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SPECIES DIVERSITY OF BASIDIOMYCETES OF DISTRICT MALAKAND SHAH HUSSAIN DEPARTMENT OF BOTANY HAZARA UNIVERSITY MANSEHRA 2016 1 HAZARA UNIVERSITY MANSEHRA Department of Botany SPECIES DIVERSITY OF BASIDIOMYCETES OF DISTRICT MALAKAKAND BY SHAH HUSSAIN This research study has been conducted and reported as partial fulfillment of the requirements of PhD degree in Botany awarded by Hazara University Mansehra, Pakistan Mansehra, The Thursday 05, May 2016 2 3 SPECIES DIVERSITY OF BASIDIOMYCETES OF DISTRICT MALAKAND A thesis submitted for fulfillment the requirements of the degree of Doctor of Philosophy in Botany SUBMITTED BY SHAH HUSSAIN PhD Scholar RESEARCH SUPERVISOR PROF. HABIB AHMAD PhD TI Chairman Department of Genetics Hazara University, Mansehra CO-SUPERVISOR DR. NAJAM-UL-SAHAR AFSHAN Assistant Professor Centre for Undergraduate Studies University of the Punjab Quaid-e-Azam Campus, Lahore DEPARTMENT OF BOTANY HAZARA UNIVERSITY MANSEHRA 2016 4 Dedication I would like to dedicate the success of this study to my family and my teachers. 5 CONTENTS Page No. List of Figures iv List of Tables viii List of Abbreviations ix Acknowledgement x Abstract xii Chapter 1 Introduction 1 1.1. The study area 1 1.2. Fungi in Pakistan 4 1.3. Taxonomy of fungi 6 1.4. Molecular biology of fungi 7 1.5. Scope and limitations of the study 8 1.6. Objectives of the study 8 Chapter 2 Materials and Methods 9 2.1. Survey and collection 9 2.1.1 Monsoon rainy season 9 2.1.2 Dry season 9 2.1.3 Spring season 9 2.2. Morphological characterization of species 9 2.3. Molecular characterization 10 2.3.1 DNA extraction, PCR and Sequencing 10 2.3.2 Phylogenetic analyses 13 2.4. Diversity index 14 Chapter 3 Results 15 3.1. Agaricus bisporiticus 18 3.2. Agaricus campestris 19 3.3. Agaricus malakandensis nom. prov. 23 i 3.4. Agaricus minorus nom. prov. 25 3.5. Hymenagaricus pakistaniensis nom. prov. 31 3.6. Leucoagaricus badius nom. prov. 36 3.7. Leucoagaricus sultanii nom. prov. 38 3.8. Leucocoprinus birnbaumii 46 3.9. Lycoperdon dermoxanthum 50 3.10. Tulostoma ahmadii 54 3.11. Conocybe papillata 60 3.12. Cantharocybe pakistanicus nom. prov. 65 3.13. Termitomyces umkowaan 70 3.14. Marasmiellus palmivorus 74 3.15. Omphalotus nidiformis 79 3.16. Pleurotus cystidiosus 83 3.17. Volvariella bombycina 87 3.18. Coprinellus curtus 91 3.19. Coprinellus disseminatus 93 3.20. Coprinellus micaceus 94 3.21. Coprinellus radians 95 3.22. Coprinopsis hispidus nom. prov. 99 3.23. Parasola auricoma 104 3.24. Parasola lentiformis nom. prov. 106 3.25. Parasola lilatincta 110 3.26. Parasola malakandensis nom. prov. 112 3.27. Parasola schroeteri 117 3.28. Psathyrella candolleana 121 3.29. Psathyrella fusiformis nom. prov. 122 3.30. Agrocybe pediades 127 3.31. Agrocybe semiorbicularis 130 3.32. Stropharia ambigua 134 ii 3.33. Geastrum velutinum 138 3.34. Phellinus badius 142 3.35. Irpex lacteus 144 3.36. Rigidoporus vinctus 146 3.37. Earliella scabrosa 148 3.38. Trametes cubensis 150 3.39. Trametes lactinae 152 3.40. Phragmidium papillatum 155 3.41. Phragmidium rubi-idaei 157 3.42. Puccinia aestivalis 159 3.43. Puccinia conclusa 161 3.44. Puccinia duthiei 164 3.45. Puccinia microspore 167 3.46. Puccinia nakanishikii 170 3.47. Puccinia striiformis var. striiformis 172 3.48. Puccinia violae 174 3.49. Puccinia melanocephala 176 3.50. Uromyces lespedezae-procumbentis 177 3.51. Urocystis avenastri 180 