DOCSLIB.ORG

Ph.D Thesis Muhammad Rafiq Microbiology 2016.Pdf

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Ph.D Thesis Muhammad Rafiq Microbiology 2016.Pdf Culture Dependent and Metagenomic study of Microbial Diversity of Glaciers in HKKH (Hindu Kush, Karakoram and Himalaya) mountain range By Muhammad Rafiq Department of Microbiology Quaid-i-Azam University Islamabad, Pakistan 2016 Culture Dependent and Metagenomic study of Microbial Diversity of Glaciers in HKKH (Hindu Kush, Karakoram and Himalaya) mountain range A thesis Submitted in the Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY IN MICROBIOLOGY By Muhammad Rafiq Department of Microbiology Quaid-i-Azam University Islamabad, Pakistan 2016 DECLARATION The material contained in this thesis is my original work and I have not presented any part of this thesis/work elsewhere for any other degree. Muhammad Rafiq DEDICATED TO My Ammi and Abbu CERTIFICATE This thesis, submitted by Mr. Muhammad Rafiq is accepted in its present form by the Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad as satisfying the thesis requirement for the degree of Doctor of Philosophy (PhD) in Microbiology. Internal Examiner: _______________________________ (Dr. Fariha Hasan) External Examiner: _____________________________ External Examiner: ______________________________ Chairperson: ____________________________________ Dated: CONTENTS S. No. Title Page No. 1. List of Abbreviations i 2. List of Tables ii 3. List of Figures iv 4. Acknowledgements vi 5. Summary viii 6. Chapter 1: Introduction 1 7. Chapter 2: Review of Literature 20 8. Chapter 3: Bacterial Diversity 89 9. Chapter 4: Fungal Diversity 182 10. Chapter 5: Metagenomic study 289 a. Abstract 289 b. Introduction 290 c. Methodology 297 d. Results 301 e. Discussion 323 f. References 335 11. Conclusions 345 12. Appendices 347 List of Abbreviations ATP Adenosine-5’-triphosphate A Adenosine BLAST Basic Local Alignment Search Tool BLASTN BLAST search using a nucleotide query BLASTX BLAST search using a translated nucleotide query bp Base pairs C Cytosine °C Degree celsius DGGE Denaturing Gradient Gel Electrophoresis DNA Deoxyribonucleic acid dNTP Deoxynucleoside triphosphate e.g. Exempli gratia, for example et al. et alii/alia, and others Fe Iron Fig. Figure G Guanine i.e. id est, that is Ion Torrent PGM Ion Torrent Personal Genome Machine KEGG Kyoto Encyclopedia of Genes and Genomes KO KEGG Orthology MEGAN 4 MEtaGenome ANalyzer MG-RAST Metagenomic Rapid Annotations using Subsystems Technology M5NR Database M5 non-redundant database NaCl Sodium Chloride NCBI National Center for Biotechnology Information NGS Next Generation Sequencing OTU Operational Taxonomic Unit PCA Principal Component Analysis PCR Polymerase Chain Reaction pH Power of Hydrogen RDP Ribosomal Database Project rRNA Ribosomal ribonucleic acid SOLiD Sequencing by Oligonucleotide Ligation and Detection SSU RNA small subunit RNA T Thymine i List of Tables No. Title Page No. 1 List of psychrophilic microbes with their habitats 3 3.1.1 Concentration of different metals in samples 98 3.1.2 Concentration of amino acids in samples 99 3.1.3 Cation and Anion concentrations in samples 99 3.1.4 Total viable cells (CFU/ml) and physiochemical conditions of the glacial 100 samples 3.1.5 16S rDNA sequence based identification and characteristics of selected 101 isolates from the Tirich