Taxonomy, Phylogeny and evolution of selected ascomycetes, with particular emphasis on saprobic fungi from marine habitats

Name: Dayarathne, Monika Chandani

Address: 333 Moo1, Thasud, Muang, Chiang Rai 57100

Organization : Mae Fah Luang University. School of Science. Biosciences

Email : ask.library@mfu.ac.th

keyword: Fungi

LCSH: Marine fungi

Classification :.LCCS: QK618

LCSH: Biology -- Research

LCSH: Fungi

LCSH: Phylogeny

LCSH: Ascomycetes

Abstract: Fungal taxonomy has undergone a revolution over the last few decades and has a long history. The proper recognition of fungi is an essential practical consequence not only in the clinical setting but also in plant pathology, biodeterioration, biotechnology, and environmental studies. A vast number of fungal species are already known; therefore, taxonomists are often attempting to recognize and describe novel species and assembling taxa into higher order taxonomical units. Still, most species have introduced mainly by traditional ways rather than numerical and has been based on readily observable morphological characteristics. Hence, name bearing type specimens constitute an integral part of fungal classification and nomenclature. To date, type specimens/old names have served as excellent exemplars and references and have been the pillar for a stable classification and appropriate nomenclature. However, with an increase in the number of species being discovered and the practical problems associated with their re-examination, there is a need to reconsider our traditional taxonomic thinking towards such an approach. It is becoming increasingly clear that loaning specimens from national herbaria, especially of rare and old species, is becoming too tedious, difficult and in some cases, practically impossible. Also, in many cases type material has been lost or is in poor condition due to repeated re-examination. This study addresses in detail some of the major practical difficulties in referring to old names from a stable nomenclatural system viewpoint, in particular, reluctance of herbaria to loan specimens and poor conditions of specimens. Therefore, as a beginning to our taxonomic study, the first chapter provides controversies associated with old fungal names furnished with relevant instances, case studies and provide potential solutions to facilitate future naming/classification of fungal species with the opinions of expertise mycologists. Our major study relies on ascomycetes which play a significant role in decomposition, breaking down lignocelluloses and releasing nutrients, and are important in ecosystem functioning. Among them our knowledge on marine ascomycetes has advanced significantly over the last two decades and comprehensive range of topics was reviewed: phylogeny of marine fungi, their biodiversity (occurrence in mangroves, on marine algae, salt marsh fungi, marine derived fungi, fungi in deep-sea environments), and their application in industry. Most of the recent studies are strongly supported by DNA sequence data and highlighted a number of new lineages of marine fungi. However, the accurate taxonomic position of a number of marine ascomycetes is still doubtful and have been tentatively placed in a class until additional sequence data becomes available to confirm their placement. Despite many studies and advances in molecular phylogenetics of fungi, the polarity of terrestrial-fresh water-marine transitions within the Ascomycota has still to be addressed. In addition, it is remarkable that the numbers of type stains of marine ascomycetes have been generated from Thailand and the species diversity is relatively high. Hence, we narrow down our study to conduct further investigations on marine ascomycetes for the identification of new species, re-collecting of existing species to provide better molecular data and to designate new types when necessary. Ascomycetes found in marine based habitats can be either sexual morphs or asexual morphs (both hyphomycetes and coelomycetes) of Dothideomycetes or Sordariomycetes or other classes. They are not a monophyletic group and phylogenetic studies reported that ascomycetes found in marine based habitats are accommodated across a range of orders and families. Dothideomycetes found from marine based habitats belong to the orders Capnodiales, Dothideales, Microthyriales, Mytilinidiales, Botryosphaeriales, Dyfrolomycetales, Hysteriales, Magnaporthales, Jahnulales, Pleosporales, Patellariales, Stigmatodiscales and Tubeufiales and Sordariomycete taxa belong to the orders Boliniales, Calosphaeriales, Coniochaetales, Coronophorales, Chaetosphaeriales, Diaporthales, Falcocladiales, Glomerellales, Hypocreales, Koralionastetales, Lulworthiales, Magnaporthales, Melanosporales, Microascales, Ophiostomatales, Phyllachorales, Savoryellales, Sordariales, Tirisporellales, Torpedosporales