The Phytophthora parasitica effector AVH195 interacts with ATG8, attenuates host autophagy, and promotes biotrophic infection

BACKGROUND

Plant pathogens secrete effector proteins into host cells to suppress immune responses and manipulate fundamental cellular processes. One of these processes is autophagy, an essential recycling mechanism in eukaryotic cells that coordinates the turnover of cellular components and contributes to the decision on cell death or survival.

RESULTS

We report the characterization of AVH195, an effector from the broad-spectrum oomycete plant pathogen, Phytophthora parasitica. We show that P. parasitica expresses AVH195 during the biotrophic phase of plant infection, i.e., the initial phase in which host cells are maintained alive. In tobacco, the effector prevents the initiation of cell death, which is caused by two pathogen-derived effectors and the proapoptotic BAX protein. AVH195 associates with the plant vacuolar membrane system and interacts with Autophagy-related protein 8 (ATG8) isoforms/paralogs. When expressed in cells from the green alga, Chlamydomonas reinhardtii, the effector delays vacuolar fusion and cargo turnover upon stimulation of autophagy, but does not affect algal viability. In Arabidopsis thaliana, AVH195 delays the turnover of ATG8 from endomembranes and promotes plant susceptibility to P. parasitica and the obligate biotrophic oomycete pathogen Hyaloperonospora arabidopsidis.

CONCLUSIONS

Taken together, our observations suggest that AVH195 targets ATG8 to attenuate autophagy and prevent associated host cell death, thereby favoring biotrophy during the early stages of the infection process.

Proteomic analysis revealed that the oomyceticide phosphite exhibits multi-modal action in an oomycete pathosystem

Phytopathogenic oomycetes constitute some of the most devastating plant pathogens and cause significant crop and horticultural yield and economic losses. The phytopathogen Phytophthora cinnamomi causes dieback disease in native vegetation and several crops. The most commonly used chemical to control P. cinnamomi is the oomyceticide phosphite. Despite its widespread use, the mode of action of phosphite is not well understood and it is unclear whether it targets the pathogen, the host, or both. Resistance to phosphite is emerging in P. cinnamomi isolates and other oomycete phytopathogens. The mode of action of phosphite on phosphite-sensitive and resistant isolates of the pathogen and through a model host was investigated using label-free quantitative proteomics. In vitro treatment of sensitive P. cinnamomi isolates with phosphite hinders growth by interfering with metabolism, signalling and gene expression; traits that are not observed in the resistant isolate. When the model host Lupinus angustifolius was treated with phosphite, proteins associated with photosynthesis, carbon fixation and lipid metabolism in the host were enriched. Increased production of defence-related proteins was also observed in the plant. We hypothesise the multi-modal action of phosphite and present two models constructed using comparative proteomics that demonstrate mechanisms of pathogen and host responses to phosphite. SIGNIFICANCE: Phytophthora cinnamomi is a significant phytopathogenic oomycete that causes root rot (dieback) in a number of horticultural crops and a vast range of native vegetation. Historically, areas infected with phosphite have been treated with the oomyceticide phosphite despite its unknown mode of action. Additionally, overuse of phosphite has driven the emergence of phosphite-resistant isolates of the pathogen. We conducted a comparative proteomic study of a sensitive and resistant isolate of P. cinnamomi in response to treatment with phosphite, and the response of a model host, Lupinus angustifolius, to phosphite and its implications on infection. The present study has allowed for a deeper understanding of the bimodal action of phosphite, suggested potential biochemical factors contributing to chemical resistance in P. cinnamomi, and unveiled possible drivers of phosphite-induced host plant immunity to the pathogen.

Fitness difference between two synonymous mutations of Phytophthora infestans ATP6 gene

BACKGROUND

Sequence variation produced by mutation provides the ultimate source of natural selection for species adaptation. Unlike nonsynonymous mutation, synonymous mutations are generally considered to be selectively neutral but accumulating evidence suggests they also contribute to species adaptation by regulating the flow of genetic information and the development of functional traits. In this study, we analysed sequence characteristics of ATP6, a housekeeping gene from 139 Phytophthora infestans isolates, and compared the fitness components including metabolic rate, temperature sensitivity, aggressiveness, and fungicide tolerance among synonymous mutations.

