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Composition and Genetic Diversity of the Nicotiana Tabacum Microbiome in Different Topographic Areas and Growth Periods
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 15 August 2018 doi:10.20944/preprints201808.0268.v1 Peer-reviewed version available at Int. J. Mol. Sci. 2018, 19, 3421; doi:10.3390/ijms19113421 Composition and Genetic Diversity of the Nicotiana tabacum Microbiome in Different Topographic Areas and Growth Periods Xiaolong Yuan 1, Xinmin Liu 1, Yongmei Du1, Guoming Shen1, Zhongfeng Zhang 1, Jinhai Li 2, Peng Zhang 1* 1.Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China, 266101. 2. China National Tobacco Corporation in Hubei province, Wuhan, China,430000. *Correspondence: Peng Zhang, [email protected]. Abstract: Fungal endophytes are the most ubiquitous plant symbionts on earth and are phylogenetically diverse. Studies on the fungal endophytes in tobacco have shown that they are widely distributed in the leaves, stems, and roots, and play important roles in the composition of the microbial ecosystem of tobacco. Herein, we analyzed and quantified the endophytic fungi of healthy tobacco leaves at the seedling (SS), resettling growth (RGS), fast-growing (FGS), and maturing (MS) stages at three altitudes [600 (L), 1000 (M), and 1300 m (H)]. We sequenced the ITS region of fungal samples to delimit operational taxonomic units (OTUs) and phylogenetically characterize the communities. The result showed the number of clustering OTUs at SS, RGS, FGS and MS were greater than 170, 245, 140, and 164, respectively. At the phylum level, species in Ascomycota and Basidiomycota had absolute predominance, representing 97.8% and 2.0 % of the total number of species. We also found the number of unique fungi at the RGS and FGS stages were higher than those in the other two stages. -
Australia Biodiversity of Biodiversity Taxonomy and and Taxonomy Plant Pathogenic Fungi Fungi Plant Pathogenic
Taxonomy and biodiversity of plant pathogenic fungi from Australia Yu Pei Tan 2019 Tan Pei Yu Australia and biodiversity of plant pathogenic fungi from Taxonomy Taxonomy and biodiversity of plant pathogenic fungi from Australia Australia Bipolaris Botryosphaeriaceae Yu Pei Tan Curvularia Diaporthe Taxonomy and biodiversity of plant pathogenic fungi from Australia Yu Pei Tan Yu Pei Tan Taxonomy and biodiversity of plant pathogenic fungi from Australia PhD thesis, Utrecht University, Utrecht, The Netherlands (2019) ISBN: 978-90-393-7126-8 Cover and invitation design: Ms Manon Verweij and Ms Yu Pei Tan Layout and design: Ms Manon Verweij Printing: Gildeprint The research described in this thesis was conducted at the Department of Agriculture and Fisheries, Ecosciences Precinct, 41 Boggo Road, Dutton Park, Queensland, 4102, Australia. Copyright © 2019 by Yu Pei Tan ([email protected]) All rights reserved. No parts of this thesis may be reproduced, stored in a retrieval system or transmitted in any other forms by any means, without the permission of the author, or when appropriate of the publisher of the represented published articles. Front and back cover: Spatial records of Bipolaris, Curvularia, Diaporthe and Botryosphaeriaceae across the continent of Australia, sourced from the Atlas of Living Australia (http://www.ala. org.au). Accessed 12 March 2019. Taxonomy and biodiversity of plant pathogenic fungi from Australia Taxonomie en biodiversiteit van plantpathogene schimmels van Australië (met een samenvatting in het Nederlands) Proefschrift ter verkrijging van de graad van doctor aan de Universiteit Utrecht op gezag van de rector magnificus, prof. dr. H.R.B.M. Kummeling, ingevolge het besluit van het college voor promoties in het openbaar te verdedigen op donderdag 9 mei 2019 des ochtends te 10.30 uur door Yu Pei Tan geboren op 16 december 1980 te Singapore, Singapore Promotor: Prof. -
Genera of Phytopathogenic Fungi: GOPHY 1