Mir glacier 3.1.6 Salt tolerance profile of the study isolates 104 3.1.7 Temperature profile of all isolates from Tirich Mir glaciers 106 3.1.8 Effect of temperature on pigment production of the isolates from Tirich 107 Mir glacier 3.1.9 Antibacterial and antifungal activity of potent bacterial isolates of Tirich 114 Mir Glacier 3.2.1 Morphological and microscopic charactarization of study isolates 138 3.2.2 Comparative study of bacteria isolates resistant to different antibiotics 144 3.2.3 Antibiotic resistance and production of antimicrobial compounds in 146 Gram negative bacteria isolated from Siachen Glacier 3.2.4 Antibiotic resistance, mutliple antibiotic resistant (MAR) index and 148 antimicrobial activity of Gram positive bacterial isolates 3.2.5 Tolerance of Gram negative and Gram positive bacteria to varying 151 concentrations of metal ions 4.1.1 Total viable count (CFU/mL or g) of fungal isolates at 15°C and 4°C 188 4.1.2 Colony morphology and microscopic characteristics of fungal isolates on 189 SDA 4.1.3 The resemblance directory of the fungal isolates with respective 194 homologous strains 4.1.4 Temperature, pH and the salt tolerance range of the fungal isolates 195 4.1.5 Antibacterial and antifungal activity of the fungal isolates by point 197 inoculation method 4.1.6 Production of various extracellular enzymes by fungal isolates 198 4.2.1 Total viable count (CFU/g or mL) of fungal isolates at 15°C and 4°C. 214 4.2.2 Similarity of the fungal isolates to their corresponding homologous 216 species and accession No. 4.2.3 Physiological analysis of the fungal isolates on different temperature, pH 217 and salt concentrations 4.2.4 Antimicrobial activity of the fungal isolates against the clinically 219 isolated bacterial and fungal strains 4.2.5 Screening of the fungal isolates for the extracellular enzymes production 220 (qualitatively). 4.3.1 Total viable count (CFU/mL or g) of fungal isolates at 15°C and 4°C 235 4.3.2 The resemblance index of strains with respective homology of the fungal 236 isolates 4.3.3 Growth responses of the fungal isolates to temperature, pH and the salt 238 4.3.4 Antibacterial and antifungal activity of the fungal isolates by point 239 inoculation 4.3.5 Production of various extracellular enzymes by fungal isolates 240 4.4.1 Total viable count (CFU/mL or g) of Tirich Mir fungal isolates at 15°C 252 and 4°C 4.4.2 Resemblance directory of the isolates with homologous strains 254 ii 4.4.3 Physiological parameters analysis of the fungal isolates on different 255 temperature, pH media and NaCl concentrations 4.4.4 Antibacterial and antifungal activity of the Tirich Mir fungal strains 257 against different bacterial and fungal strains 4.4.5 Production of various extracellular enzymes (qualitatively) by fungal 258 isolates 4.5.1 Morphological characteristics of Alternaria isolates 283 4.5.2 Percentage similarity of Alternaria isolates 285 4.5.3 Physiological analysis of the Alternaria isolates on different 286 temperature, pH and salt concentrations 4.5.4 Antibacterial and antifungal activity of the Alternaria isolates against 287 ATCC cultures 4.5.5 Production of various extracellular enzymes by Alternaria isolates 288 5.1 Sequence break down of the sequences obtained from Illumina for 303 functional categories. 5.2 Alpha diversity (Specie richness) of the study sample 306 iii List of Figure No. Page Title No. 1 Climate map of the world. 