Trichosphaeriales and Xylariales and their classification needs to be revised due to lack of molecular data and some taxa with poor morphological characterization. This study mainly concentrates on the taxonomy of ascomycetes found in marine based habitats by using modern morphological and molecular approaches. Fungal specimens associated with various hosts from marine based habitats were collected from Sweden, Thailand and UK. They were morphologically examined and their DNA sequence data from rDNA and protein loci (ITS, LSU, SSU, TEF, β-tub, ACT and RPB2) were analyzed to verify their identity and phylogenetic affinities to better understand their natural placement. Morphological examination of fresh specimens from marine based habitats including sand dunes are consolidated with multigene phylogeny yielding 80 taxa (sexual and/ or asexual morphs) accommodated in 35 families, which belong to the Dothediomycete orders; Botryosphaeriales, Dyfrolomycetales, Hysteriales, Magnaporthales, Jahnulales, Pleosporales, Patellariales, Stigmatodiscales, Tubeufiales and Sordariomycete orders; Boliniales, Calosphaeriales, Coniochaetales, Chaetosphaeriales, Hypocreales, Lulworthiales, Microascales, Torpedosporales and Xylariales. Novel fungal taxa which are described in the present study includes four new genera, 48 new species and new host records for 20 species. Additionally, this provides novel sequence data for a number of existing taxa and widens the availability of sequence data in the GenBank from marine based taxa. Our results also indicate that the abundance of Sordariomycete taxa is somewhat higher than that of Dothediomycete taxa (56% vs 43%) while the sexual morph/asexual morph ratio is 62:48. Our sample collection from marine based habitats of Krabi, Phetchaburi, Phucket, Prachuap Khiri Khan, Ranong in southern Thailand resulted in 60 taxa along with multi gene sequences while, 36 new species are recognized. Among them, Jattaea species are abundantly found from wood in terrestrial environments, while the asexual morphs are mostly reported from axenic cultures. Jattaea mucronata is the first documentation of a sexual morph of Jattaea associated with a marine habitat while Jattaea bruguierae is the first record of an asexual morph of Jattaea from mangroves. Furthermore, during this study, a sexual morph of Phaeoacremonium was collected in a mangrove forest in Krabi and morphological studies along with single ACT gene analyses of this fungus revealed that this fungus best fits in Phaeoacremonium aureum. This is the first record of asexual morph of Phaeoacremonium aureum and this is the first Phaeoacremonium species collected from a mangrove habitat. During this study we collected a marine fungal species Byssothecium obiones which lacked authentic specimens and molecular data, despite being widely reported in the literature. A novel marine genus, Halobyssothecium (Lentitheciaceae), is introduced to accommodate Byssothecium obiones (= Halobyssothecium obiones) with evidence from phylogenetic analyses of concatenated LSU, SSU, ITS rDNA and TEF1 sequence data. Further, an epitype obtained from Spartina culms in Eastney, Langstone Harbour, Hampshire, UK is designated for the precise delineation of this taxon. As a part of this study, an exhaustive morpho-molecular revision is conducted for marine based diatrypaceous taxa. Modern morphological descriptions, illustrations and a key to species of diatrypaceous taxa found in marine habitats are documented and two novel genera are introduced, Halocryptovalsa and Halodiatrype with six new species and three new combinations Cryptosphaeria bathurstensis (≡ Eutypa bathurstensis), Halocryptovalsa avicenniae (≡ Cryptovalsa avicenniae), and Halodiatrype mangrovei (≡ Cryptosphaeria mangrovei). For earlier described diatrypaceous species, current scientific names including synonyms are provided along with hosts, distribution, and notes on their taxonomy and phylogeny. DNA sequence data, phylogenetic relationships and accurately defined names will be useful for scientists working on various aspects of fungi from marine habitats, such as in conservation of mangroves and associate species, as well as screening for bioactive metabolites. Morphology, phylogeny and molecular clock analyses is carried out on Savoryellaceae in order to understand the placements of taxa in this family. Ascotaiwania and Neoascotaiwania formed a well-supported separate clade in the phylogeny of concatenated partial SSU, LSU, TEF and RPB2 gene data. These two genera share similar morphological features, especially in their asexual morphs, indicating that they are congeneric. Hence, we synonymize