Phytophthora pachypleura sp. nov., a new species causing root rot of Aucuba japonica and other ornamentals in the United Kingdom

Isolates of an unknown Phytophthora species from the ‘Phytophthora citricola complex’ have been found associated with mortality of Aucuba japonica in the UK. Based on morphological characteristics, growth–temperature relationships, sequences of five DNA regions and pathogenicity assays, the proposed novel species is described as Phytophthora pachypleura. Being homothallic with paragynous antheridia and semipapillate sporangia, P. pachypleura resembles other species in the ‘P. citricola complex’ but can be discriminated by its distinctively thick‐walled oospores with an oospore wall index of 0·71. In the phylogenetic analysis based on three nuclear (ITS, β‐tubulin, EF‐1α) and two mitochondrial (cox1, nadh1) DNA regions, P. pachypleura formed a distinct clade within the ‘P. citricola complex’ with P. citricola s. str., P. citricola E and P. acerina as its closest relatives. Phytophthora pachypleura is more aggressive to A. japonica than P. plurivora and P. multivora and has the potential to affect other ornamental species.     

Phytophthora acerina sp. nov., a new species causing bleeding cankers and dieback of Acer pseudoplatanus trees in planted forests in northern Italy

A severe dieback of Acer pseudoplatanus trees was noticed in planted forest stands in northern Italy in 2010. Affected trees showed collar rot and aerial bleeding cankers along the stems, leading to crown dieback and eventually death. An unknown Phytophthora species was consistently isolated from necrotic bark and xylem tissue and from rhizosphere soil. Based on its unique combination of morphological and physiological characters and phylogenetic analysis, this new taxon is here described as Phytophthora acerina sp. nov. Phylogenetic analysis of ITS, cox1 and β‐tubulin gene regions demonstrated that P. acerina is unique and forms a separate cluster within the ‘P. citricola complex’, closely related to P. plurivora. Phytophthora acerina is homothallic with smooth‐walled oogonia, thick‐walled, mostly aplerotic oospores with a high abortion rate, paragynous antheridia, and persistent, morphologically variable semipapillate sporangia. Four to 5‐week‐old cultures produced globose to subglobose, appressoria‐like and coralloid hyphal swellings and characteristic stromata‐like hyphal aggregations. Optimum and maximum temperatures for growth are 25°C and 32°C, respectively. Genetic uniformity of all 15 studied isolates and the apparent absence of this species in the extensive surveys of nurseries, forests and seminatural ecosystems conducted in the previous two decades across Europe indicate a recent clonal introduction to northern Italy. Under‐bark inoculation tests demonstrated high aggressiveness of P. acerina to A. pseudoplatanus indicating that this pathogen might be a serious risk to maple plantations and forests in Europe.     

Paraphoma chlamydocopiosa sp. nov. and Paraphoma pye sp. nov., two new species associated with leaf and crown infection of pyrethrum

Two new pathogens of pyrethrum, described as Paraphoma chlamydocopiosa and Paraphoma pye, isolated from necrotic leaf lesions on pyrethrum plants in northern Tasmania, Australia, were identified using morphological characters, phylogenetic analysis of the internal transcribed spacer (ITS), elongation factor 1‐α (EF1‐α) and β‐tubulin (TUB) genes, and pathogenicity bioassays. Bootstrap support in the combined and individual gene region phylogenetic trees supported the two species that were significantly different from the closely related P. chrysanthemicola and P. vinacea. Morphological characteristics also supported the two new species, with conidia of P. chlamydocopiosa being considerably longer and wider than either P. chrysanthemicola or P. vinacea, and P. pye being distinct in forming bilocular pycnidia. Glasshouse pathogenicity tests based on root dip inoculation resulted in P. chlamydocopiosa and P. pye infecting the crown and upper root tissues of pyrethrum plants, and significant reduction in biomass 2 months after inoculation. Both of these Paraphoma species caused leaf lesions during in vitro and in vivo bioassays 2 weeks after foliar spray inoculation. Although P. chlamydocopiosa and P. pye were shown to be crown rot pathogens, they were also commonly isolated from leaves of diseased plants in pyrethrum fields of northern Tasmania.     

