Phylogeny and taxonomy of Rhytisma‑like species worldwide

Rhytisma Fr.is the type genus of Rhytismataceae(Rhytismatales,Leotiomycetes,Ascomycota).Rhytisma-like species include members of Cryptomyces,Rhytisma and Vladracula.They are parasites on leaves of broadleaf trees and cause tar spot diseases.In this study,a phylogeny based on the large subunit of the ribosomal rRNA gene(nrLSU)and the mitochondrial small subunit(mtSSU)is presented,including sequences of 39 newly collected specimens from East Asia,Europe,and temperate as well as tropical America.Based on analyses of morphology,phylogeny as well as host-specificity and diversification time estimates,the family Rhytismataceae sensu stricto is proposed,and eight genera are accepted in this narrow family,including four novel genera(Densorhytisma,Fanglania,Johnstoniella and Shiqia),the type genus Rhytisma,and the reinstated genera Lophodermina,Placuntium and Xyloma.Lophodermina clusters within the main Rhytisma clade in our analyses,but is divergent in morphological terms,not having large compound stromata.Thirty species are recognized,including seven novel species(Fanglania hubeiensis,F.parasitica,Johnstoniella yunnanensis,Rhytisma japonicum,Rh.taiwanense,Xyloma globosum,and X.shennongjiaense),fifteen new combinations(Densorhytisma anhuiense,D.huangshanense,F.concova,F.himalensis,F.ilicis-integrae,F.ilicis-latifoliae,F.ilicis-pedunculosae,J.lonicerae,Rh.annuliforme,Shiqia menziesii,S.yuexiensis,X.filamentosum,X.maximum,X.muelleri,and X.polare),one new name(J.xylostei),seven known species(Lophodermina melaleuca,Placuntium andromedae,Rhytisma acerinum,Rh.americanum,Rh.punctatum,X.salicinum,and X.umbonatum).In addition,seven immature specimens were studied but not assigned to existing species,herein referred to as Fanglania sp.1,Johnstoniella sp.1,Johnstoniella sp.2,Placuntium sp.1,Placuntium sp.2,Rhytisma sp.1,and Xyloma sp.1.The systematic positions of Cryptomyces maximus,Cr.muelleri and Vladracula annuliformis are re-assigned based on phylogenetic analysis.One Rhytisma-like species from tropical America was segregated from Rhytismataceae s.str.,thus a novel genus Neorhytisma was established to accommodate this species,with the one new combinations Neorhytisma panamense.The results of the molecular phylogenetic analysis indicate that Rhytisma-like species are host-specific at genus level.Apparently,Rhytisma-like species coevolved with their hosts,and Rhytisma-like species on Ericaceae seem to be in the process of host jumping.Morphological characteristics of ascomata are important for the delimitation of species and genera of Rhytisma-like species.This study provides a key to genera and species of recognized Rhytisma-like species worldwide.

The numbers of fungi: is the descriptive curve flattening?

The recent realistic estimate of fungal numbers which used various algorithms was between 2.2 and 3.8 million.There are nearly 100,000 accepted species of Fungi and fungus-like taxa,which is between 2.6 and 4.5%of the estimated species.Several forums such as Botanica Marina series,Fungal Diversity notes,Fungal Biodiversity Profiles,Fungal Systematics and Evolution-New and Interesting Fungi,Mycosphere notes and Fungal Planet have enhanced the introduction of new taxa and nearly 2000 species have been introduced in these publications in the last decade.The need to define a fungal species more accurately has been recognized,but there is much research needed before this can be better clarified.We address the evidence that is needed to estimate the numbers of fungi and address the various advances that have been made towards its understanding.Some genera are barely known,whereas some plant pathogens comprise numerous species complexes and numbers are steadily increasing.In this paper,we examine ten genera as case studies to establish trends in fungal description and introduce new species in each genus.The genera are the ascomycetes Colletotrichum and Pestalotiopsis(with many species or complexes),Atrocalyx,Dothiora,Lignosphaeria,Okeanomyces,Rhamphoriopsis,Thozetella,Thyrostroma(rela-tively poorly studied genera)and the basidiomycete genus Lepiota.We provide examples where knowledge is incomplete or lacking and suggest areas needing further research.These include(1)the need to establish what is a species,(2)the need to establish how host-specific fungi are,not in highly disturbed urban areas,but in pristine or relatively undisturbed forests,and(3)the need to establish if species in different continents,islands,countries or regions are different,or if the same fungi occur worldwide?Finally,we conclude whether we are anywhere near to flattening the curve in new species description.

