumigation effect of Canola (Brassica napus) on soil microbial community function and structure

Thesis (MSc (Environmental Sciences))--North-West University, Potchefstroom Campus, 2012. Sunflower cultivation in South Africa is threatened to a large extent by the fungal parasite, Sclerotinia sclerotiorum, which causes extensive head rot and crop losses of up to 100%. This is a major problem for commercial farmers since it leads to a lower farm income, as the use of fungicides minimises crop damage, but increases production costs and can lead to several environmental problems. Therefore, an alternative is needed which can still control crop diseases, without harbouring health and environmental risks. Due to their biofumigation potential, Brassica plant species incorporated into the soil as green manures can be applied as alternatives for chemical pesticides. These plants produce glucosinolates that are hydrolysed upon tissue disruption by the enzyme, myrosinase, into active products for example isothiocyanates. Since isothiocyanates are highly toxic, it can be used instead of conventional pesticides for the inhibition of soil–borne pathogens. However, little is known about the effect of such biofumigants on the natural soil microbial communities required to maintain soil functions. A greenhouse experiment was conducted to assess the influence of canola (Brassica napus) green manure on soil microbial community function and structure. The study consisted of 32 pots containing four treatments of eight replicates each. The treatments included 1) only sunflowers in soil (control), 2) sunflowers in soil incorporated with canola green manure; 3) sunflowers in soil incorporated with canola and inoculated with S. sclerotiorum and 4) sunflowers in soil inoculated with S. sclerotiorum. The experiment was conducted for 120 days. From the soil physico–chemical properties conducted before the treatments were applied and after experiment completion, it was evident that the initial stimulating effect of canola manure on the soil carbon, total nitrogen and organic carbon content was not long-lasting. The overall microbial activity assessed with dehydrogenase assays and Biolog® Ecoplates, varied in relation to plant growth cycles, as root secretions differed. Multivariate analysis of the substrate utilisation patterns, distinguished among the treatments. Utilisation profiles illustrated that although different members of microorganisms were active in the various treatments, similar trends could still be observed. All four treatments showed similar diversity profiles after 120 days. Phospholipid fatty acid results indicated a significant increase in microbial biomass for all four treatments over time. The microbial community structure differed to a lesser extent between treatments, but changed over time within each treatment. Community function varied according to the changing structure. Fatty acid stress ratios for all treatments showed significantly lower stress levels just after manure amendments, as the added organic matter might have stimulated microbial growth. Chlorophyll a fluorescence measurements showed shifts occurring in the photosynthetic efficiency of the sunflowers among the treatments. S. sclerotiorum had a suppressive effect on photosystem II functionality leading to lower electron transport and ATP production. Canola green manure amendments had a slight negative effect on sunflower vitality. Overall the results obtained from this study suggest that incorporation of canola green manure into the soil has an effect on soil microbial community function and structure. Nonetheless, this biofumigation effect is short–lived and microbial communities returned to their initial compositions after the disturbance. The methods applied during this investigation indicated a possible suppressive effect of the canola manure on S. sclerotiorum. Masters