Harnessing the microbiome to control plant parasitic weeds.

Microbiomes can significantly expand the genomic potential of plants, contributing to nutrient acquisition, plant growth promotion and tolerance to (a)biotic stresses. Among biotic stressors, root parasitic weeds (RPWs), mainly of the genera Orobanche, Phelipanche and Striga, are major yield-limiting factors of a wide range of staple crops, particularly in developing countries. Here, we provide a conceptual synthesis of putative mechanisms by which soil and plant microbiomes could be harnessed to control RPWs. These mechanisms are partitioned in direct and indirect modes of action and discussed in the context of past and present studies on microbe-mediated suppression of RPWs. Specific emphasis is given to the large but yet unexplored potential of root-associated microorganisms to interfere with the chemical signalling cascade between the host plant and the RPWs. We further provide concepts and ideas for future research directions and prospective designs of novel control strategies.

Ten new species of Calonectria from Indonesia and Vietnam.

Vietnam and Indonesia have rapidly growing and extensive plantation forestry programs, especially of Acacia spp. and Eucalyptus spp. As these plantations expand, the threat from pests and diseases also increases. Calonectria species are among those pathogens causing diseases of trees in plantations and nurseries in these countries. Extensive surveys were conducted across plantations and nurseries of Vietnam and parts of Indonesia, where a large number of Calonectria isolates were retrieved from diseased leaves and soils associated with symptomatic trees. The aim of this study was to identify and resolve the phylogenetic relationships among these isolates using DNA sequence comparisons of four gene regions as well as morphological characters. From a collection of 165 isolates, the study revealed five known and 10 undescribed species. The relatively high diversity of Calonectria species found in this study supports the view that many more species in this genus remain to be discovered in other areas of Southeast Asia.

Chapter F of the International Code of Nomenclature for algae, fungi, and plants as approved by the 11th International Mycological Congress, San Juan, Puerto Rico, July 2018.

A revised version of Chapter F of the International Code of Nomenclature for algae, fungi, and plants is presented, incorporating amendments approved by the Fungal Nomenclature Session of the 11th International Mycological Congress held in San Juan, Puerto Rico in July 2018. The process leading to the amendments is outlined. Key changes in the San Juan Chapter F are (1) removal of option to use a colon to indicate the sanctioned status of a name, (2) introduction of correctability for incorrectly cited identifiers of names and typifications, and (3) introduction of option to use name identifiers in place of author citations. Examples have been added to aid the interpretation of new Articles and Recommendations, and Examples have also been added to the existing Art. F.3.7 concerning the protection extended to new combinations based on sanctioned names or basionyms of sanctioned names (which has been re-worded), and to Art. F.3.9 concerning typification of names accepted in the sanctioning works.

Diversity of yeast species from Dutch garden soil and the description of six novel Ascomycetes.

A Citizen Science initiative by the Westerdijk Fungal Biodiversity Institute and the Utrecht University Museum gave rise to a project where fungal and yeast isolates were obtained and identified from Dutch soil samples. During the current study, 386 yeast strains were isolated from 157 different locations in the Netherlands. These strains were identified using sequence data of the large-subunit rRNA gene (D1/D2 region) and the internal transcribed spacer 1 and 2 regions. A total of 53 different yeast species were found as well as 15 potentially novel species. Six novel ascomycetous species are described during this study that include Hanseniaspora mollemarum sp. nov., Ogataea degrootiae sp. nov., Pichia gijzeniarum sp. nov., Saccharomycopsis oosterbeekiorum sp. nov., Trichomonascus vanleenenius sp. nov. and Zygoascus flipseniorum sp. nov. This study made it possible to incorporate numerous yeast isolates into the CBS collection without any restrictions, which make these isolates readily available for use by others. Many of the isolates represented species of which only a few isolates or even only a single ex-type strain were available. Therefore, it is a clear indication that such biodiversity-orientated Citizen Science projects can enrich the pool of available yeasts for future research projects.

New species of Cylindrocladiella from plantation soils in South-East Asia.

