Mountain tips as reservoirs for new rock-fungal entities: Saxomyces gen. nov. and four new species from the Alps

As part of a worldwide sampling nine black fungi were isolated from rocks collected in four distinct sites of the Alps at high altitudes.Based on a nucSSU,nucLSU and mtSSU multi-locus phylogeny,seven of them were found to cluster into a distinct and wellsupported clade in a basal position within the Class Dothideomycetes.As in other rock fungi these new groups of isolates were characterized by a meristematic growth and a scarcely differentiated morphology with highly melanized and thick-walled toruloid hyphae.Nonetheless,few peculiar characters were also observed as convoluted hyphal tips and the production of spherical propagules.The new genus and species Saxomyces alpinus and S.penninicus,are here described based on morphological and molecular data,in a yet to be defined order of the Dothideomycetes.The remaining two black fungi clustered in Cryomyces,a genus previously exclusively found in rocks from the McMurdo Dry Valleys in Antarctica.These two isolates were genetically distant from other Antarctic Cryomyces species based on ITS sequences,and they showed a peculiar morphology;they are here described as the new species C.montanus and C.funiculosus.Implications of our results on the evolution,adaptation and dispersal of rock-inhabiting fungi under extreme conditions are discussed.

A multi-locus phylogenetic evaluation of Diaporthe (Phomopsis)

The genus Diaporthe(Phomopsis)includes important plant pathogenic fungi with wide host ranges and geographic distributions.In the present study,phylogenetic species recognition in Diaporthe is re-evaluated using a multi-locus phylogeny based on a combined data matrix of rDNA ITS,and partial sequences from the translation elongation factor 1-α(EF 1-α),βtubulin(TUB)and calmodulin(CAL)molecular markers.DNA sequences of available extype cultures have been included,providing a multi-locus backbone tree for future studies on Diaporthe.Four utilizable loci were analyzed individually and in combination,and ITS,EF 1-αand multi-locus phylogenetic trees are presented.The phylogenetic tree inferred by combined analysis of four loci provided the best resolution for species as compared to single gene analysis.Notes are provided for nine species previously known in Phomopsis that are transferred to Diaporthe in the present study.The unraveling of cryptic species complexes of Diaporthe based on Genealogical Concordance Phylogenetic Species Recognition(GCPSR)is emphasized.

A phylogenetic and taxonomic re-evaluation of the Bipolaris - Cochliobolus - Curvularia Complex

Three genera,Cochliobolus,Bipolaris and Curvularia form a complex that contains many plant pathogens,mostly on grasses(Poaceae)with a worldwide distribution.The taxonomy of this complex is confusing as frequent nomenclatural changes and refinements have occurred.There is no clear morphological boundary between the asexual genera Bipolaris and Curvularia,and some species show intermediate morphology.We investigated this complex based on a set of ex-type cultures and collections from northern Thailand.Combined gene analysis of rDNA ITS(internal transcribed spacer),GPDH(glyceraldehyde 3-phosphate dehydrogenase),LSU(large subunit)and EF1-α(translation elongation factor 1-α)shows that this generic complex divides into two groups.Bipolaris and Cochliobolus species clustered in Group 1 along with their type species,whereas Curvularia species(including species named as Bipolaris,Cochliobolus and Curvularia)clustered in Group 2,with its generic type.The nomenclatural conflict in this complex is resolved giving priority to the more commonly used established generic names Bipolaris and Curvularia.Modern descriptions of the genera Bipolaris and Curvularia are provided and species resolved in this study are transferred to one of these genera based on their phylogeny.

Species of the Colletotrichum gloeosporioides complex associated with anthracnose diseases of Proteaceae

Anthracnose disease of Proteaceae has in the past chiefly been attributed to infections by C.acutatum,C.boninense and C.gloeosporioides.In the present study,a multi-locus phylogenetic analysis(ACT,CAL,CHS-1,GAPDH,GS,ITS,TUB2)revealed that strains of the C.gloeosporioides complex associated with Proteaceae belong to at least six species.These include C.alienum,C.aotearoa,C.kahawae(subsp.ciggaro),C.siamense,and two new taxa,C.proteae and C.grevilleae.The most economically important pathogen of Proteaceae seems to be C.alienum,and not C.gloeosporioides as previously reported.All taxa associated with Proteaceae are morphologically described on different media in culture,except strains of C.siamense,which proved to be sterile.Furthermore,C.populi is synonymised with C.aenigma.

