Soil-dependent fate of Klebsiella pneumoniae and Listeria monocytogenes after incorporation of digestates in soil microcosms

Digestates are valuable by-products of anaerobic digestion. They can be used as fertilisers/soil improvers in agriculture. We collected six digestates from anaerobic digestors fed with biomass of diverse origins and analysed the occurrence of the process indicator bacteria E. coli and the three pathogens Salmonella enterica , Klebsiella pneumoniae sensu lato ( Klebsiella pneumoniae Species Complex, KpSC) and Listeria monocytogenes (Lm). Salmonella enterica was absent in all digestates. Low copy numbers of KpSC were PCR detected in all digestates. In digestate SMS, E. coli was present at low concentration (50 CFU/g), and K. pneumoniae sensu stricto (Kp) along with Lm were detected and isolated after selective enrichment. We designed microcosm experiments to investigate the fate of these pathogens following the application of the digestates to three soils with contrasting edaphic characteristics. After 42 days incubation, S. enterica was not detected in any microcosms, and E. coli was found only in microcosms with silty clay loam soil supplemented with SMS digestate. The frequency of molecular detection of KpSC varied, while Lm was PCR detected only once in the silty clay loam soil supplemented with SMS digestate. Further experiments with artificially contaminated digestate demonstrated that the fate of Kp and Lm was dependent on soil type and that their detection duration correlated with their initial concentration in the digestate. Additionally, we explored an integrated statistical analysis framework to uncover the relationship between soil microbial diversity and the occurrence of KpSC. This last analysis highlighted both the potential of microbial communities to act as natural barrier against pathogens, and the complexity of microbial community dynamics affecting the pathogen's presence. • Klebsiella pneumoniae species complex is detected in digestates and manure • Its fate in soil following organic fertilisation is soil-dependent • Prevalence depends on soil microbial community composition but not on diversity