利用微卫星标记研究新生隐球菌分子流行病学

目的研究国内隐球菌临床分离株的遗传多态性和分子流行病学。方法选择与新生隐球菌遗传相关的9个微卫星标记,分析这9个位点从1993～2009年国内分离到的新生隐球菌临床株遗传背景、来源及变异程度。结果 116株被研究的隐球菌临床分离株,主要归属于3个微卫星复合物(MC2,MC3和MC12),其中大部分为MC2(103株)。8株菌株属于目前为止未被国内外认识的新复合物(MC12)。结论利用微卫星DNA多态性研究新生隐球菌分子流行病学有较大的应用价值。

Classification of marine Ascomycota,Basidiomycota,Blastocladiomycota and Chytridiomycota

This paper lists the accepted names and classification of marine fungi,updating the scheme presented in 2009.The classification includes 1,112 species(in 472 genera):Ascomycota 805(in 352 genera),Basidiomycota 21 species(in 17 genera),Chytridiomycota and related phyla 26 species(in 13 genera),Zygomycota three(in two genera),Blastocladiomycota one species(one genus),asexual morphs of filamentous fungi 43(in 26 genera);and marine yeasts:Ascomycota 138 species(in 35 genera),Basidiomycota 75 species(in 26 genera).These fungi belong to 129 families and 65 orders.The Halosphaeriaceae remains the largest family of marine fungi with 141 species in 59 genera,while the most specious genera are Aspergillus(47 species),Penicillium(39 species)and the yeast genus Candida(64 species).The review includes details of recent higher order nomenclature changes,and accounts of new families,genera and species described over the past 5 years.

Notes,outline and divergence times of Basidiomycota

The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota.The present work provides an overview of all validly published,currently used basidiomycete genera to date in a single document.An outline of all genera of Basidiomycota is provided,which includes 1928 currently used genera names,with 1263 synonyms,which are distributed in 241 families,68 orders,18 classes and four subphyla.We provide brief notes for each accepted genus including information on classification,number of accepted species,type species,life mode,habitat,distribution,and sequence information.Furthermore,three phylogenetic analyses with combined LSU,SSU,5.8s,rpb1,rpb2,and ef1 datasets for the subphyla Agaricomycotina,Pucciniomycotina and Ustilaginomycotina are conducted,respectively.Divergence time estimates are provided to the family level with 632 species from 62 orders,168 families and 605 genera.Our study indicates that the divergence times of the subphyla in Basidiomycota are 406-430 Mya,classes are 211-383 Mya,and orders are 99-323 Mya,which are largely consistent with previous studies.In this study,all phylogenetically supported families were dated,with the families of Agaricomycotina diverging from 27-178 Mya,Pucciniomycotina from 85-222 Mya,and Ustilaginomycotina from 79-177 Mya.Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system,and also provide a better understanding of their phylogeny and evolution.

The world’s ten most feared fungi

An account is provided of the world’s ten most feared fungi.Within areas of interest,we have organized the entries in the order of concern.We put four human pathogens first as this is of concern to most people.This is followed by fungi producing mycotoxins that are highly harmful for humans;Aspergillus flavus,the main producer of aflatoxins,was used as an example.Problems due to indoor air fungi may also directly affect our health and we use Stachybotrys chartarum as an example.Not everyone collects and eats edible mushrooms.However,fatalities caused by mushroom intoxications often make news headlines and therefore we include one of the most poisonous of all mushrooms,Amanita phalloides,as an example.We then move on to the fungi that damage our dwellings causing serious anxiety by rotting our timber structures and flooring.Serpula lacrymans,which causes dry rot is an excellent example.The next example serves to represent all plant and forest pathogens.Here we chose Austropuccinia psidii as it is causing devastating effects in Australia and will probably do likewise in New Zealand.Finally,we chose an important amphibian pathogen which is causing serious declines in the numbers of frogs and other amphibians worldwide.Although we target the top ten most feared fungi,numerous others are causing serious concern to human health,plant production,forestry,other animals and our factories and dwellings.By highlighting ten feared fungi as an example,we aim to promote public awareness of the cost and importance of fungi.

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

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.

The evolving species concepts used for yeasts:from phenotypes and genomes to speciation networks

Here we review how evolving species concepts have been applied to understand yeast diversity.Initially,a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells,and growth profiles.Later the biological species concept was added,which applied data from mating experiments.Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology,leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA.At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy,including yeasts,because various studies revealed a relatively good correlation between the biological species concept and sequence divergence.The application of genome information is becoming increasingly common,and we strongly recommend the use of complete,rather than draft genomes to improve our understanding of species and their genome and genetic dynamics.Complete genomes allow in-depth comparisons on the evolvability of genomes and,consequently,of the species to which they belong.Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts.Note that hybrids may greatly differ in their post-hybridization development.Future in-depth studies,initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes,such as hybridization.

Delimiting species in Basidiomycota:a review

Species delimitation is one of the most fundamental processes in biology.Biodiversity undertakings,for instance,require explicit species concepts and criteria for species delimitation in order to be relevant and translatable.However,a perfect species concept does not exist for Fungi.Here,we review the species concepts commonly used in Basidiomycota,the second largest phylum of Fungi that contains some of the best known species of mushrooms,rusts,smuts,and jelly fungi.In general,best practice is to delimitate species,publish new taxa,and conduct taxonomic revisions based on as many independent lines of evidence as possible,that is,by applying a so-called unifying(or integrative)conceptual framework.However,the types of data used vary considerably from group to group.For this reason we discuss the different classes of Basidiomycota,and for each provide:(i)a general introduction with difficulties faced in species recognition,(ii)species concepts and methods for species delimitation,and(iii)community recommendations and conclusions.

