Marine Fungi from Sponges: Biodiversity, Chemodiversity and Biotechnological Applications

Total Page:16

File Type:pdf, Size:1020Kb

Marine Fungi from Sponges: Biodiversity, Chemodiversity and Biotechnological Applications Marine fungi from sponges : biodiversity, chemodiversity and biotechnological applications Elena Bovio To cite this version: Elena Bovio. Marine fungi from sponges : biodiversity, chemodiversity and biotechnological applica- tions. Other. COMUE Université Côte d’Azur (2015 - 2019); Università degli studi (Torino, Italia), 2019. English. NNT : 2019AZUR4009. tel-02514804 HAL Id: tel-02514804 https://tel.archives-ouvertes.fr/tel-02514804 Submitted on 23 Mar 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. University of Turin Department of Life Sciences and Systems Biology University of Côte d’Azur Institute of Chemistry of Nice, UMR 7272 CNRS Ph.D. Program in Biology and Applied Biotechnologies Doctoral School of Sciences Fondamentales et Appliquées Doctoral School of Sciences Fondamentales et Appliquées Marine fungi from sponges: biodiversity, chemodiversity and biotechnological applications Elena Bovio Ph.D. Coordinators: Prof. Silvia Perotto Prof. Elisabeth Taffin de Givenchy Academic years: 2015-2018 Academic disciplines: BIO/02 - Chemistry University of Turin Ph.D. Programme in Biology and Applied Biotechnologies University of Côte d’Azur Doctoral School of Sciences Fondamentales et Appliquées Marine fungi from sponges: biodiversity, chemodiversity and biotechnological applications Elena Bovio Tutors: Prof. Giovanna Cristina Varese Prof. Mohamed Mehiri XXXI Cycle: 2015 – 2018 The sea, once it casts its spell, holds one in its net of wonder forever Jacques Y. Cousteau Table of contents List of Abbreviations i List of Figures and Tables iv 1. INTRODUCTION 1 1.1 Marine environment 1 1.2 Marine fungi 2 1.2.1 Origin 2 1.2.2 Diversity and occurrence of fungi in the marine environment 5 1.2.3 Ecology 8 1.3 Marine organisms and microorganisms: an unlimited source of novel compounds 12 1.3.1 The Mycotechnology 13 1.4 The sponge holobiont 16 1.4.1 Sponges 166 1.4.1.1 Origins, anatomy and physiology 166 1.4.1.2 Sponges, as producers of secondary metabolites 18 1.4.2 Fungi associated with sponges 19 1.4.3 Secondary metabolites from marine fungi associated with sponges 23 1.5 Classical and epigenetic approach to diversify the production of secondary metabolites in marine fungi 25 2. AIM OF THE WORK 30 2.1 Project outline 32 3. The culturable mycobiota associated with 4 Atlantic sponges 33 3.1 MATERIAL AND METHODS 34 3.1.1 Sampling sites and axenic isolation 34 3.1.2 Fungal identification 36 3.1.3 Statistical analyses 38 3.2 RESULTS AND DISCUSSION 38 3.2.1 Influence of isolation techniques on the fungal community 38 3.2.2 Fungal diversity 41 3.2.3 Fungal diversity among the sponges 58 3.3 CONCLUSION 63 4. Thelebolus balaustiformis and Thelebolus spongiae: two new fungal species from the Atlantic sponge D. fragilis 65 4.1 MATERIAL AND METHODS 65 4.1.1 Thelebolus spp. growth conditions and molecular study 65 4.2 RESULTS AND DISCUSSION 65 4.2.1 Thelebolus balaustiformis and Thelebolus spongiae sp. nov. 65 4.2.2 Taxonomy 67 4.2.2.1 Description of Thelebolus balaustiformis 67 4.2.2.2 Description of Thelebolus spongiae 72 4.2.2.3 Ecology and peculiar features of Thelebolus spp. 77 5. The culturable fungal communities inhabiting the Mediterranean sponges Aplysina cavernicola, Crambe crambe and Phorbas tenacior 82 5.1 MATERIAL AND METHODS 83 5.1.1 Sampling sites and fungal isolation 83 5.1.2 Fungal identification 84 5.1.3 Statistical analyses 85 5.2 RESULTS AND DISCUSSION 85 5.2.1 Influence of isolation techniques on the fungal community 85 5.2.2 Fungal diversity 86 5.2.3 Fungal