Fungi as mutualistic partners in ant-plant interactions

Associations between fungi and ants living in mutualistic relationship with plants ("plant-ants") have been known for a long time. However, only in recent years has the mutualistic nature, frequency, and geographical extent of associations between tropical arboreal ants with fungi of the ascomycete order Chaetothyriales and Capnodiales (belonging to the so-called "Black Fungi") become clear. Two groups of arboreal ants displaying different nesting strategies are associated with ascomycete fungi: carton-building ants that construct nest walls and galleries on stems, branches or below leaves which are overgrown by fungal hyphae, and plant-ants that make their nests inside living plants (myrmecophytes) in plant provided cavities (domatia) where ants cultivate fungi in small delimited "patches". In this review we summarize the current knowledge about these unsuspected plant-ant-fungus interactions. The data suggest, that at least some of these ant-associated fungi seem to have coevolved with ants over a long period of time and have developed specific adaptations to this lifestyle.

Differences in fungal communities in the fur of two- and three-toed sloths revealed by ITS metabarcoding

Sloths have dense fur on which insects, algae, bacteria and fungi coexist. Previous studies using cultivation-dependent methods and 18S rRNA sequencing revealed that the fungal communities in their furs comprise members of the phyla Ascomycota and Basidiomycota. In this note, we increase the resolution and knowledge of the mycobiome inhabiting the fur of the two- (Choloepus hoffmanni) and three-toed (Bradypus variegatus) sloths. Targeted amplicon metagenomic analysis of ITS2 nrDNA sequences obtained from 10 individuals of each species inhabiting the same site revealed significant differences in the structure of their fungal communities and also in the alpha-diversity estimators. The results suggest a specialization by host species and that the host effect is stronger than that of sex, age and animal weight. Capnodiales were the dominant order in sloths' fur and Cladosporium and Neodevriesia were the most abundant genera in Bradypus and Choloepus, respectively. The fungal communities suggest that the green algae that inhabit the fur of sloths possibly live lichenized with Ascomycota fungal species. The data shown in this note offer a more detailed view of the fungal content in the fur of these extraordinary animals and could help explain other mutualistic relationships in this complex ecosystem.

Sooty molds from the Jurassic of Patagonia, Argentina

PREMISE

The sooty molds are a globally distributed ecological group of ascomycetes with epiphyllous, saprotrophic habit, comprising several phylogenetically distant taxa (i.e., members of the classes Dothideomycetes and Eurotiomycetes). Their fossil record extends almost continuously back to the early Cretaceous; however, they are hypothesized to have originated in the early Mesozoic. Here, we describe new specimens of sooty molds associated with conifer leaves from Jurassic hot spring deposits of Patagonia, Argentina.

METHODS

Thin sections of chert samples from the La Matilde Formation, Deseado Massif (Santa Cruz, Argentina) were observed using light microscopy.

RESULTS

The fungi occur on the surface and axils of leafy twigs with podocarpaceous affinities, forming dense subicula comprised by opaque moniliform hyphae. Additionally, several asexual and sexual reproductive structures are observed. On the basis of vegetative (i.e., dense subicula composed of moniliform hyphae; hyphae composed of opaque cells deeply constricted at the septa) and reproductive characters (i.e., poroconidial and sympodioconidial asexual stages and diverse spores), two morphotypes were identified with affinities within lineages of the subphylum Pezizomycotina that encompass the ecological group of sooty molds, and a third morphotype was within the phylum Ascomycota.

CONCLUSIONS

This finding extends the fossil record of sooty molds to the Jurassic and their geographic fossil range to the South American continent. In particular, their association with podocarpaceous conifers is shown to be ancient, dating back to the Jurassic. This new record provides an additional reference point on the diversity of interactions that characterized Jurassic forests in Patagonia.

Genome assembly of Scorias spongiosa and comparative genomics provide insights into ecological adaptation of honeydew-dependent sooty mould fungi

Sooty moulds are fungi of economic importance and with unique lifestyle mainly growing on insect honeydew. However, the lack of genomic data hinders investigation of genetic mechanisms underlying their ecological adaptation. With long-read sequencing technology, we generated the genome of Scorias spongiosa, an extraordinary sooty mould fungus associated with honeydew of colony aphids and producing large fruiting bodies. A 24.21 Mb high-quality genome assembly with a N50 length of 3.37 Mb was obtained. The genome contained 7758 protein coding genes, 97.13% of which were homologous to known genes, and approximately 0.29 Mb repeat sequences. Comparative genomics showed S. spongiosa lost relatively more gene families and contained fewer species-specific genes and gene families, with many CAZyme families and sugar transporters reduced or absent. This study not only promotes understanding of the ecological adaptation of sooty moulds, but also provides valuable genomic data resource for future comparative genomic and genetic studies.