Accepted Manuscript Genera of phytopathogenic fungi: GOPHY 1 Y. Marin-Felix, J.Z. Groenewald, L. Cai, Q. Chen, S. Marincowitz, I. Barnes, K. Bensch, U. Braun, E. Camporesi, U. Damm, Z.W. de Beer, A. Dissanayake, J. Edwards, A. Giraldo, M. Hernández-Restrepo, K.D. Hyde, R.S. Jayawardena, L. Lombard, J. Luangsa-ard, A.R. McTaggart, A.Y. Rossman, M. Sandoval-Denis, M. Shen, R.G. Shivas, Y.P. Tan, E.J. van der Linde, M.J. Wingfield, A.R. Wood, J.Q. Zhang, Y. Zhang, P.W. Crous PII: S0166-0616(17)30020-9 DOI: 10.1016/j.simyco.2017.04.002 Reference: SIMYCO 47 To appear in: Studies in Mycology Please cite this article as: Marin-Felix Y, Groenewald JZ, Cai L, Chen Q, Marincowitz S, Barnes I, Bensch K, Braun U, Camporesi E, Damm U, de Beer ZW, Dissanayake A, Edwards J, Giraldo A, Hernández-Restrepo M, Hyde KD, Jayawardena RS, Lombard L, Luangsa-ard J, McTaggart AR, Rossman AY, Sandoval-Denis M, Shen M, Shivas RG, Tan YP, van der Linde EJ, Wingfield MJ, Wood AR, Zhang JQ, Zhang Y, Crous PW, Genera of phytopathogenic fungi: GOPHY 1, Studies in Mycology (2017), doi: 10.1016/j.simyco.2017.04.002. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. -
Genome Sequencing and in Silico Characterisation of Cladosporium Sphaerospermum
GENOME SEQUENCING AND IN SILICO CHARACTERISATION OF CLADOSPORIUM SPHAEROSPERMUM YEW SU MEI Malaya of FACULTY OF MEDICINE UNIVERSITY OF MALAYA UniversityKUALA LUMPUR 2017 GENOME SEQUENCING AND IN SILICO CHARACTERISATION OF CLADOSPORIUM SPHAEROSPERMUM YEW SU MEI Malaya of THESIS SUBMITTED IN FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY FACULTY OF MEDICINE UNIVERSITY OF MALAYA KUALA LUMPUR University 2017 UNIVERSITY OF MALAYA ORIGINAL LITERARY WORK DECLARATION Name of Candidate: YEW SU MEI Registration/Matric No: MHA110037 Name of Degree: Doctor of Philosophy Title of Thesis: Genome Sequencing and in silico Characterisation of Cladosporium sphaerospermum Field of Study: MEDICAL MICROBIOLOGY I do solemnly and sincerely declare that: (1) I am the sole author/writer of this Work; (2) This Work is original; (3) Any use of any work in which copyright exists was done by way of fair dealing and for permitted purposes and any excerpt or extract from, or reference to or reproduction of any copyright work has been disclosed expressly and sufficiently and the title ofMalaya the Work and its authorship have been acknowledged in this Work; (4) I do not have any actual knowledge nor do I ought reasonably to know that the making of this work constitutesof an infringement of any copyright work; (5) I hereby assign all and every rights in the copyright to this Work to the University of Malaya (“UM”), who henceforth shall be owner of the copyright in this Work and that any reproduction or use in any form or by any means whatsoever is prohibited without the written consent of UM having been first had and obtained; (6) I am fully aware that if in the course of making this Work I have infringed any copyright whether intentionally or otherwise, I may be subject to legal action or any other action as may be determined by UM. -
New Species of the Genus Curvularia: C
pathogens Article New Species of the Genus Curvularia: C. tamilnaduensis and C. coimbatorensis from Fungal Keratitis Cases in South India Noémi Kiss 1,Mónika Homa 1,2, Palanisamy Manikandan 3,4 , Arumugam Mythili 5, Krisztina Krizsán 6, Rajaraman Revathi 7,Mónika Varga 1, Tamás Papp 1,2 , Csaba Vágvölgyi 1 , László Kredics 1,* and Sándor Kocsubé 1,* 1 Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; [email protected] (N.K.); [email protected] (M.H.); [email protected] (M.V.); [email protected] (T.P.); [email protected] (C.V.) 2 MTA-SZTE “Lendület” Fungal Pathogenicity Mechanisms Research Group, 6726 Szeged, Hungary 3 Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia; [email protected] 4 Greenlink Analytical and Research Laboratory India Private Ltd., Coimbatore, Tamil Nadu 641014, India 5 Department of Microbiology, Dr. G.R. Damodaran College of Science, Coimbatore, Tamil Nadu 641014, India; [email protected] 6 Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary; [email protected] 7 Aravind Eye Hospital and Postgraduate Institute of Ophthalmology, Coimbatore, Tamil Nadu 641014, India; [email protected] * Correspondence: [email protected]; (L.K.); [email protected]; (S.K.) Received: 6 December 2019; Accepted: 18 December 2019; Published: 20 December 2019 Abstract: Members of the genus Curvularia are melanin-producing dematiaceous fungi of increasing clinical importance as causal agents of both local and invasive infections. This study contributes to the taxonomical and clinical knowledge of this genus by describing two new Curvularia species based on isolates from corneal scrapings of South Indian fungal keratitis patients. -