RESULTS

We found that the housekeeping gene exhibited low genetic variation and was represented by two major synonymous mutants at similar frequency (0.496 and 0.468, respectively). The two synonymous mutants were generated by a single nucleotide substitution but differed significantly in fitness as well as temperature-mediated spatial distribution and expression. The synonymous mutant ending in AT was more common in cold regions and was more expressed at lower experimental temperature than the synonymous mutant ending in GC and vice versa.

CONCLUSION

Our results are consistent with the argument that synonymous mutations can modulate the adaptive evolution of species including pathogens and have important implications for sustainable disease management, especially under climate change.

In vitro and ex vivo anti-Pythium insidiosum potential of ozonated sunflower oil

This study sought to evaluate the in vitro and ex vivo susceptibility of Pythium insidiosum to ozonized sunflower oil (OSO) and verify the morphological alterations of OSO-exposed hyphae. Susceptibility assays were performed according to the broth microdilution protocol M38-A2/CLSI, and the minimal inhibitory (MIC) and minimal oomicidal (MOC) concentrations were also determined. Non-ozonated sunflower oil (SO) was used as the oil control. Additionally, kunkers from equine pythiosis were exposed to OSO. Damages caused by OSO and SO on P. insidiosum hyphae ultrastructure were verified using scanning electron microscopy. The MIC range for OSO was 7000 to 437.5 mg/mL, and the values for SO were higher, ranging from 56000 to 14000 mg/mL. The MOC was equal to MIC for both oil formulations. The OSO fully inhibited the oomycete growth from kunkers, although there was P. insidiosum growth in the kunker control in 24 h of incubation. The SEM analyses showed that both OSO and SO caused morphological alterations in P. insidiosum hyphae, highlighting the presence of cavitation along the hyphae with loss of continuity of the cell wall, which was more evident in the OSO-treated hyphae. The OSO had the best oomicidal activity, leading us to believe that our findings may support future research containing this formulation to be applied in integrative medicine protocols to control pythiosis in animals and humans.

Evaluating the efficacy of hymexazol in controlling Globisporangium spinosum, the newly identified pathogen causing root rot in Houttuynia cordata

Houttuynia cordata is a prevalent vegetable in several Asian countries and is commonly used as traditional Chinese medicinal herb for treating various diseases in China. Unfortunately, its yield and quality are adversely affected by root rot. However, the pathogen responsible for the losses remains unidentified, and effective fungicides for its management have not been thoroughly explored. In this work, we demonstrate the first report of Globisporangium spinosum as the causative agent causing root rot of H. cordata. Moreover, we evaluated the efficacy of hymexazol to manage the disease which displayed remarkable inhibitory effects against mycelial growth of G. spinosum in vitro, with EC50 values as low as 1.336 μg/mL. Furthermore, hymexazol completely inhibited sporangia in G. spinosum at a concentration of 0.3125 μg/mL. Specifically, we observed that hymexazol was highly efficacious in reducing the incidence of H. cordata root rot caused by G. spinosum, in a greenhouse setting. These findings offer a potential management tool for utilization of hymexazol in controlling H. cordata root rot in field production.

Austropotamobius pallipes can be infected by two haplotypes of Aphanomyces astaci: A key example from an outbreak at an ex-situ conservation facility

The crayfish plague, caused by the pathogen Aphanomyces astaci, is a pandemic disease endemic to North America that has been devastating susceptible crayfish populations in Europe since the 19th century. In Spain, this disease has decimated populations of the native crayfish species Austropotamobius pallipes due to introductions of North American crayfish, which act as vectors of the pathogen. To combat against these losses, several regional governments have established ex-situ breeding programs to restock wild populations of the species. In this study, we report on an outbreak of A. astaci that occurred in one of the most important A. pallipes aquaculture centers in Spain. Using a variety of detection methods, we analyzed affected crayfish and environmental samples from the facilities over a period of six months and determined that the outbreak was caused by two haplotypes of A. astaci, d1 and d2, which are both associated with the North American crayfish species Procambarus clarkii. To our knowledge, this is the first report of a two-haplotype coinfection of A. astaci outside the native range of this pathogen.

