The avocado subgroup of Phytophthora citricola constitutes a distinct species, Phytophthora mengei sp. nov

An Overview of Phytophthora Species on Woody Plants in Sweden and Other Nordic Countries

The genus Phytophthora, with 326 species in 12 phylogenetic clades currently known, includes many economically important pathogens of woody plants. Different Phytophthora species often possess a hemibiotrophic or necrotrophic lifestyle, have either a broad or narrow host range, can cause a variety of disease symptoms (root rot, damping-off, bleeding stem cankers, or blight of foliage), and occur in different growing environments (nurseries, urban and agricultural areas, or forests). Here, we summarize the available knowledge on the occurrence, host range, symptoms of damage, and aggressiveness of different Phytophthora species associated with woody plants in Nordic countries with a special emphasis on Sweden. We evaluate the potential risks of Phytophthora species to different woody plants in this geographical area and emphasize the increasing threats associated with continued introduction of invasive Phytophthora species.

Sympatric occurrence of sibling Phytophthora species associated with foot rot disease of black pepper in India

Foot rot disease caused by Phytophthora capsici is a serious threat to black pepper cultivation in India and globally. High diversity exists among the Phytophthora isolates of black pepper and hence detailed investigations of their morphology and phylogenetic taxonomy were carried out in the present study. In order to resolve the diversity, 182 isolates of Phytophthora, collected from different black pepper-growing tracts of South India during 1998-2013 and maintained in the National Repository of Phytophthora at ICAR-Indian Institute of Spices Research, Kozhikode, were subjected to morphological, molecular and phylogenetic characterization. Morphologically all the isolates were long pedicellate with umbellate/simple sympodial sporangiophores and papillate sporangia with l/b ranging from 1.63 to 2.55 µm. Maximum temperature for the growth was ~ 34 °C. Chlamydospores were observed in "tropicalis" group, whereas they were absent in "capsici" group. Initial molecular studies using internal transcribed spacer (ITS) marker gene showed two clear cut lineages-"capsici-like" and "tropicalis-like" groups among them. Representative isolates from each group were subjected to host differential test, multilocus sequence typing (MLST) and phylogeny studies. MLST analysis of seven nuclear genes (60S ribosomal protein L10, beta-tubulin, elongation factor 1 alpha, enolase, heat shock protein 90, 28S ribosomal DNA and TigA gene fusion protein) clearly delineated black pepper Phytophthora isolates into two distinct species-P. capsici and P. tropicalis. On comparing with type strains from ATCC, it was found that the type strains of P. capsici and P. tropicalis differed from black pepper isolates in their infectivity on black pepper. The high degree of genetic polymorphism observed in black pepper Phytophthora isolates is an indication of the selection pressure they are subjected to in the complex habitat which ultimately may lead to speciation. So based on the extensive analysis, it is unambiguously proved that the foot rot disease of black pepper in India is predominantly caused by two species of Phytophthora, viz. P. capsici and P. tropicalis. Presence of multiple species of Phytophthora in the black pepper agro-ecosystem warrants a revisit to the control strategy being adopted for managing this serious disease. The silent molecular evolution taking place in such an ecological niche needs to be critically studied for the sustainable management of foot rot disease.

Phytophthora theobromicola sp. nov.: A New Species Causing Black Pod Disease on Cacao in Brazil

