International Journal of Marine Science, 2024, Vol.14, No.3, 172-181 http://www.aquapublisher.com/index.php/ijms 174 Figure 1 from Luo et al.'s study shows the morphological characteristics of the newly discovered ciliate species Hemiholosticha kahli. The images, taken from in vivo observations and protargol impregnation, detail the morphological features of the species. The figure displays the species' wide oval shape, three sharp ribs on the dorsal side, and a large number of green algae inside the body. These algae give the ciliate a green appearance, enhancing its unique identification. Figure 1 also shows detailed cellular structures, such as the nucleus, cilia arrangement, and body surface texture. These morphological characteristics provide important references for the classification and study of ciliates, highlighting the importance of morphology in ciliate research. 2.2 Classification methods and criteria The classification of ciliates has traditionally relied on detailed morphological and ultrastructural analyses, including the study of ciliary structures and internal cytoskeletal derivatives (ciliary structures). The study by Chi et al. (2020) provides detailed methods and examples of ciliate classification and species diversity, demonstrating how molecular and morphological analyses can be combined to improve taxonomic diagnosis and understand phylogenetic relationships among species (Figure 2). Modern approaches combine molecular data, such as 18S rRNA gene sequences, with classical morphological methods to resolve taxonomic uncertainties and improve species identification (Zhao et al., 2016; Abraham et al., 2019). Techniques such as live cell observation, staining methods, and molecular markers (e.g., cox1 gene, ITS region) are used to delineate species and understand their phylogenetic relationships (Zhao et al., 2016; Abraham et al., 2019; Wang et al., 2020). Figure 2 from Chi et al. (2020) shows a maximum likelihood (ML) phylogenetic tree based on 18S rDNA sequences, including 91 species of heterotrich ciliates and 5 species of karyorelictean ciliates. This figure indicates that Gruberia foissneri forms a highly supported independent clade with other Gruberia species (100% ML, 1.00 BI), representing the family Gruberiidae. Additionally, Linostomella vorticella and two other Linostomella sequences form a sister group with the Condylostomides clade. These phylogenetic relationships emphasize the evolutionary differentiation among various ciliate groups, providing significant insights into their classification and evolutionary history. 2.3 Key morphological traits used in classification Key morphological traits used in the classification of ciliates include the structure and arrangement of the oral apparatus, the pattern of somatic kineties, and the presence of specific ciliary structures such as caudal cilia and undulating membranes (Chen et al., 2015; Qu et al., 2020). For instance, the novel ciliate Platynematum rossellomorai is distinguished by its large anterior oral area, two caudal cilia, and a small number of somatic kineties, which are critical for its classification within the genus Platynematum (Qu et al, 2020). Similarly, the novel species Sterkiella subtropica is identified by its unique ciliature and nuclear apparatus, as well as its ontogenetic events, which include the formation of specific cirri patterns (Chen et al., 2015). These morphological characteristics, combined with molecular data, provide a comprehensive framework for the classification and understanding of ciliate diversity and evolution (Abraham et al., 2019; Luo et al., 2019). 3 Species Diversity of Ciliate Communities 3.1 Species richness and abundance Ciliate communities exhibit significant species richness and abundance across various aquatic environments. For instance, a study conducted in the Brazilian Atlantic Forest identified 409 ciliate taxonomic units (OTUs), with a notable diversity in freshwater compared to brackish environments (Fernandes et al., 2020). Similarly, research in the Pistoia province of Italy highlighted the presence of hidden biodiversity, including rare species and resistance forms, which are often missed by traditional morphological methods but detected through molecular techniques (Rossi et al., 2016). These findings underscore the importance of employing both morphological and molecular approaches to capture the full extent of ciliate diversity. 3.2 Genetic and molecular approaches to identifying species Advancements in genetic and molecular techniques have revolutionized the identification and classification of ciliate species. The use of high-throughput sequencing and metabarcoding has provided deeper insights into ciliate diversity and taxonomy. For example, the mitochondrial cox1 gene, nuclear ITS1 and ITS2, and the hypervariable
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