A multi-locus backbone tree for Pestalotiopsis, with a polyphasic characterization of 14 new species

Pestalotiopsis is a taxonomically confused,pathogenic and chemically creative genus requiring a critical reexamination using a multi-gene phylogeny based on ex-type and ex-epitype cultures.In this study 40 isolates of Pestalotiopsis,comprised of 28 strains collected from living and dead plant material of various host plants from China were studied by means of morphology and analysis of ITS,β–tubulin and tef1 gene sequence data.Based on molecular and morphological data we describe 14 new species(Pestalotiopsis asiatica,P.chinensis,P.chrysea,P.clavata,P.diversiseta,P.ellipsospora,P.inflexa,P.intermedia,P.linearis,P.rosea,P.saprophyta,P.umberspora,P.unicolor and P.verruculosa)and three species are epitypified(P.adusta,P.clavispora and P.foedans).Of the 10 gene regions(ACT,β-tubulin,CAL,GPDH,GS,ITS,LSU,RPB 1,SSU and tef1)utilized to resolve cryptic Pestalotiopsis species,ITS,β–tubulin and tef1 proved to be the better markers.The other gene regions were less useful due to poor success in PCR amplification and/or in their ability to resolve species boundaries.As a single gene tef1 met the requirements for an ideal candidate and functions well for species delimitation due to its better species resolution and PCR success.Althoughβ-tubulin showed fairly good differences among species,a combination of ITS,β-tubulin and tef1 gene data gave the best resolution as compared to single gene analysis.This work provides a backbone tree for 22 ex-type/epitypified species of Pestalotiopsis and can be used in future studies of the genus.

Pleosporales

One hundred and five generic types of Pleosporales are described and illustrated.A brief introduction and detailed history with short notes on morphology,molecular phylogeny as well as a general conclusion of each genus are provided.For those genera where the type or a representative specimen is unavailable,a brief note is given.Altogether 174 genera of Pleosporales are treated.Phaeotrichaceae as well as Kriegeriella,Zeuctomorpha and Muroia are excluded from Pleosporales.Based on the multigene phylogenetic analysis,the suborder Massarineae is emended to accommodate five families,viz.Lentitheciaceae,Massarinaceae,Montagnulaceae,Morosphaeriaceae and Trematosphaeriaceae.

The Colletotrichum orbiculare species complex: Important pathogens of field crops and weeds

Colletotrichum orbiculare causes anthracnose of Cucurbitaceae and is phylogenetically closely related to pathogens of several other herbaceous hosts belonging to the Asteraceae,Fabaceae and Malvaceae.Most of them are known for their hemibiotrophic infection strategy and as destructive pathogens either of field crops or weeds.In order to study the phylogenetic relationships of these fungi,a multilocus analysis(ITS,GAPDH,CHS-1,HIS3,ACT,TUB2,GS)of 42 strains of C.orbiculare and related species was conducted.The analysis resulted in nine clades that confirmed the four species previously known as belonging to this species complex,C.lindemuthianum,C.malvarum,C.orbiculare and C.trifolii,and recognised four new species from weeds,namely C.bidentis,C.sidae,C.spinosum and C.tebeestii.The name C.orbiculare itself is widely used in plant pathology and science,but is invalid according to current nomenclatural rules.Therefore we described a new species with the same epithet and a type specimen that agrees with our current understanding of this species,and is linked to a living culture.Following the recent epitypification of C.lindemuthianum,we chose appropriate specimens with associated strains to serve as epitypes of C.malvarum and C.trifolii,and selected an authentic specimen of C.trifolii as lectotype.