Black pod disease, caused by Phytophthora species, is among the main limiting factors of cacao (Theobroma cacao L.) production. High incidence levels of black pod disease have been reported in Brazil, being induced by Phytophthora capsici, Phytophthora citrophthora, Phytophthora heveae, and Phytophthora palmivora. To assess the diversity of Phytophthora species affecting cacao in Brazil, 40 new isolates were obtained from cacao pods exhibiting symptoms of black pod disease collected in different smallholder farms in 2017. Further, ten cacao-infecting isolates morphologically identified as P. citrophthora and P. palmivora were molecularly characterized. The genomic regions beta-tubulin, elongation factor 1 alpha, heat shock protein 90, and internal transcribed spacer, and the mitochondrially encoded cytochrome c oxidase I and II genes were PCR-amplified and Sanger-sequenced from the cacao-infecting Phytophthora isolates. The morphological characterization and evaluation of the mycelial growth rates for the Phytophthora isolates were performed in vitro. Based on the molecular analysis and morphological comparisons, 19 isolates were identified as P. palmivora (clade 4). Interestingly, 31 isolates grouped together in the phylogenetic tree and were placed apart from previously known species in Phytophthora clade 2. Therefore, these isolates are considered as a new species herein referred to as Phytophthora theobromicola sp. nov., which produced papillate, semipapillate, and persistent sporangia on simple sporangiophores. The P. palmivora isolates were identified as A1 mating type by pairing each isolate with known A1 and A2 tester strains of P. capsici, but no oogonia/antheridia were observed when P. theobromicola was paired with the different tester strains. The P. theobromicola and P. citrophthora isolates showed higher mycelial growth rates, when compared to P. palmivora, on different media at 10, 15, and 20°C, but similar values were observed when grown on clarified CA media at 25 and 30°C. The pathogenicity tests carried out on pods of four cacao clones (CCN51, PS1319, Cepec2004, and CP49) showed significant variability among the isolates of both Phytophthora species, with P. theobromicola inducing higher rates of necrotic lesion expansion, when compared to P. palmivora. Here, two Phytophthora species were found associated with black pod disease in the state of Bahia, Brazil, and the previously undescribed P. theobromicola seems to be prevalent in field conditions. This is the first report of P. theobromicola on T. cacao. Also, these findings are crucial to improve the disease control strategies, and for the development of cacao materials genetically resistant to Phytophthora.

Novel approaches and methods for quantifying Phytophthora cinnamomi in avocado tree roots

Phytophthora cinnamomi Rands is a devastating root rot pathogen of avocado. Robust and sensitive root quantification methods are required for determining seasonal P. cinnamomi root colonization patterns and evaluating management strategies. Our study investigated four P. cinnamomi root quantification methods using a newly developed P. cinnamomi-avocado-seedling bioassay system and a P. cinnamomi-specific probe-based qPCR assay. Phytophthora cinnamomi quantification through plating of roots (root plating) or lemon leaf disks obtained from root baitings (root-baiting-plating) onto semi-selective media were the best methods. Root plating consistently yielded significant differences in P. cinnamomi quantities obtained from seedling roots inoculated with five zoospore concentrations (10-1 × 105 zoospores/ml), whereas root-baiting-plating did so less often. The two methods were comparable in yielding root quantities that were significantly correlated with the inoculated zoospore concentrations, rarely yielding false negatives and having the lowest variability between replicates of the same treatment. qPCR quantification from roots was also an effective method; however, treatment replicates were highly variable and false negatives occurred more frequently. The least effective quantification method was qPCR quantification from lemon leaf disks obtained from root baitings.

Survey in Nurseries and Irrigation Water Reservoirs as Sources of Oomycetes Found in Avocado Orchards in the Canary Islands

Nursery stocks and irrigation water are important sources of Phytophthora spp. In this study, 20 irrigation water reservoirs and 10 avocado nurseries were surveyed in the Canary Islands between 2013 and 2015 to investigate their potential role in disseminating pathogenic species in avocado orchards. Phytophthora multivora was isolated from one of the irrigation reservoirs, whereas, in two surveys conducted in nurseries, Phytophthora cinnamomi, the primary pathogen in avocado, was detected in addition to other Phytophthora species (P. lacustris, P. multivora, P. nicotianae, P. niederhauserii, and P. palmivora) and Phytopythium vexans. The species recovered from nurseries were isolated mostly from propagated plants but also from nursery irrigation water, soil used for substrate preparation, and soil samples collected in orchards that supply seeds for seedling propagation. Species recovered from nurseries correlated with those found in avocado orchards in a previous study, except for P. lacustris, suggesting that nurseries could be involved in their dissemination in avocado orchards. The improved sanitary status of nurseries resulted in reduced incidence in the second survey, indicating the importance of nursery monitoring to reduce infestations.