A Review of the Ubiquity of Ascomycetes Filamentous Fungi in Relation to Their Economic and Medical Importance
Advances in Microbiology, 2016, 6, 1140-1158 http://www.scirp.org/journal/aim ISSN Online: 2165-3410 ISSN Print: 2165-3402 A Review of the Ubiquity of Ascomycetes Filamentous Fungi in Relation to Their Economic and Medical Importance Mary Augustina Egbuta1,2*, Mulunda Mwanza3, Olubukola Oluranti Babalola1 1Department of Biological Sciences, Faculty of Agriculture, Science and Technology, North-West University, Mafikeng Campus, Mmabatho, South Africa 2Southern Cross Plant Science, Southern Cross University, Lismore Campus, Lismore, Australia 3Department of Animal Health, Faculty of Agriculture, Science and Technology, North-West University, Mafikeng Campus, Mmabatho, South Africa How to cite this paper: Egbuta, M.A., Abstract Mwanza, M. and Babalola, O.O. (2016) A Review of the Ubiquity of Ascomycetes Fila- Filamentous fungi are found in different habitats in the environment including, air, mentous Fungi in Relation to Their Econo- water and soil. This group of fungi contains organisms from different classes under mic and Medical Importance. Advances in the sub-phylum Pezizomycotina. They occur in mixtures such that you find many Microbiology, 6, 1140-1158. http://dx.doi.org/10.4236/aim.2016.614103 genera of filamentous fungi dominating a particular habitat or substrate. The wide distribution of filamentous fungi has resulted in it being used for different purposes. Received: October 31, 2016 This review aims to analyse the different genera of fungi species referred to as fila- Accepted: December 25, 2016 mentous fungi and their relevance economically and medically. Published: December 28, 2016 Copyright © 2016 by authors and Keywords Scientific Research Publishing Inc. Filamentous, Fungi, Air, Soil, Water, Distribution This work is licensed under the Creative Commons Attribution International License (CC BY 4.0). -
IV Simpósio De Biociências E Microbiologia 30 De Novembro E 01
IV Simpósio de Biociências e Microbiologia 30 de novembro e 01 e 02 de dezembro de 2020 Universidade Estadual Paulista “Júlio de Mesquita Filho” Câmpus de São José do Rio Preto IBILCE – Instituto de Biociências, Letras e Ciências Exatas ANAIS APOIO: Programa de Pós-graduação em Biociências Programa de Pós-graduação em Microbiologia IV Simpósio de Biociências e Microbiologia 30 de novembro e 01 e 02 de dezembro de 2020 Universidade Estadual Paulista “Júlio de Mesquita Filho” Câmpus de São José do Rio Preto IBILCE – Instituto de Biociências, Letras e Ciências Exatas Programa de Pós-Graduação em Biociências Programa de Pós-Graduação em Microbiologia ANAIS São José do Rio Preto - SP UNESP/IBILCE 2021 Diretor Prof. Dr. Julio Cesar Torres Vice diretor Prof. Dr. Fernando Barbosa Noll Programa de Pós-Graduação em Biociências Coordenação: Profa. Dra. Rejane Maira Góes. Vice-coordenação: Profa. Dra. Mary Massumi Itoyama Discentes: Jaqueline Alves Vieira, Flaviene Felix Torres Programa de Pós-Graduação em Microbiologia Coordenação: Profa. Dra. Eleni Gomes. Vice-coordenação: Prof. Dr. Gustavo Orlando Bonilla Rodriguez. Discentes: Lara Maria Biancheti, Graciele Ribeiro de Moraes. Comissão organizadora do evento: Discentes responsáveis Alana Della Torre da Silva, Artemiza da Silva Miranda, Bruna Emilia Roman, Carolina Gismene, Cíntia Lionela Ambrósio de Menezes, Érike Jhonnathan Pereira, Flaviene Felix Torres, Giovanna Tavares Jeronymo, Kelly Cristine Borsatto, Lara Maria Biancheti, Letícia Monteiro Bianco, Maicon Henrique Caetano, Mohammed Anas Zaiter, Olavo Henrique Petrucci Della Torre, Pâmela Jóyce Previdelli da Conceição, Rafaela dos Santos Peinado, Renan Moura Martins, Tamara de Carvalho, Victoria Simões Bernardo, Vinicius Lucatelle da Silva. Docente responsável: Profa. Dra. -
Phenotypic and Molecular Characterization of Clinical Isolates of Bipolaris, Curvularia, Exserohilum and Pithomyces
