Showing papers by "Ali H. Bahkali published in 2017"

Notes for genera: Ascomycota

Abstract: Knowledge of the relationships and thus the classification of fungi, has developed rapidly with increasingly widespread use of molecular techniques, over the past 10–15 years, and continues to accelerate. Several genera have been found to be polyphyletic, and their generic concepts have subsequently been emended. New names have thus been introduced for species which are phylogenetically distinct from the type species of particular genera. The ending of the separate naming of morphs of the same species in 2011, has also caused changes in fungal generic names. In order to facilitate access to all important changes, it was desirable to compile these in a single document. The present article provides a list of generic names of Ascomycota (approximately 6500 accepted names published to the end of 2016), including those which are lichen-forming. Notes and summaries of the changes since the last edition of ‘Ainsworth & Bisby’s Dictionary of the Fungi’ in 2008 are provided. The notes include the number of accepted species, classification, type species (with location of the type material), culture availability, life-styles, distribution, and selected publications that have appeared since 2008. This work is intended to provide the foundation for updating the ascomycete component of the “Without prejudice list of generic names of Fungi” published in 2013, which will be developed into a list of protected generic names. This will be subjected to the XIXth International Botanical Congress in Shenzhen in July 2017 agreeing to a modification in the rules relating to protected lists, and scrutiny by procedures determined by the Nomenclature Committee for Fungi (NCF). The previously invalidly published generic names Barriopsis, Collophora (as Collophorina), Cryomyces, Dematiopleospora, Heterospora (as Heterosporicola), Lithophila, Palmomyces (as Palmaria) and Saxomyces are validated, as are two previously invalid family names, Bartaliniaceae and Wiesneriomycetaceae. Four species of Lalaria, which were invalidly published are transferred to Taphrina and validated as new combinations. Catenomycopsis Tibell & Constant. is reduced under Chaenothecopsis Vain., while Dichomera Cooke is reduced under Botryosphaeria Ces. & De Not. (Art. 59).

Fungal diversity notes 603–708: taxonomic and phylogenetic notes on genera and species