Draft Genome Sequence for the Tree Pathogen Phytophthora plurivora

Species from the genus Phytophthora are well represented among organisms causing serious diseases on trees. Phytophthora plurivora has been implicated in long-term decline of woodland trees across Europe. Here we present a draft genome sequence of P. plurivora, originally isolated from diseased European beech (Fagus sylvatica) in Malmö, Sweden. When compared with other sequenced Phytophthora species, the P. plurivora genome assembly is relatively compact, spanning 41 Mb. This is organized in 1,919 contigs and 1,898 scaffolds, encompassing 11,741 predicted genes, and has a repeat content of approximately 15%. Comparison of allele frequencies revealed evidence for tetraploidy in the sequenced isolate. As in other sequenced Phytophthora species, P. plurivora possesses genes for pathogenicity-associated RXLR and Crinkle and Necrosis effectors, predominantly located in gene-sparse genomic regions. Comparison of the P. plurivora RXLR effectors with orthologs in other sequenced species in the same clade (Phytophthora multivora and Phytophthora capsici) revealed that the orthologs were likely to be under neutral or purifying selection.

Canker and decline diseases caused by soil- and airborne Phytophthora species in forests and woodlands

Most members of the oomycete genus Phytophthora are primary plant pathogens. Both soil- and airborne Phytophthora species are able to survive adverse environmental conditions with enduring resting structures, mainly sexual oospores, vegetative chlamydospores and hyphal aggregations. Soilborne Phytophthora species infect fine roots and the bark of suberized roots and the collar region with motile biflagellate zoospores released from sporangia during wet soil conditions. Airborne Phytophthora species infect leaves, shoots, fruits and bark of branches and stems with caducous sporangia produced during humid conditions on infected plant tissues and dispersed by rain and wind splash. During the past six decades, the number of previously unknown Phytophthora declines and diebacks of natural and semi-natural forests and woodlands has increased exponentially, and the vast majority of them are driven by introduced invasive Phytophthora species. Nurseries in Europe, North America and Australia show high infestation rates with a wide range of mostly exotic Phytophthora species. Planting of infested nursery stock has proven to be the main pathway of Phytophthora species between and within continents. This review provides insights into the history, distribution, aetiology, symptomatology, dynamics and impact of the most important canker, decline and dieback diseases caused by soil- and airborne Phytophthora species in forests and natural ecosystems of Europe, Australia and the Americas.

An expanded phylogeny for the genus Phytophthora

A comprehensive phylogeny representing 142 described and 43 provisionally named Phytophthora species is reported here for this rapidly expanding genus. This phylogeny features signature sequences of 114 ex-types and numerous authentic isolates that were designated as representative isolates by the originators of the respective species. Multiple new subclades were assigned in clades 2, 6, 7, and 9. A single species P. lilii was placed basal to clades 1 to 5, and 7. Phytophthora stricta was placed basal to other clade 8 species, P. asparagi to clade 6 and P. intercalaris to clade 10. On the basis of this phylogeny and ancestral state reconstructions, new hypotheses were proposed for the evolutionary history of sporangial papillation of Phytophthora species. Non-papillate ancestral Phytophthora species were inferred to evolve through separate evolutionary paths to either papillate or semi-papillate species.

Phytophthora species recovered from the Connecticut River Valley in Massachusetts, USA

