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New Methods for Improving Water Management Bonnie Bailet

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New Methods for Improving Water Management Bonnie Bailet !CTA5NIVERSITATIS!GRICULTURAE3UECIAE Acta Universitatis Agriculturae Sueciae 2021:55 No. Thesis Doctoral Doctoral Thesis No. 2021:55 Diatoms are useful bioindicators but their identification using light microscopy is time consuming Doctoral Thesis No. 2021:55 and error prone. Two alternative approaches to characterise the diatom community were Faculty of Natural Resources and Agricultural Sciences developed and applied in this thesis: a DNA metabarcoding approach and a trait-based approach. Both approaches showed potential for environmental assessment but cannot be used with tools • developed for microscopy data. New nutrient indices were developed for each novel approach and New methods for improving water management • Bonnie Bailet New methods for improving water performed well for a use in assessment of total phosphorus levels in Fennoscandia freshwater. management Bonnie Bailet received her graduate education at the Department of Aquatic Sciences and Exploring the role of diatoms in ecosystems Assessment at the Swedish University of Agricultural Sciences in Uppsala. Her M.Sc. degree in Oceanography specialised in Marine Biology was obtained at Aix-Marseille University, Marseille, France. Bonnie Bailet Acta Universitatis Agriculturae Sueciae presents doctoral theses from the Swedish University of Agricultural Sciences (SLU). SLU generates knowledge for the sustainable use of biological natural resources. Research, education, extension, as well as environmental monitoring and assessment are used to achieve this goal. Online publication of thesis summary: http://pub.epsilon.slu.se/ ISSN 1652-6880 ISBN (print version) 978-91-7760-788-5 ISBN (electronic version) 978-91-7760-789-2 New methods for improving water management Exploring the role of diatoms in ecosystems Bonnie Bailet Faculty of Natural Resources and Agricultural Sciences Department of Aquatic Sciences and Assessment Uppsala DOCTORAL THESIS Uppsala 2021 Acta Universitatis agriculturae Sueciae 2021:55 Cover: Diatom structure unfolding into DNA (Illustration: B. Bailet) ISSN 1652-6880 ISBN (print version) 978-91-7760-788-5 ISBN (electronic version) 978-91-7760-789-2 © 2021 Bonnie Bailet, Swedish University of Agricultural Sciences Uppsala Print: SLU Service/Repro, Uppsala 2021 New methods for improving water management - Exploring the role of diatoms in ecosystems Abstract Diatoms are photosynthetic microalgae which are well known to react quickly to environmental changes and are widely used as bioindicators within Water Framework Directive. However, diatom identification by light microscopy is time- consuming and error-prone, creating a need for alternative, faster and more reproducible methods for characterising diatom communities. This thesis describes the development and application of two such methods: a molecular approach using metabarcoding and a trait-based approach using combinations of different diatom morphological traits. Both approaches were shown to have potential for use in environmental assessment, as they revealed the response of diatoms to environmental change and enabled better representation of the diatom community. However, results from the two approaches were not directly comparable to results obtained by conventional microscopy and diatom DNA and trait data should not be used with tools calibrated for morphotaxa data. Discrepancies in molecular output data between laboratories revealed a strong need for standardisation and best- practice guidelines. Nutrient indices developed for each novel approach performed well and showed potential for use in assessment of total phosphorus levels in Fennoscandia freshwater. The molecular-based index showed differences in performance for stream and lake samples. The trait-based index performed equally well for both types of site, but current limitation of this index is that selection of meaningful traits must be done for each new gradient. Further work is needed on diatom traits and their response to environmental changes, to obtain reproducible and comparable molecular outputs and to continue the development of new indices calibrated to diatom DNA and trait data. Keywords: ecological status, eutrophication, Bacillariophyta, morphological identification, 18S-V4, rbcL, ISU, ASV, trait classification, ecological guilds. Author’s address: Bonnie Bailet, Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, PO Box 7050, SE750 07, Uppsala, Sweden. Nya metoder för att förbättra vattenförvaltningen - utforska kiselalgernas roll i ekosystem Abstract Kiselalger är fotosyntetiska alger och används väl som bioindikatorer inom vattendirektivet inom ramen för övervakning och miljöbedömning av europeiska vatten. Men deras identifiering