Phakopsora myrtacearum sp. nov., a newly described rust (Pucciniales) on eucalypts in eastern and southern Africa

Outbreaks of a rust disease in eucalypt forestry plantations and nurseries in Kenya, Mozambique and South Africa occurred between 2009 and 2014. The pathogen was identified using morphology and molecular phylogenetic analyses as an undescribed species in the Phakopsoraceae. A systematic study, based on nuclear ribosomal DNA, showed that it is a species of Phakopsora, herein named Phakopsora myrtacearum sp. nov. This new species of rust is the second validly described species on Eucalyptus, along with Puccinia psidii. Phakopsora myrtacearum is distinguished from P. psidii by leaf symptoms, morphology of the urediniospores and distinct phylogenetic placement. Phakopsora myrtacearum has been found on three species of Eucalyptus in Kenya, Mozambique and South Africa, and it may have future negative implications for commercial forestry in these areas.     

Phytophthora oleae sp. nov. causing fruit rot of olive in southern Italy

A homothallic Phytophthora species was found to be consistently associated with a rot of mature fruits of two local cultivars of olive (Olea europaea) in Calabria, southern Italy. The phylogenetic analysis of sequences of the ITS1‐5.8S‐ITS2 region and cox1 gene enabled its identification as a new species of clade 2, with a basal position compared to previously described subclades. The new species is described formally with the epithet Phytophthora oleae, referring to the natural matrix from which it was isolated. A unique combination of molecular and morphological characters clearly separates P. oleae from other already described Phytophthora species. This new species produced semipapillate, occasionally bipapillate, persistent sporangia on simple sympodially branching sporangiophores as well as globose and smooth‐walled oogonia, paragynous antheridia and spherical, plerotic oospores. The pathogenicity of P. oleae was confirmed in inoculation trials on fruits of three olive cultivars, including the two local cultivars from which the pathogen had been isolated.     

Phytophthora obscura sp. nov., a new species of the novel Phytophthora subclade 8d

A new Phytophthora species was detected (i) in the USA, infecting foliage of Kalmia latifolia, (ii) in substrate underneath Pieris, and (iii) in Germany in soil samples underneath Aesculus hippocastanum showing disease symptoms. The new species Phytophthora obscura sp. nov. is formally named based on phylogenetic analysis, host range, Koch’s postulates and morphology. Phytophthora obscura is homothallic with paragynous antheridia and semipapillate sporangia. It is genetically closely related to P. syringae and P. austrocedrae and together these three species define a new Phytophthora subclade 8d, with significant support for all genetic loci analysed including seven nuclear genes and the mitochondrial gene coxII. The morphological and ecological characteristics are very similar to P. syringae, and it is likely that P. obscura was not described earlier because it was identified as P. syringae. Artificial inoculations indicated that horse chestnut, kalmia, pieris and rhododendron might be hosts, and Koch’s postulates were confirmed for kalmia from which it was isolated. This pathogen was named after its elusive nature since it has to date rarely been detected in the US and Germany.     

The morphology,behaviour and molecular phylogeny of Phytophthora taxon Salixsoil and its redesignation as Phytophthora lacustris sp. nov.

Since its first isolation from Salix roots in 1972, isolates of a sexually sterile Phytophthora species have been obtained frequently from wet or riparian habitats worldwide and have also been isolated from roots of Alnus and Prunus spp. Although originally assigned to Phytophthora gonapodyides on morphological grounds, it was recognized that these isolates, informally named P. taxon Salixsoil, might represent a separate lineage within ITS Clade 6. Based on phylogenetic analyses and comparisons of morphology, growth‐temperature relationships and pathogenicity, this taxon is formally described here as Phytophthora lacustris sp. nov. Isolates of P. lacustris form a clearly resolved cluster in both ITS and mitochondrial cox1 phylogenies, basal to most other Clade 6 taxa. Phytophthora lacustris shares several unusual behavioural properties with other aquatic Clade 6 species, such as sexual sterility and tolerance of high temperatures, that have been suggested as adaptations to riparian conditions. It appears to be widespread in Europe and has also been detected in Australia, New Zealand and the USA. It was shown to be weakly or moderately aggressive on inoculation to Alnus, Prunus and Salix. The extent of P. lacustris’ activity as a saprotroph in plant debris in water and as an opportunistic pathogen in riparian habitats needs further investigation. Its pathogenic potential to cultivated fruit trees also deserves attention because P. lacustris has apparently been introduced into the nursery trade.     