Abstract: This is the sixth in a series of papers where we bring collaborating mycologists together to produce a set of notes of several taxa of fungi. In this study we introduce a new family Fuscostagonosporaceae in Dothideomycetes. We also introduce the new ascomycete genera Acericola, Castellaniomyces, Dictyosporina and Longitudinalis and new species Acericola italica, Alternariaster trigonosporus, Amarenomyces dactylidis, Angustimassarina coryli, Astrocystis bambusicola, Castellaniomyces rosae, Chaetothyrina artocarpi, Chlamydotubeufia krabiensis, Colletotrichum lauri, Collodiscula chiangraiensis, Curvularia palmicola, Cytospora mali-sylvestris, Dictyocheirospora cheirospora, Dictyosporina ferruginea, Dothiora coronillae, Dothiora spartii, Dyfrolomyces phetchaburiensis, Epicoccum cedri, Epicoccum pruni, Fasciatispora calami, Fuscostagonospora cytisi, Grandibotrys hyalinus, Hermatomyces nabanheensis, Hongkongmyces thailandica, Hysterium rhizophorae, Jahnula guttulaspora, Kirschsteiniothelia rostrata, Koorchalomella salmonispora, Longitudinalis nabanheensis, Lophium zalerioides, Magnibotryascoma mali, Meliola clerodendri-infortunati, Microthyrium chinense, Neodidymelliopsis moricola, Neophaeocryptopus spartii, Nigrograna thymi, Ophiocordyceps cossidarum, Ophiocordyceps issidarum, Ophiosimulans plantaginis, Otidea pruinosa, Otidea stipitata, Paucispora kunmingense, Phaeoisaria microspora, Pleurothecium floriforme, Poaceascoma halophila, Periconia aquatica, Periconia submersa, Phaeosphaeria acaciae, Phaeopoacea muriformis, Pseudopithomyces kunmingnensis, Ramgea ozimecii, Sardiniella celtidis, Seimatosporium italicum, Setoseptoria scirpi, Torula gaodangensis and Vamsapriya breviconidiophora. We also provide an amended account of Rhytidhysteron to include apothecial ascomata and a J+ hymenium. The type species of Ascotrichella hawksworthii (Xylariales genera incertae sedis), Biciliopsis leptogiicola (Sordariomycetes genera incertae sedis), Brooksia tropicalis (Micropeltidaceae), Bryochiton monascus (Teratosphaeriaceae), Bryomyces scapaniae (Pseudoperisporiaceae), Buelliella minimula (Dothideomycetes genera incertae sedis), Carinispora nypae (Pseudoastrosphaeriellaceae), Cocciscia hammeri (Verrucariaceae), Endoxylina astroidea (Diatrypaceae), Exserohilum turcicum (Pleosporaceae), Immotthia hypoxylon (Roussoellaceae), Licopolia franciscana (Vizellaceae), Murispora rubicunda (Amniculicolaceae) and Doratospora guianensis (synonymized under Rizalia guianensis, Trichosphaeriaceae) were re-examined and descriptions, illustrations and discussion on their familial placement are given based on phylogeny and morphological data. New host records or new country reports are provided for Chlamydotubeufia huaikangplaensis, Colletotrichum fioriniae, Diaporthe subclavata, Diatrypella vulgaris, Immersidiscosia eucalypti, Leptoxyphium glochidion, Stemphylium vesicarium, Tetraploa yakushimensis and Xepicula leucotricha. Diaporthe baccae is synonymized under Diaporthe rhusicola. A reference specimen is provided for Periconia minutissima. Updated phylogenetic trees are provided for most families and genera. We introduce the new basidiomycete species Agaricus purpurlesquameus, Agaricus rufusfibrillosus, Lactifluus holophyllus, Lactifluus luteolamellatus, Lactifluus pseudohygrophoroides, Russula benwooii, Russula hypofragilis, Russula obscurozelleri, Russula parapallens, Russula phoenicea, Russula pseudopelargonia, Russula pseudotsugarum, Russula rhodocephala, Russula salishensis, Steccherinum amapaense, Tephrocybella constrictospora, Tyromyces amazonicus and Tyromyces angulatus and provide updated trees to the genera. We also introduce Mortierella formicae in Mortierellales, Mucoromycota and provide an updated phylogenetic tree.

An updated phylogeny of Sordariomycetes based on phylogenetic and molecular clock evidence

Abstract: The previous phylogenies of Sordariomycetes by M.E. Barr, O.E. Eriksson and D.L. Hawksworth, and T. Lumbsch and S. Huhndorf, were mainly based on morphology and thus were somewhat subjective. Later outlines by T. Lumbsch and S. Huhndorf, and Maharachchikumbura and co-authors, took into account phylogenetic evidence. However, even these phylogenetic driven arrangements for Sordariomycetes, were somewhat subjective, as the arrangements in trees depended on many variables, such as number of taxa, different gene regions and methods used in the analyses. What is needed is extra evidence to help standardize ranking in the fungi. Estimation of divergence times using molecular clock methods has been proposed for providing additional rational for higher ranking of taxa. Thus, in Sordariomycetes, a divergence period (i.e. 200–300 MYA) can be used as criteria to judge when a group of related taxa evolved and what rank they should be given. In this paper, we provide an updated classification of accepted subclasses, orders of Sordariomycetes and use divergence times to provide additional evidence to stabilize ranking of taxa in the class. We point out and discuss discrepancies where the phylogenetic tree conflicts with the molecular clock.