Cylindrocladiella spp. are widely distributed especially in tropical and sub-tropical regions, where they are mainly known as saprobes although some species are plant pathogens. Very little is known about these fungi in South-East Asia. The aim of this study was to identify a collection of Cylindrocladiella isolates from soils collected in forest nurseries and plantations in Vietnam and Malaysia. This was achieved using DNA sequence comparisons and morphological observations. The study revealed two previously described species, Cy. lageniformis and Cy. peruviana as well as five novel taxa, described here as Cy. arbustasp. nov., Cy. malesianasp. nov., Cy. obpyriformissp. nov., Cy. parvisporasp. nov. and Cy. solicolasp. nov. A relatively small collection of isolates from a limited geographic sampling revealed an unexpectedly high level of Cylindrocladiella diversity suggesting that many more species in this genus await discovery in South-East Asia.

Calonectria species isolated from Eucalyptus plantations and nurseries in South China.

Diseases caused by species of Calonectria (Ca.) represent a serious threat to the growth and sustainability of Eucalyptus plantations in China. Symptoms caused by these fungi mainly include leaf blight on trees in plantations and rotting of stems and leaves in nurseries. Extensive surveys have recently been conducted where Calonectria species were collected in Eucalyptus plantations and nurseries in the FuJian, GuangDong, GuangXi, and YunNan Provinces of South China. Additional isolates were baited from soil samples in the Hong Kong Region. The aim of this study was to identify the 115 Calonectria isolates obtained using comparisons of DNA sequence data for the ß-tubulin (tub2), calmodulin (cmdA), histone H3 (his3) and partial translation elongation factor-1α (tef1) gene regions as well as their morphological features. Seven known species were identified, including Calonectria arbusta, Ca. asiatica, Ca. chinensis, Ca. eucalypti, Ca. hongkongensis, Ca. mossambicensis and Ca. pentaseptata. In addition, six novel taxa were collected and are described here as Ca. aciculata, Ca. honghensis, Ca. lantauensis, Ca. pseudoturangicola, Ca. pseudoyunnanensis, and Ca. yunnanensis spp. nov. Overall, the results reflect a high diversity of Calonectria species in China.

Pleiocarpon gen. nov. and a new species of Ilyonectria causing basal rot of Strelitzia reginae in Italy.

During 2015, a new basal rot disease was observed on potted plants of Strelitzia reginae in an ornamental nursery located in eastern Sicily. Isolations from symptomatic parts of these diseased plants consistently yielded cylindrocarpon-like isolates. Multigene analyses of the partial gene regions of 28S large subunit nrDNA, ß-tubulin, histone H3, translation elongation factor 1-alpha, internal transcribed spacer region and intervening 5.8S nrRNA gene, and RNA polymerase II second largest subunit genes, supported by morphological characters supported the recognition of a new genus, Pleiocarpon based on P. strelitziae sp. nov., and a new Ilyonectria species, described here as I. strelitziae sp. nov. The pathogenicity of both I. strelitziae and P. strelitziae were confirmed on young plants cultivated under controlled conditions in a growth chamber. Both cylindrocarpon-like fungi were pathogenic to S. reginae and reproduced symptoms similar to those observed in the nursery. Of the two species, P. strelitziae was more aggressive than I. strelitziae, resulting in the death of all inoculated plants.

Families, genera, and species of Botryosphaeriales.