Insight into the Systematics of Microfungi Colonizing Dead Woody Twigs of Dodonaea viscosa in Honghe (China)

Members of Dodonaea are broadly distributed across subtropical and tropical areas of southwest and southern China. This host provides multiple substrates that can be richly colonized by numerous undescribed fungal species. There is a severe lack of microfungal studies on Dodonaea in China, and consequently, the diversity, phylogeny and taxonomy of these microorganisms are all largely unknown. This paper presents two new genera and four new species in three orders of Dothideomycetes gathered from dead twigs of Dodonaea viscosa in Honghe, China. All new collections were made within a selected area in Honghe from a single Dodonaea sp. This suggests high fungal diversity in the region and the existence of numerous species awaiting discovery. Multiple gene sequences (non-translated loci and protein-coding regions) were analysed with maximum likelihood and Bayesian analyses. Results from the phylogenetic analyses supported placing Haniomyces dodonaeae gen. et sp. in the Teratosphaeriaceae family. Analysis of Rhytidhysteron sequences resulted in Rhytidhysteron hongheense sp. nov., while analysed Lophiostomataceae sequences revealed Lophiomurispora hongheensis gen. et sp. nov. Finally, phylogeny based on a combined dataset of pyrenochaeta-like sequences demonstrates strong statistical support for placing Quixadomyceshongheensis sp. nov. in Parapyrenochaetaceae. Morphological and updated phylogenetic circumscriptions of the new discoveries are also discussed.

A new species in the Mycosphaerellaceae from Cecidomyiidae leaf galls on Avicennia marina in South Africa

During studies to investigate the health of mangrove trees in South Africa, high numbers of Avicennia marina were found with leaf galls caused by unidentified adults and larvae of midges (Cecidomyiidae). Fungal fruiting structures were commonly observed on the abaxial areas of the galls. To determine the identity of the fungi associated with the gall midges, phylogenetic analyses using multigene sequence data were used. The nuclear large subunit (LSU), internal transcribed spacer (ITS), and a portion of the actin gene region (ACT), were amplified and analyzed. The results revealed that the fungal fruiting structures represent a new taxon in the Mycosphaerellaceae described here as Zasmidium mangrovei sp. nov. This is the first report of a species in the Mycosphaerellaceae associated with cecidomyiid leaf galls on A. marina.

A New Extremotolerant Ecotype of the Fungus Pseudotaeniolina globosa Isolated from Djoser Pyramid, Memphis Necropolis, Egypt

Most of the rock-inhabiting fungi are meristematic and melanized microorganisms often associated with monument biodeterioration. In previous microbial profiling of the Egyptian Djoser pyramid, a Pseudotaeniolina globosa isolate was found. The current study aimed to characterize the P. globosa isolated from the Djoser pyramid compared with an Italian isolate at morphological, physiological, and molecular levels. Experiments were carried out to test temperature, salinity, and pH preferences, as well as stress tolerance to UV radiation and high temperature, in addition to a multi-locus genotyping using ITS, nrSSU or 18S, nrLSU or 28S, BT2, and RPB2 markers. Morphological and molecular data confirmed the con-specificity of the two isolates. However, the Egyptian isolate showed a wider range of growth at different environmental conditions being much more tolerant to a wider range of temperature (4–37 °C) and pH values (3.0–9.0 pH) than the Italian (10–30 °C, 4.0–6.0 pH), and more tolerant to extreme salinity levels (5 M NaCl), compared to the lowest in the Italian isolate (0.2 M NaCl). Besides, the Egyptian isolate was more tolerant to high temperature than the Italian isolate since it was able to survive after exposure to up to 85 °C for 5 min, and was not affected for up to 9 h of UV exposure, while the Italian one could not regrow after the same treatments. The Pseudotaeniolina globosa species was attributed to the family Teratosphaeriaceae of the order Capnodiales, class Dothideomycetes. Our results demonstrated that the Egyptian isolate could be considered an ecotype well adapted to harsh and extreme environments. Its potential bio-deteriorating effect on such an important cultural heritage requires special attention to design and conservation plans and solutions to limit its presence and extension in the studied pyramid and surrounding archaeological sites.

Host tree organ is the primary driver of endophytic fungal community structure in a hemiboreal forest

Despite numerous studies on plant endophytes, little is known about fungal communities associated with different aboveground tissues of living trees. We used high-throughput sequencing to compare the diversity and community structure of fungi inhabiting leaves, branches and trunks of Alnus incana and Corylus avellana growing at three hemiboreal forest sites. Our analysis revealed that tree organs are the main determinants of the structure of fungal communities, whereas the effects of host species and locality remained secondary and negligible, respectively. The structure of fungal communities in trunks was the most distinct compared to that in leaves and branches. The foliar fungal communities were more similar within than between individual trees, implying that certain fungi may grow through parts of the tree crown. The weak effect of locality compared to host organs and species identity suggests that the structural variation of fungal communities in the aboveground parts of trees depends mainly on deterministic factors rather than dispersal limitation.