culturable diversity among the sponges 96 5.2.4 Mycobiotas vs metabolome 99 5.2.5 Fungi from A. cavernicola isolated by direct plating 100 5.3 CONCLUSION 105 6. Chemical diversity of the fungal community associated with the Atlantic sponge G. compressa 106 6.1 MATERIALS AND METHODS 106 6.1.1 Small scale fermentation of the fungal community and OSMAC approach 106 6.1.1.1 Multi-well culture and co-culture conditions 106 6.1.1.2 Extraction procedure and chemical analysis 107 6.1.2 Scale-up of E. chevalieri MUT 2316 and molecules purification 108 6.1.2.1 Solid media culture condition and secondary metabolites extraction and purification from E. chevalieri 108 6.1.2.2 Liquid media culture condition and secondary metabolites extraction from E. chevalieri 110 6.1.2.3 High Resolution Mass Spectrometry analysis and molecular networking 111 6.2 RESULTS AND DISCUSSION 112 6.2.1 OSMAC approach 112 6.2.1.1 Effect of media on fungal development and chemical fingerprint 112 6.2.1.2 Effect of salts on the fungal development and the chemical fingerprint 117 6.2.1.3 Effect of co-culture on the fungal development and the chemical fingerprint 119 6.2.1.4 General remarks on the OSMAC approach 120 6.2.2 Scale up of Eurotium chevalieri MUT 2316 121 6.2.2.1 E. chevalieri MUT 2316 metabolites from solid culture condition 122 6.2.2.2 E. chevalieri MUT 2316 metabolites from liquid culture condition 127 6.2.2.3 Molecular networking of E. chevalieri MUT 2316 in solid and liquid culture condition 130 6.3 CONCLUSION 134 7. The antibacterial activity of the molecules produced by E. chevalieri MUT 2316 135 7.1 INTRODUCTION 135 7.1.1 The Golden Age of antibiotics, the antibiotic crisis and the need of new medicines 135 7.1.2 Developing of AMR 139 7.1.3 What determines a bacterium to become MDR? 141 7.2 MATERIAL AND METHODS 142 7.2.1 Bacterial growth conditions and inoculum preparation 142 7.2.2 Stock solutions of the molecules isolated from E. chevalieri MUT 2316 143 7.2.3 Determination of the MIC 144 7.2.4 Determination of the Minimal Bactericidal Concentration (MBC) 146 7.3 RESULTS AND DISCUSSION 146 7.3.1 E. chevalieri MUT 2316 derived compounds show antibacterial activity 146 7.3.2 Structure-activity relationship 151 7.4 CONCLUSION AND FUTURE PERSPECTIVES 151 8. The antiviral activity of the molecules produced by E. chevalieri MUT 2316 153 8.1 INTRODUCTION 153 8.1.1 Viruses and antivirals 153 8.1.2 Influenza A virus (IAV) 155 8.1.3 Herpes Simplex virus 1 (HSV-1) 156 8.2 MATERIAL AND METHODS 158 8.2.1 Cell culture conditions and viruses titre determination 158 8.2.2 Cytotoxic assays 159 8.2.3 Antiviral assay 159 8.3 RESULTS AND DISCUSSION 161 8.3.1 Cytotoxic activity of E. chevalieri MUT 2316 compounds 161 8.3.2 E. chevalieri MUT 2316-derived compounds show antiviral activity against HSV-1 and IAV 162 8.3.3 Structure-activity relationship 164 8.4 CONCLUSION AND FUTURE PERSPECTIVES 164 9. The antifouling activity of the molecules produced by E. chevalieri MUT 2316 166 9.1 INTRODUCTION 166 9.1.1 The biofouling: definition and impact 166 9.1.2 Biofouling formation 166 9.1.3 Antifouling methods 168 9.1.4 Why sponges and their associated microorganisms as candidates for the production of new antifouling? 