Microfungi on Tectona grandis (teak) in Northern Thailand

Abstract: To date there is virtually no information available concerning the fungi associated with Tectona grandis (teak) (Lamiaceae) in Thailand. In this study, samples of microfungi were collected from both asymptomatic stems and dead wood, and symptomatic branches, stem and leaves of T. grandis from 27 sites in six provinces (Chiang Mai, Chiang Rai, Phayao, Phitsanulok, Phrae and Uttaradit Provinces). Morphology and combined multi-gene phylogeny (CAL, GAPDH, ITS, LSU, RPB2, SSU, TEF1 and TUB) were used to identify taxa. A total of 270 collections, representing 28 fungal species residing in 12 families, 7 orders and 21 genera, with three species of uncertain taxonomic placement were identified. Of these, one family, three genera and 14 species are new to science. The new family, Pseudocoleodictyosporaceae is introduced based on its distinct lineage in the Dothideomycetes and its unique morphology as compared to Roussoellaceae and Torulaceae. The new genera are Neooccultibambusa, Pseudocoleodictyospora and Subglobosporium. The newly described species are Diaporthe neoraonikayaporum, D. tectonendophytica, D. tectonae, D. tectonigena, Hermatomyces tectonae, H. thailandica, Manoharachariella tectonae, Neooccultibambusa chiangraiensis, Pseudocoleodictyospora sukhothaiensis, Ps. tectonae, Ps. thailandica, Rhytidhysteron tectonae, Subglobosporium tectonae and Tubeufia tectonae. Fourteen species are known published taxa including Alternaria tillandsiae, Berkleasmium talaumae, Boerlagiomyces macrospora, Ceratocladium purpureogriseum, Fusarium solani, Helicoma siamense, Lasiodiplodia theobromae, Macrovalsaria megalospora, Paradictyoarthrinium diffractum, Phaeoacremonium italicum, Sphaeropsis eucalypticola, Stachybotrys levispora, St. renispora and Thaxteriellopsis lignicola. Epitypifications or reference specimens are designated for Boerlagiomyces macrospora and Macrovalsaria megalospora. Macrovalsaria megalospora is transferred from Botryosphaeriaceae to Dothideomycetes genus, incertae sedis based on taxonomy and phylogenetic analysis, which indicate it is distinct from Botryosphaeriaceae. All fungal species represent first reports on T. grandis in Thailand. New taxa and taxa incertae sedis, as well as known taxa which are established as reference specimens or epitypes, are presented with phylogenetic tree analyses, habitat, known distribution, material examined, full descriptions, notes and figures. Information is also provided for known taxa to add to the body of knowledge and to assist those wishing to study fungi occurring on T. grandis in future.

The ranking of fungi: a tribute to David L. Hawksworth on his 70th birthday

Abstract: The history of assigning ranks to fungi, as well as the relative importance of using divergence time estimates is reviewed. The paper pays tribute to the major mycological players, and especially to David Hawksworth on his 70th birthday and his contribution to fungal ranking in Systema Ascomycetum from 1982 to 1998. Following the conclusion of the latter series, the ranking continued with the Outlines of Ascomycota in 2007 and 2010 and more recently with specific classes in 'Towards an outline of Sordariomycetes' and 'Families of Dothideomycetes'. Earlier classifications based on phenotype were certainly more subjective; however, remarkably many of these old arrangements have stood the test of time. More recently, phylogenetic analyses have provided evidence towards a natural classification, resulting in significant changes in many lineages. The classification arrangements however, are still subjective and dependent on the taxa analysed, resulting in different taxonomic interpretations and schemes, particularly when it comes to ranking. Thus, what have been considered as genera by some, have been introduced as families by others. More recently, estimation of divergence times using molecular clock methods have been used as objective evidence for higher ranking of taxa. A divergence period (i.e. 200-300 MYA) can be used as a criterion to infer when a group of related taxa evolved and what rank they should be given. We compiled data on divergence times for various higher ranking taxa in the Kingdom Fungi. The kingdom evolved 1000-1600 MYA (Stenian-Calymmian), while the presently accepted phyla evolved between 358 and 541 MYA (Devonian-Cambrian). Divergence times for subphyla are generally between 358 and 485 MYA (Devonian-Ordovician), those of classes 145-358 MYA (Jurassic-Carboniferous), subclasses 66-358 MYA (Cretaceous-Carboniferous), orders 23-252 MYA (Paleogene-Triassic), families 2.8-145 MYA (Neogene-Cretaceous), and genera 2.8-66 MYA (Neogene-Paleogene). Thus, there are wide discrepancies in the times different taxa diverged. We provide an overview over Ascomycota, showing how application of temporal banding could affect the recognition of higher taxa at certain rank levels. We then use Sordariomycetes as an example where we use divergence times to provide additional evidence to stabilize ranking of taxa below class level. We propose a series of evolutionary periods that could be used as a guide to determine the various higher ranks of fungi: phyla[550 MYA, subphyla 400-550 MYA; classes 300-400 MYA; subclasses 250-300 MYA, orders 150-250 MYA, and families 50-150 MYA. It is proposed that classification schemes and ranking of taxa should, where possible, incorporate a polyphasic approach including phylogeny, phenotype, and estimate of divergence times.