Evolution of lifestyles in Capnodiales

The Capnodiales, which includes fungi known as the sooty moulds, represents the second largest order in Dothideomycetes, encompassing morphologically and ecologically diverse fungi with different lifestyles and modes of nutrition. They include saprobes, plant and human pathogens, mycoparasites, rock-inhabiting fungi (RIF), lichenised, epi-, ecto- and endophytes. The aim of this study was to elucidate the lifestyles and evolutionary patterns of the Capnodiales as well as to reconsider their phylogeny by including numerous new collections of sooty moulds, and using four nuclear loci, LSU, ITS, TEF-1α and RPB2. Based on the phylogenetic results, combined with morphology and ecology, Capnodiales s. lat. is shown to be polyphyletic, representing seven different orders. The sooty moulds are restricted to Capnodiales s. str., while Mycosphaerellales is resurrected, and five new orders including Cladosporiales, Comminutisporales, Neophaeothecales, Phaeothecales and Racodiales are introduced. Four families, three genera, 21 species and five combinations are introduced as new. Furthermore, ancestral reconstruction analysis revealed that the saprobic lifestyle is a primitive state in Capnodiales s. lat., and that several transitions have occurred to evolve lichenised, plant and human parasitic, ectophytic (sooty blotch and flyspeck) and more recently epiphytic (sooty mould) lifestyles.

New species of Cladosporium associated with human and animal infections

Cladosporium is mainly known as a ubiquitous environmental saprobic fungus or plant endophyte, and to date, just a few species have been documented as etiologic agents in vertebrate hosts, including humans. In the present study, 10 new species of the genus were isolated from human and animal clinical specimens from the USA. They are proposed and characterized on the basis of their morphology and a molecular phylogenetic analysis using DNA sequences from three loci (the ITS region of the rDNA, and partial fragments of the translation elongation factor 1-alpha and actin genes). Six of those species belong to the C. cladosporioides species complex, i.e., C. alboflavescens, C. angulosum, C. anthropophilum, C. crousii, C. flavovirens and C. xantochromaticum, three new species belong to the C. herbarum species complex, i.e., C. floccosum, C. subcinereum and C. tuberosum; and one to the C. sphaerospermum species complex, namely, C. succulentum. Differential morphological features of the new taxa are provided together with molecular barcodes to distinguish them from the currently accepted species of the genus.

Exploring fungal mega-diversity: Pseudocercospora from Brazil

Although the genus Pseudocercospora has a worldwide distribution, it is especially diverse in tropical and subtropical countries. Species of this genus are associated with a wide range of plant species, including several economically relevant hosts. Preliminary studies of cercosporoid fungi from Brazil allocated most taxa to Cercospora, but with the progressive refinement of the taxonomy of cercosporoid fungi, many species were relocated to or described in Pseudocercospora. Initially, species identification relied mostly on morphological features, and thus no cultures were preserved for later phylogenetic comparisons. In this study, a total of 27 Pseudocercospora spp. were collected, cultured, and subjected to a multigene analysis. Four genomic regions (LSU, ITS, tef1 and actA) were amplified and sequenced. A multigene Bayesian analysis was performed on the combined ITS, actA and tef1 sequence alignment. Our results based on DNA phylogeny, integrated with ecology, morphology and cultural characteristics revealed a rich diversity of Pseudocercospora species in Brazil. Twelve taxa were newly described, namely P. aeschynomenicola, P. diplusodonii, P. emmotunicola, P. manihotii, P. perae, P. planaltinensis, P. pothomorphes, P. sennae-multijugae, P. solani-pseudocapsicicola, P. vassobiae, P. wulffiae and P. xylopiae. Additionally, eight epitype specimens were designated, three species newly reported, and several new host records linked to known Pseudocercospora spp.

Fodinomyces uranophilus gen. nov. sp. nov. and Coniochaeta fodinicola sp. nov., two uranium mine-inhabiting Ascomycota fungi from northern Australia

Seven acidophilic/acidotolerant fungal strains were characterized from samples of process waters (raffinate) at one of Australia's largest uranium mines, the Ranger Mine in Northern Territory. They were isolated from raffinate, which typically were very acidic (pH 1.7-1.8) and contained high concentrations of total dissolved/colloidal salts (> 100 g/L). Five of the isolates correspond to two new acidotolerant Ascomycota fungi. The first is a member of a new genus, here described as Fodinomyces (Teratosphaeriaceae, Capnodiales, Dothideomycetes) and does not show clear close affiliation with any other described fungus in the scientific literature. The second belongs to the genus Coniochaeta (Coniochaetaceae, Coniochaetales, Sordariomycetes) and is closely related to Coniochaeta hansenii.

