Environmental DNA (Edna) Monitoring of Priority Conservation Fish Species in UK Lentic Ecosystems
Total Page：16
File Type：pdf, Size：1020Kb
Environmental DNA (eDNA) monitoring of priority conservation fish species in UK lentic ecosystems being a Thesis submitted for the Degree of Ph.D. in the University of Hull by Cristina Di Muri BSc, MSc (Hons), University of Ancona October 2020 To my dad, dancing in the mind field with you Declaration of Authorship I declare that the work herein is intellectually my own. Each data chapter received contribution from my supervisors (Bernd Hӓnfling, B.H.; Lori Lawson Handley, L.L.H.), advisors (Colin W. Bean, C.W.B.; Ian J. Winfield, I.J.W.), and collaborators (Colin E. Adams, C.E.A.; Ben Aston, B.A.; Marco Benucci, M.B.; Rein Brys, R.B.; Andy Gowans; A.G.; Nathan Griffith, N.G.; Lynsey R. Harper, L.R.H.; Ben J. James, B.J.J.; Jianlong Li, J.L.; Graeme Peirson, G.P.; Glenn Rhodes, G.R.; Philip A. Rippon, P.A.R.; Graham S. Sellers, G.S.S.; Peter Shum, P.S.; Kerry Walsh, K.W.; Hayley V. Watson; H.V.W.). Chapter 2 I led the experiment which was designed by B.H., K.W. and G.P. H.V.W. assisted with sampling and initial samples processing. G.S.S. helped with optimization of DNA extraction. I performed all subsequent laboratory works and bioinformatics supervised by J.L. I analysed the data and wrote the first draft of the paper which was then revised under the advice of supervisors (B.H., L.L.H.), advisors (C.W.B., I.J.W.) and collaborators (K.W., G.P., H.V.W., J.L., G.S.S.). Chapter 3 I led the experiment which was co-designed with B.H., I.J.W. and B.J.J. H.V.W, L.R.B., J.L., M.B., I.J.W., B.J.J. assisted with fieldwork and initial samples processing. I performed all subsequent laboratory works and bioinformatics. I analysed the data and wrote the first draft of the paper which was then revised under the advice of supervisors (B.H., L.L.H.). Chapter 4 I led the experiment which was co-designed with B.H. M.B., J.L., I.J.W., B.J.J. assisted with fieldwork and initial samples processing. L.R.H. helped with the TaqMan qPCR assay design. G.R. and N.G. provided advice on qPCR experiments. R.B. provided the SYBRGreen qPCR protocol. I performed all laboratory works and bioinformatics. I analysed the data and wrote the first draft of the paper which was then revised under the advice of supervisors (B.H., L.L.H.). Chapter 5 I used data collected from the University of Hull in collaboration with the Environment Agency, Natural Resources Wales and Scottish Environment Protection Agency. B.A., P.A.R., and A.G. contributed to some data collection. I assisted with sampling and initial sample processing. I analysed the data based on information provided by C.W.B, C.E.A. and I.J.W. and wrote the first draft of the paper which was then revised under the advice of supervisors (B.H., L.L.H.). Acknowledgements This Ph.D. scholarship was funded by the Scottish Natural Heritage (SNH) with the support and scientific collaboration of the Centre of Ecology and Hydrology (CEH). The Environment Agency (EA) and Yorkshire Water provided additional funding to carry out part of this project. I would like to thank my advisors Colin W. Bean (SNH) and Ian J. Winfield (CEH), and my supervisors Bernd Hӓnfling and Lori Lawson Handley for being such inspiring people. It was a privilege and an honour to be your student and your trust and encouragement led me where I am now. To my lab mates, Marco Benucci, Rosetta Blackman, Nathan Griffiths, Lynsey R. Harper, Jianlong Li, Graham S. Sellers, Peter Shum, Michael Winter and Hayley V. Watson. I am so grateful for your personal, scientific and psychological support that I cannot even quantify how much of this PhD I owe you (Marco I know you probably kept count of the £5!). I would not have made it through without you guys! I would like to thank the EvoHull group Rob Donnelly, Africa Gómez, Domino Joyce, Dave Lunt and Katharina Wollenberg-Valero, whose invaluable source of knowledge and precious advice made me a better scientist and improved my research. A special thanks goes to Stephanie McLean without which support, inside and outside the University, I would not have survived the last two years. You are among the best things this PhD has granted me! I am so grateful for all people of the “Hull network and stuff” group that make the whole PhD experience in Hull just extraordinary. Listing all of you would be impossible, but without the little daily happy things that each of you has provided over the years, I would have struggled to keep my positivity at the top. A special thanks to Ana