Metabarcoding and development of new real‐time specific assays reveal Phytophthora species diversity in holm oak forests in eastern Spain

The evergreen holm oaks (Quercus ilex subsp. ilex and Q. ilex subsp. ballota) are the most representative tree species in the Iberian peninsula and the main tree species in oak‐rangeland ecosystems (dehesas). Oak decline in western, central and southern parts of Spain has been associated with root rot caused by Phytophthora cinnamomi for decades. However, Phytophthora species such as P.  quercina and P. psychrophila have recently been found associated with Quercus decline in eastern Spain where calcareous soils are predominant. Soil and root samples from two Quercus forests presenting decline symptoms in two different geographical areas in eastern Spain (Carrascar de la Font Roja and Vallivana) were analysed by amplicon pyrosequencing. Metabarcoding analysis showed Phytophthora species diversity, and revealed that an uncultured Phytophthora taxon, named provisionally Phytophthora taxon ballota, was the predominant species in both areas. In addition, a real‐time PCR assay, based on the pyrosequencing results, was developed for the detection of this uncultured Phytophthora taxon, and also for the detection of P. quercina. TaqMan assays were tested on soil and root samples, and on Phytophthora pure cultures. The new assays showed high specificity and were consistent with metabarcoding results. A new real‐time PCR protocol is proposed to evaluate the implication of different Phytophthora spp. in oak decline in eastern Spain.     

A new anthracnose disease of pyrethrum caused by Colletotrichum tanaceti sp. nov

A new pathogen of pyrethrum (Tanacetum cinerariifolium) causing anthracnose was described as Colletotrichum tanaceti based on morphological characteristics and a four‐gene phylogeny consisting of rDNA‐ITS, β‐tubulin (TUB2), glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH) and actin (ACT) gene sequences. The fungus produced perithecia in culture, requiring an opposite mating type isolate in a heterothallic manner. The initial infection strategy on pyrethrum leaves involved the formation of appressoria followed by production of multilobed infection vesicles in the epidermal cells. Infection and colonization then proceeded through thinner secondary hyphae, which resulted in the initial production of water‐soaked lesions followed by black necrotic lesions. The infection process was suggestive of a hemibiotrophic infection strategy. Moreover, phylogenetic analysis clearly showed that C. destructivum, C. higginsianum and C. panacicola were separate species that also had similar intracellular hemibiotrophic infection strategies as C. tanaceti, which all clustered in the C. destructivum complex. Colletotrichum spp. were detected at 1% incidence in seed of 1 of 19 seed lines, indicating the potential for seed as a source of inoculum into crops. Colletotrichum tanaceti was detected in leaf lesions from 11 of 24 pyrethrum fields surveyed between April and July 2012, at a frequency of 1·3–25·0% of lesions. Anthracnose probably contributes to the complex of foliar diseases reducing green leaf area in pyrethrum fields in Australia.     

Pineapple heart rot isolates from Ecuador reveal a new genotype of Phytophthora nicotianae

Pineapple heart rot disease, caused by Phytophthora nicotianae (syn. P. parasitica), is responsible for significant annual reductions in crop yield due to plant mortality. In Ecuador, new infections arise during the rainy season and increase production costs due to the need for biocontrol and fungicide applications. Studies of P. nicotianae population structure suggest that certain genetic groups are associated with host genera; however, it is not clear how many host‐specific lineages of the pathogen exist or how they are related. The objectives of this study were to determine the level of genetic variation in the P. nicotianae population causing heart rot disease of pineapple in Ecuador and compare the genotypes found on pineapple to those previously reported from citrus, tobacco and ornamentals. Thirty P. nicotianae isolates collected from infected pineapple leaves from four farms were genotyped using nine simple sequence repeat loci. In addition, the DNA sequences of mitochondrial loci cox2 + spacer and trnG‐rns were analysed. Together, these loci supported a single clonal lineage with two multilocus genotypes differing in a single allele and low mitochondrial diversity. This lineage was distinct but closely related to isolates collected from vegetables and ornamentals in Italy. The results support the hypothesis of host specialization of P. nicotianae in intensive cropping systems and contribute to the understanding of population structure of this important pathogen.     

