DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly important if molecular identification tools are to be implemented in biomonitoring and reports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). We analysed gaps in the two most important reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses show that coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, caddisflies and vascular plants) are well represented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also found that species monitored in several countries often are represented by barcodes in reference libraries, while species monitored in a single country frequently lack sequence records. A large proportion of species (up to 50%) in several taxonomic groups are only represented by private data in BOLD. Our results have implications for the future strategy to fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species relevant to monitoring in multiple countries should be prioritized for future collaborative programs. We also discuss why a strategy for quality control and quality assurance of barcode reference libraries is needed and recommend future steps to ensure full utilisation of metabarcoding in aquatic biomonitoring.This paper is a deliverable of the European Cooperation in Science and Technology (COST) Action DNAqua-Net (CA15219) Working Group 1, led by Torbjørn Ekrem and Fedor Čiampor. Thanks to the University of Minho and University of Pécs for hosting workshops and working group meetings. We also thank staff at National Environment Agencies and others that provided national checklists of taxa used in biomonitoring, and otherwise assisted with checklist proof-reading: Jarmila Makovinská and Emília Mišíková Elexová (Slovakia); Steinar Sandøy and Dag Rosland (Norway); Mišel Jelič (Croatia); Marlen Vasquez (Cyprus); Adam Petrusek (Czech Republic); Kristel Panksep (Estonia); Panagiotis Kaspiditis (Greece); Matteo Montagna (Italy); Marija Katarzyte (Lithuania); Ana Rotter (Slovenia); Rosa Trabajo (Spain); Florian Altermatt (Switzerland); Kristian Meissner (Finland), Rigers Bakiu (Albania), Valentina Stamenkovic and Jelena Hinic (Macedonia); Patricia Mergen (Belgium); Gael Denys & the French Biodiversity Agency (France); Mary Kelly-Quinn (Ireland); Piotr Panek and Andrzej Zawal (Poland); Cesare Mario Puzzi (Italy); Carole Fitzpatrick (United Kingdom); Simon Vitecek (Austria); Ana Filipa Filipe (Portugal); Peter Anton Stæhr & Anne Winding (Denmark); Michael Monaghan (Germany); Alain Dohet, Lionel L'Hoste, Nora Welschbillig & Luc Ector (Luxembourg), Lujza Keresztes, (Romania). The authors also want to thank Dirk Steinke for providing the original European ERMS list for marine taxa and Florian Malard for comments on the manuscript. The preparation of the AMBI checklist was carried out in the scope of a Short-term Scientific Mission (ECOST-STSM-CA15219-150217- 082111) granted to SD visiting AZTI, Spain. ZC was supported by grants EFOP-3.6.1.-16-2016-00004 and 20765-3/2018/FEKUTSTRAT. TE was supported by the NorBOL-grant (226134/F50) from the Research Coun cil of Norway. BR, FL and MFG contributed through support from the GBOL project, which is generously funded by the German Federal Min istry of Education and Research (FKZ 01LI1101 and 01LI1501). MG contributed through support of the Polish National Science Centre, grants N N303 5794 39 and 2014/15/B/NZ8/00266. SF was funded by the project PORBIOTA - Portuguese E-Infrastructure for Information and Research on Biodiversity (POCI-01-0145-FEDER-022127), supported by Operational Thematic Program for Competitiveness and Internationalization (POCI), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (FEDER)

Mutual Role Expectations by Patients and General Practitioners—A Mixed Methods Study on Complementarity

Background: Changes in public attitudes toward “authorities” in general, as well as shifts in medical practice toward participative models of diagnosis and treatment, imply fundamental transformations in the patient–doctor relationship. However, consistency in reciprocal role expectations cannot be assumed, and this study reveals significant discrepancies in attitudes and behaviors in primary health consultations. Methods: We conducted a study in the tri-lingual northeastern Italian region of South Tyrol to determine whether perceptions of the patient’s role were congruent or differed. In a mixed method approach, the quantitative research part consisted of a survey with 34 identical questions for general practitioners (n = 109) and adult primary care patients (n = 506) on verbal communication, self-initiative and health literacy, interpersonal and social qualities of the patient–physician relationship, and formal aspects of the consultation. Patients were interviewed via telephone, and general practitioners responded online. In the qualitative part, 26 semi-structured in-depth interviews were conducted with the patients and analyzed. Results: General practitioners considered patients’ communicative efforts (p < 0.001), self-initiative (p < 0.001), compliance (p = 0.0026), and openness regarding psychosocial issues (p < 0.001) to be significantly more important, whereas patients showed a tendency to give increased importance to formal aspects such as politeness and hygiene (p < 0.001). Perception of the patient’s role differed significantly between the Italian and German linguistic groups. Conclusions: Patients and general practitioners differ in their understanding of patients’ roles. These data suggest that a considerable proportion of the population lacks a clear and tangible idea of the active role they could play in consultations. Targeted information on the identified aspects of patient–provider communication may facilitate participatory behavior and positively impact the longitudinal quality of the patient–general practitioner relationship

