Monitoring rhizosphere microbial communities in healthy and Pythium ultimum inoculated tomato plants in soilless growing systems

• CLPP and DGGE were used to see change in microbial communities in response to pathogen.
• Introduction of Pythium ultimum changed the utilization of nutrients by the microflora.
• Utilization changes were more evident for plant stage than for pathogen introduction.

Closed hydroponic growing systems are commonly used for greenhouse production of vegetables. One of the main problems associated with these systems is the potential spread of plant root pathogens. The purpose of this study was to investigate whether Community Level Physiological Profiling (CLPP) can be used as a method to monitor changes in the rhizosphere microbial communities inflicted by a pathogen. We studied the microbial communities of the roots from three different physiological stages of Pythium ultimum inoculated and non-inoculated tomato plants, with culture-dependent (CLPP and viable counts) and culture-independent methods (PCR–DGGE). The results showed that the presence of P. ultimum changed the utilization of carbon sources by the root microbiota, and significant differences were found between inoculated and non-inoculated plants. However, the differences in utilization patterns were larger between plant physiological stages than between treatments. Also with the results from PCR–DGGE it was confirmed that plant age was a stronger driver of the community structure than the introduction of a pathogen. CLPP is hence a good method for examining changes in microbial communities related to plant development, but regarding changes caused by the presence of a pathogen the method shows less potential.