Microfungi on Tamarix

Abstract: Tamarix species are small trees that grow in various natural habitats and have a wide geographic distribution. Microfungal species previously found on Tamarix and recently collected in Italy and Russia were identified based on morphological characters and analyses of gene sequence data. The sexual morph of the coelomycetous genus Homortomyces was collected for the first time and is described and illustrated. A new family, Homortomycetaceae (Dothideomycetes, families incertae sedis) is introduced to accommodate Homortomyces. Two new genera Neomicrosphaeropsis (Didymellaceae) and Tamaricicola (Pleosporaceae) are introduced in this paper. Phoma tamaricicola was recollected and is placed in Neomicrosphaeropsis based on morphology and molecular data. Ten new species, Cytospora italica, C. unilocularis, Diaporthe ravennica, Eutypella tamaricis, Neomicrosphaeropsis italica, N. novorossica, N. rossica, Keissleriella tamaricicola, Paracamarosporium tamaricis and Tamaricicola muriformis are introduced, while Alternaria tenuissima, Dothiorella sarmentorum, Neofusicoccum luteum, Paraepicoccum amazonense, Pleospora herbarum and Pseudocamarosporium propinquum are reported for the first time on Tamarix spp. with descriptions and illustrations. Multi-gene analyses show that Paraepicoccum amazonense should be placed in Pleosporineae, Pleosporales, where it is closely related to Camarosporium sensu stricto. Several herbarium specimens were studied to illustrate other fungal species recorded on Tamarix species. A comprehensive account of microfungi on Tamarix is provided, which includes a list with data from the literature, as well as those identified in the present study. The taxonomic placement of most taxa discussed in this study is based on a modern taxonomic framework based on analysis of multi-gene sequence data.

Efficacy of neutral and negatively charged liposome-loaded gentamicin on planktonic bacteria and biofilm communities.

Abstract: We investigated the efficacy of liposomal gentamicin formulations of different surface charges against Pseudomonas aeruginosa and Klebsiella oxytoca. The liposomal gentamicin formulations were prepared by the dehydration-rehydration method, and their sizes and zeta potential were measured. Gentamicin encapsulation efficiency inside the liposomal formulations was determined by microbiologic assay, and stability of the formulations in biologic fluid was evaluated for a period of 48 h. The minimum inhibitory concentration and the minimum bactericidal concentration were determined, and the in vitro time kill studies of the free form of gentamicin and liposomal gentamicin formulations were performed. The activities of liposomal gentamicin in preventing and reducing biofilm-forming P. aeruginosa and K. oxytoca were compared to those of free antibiotic. The sizes of the liposomal formulations ranged from 625 to 806.6 nm in diameter, with the zeta potential ranging from -0.22 to -31.7 mV. Gentamicin encapsulation efficiency inside the liposomal formulation ranged from 1.8% to 43.6%. The liposomes retained >60% of their gentamicin content during the 48 h time period. The minimum inhibitory concentration of neutral formulation was lower than that of free gentamicin (0.25 versus 1 mg/L for P. aeruginosa and 0.5 versus 1 mg/L for K. oxytoca). The negatively charged formulation exhibited the same bacteriostatic concentration as that of free gentamicin. The minimum bactericidal concentration of neutral liposomes on planktonic bacterial culture was twofold lower than that of free gentamicin, whereas the negatively charged formulations were comparable to free gentamicin. The killing time curve values for the neutral negatively charged formulation against planktonic P. aeruginosa and K. oxytoca were better than those of free gentamicin. Furthermore, liposomal formulations prevent the biofilm-formation ability of these strains better than free gentamicin. In summary, liposomal formulations could be an effective lipid nanoparticle to combat acute infections where planktonic bacteria are predominant.