3.52. Diversity of basidiomycetous fungi 182 3.52.1 Diversity of basidiomycetous fungi in Dargai tehsil 182 3.52.2 Diversity of basidiomycetous fungi in Batkhela tehsil 182 Chapter 4 Discussion 190 Conclusion 206 Recommendations 207 Chapter 5 References 208 iii LIST OF FIGURES Page No. Figure 1. Map of district Malakand 2 Figure 2. Basidiomata of Agaricus bisporiticus and A. campestris 21 Figure 3. Anatomical features of Agaricus bisopriticus and A. campestris 22 Figure 4. Basidiomata of Agaricus malakandensis and A. minorus 27 Figure 5. Anatomical features of Agaricus malakandensis and A. minorus 28 Figure 6. Phylogenetic tree of Agaricus spp. 30 Figure 7. Basidiomata of Hymenagaricus pakistaniensis 33 Figure 8. Anatomical features of Hymenagaricus pakistaniensis 34 Figure 9. Phylogenetic tree of Hymenagaricus and allied genera 35 Figure 10. Basidiomata of Leucoagaricus species 40 Figure 11. Anatomical features of Leucoagaricus species 41 Figure 12. Phylogenetic tree based on ITS dataset of Leucoagaricus spp. 44 Figure 13. Phylogenetic tree based four genes regions of Leucoagaricus spp. 45 Figure 14. Morpho-anatomical features of Leucocoprinus birnbaumii 48 Figure 15. Phylogenetic tree of Leucocoprinus spp. 49 Figure 16. Morpho-anatomical features of Lycoperdon dermoxanthum 52 Figure 17. Phylogenetic tree of Lycoperdon spp. 53 Figure 18. Basidiomata and basidiospores of Tulostoma ahmadii 57 Figure 19. Morpho-anatomical features of Tulostoma ahmadii 58 Figure 20. Phylogenetic tree of Tulostama spp. 59 Figure 21. Basidiomata of Conocybe papillata 62 Figure 22. Anatomical features of Conocybe papillata 63 Figure 23. Phylogenetic tree of Conocybe spp. 64 Figure 24. Basidiomata of Cantharocybe pakistanicus 67 Figure 25. Anatomical features of Cantharocybe pakistanicus 68 Figure 26. Phylogenetic tree of Hygrophoraceae 69 Figure 27. Morpho-anatomical features of Termitomyces umkowaan 72 iv Figure 28. Phylogenetic tree of Termitomyces spp. 73 Figure 29. Sporophores of Marasmiellus palmivorus 76 Figure 30. Anatomical features of Marasmiellus palmivorus 77 Figure 31. Phylogenetic tree of Marasmiellus palmivorus and allied genera 78 Figure 32. Morpho-anotmical features of Omphalotus nidiformis 81 Figure 33. Phylogenetic tree of Omphalotus spp. 82 Figure 34. Morpho-anatomical features of Pleurotus cystidiosus 85 Figure 35. Phylogenetic tree of Pleurotus spp. 86 Figure 36. Basidiomata of Volvariella bombycina 88 Figure 37. Anatomical features of Volvariella bombycina 89 Figure 38. Phylogenetic tree of Volvariella spp. 90 Figure 39. Anatomical features of Coprinellus curtus 92 Figure 40. Basidiomata of Coprinellus spp. 96 Figure 41. Anatomical features of Coprinellus spp. 97 Figure 42. Phylogenetic tree of Coprinellus species 98 Figure 43. Basidiomata and basidiospores of Coprinopsis hispidus 101 Figure 44. Anatomical features of Coprinopsis hispidus 102 Figure 45. Phylogenetic tree of Coprinopsis spp. 103 Figure 46. Figure 46. Basidiomata of Parasola auricoma and Pa. lentiformis 108 Figure 47. Anatomical features of Parasola auricoma and Pa lentiformis 109 Figure 48. Basidiomata and anatomical features Parasola lilatincta 111 Figure 49. Basidiomata of Parasola malakandensis 114 Figure 50. Morpho-anatomical features of Parasola malakandensis 115 Figure 51. Three gene phylogeny (ITS-LSU-tef-1α) of Pa. malakandensis 116 Figure 52. Basidiomata and anatomical features of Parasola schroeterii 118 Figure 