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Review
. 2022 Dec 19;10(12):2512.
doi: 10.3390/microorganisms10122512.

Ciliate Morpho-Taxonomy and Practical Considerations before Deploying Metabarcoding to Ciliate Community Diversity Surveys in Urban Receiving Waters

Yan Zhao  1 , Gaytha A Langlois  2
Affiliations
Review

Ciliate Morpho-Taxonomy and Practical Considerations before Deploying Metabarcoding to Ciliate Community Diversity Surveys in Urban Receiving Waters

Yan Zhao et al. Microorganisms. .

Abstract

Disentangling biodiversity and community assembly effects on ecosystem function has always been an important topic in ecological research. The development and application of a DNA metabarcoding method has fundamentally changed the way we describe prokaryotic communities and estimate biodiversity. Compared to prokaryotes (bacteria and archaea), the eukaryotic microbes (unicellular eukaryotes) also fulfill extremely important ecological functions in different ecosystems regarding their intermediate trophic positions. For instance, ciliated microbes (accounting for a substantial portion of the diversity of unicellular eukaryotes) perform pivotal roles in microbial loops and are essential components in different ecosystems, especially in water purification processes. Therefore, the community composition of ciliated species has been widely utilized as a proxy for water quality and biological assessment in urban river ecosystems and WWTPs (wastewater treatment plants). Unfortunately, investigating the dynamic changes and compositions in ciliate communities relies heavily on existing morpho-taxonomical descriptions, which is limited by traditional microscopic approaches. To deal with this dilemma, we discuss the DNA-based taxonomy of ciliates, the relative merits and challenges of deploying its application using DNA metabarcoding for surveys of ciliate community diversity in urban waterbodies, and provide suggestions for minimizing relevant sources of biases in its implementation. We expect that DNA metabarcoding could untangle relationships between community assembly and environmental changes affecting ciliate communities. These analyses and discussions could offer a replicable method in support of the application of evaluating communities of ciliated protozoa as indicators of urban freshwater ecosystems.

Keywords: DNA metabarcoding; biomonitoring; ciliated protozoa; molecular-based taxonomy; urban receiving waters; water quality.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The flow chart of the metabarcoding processing steps (water sampling collection, sample pretreatment, DNA extraction, and PCR amplification, NGS-Illumina sequencing for example, reference database selection, and taxonomic assignment) of ciliate biodiversity. Factors that might distort biodiversity assessments are marked with an asterisk. The interior pictures in terms of “Barcode markers & Group specific primers”, “The ‘best match’ similarity threshold for species level” and “High variability in SSU rDNA copy number” are modified after the work of Dunthorn et al. [55] and Zhan et al. [70] and Wang et al. [71].
See this image and copyright information in PMC

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