International Journal of Marine Science, 2024, Vol.14, No.3, 172-181 http://www.aquapublisher.com/index.php/ijms 177 than in brackish environments, with a considerable fraction of the detected diversity not represented in current molecular databases (Fernandes et al., 2020). These findings highlight the importance of freshwater ciliates in ecosystem functioning and their potential as bioindicators for environmental monitoring. 5.2 Marine ecosystems Marine ciliate communities are equally diverse and play essential roles in marine food webs, particularly in nutrient cycling and primary production. Studies in coastal waters of China have documented over 100 new species of marine ciliates, emphasizing the large, undiscovered diversity in these habitatsn (Liu et al., 2017). The application of taxonomic relatedness indices, such as taxonomic distinctness (Δ*) and average taxonomic distinctness (Δ+), has proven effective in assessing the impact of environmental stressors like eutrophication on marine ciliate communities. These indices showed significant correlations with changes in nutrient levels, demonstrating their robustness as indicators for marine environmental assessment (Xu et al., 2011). Furthermore, the functional diversity of marine ciliates, including their roles as predators and mixotrophs, underscores their ecological significance in maintaining the balance of marine ecosystems (Weisse et al., 2017). 5.3 Soil and terrestrial habitats Soil and terrestrial habitats host a remarkable diversity of ciliates, with many species yet to be discovered. Soil ciliates contribute to ecosystem functioning by participating in nutrient cycling and responding to environmental changes. Studies have shown that soil ciliate communities are influenced by factors such as soil type and vegetation cover. For example, grasslands and hardwood forests are characterized by a higher abundance of K-strategist ciliates, while more stressed ecosystems like arable lands and deserts have a higher proportion of r-strategist ciliates. Recent research in South Korea has identified 18 newly recorded ciliate species from soil and inland waters, further highlighting the high ciliate diversity in these habitats. The hidden biodiversity of soil ciliates, often missed by traditional morphological methods, can be better understood through molecular techniques, which reveal a more comprehensive picture of their community structure and ecological roles (Rossi et al., 2016). 6 Methods for Studying Ciliate Communities 6.1 Sampling techniques and protocols Sampling techniques for studying ciliate communities are crucial for obtaining representative and reliable data. In freshwater biotopes, prolonged observations of differentially treated sample aliquots are often employed to capture the hidden biodiversity, including rare species and resistance forms. This approach combines morphological identification with molecular techniques such as Sanger sequencing to provide comprehensive insights into ciliate fauna (Rossi et al., 2016). In stream biofilms, samples are collected from various streams with different levels of human impact, and both microscopy and terminal restriction fragment length polymorphism (T-RFLP) analysis of 18S rRNA sequences are used to assess ciliate diversity. Additionally, periphyton samples from light- and dark-exposed lithified tufa/stones in karstic rivers are collected to investigate ciliate community structure, with environmental DNA (eDNA) metabarcoding being employed alongside traditional microscopy analyses (Kulaš et al., 2021). 6.2 Microscopic and imaging technologies Microscopy remains a fundamental tool for studying ciliate communities, allowing for the direct observation and identification of ciliates based on their morphological characteristics. Traditional microscopy analyses are used to investigate ciliate community structures in various aquatic environments, such as biofilms and periphyton samples (Kulaš et al., 2021). However, microscopy alone may not capture the full extent of ciliate diversity, as it can miss rare species and those with subtle morphological differences (Rossi et al., 2016). To address this limitation, advanced imaging technologies and error-correcting algorithms for pyrosequences are employed to enhance the accuracy of taxon identification and reduce discrepancies in richness estimates (Santoferrara et al., 2014). These technologies provide a more detailed and accurate representation of ciliate communities, complementing traditional microscopy methods.
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