scholarly journals Is the ecological status assessment result the same using genomic- and morphology-based benthic biotic indices?

2021 ◽  
Vol 4 ◽  
Author(s):  
Ángel Borja ◽  
Iñigo Muxika ◽  
Anders Lanzén
Keyword(s):  
European Commission ◽  
Marine Biology ◽  
Reference Conditions ◽  
Ecological Status ◽  
Assessment Method ◽  
Biotic Index ◽  
Official Journal ◽  
Commission Decision ◽  
Ecological Status Assessment ◽  
Status Assessment

Monitoring and assessment of benthic communities have been routinely undertaken using morphology-based benthic indices, among which AZTI’s Marine Biotic Index (AMBI) and multivariate-AMBI (M-AMBI), are the most successful worldwide (Borja et al., 2019). They are used officially in routine monitoring in many European countries, where they have been intercalibrated (European Commission, 2018). AMBI has been mirrored by metabarcoding, and the genomic version (gAMBI; Aylagas et al., 2014) has demonstrated to yield results comparable to the morphological version. However, we have so far failed to develop a reliable genomic version of M-AMBI (M-gAMBI), which includes gAMBI, richness and diversity (Aylagas et al., 2018). This is because richness and diversity present very different results in morphological and genomic analyses. Since the multivariate method needs reference conditions, these must be set specifically for M-gAMBI to make its results comparable to those obtained with M-AMBI. To this aim, we started annual surveys in 2018, in 22 sampling locations, in Basque estuaries and coast. We present the results from the first three years of these surveys and discuss the problems faced when developing genomic reference conditions for M-gAMBI. The findings are of paramount importance for managers, since any new method or modification of an existing assessment method, needs to demonstrate that the results obtained when assessing the status are similar to those morphological-based methods, already approved and intercalibrated. Aylagas, E., Á. Borja, N. Rodríguez-Ezpeleta, 2014. Environmental Status Assessment Using DNA Metabarcoding: Towards a Genetics Based Marine Biotic Index (gAMBI). PLoS ONE, 9: e90529. Aylagas, E., Á. Borja, I. Muxika, N. Rodríguez-Ezpeleta, 2018. Adapting metabarcoding-based benthic biomonitoring into routine marine ecological status assessment networks. Ecological Indicators, 95: 194-202. Borja, A., G. Chust, I. Muxika, 2019. Chapter Three - Forever young: The successful story of a marine biotic index. Advances in Marine Biology, 82: 93-127. European Commission, 2018. Commission Decision (EU) 2018/229 of 12 February 2018 establishing, pursuant to Directive 2000/60/EC of the European Parliament and of the Council, the values of the Member State monitoring system classifications as a result of the intercalibration exercise and repealing Commission Decision 2013/480/EU. Official Journal of the European Communities, L47: 1-91.

scholarly journals Further improvement, validation, and application of CymoSkew biotic index for the ecological status assessment of the Greek coastal and transitional waters

2020 ◽  
Vol 118 ◽  
pp. 106727 ◽  
Author(s):  
Sotiris Orfanidis ◽  
Vasillis Papathanasiou ◽  
Nikolaos Mittas ◽  
Theodosios Theodosiou ◽  
Alexis Ramfos ◽  
...  
Keyword(s):  
Ecological Status ◽  
Biotic Index ◽  
Transitional Waters ◽  
Ecological Status Assessment ◽  
Status Assessment ◽  
Coastal And Transitional Waters

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.

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