Faculty of Biosciences, Fisheries and Economics The Norwegian College of Fishery Science Bioprospecting of marine fungi from the High Arctic A study of high latitude marine fungi from understudied taxa; bioactivity potential, taxonomy and genomics Ole Christian Hagestad A dissertation for the degree of Philosophiae Doctor April 2021 Cover page “A true teacher would never tell you what to do. But he would give you the knowledge with which you could decide what would be best for you to do.” ― Christopher Pike, Sati Bioprospecting of marine fungi from the High Arctic A study of high latitude marine fungi from understudied taxa; bioactivity potential, taxonomy and genomics A dissertation submitted in partial fulfilment of the requirement for the degree of Philosophiae Doctor. Ole Christian Hagestad Tromsø April 2021 The work presented in this thesis was carried out at the Norwegian College of Fishery Sciences (NFH), UiT – The Arctic University of Norway from January 2017 to April 2021. The work was funded by UiT - The Arctic University of Norway as an independent PhD position. i Summary Marine fungi comprise a group of organisms that have been overlooked for a long time. Research interest has increased with the realization of the important ecological role and rich chemistry of marine fungi. Marine fungi have yielded thousands of new natural products the last decade, but many taxa remain unstudied. Marine fungi from the Arctic have not been reported in literature in regard to bioprospecting campaigns and represent a novel source of natural products. The aim of this thesis is to assess the potential of Arctic marine fungi to produce bioactive secondary metabolites by fermentation and genome analysis. This was achieved in three steps. First, fungi were isolated from the Svalbard archipelago. The 20 isolates obtained were characterized based on molecular markers and their antibacterial activity was tested using an agar diffusion assay (Paper 1). Secondly, three distinct marine fungi were whole genome sequenced and characterized. One of the fungi represented a putatively novel species which was circumscribed based on morphology and phylogenetic inference (Paper 2). Finally, a metabolite from one fungus among the 20 obtained around Svalbard was isolated and the bioactivities characterized (Paper 3). In Paper 1, half of the fungal isolates showed activity against pathogenic bacteria and every third isolate represents potentially new species of fungi. Five of these isolates are strictly marine fungi belonging to the order of Lulworthiales. The study showed that the Arctic can yield novel marine fungal diversity that can be utilized in bioprospecting. For Paper 2, three marine fungi were whole genome sequenced and their biosynthetic gene clusters were characterized. Mapping of the biosynthetic gene clusters (BGCs) within the Emericellopsis genome confirmed the detection of the secondary metabolite helvolic acid produced during fermentation. The study revealed numerous unknown biosynthetic gene clusters and a range of carbohydrate active enzymes. Each of the three genomes provides the first genome of their respective taxa and can contribute to understanding their evolutionary adaption to the marine environment. In Paper 3, a novel compound from the fermentation broth of Mytilinidion sp. was isolated and its bioactivity was characterized using seven different bioactivity assays. The compound turned out to be a modified medium component with IC50 of 43 µM in an ACE- inhibitory assay. The compound was novel and this is the first report of its bioactivity. Molecular networking could perhaps have provided early indications that the compound was a modified medium component. ii Sammendrag Marin sopp er en gruppe av organismer som har vært oversett i lang tid. Interessen for marin sopp har steget i takt med økt forståelse for dens økologi og rike kjemi. Mange tusen nye naturprodukter har blitt beskrevet fra marin sopp de siste tiårene, men det er fremdeles mange grupper som ikke er godt studert. Marin sopp fra Arktis er ikke godt undersøkt i forbindelse med bioprospektering og representerer en ny kilde til naturprodukter. Målet med avhandlingen var å vurdere potensialet til Arktisk marin sopp for å produsere bioaktive metabolitter ved å bruke fermentering og genomanalyse. Dette ble gjennomført i tre steg. Først ble 20 marine sopp isolert i løpet av ett forskningstokt rundt Svalbard. Disse soppene ble karakterisert ved hjelp av molekylære markører og evnen til å produsere antibakterielle forbindelser ble undersøkt ved å bruke agar-diffusjons analyse (Artikkel 1). Det neste som ble gjort var at tre forskjellige marine sopp ble helgenomsekvensert og genomene ble karakterisert. En av soppene er antageligvis ny for vitenskapen og ble