EARTHWORM AND SOIL POLLUTION Mutual interactions of E. andrei earthworm and pathogens during the process of vermicomposting Radka Roubalová 1 & Petra Procházková 1 & Aleš Hanč 2 & Jiří Dvořák 1 & Martin Bilej 1 Received: 1 November 2018 /Accepted: 22 January 2019 # Springer-Verlag GmbH Germany, part of Springer Nature 2019 Abstract Vermicomposting is a process by which earthworms together with microorganisms degrade organic wastes into a humus- like material called vermicompost. This process does not include a thermophilic stage, and therefore, the possible presence of pathogens represents a potential health hazard. To elucidate the effect of earthworms in the selective reduction of pathogens, grape marc substrate was artificially inoculated with Escherichia coli, Enterococcus spp., thermotolerant coliform bacteria (TCB), and Salmonella spp., and their reduction during vermicomposting was moni- tored. Various defense mechanisms eliminating microorganisms in the earthworm gut were assumed to be involved in the process of pathogen reduction. Therefore, we followed the expression of three pattern recognition receptors (coelo- mic cytolytic factor (CCF), lipopolysaccharide-binding protein (LBP), and Toll-like receptor (v-TLR)), two antimicrobial molecules (fetidin/lysenins and lysozyme), and heat shock protein HSP70. We detected the significant decrease of some defense molecules (fetidin/lysenins and LBP) in all pathogen-inoculated substrates, and the increase of CCF and LBP in the Salmonella spp.-inoculated substrate. At the same time, the reduction of pathogens during vermicomposting was assessed. We observed the accelerated reduction of E. coli, Enterococcus spp., and TCB in pathogen-inoculated sub- strates with earthworms compared to that without earthworms. Moreover, the differences between the microbiome of grape marc substrate and earthworm intestines were determined by high throughput sequencing. This analysis revealed that the bacterial composition of grape marc substrate differed from the composition of the content of earthworm intestines, suggesting the elimination of specific bacterial species during food passage through the gut. Keywords Eisenia . Grape marc . Bacteria . Defense molecules . Microbiome Abbreviations CCF Coelomic cytolytic factor CFU Colony-forming unit LBP Lipopolysaccharide-binding protein PRR Pattern recognition receptor TCB Thermotolerant coliform bacteria TLR Toll-like receptor Introduction Vermicomposting is a process of degradation of organic matter that involves complex interactions between earth- worms and microorganisms. In comparison with the composting process, in which the organic material un- dergoes a thermophilic phase (45–65 °C) that should inactivate pathogenic microorganisms (Lung et al. 2001), vermicomposting takes place at temperatures up Highlights Earthworms accelerated the reduction of pathogens in most of the tested substrates. Some defense molecules were upregulated in earthworms kept in the pathogen-inoculated substrate. Under great bacterial load, the earthworm gut underwent reversible histological changes. The microbiome of the earthworm gut differed from that of grape marc substrate. Responsible editor: Philippe Garrigues Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11356-019-04329-5) contains supplementary material, which is available to authorized users. * Radka Roubalová r.roubalova@biomed.cas.cz 1 Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic 2 Czech University of Life Sciences Prague, Kamýcká 129, CZ-165 00 Prague 6, Czech Republic Environmental Science and Pollution Research https://doi.org/10.1007/s11356-019-04329-5