The Suppressive Nature of Compost against Pythium spp: evaluation of compost-based applications in two host pathogen systems using bioassays and molecular fingerprinting

The suppressive effect of composts on soil-borne plant pathogens has been widely reported in the scientific literature. However, the role of the compost microbiome, in this respect, is still not well understood. The general goal of this research was the molecular-biological characterisation of the microbiomes of two compost types within the host-pathogen system Pythium ultimum and cucumber, thereby contributing to understanding the role of the microbial structure of the chosen composts in this specific system. An additional goal included the definition, development and testing of new host-pathogen systems using the pathogen Pythium aphanidermatum in tomato and cucumber in order to test the suppressive effects of composts against this pathogen. The two chosen composts were made from either organic household waste or organic green waste and the composting process was well known and documented. The composts were mixed together with a reference substrate (peat) in a 50:50 volume ratio. In order to characterise the bacterial (16S rRNA) and fungal (ITS rRNA Amplicons) communities involved in suppressiveness within a P. ultimum and cucumber system, the influence of the composts using DGGE-Fingerprints (Denaturating Gradient Gel Electrophoresis) was analysed on the substrate, as well as at the rhizosphere level of the host plant. Additionally, the effects of gamma irradiation on compost suppressiveness, microbial structure and substrate activity were tested at the end of the experiment.
A clear suppressive effect on the pathogen was found when the composts were mixed with the peat substrate; however, this suppressive effect was no longer present when the sterilised compost (gamma irradiated) and was mixed with the peat. Cluster analysis results from the DGGE fingerprints of the bacterial and fungal communities showed a clear differentiation between the untreated and gamma irradiated composts and peat mixtures. Similar differentiation between the microbial communities of the rhizosphere was found when comparing the untreated and irradiated compost mixtures; however, greater differences in microbial community structures were found when comparing the two different compost and peat mixtures to one another. Results from the rhizosphere fingerprinting for the organic household waste compost indicated a clear differentiation between the fungal and bacterial community structures when comparing the untreated compost mixture to the irradiated compost mixture. Similar results were found when comparing rhizosphere fingerprinting results for the organic green waste compost; however, unlike the organic household compost, the bacterial community structure shared both a main, as well as sub-clusters, between both the untreated and irradiated organic green waste compost samples. Interestingly, no changes in the grouping of the microbial communities were found in the presence of the pathogen i.e. with the addition of the inoculum, in either the substrate or the rhizosphere samples. Differences in substrate composition (e.g. household waste vs. green waste compost) tended to be the greatest factor affecting the fingerprinting grouping. However, the fact that the different microbial communities found for each compost led to similar pathogen suppression in this particular host-pathogen system is of great interest. Apart from the identification of the involved bacteria and fungal species, the analysis of functional diversity is in this way an important step in the elucidation of the mechanisms of the suppressive effects of composts. Results using Fluorescein-Diacetat-Hydrolserate (FDA-HR) as a measure of suppression after 21 days of experimental testing showed that although microbial activity in the compost substrates was higher than found in the reference substrate (peat), microbial activity was similar between both the untreated and irradiated compost mixtures, although the latter was not found to have any suppressive effect on the pathogen. This further indicates the importance of microbial and functional diversity identification in suppressive substrates, as well as the limitations of the FDA-HR per se as a measure of suppressiveness. In a follow-up study, the suppressive potential of both an organic green waste compost and a compost tea made from the same green waste compost were compared using the before-mentioned methodological approach. Results indicated a clear suppressive effect of the compost (50% volume) in comparison to the compost tea and the addition of compost tea to the compost and peat mixture did not improve the initial suppressiveness of the substrate. Results from the molecular-biological study showed no changes with the addition of compost tea to the compost substrate; however, a clear differentiation was found in the microbial community structure of the rhizosphere when the compost tea was added to the control substrate (peat). Although there were differences in the microbial community found, no differences in plant health were observed.
A further system using Pythium aphanidermatum in tomato and cucumber was also developed. This system, which closely resembled that developed for Pythium ultimum and cucumber and using the same peat substrate, differed in the sense that the substrate was inoculated with the pathogen. The reproducibility and success of this new method with regards to optimum temperatures for pathogen proliferation, pathogen inoculation concentrations, as well as cultivation temperatures for both cucumber and tomato (multiple varieties) in the greenhouse was developed and optimised. However, the results obtained using the newly developed system with Pythium aphanidermatum and 4 tomato and cucumber varieties in numerous trial runs and using the same green household waste compost with known suppressive effects on Pythium ultimum, should be taken as preliminary. Although, disease suppression in tomato and cucumber through the use of the compost was evident, the high variation in the bioassay results indicate that further testing and development is necessary to achieve a stable and reliable test with clear results.