Phytophthora urerae sp. nov., a new clade 1c relative of the Irish famine pathogen Phytophthora infestans from South America

An unknown Phytophthora species was discovered in the central Peruvian Andes on blighted foliage of the native South American plant species Urera lacineata. Urera is a genus of native flowering shrubs in the nettle family Urticaceae. This new taxon Phytophthora urerae sp. nov. is herewith formally described based on extensive morphological analysis, phylogenetic analysis of nuclear and mitochondrial loci, and AFLP analysis. Phytophthora urerae sp. nov. is a close relative of the Irish famine pathogen, Phytophthora infestans, and only the third clade 1c taxon described from South America to date. In contrast to the clade 1c taxon Phytophthora andina, first described in South America as a hybrid, P. urerae does not appear to be a hybrid based on cloning and sequencing nuclear loci. Findings of new species in South America may provide novel insights into the origin and evolutionary history of clade 1c Phytophthora species.     

Two new species,Phytophthora nagaii sp. nov. and P. fragariaefolia sp. nov., causing serious diseases on rose and strawberry plants,respectively, in Japan

A new disease of rose was noticed in Chiba Prefecture of Japan in 1968, and the pathogen was initially identified as Phytophthora megasperma based on morphological characteristics. Similar Phytophthora isolates have since been collected from rose plants in Chiba, Kanagawa, and Shizuoka Prefectures. In 2005, several Phytophthora isolates were recovered from crowns of strawberry plants in Hokkaido Prefecture. These were considered to be members of a new species. In this study, we re-examined all these isolates using morphological and physiological studies and a multilocus phylogenetic analysis. The rose and strawberry isolates were mostly similar morphologically and physiologically, with some exceptions. The rose isolates differed significantly from P. megasperma sensu stricto and other related Phytophthora species. The rose and strawberry isolates had external proliferation of sporangia, characteristic funnel-shaped oogonia, predominantly paragynous antheridia, and fast growth rates of 10.5 mm/24 h at an optimum temperature of 28 °C. In the multilocus phylogenetic tree constructed using sequences from the rDNA ITS regions, rDNA LSU, and the translation elongation factor 1-α, β-tubulin and coxI genes, they formed a distinct monophyletic group in clade 7 with strong bootstrap support. The rose and strawberry isolates separated into two distinct groups. The results indicate that the rose and strawberry isolates constitute two separate species, designated here as Phytophthora nagaii and P. fragariaefolia.     

Phytophthora bilorbang sp. nov., a new species associated with the decline of Rubus anglocandicans (European blackberry) in Western Australia

A new homothallic Phytophthora species, isolated from rhizosphere soil and roots of declining or dead Rubus anglocandicans (European blackberry) in south-west Western Australia, is described as Phytophthora bilorbang sp. nov. It produces non-papillate sporangia, smooth-walled oogonia containing thick-walled oospores, and paragynous antheridia. Although morphologically similar to several species within ITS Clade 6 and sub-clade II, namely P. gibbosa, P. gregata and P. megasperma, phylogenetic analyses of the ITS, cox1, HSP90, BT and NADH gene regions demonstrate that P. bilorbang sp. nov. is a distinct species. Additionally, P. bilorbang differs from these species in its growth and colony morphology on several media. Pathogenicity tests indicate that P. bilorbang could be responsible for the decline syndrome of blackberry within the Warren and Donnelly River catchments in the south-west of Western Australia.     

Characterization and taxonomic reassessment of the box blight pathogen Calonectria pseudonaviculata,introducing Calonectria henricotiae sp. nov.