Members of Botryosphaeriales are ecologically diverse, but most commonly associated with leaf spots, fruit and root rots, die-back or cankers of diverse woody hosts. Based on morphology and DNA sequence data, the Botryosphaeriales have to date been shown to contain eight families, with an additional two, Endomelanconiopsisaceae (Endomelanconiopsis) and Pseudofusicoccumaceae (Pseudofusicoccum) being newly described in this study. Furthermore, Oblongocollomyces is introduced as new genus, while Spencermartinsia is reduced to synonymy under Dothiorella. Novel species include Diplodia pyri (Pyrus sp., the Netherlands), Diplodia citricarpa (Citrus sp., Iran), Lasiodiplodia vitis (Vitis vinifera, Italy), L. sterculiae (Sterculia oblonga, Germany), Neofusicoccum pistaciarum (Pistacia vera, USA), N. buxi (Buxus sempervirens, France), N. stellenboschiana (Vitis vinifera, South Africa), and Saccharata hawaiiensis (Protea laurifolia, Hawaii). New combinations are also proposed for Camarosporium pistaciae (associated with fruit rot of Pistacia vera) in Neofusicoccum, and Sphaeria gallae (associated with galls of Quercus) in Diplodia. The combination of large subunit of the nuclear ribosomal RNA gene (LSU)-rpb2 proved effective at delineating taxa at family and generic level. Furthermore, rpb2 also added additional resolution for species delimitation, in combination with ITS, tef1 and tub2. In this study we analysed 499 isolates, and produce an expanded phylogenetic backbone for Botryosphaeriales, which will help to delimit novelties at species, genus and family level in future.

Overlooked competing asexual and sexually typified generic names of Ascomycota with recommendations for their use or protection.

With the change to one scientific name for fungal species, numerous papers have been published with recommendations for use or protection of competing generic names in major groups of ascomycetes. Although genera in each group of fungi were carefully considered, some competing generic names were overlooked. This paper makes recommendations for additional competing genera not considered in previous papers. Chairs of relevant Working Groups of the ICTF were consulted in the development of these recommendations. A number of generic names need protection, specifically Amarenographium over Amarenomyces, Amniculicola over Anguillospora, Balansia over Ephelis, Claviceps over Sphacelia, Drepanopeziza over Gloeosporidiella and Gloeosporium, Golovinomyces over Euoidium, Holwaya over Crinium, Hypocrella over Aschersonia, Labridella over Griphosphaerioma, Metacapnodium over Antennularia, and Neonectria over Cylindrocarpon and Heliscus. The following new combinations are made: Amniculicola longissima, Atichia maunauluana, Diaporthe columnaris, D. liquidambaris, D. longiparaphysata, D. palmicola, D. tersa, Elsinoë bucidae, E.caricae, E. choisyae, E. paeoniae, E. psidii, E. zorniae, Eupelte shoemakeri, Godronia myrtilli, G. raduloides, Sarcinella mirabilis, S. pulchra, Schizothyrium jamaicense, and Trichothallus niger. Finally, one new species name, Diaporthe azadirachte, is introduced to validate an earlier name, and the conservation of Discula with a new type, D. destructiva, is recommended.

Mycoparasitic species of Sphaerellopsis, and allied lichenicolous and other genera.

Species of Sphaerellopsis (sexual morph Eudarluca) are well-known cosmopolitan mycoparasites occurring on a wide range of rusts. Although their potential role as biocontrol agents has received some attention, the molecular phylogeny of the genus has never been resolved. Based on morphology and DNA sequence data of the large subunit nuclear ribosomal RNA gene (LSU, 28S) and the internal transcribed spacers (ITS) and 5.8S rRNA gene of the nrDNA operon, the genus Sphaerellopsis is shown to belong to Leptosphaeriaceae in Dothideomycetes. Sphaerellopsis is circumscribed, and the sexually typified generic name Eudarluca treated as a synonym on the basis that Sphaerellopsis is more commonly used in literature, is the older generic name, and is the morph commonly encountered by plant pathologists in the field. A neotype is designated for Sphaerellopsis filum, and two new species are introduced, S. macroconidialis and S. paraphysata spp. nov. Species previously incorrectly placed in Sphaerellopsis are allocated to Neosphaerellopsis gen. nov. as N. thailandica, and to the genus Acrocalymma, as A. fici. The genus Rhizopycnis is nestled among species of Acrocalymma, and reduced to synonymy based on its morphology and DNA phylogeny, while Acrocalymmaceae is introduced as novel family to accommodate members of this genus in the Dothideomycetes. Furthermore, Sphaerellopsis proved to be phylogenetically closely allied to a lichenicolous complex of phoma-like taxa, for which the new genera Diederichomyces and Xenophoma are established. Several new combinations are introduced, namely D. xanthomendozae, D. ficuzzae, D. caloplacae, D. cladoniicola, D. foliaceiphila, and X. puncteliae combs. nov, while Paraphaeosphaeria parmeliae sp. nov. is newly described.