PHENOTYPIC AND MOLECULAR CHARACTERIZATION OF CLINICAL ISOLATES OF BIPOLARIS, CURVULARIA, EXSEROHILUM AND PITHOMYCES Keith Cassia Da Cunha Dipòsit Legal: T 1479-2014 ADVERTIMENT. L'accés als continguts d'aquesta tesi doctoral i la seva utilització ha de respectar els drets de la persona autora. Pot ser utilitzada per a consulta o estudi personal, així com en activitats o materials d'investigació i docència en els termes establerts a l'art. 32 del Text Refós de la Llei de Propietat Intel·lectual (RDL 1/1996). Per altres utilitzacions es requereix l'autorització prèvia i expressa de la persona autora. En qualsevol cas, en la utilització dels seus continguts caldrà indicar de forma clara el nom i cognoms de la persona autora i el títol de la tesi doctoral. No s'autoritza la seva reproducció o altres formes d'explotació efectuades amb finalitats de lucre ni la seva comunicació pública des d'un lloc aliè al servei TDX. Tampoc s'autoritza la presentació del seu contingut en una finestra o marc aliè a TDX (framing). Aquesta reserva de drets afecta tant als continguts de la tesi com als seus resums i índexs. ADVERTENCIA. El acceso a los contenidos de esta tesis doctoral y su utilización debe respetar los derechos de la persona autora. Puede ser utilizada para consulta o estudio personal, así como en actividades o materiales de investigación y docencia en los términos establecidos en el art. 32 del Texto Refundido de la Ley de Propiedad Intelectual (RDL 1/1996). Para otros usos se requiere la autorización previa y expresa de la persona autora. -
Banana Weevil Borer (Cosmopolites Sordidus): Plant Defense Responses
FACULTY OF AGRICULTURAL SCIENCES INSTITUTE OF CROP SCIENCE SECTION of CROP PHYSIOLOGY OF SPECIALTY CROPS (340F) UNIVERSITY OF HOHENHEIM SUPERVISOR: PROF. DR. JENS NORBERT WÜNSCHE (RIP)/ PROF. DR. CHRISTIAN ZÖRB Banana weevil borer (Cosmopolites sordidus): Plant defense responses and Control options Dissertation Submitted in fulfillment of the regulation to acquire the degree “Doktor der Agrarwissenschaften” (Dr.Sc.agr.in Agricultural Sciences) to the Faculty of Agricultural Sciences Presented by Elyeza Bakaze Born in Luwero, Uganda -2021- i This thesis was accepted as a doctoral dissertation in fulfilment of the requirement for the degree ‘Doktor der Agrarwissenschaften’ by the Faculty of Agricultural Sciences at University of Hohenheim on 14h October 2020. Date of Oral examination: 15th March 2021 Examination Committee Supervisor and Reviewer: Prof. Dr. Jens Wünsche (RIP)/ Prof. Dr. Christian Zörb Co-Reviewer: Prof. Dr. Jens Poetsch Additional examiner: Prof. Dr. Claus P.W. Zebitz Dean and Head of the committee: Prof. Dr. Martin Hasselmann ii ACKNOWLEDGMENT I extend my sincere gratitude to Prof. Dr. Jens Wünsche (RIP) for his relentless kindness and moral support, encouragement, and guidance that made this research possible. Also, I thank Prof. Dr. Christian Zörb, who accepted to take up the supervisory role of Prof. Dr. Jens Wünsche when his creator called him, thank you sir. I would like to thank Prof. Dr. Dr. C.P.W Zebitz for being my second supervisor and his knowledge about entomopathogenic fungi that greatly complimented my work substantially. And Prof. Dr. Jens Poetsch thank you for reviewing this thesis. This research would not have been possible without the help of Beloved Dzomeku and his team at CSIR-Crops Research Institute Kumasi. -
Novel Curvularia Species from Clinical Specimens
Persoonia 33, 2014: 48–60 www.ingentaconnect.com/content/nhn/pimj RESEARCH ARTICLE http://dx.doi.org/10.3767/003158514X683538 Novel Curvularia species from clinical specimens H. Madrid1, K.C. da Cunha2, J. Gené2, J. Dijksterhuis1, J. Cano2, D.A. Sutton3, J. Guarro2, P.W. Crous1,4 Key words Abstract The fungal genus Curvularia includes numerous plant pathogens and some emerging opportunistic pathogens of humans. In a previous study we used morphology and sequences of the nuclear ribosomal internal Bipolaris transcribed spacer region (ITS) and the glyceraldehyde-3-phosphate dehydrogenase (gpd) gene to identify spe- Curvularia cies within a set of 99 clinical Curvularia isolates from the USA. Seventy-two isolates could be identified while the gpd remaining 27 isolates belonged in three unclassified clades that were tentatively labelled Curvularia sp. I, II and ITS III. In the present study, we further assess the taxonomic placement