scholarly journals TREHS: An open-access software tool for investigating and evaluating temporary river regimes as a first step for their ecological status assessment

2017 ◽  
Vol 607-608 ◽  
pp. 519-540 ◽  
Author(s):  
Francesc Gallart ◽  
Núria Cid ◽  
Jérôme Latron ◽  
Pilar Llorens ◽  
Núria Bonada ◽  
...  
Keyword(s):  
Open Access ◽  
Ecological Status ◽  
Software Tool ◽  
Ecological Status Assessment ◽  
Status Assessment ◽  
Temporary River

scholarly journals Applicability of diatom metabarcoding in the ecological status assessment of Hungarian lotic and soda pan habitats

2021 ◽  
Vol 130 ◽  
pp. 108105
Author(s):  
Mónika Duleba ◽  
Angéla Földi ◽  
Adrienn Micsinai ◽  
Gábor Várbíró ◽  
Anita Mohr ◽  
...  
Keyword(s):  
Ecological Status ◽  
Ecological Status Assessment ◽  
Status Assessment ◽  
Soda Pan

scholarly journals The Fellowship of the Ring Test: DNAqua-Net WG2 initiative to compare diatom metabarcoding protocols used in routine freshwater biomonitoring for standardisation

2021 ◽  
Vol 4 ◽  
Author(s):  
Valentin Vasselon ◽  
Éva Ács ◽  
Salomé Almeida ◽  
Karl Andree ◽  
Laure Apothéloz-Perret-Gentil ◽  
...  
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Aquatic Ecosystems ◽  
Quality Index ◽  
Ecological Status ◽  
Pcr Amplification ◽  
Ring Test ◽  
Dna Metabarcoding ◽  
Ecological Status Assessment ◽  
Status Assessment

During the past decade genetic approaches have been developed to monitor biodiversity in aquatic ecosystems. These enable access to taxonomic and genetic information from biological communities using DNA from environmental samples (e.g. water, biofilm, soil) and methods based on high-throughput sequencing technologies, such as DNA metabarcoding. Within the context of the Water Framework Directive (WFD), such approaches could be applied to assess Biological Quality Elements (BQE). These are used as indicators of the ecological status of aquatic ecosystems as part of national monitoring programs of the european network of 110,000 surface water monitoring sites with 79.5% rivers and 11% lake sites (Charles et al. 2020). A high-throughput method has the potential to increase our spatio-temporal monitoring capacity and to accelerate the transfer of information to water managers with the aim to increase protection of aquatic ecosystems. Good progress has been made with developing DNA metabarcoding approaches for benthic diatom assemblages. Technological innovation and protocol optimization have allowed robust taxonomic (species) and genetic (OTU, ESV) information to be obtained from which diatom quality indices can be calculated to infer ecological status to rivers and lakes. Diatom DNA metabarcoding has been successfully applied for biomonitoring at the scale of national river monitoring networks in several countries around the world and can now be considered technically ready for routine application (e.g. Apothéloz-Perret-Gentil et al. 2017, Bailet et al. 2019, Mortágua et al. 2019, Vasselon et al. 2019, Kelly et al. 2020, Pérez-Burillo et al. 2020, Pissaridou et al. 2021). However, protocols and methods used by each laboratory still vary between and within countries, limiting their operational transferability and the ability to compare results. Thus, routine use of DNA metabarcoding for diatom biomonitoring requires standardization of all steps of the metabarcoding procedure, from the sampling to the final ecological status assessment in order to define good practices and standards. Following previous initiatives which resulted in a CEN technical report for biofilm sampling and preservation (CEN 2018), a set of experiments was initiated during the DNAqua-Net WG2 diatom workshop (Cyprus, 2019) to focus on DNA extraction and PCR amplification steps in order to evaluate: i) the transferability and reproducibility of a protocol between different laboratories; ii) the variability introduced by different protocols currently applied by the scientific community. 19 participants from 14 countries performed DNA extraction and PCR amplification in parallel, using i) the same fixed protocol and ii) their own protocol. Experiments were performed by each participant on a set of standardized DNA and biofilm samples (river, lake, mock community). In order to specifically test the variability of DNA extraction and PCR amplification steps, all other steps of the metabarcoding process were fixed and the preparation of the Miseq sequencing was performed by only one laboratory. The variability within and between participants will be evaluated on DNA extracts quantity, taxonomic (genus, species) and genetic richness, community structure comparison and diatom quality index scores (IPS). We will also evaluate the variability introduced by different DNA extraction and PCR amplification protocols on diatom quality index scores and the final ecological status assessment. The results from this collaborative work will not serve to define “one protocol to rule them all”, but will provide valuable information to define guidelines and minimum requirements that should be considered when performing diatom metabarcoding for biomonitoring.

scholarly journals Benthic diatoms of the Vrla River (Serbia) and their application in the water ecological status assessment

2016 ◽  
Vol 45 (3) ◽  
Author(s):  
Olga Jakovljević ◽  
Slađana Popović ◽  
Ivana Živić ◽  
Katarina Stojanović ◽  
Jelena Krizmanić
Keyword(s):  
Dominant Species ◽  
Ecological Status ◽  
Benthic Diatoms ◽  
Epilithic Diatoms ◽  
Ecological Status Assessment ◽  
Status Assessment

AbstractEpilithic diatoms from the Vrla River (Serbia) have been used to assess the ecological status of water. A total of 227 diatom taxa belonging to 50 genera were identified in the Vrla River during six research seasons with 13 dominant species recorded.

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