Neoascotaiwania under Ascotaiwania. Ascotaiwania hughesii (and its asexual morph, Helicoon farinosum) and Monotosporella setosa grouped in a clade sister to Pleurotheciales and are excluded from Ascotaiwania which becomes monophyletic. A novel genus Helicoascotaiwania is introduced to accommodate Ascotaiwania hughesii and its asexual morph, Helicoon farinosum. In addition, we provided evolutionary divergence estimates for Savoryellomycetidae taxa and major marine based taxa to support our phylogenetic and morphological investigations. The taxonomic placement of these marine-based taxa is briefly discussed. This study moreover extends towards herbarium types studies of selected Sordariomycete families which comprises mostly marine taxa, Etheirophoraceae, Gondwanamycetaceae, Hispidicarpomyceae, Jobellisiaceae, Juncigenaceae, Tirisporellaceae, Koralionastetacea, Lautosporaceae, Microascaceae, Papulosaceae, Spathulosporaceae, Torpedosporaceae. Taxonomic information obtained from the morphological characters from authentic specimens, protologues, original illustrations and molecular data obtained from GenBank are used to establish their placements within the natural classification system and updated phylogenetic trees are provided for each family. Extending from the single gene analyses to multigene phylogeny of the Halosphaeriaceae and Lulworthiaceae, several attempts are documented in resolving the phylogenetic relationships of these families by examining selected genera and related taxa. Some of the described species in Lulworthiaceae and Halosphaeriaceae lack molecular data or controversial due to inadequate morphological studies. We have prepared morphological accounts for hitherto observed poorly illustrated materials with highly improved microscopes and software, which allow more reliable phenotypic characterization. Therefore, my preliminary study on taxa in the Lulworthiaceae and Halosphaeriaceae provides summarized accounts for their current taxonomic status. Hence, my study has enabled the introduction of the sub class Lulworthiomycetidae to include orders Lulworthiales and Koralionastetales. Further, herbarium type material for the generic types and fresh specimens are studied in order to resolve the taxonomic confusions of various genera within Lulworthiaceae and Halosphaeriaceae and infer their taxonomic relationships. Ultimately, I aim to provide monographs for Lulworthiaceae and Halosphaeriaceae, in a post-doctoral study. Asian/Australasian lignicolous freshwater fungi have been relatively well-surveyed and a number of types have been generated. We observed some lignicolous freshwater species collected form Queensland, Australia as a partial objective of this study, and yielded a number of interesting taxa. Our observation of the holotype of Annulatascus velatisporus, the type species of the genus Annulatascus, showed that there are few ascomata remaining on the material and no molecular data was generated from the holotype. We were able investigate Annulatascus velatisporus from the holotype location and obtain DNA sequences for LSU, SSU and ITS, gene regions. Therefore, this specimen merits use as an interpretive type (epitype) for the holotype of A. velatisporus. Moreover, this study introduces two interesting novel taxa Ascitendus aquaticus and Jahnula queenslandica from fresh water habitats in Queensland. Despite the fact my study is based marine and fresh water taxa, I also studied the somewhat controversial group of fungi known as Phyllachorales, which is often comprises biotrophs. Some marine based species have also been reported from this order. Under this, I provide morpho-molecular accounts for the families Phyllachoraceae and Telimenaceae supported by authentic type studies. The genus Polystigma is excluded from Phyllachoraceae and placed in the re-instated family Polystigmataceae, within Xylariales and a reference specimen is provided for the type Polystigma rubrum. This study also inaugurates one new genus Neophyllachora and three novel species Phyllachora chloridis, Phyllachora cynodonticola and Phyllachora panicicola. Hence, provided a well resolved phylogenetic tree for the order.

Mae Fah Luang University. Learning Resources and Educational Media Center

Address: CHIANG RAI

Email: library@mfu.ac.th

Name: Kitiphong Khongphinitbunjong

Role: Advisor

Email : ask.library@mfu.ac.th

Name: Jones, Gareth

Role: Co-Advisor

Email : ask.library@mfu.ac.th

Created: 2019

Issued: 2563

Modified: 2020-03-03

Issued: 2020-03-03

วิทยานิพนธ์/Thesis

application/pdf

CallNumber: Thesis QK618 D275t 2019

eng

DegreeName: Dotor of Philosophy

Level: Doctoral Degree

Descipline: Biosciences

Grantor: Mae Fah Luang University

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