Molecular taxonomy and morphological characterization reveal new species and new host records of Torula species (Torulaceae, Pleosporales)

Abstract: Four new species and two new host records of Torula (Torulaceae, Pleosporales) are described and illustrated from herbaceous litter collected in Italy and Thailand. The new species possess colony, conidiophore and conidial characteristics that fit within the generic concept of Torula. Detailed morphological observations clearly demarcate four of these from extant species and are hence described as new (Torula chiangmaiensis sp. nov., Torula pluriseptata sp. nov., Torula chromolaenae sp. nov., Torula mackenziei sp. nov.). Details of asexual morphs are described, and justifications for establishing these new species are provided. The nuclear are sequenced ribosomal RNA genes as well as protein coding genes to infer phylogenetic relationships and discuss phylogenetic affinities with morphologically similar species. Our morphological distinction is further supported by phylogenetic discrimination. In particular, phylogenies depict a close relationship of Torula chiangmaiensis and T. pluriseptata to T. hollandica, while T. chromolaenae and T. mackenziei constitute an independent phylogenetic lineage basal to T. herbarum and T. ficus. Torula ficus and T. masonii are also described and their phylogeny investigated as new host records from Bidens pilosa and Iris germanica, respectively.

New saprobic marine fungi and a new combination

Abstract: Abstract This paper documents five new saprobic marine fungi occurring on various substrata in the marine environment. Bacusphaeria nypae gen. et sp. nov. was discovered on bases of fronds of Nypa fruticans in Malaysia and phylogenetically, it belongs to the Tirisporellaceae (Tirisporellales, Diaporthomycetidae, Sordariomycetes) based on 18S and 28S rDNA. Cryptovalsa avicenniae, Ceriosporopsis minuta and Jattaea mucronata also belong to the Sordariomycetes; Cr. avicenniae was saprobic on Avicennia marina collected in Saudi Arabia, J. mucronata on intertidal decaying bark of Rhizophora mucronata while Ce. minuta was found on driftwood collected on a sandy beach in Japan. Phylogeny based on 18S and 28S rDNA placed Cr. avicenniae with other Cryptovalsa species in the Diatrypaceae. Jattaea mucronata groups well in the Calosphaeriales and is closely related to J. algeriensis based on a phylogeny using ITS and 28S rRNA and RPB2 genes. Aegeanispora elanii gen. et sp. nov. is an asexual fungus which produces pycnidia on decaying driftwood collected in the Aegean Sea. Combined 18S and 28S rDNA phylogenetic analyses suggest that it is a member of the Pleosporales, Dothideomycetes. Ceriosporopsis minuta resembles C. capillacea with its tubular, long polar appendages of ascospores but dimensions of ascomata and ascospores for the former species are considerably smaller. Ceriosporopsis is considered the best genus to accommodate C. minuta without support from sequence data. Sammeyersia is established as a new genus to accommodate Lulworthia grandispora, a species unrelated to Lulworthia fucicola, the type species. The diagnostic characteristic for the genus is a melanized region at the base of the neck of the ascomata.

A new species of Colletotrichum from Sonchus sp. in Italy

Abstract: Colletotrichum sonchicola , sp. nov . from Sonchus sp. (dandelion tribe) in Forli-Cesena Province, Italy, is introduced using morphological and molecular data. Combined phylogenetic analysis of ITS, GAPDH, CHS, ACT and TUB2 sequence data demonstrate that C. sonchicola is a distinct species within the dematium species complex. The new species is illustrated and compared with related taxa. This provides the first record of a Colletotrichum species from the genus Sonchus .

Life-history Traits of the Blacktrip sardinella, Sardinella melanura (Clupeidae) in the Gwadar, Balochistan Coast, Pakistan