Phyllosticta species associated with freckle disease of banana

The identity of the casual agent of freckle disease of banana was investigated.The pathogen is generally referred to in literature under its teleomorphic name,Guignardia musae,or that of its purported anamorph,Phyllosticta musarum.Based on morphological and molecular data from a global set of banana specimens,several species were found associated with freckle disease.Phyllosticta maculata(from Southeast Asia and Oceania)is introduced as a new name for Guignardia musae,and an epitype is designated from Australia.Phyllosticta musarum(from India and Thailand)is shown to represent a distinct species,and the name is fixed by designation of an epitype from India.Guignardia stevensii is confirmed as distinct species from Hawaii,while Guignardia musicola from northern Thailand is shown to contain different taxa and is regarded as nomen confusum.Phyllosticta cavendishii is described as a new,widely distributed species,appearing primarily on Cavendish,but also on non-Cavendish banana cultivars.

Phyllosticta capitalensis,a widespread endophyte of plants

Phyllosticta capitalensis is an endophyte and weak plant pathogen with a worldwide distribution presently known from 70 plant families.This study isolated P.capitalensis from different host plants in northern Thailand,and determined their different life modes.Thirty strains of P.capitalensis were isolated as endophytes from 20 hosts.An additional 30 strains of P.capitalensis from other hosts and geographic locations were also obtained from established culture collections.Phylogenetic analysis using ITS,ACTand TEF gene data confirmed the identity of all isolates.Pathogenicity tests with five strains of P.capitalensis originating from different hosts were completed on their respective host plants.In all cases there was no infection of healthy leaves,indicating that this endophyte does not cause disease on healthy,unstressed host plants.That P.capitalensis is often isolated as an endophyte has important implications in fungal biology and plant health.Due to its endophytic nature,P.capitalensisis commonly found associated with lesions of plants,and often incorrectly identified as a species of quarantine importance,which again has implications for trade in agricultural and forestry production.

Extremotolerant rock inhabiting black fungi from Italian monumental sites

A wide sampling for isolating highly destructive and extremotolerant black fungi was performed from Italian monuments in selected historical sites which include the "Cortile della Pigna",Vatican Museum and the St Peter colonnade(Vatican City State),the monumental cemetery of Bonaria(Cagliari),and other monuments in the city of Cagliari.Thirty out of seventy-four strains isolated were identified basing on ITS Blastn comparison.Based on multilocus phylogeny and morphological data,one new genus and species Lithophila guttulata,five new species Knufia marmoricola,K.vaticanii,K.karalitana,K.mediterranea and Exophiala bonariae,order Chaetothyriales and one new genus and species,Saxophila tyrrhenica,and two new species Vermiconia calcicola and Devriesia sardiniae,order Capnodiales,were proposed.Ecological considerations are put forward.

Phylogeny of the industrial relevant,thermophilic genera Myceliophthora and Corynascus

Species of the genus Myceliophthora and its teleomorph Corynascus have attracted increasing interest due to their potential to produce thermostable enzymes.This study re-assessed the phylogenetic relationship of 49 isolates of nine species belonging to Myceliophthora and Corynascus.One species,M.vellerea,was shown not to belong to the genus Myceliophthora and should be placed in the genus Ctenomyces.The other species belonged to two phylogenetic clusters:mesophilic fungi with the type species M.lutea and C.sepedonium,and thermophilic fungi with M.thermophila,M.hinnulea and C.thermophilus.The phylogenetic data provides no clear separation of the two genera Corynascus and Myceliophthora.To avoid confusion in future taxonomic studies,it is proposed that all existing Corynascus species be renamed to Myceliophthora,which is the old name and the one more frequently used.Furthermore,this study identified two groups within the isolates listed as M.thermophila and assigned one group(five isolates)to M.heterothallica based on AFLP analysis and mating behavior.This study provides new insights into the genetic differences within the genus Myceliophthora and will therefore be essential for the interpretation of future genomic and physiological studies of these species.

