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).