med ett ljussmikroskop mikroskopiskt är tidskrävande och har felkällor, vilket skapar ett behov av alternativa, snabbare och mer reproducerbara metoder för att karaktärisera kiselalgssamhället ökat. I denna avhandling testar vi utvecklingen och tillämpningen av två nya tillvägagångssätt: ett molekylärt tillvägagångssätt med metabarkodningsmetoden och ett egenskapsbaserat tillvägagångssätt med kombinationer av olika morfologiska drag. Båda tillvägagångssätten har potential för användning i miljöbedömning eftersom de visat starka responser från kiselalgerna på miljöförändringar, en bättre representation av kiselalgssamhället. Resultat från de två nya tillvägagångssätten är emellertid inte jämförbara med dem i den traditionella mikrokopimetoden. Alltså, kiselalgernas DNA-data och drag ska inte användas med verktyg kalibrerade för taxonomiska data. Skillnader i molekylära utdata mellan laboratorier skiljer sig åt och att det finns ett stort behov av standardisering och riktlinjer för bästa praxis. De nya indexen fungerar bra och visar potential för bedömning av totala fosforhalter i Fennoscandias sötvatten. Det molekylärbaserade indexet visade en differentiell prestanda i bäckar och sjöar. Det egenskaper indexet å andra sidan fungerade lika bra för båda typerna av vattenförekomster, men nuvarande begränsningar för detta index är att valet av meningsfulla egenskaper måste göras för varje ny gradient. Ytterligare arbete behövs med kiselalger egenskaper och deras reaktion på miljön för att utveckla mer reproducerbara och jämförbara molekylära utdata och för att hjälpa utvecklingen av nya index kalibrerade till kiselalgernas DNA och egenskaper. Nyckelord: ekologisk status, eutrofiering, Bacillariophyta, morfologisk identifiering, 18S-V4, rbcL, ISU, ASV, egenskapsklassificering, ekologiska guilds. De nouvelles méthodes améliorant la gestion de l'eau – explorer le rôle des diatomées dans les écosystèmes Résumé Les diatomées sont des algues photosynthétiques et utilisées comme bioindicateurs pour l'évaluation environnementale des eaux européennes. Cependant, leur identification au microscope optique est chronophage et sujette à des erreurs, générant un besoin de méthodes alternatives, plus rapides et plus reproductibles pour caractériser les communautés des diatomées. Dans cette thèse, nous testons le développement et l'application de deux nouvelles approches : une approche moléculaire utilisant la méthode du « metabarcoding » et une approche basée sur les traits utilisant des combinaisons de différents traits morphologiques des diatomées. Les deux nouvelles approches ont un bon potentiel d'utilisation dans l'évaluation environnementale car elles reflètent clairement la réponse des diatomées aux changements environnementaux et offrent une meilleure représentation de la communauté des diatomées. Cependant, les résultats des deux nouvelles approches ne sont pas comparables à ceux de l'approche de microcopie traditionnelle et les données ADN et de traits de diatomées ne devraient pas être utilisées avec des outils calibrés pour les données de microscopie. En outre, nous avons constaté un fort besoin de standardisation et de lignes directrices sur les meilleures pratiques à adopter. Un indice écologique pour chaque approche a aussi été développé et testé. Les nouveaux indices montrent un fort potentiel pour l'évaluation des niveaux de phosphore total dans les eaux douces de la Fennoscandie. L'indice moléculaire a montré une performance différentielle entre les sites de cours d'eau et de lacs. L'indice basé sur les traits, en revanche, a donné de bons résultats pour les deux types de sites, mais des traits représentatifs doivent être sélectionnés pour chaque nouveau gradient. De futures travaux devront approfondir notre compréhension des traits des diatomées et de leur réponse à l'environnement, permettre des résultats moléculaires plus reproductibles et comparables, et aider au développement de nouveaux indices calibrés sur les données d'ADN et de traits des diatomées. Mots clés: état écologique, eutrophisation, Bacillariophyta, identification morphologique, 18S-V4, rbcL, ISU, ASV, classification des traits, guildes écologiques. Dedication À mon Papi Caillou, qui était là au début de cette aventure et qui aurait aimé être là pour la fin. “The truth is everyone is winging it. So, I say spread your wings and follow your dreams.” Charlie Mackesy. Contents List of Publications ........................................................................ 13 Abbreviations ................................................................................ 15 1. Explanation of frequently used terms and abbreviations ...... 17 Environmental assessment .................................................................... 17 (Bio)monitoring......................................................................................
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