Future prospects for investigating ciliate biodiversity

Abstract

Ciliates have a long history of being central in evolutionary and ecological studies on eukaryotic microorganisms. Although thousands of species have been discovered, their total diversity still remains unknown. Here, we will discuss two unsolved problems that hinder the further exploration of ciliate diversity at the species level, and potential solutions to these problems are proposed. First, ciliate morphospecies are difficult to identify because the different silver stains are not scalable (they do not represent high-throughput methods) and basic supplies are lacking (e.g., protargol); a solution may be the development of fluorescent staining techniques. Second, ciliate phylogenetic species are difficult to identify because of extensive paralogy in nuclear-protein-coding genes; a solution may be to concentrate on sequencing mitochondrial genomes. These two approaches could be integrated into a high-throughput fluorescent-single-cell sorting and mitochondrial genomes sequencing process that would enable the observation and better understanding of ciliate species on a massive scale.

Insights into freshwater ciliate diversity through high throughput DNA metabarcoding

“…Taxa that are low to very low in abundance are either lost in multiple steps involved in staining, or remain unnoticed. Sometimes, cells are inevitably contracted, swollen, or broken after the fixation or bleaching process, leading to discrepancies in morphology-based identifications (Dunthorn et al 2014 , Abraham et al 2019 , Rajter et al 2022 ). Moreover, some ciliates groups, such as free-living litostomateans, members of the genera Pseudoprorodon and Cryptolophosis cannot be sufficiently stained at all (Abraham et al 2019 ).…”

“…The taxonomic identifications of ciliates traditionally relies on microscopic techniques involving observation of live or fixed cells, with a focus on ciliature or silver-line system (Foissner 2016 ). However, relying solely on microscopy for identification presents certain limitations, including the time-intensive process of culturing ciliates, complex staining procedures, and the existence of morphospecies and cryptic species that can only be distinguished at the genetic level, posing challenges to accurate identifications (Rajter et al 2022 ). Consequently, the identification of ciliates and other microorganisms has proposed DNA-based methods as an alternative taxonomic approach to unveil their vast diversity (Medinger et al 2010 , Cahoon et al 2018 , Pitsch et al 2019 , Antil et al 2023 ).…”