beskrevet basert på morfologisk og fylogenetisk analyser (Artikkel 2). Til sist ble ett stoff fra en av soppene fra Artikkel 1 isolert og bioaktiviteten til stoffet ble beskrevet (Artikkel 3). I den første artikkelen viste halvparten av de isolerte soppene antibakteriell aktivitet mot sykdomsfremkallende bakterier. Hvert tredje isolat representerer muligens nye arter basert på tilgjengelige referansesekvenser. Fem av de potensielt nye artene tilhører ordenen Lulworthiales som kun finnes i havet. Studien har vist at det er stort potensiale for å avdekke nye arter og at mange av disse viser evne til å produsere antibakterielle forbindelser. Dette viser at de kan utnyttes i bioprospektering. I Artikkel 2 ble tre ulike marine sopper helgenomsekvenseert og genomet ble karakterisert med tanke på hvilke biosyntetiske genklynger og karbohydrat-aktive enzymer som ble detektert. Karakteriseringen av genklyngene i Emericellopsis bekreftet deteksjonen av metabolitten helvolsyre som soppen produserte under fermentering. Studien avslørte mange ukjente genklynger og en rekke karbohydrat-aktive enzymer. De tre genomene er de første helsekvenserte genomene i deres respektive slekter og kan bidra til å gi ny kunnskap om de evolusjonære tilpasningene de har til det marine miljø. I den siste artikkelen ble ett ukjent stoff fra fermenteringen av Mytilinidion isolert. Bioaktiviteten til stoffet ble karakterisert ved hjelp av syv forskjellige bioaktivitetstester. Stoffet viste seg å være en delvis nedbrutt og modifisert mediekomponent som hadde en IC50 verdi på 42.3 µM i en ACE-inhiberingstest. Analyse ved hjelp av molekylært nettverk kunne kanskje avdekket at stoffet var relatert til dyrkningsmediumet. iii Acknowledgements Ever since I was a young boy I have always wanted to become a scientist and complete a PhD, mainly due to my parent’s supply of Science Illustrated1 issues. I was delighted when I got the opportunity to fulfil this dream at Marbio. I do not believe many research groups have the same team spirit on both professional and social levels as Marbio. First and foremost, I would like to express my thanks and highlight my main supervisor Dr. Teppo Rämä, who introduced me to the wonderful world of marine fungi, and was always prepared to answer questions even late in the weekend evenings. I am also deeply appreciative for my co-supervisors Prof. Dr. Jeanette H. Andersen, Prof. Dr. Espen H. Hansen and Dr. Bjørn Altermark. Your knowledge and feedback have been invaluable in pushing me forward and keeping me on track in this work. It was always possible for you to make me take a step back and look at the bigger picture when I got too hung up on details. Secondly, I would like to express my gratitude to all of my colleagues who have contributed to my work in different ways. Thanks to Marte Albrigtsen, Kirsti Helland, Dr. Kine Ø. Hansen, Dr. Johan Isaksson, Dr. Ruth Hendus-Altenburger, Dr, Chun Li and Dr. Sara Ullsten Wahlund for their work and help on bioassays, NMR, DNA extraction and PCR. I would also like to thank everyone else at Marbio and MarBank for making these four years as enjoyable as they were. A very heartfelt thanks to the other PhD students Marte, Yannik (now Dr.), Renate and Venke that shared the PhD life with me. A special thanks to Marte and André for proofreading my thesis. I also want to express my gratitude to the external collaborators that participated in parts of the project. A special thanks to Prof. Dr. Russell Cox and Dr. Eric Kuhnert at Leibniz Universität Hannover that allowed me to have a 3-months research stay in their group, digging into the biosynthetic potential of fungi (unfortunately cut short by corona). Thanks to Prof. Dr. Alan Dobson and his group at University College Cork for providing a deep-sea sponge isolate for our study and Lingwei Hou and Prof. Dr. Pedro Crous at Westerdijk Fungal Biodiversity Institute for providing assistance in morphological descriptions. Additionally, I would like to thank Prof. Dr. Joseph Spatafora and JGI collaborators in the 1KFG project that enabled the sequencing of the genomes. Lastly, I would like to thank all my friends and family for checking in on me, keeping me grounded, cheering me on and giving me support and encouragement through my PhD. Thank you for letting me share my happiness and frustrations with you. Thanks to everyone who has made this journey possible. I look forward to new adventures with you in the future! Tromsø, April 2021 Ole Christian Hagestad 1 Science Illustrated (Norwegian: Illustrert Vitenskap) is a popular science magazine that is given out monthly covering all areas of science. iv Abbreviations 18S Small ribosomal subunit 1KFG 1000 fungal genomes project 1D/2D NMR One and two dimensional nuclear magnetic resonance 28S Large ribosomal