Maria for our daily walks to the University (and much more of course!), to Barbara who tried to educate me to a correct work-life balance (sorry if I miserably failed!), to Ola and our glasses of wine (waiting for the next cheer!), to Angelo for being my Italian family in Hull and finally to my beloved “husband” Pili, I am not sure where this unpredictable life will take us, but I know that we’ll always be there for each other! Love you so much! Time to move on to my Italian supporters, therefore, I shall switch to Italian. Mamma grazie per il tuo continuo supporto che non è venuto a mancare mai, neanche negli ultimi anni che sono stati così difficili per noi. Grazie per avermi coccolata (con cibo e non solo!) e protetta sempre. Grazie alla mia famiglia ed in particolare alle zie (Teresa, Franca ed Ester) e a mia cugina Chiara per avermi aiutata ad affrontare questi ultimi duri mesi in assenza di una figura essenziale della mia vita. Tanto Matti, la mia famiglia adottiva, rimarrete sempre una delle cose più preziose che ho. Il reciproco amore, la stima e il supporto che da anni ci uniscono sono sicura ci accompagneranno sempre in futuro e, nonostante le distanze, riusciremo a gioire reciprocamente per ogni prossimo traguardo. Ultimo, solo in ordine di arrivo, grazie a Matteo che negli ultimi mesi ha portato qualcosa di inaspettato e bellissimo nella mia vita. Non avrei mai pensato di poter incontrare una persona così speciale da decidere di volerla accanto a me come compagno di questo viaggio che è la vita, ma ora ci sei, e non ti lascerò andare via tanto facilmente. Grazie per tutte le piacevoli distrazioni che mi hai regalato in questi mesi e per l’affetto immenso che giornalmente mi dimostri. Papà questa tesi è dedicata a te e a tutti i nostri sogni, spero che tu possa essere orgoglioso di me come lo sei sempre stato. Grazie a te per avermi reso la persona che sono oggi, essere la tua “copia”, come molti dicono, è ciò che mi rende più orgogliosa. Table of contents Abstract 1 Chapter 1 2 General introduction 2 1.1 Freshwater ecosystems 2 1.2 Freshwaters fish monitoring - from conventional methods to molecular investigation 3 1.3 Environmental DNA research in lentic systems 5 1.4 Thesis rationale 7 1.5 Data chapter summaries 12 Chapter 2 15 Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds 15 2.1 Abstract 16 2.2 Introduction 17 2.3 Materials and methods 19 2.4 Results 27 2.5 Discussion 35 2.6 Conclusion 40 Chapter 3 43 Detection of Arctic charr (Salvelinus alpinus L.) spawning activity in England’s biggest lake: a spatio-temporal study using environmental DNA metabarcoding 43 3.1 Abstract 43 3.2 Introduction 44 3.3 Materials and methods 49 3.4 Results 55 3.5 Discussion 59 3.6 Conclusion 64 Chapter 4 66 Targeted or whole-community? A “sensitive” matter for environmental DNA samples. 66 4.1 Abstract 66 4.2 Introduction 67 4.3 Materials and methods 70 4.4 Results 77 4.5 Discussion 81 4.6 Conclusion 85 Chapter 5 87 Environmental DNA (eDNA) metabarcoding provides accurate information on distribution and abundance of UK priority conservation fish 87 5.1 Abstract 87 5.2 Introduction 88 5.3 Materials and methods 91 5.4 Results 97 5.5 Discussion 103 5.6 Conclusion 111 Chapter 6 112 General discussion 112 6.1 Environmental DNA metabarcoding provides reliable estimates of fish biomass and abundance 112 6.2 Environmental DNA metabarcoding determines spawning location and timing of endangered fish species 114 6.3 Environmental DNA metabarcoding effectively monitors UK priority conservation fish species in sensitive sites 116 6.4 Closing remarks: understanding limitations and future directions of eDNA 117 References 122 Appendix 1: Additional information for Chapter 2 164 Appendix 2: Additional information for Chapter 3 171 Appendix 3: Additional information for Chapter 4 173 Appendix 4: Additional information for Chapter 5 178 Abstract Freshwater environments cover only a tiny fraction of the planet’s surface, yet they are biodiversity hotspots and support almost half of the global fish diversity, including globally and locally endangered species. In the UK, three species of national conservation value namely, Arctic charr (Salvelinus alpinus L.), European whitefish (Coregonus lavaretus L.) and vendace (Coregonus albula L.), are threatened throughout their limited distribution range by a number of human-driven environmental changes. To combat a further loss of these priority conservation fish, non-invasive, sensitive and reliable monitoring tools are required to assess their status and guide appropriate conservation measures.