Abstract: The present study describes the first complete and comprehensive description on life-history traits of Sardinella melanura including length-frequency distributions (LFDs), length-weight relationships (LWRs), condition factors (allometric condition, KA; Fulton’s condition, KF; relative condition, KR), and relative weight (WR) in the Gwadar, Balochistan Coast, Pakistan. Additionally, form factor (a3.0) using available a and b regression parameters of LWRs and size at first sexual maturity (Lm) using available maximum length for 07 Sardinella spp. in 23 water-bodies were calculated. Seasonal samples of S. melanura were collected from the Gwadar, Balochistan Coast, Pakistan using gill nets during July 2013 to J u n e 2014. Total length (TL) was measured to nearest 0.1 cm using digital slide calipers and total body weight (BW) was measured using an electronic balance with 0.1 g accuracy for each individual. A total of 600 individuals of S. melanura were analyzed, where minimum and maximum TL was 12.5 cm and 23.00 cm, respectively and BW was 16.5g and 114.8 g, correspondingly. Highest number (25.83%) of its population stands at 17.00 cm to 18.00 cm size group. The b value of LWR indicated negative allometric growth in the population. All the condition factors (KA, KF, KR, and WR) were significantly correlated with TL and BW (P < 0.001). WR showed significant difference from 100 (P < 0.001) representing imbalanced population in presence of prey and predator. In addition, the a3.0 for S. melanura was 0.0078. The size at first sexual maturity (Lm) was 14.43 cm in TL of S. melanura in the Gwadar, Balochistan coast, Pakistan.

A new species of Trichoglossum (Geoglossales, Ascomycota) from Thailand

Abstract: The genus Trichoglossum ( Geoglossaceae ) is characterized by black, clavate, stipitate apothecia with hymenial setae. We collected T. cf. octopartitum from China and a new species of Trichoglossum from Thailand, the latter named as T. septatum. According to morphological examination and molecular phylogenetic analyses of ITS sequence data, T. septatum diverges from other Trichoglossum species. Full descriptions, colour figures, and a phylogenetic tree to show the positions of T. cf. octopartitum and T. septatum are provided, and the two species are compared with allied taxa. The important morphological characteristics of Trichoglossum species are also summarized.

Seasonal Variations of Growth Pattern and Condition of Paradise threadfin Polynemus paradiseus (Polynemidae) from Tetulia River in Southern Bangladesh

Abstract: A total of 900 individuals (pre-monsoon = 250, monsoon = 350, post-monsoon = 300) of P. paradiseus were collected from the fishers catches during January to December 2014. For each individual, TL (total length) and BW (body weight) were measured with 0.1 cm and 0.1 g accuracy, respectively. Length weight relationship (LWR) was estimated by the equation, W = a × L. Length-frequency distributions (LFD) were significantly different between the seasons (P < 0.001). Allometric coefficient (b values) of LWRs (TL vs. BW) indicated isometric growth in pre-monsoon and post-monsoon (b ≈ 3), but negative allometric growth was found in monsoon (b < 3). All LWRs were highly significant (P < 0.001) with all r values ≥ 0.984. The LWRs were significantly difference between the seasons (ANCOVA, P < 0.001). The KF is highly correlated with TL (Spearman rank test, P < 0.001) in all the seasons, thus suggesting the best condition factor for assessing the wellbeing of this fish in our study area. Additionally, the WR was significantly different from 100 (Wilcoxon rank test, P = 0.003) in pre-monsoon, which indicates the habitat was in poor condition for P. paradiseus, nevertheless it was not significantly differed in monsoon (P = 0.0186) and post-monsoon (P = 0.423). The calculated Lm was 12.1 cm in TL and form factor was 0.0061 for P. paradiseus in the Tetulia River.

Alfaria avenellae sp. nov. from Italy

Abstract: A new species Alfaria avenellae , is described, illustrated and compared with other Alfaria species. Evidence for the new species is provided by morphological comparison and sequence data analyses. Alfaria avenellae can easily be distinguished from other Alfaria species by its distinct synnemata, long conidiophores (up to 350 μm) and pale green to dark green conidia. Phylogenetic analysis of combined LSU and ITS sequence data was carried out to determine the phylogenetic placement of this new species within the genus Alfaria and provide evidence to support the establishment of our new species.

Temporal variations of condition and prey-predator status for two Halfbeaks ( Hemiramphus archipelagicus and H. lutkei ) in the Karachi Coast of Pakistan through multi-model inference

Abstract: Department of Zoology, Federal Urdu University of Arts, Science and Technology, Gulshan-e-Iqbal Campus, Karachi 75300, Pakistan Department of Zoology, University of Karachi, Karachi 75270, Pakistan Department of Fisheries, Faculty of Agriculture, University of Rajshahi, Rajshahi 6205, Bangladesh School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia