A Parasite-Rich Microeukaryome Shows Tribe-Structured Covariation with the Bacteriome in Non-Urban Mosquitoes (Culicinae) from Colombia

The eukaryotic component of the mosquito microbiota, which includes parasites, remains poorly characterized, partly because amplicon surveys suffer from host co-amplification and primer bias. To describe their microeukaryome, we re-analysed total-RNA sequencing libraries from non-urban Culicinae collected in Antioquia, Colombia, whose virome and bacteriome were previously characterized. Ribosomal 18S and 28S reads were mined from 26 pooled samples representing 18 morphotypes and four tribes. The curated 18S matrix comprised 1350 reads across 45 taxonomic features, and a rank-aware inventory retained 29 non-redundant lineages. Stramenopiles (Gyrista and Bigyra) accounted for 43.0% of curated 18S reads and Microsporidia for 20.0%. Seven features with best-hit labels of insect parasites occurred in 15 samples; Amblyospora was supported at the genus level, whereas a Coelomomyces-labelled signal was corroborated by 28S evidence only at the order Blastocladiales. Community composition differed among tribes after rarefaction; in non-rarefied data, this difference depended mainly on an Aspergillus-labelled feature of uncertain provenance. In 21 matched samples, microeukaryome and bacteriome ordinations were concordant (Procrustes correlation = 0.507; p = 0.0047), but not within tribes, and no concordance with the virome was detected. These results provide a baseline for the microeukaryome of non-urban Neotropical Culicinae and its tribe-structured covariation with the bacteriome.