171 9.2 MATERIAL AND METHODS 172 9.2.1 Marine Antibacterial Assays 173 9.2.1.1 Growth inhibition 174 9.2.1.2 Adhesion inhibition 175 9.2.2 Microalgal assay 176 9.2.2.1 Growth inhibition 176 9.2.2.2 Adhesion inhibition 177 9.2.3 Inhibition of blue mussel M. edulis settlement – tyrosinase assay 177 9.3 RESULTS AND DISCUSSION 178 9.3.1 The molecules produced by E. chevalieri MUT 2316 display antifouling activity 178 9.4 CONCLUSION AND FUTURE PERSPECTIVES 184 10. GENERAL CONCLUSION AND FUTURE PERSPECTIVES 186 References 190 Annexe 226 Annexe 2 242 Ph.D. activities 245 PUBLICATIONS 247 ACKNOWLEDGEMENTS 250 List of Abbreviations AC Algobank of Caen ACT Actin gene AIC Akaike Information Criterion AMR Antimicrobial resistance ANOVA Analysis of variance ATCC American type culture collection BHI Brain-Heart Infusion BPP Bayesian posterior probabilities CA Carrot Agar CAL Calmodulin gene CAP Canonical analysis of principal coordinates CFU Colony forming unit CLSI Clinical and laboratory standards institute CMASW Corn meal agar seawater cRNP Ribonucleoprotein DAAs Directly acting antivirals DBIOS Department of life sciences and system biology DDD 1,1-dichloro-2,2-bis-(4-chlorophenyl)ethane DMEM Dulbecco’s Modified Eagle Medium DMSO Dimethyl sulfoxide DNA Deoxyribonucleic acid DNMT DNA methyltransferase dNTPs Deoxynucleotides EPS Extracellular polymeric substances FA Formic acid FBS Fetal bovine serum FDA Food and Drug Administration GA Gelatin agar GAPDH Glyceraldehyde-3-phosphate dehydrogenase gene GAS Gelatin agar added with 3% NaCl GASW Gelatin agar seawater i GNPS Global natural products social molecular networking HAAs Host-acting antivirals HBV Hepatitis B virus HCV Hepatitis C virus HDAC Histone deacethylase HIV Human immunodeficiency virus HPLC High Performance Liquid Chromatography HR-MS/MS High-resolution tandem mass spectrometry HSV1 Herpes simplex virus 1 HSV2 Herpes simplex virus 2 IAV Influenza A virus IBV Influenza virus B IC Inhibitor concentration ITS Internal transcribed spacer regions LBCM Laboratoire de Biotechnologie et Chimie Marines LC-MS Liquid chromatography - mass spectrometry LOEC Low observable effect concentration LSU Large subunit MBC Minimal bactericidal concentration MBM Marine bacterial medium MCMC Markov chains monte carlo MDCK Madin darby canine kidney cells MDR Multi drug resistant
Recommended publications
  • Leaf-Associated Shifts in Bacterial and Fungal Communities in Response to Chicken Rearing Under Moso Bamboo Forests in Subtropical China
    Article Leaf-Associated Shifts in Bacterial and Fungal Communities in Response to Chicken Rearing Under Moso Bamboo Forests in Subtropical China Xiaoping Zhang 1, Zheke Zhong 1,*, Xu Gai 1, Jiafu Ying 2, Weifen Li 2, Xuhua Du 1, Fangyuan Bian 1 and Chuanbao Yang 1 1 China National Bamboo Research Center, Key Laboratory of Resources and Utilization of Bamboo of State Forestry Administration, Hangzhou 310012, China; [email protected] (X.Z.); [email protected] (X.G.); [email protected] (X.D.); [email protected] (F.B.); [email protected] (C.Y.) 2 College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; [email protected] (J.Y.); wfl[email protected] (W.L.) * Correspondence: [email protected]; Tel.: +86-0571-88860734 Received: 25 January 2019; Accepted: 25 February 2019; Published: 1 March 2019 Abstract: Integrated bamboo-chicken farming (BCF) systems are a traditional agroforestry pattern with large economic benefits in subtropical China. However, little is known regarding the effect of this integration on the bamboo leaf-associated microbiome, which can be very important for disease control and nutrient turnover. In the present study, we compared the leaf-associated bacterial and fungal communities of moso bamboo (Phyllostachys edulis) in a BCF system and an adjacent moso bamboo forest (MBF). The results showed that Cyanobacteria and Ascomycota were the predominant microbial phyla associated with bamboo leaves. Chicken farming under the bamboo forest significantly increased the bacterial and fungal alpha diversity (observed operational taxonomic units (OTUs) and Simpson’s index) associated with bamboo leaves. Principal components analysis (PCoA) further confirmed the shifts in the bacterial and fungal communities caused by chicken farming.