Cryptococcus gattii infections in China： extent of the problem？

Approximately 70 species are accepted in the genus Cryptococcus; however, only two species,Cryptococcus neoformans （ C. neoformans, AD and D） and C. gattii （serotypes B responsible for almost all human infections,2,3 and resulted in over 1 million cryptococcosis in the world each year with casualties.4 It is generally assumed that serotypes A, and C） are cryptococcal new cases of over 600000 cryptococcal infections are acquired by inhalation of fungal spores, desiccated cells, or poorly encapsulated yeasts from environmental niches, such as decayed wood debris of certain tree species or bird droppings.5 Epidemiological surveys have shown that C. neoformans caused about 80% of cryptococcosis cases globally each year, particularly in immunocompromised persons, such as human immunodeficiency virus （HIV）-infected people and acquired immunodeficiency syndrome （AIDS） patients,2＇3 while C. gattii primarily infects apparently immunocompetent hosts, and is mainly responsible for the remaining cases of cryptococcosls6,7

A multigene phylogeny reveals that Ochroconis belongs to the family Sympoventuriaceae (Venturiales,Dothideomycetes)

Ochroconis is a genus of ascomycete fungi that includes oligotrophic saprobes and some opportunistic species causing infections in vertebrates.The most important of these opportunists is the neurotropic species Ochroconis gallopava,which occurs in birds and occasionally in immunocompromised humans.Other Ochroconis species have been isolated from superficial infections of cats,dogs and fish.In their natural environment,these species are found in litter,soil,and on moist surfaces.Some thermophilic species have been isolated from hot springs,industrial effluents,and self-heated plant material.Although their ecology and epidemiology has been investigated,their classification within the ascomycetes is still unknown.Here,the phylogenetic placement of Ochroconis is investigated using a four-gene phylogeny(nuLSU,nuSSU,mtSSU and RPB2).The results show that Ochroconis and its recently described sister genus Verruconis belong to the order Venturiales(Dothideomycetes)and are nested within the Sympoventuriaceae,a family recently erected for a group of plant-saprobes or-pathogens sister to the Venturiaceae.They form a well-supported monophyletic group together with five species of the anamorphic genus Fusicladium isolated from leaf and needle litters.

European Species of Hebeloma Section Theobromina

This paper addresses section Theobromina within the genus Hebeloma(Agaricales).We recognise seven European species within this section,three of which are described as new:Hebeloma alboerumpens,H.griseopruinatum and H.parvicystidiatum.The first two of these species appear to be ectomycorrhizal with Cistaceae:Cistus and Helianthemum.Hebeloma parvicystidiatum is more likely to be in mycorrhizal association with Quercus spp.We also provide a key to the European species within sect.Theobromina and an updated key of known Hebeloma associates of Cistus.Molecular analyses based on multiple loci further illustrate the distinctness of the newly described taxa and provide molecular evidence,supporting the morphological evidence,for the relationship that exists among species of this section.The ITS is the only one from the sequenced loci that,alongside with morphology,distinguishes among all of the species of sect.Theobromina.The section gains most of its molecular support from the MCM7 locus,followed by RPB2.

Taxonomy of Ochroconis, genus including opportunistic pathogens on humans and animals

The genus Ochroconis(Sympoventuriaceae,Venturiales)is revised and currently contains 13 species for which the phylogenetic position has been determined using multilocus sequencing.The older generic name Scolecobasidium is considered to be of doubtful identity because the type specimen is ambiguous.Within the Ochroconis lineage,phylogenetic distances of all markers analyzed are exceptionally large,both between and within species.A new genus Verruconis is proposed for the neurotropic opportunist Ochroconis gallopava.Species accepted within the lineages are keyed out on the basis of phenotypic characters.Main ecological traits within each species are discussed.Verruconis species are thermophilic and one of them is an important agent of infection in the brain,while Ochroconis is mesophilic,several species causing infections in cold-blooded animals.

One stop shop:backbones trees for important phytopathogenic genera:Ⅰ(2014)

