Ciliated microeukaryotes of the subclass peritrichia (ciliophora: oligohymenophorea): integrative taxonomy, genomic analysis, and environmental applications

Abstract

The ciliates (Alveolata, Ciliophora) are cosmopolitan, ecologically diverse, and genetically complex microeukaryotes, with more than 10,000 described species. Due to their wide distribution, variety of life habits, and sensitivity to environmental stressors, they represent an excellent model for studies on biodiversity, evolution, and biomonitoring. The subclass Peritrichia, one of the most diverse groups within Ciliophora, is particularly notable for its predominantly sessile lifestyle and its utility as a bioindicator of organic pollution. However, knowledge regarding their taxonomy, evolution, and biotechnological potential still presents gaps, often due to morphological complexity and a lack of data, ranging from taxonomy to genomics. The increasing application of next-generation sequencing (NGS) methodologies, such as comparative genomics and metabarcoding, offers new frontiers to resolve taxonomic deadlocks and explore the functional and ecological diversity of peritrichs. Therefore, the general objective of this thesis was to expand the knowledge of the taxonomic and genetic diversity of ciliates in the subclass Peritrichia in aquatic ecosystems of south and southeastern Brazil and to improve the understanding of their evolution in a genomic context. To this end, microscopy and molecular techniques were employed, resulting in three chapters. The first chapter documented the first occurrence of a high natural infestation of the peritrich Epistylis sp. on the crustacean Aegla serrana in a natural habitat. Through morphological characterization and phylogenetic analysis based on the 18S rRNA gene, the study confirmed the occurrence of superinfestation in the wild, highlighting the potential ecological importance of this interaction, which may affect the fitness of the basibiont, and demonstrating the applicability of molecular techniques to resolve taxonomic impasses. The second chapter investigated the genomic and evolutionary landscape of Peritrichia through the sequencing and analysis of the genomes of seven Brazilian peritrich species, comparing them with data from other Oligohymenophorea. Phylogenomic analysis confirmed the monophyly of the subclass Peritrichia and corroborated previously established internal relationships. Functional analysis, focused on Carbohydrate-Active Enzymes (CAZymes), revealed the adaptation of peritrichs to bacterivory (evidenced by the high frequency of Glycoside Hydrolases – GHs) and suggested metabolic specializations, such as the increased presence of chitin-degradation enzymes in mobilids (Trichodina), possibly linked to feeding on the host's integument, and an abundance of Glycosyl Transferases (GTs) in Vaginicolidae, likely associated with lorica synthesis. The third chapter evaluated the efficacy of 18S rRNA gene metabarcoding (V4 region) for water quality biomonitoring using the Ciliophora community, with a focus on Peritrichia, in reservoirs of the Tietê River with distinct levels of organic contamination. The results demonstrated the capacity of high-throughput sequencing to detect variations in the composition of the microeukaryotic community in response to organic pollution, with different Peritrichia taxa acting as potential bioindicators in a regional and seasonal context, reinforcing the utility of ciliates as a practical and effective tool for biomonitoring impacted tropical ecosystems. In summary, this thesis employed an integrative taxonomic, genomic, and ecological approach to provide deeper insight into the diversity, adaptive potential, and functional role of peritrichs. The findings reinforce the evolutionary complexity of the group, elucidate new perspectives on their metabolism, and validate the application of advanced molecular methodologies for conservation and environmental biomonitoring in Neotropical aquatic ecosystems.