Little is currently known about the assemblage of Phytophthora species in northeastern North America, representing a gap in our understanding of species incidence. Therefore, Phytophthora species were surveyed at 20 sites in Massachusetts, with 16 occurring in the Connecticut River Valley. Many of the sampled waterways were adjacent to active agricultural lands, yet were buffered by mature floodplain forests composed of Acer, Platanus, Populus and Ulmus. Isolates were recovered with three types of baits (rhododendron leaves, pear, green pepper) in 2013 and water filtration in 2014. Overall, 457 isolates of Phytophthora were recovered and based on morphological characters and rDNA internal transcribed spacer (ITS), β-tubulin (β-tub) and cytochrome oxidase c subunit I (cox1) sequences, 18 taxa were identified, including three new species: P. taxon intercalaris, P. taxon caryae and P. taxon pocumtuck. In addition, 49 isolates representing five species of Phytopythium also were identified. Water filtration captured a greater number of taxa (18) compared to leaf and fruit baits (12). Of the three bait types rhododendron leaves yielded the greatest number of isolates and taxa, followed by pear and green pepper, respectively. Despite the proximity to agricultural lands, none of the Phytophthora species baited are considered serious pathogens of vegetable crops in the region. However, many of the recovered species are known woody plant pathogens, including four species in the P. citricola s.l. complex that were identified: P. plurivora, P. citricola III, P. pini and a putative novel species, referred to here as P. taxon caryae. An additional novel species, P. taxon pocumtuck, is a close relative of P. borealis based on cox1 sequences. The results illustrate a high level of Phytophthora species richness in the Connecticut River Valley and that major rivers can serve as a source of inoculum for pathogenic Phytophthora species in the northeast.

Development of a multiplex assay for genus- and species-specific detection of Phytophthora based on differences in mitochondrial gene order

A molecular diagnostic assay for Phytophthora spp. that is specific, sensitive, has both genus- and species-specific detection capabilities multiplexed, and can be used to systematically develop markers for detection of a wide range of species would facilitate research and regulatory efforts. To address this need, a marker system was developed based on the high copy sequences of the mitochondrial DNA utilizing gene orders that were highly conserved in the genus Phytophthora but different in the related genus Pythium and plants to reduce the importance of highly controlled annealing temperatures for specificity. An amplification primer pair designed from conserved regions of the atp9 and nad9 genes produced an amplicon of ≈340 bp specific for the Phytophthora spp. tested. The TaqMan probe for the genus-specific Phytophthora test was designed from a conserved portion of the atp9 gene whereas variable intergenic spacer sequences were used for designing the species-specific TaqMan probes. Specific probes were developed for 13 species and the P. citricola species complex. In silico analysis suggests that species-specific probes could be developed for at least 70 additional described and provisional species; the use of locked nucleic acids in TaqMan probes should expand this list. A second locus spanning three tRNAs (trnM-trnP-trnM) was also evaluated for genus-specific detection capabilities. At 206 bp, it was not as useful for systematic development of a broad range of species-specific probes as the larger 340-bp amplicon. All markers were validated against a test panel that included 87 Phytophthora spp., 14 provisional Phytophthora spp., 29 Pythium spp., 1 Phytopythium sp., and 39 plant species. Species-specific probes were validated further against a range of geographically diverse isolates to ensure uniformity of detection at an intraspecific level, as well as with other species having high levels of sequence similarity to ensure specificity. Both diagnostic assays were also validated against 130 environmental samples from a range of hosts. The only limitation observed was that primers for the 340 bp atp9-nad9 locus did not amplify Phytophthora bisheria or P. frigida. The identification of species present in a sample can be determined without the need for culturing by sequencing the genus-specific amplicon and comparing that with a reference sequence database of known Phytophthora spp.

The genus Phytophthora anno 2012

Plant diseases caused by Phytophthora species will remain an ever increasing threat to agriculture and natural ecosystems. Phytophthora literally means plant destroyer, a name coined in the 19th century by Anton de Bary when he investigated the potato disease that set the stage for the Great Irish Famine. Phytophthora infestans, the causal agent of potato late blight, was the first species in a genus that at present has over 100 recognized members. In the last decade, the number of recognized Phytophthora species has nearly doubled and new species are added almost on a monthly basis. Here we present an overview of the 10 clades that are currently distinguished within the genus Phytophthora with special emphasis on new species that have been described since 1996 when Erwin and Ribeiro published the valuable monograph 'Phytophthora diseases worldwide' (35).

