Survival of plant pathogens during composting of bio-waste: a case study for oomycetes and fungi

European countries have implemented national strategies to reduce the use of peat in horticulture due to its environmental impact. Studies demonstrated the possibility of reducing peat consumption by using compost as a substitute without affecting the growth and development of potted horticulture plants. However, any substitute must be produced considering quality standards and requirements that are adopted for peat. Among others, the risk of contamination of compost with plant pathogens is particularly high. Furthermore, the assessment of the survival of specific plant pathogens during the composting process requires proper detection methods. This study evaluated the survival/presence of the oomycete Phytophthora cinnamomi, as a model plant pathogen, in woody chips of artificially inoculated Castanea sativa saplings used as a bulking agent in composting processes. Detection techniques for assessment included isolation in pure culture, quantitative PCR (qPCR) and High Throughput Sequencing (HTS). The pathogen was easily detected in woody chips at the beginning of the composting process with baiting and molecular barcoding. By the end of the maturation phase, no P. cinnamomi was detectable by any diagnostic method including baiting, confirming the efficacy of a proper composting process in eradicating the pathogen. HTS approach was also able to detect throughout the process the DNA of plant pathogenic fungal genera naturally present in the green residues and bulk agents. These findings are crucial for developing diagnostic pipelines to be included in protocols for compost biosafety certification. Finally, the present study demonstrated the possibility of processing recycled horticulture biowaste to obtain high-quality and safe compost without the need for complex and expensive composting plants.