Septoria-like pathogens causing leaf and fruit spot of pistachio

Several species of Septoria are associated with leaf and fruit spot of pistachio (Pistacia vera), though their identity has always been confused, making identification problematic. The present study elucidates the taxonomy of the Septoria spp. associated with pistachio, and distinguishes four species associated with this host genus. Partial nucleotide sequence data for five gene loci, ITS, LSU, EF-1α, RPB2 and Btub were generated for a subset of isolates. Cylindroseptoria pistaciae, which is associated with leaf spots of Pistacia lentiscus in Spain, is characterised by pycnidial conidiomata that give rise to cylindrical, aseptate conidia. Two species of Septoria s. str. are also recognised on pistachio, S. pistaciarum, and S. pistaciae. The latter is part of the S. protearum species complex, and appears to be a wide host range pathogen occurring on hosts in several different plant families. Septoria pistacina, a major pathogen of pistachio in Turkey, is shown to belong to Pseudocercospora, and not Septoria as earlier suspected. Other than for its pycnidial conidiomata, it is a typical species of Pseudocercospora based on its smooth, pigmented conidiogenous cells and septate conidia. This phenomenon has also been observed in Pallidocercospora, and seriously questions the value of conidiomatal structure at generic level, which has traditionally been used to separate hyphomycetous from coelomycetous ascomycetes. Other than DNA barcodes to facilitate the molecular identification of these taxa occurring on pistachio, a key is also provided to distinguish species based on morphology.

Phylogenetic lineages in Pseudocercospora

Pseudocercospora is a large cosmopolitan genus of plant pathogenic fungi that are commonly associated with leaf and fruit spots as well as blights on a wide range of plant hosts. They occur in arid as well as wet environments and in a wide range of climates including cool temperate, sub-tropical and tropical regions. Pseudocercospora is now treated as a genus in its own right, although formerly recognised as either an anamorphic state of Mycosphaerella or having mycosphaerella-like teleomorphs. The aim of this study was to sequence the partial 28S nuclear ribosomal RNA gene of a selected set of isolates to resolve phylogenetic generic limits within the Pseudocercospora complex. From these data, 14 clades are recognised, six of which cluster in Mycosphaerellaceae. Pseudocercospora s. str. represents a distinct clade, sister to Passalora eucalypti, and a clade representing the genera Scolecostigmina, Trochophora and Pallidocercospora gen. nov., taxa formerly accommodated in the Mycosphaerella heimii complex and characterised by smooth, pale brown conidia, as well as the formation of red crystals in agar media. Other clades in Mycosphaerellaceae include Sonderhenia, Microcyclosporella, and Paracercospora. Pseudocercosporella resides in a large clade along with Phloeospora, Miuraea, Cercospora and Septoria. Additional clades represent Dissoconiaceae, Teratosphaeriaceae, Cladosporiaceae, and the genera Xenostigmina, Strelitziana, Cyphellophora and Thedgonia. The genus Phaeomycocentrospora is introduced to accommodate Mycocentrospora cantuariensis, primarily distinguished from Pseudocercospora based on its hyaline hyphae, broad conidiogenous loci and hila. Host specificity was considered for 146 species of Pseudocercospora occurring on 115 host genera from 33 countries. Partial nucleotide sequence data for three gene loci, ITS, EF-1α, and ACT suggest that the majority of these species are host specific. Species identified on the basis of host, symptomatology and general morphology, within the same geographic region, frequently differed phylogenetically, indicating that the application of European and American names to Asian taxa, and vice versa, was often not warranted.