    [Show full text]
  • Taxonomy and Diversity of the Sponge Fauna from Walters Shoal, a Shallow Seamount in the Western Indian Ocean Region
    Taxonomy and diversity of the sponge fauna from Walters Shoal, a shallow seamount in the Western Indian Ocean region By Robyn Pauline Payne A thesis submitted in partial fulfilment of the requirements for the degree of Magister Scientiae in the Department of Biodiversity and Conservation Biology, University of the Western Cape. Supervisors: Dr Toufiek Samaai Prof. Mark J. Gibbons Dr Wayne K. Florence The financial assistance of the National Research Foundation (NRF) towards this research is hereby acknowledged. Opinions expressed and conclusions arrived at, are those of the author and are not necessarily to be attributed to the NRF. December 2015 Taxonomy and diversity of the sponge fauna from Walters Shoal, a shallow seamount in the Western Indian Ocean region Robyn Pauline Payne Keywords Indian Ocean Seamount Walters Shoal Sponges Taxonomy Systematics Diversity Biogeography ii Abstract Taxonomy and diversity of the sponge fauna from Walters Shoal, a shallow seamount in the Western Indian Ocean region R. P. Payne MSc Thesis, Department of Biodiversity and Conservation Biology, University of the Western Cape. Seamounts are poorly understood ubiquitous undersea features, with less than 4% sampled for scientific purposes globally. Consequently, the fauna associated with seamounts in the Indian Ocean remains largely unknown, with less than 300 species recorded. One such feature within this region is Walters Shoal, a shallow seamount located on the South Madagascar Ridge, which is situated approximately 400 nautical miles south of Madagascar and 600 nautical miles east of South Africa. Even though it penetrates the euphotic zone (summit is 15 m below the sea surface) and is protected by the Southern Indian Ocean Deep- Sea Fishers Association, there is a paucity of biodiversity and oceanographic data.
    [Show full text]
  • Review of Oxepine-Pyrimidinone-Ketopiperazine Type Nonribosomal Peptides
    H OH metabolites OH Review Review of Oxepine-Pyrimidinone-Ketopiperazine Type Nonribosomal Peptides Yaojie Guo , Jens C. Frisvad and Thomas O. Larsen * Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, DK-2800 Kgs. Lyngby, Denmark; [email protected] (Y.G.); [email protected] (J.C.F.) * Correspondence: [email protected]; Tel.: +45-4525-2632 Received: 12 May 2020; Accepted: 8 June 2020; Published: 15 June 2020 Abstract: Recently, a rare class of nonribosomal peptides (NRPs) bearing a unique Oxepine-Pyrimidinone-Ketopiperazine (OPK) scaffold has been exclusively isolated from fungal sources. Based on the number of rings and conjugation systems on the backbone, it can be further categorized into three types A, B, and C. These compounds have been applied to various bioassays, and some have exhibited promising bioactivities like antifungal activity against phytopathogenic fungi and transcriptional activation on liver X receptor α. This review summarizes all the research related to natural OPK NRPs, including their biological sources, chemical structures, bioassays, as well as proposed biosynthetic mechanisms from 1988 to March 2020. The taxonomy of the fungal sources and chirality-related issues of these products are also discussed. Keywords: oxepine; nonribosomal peptides; bioactivity; biosynthesis; fungi; Aspergillus 1. Introduction Nonribosomal peptides (NRPs), mostly found in bacteria and fungi, are a class of peptidyl secondary metabolites biosynthesized by large modularly organized multienzyme complexes named nonribosomal peptide synthetases (NRPSs) [1]. These products are amongst the most structurally diverse secondary metabolites in nature; they exhibit a broad range of activities, which have been exploited in treatments such as the immunosuppressant cyclosporine A and the antibiotic daptomycin [2,3].
