Cyprus’ diatom diversity and the association of environmental and anthropogenic influences for ecological assessment of rivers using DNA metabarcoding

Pissaridou, Panayiota; Vasselon, Valentin; Christou, Andreas; Chonova, Teofana; Papatheodoulou, Athina; Drakou, Katerina; Tziortzis, Iakovos; Dörflinger, Gerald; Rimet, Frédéric; Bouchez, Agnès; Vasquez, Marlen I.

doi:10.1016/j.chemosphere.2021.129814

Cited by 15 publications

(13 citation statements)

References 45 publications

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“…Identification of diatom communities in environmental samples through DNA metabarcoding is nowadays becoming a reliable approach that has been successfully tested on a large variety of ecological contexts through numerous pilot studies for freshwater biomonitoring (Vasselon et al 2019, Rivera et al 2020, Pissaridou et al 2021, Tapolczai et al 2021, Pérez-Burillo et al 2020), while less has been done for phytoplankton in marine ecosystems (Piredda et al 2018, 2022). With sample preservation and storage being at the beginning of this metabarcoding approach, this experiment aimed at identifying potential key points in preservation methods and preservation duration that may blur the ability of DNA metabarcoding to produce accurate diatoms inventories and, as a result, produce reliable quality assessment of aquatic ecosystems.…”

Section: Discussionmentioning

confidence: 99%

Best practice recommendations for sample preservation in metabarcoding studies: a case study on diatom environmental samples

Baričević

Chardon

Kahlert

et al. 2022

Preprint

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The development of DNA metabarcoding and High-Throughput Sequencing for diatoms is nowadays offering an interesting approach to assess their communities in freshwater and marine ecosystems. In the context of the implementation of these genomic methods to environmental monitoring, protocol constraints are moving from scientific to operational applications, requiring operational guidelines and standards. In particular, the first steps of the diatom metabarcoding process, which consist of sampling and storage, have been addressed in various ways in scientific and pilot studies. The objective of this study was to compare three currently applied preservation protocols through different storage durations (ranging from one day to one year) for phytobenthos and phytoplankton samples intended for diatom DNA metabarcoding analysis. The experimental design included four freshwater and two marine samples from sites of diverse ecological characteristics. The impact of the preservation and storage was assessed through diatom metabarcoding endpoints: DNA quality and quantity, diversity and richness, community composition and ecological index values (for freshwater samples). The yield and quality of extracted DNA only decreased for freshwater phytobenthos samples preserved with ethanol. Diatom diversity was not affected and their taxonomic composition predominantly reflects the site origin. Only rare taxa (below 100 reads) differed among methods and durations. Thus, importance of preservation method choice is important for low-density species (rare, invasive, threatened or toxic species). However, for biomonitoring purposes, freshwater ecological index values were not affected whatever the preservation method and duration considered (including ethanol preservation), reflecting the site ecological status. This study proved that diatom metabarcoding is robust enough to replace or complement the current approach based on morphotaxonomy, paving the way to new possibilities for biomonitoring. Thus, accompanied by operational standards, the method will be ready to be confidently deployed and prescribed in future regulatory monitoring.

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Section: Discussionmentioning

confidence: 99%

Best practice recommendations for sample preservation in metabarcoding studies: a case study on diatom environmental samples

Baričević

Chardon

Kahlert

et al. 2022

Preprint

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“…Correlations between diatom species and environmental factors such as TP and soluble reactive phosphorus are quantifiable based on autecological preferences of species in the different trophic gradients from reference sites to highly disturbed sites (Çelekli, Lekesiz, & Çetin, 2021; Çelekli, Lekesiz, & Yavuzatmaca, 2021; Charles et al, 2021). Among the European diatom indices, IPS having more diatom species has been commonly used to evaluate the surface waters of the Eastern Mediterranean Region such as Cyprus (Cantonati et al, 2020; Pissaridou et al, 2021) and Greece (Karaouzas et al, 2019). The European indices cannot efficiently adapt to the particular hydrological and climatic conditions of the Eastern Mediterranean Region (Çelekli et al, 2018; Çelekli & Bilgi, 2019; Çelekli & Lekesiz, 2020; Lazaridou et al, 2018) because ecoregional factors influence the trophic weight of diatom taxa.…”

Section: Discussionmentioning

confidence: 99%

Eco‐assessment of Değirmendere and Bulaklı streams using diatom indices from different ecoregions

