New molecular methods to assess biodiversity. Potentials and pitfalls of DNA metabarcoding: a workshop report

Kahlert, Maria; Alfjorden, Anders; Apunte-Ramos, Katherine; Bailet, Bonnie; Pérez-Burillo, Javier; Carrera-Gonzalez, Andrea; Castro, David; Bernardi, Cecilia Di; Dully, Verena; Fekete, Judit; Frühe, Larissa; González, Raquel Fernández; Gratsia, Eirini; Hanjalić, Jasna; Kamberović, Jasmina; Kelly, Ann-Marie; Meriggi, Carlotta; Nousiainen, Ilkka; Ørberg, Sarah B.; Orr, James; Quintana, Cintia Organo; Papatheodoulou, Athina; Šargač, Jasmina; Shahbaz, Muhammad; Tapolczai, Kálmán; Tosic, Katarina; Wallin, Isa; Zupančič, Maša; Bohman, Patrik; Buttigieg, Pier Luigi; Häubner, Norbert; Leese, Florian; Macher, Jan Niklas; Peura, Sari; Roslin, Tomas; Strand, Malin; Terenius, Olle; Vasselon, Valentin; Weigand, Alexander

doi:10.3897/rio.5.e38915

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“…However, in addition to standardization for reporting taxonomic, genomic and metadata, we also see the need for both procedures and best practices for the generation of site‐based metabarcoding data to be similarly standardized. Standardization is fundamental to maximize the potential for integration and global syntheses, as limited integration of genomic approaches in biodiversity observation networks is mainly attributed to the lack of global, standardized and well‐contextualized data sets and accompanying best practices (Canonico et al, 2019; Kahlert et al, 2019).…”

Section: A Framework For Harmonized Data Generation Within a Spatiallmentioning

confidence: 99%

Connecting high‐throughput biodiversity inventories: Opportunities for a site‐based genomic framework for global integration and synthesis

et al. 2021

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High‐throughput sequencing (HTS) is increasingly being used for the characterization and monitoring of biodiversity. If applied in a structured way, across broad geographical scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated independently at local, regional and global scales. The universality, reliability and efficiency of HTS data can potentially facilitate the seamless linking of data among species assemblages from different sites, at different hierarchical levels of diversity, for any taxonomic group and regardless of prior taxonomic knowledge. However, collective international efforts are required to optimally exploit the potential of site‐based HTS data for global integration and synthesis, efforts that at present are limited to the microbial domain. To contribute to the development of an analogous strategy for the nonmicrobial terrestrial domain, an international symposium entitled “Next Generation Biodiversity Monitoring” was held in November 2019 in Nicosia (Cyprus). The symposium brought together evolutionary geneticists, ecologists and biodiversity scientists involved in diverse regional and global initiatives using HTS as a core tool for biodiversity assessment. In this review, we summarize the consensus that emerged from the 3‐day symposium. We converged on the opinion that an effective terrestrial Genomic Observatories network for global biodiversity integration and synthesis should be spatially led and strategically united under the umbrella of the metabarcoding approach. Subsequently, we outline an HTS‐based strategy to collectively build an integrative framework for site‐based biodiversity data generation.

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Section: A Framework For Harmonized Data Generation Within a Spatiallmentioning

confidence: 99%

Connecting high‐throughput biodiversity inventories: Opportunities for a site‐based genomic framework for global integration and synthesis

et al. 2021

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New trends in bioassessment of aquatic ecosystems: from organisms to DNA-based metrics

Pawłowski¹,

Kahlert²

2021

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Traditionally, the biological quality of aquatic ecosystems is assessed using selected groups of organisms that can be identified morphologically. Recent advances in high-throughput genomic approaches offered new opportunities to monitor biodiversity and assess ecological status using DNA barcoding and metabarcoding. The DNA-based tools have been used in three different ways: (1) to replace morphological identification of biological quality elements in existing biotic indices, (2) to develop new molecular indices based on morphologically inconspicuous groups of potential environmental indicators, and (3) to predict biotic indices from environmental DNA datasets using machine learning methods (Pawlowski et al. 2018). The next steps need to take advantages and challenges of these different approaches into account in view of their future application in routine bioassessment.The Working Group 2 of DNAqua-Net, Biotic Indices & Metrics, has worked with several task forces tackling different organism groups (fish, macroinvertebrates, diatoms, bacteria, protists, meiofauna), because challenges have been shown to be quite different dependent on the target organisms Kahlert et al. 2019. For the fish the eDNA-metabarcoding methods are well developed and give very good results in terms of species detection. The important question is to see if the semi-quantitative data retrieved from the metabarcoding (proportion in eDNA sequences) could be translated to proportions in biomass/numbers that are now used in many indices. The fish researchers are trying to fit these data in, but some correction factors might be needed to correct for differences between molecular and conventional methodsRegarding the macroinvertebrates, much discussion regarding index development was focusing on the importance of abundance measurements, and it was tested how existing indices would perform if barcoding data would be used instead of morphological data. Still discussion is ongoing on several technical issues, including the use of preservative for DNA extraction from bulk samples, the choice of primers for PCR amplification and the incompleteness of reference databases which impedes the correct assignment of eDNA sequences. Also minimum standards for routine operation are still missing.The diatom group has worked much on practical issues, starting a large initiative to compare diatom metabarcoding protocols used in routine freshwater biomonitoring for standardization (Bailet et al. 2019, Keck et al. 2018, Vasselon et al. 2017). With diatoms, all three approaches to develop molecular indices have been tested and seem promising, i.e. using existing indices with taxa names derived by matching sequences with reference databases, developing new indices based on molecular data only with traditional fixed scores, and using machine-learning techniques (Bailet et al. 2020, Vasselon et al. 2018, Tapolczai et al. 2019, Keck et al. 2018) The micro- and meiobiota group has worked towards an inclusion of microorganisms into aquatic assessment, because the microbial community dynamics are a missing link important for our understanding of rapid changes in the structure and function of aquatic ecosystems, and should be addressed in the future environmental monitoring of freshwater ecosystems (Sagova-Mareckova et al. 2021). Another focus was on how sediment DNA analysis can be integrated into stated goals of routine monitoring applications. It has been an interesting journey, and we WG2 coordinators would like to thank all the people for their engagement! Keep up the good work!

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New molecular methods to assess biodiversity. Potentials and pitfalls of DNA metabarcoding: a workshop report

Cited by 2 publications

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Connecting high‐throughput biodiversity inventories: Opportunities for a site‐based genomic framework for global integration and synthesis

Connecting high‐throughput biodiversity inventories: Opportunities for a site‐based genomic framework for global integration and synthesis

New trends in bioassessment of aquatic ecosystems: from organisms to DNA-based metrics

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