Calonectria pseudonaviculata, the causal agent of the disease of Buxus spp. known as ‘box blight’, was first detected in the mid‐1990s in the UK and New Zealand. Since then, the geographic range of box blight has rapidly expanded to at least 21 countries throughout temperate regions of the world, causing significant losses in nurseries, gardens and wild boxwood populations. This study determined the genetic diversity in a collection of 234 Calonectria isolates from diseased Buxus plants, originating from 15 countries and four continents. Two genetic clades, G1 and G2, were identified within this sample using multilocus phylogenetic analysis. The application of genealogical concordance phylogenetic species recognition criteria using four independent nuclear loci determined that the Calonectria isolates in these two clades are separate phylogenetic species. The isolates in the G1 clade were upheld as C. pseudonaviculata sensu stricto. Based on phylogenetic distinctiveness and the lack of mating, a new species is proposed, Calonectria henricotiae sp. nov., for the Calonectria isolates in the G2 clade. A PCR‐RFLP assay and real‐time PCR assays were developed to easily and reproducibly differentiate these species. To assess the practical implications of the identification of the two species, their physiology, fungicide susceptibility and pathogenicity were compared. No differences in pathogenicity were observed. However, C. henricotiae isolates exhibited greater thermotolerance and reduced sensitivity to specific triazole as well as strobilurin fungicides. The identification of a second phylogenetic species causing box blight may have a substantial impact on the epidemiology and control of this destructive disease.     

Diversity and populations of Phytophthora,Phytopythium and Pythium species recovered from sediments in an agricultural run‐off sedimentation reservoir

Agricultural run‐off sedimentation reservoirs are an emerging aquatic system of critical importance to plant biosecurity, water and environmental sustainability. Oomycete pathogens such as Phytophthora and Pythium species in irrigation water have been demonstrated to pose significant risks to ornamental crops, but little is known about their diversity and populations in sediments of agricultural irrigation systems. This study investigated the oomycete communities including Phytophthora (Ph.), Phytopythium (Pp.) and Pythium (Py.) species in sediments at various depths of an agricultural run‐off sedimentation reservoir in Virginia during the winters of 2011 and 2015. The recovery of these oomycetes declined sharply with sediment depth from surface to 0·8 m and none was recovered from sediments deeper than 1·4 m. A total of 47 oomycete species were recovered, with all four species of Phytophthora and five of Phytopythium exclusively from the surface. Recovered species included many important plant pathogens such as Ph. nicotianae, Ph. pini, Ph. tropicalis, Pp.  vexans, Py. irregulare and Py. monospermum. These results underline the importance of decontaminating sediments excavated from top layers (0–1·4 m) of the sedimentation reservoir before reuse in plant production.     

Reassessment of rust fungi on weeping willows in the Americas and description of Melampsora ferrinii sp. nov.

Rust fungi in the genus Melampsora usually cause disease on hosts in the Salicaceae. Identification of Melampsora species is often complicated due to few differences in spore morphology and little publicly available comparative sequence data. Weeping willow trees (primarily Salix babylonica and its hybrids) have been reported to be infected by 11 Melampsora species; however, most of these records are based on morphological characterization. New collections of rust fungi on weeping willows from the central USA were analysed using a combination of morphology, ITS and LSU rDNA sequencing, and host data to determine that they represent an undescribed rust fungus, Melampsora ferrinii sp. nov. Additional studies of herbarium material revealed that M. ferrinii has occasionally been collected but identified as M. epitea. In addition to North America, M. ferrinii is also present in South America and has been infecting weeping willows there since at least the 1990s.     