TAXONOMIC NOVELTIES

New genera - Pallidocercospora Crous, Phaeomycocentrospora Crous, H.D. Shin & U. Braun; New species - Cercospora eucommiae Crous, U. Braun & H.D. Shin, Microcyclospora quercina Crous & Verkley, Pseudocercospora ampelopsis Crous, U. Braun & H.D. Shin, Pseudocercospora cercidicola Crous, U. Braun & C. Nakash., Pseudocercospora crispans G.C. Hunter & Crous, Pseudocercospora crocea Crous, U. Braun, G.C. Hunter & H.D. Shin, Pseudocercospora haiweiensis Crous & X. Zhou, Pseudocercospora humulicola Crous, U. Braun & H.D. Shin, Pseudocercospora marginalis G.C. Hunter, Crous, U. Braun & H.D. Shin, Pseudocercospora ocimi-basilici Crous, M.E. Palm & U. Braun, Pseudocercospora plectranthi G.C. Hunter, Crous, U. Braun & H.D. Shin, Pseudocercospora proteae Crous, Pseudocercospora pseudostigmina-platani Crous, U. Braun & H.D. Shin, Pseudocercospora pyracanthigena Crous, U. Braun & H.D. Shin, Pseudocercospora ravenalicola G.C. Hunter & Crous, Pseudocercospora rhamnellae G.C. Hunter, H.D. Shin, U. Braun & Crous, Pseudocercospora rhododendri-indici Crous, U. Braun & H.D. Shin, Pseudocercospora tibouchinigena Crous & U. Braun, Pseudocercospora xanthocercidis Crous, U. Braun & A. Wood, Pseudocercosporella koreana Crous, U. Braun & H.D. Shin; New combinations - Pallidocercospora acaciigena (Crous & M.J. Wingf.) Crous & M.J. Wingf., Pallidocercospora crystallina (Crous & M.J. Wingf.) Crous & M.J. Wingf., Pallidocercospora heimii (Crous) Crous, Pallidocercospora heimioides (Crous & M.J. Wingf.) Crous & M.J. Wingf., Pallidocercospora holualoana (Crous, Joanne E. Taylor & M.E. Palm) Crous, Pallidocercospora konae (Crous, Joanne E. Taylor & M.E. Palm) Crous, Pallidoocercospora irregulariramosa (Crous & M.J. Wingf.) Crous & M.J. Wingf., Phaeomycocentrospora cantuariensis (E.S. Salmon & Wormald) Crous, H.D. Shin & U. Braun, Pseudocercospora hakeae (U. Braun & Crous) U. Braun & Crous, Pseudocercospora leucadendri (Cooke) U. Braun & Crous, Pseudocercospora snelliana (Reichert) U. Braun, H.D. Shin, C. Nakash. & Crous, Pseudocercosporella chaenomelis (Y. Suto) C. Nakash., Crous, U. Braun & H.D. Shin; Typifications: Epitypifications - Pseudocercospora angolensis (T. Carvalho & O. Mendes) Crous & U. Braun, Pseudocercospora araliae (Henn.) Deighton, Pseudocercospora cercidis-chinensis H.D. Shin & U. Braun, Pseudocercospora corylopsidis (Togashi & Katsuki) C. Nakash. & Tak. Kobay., Pseudocercospora dovyalidis (Chupp & Doidge) Deighton, Pseudocercospora fukuokaensis (Chupp) X.J. Liu & Y.L. Guo, Pseudocercospora humuli (Hori) Y.L. Guo & X.J. Liu, Pseudocercospora kiggelariae (Syd.) Crous & U. Braun, Pseudocercospora lyoniae (Katsuki & Tak. Kobay.) Deighton, Pseudocercospora lythri H.D. Shin & U. Braun, Pseudocercospora sambucigena U. Braun, Crous & K. Schub., Pseudocercospora stephanandrae (Tak. Kobay. & H. Horie) C. Nakash. & Tak. Kobay., Pseudocercospora viburnigena U. Braun & Crous, Pseudocercosporella chaenomelis (Y. Suto) C. Nakash., Crous, U. Braun & H.D. Shin, Xenostigmina zilleri (A. Funk) Crous; Lectotypification - Pseudocercospora ocimicola (Petr. & Cif.) Deighton; Neotypifications - Pseudocercospora kiggelariae (Syd.) Crous & U. Braun, Pseudocercospora lonicericola (W. Yamam.) Deighton, Pseudocercospora zelkovae (Hori) X.J. Liu & Y.L. Guo.

Sizing up Septoria

Septoria represents a genus of plant pathogenic fungi with a wide geographic distribution, commonly associated with leaf spots and stem cankers of a broad range of plant hosts. A major aim of this study was to resolve the phylogenetic generic limits of Septoria, Stagonospora, and other related genera such as Sphaerulina, Phaeosphaeria and Phaeoseptoria using sequences of the the partial 28S nuclear ribosomal RNA and RPB2 genes of a large set of isolates. Based on these results Septoria is shown to be a distinct genus in the Mycosphaerellaceae, which has mycosphaerella-like sexual morphs. Several septoria-like species are now accommodated in Sphaerulina, a genus previously linked to this complex. Phaeosphaeria (based on P. oryzae) is shown to be congeneric with Phaeoseptoria (based on P. papayae), which is reduced to synonymy under the former. Depazea nodorum (causal agent of nodorum blotch of cereals) and Septoria avenae (causal agent of avenae blotch of barley and rye) are placed in a new genus, Parastagonospora, which is shown to be distinct from Stagonospora (based on S. paludosa) and Phaeosphaeria. Partial nucleotide sequence data for five gene loci, ITS, LSU, EF-1α, RPB2 and Btub were generated for all of these isolates. A total of 47 clades or genera were resolved, leading to the introduction of 14 new genera, 36 new species, and 19 new combinations.