    [Show full text]
  • A Novel Bambusicolous Fungus from China, Arthrinium Chinense (Xylariales)
    DOI 10.12905/0380.sydowia72-2020-0077 Published online 4 February 2020 A novel bambusicolous fungus from China, Arthrinium chinense (Xylariales) Ning Jiang1, Ying Mei Liang2 & Cheng Ming Tian1,* 1 The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China 2 Museum of Beijing Forestry University, Beijing Forestry University, Beijing 100083, China * e-mail: [email protected] Jiang N., Liang Y.M. & Tian C.M. (2020) A novel bambusicolous fungus from China, Arthrinium chinense (Xylariales). – Sydowia 72: 77–83. Arthrinium (Apiosporaceae, Xylariales) is a globally distributed genus inhabiting various substrates, mostly plant tissues. Arthrinium specimens from bamboo culms were characterized on the basis of morphology and phylogenetic inference, which suggested that they are different from all known species. Hence, the new taxon, Arthrinium chinense, is proposed. Arthrinium chinense can be distinguished from the phylogenetically close species, A. paraphaeospermum and A. rasikravindrae, by much shorter conidia. Keywords: Apiosporaceae, bamboo, taxonomy, molecular phylogeny. – 1 new species. Bambusoideae (bamboo) is an important plant ium qinlingense C.M. Tian & N. Jiang, a species de- subfamily comprising multiple genera and species scribed from Fargesia qinlingensis in Qinling moun- widely distributed in China. Taxonomy of bamboo- tains (Shaanxi, China; Jiang et al. 2018), we also associated fungi has been studied worldwide in the collected dead and dying culms of Fargesia qinlin- past two decades, and more than 1000 fungal spe- gensis in order to find it. cies have been recorded (Hyde et al. 2002a, b). Re- cently, additional fungal species from bamboo were Materials and methods described in China on the basis of morphology and molecular evidence (Dai et al.
    [Show full text]
  • Genomic Analysis of Ant Domatia-Associated Melanized Fungi (Chaetothyriales, Ascomycota) Leandro Moreno, Veronika Mayer, Hermann Voglmayr, Rumsais Blatrix, J
    Genomic analysis of ant domatia-associated melanized fungi (Chaetothyriales, Ascomycota) Leandro Moreno, Veronika Mayer, Hermann Voglmayr, Rumsais Blatrix, J. Benjamin Stielow, Marcus Teixeira, Vania Vicente, Sybren de Hoog To cite this version: Leandro Moreno, Veronika Mayer, Hermann Voglmayr, Rumsais Blatrix, J. Benjamin Stielow, et al.. Genomic analysis of ant domatia-associated melanized fungi (Chaetothyriales, Ascomycota). Mycolog- ical Progress, Springer Verlag, 2019, 18 (4), pp.541-552. 10.1007/s11557-018-01467-x. hal-02316769 HAL Id: hal-02316769 https://hal.archives-ouvertes.fr/hal-02316769 Submitted on 15 Oct 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Mycological Progress (2019) 18:541–552 https://doi.org/10.1007/s11557-018-01467-x ORIGINAL ARTICLE Genomic analysis of ant domatia-associated melanized fungi (Chaetothyriales, Ascomycota) Leandro F. Moreno1,2,3 & Veronika Mayer4 & Hermann Voglmayr5 & Rumsaïs Blatrix6 & J. Benjamin Stielow3 & Marcus M. Teixeira7,8 & Vania A. Vicente3 & Sybren de Hoog1,2,3,9 Received: 20 August 2018 /Revised: 16 December 2018 /Accepted: 19 December 2018 # The Author(s) 2019 Abstract Several species of melanized (Bblack yeast-like^) fungi in the order Chaetothyriales live in symbiotic association with ants inhabiting plant cavities (domatia) or with ants that use carton-like material for the construction of nests and tunnels.
    [Show full text]
  • Fungal Planet Description Sheets: 716–784 By: P.W
    Fungal Planet description sheets: 716–784 By: P.W. Crous, M.J. Wingfield, T.I. Burgess, G.E.St.J. Hardy, J. Gené, J. Guarro, I.G. Baseia, D. García, L.F.P. Gusmão, C.M. Souza-Motta, R. Thangavel, S. Adamčík, A. Barili, C.W. Barnes, J.D.P. Bezerra, J.J. Bordallo, J.F. Cano-Lira, R.J.V. de Oliveira, E. Ercole, V. Hubka, I. Iturrieta-González, A. Kubátová, M.P. Martín, P.-A. Moreau, A. Morte, M.E. Ordoñez, A. Rodríguez, A.M. Stchigel, A. Vizzini, J. Abdollahzadeh, V.P. Abreu, K. Adamčíková, G.M.R. Albuquerque, A.V. Alexandrova, E. Álvarez Duarte, C. Armstrong-Cho, S. Banniza, R.N. Barbosa, J.-M. Bellanger, J.L. Bezerra, T.S. Cabral, M. Caboň, E. Caicedo, T. Cantillo, A.J. Carnegie, L.T. Carmo, R.F. Castañeda-Ruiz, C.R. Clement, A. Čmoková, L.B. Conceição, R.H.S.F. Cruz, U. Damm, B.D.B. da Silva, G.A. da Silva, R.M.F. da Silva, A.L.C.M. de A. Santiago, L.F. de Oliveira, C.A.F. de Souza, F. Déniel, B. Dima, G. Dong, J. Edwards, C.R. Félix, J. Fournier, T.B. Gibertoni, K. Hosaka, T. Iturriaga, M. Jadan, J.-L. Jany, Ž. Jurjević, M. Kolařík, I. Kušan, M.F. Landell, T.R. Leite Cordeiro, D.X. Lima, M. Loizides, S. Luo, A.R. Machado, H. Madrid, O.M.C. Magalhães, P. Marinho, N. Matočec, A. Mešić, A.N. Miller, O.V. Morozova, R.P. Neves, K. Nonaka, A. Nováková, N.H.
