The core microbiome of Ips typographus in respect to season
Only ASVs that accounted for at least 0.5 % of total ASVs number and were present in at least in five samples were considered part ofI. typographus bacterial or fungal core microbiome in the respective season. Bacterial and fungal communities were significantly affected by seasonality (Fig. 3B, p < 0.005, permanova Jaccard and Bray-Curtis distance).
In both seasons (Fig. 2, 3A), most of the bacterial ASVs belonged to the phylum Proteobacteria (98 % in spring and 96 % in summer season), other phyla were presented only marginally (Bacteroidetes up to 2 %, Actinobacteria up to 1 %, Patescibacteria up to 0.2 and Firmicutes up to 2 %). Proteobacteria were represented by the classes Alphaproteobacteria and Gammaproteobacteria. The last one dominated in both seasons as it accounted for more than 95 % of bacterial ASVs. Gammaproteobacteria were further represented mostly by the orders Enterobacteriales and Xanthomonadales in summer and additionally with Pseudomonadales (represented by Pseudomonas bohemica ) in the spring season. The family Enterobacteriaceae largely dominated in both seasons and was mostly represented by species of Erwinia (around 70 % of the total bacterial reads) and Serratia (6.4 % of reads in spring and 2 % in summer). Pseudoxanthomonas(Xanthomonadales, Xanthomonadaceae) was the second most abundant genus in spring (5.5 %) and summer season (19.2%). Bacterial spring community further differed from the summer by presence of the genusStenotrophomonas (Xanthomonadales) and by almost absence of the genus Taibaiella (Chitinophagales) and the family Lachnospiraceae (Clostridiales).
Ascomycetous fungi dominated in both seasons (Fig. 2, 3A). Saccharomycetes represented 81 % of diversity in the spring and 91 % in the summer season. The second most common class was Sordariomycetes which took almost the rest of the reads. The taxonomic representation was strongly biased toward several species that largely dominated the samples. In both seasons, the most abundant yeasts wereWickerhamomyces bisporus , Kuraishia molischiana andNakazawaea ambrosiae ; however, their proportions differ between seasons. Spring season was characterized by high incidence of yeastsWickerhamomyces bisporus and Yamadazyma species (Saccharomycetales) and filamentous fungi Endoconidiophora polonica and Graphium fimbriasporum (both Microascales). The proportion of these fungi largely decreases in the summer season. The proportion of the yeasts Kuraishia molischiana andNakazawaea ambrosiae increased as the proportion of W. bisporus decreased. A similar course was found for E. polonicathat was almost absent in the summer seasons and was replaced byO. bicolor (Ophiostomatales).