of these isolates using sequences of ITS, LSU gpd, the large subunit rDNA, and the second largest subunit of RNA polymerase II. DNA sequence comparisons phylogeny with a set of 87 isolates representing 33 Curvularia spp. and members of the closely-related genera Bipolaris and RPB2 Exserohilum revealed that Curvularia sp. I, II and III represent novel lineages in Curvularia. These lineages are systematics morphologically different from the currently accepted species. In the phylogenetic tree, Curvularia sp. I and sp. III were each split into two distinct lineages. Morphology and phylogeny supported the proposal of five new species, to be named C. americana, C. chlamydospora, C. hominis, C. muehlenbeckiae and C. pseudolunata. The concaten- ated 4-locus phylogeny revealed the existence of six clades in Curvularia, which are associated with particular morphological features. -
A Five-Year Survey of Dematiaceous Fungi in a Tropical Hospital Reveals Potential Opportunistic Species
A Five-Year Survey of Dematiaceous Fungi in a Tropical Hospital Reveals Potential Opportunistic Species Su Mei Yew1, Chai Ling Chan1, Kok Wei Lee2, Shiang Ling Na1, Ruixin Tan1, Chee-Choong Hoh2, Wai-Yan Yee2, Yun Fong Ngeow1, Kee Peng Ng1* 1 Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia, 2 Codon Genomics SB, Jalan Bandar Lapan Belas, Pusat Bandar Puchong, Selangor Darul Ehsan, Malaysia Abstract Dematiaceous fungi (black fungi) are a heterogeneous group of fungi present in diverse environments worldwide. Many species in this group are known to cause allergic reactions and potentially fatal diseases in humans and animals, especially in tropical and subtropical climates. This study represents the first survey of dematiaceous fungi in Malaysia and provides observations on their diversity as well as in vitro response to antifungal drugs. Seventy-five strains isolated from various clinical specimens were identified by morphology as well as an internal transcribed spacer (ITS)-based phylogenetic analysis. The combined molecular and conventional approach enabled the identification of three classes of the Ascomycota phylum and 16 genera, the most common being Cladosporium, Cochliobolus and Neoscytalidium. Several of the species identified have not been associated before with human infections. Among 8 antifungal agents tested, the azoles posaconazole (96%), voriconazole (90.7%), ketoconazole (86.7%) and itraconazole (85.3%) showed in vitro activity (MIC #1 mg/mL) to the largest number of strains, followed by anidulafungin (89.3%), caspofungin (74.7%) and amphotericin B (70.7%). Fluconazole appeared to be the least effective with only 10.7% of isolates showing in vitro susceptibility. -
The Magnitude and Diversity of Infectious Diseases
Chapter 1 The Magnitude and Diversity of Infectious Diseases “All interest in disease and death is only another expression of interest in life.” Thomas Mann THE IMPORTANCE OF INFECTIOUS DISEASES IN TERMS OF HUMAN MORTALITY According to the U.S. Census Bureau, on July 20, 2011, the USA population was 311 806 379, and the world population was 6 950 195 831 [2]. The U.S. Central Intelligence agency estimates that the USA crude death rate is 8.36 per 1000 and the world crude death rate is 8.12 per 1000 [3]. This translates to 2.6 million people dying in 2011 in the USA, and 56.4 million people dying worldwide. These numbers, calculated from authoritative sources, correlate surprisingly well with the widely used rule of thumb that 1% of the human population dies each year. How many of the world’s 56.4 million deaths can be attributed to infectious diseases? According to World Health Organization, in 1996, when the global death toll was 52 million, “Infectious diseases remain the world’s leading cause of death, accounting for at least 17 million (about 33%) of the 52 million people who die each year” [4]. Of course, only a small fraction of infections result in death, and it is impossible to determine the total incidence of infec- tious diseases that occur each year, for all organisms combined. Still, it is useful to consider some of the damage inflicted by just a few of the organisms that infect humans. Malaria infects 500 million people. About 2 million people die each year from malaria [4].