Grant Proposal
Research Ideas and Outcomes 2: e11321
https://doi.org/10.3897/rio.2.e11321 (29 Nov 2016)
https://doi.org/10.3897/rio.2.e11321 (29 Nov 2016)
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BAGS: An automated Barcode, Audit & Grade System for DNA barcode reference libraries. Molecular Ecology Resources 21: 573.
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Beyond taxonomy: Validating functional inference approaches in the context of fish‐farm impact assessments. Molecular Ecology Resources 21: 2264.
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Innovating transcriptomics for practitioners in freshwater fish management and conservation: best practices across diverse resource-sector users. Reviews in Fish Biology and Fisheries 32: 921.
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Assessing pollution of aquatic environments with diatoms’ DNA metabarcoding: experience and developments from France water framework directive networks. Metabarcoding and Metagenomics 3: .
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Species diversity and DNA barcode library of freshwater Molluscs of South Caucasus. Biodiversity Data Journal 10: .
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The Effect of Activity, Energy Use, and Species Identity on Environmental DNA Shedding of Freshwater Fish. Frontiers in Ecology and Evolution 9: .
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A validation scale to determine the readiness of environmental DNA assays for routine species monitoring. Environmental DNA 3: 823.
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The influence of macroinvertebrate abundance on the assessment of freshwater quality in The Netherlands. Metabarcoding and Metagenomics 2: .
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Gap-analysis and annotated reference library for supporting macroinvertebrate metabarcoding in Atlantic Iberia. Regional Studies in Marine Science 36: 101307.
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Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates. Water 13: 331.
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Assessment of species gaps in DNA barcode libraries of non-indigenous species (NIS) occurring in European coastal regions. Metabarcoding and Metagenomics 4: .
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Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding. Science of The Total Environment 751: 141729.
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Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive. Water Research 138: 192.
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DNAqua-Net: Advancing Methods, Connecting Communities and Envisaging Standards. Proceedings of TDWG 1: e20310.
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Assessing changes in stream macroinvertebrate communities across ecological gradients using morphological versus DNA metabarcoding approaches. Science of The Total Environment 797: 149030.
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Managing the small stream network for improved water quality, biodiversity and ecosystem services protection (SSNet). Research Ideas and Outcomes 5: .
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Metabarcoding data allow for reliable biomass estimates in the most abundant animals on earth. Metabarcoding and Metagenomics 3: .
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Freshwater diatom biomonitoring through benthic kick-net metabarcoding. PLOS ONE 15: e0242143.
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Meta‐analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment. Molecular Ecology 31: 1820.
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Environmental DNA metabarcoding: Transforming how we survey animal and plant communities . Molecular Ecology 26: 5872.
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Nematodes as bioindicators of polluted sediments using metabarcoding and microscopic taxonomy. Environment International 143: 105922.
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Zooplankton biodiversity monitoring in polluted freshwater ecosystems: A technical review. Environmental Science and Ecotechnology 1: 100008.
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The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada. Science of The Total Environment 710: 135906.
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Exploring the eDNA dynamics of the host-pathogen pair Pacifastacus leniusculus (Decapoda) and Aphanomyces astaci (Saprolegniales) under experimental conditions. NeoBiota 79: 1.
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COI metabarcoding primer choice affects richness and recovery of indicator taxa in freshwater systems. PLOS ONE 14: e0220953.
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An Overview of DNA-Based Applications for the Assessment of Benthic Macroinvertebrates Biodiversity in Mediterranean Aquatic Ecosystems. Diversity 13: 112.
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Towards a holistic and solution-oriented monitoring of chemical status of European water bodies: how to support the EU strategy for a non-toxic environment?. Environmental Sciences Europe 30: .
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Estimating intraspecific genetic diversity from community DNA metabarcoding data. PeerJ 6: e4644.
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Development of an autonomous biosampler to capture in situ aquatic microbiomes. PLOS ONE 14: e0216882.
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Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life. Metabarcoding and Metagenomics 5: .
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Human access impacts biodiversity of microscopic animals in sandy beaches. Communications Biology 3: .
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A New Network for the Advancement of Marine Biotechnology in Europe and Beyond. Frontiers in Marine Science 7: .
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European large perialpine lakes under anthropogenic pressures and climate change: present status, research gaps and future challenges. Hydrobiologia 824: 1.