TAXONOMIC NOVELTIES

New genera - Acicuseptoria Quaedvlieg, Verkley & Crous, Cylindroseptoria Quaedvlieg, Verkley & Crous, Kirstenboschia Quaedvlieg, Verkley & Crous, Neoseptoria Quaedvlieg, Verkley & Crous, Neostagonospora Quaedvlieg, Verkley & Crous, Parastagonospora Quaedvlieg, Verkley & Crous, Polyphialoseptoria Quaedvlieg, R.W. Barreto, Verkley & Crous, Ruptoseptoria Quaedvlieg, Verkley & Crous, Septorioides Quaedvlieg, Verkley & Crous, Setoseptoria Quaedvlieg, Verkley & Crous, Stromatoseptoria Quaedvlieg, Verkley & Crous, Vrystaatia Quaedvlieg, W.J. Swart, Verkley & Crous, Xenobotryosphaeria Quaedvlieg, Verkley & Crous, Xenoseptoria Quaedvlieg, H.D. Shin, Verkley & Crous. New species - Acicuseptoria rumicis Quaedvlieg, Verkley & Crous, Caryophylloseptoria pseudolychnidis Quaedvlieg, H.D. Shin, Verkley & Crous, Coniothyrium sidae Quaedvlieg, Verkley, R.W. Barreto & Crous, Corynespora leucadendri Quaedvlieg, Verkley & Crous, Cylindroseptoria ceratoniae Quaedvlieg, Verkley & Crous, Cylindroseptoria pistaciae Quaedvlieg, Verkley & Crous, Kirstenboschia diospyri Quaedvlieg, Verkley & Crous, Neoseptoria caricis Quaedvlieg, Verkley & Crous, Neostagonospora caricis Quaedvlieg, Verkley & Crous, Neostagonospora elegiae Quaedvlieg, Verkley & Crous, Paraphoma dioscoreae Quaedvlieg, H.D. Shin, Verkley & Crous, Parastagonospora caricis Quaedvlieg, Verkley & Crous, Parastagonospora poae Quaedvlieg, Verkley & Crous, Phlyctema vincetoxici Quaedvlieg, Verkley & Crous, Polyphialoseptoria tabebuiae-serratifoliae Quaedvlieg, Alfenas & Crous, Polyphialoseptoria terminaliae Quaedvlieg, R.W. Barreto, Verkley & Crous, Pseudoseptoria collariana Quaedvlieg, Verkley & Crous, Pseudoseptoria obscura Quaedvlieg, Verkley & Crous, Sclerostagonospora phragmiticola Quaedvlieg, Verkley & Crous, Septoria cretae Quaedvlieg, Verkley & Crous, Septoria glycinicola Quaedvlieg, H.D. Shin, Verkley & Crous, Septoria oenanthicola Quaedvlieg, H.D. Shin, Verkley & Crous, Septoria pseudonapelli Quaedvlieg, H.D. Shin, Verkley & Crous, Setophoma chromolaenae Quaedvlieg, Verkley, R.W. Barreto & Crous, Setoseptoria phragmitis Quaedvlieg, Verkley & Crous, Sphaerulina amelanchier Quaedvlieg, Verkley & Crous, Sphaerulina pseudovirgaureae Quaedvlieg, Verkley & Crous, Sphaerulina viciae Quaedvlieg, H.D. Shin, Verkley & Crous, Stagonospora duoseptata Quaedvlieg, Verkley & Crous, Stagonospora perfecta Quaedvlieg, Verkley & Crous, Stagonospora pseudocaricis Quaedvlieg, Verkley, Gardiennet & Crous, Stagonospora pseudovitensis Quaedvlieg, Verkley & Crous, Stagonospora uniseptata Quaedvlieg, Verkley & Crous, Vrystaatia aloeicola Quaedvlieg, Verkley, W.J. Swart & Crous, Xenobotryosphaeria calamagrostidis Quaedvlieg, Verkley & Crous, Xenoseptoria neosaccardoi Quaedvlieg, H.D. Shin, Verkley & Crous. New combinations - Parastagonospora avenae (A.B. Frank) Quaedvlieg, Verkley & Crous, Parastagonospora nodorum (Berk.) Quaedvlieg, Verkley & Crous, Phaeosphaeria papayae (Speg.) Quaedvlieg, Verkley & Crous, Pseudocercospora domingensis (Petr. & Cif.) Quaedvlieg, Verkley & Crous, Ruptoseptoria unedonis (Roberge ex Desm.) Quaedvlieg, Verkley & Crous, Septorioides pini-thunbergii (S. Kaneko) Quaedvlieg, Verkley & Crous, Sphaerulina abeliceae (Hiray.) Quaedvlieg, Verkley & Crous, Sphaerulina azaleae (Voglino) Quaedvlieg, Verkley & Crous, Sphaerulina berberidis (Niessl) Quaedvlieg, Verkley & Crous, Sphaerulina betulae (Pass.) Quaedvlieg, Verkley & Crous, Sphaerulina cercidis (Fr.) Quaedvlieg, Verkley & Crous, Sphaerulina menispermi (Thüm.) Quaedvlieg, Verkley & Crous, Sphaerulina musiva (Peck) Quaedvlieg, Verkley & Crous, Sphaerulina oxyacanthae (Kunze & J.C. Schmidt) Quaedvlieg, Verkley & Crous, Sphaerulina patriniae (Miura) Quaedvlieg, Verkley & Crous, Sphaerulina populicola (Peck) Quaedvlieg, Verkley & Crous, Sphaerulina quercicola (Desm.) Quaedvlieg, Verkley & Crous, Sphaerulina rhabdoclinis (Butin) Quaedvlieg, Verkley & Crous, Stromatoseptoria castaneicola (Desm.) Quaedvlieg, Verkley & Crous. Typifications: Epitypifications - Phaeosphaeria oryzae I. Miyake, Phaeoseptoria papayae Speg.; Neotypification - Hendersonia paludosa Sacc. & Speg.

