Marta Wrzosek

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. Lineage-specific 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.

Fungal Planet description sheets: 154–213

Novel species of microfungi described in the present study include the following from South Africa: Camarosporium aloes, Phaeococcomyces aloes and Phoma aloes from Aloe, C. psoraleae, Diaporthe psoraleae and D. psoraleae-pinnatae from Psoralea, Colletotrichum euphorbiae from Euphorbia, Coniothyrium prosopidis and Peyronellaea prosopidis from Prosopis, Diaporthe cassines from Cassine, D. diospyricola from Diospyros, Diaporthe maytenicola from Maytenus, Harknessia proteae from Protea, Neofusicoccum ursorum and N. cryptoaustrale from Eucalyptus, Ochrocladosporium adansoniae from Adansonia, Pilidium pseudoconcavum from Greyia radlkoferi, Stagonospora pseudopaludosa from Phragmites and Toxicocladosporium ficiniae from Ficinia. Several species were also described from Thailand, namely: Chaetopsina pini and C. pinicola from Pinus spp., Myrmecridium thailandicum from reed litter, Passalora pseudotithoniae from Tithonia, Pallidocercospora ventilago from Ventilago, Pyricularia bothriochloae from Bothriochloa and Sphaerulina rhododendricola from Rhododendron. Novelties from Spain include Cladophialophora multiseptata, Knufia tsunedae and Pleuroascus rectipilus from soil and Cyphellophora catalaunica from river sediments. Species from the USA include Bipolaris drechsleri from Microstegium, Calonectria blephiliae from Blephilia, Kellermania macrospora (epitype) and K. pseudoyuccigena from Yucca. Three new species are described from Mexico, namely Neophaeosphaeria agaves and K. agaves from Agave and Phytophthora ipomoeae from Ipomoea. Other African species include Calonectria mossambicensis from Eucalyptus (Mozambique), Harzia cameroonensis from an unknown creeper (Cameroon), Mastigosporella anisophylleae from Anisophyllea (Zambia) and Teratosphaeria terminaliae from Terminalia (Zimbabwe). Species from Europe include Auxarthron longisporum from forest soil (Portugal), Discosia pseudoartocreas from Tilia (Austria), Paraconiothyrium polonense and P. lycopodinum from Lycopodium (Poland) and Stachybotrys oleronensis from Iris (France). Two species of Chrysosporium are described from Antarctica, namely C. magnasporum and C. oceanitesii. Finally, Licea xanthospora is described from Australia, Hypochnicium huinayensis from Chile and Custingophora blanchettei from Uruguay. Novel genera of Ascomycetes include Neomycosphaerella from Pseudopentameris macrantha (South Africa), and Paramycosphaerella from Brachystegia sp. (Zimbabwe). Novel hyphomycete genera include Pseudocatenomycopsis from Rothmannia (Zambia), Neopseudocercospora from Terminalia (Zambia) and Neodeightoniella from Phragmites (South Africa), while Dimorphiopsis from Brachystegia (Zambia) represents a novel coelomycetous genus. Furthermore, Alanphillipsia is introduced as a new genus in the Botryosphaeriaceae with four species, A. aloes, A. aloeigena and A. aloetica from Aloe spp. and A. euphorbiae from Euphorbia sp. (South Africa). A new combination is also proposed for Brachysporium torulosum (Deightoniella black tip of banana) as Corynespora torulosa. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.

Bringing Laboulbeniales into the 21st century: enhanced techniques for extraction and PCR amplification of DNA from minute ectoparasitic fungi

Laboulbeniales is one of the most peculiar orders of Ascomycota. These fungi are characterized by an ectoparasitic life-style on arthropods, determinate growth, lack of an asexual stage, high species richness, and intractability to culture. The order Laboulbeniales, sister to Pyxidiophorales, has only recently been assigned a separate class, the Laboulbeniomycetes, based on very few ribosomal DNA sequences. So far, DNA isolations and PCR amplifications have proven difficult. Here, we provide details of isolation techniques and the application of commercially available kits that enable efficient and reliable genetic analyses of these fungi. We provide 43 newly generated Laboulbeniales ribosomal DNA sequences, among which are the first published sequences for species in the genera Gloeandromyces, Herpomyces, Laboulbenia, Monoicomyces, and Polyandromyces. DNA extractions were possible using from 1 to 30 thalli from hosts preserved in ethanol (70–100 %). In two cases, we successfully isolated DNA from thalli on dried insect collections. Laboulbeniales molecular systematics could be substantially enhanced through these improved methods by allowing more complete sampling of both taxa and gene regions.

Biodegradation of nonylphenol by a novel entomopathogenic Metarhizium robertsii strain

The biodegradation of nonylphenol (NP) by a newly isolated form of the larva fungal strain Metarhizium robertsii IM 6519 was investigated in this study. This isolate was capable of degrading 4-n-NP, and multiple metabolites were detected. The coexistence of parallel degradation pathways with versatile hydroxylation in different positions of the alkyl chain is a unique feature of this strain. Moreover, several metabolites previously described only in higher eukaryotes were detected in the fungal cultures. The degradation process led to the mineralization of 4-n-NP (with an efficiency of 36%), a great advantage of this strain that results in complete removal of toxic substrate from the environment.

Diversity of acaropathogenic fungi in Poland and other European countries.

