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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.
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  • Biological Albedo Reduction on Ice Sheets, Glaciers, and Snowfields

    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.