21 2 North and South poles of the world 22 3 Locations of Permafrost land across the world 23 4 Hindu Kush, Karakoram and Himalaya (HKKH) region, considered as the 25 ‘Third Pole’ of the world. 5 Structure of Valley glacier, demonstrate its different parts 27 6 Various physiological adaptations in psychrophilic Bacteria 33 7 Adaptation mechanisms in psychrophilic fungi to survive the harsh 34 environment of low temperature 3.1.1 Location of the sampling site (A), photograph of the glacier from where 94 samples were collected (B) 3.1.2 Distribution of phylogenetic groups (%) of the culturable isolates of the 109 study isolates from Tirich Mir glacier 3.1.3 Evolutionary relationships of taxa of Proteobacteria group. 110 3.1.4 Evolutionary relationships of taxa of Firmicutes group. 111 3.1.5 Evolutionary relationships of taxa of Actinobacteria group 112 3.1.6 Evolutionary relationships of taxa of Bacteroidetes group 112 3.1.7 Metal tolerance of Tirich Mir low- temperature isolates 115 3.1.8 Metal tolerance of Tirich Mir high- temperature isolates. 116 3.2.1 Molecular Phylogenetic analysis of HTS (15°C) by Maximum Likelihood 142 method 3.2.2 Molecular Phylogenetic analysis of low temperature isolates (LTS) by 143 Maximum Likelihood method 3.3.1 Molecular phylogenetic analysis of HTP6 (Alcaligenes faecalis) by 168 Maximum Likelihood method. 3.3.2 Antibiotic sensitivity profile of Alcaligenes faecalis HTP6, showing 169 variable zones of inhibition against different antibiotics. 3.3.3 Zone of inhibition (mm) of Alcaligenes faecalis HTP6 against tested 170 ATCC cultures and clinically isolated bacterial strains 3.3.4 Optimization of isolate for biomass production with different parameters, 171 these parameters 3.3.5 Optimization of parameters for the maximum production of antimicrobial 172 compounds 3.3.6 The effect of incubation time on the antimicrobial compounds activity 173 showed best inhibition at 96 hours of incubation 3.3.7 Zone of inhibition (mm) of crude extract of Alcaligenes faecalis HTP6 174 against the test bacterial and fungal strains. Best inhibition was found against A. fumigatus followed by S. aureus 3.3.8 The tolerance of Alcaligenes faecalis HTP6 to different metal ions(ppm) 174 showed best tolerance against Fe++.and least against Hg++ 3.3.9 FTIR analysis of the antimicrobial metabolite produced by Alcaligenes 175 faecalis HTP6 showing the presence of various functional groups 3.3.10 Multiple bands of the antimicrobial crude extract under (a) UV 365 nm 176 and (b) 254 nm. The arrows showed metabolites of different molecular weight, probably having antimicrobial activity. 4.1.1 Molecular Phylogenetic analysis of the Batura fungal isolates by 201 Maximum Likelihood method 4.2.1 Phylogenetic tree of the fungal isolates prepared by Maximum Likelihood 215 iv analysis of ITS1 and ITS4 sequences 4.3.1 Phylogenetic analysis of the Siachen isolates using Maximum Likely hood 237 4.4.1 Molecular Phylogenetic analysis by Maximum Likelihood method 253 4.5.1 Phylogenetic relationships of Alternaria taxa isolated from Tirich Mir 282 Glacier 5.1 Distribution of sequences of all 4 samples into functional categories 305 5.2 Rare faction curve showing specie richness of the study samples 306 5.3 Domain distribution of all the samples, all samples indicates the absolute 307 abundance of domain bacteria.
