The contribution of the apple microbiome to the production chain of apple was so far largely unknown. Here, we describe the apple fruit microbiome and influences on its composition by parameters such as storage season, storage duration, storage technology, apple variety, and plant protection schemes. A combined culturing and metabarcoding approach revealed significant differences in the abundance, composition, and diversity of the apple fruit microbiome. We showed that relatively few genera contribute a large portion of the microbiome on fruit and that the fruit microbiome changes during the storage season depending on the storage conditions. In addition, we show that the plant protection regime has an influence on the diversity of the fruit microbiome and on the dynamics of pathogenic fungal genera during the storage season. For the genus Neofabraea, the quantitative results from the metabarcoding approach were validated with real-time PCR. In conclusion, we identified key parameters determining the composition and temporal changes of the apple fruit microbiome, and the main abiotic driving factors of microbiome diversity on apple fruit were characterized.

The recently discovered prevalence of Rozellomycota in aquatic ecosystems establishes this poorly understood, holomycotan lineage as a group of critical importance for understanding aquatic ecology and fungal evolution. While gradually more genomes become available, knowledge on the ecology of Rozellomycota is still very scarce. After compiling their occurrences from public databases, we can clearly establish their abundance in aquatic environments, interestingly, with a dominance in carbon-rich sediments. Similarly, the carbon and nutrient rich artificial wastewater environment may serve as an example for a highly reduced environment that is inhabited by a diverse range of Rozellomycota lineages, despite being a prokaryote dominated environment. As the Rozellomycota from anaerobic environments are not monophyletic, the questions arise how the Rozellomycota adapt to differing redox conditions and if their parasitism could also have led to anaerobiosis.

Known for its remarkable diversity and ecological importance, the fungal kingdom remains largely unexplored. In fact, the number of unknown and undescribed fungi is predicted to exceed the number of known fungal species by far. Despite efforts to uncover these dark fungal taxa, we still face inherent sampling biases and methodological limitations. Here, we present a framework that combines taxonomic knowledge, molecular biology, and data processing to explore the fungal biodiversity of enigmatic aquatic fungal lineages. Our work is based on serial screening of environmental fungal cells to approach unknown fungal taxa. Microscopic documentation is followed by DNA analysis of laser micro-dissected cells, coupled with a ribosomal operon barcoding step realized by long-read sequencing, followed by an optional whole genome sequencing step. We tested this approach on a range of aquatic fungal cells mostly belonging to the group of aquatic hyphomycetes derived from environmental samples. From this initial screening, we were able to identify thirty-two potentially new fungal taxa in the target dataset. By extending this methodology to other fungal lineages associated with different habitats, we expect to increasingly characterize the molecular barcodes of dark fungal taxa in diverse environmental samples. This work offers a promising solution to the challenges posed by unknown and unculturable fungi and holds the potential to be applied to the diverse lineages of undescribed microeukaryotes.

ISHS IV International Symposium on Postharvest Pathology: Next Generation Innovation and Commercial Solutions for Postharvest Pathology to Reduce Losses, Enhance Quality, and Ensure Product Safety A metagenomic approach to assess Neofabraea infection and dynamics on stored apples