Stem rot of jewel orchids caused by a new forma specialis,Fusarium oxysporum f. sp. anoectochili in Taiwan

Stem rot of Anoectochilus formosanus (Af) caused by Fusarium oxysporum (Fo) is a major limiting factor to jewel orchid production in Taiwan. Fo causes discoloration in vascular tissues. However, some newly collected Fo isolates from Af stem rot do not cause vascular discoloration, suggesting changes may have occurred in the pathogen. Among recent Fo isolates from Af there are two colony types, the cottony alba (CA) and the sporodochial (S). In order to confirm that both colony types cause Af stem rot, 200 isolates were obtained from diseased stems in Nantou County and characterized by colony type and whether or not the infected plants had vascular discoloration. Isolates of both the CA and S types caused stem rot of Af; some isolates in each colony type caused vascular discoloration whilst others did not. Pathogenicity tests with 22 isolates resulted in stem rot disease severity ratings on Af of 3·1–4·0 and 2·1–4·0 with CA and S type colonies, respectively. The same isolates failed to cause disease on Cattleya, Dendrobium or Phalaenopsis plants. Phylogenetic analysis of partial intergenic spacer sequences showed that these isolates were distinguishable from other formae speciales of Fo and could be separated into two groups correlated with the CA or S type colonies with high bootstrap. Based on pathogenic, morphological and molecular characterizations, the Fo that causes stem rot of Af is proposed to be a new forma specialis, F. oxysporum f. sp. anoectochili, with different pathotypes.     

Fusarium solani f. sp. passiflorae: a new forma specialis causing collar rot in yellow passion fruit

The aim of this study was to characterize a Fusarium population obtained from yellow passion fruit (YPF) with collar rot using pathogenicity, morphocultural characteristics and molecular tests. Pathogenicity and disease severity were assessed in six plant species: YPF, zucchini, tomato, bean, soya bean and cucumber. Potato dextrose agar medium (PDA) was used to determine mycelial growth at five temperatures (15–35°C). The colour produced by isolates was also determined on PDA at 25°C. Synthetic nutrient agar medium was used to evaluate: (i) type of mycelium and phialides; (ii) size, shape and number of septa from conidia; and (iii) production of chlamydospores and perithecia. Molecular tests consisted of sequencing the ITS–5·8S rDNA region and elongation factor 1α (EF‐1α) gene. The isolates caused large lesions on YPF, zucchini and tomato, with YPF having the highest mean disease severity and being the only one that showed wilt symptoms and death of the plant. Thus the isolates showed host specificity. Maximum mycelial growth occurred at 25°C and the predominant colour was bluish‐white. The isolates produced long phialides, dense aerial mycelium, oval microconidia with a mean size of 9·5 × 2·6 μm, macroconidia of 32·7 × 3·4 μm with 3·3 septa, and chlamydospores; only one isolate lacked perithecia. Phylogenetic trees of the ITS region and EF‐1α gene showed that isolates from YPF formed a distinct group within the F. solani group and the formae speciales of F. solani. It is proposed to name all isolates from YPF as F. solani f. sp. passiflorae.     

Phytophthora andina sp. nov., a newly identified heterothallic pathogen of solanaceous hosts in the Andean highlands

A blight disease on fruits and foliage of wild and cultivated Solanum spp. was found to be associated with a new species of Phytophthora. The proposed novel species is named Phytophthora andina Adler & Flier, sp. nov. based on morphological characteristics, pathogenicity assays, mitochondrial DNA haplotyping, AFLP fingerprinting and nuclear and mitochondrial DNA sequence analyses. Isolates of P. andina (n = 48) from the Andean highland tropics of Ecuador were collected from 1995 to 2006. Phytophothora andina is closely related to P. infestans and has semipapillate, ellipsoidal sporangia borne on sympodially branched sporangiophores. It is heterothallic and produces amphigynous antheridia. The species consists of several clonal lineages, including the EC‐2 and EC‐3 RFLP lineages, which were described previously as P. infestans. Approximately 75% of isolates react as compatibility type A2 when paired with an A1 compatibility type isolate of P. infestans. However, when A2 isolates from the Anarrhichomenum section of Solanum were paired in all combinations, viable oospores were obtained in several crosses, suggesting that there is a unique compatibility interaction in P. andina that is complementary to that described in P. infestans. Nuclear and mitochondrial sequence analysis supported the species designation of P. andina. This newly identified heterothallic pathogen shares a common ancestor with P. infestans and may have arisen from hybridization events with sister taxa in the Andes.