Load more

Recommended publications
  • Chilling Out: the Evolution and Diversification of Psychrophilic Algae with a Focus on Chlamydomonadales
    Polar Biol DOI 10.1007/s00300-016-2045-4 REVIEW Chilling out: the evolution and diversification of psychrophilic algae with a focus on Chlamydomonadales 1 1 1 Marina Cvetkovska • Norman P. A. Hu¨ner • David Roy Smith Received: 20 February 2016 / Revised: 20 July 2016 / Accepted: 10 October 2016 Ó Springer-Verlag Berlin Heidelberg 2016 Abstract The Earth is a cold place. Most of it exists at or Introduction below the freezing point of water. Although seemingly inhospitable, such extreme environments can harbour a Almost 80 % of the Earth’s biosphere is permanently variety of organisms, including psychrophiles, which can below 5 °C, including most of the oceans, the polar, and withstand intense cold and by definition cannot survive at alpine regions (Feller and Gerday 2003). These seemingly more moderate temperatures. Eukaryotic algae often inhospitable places are some of the least studied but most dominate and form the base of the food web in cold important ecosystems on the planet. They contain a huge environments. Consequently, they are ideal systems for diversity of prokaryotic and eukaryotic organisms, many of investigating the evolution, physiology, and biochemistry which are permanently adapted to the cold (psychrophiles) of photosynthesis under frigid conditions, which has (Margesin et al. 2007). The environmental conditions in implications for the origins of life, exobiology, and climate such habitats severely limit the spread of terrestrial plants, change. Here, we explore the evolution and diversification and therefore, primary production in perpetually cold of photosynthetic eukaryotes in permanently cold climates. environments is largely dependent on microbes. Eukaryotic We highlight the known diversity of psychrophilic algae algae and cyanobacteria are the dominant photosynthetic and the unique qualities that allow them to thrive in severe primary producers in cold habitats, thriving in a surprising ecosystems where life exists at the edge.
    [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]
  • A Metagenomic Approach to Understand Stand Failure in Bromus Tectorum
    Brigham Young University BYU ScholarsArchive Theses and Dissertations 2019-06-01 A Metagenomic Approach to Understand Stand Failure in Bromus tectorum Nathan Joseph Ricks Brigham Young University Follow this and additional works at: https://scholarsarchive.byu.edu/etd BYU ScholarsArchive Citation Ricks, Nathan Joseph, "A Metagenomic Approach to Understand Stand Failure in Bromus tectorum" (2019). Theses and Dissertations. 8549. https://scholarsarchive.byu.edu/etd/8549 This Thesis is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. A Metagenomic Approach to Understand Stand Failure in Bromus tectorum Nathan Joseph Ricks A thesis submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Master of Science Craig Coleman, Chair John Chaston Susan Meyer Department of Plant and Wildlife Sciences Brigham Young University Copyright © 2019 Nathan Joseph Ricks All Rights Reserved ABSTACT A Metagenomic Approach to Understand Stand Failure in Bromus tectorum Nathan Joseph Ricks Department of Plant and Wildlife Sciences, BYU Master of Science Bromus tectorum (cheatgrass) is an invasive annual grass that has colonized large portions of the Intermountain west. Cheatgrass stand failures have been observed throughout the invaded region, the cause of which may be related to the presence of several species of pathogenic fungi in the soil or surface litter. In this study, metagenomics was used to better understand and compare the fungal communities between sites that have and have not experienced stand failure.
    [Show full text]
  • Alternaria Alternata
    Published on INSPQ (https://www.inspq.qc.ca) Home > Compendium sur les moisissures > Fiches sur les moisissures > Alternaria alternata Alternaria alternata Alternaria alternata [1] [2] [3] [4] [5] [6] Introduction Laboratoire Métabolites Problèmes de santé Milieux Diagnostic Bibliographie Introduction Alternaria est un genre comportant approximativement 50 espèces {813, 816, 3318}. A. alternata est l’espèce la plus fréquemment rencontrée et un des mycètes les plus communs de la flore fongique aéroportée {989, 813}. Alternaria spp. est connu mondialement à la fois comme organisme phytopathogène courant et comme allergène aéroporté; plus particulièrement, l’A. alternata est reconnu comme l’espèce aéroallergène type, et, dans une majorité de cas, les problèmes de santé chez les humains et les animaux ont été associés à cette espèce. Taxonomie Règne Fungi Famille Pleosporaceae Phylum Ascomycota Genre Alternaria Classe Euascomycetes (ou Dothideomycetes) Espèce alternata Ordre Pleosporales Le Comoclathris permunda est la forme sexuée ou télémorphe del’Alternaria alternata et le Lewia sp. est la forme parfaite de plusieurs autres Alternaria sp. {3842}; d’autres genres télémorphes comprennent le Graphyllium et le Pleospora. Le genre comporte 44 espèces bien étudiées et dont l’identification est établie, mais il se peut qu’il en existe des centaines de plus; de fait, la banque de données universelle de l’Universal Protein Resource (UniProt) rapporte 95 espèces nommées parmi les 433 souches enregistrées {3318}. Certains taxonomistes suggèrent également que l’A. alternata est une espèce représentative d’un complexe d’espèces plutôt qu’une espèce unique, et ce groupe pourrait comprendre plusieurs espèces hétérogènes {816}. Écologie Les espèces d’Alternaria sont des mycètes dématiacés cosmopolites fréquemment isolés d’échantillons de plantes, de terre, de nourriture et d’air intérieur.