Morphological and molecular characterization of Phytophthora glovera sp. nov. from tobacco in Brazil

A root rot disease of cultivated tobacco called yellow stunt has been observed in the burley tobacco production areas of Brazil since the early 1990s. Root infecting fungi and straminipiles were isolated from the roots of diseased tobacco plants, including a semi-papillate, homothallic, slow growing Phytophthora species. Pathogenicity trials confirmed that Phytophthora sp. caused root rot and stunting of burley and flue-cured tobaccos. Morphological characteristics of the asexual and sexual stages of this organism did not match any reported Phytophthora species and were very different from the widely known tobacco black shank pathogen P. nicotianae. Phylogenetic analysis based on sequences of the internal transcribed spacer rDNA, β-tubulin and translation elongation factor 1-α regions indicated that this organism represents a previously unreported Phytophthora species that is significantly supported in clade 2 and most closely related to P. capsici. However P. glovera differs from P. capsici in a number of morphological characters, most significantly P. glovera is homothallic and produces both paragynous and amphigynous antheridia while P. capsici is heterothallic and produces only amphigynous antheridia. In this paper we confirmed pathogenicity of this species on tobacco and describe the morphological and molecular characteristics of Phytophthora glovera sp. nov.

Phytophthora taxa associated with cultivated Agathosma, with emphasis on the P. citricola complex and P. capensis sp. nov

Agathosma species, which are indigenous to South Africa, are also cultivated for commercial use. Recently growers experienced severe plant loss, and symptoms shown by affected plants suggested that a soilborne disease could be the cause of death. A number of Phytophthora taxa were isolated from diseased plants, and this paper reports their identity, mating type, and pathogenicity to young Agathosma plants. Using morphological and sequence data seven Phytophthora taxa were identified: the A1 mating type of P. cinnamomi var. cinnamomi, P. cinnamomi var. parvispora and P. cryptogea, the A2 mating type of P. drechsleri and P. nicotianae, and two homothallic taxa from the P. citricola complex. The identity of isolates in the P. citricola complex was resolved using reference isolates of P. citricola CIT groups 1 to 5 sensu Oudemans et al. (1994) along with multi-locus phylogenies (three nuclear and two mitochondrial regions), isozyme analyses, morphological characteristics and temperature-growth studies. These analyses revealed the isolates from Agathosma to include P. multivora and a putative novel species, P. taxon emzansi. Furthermore, among the P. citricola reference isolates the presence of a new species was revealed, described here as P. capensis. Findings of our study, along with some recent other studies, have contributed to resolving some of the species complexity within the P. citricola complex, resulting in the identification of a number of phylogenetically distinct taxa. The pathogenicity of representative isolates of the taxa from Agathosma was tested on A. betulina seedlings. The putative novel species, P. taxon emzansi, and P. cinnamomi var. parvispora were non-pathogenic, whereas the other species were pathogenic to this host.

Aggressiveness of Phytophthora cactorum, P. citricola I, and P. plurivora from European Beech

Phytophthora cactorum, P. citricola I, and P. plurivora cause bleeding cankers on mature European beech (Fagus sylvatica) trees in the northeastern United States. Inoculation experiments were conducted to compare the aggressiveness of the three Phytophthora spp. on stems, leaf disks, and roots of European beech and common lilac (Syringa vulgaris) seedlings. Isolates were obtained from bleeding cankers on European beech from five cities in New York (Albany, Ithaca, Oyster Bay, Plainview, and Rochester) and from a bleeding canker on sugar maple in Ithaca, NY. Stems were inoculated with colonized agar plugs, leaf disks with a zoospore suspension, and roots via infested soil at three inoculum levels. All organs of inoculated beech and lilac developed disease except for lilac roots inoculated with zoospores of P. cactorum. Disease incidence, severity, and plant survival were dependent on isolate and were also influenced by the tissue inoculated and host. Isolates of P. cactorum were the least aggressive and caused less necrosis than isolates of P. citricola I and P. plurivora. Results emphasize the utility of stem and root inoculation for evaluation of this canker disease and underscore critical differences in species aggressiveness.