Çelekli

Yıldız

2022

Ecological Research

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Diatom metrics are important tools for evaluating the environmental conditions of streams for the achievement of environmental sustainability. Aim of the present study was to assess the ecological status of De girmendere and Bulaklı streams using diatom indices developed in different ecoregions and to elucidate responses of diatom assemblages to stressors using multivariate approaches. Analysis of similarity percentage indicated a 74% dissimilarity between De girmendere and Bulaklı streams with the most contribution of Encyonopsis minuta, Achnanthidium minutissimum, Achnanthidium druartii, Amphora indistincta, and Gomphonema cuneolus species to this dissimilarity.The first two axes of canonical correspondence analysis exhibited a strong correlation (93.1%) between diatom assemblages and environment variables. Pollution-tolerant species were associated with Bulaklı stream, whereas pollution-sensitive species displayed relatedness to De girmendere stream. Conductivity, salinity, oxidation-reduction potential, total phosphorus (TP), and orthophosphate were the significant effective environmental factors on the spatiotemporal distribution of diatom assemblages. Used diatom indices showed significantly positive and negative correlations with TP gradient. The results of bioassessment exhibited that diatom indices have different scores for the ecological status of the sampling stations. European diatom indices except Trophic Diatom Index and Duero Diatom Index mainly showed similar behavior in the bioassessment of ecological conditions of De girmendere and Bulaklı streams. Among European diatom indices, Trophic Index Turkey was more competitive and could give better results in the bioassessment of streams. Results indicated that ecoregional specific diatom index could be used as a suitable tool to accurately evaluate the surface water quality.

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“…For instance, the non-invasive nature of some eDNA methods can be a strong argument. To clarify all these points, in Europe and beyond, numerous projects to compare traditional and DNA-based methods have been or are being implemented (e.g., Elbrecht et al 2017;Pont et al 2018;Bailet et al 2019;Vasselon et al 2019;Griffiths et al 2021;Martins et al 2021;Pissaridou et al 2021;Weigand 2021).…”

Section: Highlight the Effectiveness And Benefits Of Dnabased Methodsmentioning

confidence: 99%

“…Thanks to numerous pilot projects throughout Europe (e.g., Mortágua et al 2019;Pérez-Burillo et al 2020;Meissner et al 2021;Pissaridou et al 2021), it is now commonly accepted that, from a general perspective and for the time being, traditional and DNA-based methods bring complementary information. However, when it comes to biodiversity estimates or detection of certain indicator taxa, in many cases the molecular method is often more accurate (e.g.…”

Section: Highlight the Effectiveness And Benefits Of Dnabased Methodsmentioning

confidence: 99%

A strategy for successful integration of DNA-based methods in aquatic monitoring

Blancher¹,

Lefrançois²,

Rimet³

et al. 2022

MBMG

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Recent advances in molecular biomonitoring open new horizons for aquatic ecosystem assessment. Rapid and cost-effective methods based on organismal DNA or environmental DNA (eDNA) now offer the opportunity to produce inventories of indicator taxa that can subsequently be used to assess biodiversity and ecological quality. However, the integration of these new DNA-based methods into current monitoring practices is not straightforward, and will require coordinated actions in the coming years at national and international levels. To plan and stimulate such an integration, the European network DNAqua-Net (COST Action CA15219) brought together international experts from academia, as well as key environmental biomonitoring stakeholders from different European countries. Together, this transdisciplinary consortium developed a roadmap for implementing DNA-based methods with a focus on inland waters assessed by the EU Water Framework Directive (2000/60/EC). This was done through a series of online workshops held in April 2020, which included fifty participants, followed by extensive synthesis work. The roadmap is organised around six objectives: 1) to highlight the effectiveness and benefits of DNA-based methods, 2) develop an adaptive approach for the implementation of new methods, 3) provide guidelines and standards for best practice, 4) engage stakeholders and ensure effective knowledge transfer, 5) support the environmental biomonitoring sector to achieve the required changes, 6) steer the process and harmonise efforts at the European level. This paper provides an overview of the forum discussions and the common European views that have emerged from them, while reflecting the diversity of situations in different countries. It highlights important actions required for a successful implementation of DNA-based biomonitoring of aquatic ecosystems by 2030.

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Cyprus’ diatom diversity and the association of environmental and anthropogenic influences for ecological assessment of rivers using DNA metabarcoding

Cited by 15 publications

References 45 publications

Best practice recommendations for sample preservation in metabarcoding studies: a case study on diatom environmental samples

Best practice recommendations for sample preservation in metabarcoding studies: a case study on diatom environmental samples

Eco‐assessment of Değirmendere and Bulaklı streams using diatom indices from different ecoregions

A strategy for successful integration of DNA-based methods in aquatic monitoring

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Cyprus’ diatom diversity and the association of environmental and anthropogenic influences for ecological assessment of rivers using DNA metabarcoding

Cited by 15 publications

References 45 publications

Best practice recommendations for sample preservation in metabarcoding studies: a case study on diatom environmental samples

Best practice recommendations for sample preservation in metabarcoding studies: a case study on diatom environmental samples

Eco‐assessment of Değirmendere and Bulaklı streams using diatom indices from different ecoregions

﻿A strategy for successful integration of DNA-based methods in aquatic monitoring

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A strategy for successful integration of DNA-based methods in aquatic monitoring