    [Show full text]
  • 157-21(5-20-00) Red Snow, Green Snow: It's Truly Spring When Those
    May 20, 2000 BROWSE BROWSE TABLE OF BY YEAR 2000 ISSUES CONTENTS 2000 Vol. 157 No. 21 p. 328 Red Snow, Green Snow It’s truly spring when those last white drifts go technicolor By SUSAN MILIUS Microbiologist Brian Duval hates this part, so let’s just deal with the snickering up front. Yes, he studies yellow snow. He also studies red, green, and orange snow and would love to examine other colors if he were lucky enough to dis- cover them. His palette comes from springtime blooms of algae that live only in deep, persistent snowfields. And yes, even a professional sometimes gets fooled. “I was outside a penguin rookery in Antarctica, and I thought I was collecting this greenish-yellow algae,” recalls the microbiologist now at the Massachusetts Department of Environmental Protection in Worcester. “I was saying, ‘Yeah, yeah, this looks like the stuff.’” When he checked his trea- sures under a microscope, however, he diagnosed the obvious nonalgal origin. “It gets embarrassing,” he admits. Despite the yellow-snow raillery, Duval and his colleagues stay with their studies of snow algae because of the marvels of the chilly lifestyle. Somehow the 350 species of snow algae thrive in the near- freezing, nutrient-poor, acidic, sun-blasted slush of melting snowfields around the world. The algae support a food web in the snow—a world of tiny, wormy, crawly beings as odd as Spielberg-movie creatures. Duval Algal life cycles combine the drama of salmon runs and No, it’s not a murder scene. A the nightmare of icebound explorers.
    [Show full text]
  • A Molecular and Morphological Reassessment of Diademaceae
    Hindawi Publishing Corporation e Scientific World Journal Volume 2014, Article ID 675348, 11 pages http://dx.doi.org/10.1155/2014/675348 Research Article A Molecular and Morphological Reassessment of Diademaceae Hiran A. Ariyawansa,1,2,3 Rungtiwa Phookamsak,2,3 Saowaluck Tibpromma,2,3 Ji-Chuan Kang,1 and Kevin D. Hyde2,3 1 The Engineering and Research Center for Southwest Bio-Pharmaceutical Resources of National Education Ministry of China, Guizhou University, Guiyang, Guizhou 550025, China 2 School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand 3 Institute of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand Correspondence should be addressed to Ji-Chuan Kang; [email protected] and Kevin D. Hyde; [email protected] Received 6 August 2013; Accepted 8 October 2013; Published 12 January 2014 Academic Editors: R. Jeewon and S. J. Suh Copyright © 2014 Hiran A. Ariyawansa et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. We revisit the family Diademaceae based on available sequence data and morphology. Diademaceae is characterized by ascomata opening with a flat circular lid and fissitunicate, short orbicular frequently cylindrical, pedicellate asci. Ascospores are frequently circular in section but narrowing to one end with three or more transverse septa, without longitudinal septa, and mostly with a thick sheath. In recent treatments Clathrospora, Comoclathris, Diadema, Diademosa,andGraphyllium were placed in the family. Following molecular and morphological study, Clathrospora, Comoclathris,andDiademosa, are excluded from the family and referred to Pleosporaceae.
