Dothideomycetes comprise a highly diverse range of fungi characterized mainly by asci with two wall layers (bitunicate asci) and often with fissitunicate dehiscence. Many species are saprobes, with many asexual states comprising important plant pathogens. They are also endophytes, epiphytes, fungicolous, lichenized, or lichenicolous fungi. They occur in terrestrial, freshwater and marine habitats in almost every part of the world. We accept 105 families in Dothideomycetes with the new families Anteagloniaceae, Bambusicolaceae, Biatriosporaceae, Lichenoconiaceae, Muyocopronaceae, Paranectriellaceae, Roussoellaceae, Salsugineaceae, Seynesiopeltidaceae and Thyridariaceae introduced in this paper. Each family is provided with a description and notes, including asexual and asexual states, and if more than one genus is included, the type genus is also characterized. Each family is provided with at least one figure-plate, usually illustrating the type genus, a list of accepted genera, including asexual genera, and a key to these genera. A phylogenetic tree based on four gene combined analysis add support for 64 of the families and 22 orders, including the novel orders, Dyfrolomycetales, Lichenoconiales, Lichenotheliales, Monoblastiales, Natipusillales, Phaeotrichales and Strigulales. The paper is expected to provide a working document on Dothideomycetes which can be modified as new data comes to light. It is hoped that by illustrating types we provide stimulation and interest so that more work is carried out in this remarkable group of fungi.

Families of Dothideomycetes

Notes on 113 fungal taxa are compiled in this paper, including 11 new genera, 89 new species, one new subspecies, three new combinations and seven reference specimens. A wide geographic and taxonomic range of fungal taxa are detailed. In the Ascomycota the new genera Angustospora (Testudinaceae), Camporesia (Xylariaceae), Clematidis, Crassiparies (Pleosporales genera incertae sedis), Farasanispora, Longiostiolum (Pleosporales genera incertae sedis), Multilocularia (Parabambusicolaceae), Neophaeocryptopus (Dothideaceae), Parameliola (Pleosporales genera incertae sedis), and Towyspora (Lentitheciaceae) are introduced. Newly introduced species are Angustospora nilensis, Aniptodera aquibella, Annulohypoxylon albidiscum, Astrocystis thailandica, Camporesia sambuci, Clematidis italica, Colletotrichum menispermi, C. quinquefoliae, Comoclathris pimpinellae, Crassiparies quadrisporus, Cytospora salicicola, Diatrype thailandica, Dothiorella rhamni, Durotheca macrostroma, Farasanispora avicenniae, Halorosellinia rhizophorae, Humicola koreana, Hypoxylon lilloi, Kirschsteiniothelia tectonae, Lindgomyces okinawaensis, Longiostiolum tectonae, Lophiostoma pseudoarmatisporum, Moelleriella phukhiaoensis, M. pongdueatensis, Mucoharknessia anthoxanthi, Multilocularia bambusae, Multiseptospora thysanolaenae, Neophaeocryptopus cytisi, Ocellularia arachchigei, O. ratnapurensis, Ochronectria thailandica, Ophiocordyceps karstii, Parameliola acaciae, P. dimocarpi, Parastagonospora cumpignensis, Pseudodidymosphaeria phlei, Polyplosphaeria thailandica, Pseudolachnella brevifusiformis, Psiloglonium macrosporum, Rhabdodiscus albodenticulatus, Rosellinia chiangmaiensis, Saccothecium rubi, Seimatosporium pseudocornii, S. pseudorosae, Sigarispora ononidis and Towyspora aestuari. New combinations are provided for Eutiarosporella dactylidis (sexual morph described and illustrated) and Pseudocamarosporium pini. Descriptions, illustrations and / or reference specimens are designated for Aposphaeria corallinolutea, Cryptovalsa ampelina, Dothiorella vidmadera, Ophiocordyceps formosana, Petrakia echinata, Phragmoporthe conformis and Pseudocamarosporium pini. The new species of Basidiomycota are Agaricus coccyginus, A. luteofibrillosus, Amanita atrobrunnea, A. digitosa, A. gleocystidiosa, A. pyriformis, A. strobilipes, Bondarzewia tibetica, Cortinarius albosericeus, C. badioflavidus, C. dentigratus, C. duboisensis, C. fragrantissimus, C. roseobasilis, C. vinaceobrunneus, C. vinaceogrisescens, C. wahkiacus, Cyanoboletus hymenoglutinosus, Fomitiporia atlantica, F. subtilissima, Ganoderma wuzhishanensis, Inonotus shoreicola, Lactifluus armeniacus, L. ramipilosus, Leccinum indoaurantiacum, Musumecia alpina, M. sardoa, Russula amethystina subp. tengii and R. wangii are introduced. Descriptions, illustrations, notes and / or reference specimens are designated for Clarkeinda trachodes, Dentocorticium ussuricum, Galzinia longibasidia, Lentinus stuppeus and Leptocorticium tenellum. The other new genera, species new combinations are Anaeromyces robustus, Neocallimastix californiae and Piromyces finnis from Neocallimastigomycota, Phytophthora estuarina, P. rhizophorae, Salispina, S. intermedia, S. lobata and S. spinosa from Oomycota, and Absidia stercoraria, Gongronella orasabula, Mortierella calciphila, Mucor caatinguensis, M. koreanus, M. merdicola and Rhizopus koreanus in Zygomycota.

Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa

This article provides an outline of the classification of the kingdom Fungi (including fossil fungi. i.e. dispersed spores, mycelia, sporophores, mycorrhizas). We treat 19 phyla of fungi. These are Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota. The placement of all fungal genera is provided at the class-, order- and family-level. The described number of species per genus is also given. Notes are provided of taxa for which recent changes or disagreements have been presented. Fungus-like taxa that were traditionally treated as fungi are also incorporated in this outline (i.e. Eumycetozoa, Dictyosteliomycetes, Ceratiomyxomycetes and Myxomycetes). Four new taxa are introduced: Amblyosporida ord. nov. Neopereziida ord. nov. and Ovavesiculida ord. nov. in Rozellomycota, and Protosporangiaceae fam. nov. in Dictyosteliomycetes. Two different classifications (in outline section and in discussion) are provided for Glomeromycota and Leotiomycetes based on recent studies. The phylogenetic reconstruction of a four-gene dataset (18S and 28S rRNA, RPB1, RPB2) of 433 taxa is presented, including all currently described orders of fungi.

https://biblio.ugent.be/publication/8660838/file/8660843.pdf

Outline of Fungi and fungus-like taxa

Research on the mechanisms employed by the biocontrol agent Trichoderma virens to suppress cotton (Gossypium hirsutum) seedling disease incited by Rhizoctonia solani has shown that mycoparasitism and antibiotic production are not major contributors to successful biological control. In this study, we examined the possibility that seed treatment with T. virens stimulates defense responses, as indicated by the synthesis of terpenoids in cotton roots. We also examined the role of these terpenoid compounds in disease control. Analysis of extracts of cotton roots and hypocotyls grown from T. virens-treated seed showed that terpenoid synthesis and peroxidase activity were increased in the roots of treated plants, but not in the hypocotyls of these plants or in the untreated controls. Bioassay of the terpenoids for toxicity to R. solani showed that the pathway intermediates desoxyhemigossypol (dHG) and hemigossypol (HG) were strongly inhibitory to the pathogen, while the final product gossypol (G) was toxic only at a much higher concentration. Strains of T. virens and T. koningii were much more resistant to HG than was R. solani, and they thoroughly colonized the cotton roots. A comparison of biocontrol efficacy and induction of terpenoid synthesis in cotton roots by strains of T. virens, T. koningii, T. harzianum, and protoplast fusants indicated that there was a strong correlation (+0.89) between these two phenomena. It, therefore, appears that induction of defense response, particularly terpenoid synthesis, in cotton roots by T. virens may be an important mechanism in the biological control by this fungus of R. solani-incited cotton seedling disease.

Induction of terpenoid synthesis in cotton roots and control of Rhizoctonia solani by seed treatment with Trichoderma virens. [Erratum: 2003 Dec., v. 93, no. 12, p. 1606.]

http://rmf.smf.org.mx/suplemento/docs/Volumen332015/sh/CM2.pdf

Generic concepts in Nectriaceae

This is the first high-throughput amplicon sequencing study of mycobiome associated with leaves of the seagrass Halophila stipulacea. Five leaf samples were collected from the Al-Leith mangroves along the Red Sea coast of Saudi Arabia. Total DNA was extracted from 250 mg of each sample, and the first 300 bp (contains D1-D2 variable regions) of the LSU rDNA amplicon was sequenced with the Illumina MiSeq (bTEFAP). A total of 928,626 reads were obtained from the five samples. The sequence reads belonged to Metazoa (48.1% of the total reads), Viridiplantae (41.1%), Eukaryota (8.8%), Fungi (1.96%), Bacteria (0.09%), and Archaea (0.0001%). Fungi represented between 1.1% and 5.8% of the total reads in the five samples. A total of 18,279 reads (representing 1.96% of the total reads) were recorded from the 5 samples representing 296 molecular species (OTUs) that belong to 13 fungal phyla. At the phylum level, Basidiomycota dominated the community (37.2–51.6%) in three samples, while Neocallimastigomycota (37.5%) and Mucoromycota (42.1%) dominated the community in the fourth and the fifth samples, respectively. High diversity of OTUs (28 molecular species) were recorded from the monokaryotic subkingdom with five unknown basal lineages that are not aligning with any known taxa. Total number of sequence reads of microbial eukaryote organisms (Stramenopiles) from the five samples ranged between 0.16 of total reads in the fifth sample (AL-Hs05) to 2.9% in the first one (AL-Hs01). Majority of the microbial eukaryote reads (93.6%) belong to the phylum Oomycota, followed by Opisthokonts (Fungi/Metazoa group) representing 6.4% of microbial eukaryote reads. Monokaryon phyla (i.e., Chytridiomycota, Mucoromycota, and Neocallimastigomycota) and microbial eukaryotes occupied a major portion of the sequence reads followed by Basidiomycota and Ascomycota. Our results support the findings that the majority of fungi and microbial eukaryotes communities are so far unknown with seven deep branching lineages remain to be cultivated.