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Toward eDNA‐based bioassessment of freshwater reservoirs with small volumes of water: Robust molecular protocols. Environmental DNA 5: 264.
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Open science in practice: 300 published research ideas and outcomes illustrate how RIO Journal facilitates engagement with the research process. Research Ideas and Outcomes 7: .
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Diatom metabarcoding applied to large scale monitoring networks: Optimization of bioinformatics strategies using Mothur software. Ecological Indicators 109: 105775.
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DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work. Science of The Total Environment 678: 499.
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eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects. Science of The Total Environment 820: 153223.
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Environmental genomics applications for environmental management activities in the oil and gas industry: state-of-the-art review and future research needs. The APPEA Journal 62: S310.
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Compilation, Revision, and Annotation of DNA Barcodes of Marine Invertebrate Non-Indigenous Species (NIS) Occurring in European Coastal Regions. Diversity 15: 174.
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Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill. Molecular Ecology 27: 146.
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Non-indigenous Species in the Mediterranean Sea: Turning From Pest to Source by Developing the 8Rs Model, a New Paradigm in Pollution Mitigation. Frontiers in Marine Science 7: .
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Environmental DNA (eDNA) Monitoring of Noble Crayfish Astacus astacus in Lentic Environments Offers Reliable Presence-Absence Surveillance – But Fails to Predict Population Density. Frontiers in Environmental Science 8: .
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Development and implementation of eco-genomic tools for aquatic ecosystem biomonitoring: the SYNAQUA French-Swiss program. Environmental Science and Pollution Research 25: 33858.
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A comparison of genetically and morphometrically identified macroinvertebrate community index scores with implications for aquatic life use attainment. Environmental Monitoring and Assessment 194: .
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DNA metabarcoding from sample fixative as a quick and voucher-preserving biodiversity assessment method. Genome 62: 122.
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Exploring the potential of metabarcoding to disentangle macroinvertebrate community dynamics in intermittent streams. Metabarcoding and Metagenomics 4: .
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Marine health of the Arabian Gulf: Drivers of pollution and assessment approaches focusing on desalination activities. Marine Pollution Bulletin 164: 112085.
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The impact of OTU sequence similarity threshold on diatom-based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean). Ecology and Evolution 9: 166.
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Gaps in DNA sequence libraries for Macaronesian marine macroinvertebrates imply decades till completion and robust monitoring. Diversity and Distributions 27: 2003.
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Translational Molecular Ecology in practice: Linking DNA-based methods to actionable marine environmental management. Science of The Total Environment 744: 140780.
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A triad of kicknet sampling, eDNA metabarcoding, and predictive modeling to assess richness of mayflies, stoneflies and caddisflies in rivers. Metabarcoding and Metagenomics 6: .
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A DNA metabarcoding protocol for hyporheic freshwater meiofauna: Evaluating highly degenerate COI primers and replication strategy. Metabarcoding and Metagenomics 2: .
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Enhancing DNA metabarcoding performance and applicability with bait capture enrichment and DNA from conservative ethanol. Molecular Ecology Resources 20: 79.
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Revision and annotation of DNA barcode records for marine invertebrates: report of the 8th iBOL conference hackathon. Metabarcoding and Metagenomics 5: .
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The European Water Framework Directive facing current challenges: recommendations for a more efficient biological assessment of inland surface waters. Inland Waters 9: 95.
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Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary. PLOS ONE 12: e0175186.
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Choice of DNA extraction method affects DNA metabarcoding of unsorted invertebrate bulk samples. Metabarcoding and Metagenomics 2: .
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Assessing strengths and weaknesses of DNA metabarcoding‐based macroinvertebrate identification for routine stream monitoring. Methods in Ecology and Evolution 8: 1265.
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Simultaneous detection of native and invasive crayfish and Aphanomyces astaci from environmental DNA samples in a wide range of habitats in Central Europe. NeoBiota 58: 1.
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The potential of exact sequence variants (ESVs) to interpret and assess the impact of agricultural pressure on stream diatom assemblages revealed by DNA metabarcoding. Ecological Indicators 122: 107322.
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DNAqua-Net or how to navigate on the stormy waters of standards and legislations. Biodiversity Information Science and Standards 2: e25953.
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