    [Show full text]
  • Proposal for a Revised Classification of the Demospongiae (Porifera) Christine Morrow1 and Paco Cárdenas2,3*
    Morrow and Cárdenas Frontiers in Zoology (2015) 12:7 DOI 10.1186/s12983-015-0099-8 DEBATE Open Access Proposal for a revised classification of the Demospongiae (Porifera) Christine Morrow1 and Paco Cárdenas2,3* Abstract Background: Demospongiae is the largest sponge class including 81% of all living sponges with nearly 7,000 species worldwide. Systema Porifera (2002) was the result of a large international collaboration to update the Demospongiae higher taxa classification, essentially based on morphological data. Since then, an increasing number of molecular phylogenetic studies have considerably shaken this taxonomic framework, with numerous polyphyletic groups revealed or confirmed and new clades discovered. And yet, despite a few taxonomical changes, the overall framework of the Systema Porifera classification still stands and is used as it is by the scientific community. This has led to a widening phylogeny/classification gap which creates biases and inconsistencies for the many end-users of this classification and ultimately impedes our understanding of today’s marine ecosystems and evolutionary processes. In an attempt to bridge this phylogeny/classification gap, we propose to officially revise the higher taxa Demospongiae classification. Discussion: We propose a revision of the Demospongiae higher taxa classification, essentially based on molecular data of the last ten years. We recommend the use of three subclasses: Verongimorpha, Keratosa and Heteroscleromorpha. We retain seven (Agelasida, Chondrosiida, Dendroceratida, Dictyoceratida, Haplosclerida, Poecilosclerida, Verongiida) of the 13 orders from Systema Porifera. We recommend the abandonment of five order names (Hadromerida, Halichondrida, Halisarcida, lithistids, Verticillitida) and resurrect or upgrade six order names (Axinellida, Merliida, Spongillida, Sphaerocladina, Suberitida, Tetractinellida). Finally, we create seven new orders (Bubarida, Desmacellida, Polymastiida, Scopalinida, Clionaida, Tethyida, Trachycladida).
    [Show full text]
  • University of California Santa Cruz Responding to An
    UNIVERSITY OF CALIFORNIA SANTA CRUZ RESPONDING TO AN EMERGENT PLANT PEST-PATHOGEN COMPLEX ACROSS SOCIAL-ECOLOGICAL SCALES A dissertation submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in ENVIRONMENTAL STUDIES with an emphasis in ECOLOGY AND EVOLUTIONARY BIOLOGY by Shannon Colleen Lynch December 2020 The Dissertation of Shannon Colleen Lynch is approved: Professor Gregory S. Gilbert, chair Professor Stacy M. Philpott Professor Andrew Szasz Professor Ingrid M. Parker Quentin Williams Acting Vice Provost and Dean of Graduate Studies Copyright © by Shannon Colleen Lynch 2020 TABLE OF CONTENTS List of Tables iv List of Figures vii Abstract x Dedication xiii Acknowledgements xiv Chapter 1 – Introduction 1 References 10 Chapter 2 – Host Evolutionary Relationships Explain 12 Tree Mortality Caused by a Generalist Pest– Pathogen Complex References 38 Chapter 3 – Microbiome Variation Across a 66 Phylogeographic Range of Tree Hosts Affected by an Emergent Pest–Pathogen Complex References 110 Chapter 4 – On Collaborative Governance: Building Consensus on 180 Priorities to Manage Invasive Species Through Collective Action References 243 iii LIST OF TABLES Chapter 2 Table I Insect vectors and corresponding fungal pathogens causing 47 Fusarium dieback on tree hosts in California, Israel, and South Africa. Table II Phylogenetic signal for each host type measured by D statistic. 48 Table SI Native range and infested distribution of tree and shrub FD- 49 ISHB host species. Chapter 3 Table I Study site attributes. 124 Table II Mean and median richness of microbiota in wood samples 128 collected from FD-ISHB host trees. Table III Fungal endophyte-Fusarium in vitro interaction outcomes.