Trends in yeast diversity discovery

Yeasts,usually defined as unicellular fungi,occur in various fungal lineages.Hence,they are not a taxonomic unit,but rather represent a fungal lifestyle shared by several unrelated lineages.Although the discovery of new yeast species occurs at an increasing speed,at the current rate it will likely take hundreds of years,if ever,before they will all be documented.Many parts of the earth,including many threatened habitats,remain unsampled for yeasts and many others are only superficially studied.Cold habitats,such as glaciers,are home to a specific community of cold-adapted yeasts,and,hence,there is some urgency to study such environments at locations where they might disappear soon due to anthropogenic climate change.The same is true for yeast communities in various natural forests that are impacted by deforestation and forest conversion.Many countries of the so-called Global South have not been sampled for yeasts,despite their economic promise.However,extensive research activity in Asia,especially China,has yielded many taxonomic novelties.Comparative genomics stud-ies have demonstrated the presence of yeast species with a hybrid origin,many of them isolated from clinical or industrial environments.DNA-metabarcoding studies have demonstrated the prevalence,and in some cases dominance,of yeast species in soils and marine waters worldwide,including some surprising distributions,such as the unexpected and likely common presence of Malassezia yeasts in marine habitats.

Forecasting the number of species of asexually reproducing fungi(Ascomycota and Basidiomycota)

Asexually reproducing fungi play a significant role in essential processes in managed and wild ecosystems such as nutrients cycling and multitrophic interactions.A large number of such taxa are among the most notorious plant and animal pathogens.In addition,they have a key role in food production,biotechnology and medicine.Taxa without or rare sexual reproduction are distinguished based on their sporulating structures and conidiomata in traditional morphology-based taxonomy.The number,variation and diversity of asexually reproducing taxa are insufficiently known,even though fungi capable of asexual reproduction may provide an untapped,rich biological resource for future exploitation.Currently,ca.30,000 asexual species belonging to ca.3800 genera have been reported(including 1388 coelomycetous and 2265 hyphomycetous genera).Recent reports(2017–2020)reiterate that the number of asexually producing fungi is higher than the number of frequently sexually-reproducing fungi.With the advent of molecular tools and the abandonment of the dual nomenclature system for pleomorphic fungi,priority criteria were established and revisited in the latest outline of fungi and fungus-like taxa.However,species numbers and taxonomic boundaries of pleomorphic taxa and their synanamorphs or synasexual morphs have yet to be addressed.The number of species of speciose genera(e.g.Alternaria,Aspergillus,Cercospora,Fusarium,Phoma and Pseudocercospora),cryptic species,species of pleomorphic genera,less studied life modes(such as lichenicolous taxa,taxa from extreme environments)and species from biodiversity-rich areas still need evaluation to achieve more reliable estimates of their diversity.This paper discusses the current knowledge on the matter,with diversity estimates,and potential obstacles in several chapters on(1)speciose genera;(2)pleomorphic genera;(3)cryptic species;(4)well-studied but insufficiently resolved taxa,e.g.leaf inhabiting species,marine fungi,(5)less studied life modes,e.g.lichenicolous,rock-inhabiting fungi,insect-associated and yeast-forming taxa and(6)species from biodiversity-rich areas.

An online resource for marine fungi

Index Fungorum,Species Fungorum and MycoBank are the key fungal nomenclature and taxonomic databases that can be sourced to find taxonomic details concerning fungi,while DNA sequence data can be sourced from the NCBI,EBI and UNITE databases.Nomenclature and ecological data on freshwater fungi can be accessed on http://fungi.life.illinois.edu/,while http://www.marinespecies.org/provides a comprehensive list of names of marine organisms,including information on their synonymy.Previous websites however have little information on marine fungi and their ecology,beside articles that deal with marine fungi,especially those published in the nineteenth and early twentieth centuries may not be accessible to those working in third world countries.To address this problem,a new website www.marinefungi.org was set up and is introduced in this paper.This website provides a search facility to genera of marine fungi,full species descriptions,key to species and illustrations,an up to date classification of all recorded marine fungi which includes all fungal groups(Ascomycota,Basidiomycota,Blastocladiomycota,Chytridiomycota,Mucoromycota and fungus-like organisms e.g.Thraustochytriales),and listing recent publications.Currently,1257 species are listed in the marine fungi website(www.marinefungi.org),in 539 genera,74 orders,168 families,20 classes and five phyla,with new taxa continuing to be described.The website has curators with specialist mycological expertise who help to provide update data on the classification of marine fungi.This article also reviews knowledge of marine fungi covering a wide range of topics:their higher classification,ecology and world distribution,role in energy transfer in the oceans,origin and new chemical structures.An updated classification of marine fungi is also included.We would like to invite all mycologists to contribute to this innovative website.

Correction to:The evolving species concepts used for yeasts:from phenotypes and genomes to speciation networks

The name of the second author was incorrectly captured in the initial online publication,and due to an error at the proofs stage,several proof corrections had been left undone.The original online article has been corrected.