53. Phylogeny of Parasola spp., based on ITS sequences 120 Figure 54. Basidiomata of Psathyrella candolleana and Ps. fusiformis 124 Figure 55. Anatomical features of Psathyrella candolleana and Ps. fusiformis 125 Figure 56. Phylogenetic tree of Psathyrella species 126 v Figure 57. Morpho-anatomical features of Agrocybe pediades 128 Figure 58. Phylogenetic tree of Agrocybe spp. 129 Figure 59. Basidiomata and spores of Agrocybe semiobricularis 131 Figure 60. Anatomical features of Agrocybe semiobricularis 132 Figure 61. Phylogenetic tree of Agrocybe spp. 133 Figure 62. Morpho-anatomical features of Stropharia ambigua 136 Figure 63. Phylogenetic tree of Stropharia and Hypholoma 137 Figure 64. Morpho-anatomical features of Geastrum velutinum 140 Figure 65. Phylogenetic tree of Geastrum spp. 141 Figure 66. Morpho-anatomical features of Phellinus badius 143 Figure 67. Morpho-anatomical features of Irpex lacteus 145 Figure 68. Morpho-anatomical features of Rigidoporus vinctus 147 Figure 69. Morpho-anatomical features of Earliella scabrosa 149 Figure 70. Morpho-anatomical features of Trametes cubensis 151 Figure 71. Morpho-anatomical features of Trametes lactinea 153 Figure 72. Phylogenetic tree of Polyporales 154 Figure 73. Phragmidium papillatum Potentilla geradiana 156 Figure 74. Phragmidium rubi-idaei on Rubus fruiticosus 158 Figure 75. Puccinia aestivalis on Microstegium nudum 160 Figure 76. Puccinia conclusa on Cyperus iria 162 Figure 77. Line drawings Puccinia conclusa 163 Figure 78. Puccinia duthiei on Dichanthium annulatum 165 Figure 79. Line drawings of Puccinia duthiei 166 Figure 80. Puccinia microspora on Imperata cylindrica 168 Figure 81. Drawings of Puccinia microspora 169 Figure 82. Puccinia nakanishikii on Sorghum halepense 171 Figure 83. Puccinia striiformis var. striiformis on Triticum aestivum 173 Figure 84. Puccinia violae on Viola canescense 175 Figure 85. Puccinia sp. on Saccharum bengalense 177 vi Figure 86. Uromyces lespedezae-procumbentis on Lespedeza juncea var. sericea 179 Figure 87. Urocystis avenastri 181 Figure 88. Species diversity index of Dargai tehsil 187 Figure 89. Species diversity index of Batkhela tehsil 188 Figure 90. Diversity index of different families of Basidiomycota of Malakand 189 vii List of Tables Page No. Table 1. Primers used in this study 12 Table 2. Diversity Indices of fungal species of tehsil Dargai, district Malakaknd 183 Table 3. Diversity Indices of fungal species of tehsil Batkhela, district Malakaknd 185 Table 4. Diversity Indices of different fungal families of district Malakaknd 186 viii List of abbreviations A. Agaricus BPP Bayesian Posterior Probabilities Beast Bayesian evolutionary analysis sampling trees Co. 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  • Revised Taxonomy and Phylogeny of an Avian-Dispersed Neotropical Rhizomorph-Forming Fungus

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    Mycological Progress https://doi.org/10.1007/s11557-018-1411-8 ORIGINAL ARTICLE Tying up loose threads: revised taxonomy and phylogeny of an avian-dispersed Neotropical rhizomorph-forming fungus Rachel A. Koch1 & D. Jean Lodge2,3 & Susanne Sourell4 & Karen Nakasone5 & Austin G. McCoy1,6 & M. Catherine Aime1 Received: 4 March 2018 /Revised: 21 May 2018 /Accepted: 24 May 2018 # This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2018 Abstract Rhizomorpha corynecarpos Kunze was originally described from wet forests in Suriname. This