New fungal core microbiome members of the ground nesting bee Andrena vaga: The key to oligolecty?

This dataset contains lists of yeast species associated with the oligolectic mining bee Andrena vaga, which is specialised on willow pollen (Salix spec.). We analysed the yeast community of seven different matrices of the early nest stage, using two methodological approaches (classical cultivation and DNA-metabarcoding). In May 2022, ten brood cells were excavated at one nesting site of A. vaga, and separated into pollen provision, egg and brood cell wall. On the same nesting site, ten pollen collecting adult females were sampled. The pollen from their scopae was scraped into individual collection tubes and their guts were dissected. Additionally, we sampled ten samples of catkin pollen from four male Salix alba trees. To recover the viable yeast community, we used classical cultivation. All seven matrices (pollen of willow catkins, inner brood cell walls, provisions, eggs, adult bee guts, and pollen collected on their scopae) are represented by ten sub-samples. For the cultivation of the brood cells, the inner wall was carefully washed with sterile Tween-water and a cotton bud in a sterile Petri dish, and the collected Tween-water was used for cultivation. All other sub-samples were suspended in Tween-water and cultivated on yeast extract–malt extract (YM) medium, supplemented with 500 mg/l chloramphenicol to prevent bacterial growth. Pure cultures were prepared for Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) using the Biotyper platform (Bruker Daltonics). Yeast isolates showing high confidence scores in pair-wise comparisons of MALDI-ToF MS spectra, were considered conspecifics and 1-2 representatives of each group were additionally identified using ribosomal gene sequencing. ITS2 DNA-metabarcoding was performed for the same set of matrices, but with pooled sub-samples. It was technically impossible to separate the brood cell wall from the surrounding soil matrix for DNA extraction. Thus, we analysed the consolidated soil of the brood cell wall; it is referred to as ‘soil matrix’ in the following. For ITS2 sequences, paired-end reads assembly, quality filtering, chimera checks, ITS2 region extraction, clustering of OTUs (3% dissimilarity), and taxonomic assignment were performed using the Pipits pipeline (Gweon et al., 2015). Representative OTU sequences were identified employing the NCBI GenBank sequence database, and in parallel employing the MycoBank sequence database. Unfortunately, the sequencing of the pollen from the catkin failed. Further methodological and analytical details are described in the associated paper by Gardein et al. (2025). The dataset compromises two tables: Table “Rawdata_cultivation” includes columns for the seven matrices, the ten sub-sample for each matrix, the yeast species identified using MALDI-ToF MS, yeast species identified with ribosomal gene sequencing, identifier from the Catalogue of Life (COL), and an accession number of the strain for the collection of the German Collection of Microorganisms and Cell Cultures (DSMZ, Braunschweig, GER). For Holtermanniella takashimae and Triodiomyces crassus the COL identifier were not available, why the identifier from Mycobank.org are mentioned. Table “Rawdata_metabarcoding” includes columns for the matrices, species identified with ITS2 DNA-metabarcoding, identifier from the Catalogue of Life (COL), number of reads (summarised for all Operational Taxonomic Units (OTUs) of this species) and the proportion of reads per species relative to the total read number per matrix in percent. For Aspergillus candidus, Holtermanniella takashimae, Diddensiella parasantjacobensis, Penicillum soosanum and Thelonectria blackeriella the COL identifier were not available, why the identifier from Mycobank.org are mentioned. The COL identifier can be used with the following URL link: https://www.catalogueoflife.org/data/taxon/[Identifier]

Tags: associated-microbiota, bee-fungi-interaction, fungal-symbionts, microbiome, solitary-bee, yeast-species
Organization: OpenAgrar