    [Show full text]
  • Proposed Generic Names for Dothideomycetes
    Naming and outline of Dothideomycetes–2014 Nalin N. Wijayawardene1, 2, Pedro W. Crous3, Paul M. Kirk4, David L. Hawksworth4, 5, 6, Dongqin Dai1, 2, Eric Boehm7, Saranyaphat Boonmee1, 2, Uwe Braun8, Putarak Chomnunti1, 2, , Melvina J. D'souza1, 2, Paul Diederich9, Asha Dissanayake1, 2, 10, Mingkhuan Doilom1, 2, Francesco Doveri11, Singang Hongsanan1, 2, E.B. Gareth Jones12, 13, Johannes Z. Groenewald3, Ruvishika Jayawardena1, 2, 10, James D. Lawrey14, Yan Mei Li15, 16, Yong Xiang Liu17, Robert Lücking18, Hugo Madrid3, Dimuthu S. Manamgoda1, 2, Jutamart Monkai1, 2, Lucia Muggia19, 20, Matthew P. Nelsen18, 21, Ka-Lai Pang22, Rungtiwa Phookamsak1, 2, Indunil Senanayake1, 2, Carol A. Shearer23, Satinee Suetrong24, Kazuaki Tanaka25, Kasun M. Thambugala1, 2, 17, Saowanee Wikee1, 2, Hai-Xia Wu15, 16, Ying Zhang26, Begoña Aguirre-Hudson5, Siti A. Alias27, André Aptroot28, Ali H. Bahkali29, Jose L. Bezerra30, Jayarama D. Bhat1, 2, 31, Ekachai Chukeatirote1, 2, Cécile Gueidan5, Kazuyuki Hirayama25, G. Sybren De Hoog3, Ji Chuan Kang32, Kerry Knudsen33, Wen Jing Li1, 2, Xinghong Li10, ZouYi Liu17, Ausana Mapook1, 2, Eric H.C. McKenzie34, Andrew N. Miller35, Peter E. Mortimer36, 37, Dhanushka Nadeeshan1, 2, Alan J.L. Phillips38, Huzefa A. Raja39, Christian Scheuer19, Felix Schumm40, Joanne E. Taylor41, Qing Tian1, 2, Saowaluck Tibpromma1, 2, Yong Wang42, Jianchu Xu3, 4, Jiye Yan10, Supalak Yacharoen1, 2, Min Zhang15, 16, Joyce Woudenberg3 and K. D. Hyde1, 2, 37, 38 1Institute of Excellence in Fungal Research and 2School of Science, Mae Fah Luang University,
    [Show full text]
  • Multi-Locus Phylogeny of Pleosporales: a Taxonomic, Ecological and Evolutionary Re-Evaluation
    available online at www.studiesinmycology.org StudieS in Mycology 64: 85–102. 2009. doi:10.3114/sim.2009.64.04 Multi-locus phylogeny of Pleosporales: a taxonomic, ecological and evolutionary re-evaluation Y. Zhang1, C.L. Schoch2, J. Fournier3, P.W. Crous4, J. de Gruyter4, 5, J.H.C. Woudenberg4, K. Hirayama6, K. Tanaka6, S.B. Pointing1, J.W. Spatafora7 and K.D. Hyde8, 9* 1Division of Microbiology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P.R. China; 2National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, MSC 6510, Bethesda, Maryland 20892-6510, U.S.A.; 3Las Muros, Rimont, Ariège, F 09420, France; 4CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD, Utrecht, The Netherlands; 5Plant Protection Service, P.O. Box 9102, 6700 HC Wageningen, The Netherlands; 6Faculty of Agriculture & Life Sciences, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan; 7Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 93133, U.S.A.; 8School of Science, Mae Fah Luang University, Tasud, Muang, Chiang Rai 57100, Thailand; 9International Fungal Research & Development Centre, The Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, Yunnan, P.R. China 650034 *Correspondence: Kevin D. Hyde, [email protected] Abstract: Five loci, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, are used for analysing 129 pleosporalean taxa representing 59 genera and 15 families in the current classification ofPleosporales . The suborder Pleosporineae is emended to include four families, viz. Didymellaceae, Leptosphaeriaceae, Phaeosphaeriaceae and Pleosporaceae. In addition, two new families are introduced, i.e.
