Understanding disease suppression by compost microbes: quantifying pathogen reduction by compost and testing Sphingopyxis spp. associated with disease suppression

MSC Monica

MSc Mònica Camareno Rodríguez


Supervision: Dr. Pascale Flury, Anja Logo, Dr. Thomas Oberhänsli (FiBL)


Pathogens causing soilborne diseases are difficult to manage and they represent a big challenge for the cropping systems. Some of the most common soilborne pathogens are Globisporangium ultimum (former Pythium ultimum) and Rhizoctonia solani (Kühn), affecting a wide range of host plants. Composts have demonstrated the capacity to reduce disease incidence and have a suppressive effect against these pathogens. This characteristic is attributed in most cases to the microbial composition in the compost. However, the microbes and mechanisms that make compost suppressive remain elusive. The study aimed to analyze the development of G. ultimum in compost-substrate mixes as an indicator of disease suppression happening in the substrate. For this purpose, a qPCR was used to quantify the pathogen in the compost substrate mixes. Further analysis between pathogen quantification in the compost substrate mixes and cress/ cucumber biomass was carried out to try to find a correlation between the disease incidence and pathogen development in the substrate. In the second part of the thesis, strains of Sphingopyxis were isolated, a bacterial genus that is associated with disease suppressive compost. The isolates were tested for their disease suppressive properties in vitro and in vivo.

In this study, we found an inconsistent reduction of G. ultimum among the composts after 7 days in the compost/mix substrate. Also, no correlation between the pathogen amount and the disease suppression of the compost in cress nor cucumber was found. Three isolates from the indicative genus Sphingopyxis were successfully identified and tested in vitro, in which one of them could significantly reduce the growth of G. ultimum in an in vitro assay. All three isolates were also tested in vivo but no clear results were obtained due to experimental challenges.

The results of this study showed that the pathogen amount in the bulk substrate is not representative of the strength of the disease suppressive properties of the compost when correlated with the amount of the pathogen in the substrate and the relative biomass in plant assays. Nevertheless, this type of study can be used as a base for the analysis of the pathogen in the composts since there is not much information about the suppression of soilborne diseases happening directly in the compost. Moreover, the role of the isolated Sphingopyxis strains in disease suppression cannot be defined based on our results, and further testing is required.