Fungicolous fungi:terminology,diversity,distribution,evolution,and species checklist

Fungicolous fungi are a very large,diverse,ecological and trophic group of organisms that are associated with other fungi.This association occurs with species of different lineages across the fungal kingdom.They are recognized as symbionts,mycoparasites,saprotrophs,and even neutrals.Wherever fungi have been found,fungicolous taxa have also been found.Homogeneous environments favour the development of highly adapted and coevolved fungicolous species,which could have led to host-specificity aspects.As a primary consumer,fungicolous fungi decrease the turnaround time of certain nutrients in food webs,due to their special often-rapid life cycles.They may also significantly affect population dynamics and population sizes of their hosts in aquatic or terrestrial ecosystems.As mycoparasites of pathogenic fungi,some fungicolous fungi have been explored as biocontrol agents.They may also cause serious diseases of cultivated edible and medicinal mushrooms,decreasing both yield and quality.Fungicolous fungi could be used as model organisms that may help determine better understanding of species interactions,fungal evolution and divergence,and fungicolous mechanisms.This review summarizes our current understanding of fungicolous fungi,with a particular focus on the terminology,diversity,global distribution,and interaction with their hosts.We also provide a checklist including 1552 fungicolous fungal taxa so far recorded following the updated classification schemes.There is a need for further investigations on this ecologically important group of fungi to better understand their biology,ecological aspects,origin and divergence,hostspecificity and application in biocontrol.Accurate identification of these fungi as pathogens and their significance in quarantine purposes on the mushroom industry need further evaluations so that efficient control measures can be developed for better disease management purposes.

The numbers of fungi:are the most speciose genera truly diverse?

Fungi play vital roles in ecosystems as endophytes,pathogens and saprobes.The current estimate of fungal diversity is highly uncertain,ranging from 1.5 to 12 million,but only around 150,000 species have been named and classified to date.Since the introduction of DNA based methods for species identification,the number of newly described taxa has increased from approximately 1000 to around 2000 yearly.This demonstrates the importance of DNA based methods to identify and distin-guish species,especially cryptic species.Many novel species from recent studies have been found in historically understudied regions and habitats,but these still represent only a small percentage of the estimated species.In this paper,we examine 16 genera from the top 40 most speciose genera as listed in Species Fungorum as case studies to examine the diversity of taxa in each genus.The genera treated herein are Cercospora,Diaporthe,Meliola,Passalora,Phyllachora,Phyllosticta,Pseudocer-cospora,Ramularia(ascomycetes)and Cortinarius,Entoloma,Inocybe,Marasmius,Psathyrella,Puccinia,Russula,Uromyces(basidiomycetes).We critically evaluate the number of species in these genera and correlate these numbers with the number of entries in GenBank.We introduce 18 new species Apiospora multiloculata,Candolleomyces thailandensis,Cortinarius acutoproximus,Cortinarius melleoalbus,Cortinarius pacificus,Cortinarius parvoacetosus,Diaporthe guizhouensis,Entoloma pseudosubcorvinum,Inocybe meirensongia,Marasmius albulus,Marasmius obscuroaurantiacus,Meliola camporesii,Phyl-lachora siamensis,Phyllosticta doitungensis,Picipes yuxiensis,Pseudocercospora vignae,Puccinia maureanui and Russula inornata.We also introduce a new record of Candolleomyces cladii-marisci and Inocybe iringolkavensis.We discuss the genera Colletotrichum and Pleurotus that are speciose,but do not occur in the top 40.We hypothesize whether there might be more species in these genera and discuss why these genera have some of the largest number of species.