Many fungi are pathogenic on plants and cause significant damage in agriculture and forestry.They are also part of the natural ecosystem and may play a role in regulating plant numbers/density.Morphological identification and analysis of plant pathogenic fungi,while important,is often hampered by the scarcity of discriminatory taxonomic characters and the endophytic or inconspicuous nature of these fungi.Molecular(DNA sequence)data for plant pathogenic fungi have emerged as key information for diagnostic and classification studies,although hampered in part by non-standard laboratory practices and analytical methods.To facilitate current and future research,this study provides phylogenetic synopses for 25 groups of plant pathogenic fungi in the Ascomycota,Basidiomycota,Mucormycotina(Fungi),and Oomycota,using recent molecular data,up-to-date names,and the latest taxonomic insights.Lineagespecific laboratory protocols together with advice on their application,as well as general observations,are also provided.We hope to maintain updated backbone trees of these fungal lineages over time and to publish them jointly as new data emerge.Researchers of plant pathogenic fungi not covered by the present study are invited to join this future effort.Bipolaris,Botryosphaeriaceae,Botryosphaeria,Botrytis,Choanephora,Colletotrichum,Curvularia,Diaporthe,Diplodia,Dothiorella,Fusarium,Gilbertella,Lasiodiplodia,Mucor,Neofusicoccum,Pestalotiopsis,Phyllosticta,Phytophthora,Puccinia,Pyrenophora,Pythium,Rhizopus,Stagonosporopsis,Ustilago and Verticillium are dealt with in this paper.

Dishwashers provide a selective extreme environment for human-opportunistic yeast-like fungi

Urban life has led to the creation of human-made environments that,from a microbiological perspective,provide extreme life conditions.Certain non-ubiquitous microorganisms such as thermophilic members of the black yeast genus Exophiala are enriched within these habitats for which no counterpart is known in nature.Dishwashers consistently accumulate a number of specific black,white and red yeasts on the rubber seals of doors and in stagnant water at the interior.Several of these yeasts are primarily known as agents of human opportunistic infections.In this review,the literature data are supported by a screening study involving 937 households in 15 cities in Turkey.Fungi were detected in 230 samples(24.5%).Using rDNA sequencing,the prevalent species were identified as Exophiala dermatitidis(n=116),Candida parapsilosis(n=44),E.phaeomuriformis(n=35),Magnusiomyces capitatus(n=22),Rhodotorula mucilaginosa(n=15),and C.lusitaniae(n=14).The possible role of dishwashers in transmitting disease is discussed.

Environmental siblings of black agents of human chromoblastomycosis

Agents of human chromoblastomycosis,a skin disease almost exclusively caused by members of the order Chaetothyriales,are assumed to be traumatically inoculated into the skin with sharp environmental materials such as plant thorns or wooden splinters carrying the respective opportunist.In the supposition that such fungi should have their main habitat in the environment,we investigated the occurrence of black fungi in living areas of patients with chromoblastomycosis.In South America Fonsecaea agents are prevalent as agents of the disease,while also related Cladophialophora species,known from other types of skin infections,are known from the continent.Ninety environmental isolates were preliminarily selected as possible agents of chromoblastomycosis,based on morphology.Judging from ITS sequence data isolates were attributed to the genera Cladophialophora,Cyphellophora,Exophiala,Fonsecaea,Phialophora,and Veronaea.A total of 45 fungi morphologically identified as Fonsecaea or Cladophialophora isolated from debris and thorns of living prickly plants in Brazil were processed for taxonomic studies.Phylogenetic analysis revealed that the isolates indeed belonged to the Chaetothyriales,but only rarely an agent of chromoblastomycosis was concerned;only two strains of F.pedrosoi and one F.monophora were isolated from debris plants.The remaining isolates belonged to hitherto unknown molecular siblings of Fonsecaea.Two novel taxa are introduced.

Diversity and delimitation of Rhizopus microsporus

Rhizopus microsporus has been used for centuries in the production of oriental fermented foods,but the species is also known as a toxin producer and from severe human infections.To study the diversity and species delimitation of Rhizopus microsporus,48 isolates from the reference collection of the CBS-KNAW Fungal Biodiversity Centre,comprising nine environmental,ten clinical,and 23 foodborne strains,in addition to six strains from unknown sources and representing all existing varieties of the species,were examined.Sequence diversity was based on the internal transcribed spacer(ITS),and on a part of the actin(ACT)and translation elongation factor 1-α(TEF)genes.Differences in physiological properties were assessed including temperature relationships.Spore morphology was studied,mating type tests were performed,and MALDI-ToF profiles were generated.Clinical and food-associated strains as well as members of different varieties mated successfully and consequently they belong to a single biological species.Molecular differences did not match with any other parameter investigated.Based on these results the varieties of Rhizopus microsporus are reduced to synonyms.

Families of Dothideomycetes

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.