    [Show full text]
  • Study on Snowmelt and Algal Growth in the Antarctic Peninsula Using
    RESEARCH COMMUNICATIONS Study on snowmelt and algal growth during February 2020 due to algal growth. Scientists from Ukraine have explained that due to red colour, snow in the Antarctic Peninsula using spatial reflects less sunlight and melts at a faster rate producing approach more bright algae7. Red snow was discovered by John Ross in 1818 at M. Geetha Priya1,*, N. Varshini2, G. Chandhana2, Crimson cliff in Baffin’s bay near the Arctic region. Later Robert Brown reported that the red colour was caused by G. Deeksha2, K. Supriya2 and D. Krishnaveni2 algae. At the beginning of the 20th century, Johan Nordal 1 School of Electronics Engineering, Vellore Institute of Technology, Fischer-Wille proved that the red colour of snow was due Chennai 600 127, India 2Centre for Incubation, Innovation, Research and Consultancy and to algae that he named Chlamydomonas nivalis (photo- 8,9 Department of ECE, Jyothy Institute of Technology, Thataguni, synthetic green algae) . Green algae grow in snowfields Bengaluru 560 082, India of the Alps and polar regions which consist of red carote- noid pigment that is responsible for the red colour pro- In recent times, global warming across the world is tecting it from UV radiation10,11. The present study is an one of the major factors that triggers surface snow immediate response to observations on the effect of rise melting. According to the reports, climate change in temperature on snow cover of Eagle Island and the across the globe has a major impact on the poles, change in snow reflectance due to red algal growth which which has resulted in rapid snowmelt and red- has been reported by polar researchers in February 2020.
    [Show full text]
  • A New Genus and Three New Species of Hysteriaceous Ascomycetes from the Semiarid Region of Brazil
    Phytotaxa 176 (1): 298–308 ISSN 1179-3155 (print edition) www.mapress.com/phytotaxa/ Article PHYTOTAXA Copyright © 2014 Magnolia Press ISSN 1179-3163 (online edition) http://dx.doi.org/10.11646/phytotaxa.176.1.28 A new genus and three new species of hysteriaceous ascomycetes from the semiarid region of Brazil DAVI AUGUSTO CARNEIRO DE ALMEIDA1, LUÍS FERNANDO PASCHOLATI GUSMÃO1 & ANDREW NICHOLAS MILLER2 1 Universidade Estadual de Feira de Santana, Av. Transnordestina, S/N – Novo Horizonte, 44036-900. Feira de Santana, BA, Brazil. 2 Illinois Natural History Survey, University of Illinois, 1816 S. Oak St., Champaign, IL 61820 * email: [email protected] Abstract During an inventory of ascomycetes in the semi-arid region of Brazil, one new genus and three new species of hysteriaceous ascomycetes were found. Maximum likelihood and Bayesian phylogenetic analyses of the nuclear ribosomal 28S large subunit were performed to investigate the placement of the new taxa within the class Dothideomycetes. Anteaglonium brasiliense is described as a new species within the order Pleosporales, and Graphyllium caracolinense is described as a new species nested inside Hysteriales. Morphological and molecular data support Hysterodifractum as a new monotypic genus in the Hysteriaceae. The type species, H. partisporum, is characterized by navicular, carbonaceous, gregarious hysterothecia and pigmented, fusiform ascospores that disarticulate into 16 ovoid or obovoid, septate, part-spores. This is the first report of a hysteriaceous fungus producing part-spores. Key words: Dothideomycetes, LSU, phylogeny, Pleosporomycetidae, taxonomy, tropical microfungi Introduction Hysteriaceous ascoloculares ascomycetes produce navicular, carbonaceous, persistent ascomata that are superficial or erumpent and dehisce through a longitudinal slit (Boehm et al.