The numbers of fungi:contributions from traditional taxonomic studies and challenges of metabarcoding

The global diversity of fungi has been estimated using several different approaches.There is somewhere between 2–11 million estimated species,but the number of formally described taxa is around 150,000,a tiny fraction of the total.In this paper,we examine 12 ascomycete genera as case studies to establish trends in fungal species descriptions,and introduce new species in each genus.To highlight the importance of traditional morpho-molecular methods in publishing new species,we introduce novel taxa in 12 genera that are considered to have low species discovery.We discuss whether the species are likely to be rare or due to a lack of extensive sampling and classification.The genera are Apiospora,Bambusicola,Beltrania,Capronia,Distoseptispora,Endocalyx,Neocatenulostroma,Neodeightonia,Paraconiothyrium,Peroneutypa,Phaeoacremonium and Vanakripa.We discuss host-specificity in selected genera and compare the number of species epithets in each genus with the number of ITS(barcode)sequences deposited in GenBank and UNITE.We furthermore discuss the relationship between the divergence times of these genera with those of their hosts.We hypothesize whether there might be more species in these genera and discuss hosts and habitats that should be investigated for novel species discovery.

What is a species in fungal plant pathogens?

Scientific names are crucial for communicating knowledge concerning fungi and fungus-like organisms.In plant pathology,they link information regarding biology,host range,distribution and potential risk to agriculture and food security.In the past,delimitation among pathogenic taxa was primarily based on morphological characteristics.Due to distinct species sharing overlapping characteristics,the morphological identification of species is often neither straightforward nor reliable.Hence,the phylogenetic species concept based on molecular phylogenetic reconstructions gained importance.The present opinion discusses what a fungal species is and how identification of species in plant pathology has changed over the past decades.In this context,host-specialization and species complexes are discussed.Furthermore,species concepts in plant pathology are examined using case studies from Bipolaris,Colletotrichum,Curvularia,Diaporthe,Diplodia,Meliola,Plasmopara,rust fungi and Trichoderma.Each entry contains a brief introduction to the genus,concepts used in species identification so far and the problems in describing a species followed by recommendations.The importance of correctly naming and identifying a species is addressed in the context of recent introductions,and we also discuss whether the introduction of new species in pathogenic genera has been overestimated.We also provide guidelines to be considered when introducing a new species in a plant pathogenic genus.

Seed priming with Pseudomonas putida isolated from rhizosphere triggers innate resistance against Fusarium wilt in tomato through pathogenesis-related protein activation and phenylpropanoid pathway

Pathogenesis-related(PR)proteins are one of the major and preliminary proteins accumulated as a defense against biotic stress.This defense response can be induced by using beneficial rhizobacteria,which has been studied in various host-pathogen interactions.In the present study,eleven Pseudomonas isolates were assessed for their potential to ferment sorbitol,reduce nitrate,and produce mycolytic enzymes,1-aminocyclopropane-l-carboxylic acid(ACC)deaminase,phenazine antibiotics,and N-acyl homoserine lactones(AHLs).All isolates were tested against the host-specific pathogen Fusarium oxysporum MTCC1755 in tomato under greenhouse conditions,and shortlisted isolates were tested for their rhizosphere competence.In-vitro test results showed that the isolates were able to produce mycolytic enzymes,including protease,lipase,chitinase,cellulase,and amylase,and the antibiotic phenazine and were negative for pyoluteorin.All the isolates except two were positive for ACC deaminase production.Greenhouse results showed that the isolates M80,M96,and T109 significantly reduced symptoms of Fusarium wilt.Extended greenhouse tests under autoclaved and unautoclaved soil conditions showed that M80,M96,and T109 were excellent rhizosphere competitors and were identified as Pseudomonas putida.In brief,the defense-specific biochemical variations in the host could describe the improved defense against Fusarium wilt occurring in the primed plants.These three Pseudomonas strains could be used as potential biocontrol agents,along with their rhizosphere competence.