unusual fungus forms white, sterile rhizomorphs bearing abundant club-shaped branches. Its evolutionary origins are unknown because reproductive struc- tures have never been found. Recent collections and observations of R. corynecarpos were made from Belize, Brazil, Ecuador, Guyana, and Peru. Phylogenetic analyses of three nuclear rDNA regions (internal transcribed spacer, large ribosomal subunit, and small ribosomal subunit) were conducted to resolve the phylogenetic relationship of R. corynecarpos. Results show that this fungus is sister to Brunneocorticium bisporum—a widely distributed, tropical crust fungus. These two taxa along with Neocampanella blastanos form a clade within the primarily mushroom-forming Marasmiaceae. Based on phylogenetic evidence and micromorphological similarities, we propose the new combination, Brunneocorticium corynecarpon, to accommodate this species. Brunneocorticium corynecarpon is a pathogen, infecting the crowns of trees and shrubs in the Neotropics; the long, dangling rhizomorphs with lateral prongs probably colonize neighboring trees. Longer-distance dispersal can be accomplished by birds as it is used as construction material in nests of various avian species. Keywords Agaricales . Fungal systematics .
  • Metabolites from Nematophagous Fungi and Nematicidal Natural Products from Fungi As Alternatives for Biological Control

    Metabolites from Nematophagous Fungi and Nematicidal Natural Products from Fungi As Alternatives for Biological Control

    Appl Microbiol Biotechnol (2016) 100:3813–3824 DOI 10.1007/s00253-015-7234-5 MINI-REVIEW Metabolites from nematophagous fungi and nematicidal natural products from fungi as alternatives for biological control. Part II: metabolites from nematophagous basidiomycetes and non-nematophagous fungi Thomas Degenkolb1 & Andreas Vilcinskas1,2 Received: 4 October 2015 /Revised: 29 November 2015 /Accepted: 2 December 2015 /Published online: 4 January 2016 # The Author(s) 2016. This article is published with open access at Springerlink.com Abstract In this second section of a two-part mini-re- Introduction view article, we introduce 101 further nematicidal and non-nematicidal secondary metabolites biosynthesized Metabolites from nematophagous basidiomycetes by nematophagous basidiomycetes or non- nematophagous ascomycetes and basidiomycetes. Sev- General remarks eral of these compounds have promising nematicidal activity and deserve further and more detailed analy- The chemical ecology of nematophagous fungi is still far from sis. Thermolides A and B, omphalotins, ophiobolins, understood. Little has been done to screen for metabolites in bursaphelocides A and B, illinitone A, pseudohalonectrins A nematophagous fungi, or nematicidal metabolites in other fun- and B, dichomitin B, and caryopsomycins A–Careex- gi, since the pioneering studies by Stadler and colleagues pub- cellent candidates or lead compounds for the develop- lished in the 1990s (Stadler et al. 1993a, b, 1994a, b, c, d). In ment of biocontrol strategies for phytopathogenic the first part of this review, we discussed 83 primary and nematodes. Paraherquamides, clonostachydiol, and secondary metabolites from nematophagous ascomycetes nafuredins offer promising leads for the development (Degenkolb and Vilcinskas, in press). In this second install- of formulations against the intestinal nematodes of ment, we consider nematicidal metabolites from ruminants.