Development of a novel metric for evaluating diatom assemblages in rivers using DNA metabarcoding

Kelly, Mahlon G.; Juggins, Steve; Mann, David G.; Sato, Shinya; Glover, R.; Boonham, Neil; Sapp, Melanie; Lewis, E. L. V.; Hany, U.; Kille, Peter; Jones, Tim; Walsh, Kerry

doi:10.1016/j.ecolind.2020.106725

Cited by 44 publications

(36 citation statements)

References 60 publications

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“…The Trophic Diatom Index (TDI5NGS) was calculated following Kelly et al (2020) using the R package DAR-LEQ3 available at https://github.com/nsj3/darleq3. When evaluating the scale of variation in TDI5NGS, we used data from the Environment Agency (2018) which showed the average level of variation measured at a site on a single day.…”

Section: Discussionmentioning

confidence: 99%

“…Based on experience at a number of locations, sampling a thick biofilm where there are entangling filamentous algae and then using the same toothbrush at a subsequent site with a very thin biofilm is more likely to lead to problems than the reverse situation. Similarly, given that the TDI is based on a weighted average equation where taxa tolerant to nutrient enrichment have higher scores than those associated with low nutrients (Kelly et al 2008b;Kelly et al 2020), sampling a 'clean' site after a visit to a 'polluted' one is more likely to result in problems than the other way around.…”

Section: Discussionmentioning

confidence: 99%

“…Samples were then transferred to the laboratory in a cool box and frozen at -30 °C prior to DNA extraction. The methods used for DNA extraction, amplification and analysis followed methods described in Kelly et al (2020).…”

Section: Sampling and Analysis Of Benthic Diatomsmentioning

confidence: 99%

“…Although DNA-based technologies have potential to improve ecological assessment (Hänfling et al 2016;Bista et al 2017Bista et al , 2018Blackman 2017;Valentin et al 2019;Kelly et al 2020, Di Muri et al 2020, regulators are still concerned about these technologies, particularly when they are replacing established methods. Challenges associated with metabarcoding methods include differences in the mode of quantification compared to traditional approaches (Kelly et al 2020;Vasselon et al 2018), in optimising bioinformatics pipelines (Baillet et al 2020), in curating barcode libraries (Rimet et al 2019(Rimet et al , 2021 and in the lack of robust models to quantify uncertainties in DNA-based workflows. These technical challenges are being addressed by the research community, but some of the more subtle challenges and bottlenecks to implementing these technologies are less widely-recognised.…”

Section: Introductionmentioning

confidence: 99%

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Potential for cross-contamination of diatom DNA samples when using toothbrushes

Kelly¹,

Jones²,

Walsh³

2021

MBMG

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The use of toothbrushes and similar devices for sampling diatoms from hard surfaces is a well-established approach. Toothbrushes are routinely cleaned and reused when sampling for analysis by light microscopy. This paper looks at the scale of contamination encountered when this technique is used to sample diatoms for metabarcoding analyses, as well as at the scale of contamination to be expected if stream, rather than distilled water, is used to wash diatoms from stones. Although some contamination attributable to toothbrushes was detected, read numbers were low and had no effect on index calculation or ecological status estimates. However, if the primary focus of a study is to thoroughly document diversity in a sample, then even this small level of contamination may be unacceptable and more stringent measures may be required.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Sampling and Analysis Of Benthic Diatomsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Potential for cross-contamination of diatom DNA samples when using toothbrushes

Kelly¹,

Jones²,

Walsh³

2021

MBMG

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“…In recent times, many studies have shown the advantages of DNA barcoding combined with High-Throughput Sequencing (HTS) methods, compared to conventional approaches [3][4][5][6][7], and thus DNA-based monitoring has been postulated as a promising tool in recent years for the assessment of aquatic ecosystems [8][9][10][11][12]. The development of high-throughput techniques have made this process quicker and easier, and now there are studies available evaluating its application in the biomonitoring of rivers [8][9][10][11][13][14][15] and large lakes [16].…”

Section: Introductionmentioning

confidence: 99%

Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches

Borrego-Ramos

Bécares

Garcı́a

et al. 2021

Water

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Benthic diatoms have traditionally been used as bioindicators of aquatic ecosystems. Because diatom-based monitoring of water quality is required by European legislation, molecular-based methods had emerged as useful alternatives to classical methods based on morphological identification using light microscopy. The aim of this study was to test the reliability of DNA metabarcoding combined with High-Throughput Sequencing (HTS) techniques in the bioassessment of the trophic status of 22 Mediterranean shallow ponds in NW Spain. For each pond, the Trophic Diatom Index (TDI) was calculated from inventories obtained by identification using light microscopy (LM) followed by high-throughput sequencing (HTS) at the molecular level. Ponds were subsequently classified into five water quality classes. The results showed a good correspondence between both methods, especially after applying a correction factor that depended on the biovolume of the cells. This correspondence led to the assignment to the same quality class in 59% of the ponds. The determination and quantification of valves or DNA sequences was one of the main pitfalls, which mainly included those related to the variability in the relative abundances of some species. Accordingly, ponds with similar relative abundances for the dominant species were assigned to the same quality class. Moreover, other difficulties leading the discrepancies were the misidentification of some species due to the presence of semi-cryptic taxa, the incompleteness of the reference database and the bioinformatic protocol. Thus, the validation of DNA-based methods for the identification of freshwater diatoms represents an important goal, as an alternative to using traditional methods in Mediterranean shallow ponds.

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Present and Future Perspectives for Bioassessment of Running Water Using Diatoms

Almeida,

Feio

2024

Diatom Photosynthesis

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Development of a novel metric for evaluating diatom assemblages in rivers using DNA metabarcoding

Cited by 44 publications

References 60 publications

Potential for cross-contamination of diatom DNA samples when using toothbrushes

Potential for cross-contamination of diatom DNA samples when using toothbrushes

Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches

Present and Future Perspectives for Bioassessment of Running Water Using Diatoms

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