BackgroundThe microbiota of liverworts provides an interesting model for plant symbioses; however, their microbiome assembly is not yet understood. Here, we assessed specific factors that shape microbial communities associated withRicciatemporary agricultural crusts in harvested fields by investigating bacterial, fungal and archaeal communities in thalli and adhering soil from different field sites in Styria and Burgenland, Austria combining qPCR analyses, amplicon sequencing and advanced microscopy.ResultsRiccia spec. div.was colonized by a very high abundance of bacteria (101016S rRNA gene copies per g of thallus) as well as archaea and fungi (108ITS copies per g of thallus). EachRicciathallus contain approx. 1000 prokaryotic and fungal ASVs. The field type was the main driver for the enrichment of fungal taxa, likely due to an imprint on soil microbiomes by the cultivated crop plants. This was shown by a higher fungal richness and different fungal community compositions comparing liverwort samples collected from pumpkin fields, with those from corn fields. In contrast, bacterial communities linked to liverworts are highly specialized and the soil attached to them is not a significant source of these bacteria. Specifically, enrichedCyanobacteria, BacteroidetesandMethylobacteriasuggest a symbiotic interaction. Intriguingly, compared to the surrounding soil, the thallus samples were shown to enrich several well-known bacterial and fungal phytopathogens indicating an undescribed role of liverworts as potential reservoirs of crop pathogens.ConclusionsOur results provide evidence that a stable bacterial community but varying fungal communities are colonizing liverwort thalli. Post-harvest, temporary agricultural biocrusts are important reservoirs for microbial biodiversity but they have to be considered as potential reservoirs for pathogens as well.Supplementary InformationThe online version contains supplementary material available at 10.1186/s40793-023-00501-0.