Diatom eDNA metabarcoding and morphological methods for bioassessment of karstic river

Kulaš, Antonija; Udovič, Marija Gligora; Tapolczai, Kálmán; Žutinić, Petar; Orlić, Sandi; Levkov, Zlatko

doi:10.1016/j.scitotenv.2022.154536

Cited by 18 publications

(6 citation statements)

References 71 publications

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“…Analysis via Illumina MiSeq does not require skilled observers; therefore, there are no concerns about the reliability of data, which would vary depending on their level of expertise [13]. In addition, this method allows researchers who are inexperienced in taxonomic identi cation to easily analyze microbial communities [11,39]. Furthermore, compared with microscopy, Illumina MiSeq can effectively process large amounts of data in a relatively short time [13,37].…”

Section: Discussionmentioning

confidence: 99%

“…Microscopy studies, which are based on morphology, have led to the development of phylogenetic systematics for the taxonomic classi cation of diatoms [9]. However, community analysis based on morphology has many limitations [10,11]. Although the morphological characteristics of each diatom species are relatively clear, extensive knowledge and expertise are still required for identi cation [10].…”

Section: Introductionmentioning

confidence: 99%

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Comparison of Illumina MiSeq and microscopy methodologies for the analysis of diatom communities in five estuaries along the southern coast of the Korean Peninsula

Kim,

Yun,

Lee

et al. 2024

Preprint

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The study of microalgal communities is critical for understanding aquatic ecosystems. These communities are primarily composed of diatoms (Bacillariophyta), and two methods are commonly used to study them: microscopy and Illumina MiSeq. These two methods are distinct, and their differences are reflected in the results they yield. Thus, their suitability for analyzing diatom communities is often debated and evaluated. In this study, these two methods were used to analyze the diatom communities in the same water samples, and the results obtained were compared. The taxonomy of the species constituting the diatom communities was confirmed, and both methods showed that the species belonging to the Bacillariales and Naviculales orders (class Bacillariophyceae) are diverse. However, at the lower taxonomic levels (family, genus, and species), microscopy tended to show a bias toward detecting diatom species belonging to the Bacillariaceae and Naviculaceae families. The results obtained from the two methods differed in terms of the identification of each diatom present in the communities and the analysis of their structural characteristics. These results are consistent with the fact that diatoms belonging to the Nitzschia and Navicula genera are abundant in the communities, furthermore, only the Illumina MiSeq showed the abundance of the Melosira, Entomonis, and Amphiprora genera. Although the results obtained from microscopy tended to be biased, they were superior to those of Illumina MiSeq regarding species-level identification. Based on the results obtained via microscopy and Illumina MiSeq, it was revealed that neither method is perfect and that each has clear strengths and weaknesses. Therefore, for the effective and accurate analysis of diatom communities, it is desirable to combine the two methods.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comparison of Illumina MiSeq and microscopy methodologies for the analysis of diatom communities in five estuaries along the southern coast of the Korean Peninsula

Kim,

Yun,

Lee

et al. 2024

Preprint

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“…Baković et al [77] already found that karst underground habitats of Croatia and Bosnia and Herzegovina are a hotspot of protist biodiversity; therefore, it is likely that the influx of groundwater served as a mechanism of ciliate colonization at Krka spring. Interestingly, Kulaš et al [78] recorded diatom species (Aulacoseira granulata (Ehrenberg) Simonsen and Navicula cryptotenella Lange-Bertalot) at Krka spring that tolerate higher phosphate concentrations. This supports the idea that phosphate concentration, along with discharge rate, may be one of the main factors determining the ciliate functional community composition at Krka spring.…”

Section: Discussionmentioning

confidence: 99%

Changes in Phylogenetic and Functional Diversity of Ciliates along the Course of a Mediterranean Karstic River

et al. 2022

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Ciliates are a group of phagotrophic protists found in a wide variety of ecosystems. This study builds on recent studies of ciliates in the Krka river and investigates changes in the phylogenetic and functional diversity of ciliates in biofilm to predict the phylogenetic and functional structure of ciliates in other karstic rivers. Biofilm samples were collected from four representative locations: upstream (Krka spring), midstream (Marasovine), and downstream (Roški slap, Skradinski buk) of the Krka river to test for differences in phylogenetic and functional diversity of ciliates in relation to location and positioning on tufa stones (light/dark-exposed side of tufa stone). Our results showed that Krka spring had higher phylogenetic species variability, lower phylogenetic diversity, and lower functional richness than Skradinski buk, suggesting phylogenetic overdispersal at Krka spring. This could be due to environmental filtering, competitive exclusion, or a combination of these factors. As the first study of its kind in the Mediterranean, our results shed light on the phylogenetic and functional diversity of ciliates in karst ecosystems and provide a basis for future ecological and conservation efforts.

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“…The prepared slides were then scanned into the Olympus Slideview VS200 (EVIDENT, Tokyo, Japan) using the pipeline described in the paper of Burfeid-Castellanos et al (2022) on a surface of 16-25 mm² depending on density. The stitched and stacked virtual slides were then uploaded onto the browser-based annotation platform BIIGLE 2.0 (Langenkämper et al, 2017).…”

Section: Diatom Microscopy Preparation and Manual Digital Microscopymentioning

confidence: 99%

Non-perennial rivers and streams in extreme hydrological conditions—comparing the effectiveness of amplicon sequencing and digital microscopy for diatom biodiversity appraisal

Burfeid-Castellanos,

Mones,

Dani

et al. 2024

Front. Ecol. Evol.

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IntroductionNon-perennial rivers and streams are increasingly present, in part because of climate change, even in the temperate climate. However, how the loss of connectivity and complete drying affect microphytobenthos in general and diatom communities in particular has gone mostly unstudied. MethodsWith this paper, we aim to close this gap, identifying diatom biodiversity through manual digital microscopy and rbcL amplicon sequencing, to observe a) which method is better suited to it and b) how the ecotone flow-pool-dry affects diatom diversity under duress. Three karstic, non-perennial rivers and streams with a gradient from natural to anthropogenically disturbed were sampled under flooding conditions and after a long and intense drought in 2022.ResultsOur results show that digital microscopy shows a higher diversity and species richness than amplicon sequencing. We posit that this might be due to a reduced pool of subaerophile taxa having been sequenced and being part of the reference database. Furthermore, the effect of drying only resulted in a reduction in diversity after this drought, although the biofilm was still alive under these conditions. DiscussionTo use amplicon sequencing for non-perennial river diatom diversity monitoring, the reference databases will have to be adapted to such systems, as most rivers may be subjected to drying regularly in the future.

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Diatom eDNA metabarcoding and morphological methods for bioassessment of karstic river

Cited by 18 publications

References 71 publications

Comparison of Illumina MiSeq and microscopy methodologies for the analysis of diatom communities in five estuaries along the southern coast of the Korean Peninsula

Comparison of Illumina MiSeq and microscopy methodologies for the analysis of diatom communities in five estuaries along the southern coast of the Korean Peninsula

Changes in Phylogenetic and Functional Diversity of Ciliates along the Course of a Mediterranean Karstic River

Non-perennial rivers and streams in extreme hydrological conditions—comparing the effectiveness of amplicon sequencing and digital microscopy for diatom biodiversity appraisal

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