The occurrence, species diversity and some aspects of taxonomical affinity and host selectivity of acaropathogenic fungi associated with phytophagous, saprotrophic and predacious mites in Poland and other European countries were investigated on wild and cultivated plants, in insect feeding sites under the bark and in decayed wood. From among 33 species of fungi affecting mites only five species of Entomophthorales were separated and the most numerous were Neozygites floridana mostly on Tetranychus urticae, N. abacaridis on a few eriophyid species, and Conidiobolus coronatus attacking gamasid mites most frequently of the genus Dendrolaelaps. The most frequent mite pathogens occurring in mite communities on plants and in wood infested by insects were of the genus Hirsutella. Until now 13 of their form-species have been recognized in these habitats, but only H. kirchneri, H. necatrix and H. thompsonii (including its variety synnematosa) can be treated as exclusive oligophagous pathogens of phytophagous mites, though their potential host range seems to embrace only selected eriophyid or tarsonemid mites. Taxonomical differentiation of fungal strains was based on close morphological observations and molecular analysis of ITS region sequences. Two new species of acaropathogenic fungi were described in these studies. Hirsutella danubiensis sp. nov. was found in the tetranychid T. urticae, whereas H. vandergeesti sp. nov. affected phytoseiid mites of the genera Amblyseius, Neoseiulus, Seiulus and Typhlodromus, and the tarsonemid Tarsonemus lacustris.

Paraconiothyrium babiogorense sp. nov., a new endophyte from fir club moss Huperzia selago (Huperziaceae)

Paraconiothyrium is a recently established genus within the order Pleosporales. Species from this genus are commonly associated with plants but can also be found in soil samples and be parasitic on fungi. Several isolates of a Paraconiothyrium sp. were obtained from Huperzia selago in Poland. Strains were characterized based on morphological characteristics and molecular data (SSU rDNA, ITS1, 5.8S rDNA, ITS2). Based on its unique morphology and DNA phylogeny, isolates were described as a new species: Paraconiothyrium babiogorense, which represents the first report of a Paraconiothyrium species from fir club moss. Comparison of characters with other Paraconiothyrium species is provided as well as a signature sequence for the new species.

The diversity of endophytic fungi in the above-ground tissue of two Lycopodium species in Poland

Endophytes are a large and diverse group of fungi that colonize healthy plant tissues without causing any symptoms. The majority of studies have focused on angiosperm and conifer hosts and few have examined the endophytes of lycophytes. In the present study, we characterized culturable endophytic fungi in two closely related Lycopodium species (L. annotinum and L. clavatum) from pine, beech, oak and spruce forests across Poland. More than 400 strains were isolated but only 18 Ascomycete species were identified. Members of the Dothideomycetes dominated the fungal endophyte communities in Lycopodium. The most abundant taxa cultured were Phoma brasiliensis (from L. clavatum) and Paraconiothyrium lycopodinum (from L. annotinum). Five taxa were isolated exclusively from L. annotinum, but only two of them (Paraconiothyrium lycopodinum and Mycosphaerella sp.) were relatively abundant. Two taxa were only found in L. clavatum, namely: Stagonospora pseudovitensis and an unidentified Dothideomycete. The taxon assigned as Ascomycota 2 (SH219457.06FU) was isolated only from strobili of both host species. Direct PCR and cloning from L. annotinum shoots revealed a substantially greater endophyte richness compared with the results from culturing.

Preliminary studies on the evolution of carbon assimilation abilities within Mucorales

Representatives of Mucorales belong to one of the oldest lineages of terrestrial fungi. Although carbon is of fundamental importance for fungal growth and functioning, relatively little is known about enzymatic capacities of Mucorales. The evolutionary history and the variability of the capacity to metabolize different carbon sources among representatives of the order Mucorales was studied using Phenotypic Microarray Plates. The ability of 26 strains belonging to 23 nonpathogenic species of Mucorales to use 95 different carbon sources was tested. Intraspecies variability of carbon assimilation profiles was lower than interspecies variation for some selected strains. Although similarities between the phylogenetic tree and the dendrogram created from carbon source utilization data were observed, the ability of the various strains to use the analyzed substrates did not show a clear correlation with the evolutionary history of the group. Instead, carbon assimilation profiles are probably shaped by environmental conditions.

The plasticity of fungal interactions

Their hyphal structure, the common events of hybridization and horizontal gene transfer, as well as intimate associations with prokaryotes (including endobiotic bacteria) and cooperation with eukaryotes have made fungi very flexible at the genetic, physiological, and ecological levels. It is manifested with the fungal ability to perfectly exploit existing nutrient sources and plastically fit into a changing environment. Although the links between fungi and other ecosystem components are rarely clearly visible and unambiguous, fungi can be ecosystem buffers playing a homeostatic role throughout global ecosystems, reacting to changes in various ways, not only by modifications of gene expression but also by nuclear status and “extended phenotype”. The goal of this review is to underline some ecological interactions involving fungi and other organisms and to indicate high fungal plasticity in terms of ontogenetic perspective.

The use of compensatory base change analysis of ITS2 as a tool in the phylogeny of Mucorales, illustrated by the Mucor circinelloides complex

Compensatory base changes (CBCs) in helix II of rDNA ITS2, suggested as a molecular classifier for fungi, were analyzed in Mucor circinelloides and its varieties. Only a few CBCs were found in the complex. Three out of the four accepted formae (f. circinelloides, f. lusitanicus, f. janssenii) did not exhibit CBCs. One CBC was found between strains that form zygospores; consequently, CBC is not always concordant with mating experiments. Strains with two CBC are unable to breed. It is suggested that some strains of the M. circinelloides complex are at the beginning of speciation.