Genera in Bionectriaceae, Hypocreaceae, and Nectriaceae (Hypocreales) proposed for acceptance or rejection.

With the recent changes concerning pleomorphic fungi in the new International Code of Nomenclature for algae, fungi, and plants (ICN), it is necessary to propose the acceptance or protection of sexual morph-typified or asexual morph-typified generic names that do not have priority, or to propose the rejection or suppression of competing names. In addition, sexual morph-typified generic names, where widely used, must be proposed for rejection or suppression in favour of asexual morph-typified names that have priority, or the latter must be proposed for conservation or protection. Some pragmatic criteria used for deciding the acceptance or rejection of generic names include: the number of name changes required when one generic name is used over another, the clarity of the generic concept, their relative frequencies of use in the scientific literature, and a vote of interested mycologists. Here, twelve widely used generic names in three families of Hypocreales are proposed for acceptance, either by conservation or protection, despite their lack of priority of publication, or because they are widely used asexual morph-typified names. Each pair of generic names is evaluated, with a recommendation as to the generic name to be used, and safeguarded, either through conservation or protection. Four generic names typified by a species with a sexual morph as type that are younger than competing generic names typified by a species with an asexual morph type, are proposed for use. Eight older generic names typified by species with an asexual morph as type are proposed for use over younger competing generic names typified by a species with a sexual morph as type. Within Bionectriaceae, Clonostachys is recommended over Bionectria; in Hypocreaceae, Hypomyces is recommended over Cladobotryum, Sphaerostilbella over Gliocladium, and Trichoderma over Hypocrea; and in Nectriaceae, Actinostilbe is recommended over Lanatonectria, Cylindrocladiella over Nectricladiella, Fusarium over Gibberella, Gliocephalotrichum over Leuconectria, Gliocladiopsis over Glionectria, Nalanthamala over Rubrinectria, Nectria over Tubercularia, and Neonectria over Cylindrocarpon.

Homortomyces gen. nov., a new dothidealean pycnidial fungus from the Cradle of Humankind.

Homortomyces is introduced as a new coelomycetous genus associated with leaf spots onCombretum erythrophyllum trees growing near and around the Sterkfontein caves, Maropeng, South Africa. Based on its transversely septate, brown conidia, the presence of paraphyses, and percurrent proliferation of the conidiogenous cells, the genus resembles Stilbospora (Melanoconidaceae, Diaporthales). It is distinct in having pycnidial condiomata, conidia lacking mucoid sheaths, and becoming muriform when mature. Its morphology and phylogenetic placement based on analyses of sequence data for the large subunit nuclear ribosomal RNA gene (LSU, 28S) as well as the ITS and 5.8S rRNA gene of the nrDNA operon, show that Homortomyces represents a novel genus in Dothideomycetes, although its familial relationships remain unresolved.

One fungus, one name promotes progressive plant pathology.

The robust and reliable identification of fungi underpins virtually every element of plant pathology, from disease diagnosis to studies of biology, management/control, quarantine and, even more recently, comparative genomics. Most plant diseases are caused by fungi, typically pleomorphic organisms, for which the taxonomy and, in particular, a dual nomenclature system have frustrated and confused practitioners of plant pathology. The emergence of DNA sequencing has revealed cryptic taxa and revolutionized our understanding of relationships in the fungi. The impacts on plant pathology at every level are already immense and will continue to grow rapidly as new DNA sequencing technologies continue to emerge. DNA sequence comparisons, used to resolve a dual nomenclature problem for the first time only 19 years ago, have made it possible to approach a natural classification for the fungi and to abandon the confusing dual nomenclature system. The journey to a one fungus, one name taxonomic reality has been long and arduous, but its time has come. This will inevitably have a positive impact on plant pathology, plant pathologists and future students of this hugely important discipline on which the world depends for food security and plant health in general. This contemporary review highlights the problems of a dual nomenclature, especially its impact on plant pathogenic fungi, and charts the road to a one fungus, one name system that is rapidly drawing near.