High-throughput amplicon sequencing of fungi and microbial eukaryotes associated with the seagrass Halophila stipulacea (Forssk.) Asch. from Al-Leith mangroves, Saudi Arabia

Strain SY-07 was isolated from decaying leaves of Avicennia marina collected from Syhat mangroves, Dammam city, Arabian Gulf, Saudi Arabia. Phylogenetic analyses of three genes [D1/D2 region of the LSU and SSU rRNA genes and internal transcribed spacer (ITS) region] showed that strain SY-07 represents a novel species of the genus Saturnispora distinct from closely related species. Saturnispora mendoncae was the most closely related species with an LSU gene sequence similarity of 89.3 % (58 nucleotide substitutions and four indels out of 578 nt), 97 % similarity for the SSU gene (42 nucleotide substitutions and 10 indels out of 1614 nt) and 88 % similarity for the ITS region (15 nucleotide substitutions and eight indels out of 430 nt). In addition, strain SY-07 differed from S. mendoncae by its ability to assimilate d-galactose (weak), d-xylose (weak), meso-erythritol (delayed), glucono-δ-lactone, citrate (delayed) and ethylamine. S. mendoncae produced persistent asci that contain two to four spherical ascospores and lacked pseudohyphae, while sexual reproduction was not observed in strain SY-07 and extensive and pseudohyphae were present. Strain SY-07 was able to grow at between 25 and 40 °C, while S. mendoncae did not grow at 37 °C. The name Saturnispora mangrovi f.a., sp. nov. is proposed for strain SY-07. The holotype is CBS 15874, with the ex-type culture AUMC 12005. The MycoBank number for Saturnispora mangrovi f.a., sp. nov. is MB 827036.

Saturnispora mangrovi f.a., sp. nov. from Syhat mangrove, Saudi Arabia.

In this paper, a video object segmentation method utilizing the motion of superpixel centroids is proposed. Our method achieves the same advantages of methods based on clustering point trajectories, furthermore obtaining dense clustering labels from sparse ones becomes very easy. Simply for each superpixel the label of its centroid is propagated to all its entire pixels. In addition to the motion of superpixel centroids, histogram of oriented optical flow, HOOF, extracted from superpixels is used as a second feature. After segmenting each object, we distinguish between foreground objects and the background utilizing the obtained clustering results.

Video Object Segmentation Based on Superpixel Trajectories

An enhanced feature space to represent visual complexity of images, as would the HVS, is presented. Specifically, the ratio between the coherent and incoherent pixels in an image was used as a measure of the chromatic contributions to the visual complexity of an image. Similarly, the contrast, energy, entropy and homogeneity were modelled as the textural attributes of an image's visual complexity. Integrated into the SND feature space, these new (chromatic and textural) features facilitate a better and enhanced representation of visual complexity. Using the Corel 1000A dataset to validate the veracity of the proposal, the enhanced visual complexity space, the SND+ space, improves the capability to better represent visual complexity by a 16.7% increase in the exact correlation with a subjective (human) evaluation of the same dataset over the original SND space. Pursued further, the effective representation of visual complexity would have profound impacts in many areas of image processing and computer vision.

Mohamed A. Abdel-Wahab

Papers

High-throughput amplicon sequencing of fungi and microbial eukaryotes associated with the seagrass Halophila stipulacea (Forssk.) Asch. from Al-Leith mangroves, Saudi Arabia

Saturnispora mangrovi f.a., sp. nov. from Syhat mangrove, Saudi Arabia.

Video Object Segmentation Based on Superpixel Trajectories

Mining visual complexity of images based on an enhanced feature space representation

Thraustochytrids from the Red Sea mangroves in Saudi Arabia and their abilities to produce docosahexaenoic acid