Asperisporium and Pantospora (Mycosphaerellaceae): epitypifications and phylogenetic placement

The species-rich family Mycosphaerellaceae contains considerable morphological diversity and includes numerous anamorphic genera, many of which are economically important plant pathogens. Recent revisions and phylogenetic research have resulted in taxonomic instability. Ameliorating this problem requires phylogenetic placement of type species of key genera. We present an examination of the type species of the anamorphic Asperisporium and Pantospora. Cultures isolated from recent port interceptions were studied and described, and morphological studies were made of historical and new herbarium specimens. DNA sequence data from the ITS region and nLSU were generated from these type species, analysed phylogenetically, placed into an evolutionary context within Mycosphaerellaceae, and compared to existing phylogenies. Epitype specimens associated with living cultures and DNA sequence data are designated herein. Asperisporium caricae, the type of Asperisporium and cause of a leaf and fruit spot disease of papaya, is closely related to several species of Passalora including P. brachycarpa. The status of Asperisporium as a potential generic synonym of Passalora remains unclear. The monotypic genus Pantospora, typified by the synnematous Pantospora guazumae, is not included in Pseudocercospora sensu stricto or sensu lato. Rather, it represents a distinct lineage in the Mycosphaerellaceae in an unresolved position near Mycosphaerella microsora.

What is Scirrhia?

The ascomycetous genus Scirrhia is presently treated as a member of Dothideomycetidae, though uncertainty remains as to which family it belongs in Capnodiales, Ascomycota. Recent collections on stems of a fern, Pteridium aquilinum (Dennstaedtiaceae) in Brazil, led to the discovery of a new species of Scirrhia, described here as S.brasiliensis. Based on DNA sequence data of the nuclear ribosomal DNA (LSU), Scirrhia is revealed to represent a member of Dothideomycetes, Capnodiales, Mycosphaerellaceae. Scirrhia is the first confirmed genus in Mycosphaerellaceae to have well developed pseudoparaphyses and a prominent hypostroma in which ascomata are arranged in parallel rows. Given the extremely slow growth rate and difficulty in obtaining cultures of S. brasiliensis on various growth media, it appears that Scirrhia represents a genus of potentially obligate plant pathogens within Mycosphaerellaceae.

Phylogeny of rock-inhabiting fungi related to Dothideomycetes

The class Dothideomycetes (along with Eurotiomycetes) includes numerous rock-inhabiting fungi (RIF), a group of ascomycetes that tolerates surprisingly well harsh conditions prevailing on rock surfaces. Despite their convergent morphology and physiology, RIF are phylogenetically highly diverse in Dothideomycetes. However, the positions of main groups of RIF in this class remain unclear due to the lack of a strong phylogenetic framework. Moreover, connections between rock-dwelling habit and other lifestyles found in Dothideomycetes such as plant pathogens, saprobes and lichen-forming fungi are still unexplored. Based on multigene phylogenetic analyses, we report that RIF belong to Capnodiales (particularly to the family Teratosphaeriaceae s.l.), Dothideales, Pleosporales, and Myriangiales, as well as some uncharacterised groups with affinities to Dothideomycetes. Moreover, one lineage consisting exclusively of RIF proved to be closely related to Arthoniomycetes, the sister class of Dothideomycetes. The broad phylogenetic amplitude of RIF in Dothideomycetes suggests that total species richness in this class remains underestimated. Composition of some RIF-rich lineages suggests that rock surfaces are reservoirs for plant-associated fungi or saprobes, although other data also agree with rocks as a primary substrate for ancient fungal lineages. According to the current sampling, long distance dispersal seems to be common for RIF. Dothideomycetes lineages comprising lichens also include RIF, suggesting a possible link between rock-dwelling habit and lichenisation.

Molecular phylogenetic studies on the lichenicolous Xanthoriicola physciae reveal Antarctic rock-inhabiting fungi and Piedraia species among closest relatives in the Teratosphaeriaceae

The phylogenetic placement of the monotypic dematiaceous hyphomycete genus Xanthoriicola was investigated. Sequences of the nLSU region were obtained from 11 specimens of X. physciae, which formed a single clade supported both by parsimony (91 %), and maximum likelihood (100 %) bootstraps, and Bayesian Posterior Probabilities (1.0). The closest relatives in the parsimony analysis were species of Piedraria, while in the Bayesian analysis they were those of Friedmanniomyces. These three genera, along with species of Elasticomyces, Recurvomyces, Teratosphaeria, and sequences from unnamed rock-inhabiting fungi (RIF), were all members of the same major clade within Capnodiales with strong support in both analyses, and for which the family name Teratosphaeriaceae can be used pending further studies on additional taxa.

Racoleus, a new genus of sterile filamentous lichen-forming fungi from the tropics, with observations on the nomenclature and typification of Cystocoleus and Racodium

Racoleus trichophorus gen. sp. nov. is described for a tropical sterile filamentous lichenized fungus which overgrows various crustose lichens on bark. It shares some features with Cystocoleus and Racodium, but is unique in having non-lichenized long lateral spines. The genus, which is known from China, the Ivory Coast, and Peru, is of uncertain systematic position; on the basis of morphological similarities, however, it may be referred to "? Capnodiales (incertae sedis)" ad interim. In addition, the nomenclature and typification of the monotypic genera Cystocoleus and Racodium are reviewed, and lectotypes selected for the type of each. The available information on the ecology and distribution of these two genera is also summarized, and scanning electron micrographs (SEM) of all three species are presented for the first time.