First limnological characterization of Lakes Leqinat and Drelaj in Bjeshkët e Nemuna National Park, Kosovo

The Balkan Peninsula is a biodiversity hotspot and hosts numerous mountain lakes, which offer a refuge for a multitude of species. However, previous pristine habitats have been deeply affected by anthropogenic change, such as non-native fish introductions, which calls for multi-species considerations in the last remaining unaltered habitats. We carried out abiotic measurements and biodiversity assessments in two neighbouring alpine lakes, Lakes Leqinat and Drelaj in the Bjeshkët e Nemuna National Park in Kosovo, in August 2018. Lake Leqinat is a permanent, stratified water body and exhibits weak oxygen depletion below 3 m. Phytoplankton was dominated by chrysophycean, cryptophycean and chlorophycean algae. Zooplankton consisted of five rotifer species and Daphnia longispina. A mark-recapture experiment yielded a population of alpine newts (Ichthyosaura alpestris) of nearly 4 000 adult individuals. In contrast, cold water from the surrounding karst seeps into Lake Drelaj, which is a well-oxygenated temporary lake. Hence phytoplankton and zooplankton biomasses were considerably lower than in Lake Leqinat. Phytoplankton was dominated by cryptophycean, chlorophycean, and bacillariophycean algae. Zooplankton consisted of the diaptomid copepod Mixodiaptomus tatricus, the cladoceran Daphnia rosea, and the anostracan Chirocephalus diaphanus. Conservation efforts should ensure that Lake Leqinat remains unstocked as introduced fish would probably destroy the natural community

Long-term trends in the prescription of antidiabetic drugs: real-world evidence from the Diabetes Registry Tyrol 2012–2018

Introduction Prescription patterns of antidiabetic drugs in the period from 2012 to 2018 were investigated based on the Diabetes Registry Tyrol. To validate the findings, we compared the numbers with trends of different national registries conducted in a comparable period of time.Research design and methods Medication data, prescription patterns, age groups, antidiabetic therapies and quality parameters (hemoglobin A1c, body mass index, complications) of 10 875 patients with type 2 diabetes from 2012 to 2018 were retrospectively assessed and descriptively analyzed. The changes were assessed using a time series analysis with linear regression and prescription trends were plotted over time.Results Sodium/glucose cotransporter 2 inhibitors (SGLT-2i) showed a significant increase in prescription from 2012 to 2018 (p<0.001), as well as metformin (p=0.002), gliptins (p=0.013) and glucagon-like peptide-1 agonists (GLP-1a) (p=0.017). Significant reduction in sulfonylurea prescriptions (p<0.001) was observed. Metformin was the most frequently prescribed antidiabetic drug (51.3%), followed by insulin/analogs (34.6%), gliptins (28.2%), SGLT-2i (11.7%), sulfonylurea (9.1%), glitazones (3.7%), GLP-1a (2.8%) and glucosidase inhibitors (0.4%).Conclusions In this long-term, real-world study on prescription changes in the Diabetes Registry Tyrol, we observed significant increase in SGLT-2i, metformin, gliptins and GLP-1a prescriptions. In contrast prescriptions for sulfonylureas declined significantly. Changes were consistent over the years 2012–2018. Changes in prescription patterns occurred even before the publication of international and national guidelines. Thus, physicians change their prescription practice not only based on published guidelines, but even earlier on publication of cardiovascular outcome trials

Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring

Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have been recognized for their importance in environmental processes. Recently, the use of molecular methods has revealed unexpected diversity within known functional groups and novel metabolic pathways that are particularly important in energy and nutrient cycling. In various habitats, microbial communities respond to eutrophication, metals, and natural or anthropogenic organic pollutants through changes in diversity and function. In this review, we evaluated the common trends in these changes, documenting that they have value as bioindicators and can be used not only for monitoring but also for improving our understanding of the major processes in lotic and lentic environments. Current knowledge provides a solid foundation for exploiting microbial taxa, community structures and diversity, as well as functional genes, in novel monitoring programs. These microbial community measures can also be combined into biotic indices, improving the resolution of individual bioindicators. Here, we assess particular molecular approaches complemented by advanced bioinformatic analysis, as these are the most promising with respect to detailed bioindication value. We conclude that 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