    [Show full text]
  • Isolation of an Emerging Thermotolerant Medically Important Fungus, Lichtheimia Ramosa from Soil
    Vol. 14(6), pp. 237-241, June, 2020 DOI: 10.5897/AJMR2020.9358 Article Number: CC08E2B63961 ISSN: 1996-0808 Copyright ©2020 Author(s) retain the copyright of this article African Journal of Microbiology Research http://www.academicjournals.org/AJMR Full Length Research Paper Isolation of an emerging thermotolerant medically important Fungus, Lichtheimia ramosa from soil Imade Yolanda Nsa*, Rukayat Odunayo Kareem, Olubunmi Temitope Aina and Busayo Tosin Akinyemi Department of Microbiology, Faculty of Science, University of Lagos, Nigeria. Received 12 May, 2020; Accepted 8 June, 2020 Lichtheimia ramosa, a ubiquitous clinically important mould was isolated during a screen for thermotolerant fungi obtained from soil on a freshly burnt field in Ikorodu, Lagos State. In the laboratory, as expected it grew more luxuriantly on Potato Dextrose Agar than on size limiting Rose Bengal Agar. The isolate had mycelia with a white cottony appearance on both media. It was then identified based on morphological appearance, microscopy and by fungal Internal Transcribed Spacer ITS-5.8S rDNA sequencing. This might be the first report of molecular identification of L. ramosa isolate from soil in Lagos, as previously documented information could not be obtained. Key words: Soil, thermotolerant, Lichtheimia ramosa, Internal Transcribed Spacer (ITS). INTRODUCTION Zygomycetes of the order Mucorales are thermotolerant L. ramosa is abundant in soil, decaying plant debris and moulds that are ubiquitous in nature (Nagao et al., 2005). foodstuff and is one of the causative agents of The genus Lichtheimia (syn. Mycocladus, Absidia) mucormycosis in humans (Barret et al., 1999). belongs to the Zygomycete class and includes Mucormycosis is an opportunistic invasive infection saprotrophic microorganisms that can be isolated from caused by Lichtheimia, Mucor, and Rhizopus of the order decomposing soil and plant material (Alastruey-Izquierdo Mucorales.
    [Show full text]
  • Protistology Molecular Phylogeny of Aphelidium Arduennense Sp. Nov
    Protistology 13 (4), 192–198 (2019) Protistology Molecular phylogeny of Aphelidium arduennense sp. nov. – new representative of Aphelida (Opis- thosporidia) Victoria S. Tcvetkova1, Natalia A. Zorina1, Maria A. Mamkaeva1 and Sergey A. Karpov1,2 1 St. Petersburg State University, St. Petersburg 199034, Russia 2 Zoological Institute, Russian Academy of Sciences, St. Petersburg 199034, Russia | Submitted November 14, 2019 | Accepted December 2, 2019 | Summary Aphelids (Aphelida) are poorly known parasitoids of algae that have raised considerable interest because of their phylogenetic position as phagotrophic protists sister to Fungi. Together with Rozellida and Microsporidia they have been classified in the Opisthosporidia but seem to be more closely related to the Fungi rather than to the Cryptomycota and Microsporidia, the other members of the Opisthosporidia. Molecular environmental studies have revealed high genetic diversity within the aphelids, but only four genera have been described: Aphelidium, Amoeboaphelidium, Paraphelidium and Pseudaphelidium. Here, we describe the life cycle of a new species of Aphelidium, Aph. arduennense. Molecular phylogenetic analysis of its 18S rRNA indicates that Aph. arduennense is sister to Aph. tribonematis, and together with Aph. melosirae they form a monophyletic cluster. Within the aphelids, this cluster is distantly related to Paraphelidium and Amoeboaphelidium. Key words: aphelids, Holomycota, Opisthosporidia, Rozellosporidia, taxonomy Introduction Rozellosporidia (Cryptomycota) formed the super- phylum Opisthosporidia, the deepest branch Aphelids are a divergent group of intracellular of the Holomycota lineage, separated from the parasitoids of green, yellow-green and diatom algae Fungi (Karpov et al., 2014a; Letcher et al., 2015; (Gromov, 2000; Karpov et al., 2014a). The four 2017; Torruella et al., 2015). Several biological known genera have different ecological preferences: peculiarities of the aphelids do not conform the Aphelidium, Amoeboaphelidium and Paraphelidium classical definition of the Fungi.