Cymadothea trifolii, an obligate biotrophic leaf parasite of Trifolium, belongs to Mycosphaerellaceae as shown by nuclear ribosomal DNA analyses

The ascomycete Cymadothea trifolii, a member of the Dothideomycetes, is unique among obligate biotrophic fungi in its capability to only partially degrade the host cell wall and in forming an astonishingly intricate interaction apparatus (IA) in its own hyphae, while the attacked host plant cell is triggered to produce a membranous bubble opposite the IA. However, no sequence data are currently available for this species. Based on molecular phylogenetic results obtained from complete SSU and partial LSU data, we show that the genus Cymadothea belongs to the Mycosphaerellaceae (Capnodiales, Dothideomycetes). This is the first report of sequences obtained for an obligate biotrophic member of Mycosphaerellaceae.

Phylogenetic lineages in the Capnodiales

The Capnodiales incorporates plant and human pathogens, endophytes, saprobes and epiphytes, with a wide range of nutritional modes. Several species are lichenised, or occur as parasites on fungi, or animals. The aim of the present study was to use DNA sequence data of the nuclear ribosomal small and large subunit RNA genes to test the monophyly of the Capnodiales, and resolve families within the order. We designed primers to allow the amplification and sequencing of almost the complete nuclear ribosomal small and large subunit RNA genes. Other than the Capnodiaceae (sooty moulds), and the Davidiellaceae, which contains saprobes and plant pathogens, the order presently incorporates families of major plant pathological importance such as the Mycosphaerellaceae, Teratosphaeriaceae and Schizothyriaceae. The Piedraiaceae was not supported, but resolves in the Teratosphaeriaceae. The Dissoconiaceae is introduced as a new family to accommodate Dissoconium and Ramichloridium. Lichenisation, as well as the ability to be saprobic or plant pathogenic evolved more than once in several families, though the taxa in the upper clades of the tree lead us to conclude that the strictly plant pathogenic, nectrotrophic families evolved from saprobic ancestors (Capnodiaceae), which is the more primitive state.

High diversity and morphological convergence among melanised fungi from rock formations in the Central Mountain System of Spain

Melanised fungi were isolated from rock surfaces in the Central Mountain System of Spain. Two hundred sixty six isolates were recovered from four geologically and topographically distinct sites. Microsatellite-primed PCR techniques were used to group isolates into genotypes assumed to represent species. One hundred and sixty three genotypes were characterised from the four sites. Only five genotypes were common to two or more sites. Morphological and molecular data were used to characterise and identify representative strains, but morphology rarely provided a definitive identification due to the scarce differentiation of the fungal structures or the apparent novelty of the isolates. Vegetative states of fungi prevailed in culture and in many cases could not be reliably distinguished without sequence data. Morphological characters that were widespread among the isolates included scarce micronematous conidial states, endoconidia, mycelia with dark olive-green or black hyphae, and mycelia with torulose, isodiametric or moniliform hyphae whose cells develop one or more transverse and/or oblique septa. In many of the strains, mature hyphae disarticulated, suggesting asexual reproduction by a thallic micronematous conidiogenesis or by simple fragmentation. Sequencing of the internal transcribed spacers (ITS1, ITS2) and 5.8S rDNA gene were employed to investigate the phylogenetic affinities of the isolates. According to ITS sequence alignments, the majority of the isolates could be grouped among four main orders of Pezizomycotina: Pleosporales, Dothideales, Capnodiales, and Chaetothyriales. Ubiquitous known soil and epiphytic fungi species were generally absent from the rock surfaces. In part, the mycota of the rock surfaces shared similar elements with melanised fungi from plant surfaces and fungi described from rock formations in Europe and Antarctica. The possibility that some of the fungi were lichen mycobionts or lichen parasites could not be ruled out.

An RFLP-Based Technique for Identifying Fungi in the Sooty Blotch and Flyspeck Complex on Apple

A restriction fragment length polymorphism (RFLP)-based technique was developed to identify members of the sooty blotch and flyspeck (SBFS) disease complex on apple because these fungi are difficult to identify using agar-plate isolation and morphological description. The method includes polymerase chain reaction (PCR) amplification of the internal transcribed spacer (ITS) region of ribosomal DNA (rDNA) using a fungal-specific forward primer (ITS1-F) and an SBFS-specific reverse primer (Myc1-R), followed by digestion of the PCR product by the HaeIII restriction enzyme. When applied to previously identified isolates of 24 SBFS-causing species in nine genera, the PCR-RFLP assay produced 14 unique banding patterns. Different genera never shared the same RFLP pattern. To evaluate performance in vivo, the technique was applied to DNA extracted directly from SBFS colonies on apple fruit from three Iowa orchards. The primers amplified the rDNA of only SBFS fungi, with the exception of a Cladosporium sp.; however, its RFLP banding pattern was distinct from those of SBFS fungi. The majority (60%) of SBFS colonies in the in vivo trial were identified to genus by RFLP analysis. The PCR-RFLP assay greatly streamlined the identification process by minimizing the need for culturing, indicating its value as a tool for field studies of the SBFS complex.