    [Show full text]
  • Morphological and Physicochemical Diversity of Snow Algae from Alaska Marta J
    www.nature.com/scientificreports OPEN Morphological and physicochemical diversity of snow algae from Alaska Marta J. Fiołka1*, Nozomu Takeuchi2, Weronika Sofńska‑Chmiel3, Sylwia Mieszawska1 & Izabela Treska1 Snow algae are photosynthetic microbes growing in thawing snow. They usually show various morphological cell types. The aim of this study was to carry out microscopic and spectroscopic analysis of diferent forms of cells of snow algae collected on glaciers in Alaska. Four diferent shapes of algal cells were observed with the use of bright feld LM (Light Microscopy), DIC (Diferential Interference Contrast), EDF (Extended Depth Focus), fuorescence microscopy, and SEM (Scanning Electron Microscopy). The cells exhibited the strongest autofuorescence after the exposure to 365‑nm excitation light, and the intensity difered among the cell types. Zygotes (cysts) showed the most intense fuorescence. Acridine orange staining revealed the acid nature of the algal cells. The use of Congo red and Calcofuor white fuorochromes indicated diferences in the structure of polysaccharides in the cell wall in the individual types of algal cells. FTIR (Fourier‑Transform Infrared Spectroscopy) analyses showed the presence of polysaccharides not only in the algal cells but also in the fxative solution. The presence of polysaccharides in the extracellular algal fraction was confrmed by X‑ray dispersion spectroscopy (EDS), X‑ray photoelectron spectroscopy (XPS), and scanning electron microscopy imaging (SEM). The diferences observed in the structure of the cell wall of the diferent forms of red snow algae prompt further analysis of this structure. Te red or pink color of snow caused by blooms of snow algae is commonly observed during summer in alpine and coastal polar regions.
    [Show full text]
  • Biological Albedo Reduction on Ice Sheets, Glaciers, and Snowfields
    Biological albedo reduction on ice sheets, glaciers, and snowfields Scott Hotaling1, Stefanie Lutz2, Roman J. Dial3, Alexandre M. Anesio4, Liane G. Benning2,5, Andrew G. Fountain6, Joanna L. Kelley1, Jenine McCutcheon7, S. McKenzie Skiles8, Nozomu Takeuchi9, and Trinity L. Hamilton10 Affiliations: 1 School of Biological Sciences, Washington State University, Pullman, WA, USA 2 GFZ German Research Center for Geosciences, Telegrafenberg, 14473 Potsdam, Germany 3 Institute of Culture and Environment, Alaska Pacific University, Anchorage, AK, USA 4 Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark 5 Department of Earth Sciences, Free University of Berlin, 12249 Berlin, Germany 6 Departments of Geology and Geography, Portland State University, Portland, OR, USA 7 Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Canada 8 Department of Geography, University of Utah, Salt Lake City, UT, USA 9 Department of Earth Sciences, Graduate School of Science, Chiba University, Chiba, Japan 10 Department of Plant and Microbial Biology and The BioTechnology Institute, University of Minnesota, Saint Paul, MN, USA Correspondence: Scott Hotaling, School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA; Email: [email protected]; Phone: (828) 507-9950; ORCID: 0000-0002-5965- 0986 Trinity Hamilton, Department of Plant and Microbial Biology and the BioTechnology Institute, University of Minnesota, Saint Paul, MN, USA; Email: [email protected]; Phone: (612) 625- 6372; ORCID: 0000-0002-2282-4655 Note: This article is a non-peer reviewed preprint submitted to EarthArXiv. It was submitted for peer review to Earth-Science Reviews in January 2021. 1 Abstract: 2 The global cryosphere, Earth’s frozen water, is in precipitous decline.
    [Show full text]