    [Show full text]
  • Identification of Fungi Storage Types by Sequencing Method
    Zh. T. Abdrassulova et al /J. Pharm. Sci. & Res. Vol. 10(3), 2018, 689-692 Identification of Fungi Storage Types by Sequencing Method Zh. T. Abdrassulova, A. M. Rakhmetova*, G. A. Tussupbekova#, Al-Farabi Kazakh national university, 050040, Republic of Kazakhstan, Almaty, al-Farabi Ave., 71 *Karaganda State University named after the academician E.A. Buketov #A;-Farabi Kazakh National University, 050040, Republic of Kazakhstan, Almaty, al0Farabi Ave, 71 E. M. Imanova, Kazakh State Women’s Teacher Training University, 050000, Republic of Kazakhstan, Almaty, Aiteke bi Str., 99 M. S. Agadieva, R. N. Bissalyyeva Aktobe regional governmental university named after K.Zhubanov, 030000, Republic of Kazakhstan, Аktobe, A. Moldagulova avenue, 34 Abstract With the use of classical identification methods, which imply the identification of fungi by cultural and morphological features, they may not be reliable. With the development of modern molecular methods, it became possible to quickly and accurately determine the species and race of the fungus. The purpose of this work was to study bioecology and refine the species composition of fungi of the genus Aspergillus, Penicillium on seeds of cereal crops. The article presents materials of scientific research on morphological and molecular genetic peculiarities of storage fungi, affecting seeds of grain crops. Particular attention is paid to the fungi that develop in the stored grain. The seeds of cereals (Triticum aestivum L., Avena sativa L., Hordeum vulgare L., Zea mays L., Oryza sativa L., Sorghum vulgare Pers., Panicum miliaceum L.) were collected from the granaries of five districts (Talgar, Iliysky, Karasai, Zhambul, Panfilov) of the Almaty region. The pathogens of diseases of fungal etiology were found from the genera Penicillium, Aspergillus influencing the safety, quality and safety of the grain.
    [Show full text]
  • Protistology an International Journal Vol
    Protistology An International Journal Vol. 10, Number 2, 2016 ___________________________________________________________________________________ CONTENTS INTERNATIONAL SCIENTIFIC FORUM «PROTIST–2016» Yuri Mazei (Vice-Chairman) Welcome Address 2 Organizing Committee 3 Organizers and Sponsors 4 Abstracts 5 Author Index 94 Forum “PROTIST-2016” June 6–10, 2016 Moscow, Russia Website: http://onlinereg.ru/protist-2016 WELCOME ADDRESS Dear colleagues! Republic) entitled “Diplonemids – new kids on the block”. The third lecture will be given by Alexey The Forum “PROTIST–2016” aims at gathering Smirnov (Saint Petersburg State University, Russia): the researchers in all protistological fields, from “Phylogeny, diversity, and evolution of Amoebozoa: molecular biology to ecology, to stimulate cross- new findings and new problems”. Then Sandra disciplinary interactions and establish long-term Baldauf (Uppsala University, Sweden) will make a international scientific cooperation. The conference plenary presentation “The search for the eukaryote will cover a wide range of fundamental and applied root, now you see it now you don’t”, and the fifth topics in Protistology, with the major focus on plenary lecture “Protist-based methods for assessing evolution and phylogeny, taxonomy, systematics and marine water quality” will be made by Alan Warren DNA barcoding, genomics and molecular biology, (Natural History Museum, United Kingdom). cell biology, organismal biology, parasitology, diversity and biogeography, ecology of soil and There will be two symposia sponsored by ISoP: aquatic protists, bioindicators and palaeoecology. “Integrative co-evolution between mitochondria and their hosts” organized by Sergio A. Muñoz- The Forum is organized jointly by the International Gómez, Claudio H. Slamovits, and Andrew J. Society of Protistologists (ISoP), International Roger, and “Protists of Marine Sediments” orga- Society for Evolutionary Protistology (ISEP), nized by Jun Gong and Virginia Edgcomb.
    [Show full text]