Cross-kingdom analyses of transmembrane protein kinases show their functional diversity and distinct origins in protists

Transmembrane kinases (TMKs) are important mediators of cellular signaling cascades. The kinase domains of most metazoan and plant TMKs belong to the serine/threonine/tyrosine kinase (S/T/Y-kinase) superfamily. They share a common origin with prokaryotic kinases and have diversified into distinct subfamilies. Diverse members of the eukaryotic crown radiation such as amoebae, ciliates, and red and brown algae (grouped here under the umbrella term "protists") have long diverged from higher eukaryotes since their ancient common ancestry, making them ideal organisms for studying TMK evolution. Here, we developed an accurate and high-throughput pipeline to predict TMKomes in cellular organisms. Cross-kingdom analyses revealed distinct features of TMKomes in each grouping. Two-transmembrane histidine kinases constitute the main TMKomes of bacteria, while metazoans, plants, and most protists have a large proportion of single-pass TM S/T/Y-kinases. Phylogenetic analyses classified most protist S/T/Y-kinases into three clades, with clades II and III specifically expanded in amoebae and oomycetes, respectively. In contrast, clade I kinases were widespread in all protists examined here, and likely shared a common origin with other eukaryotic S/T/Y-kinases. Functional annotation further showed that most non-kinase domains were grouping-specific, suggesting that their recombination with the more conserved kinase domains led to the divergence of S/T/Y-kinases. However, we also found that protist leucine-rich repeat (LRR)- and G-protein-coupled receptor (GPCR)-type TMKs shared similar sensory domain architectures with respective plant and animal TMKs, despite that they belong to distinct kinase subfamilies. Collectively, our study revealed the functional diversity of TMKomes and the distinct origins of S/T/Y-kinases in protists.

First report of Achlya bisexualis infection in captive-reared Endangered golden mahseer Tor putitora

Achlya bisexualis is a notorious oomycete pathogen with the potential to cause emerging disease in fish farms. In this study, we report the first isolation of A. bisexualis from captive-reared golden mahseer Tor putitora, an Endangered fish species. The infected fish showed a cotton-like growth of mycelia at the site of infection. The mycelium when cultured on potato dextrose agar produced radially growing white hyphae. The hyphae were non-septate, and some of them carried matured zoosporangium with dense granular cytoplasmic contents. Spherical gemmae with stout stalks were also observed. All the isolates had 100% identity in internal transcribed spacer (ITS)-rDNA sequence and showed highest similarity to that of A. bisexualis. In molecular phylogeny, all the isolates formed a monophyletic group with A. bisexualis which was supported by a bootstrap value of 99%. Based on the molecular and morphological findings, all the isolates were confirmed as A. bisexualis. Further, the anti-oomycete effect of boric acid, a known antifungal agent, against the isolate was evaluated. The minimum inhibitory concentration and minimum fungicidal concentration were found to be 1.25 and >2.5 g l-1, respectively. Isolation of A. bisexualis from a new fish species indicates its possible occurrence in other unreported hosts. Considering its wide infectivity and the potential to cause disease in farmed fishes, its probable prevalence in a new environment and host needs to be closely monitored to prevent the spread of infection, if any, by adopting suitable control measures.

A Nicotiana benthamiana receptor-like kinase regulates Phytophthora resistance by coupling with BAK1 to enhance elicitin-triggered immunity

Cell-surface-localized leucine-rich-repeat receptor-like kinases (LRR-RLKs) are crucial for plant immunity. Most LRR-RLKs that act as receptors directly recognize ligands via a large extracellular domain (ECD), whereas LRR-RLK that serve as regulators are relatively small and contain fewer LRRs. Here, we identified LRR-RLK regulators using high-throughput tobacco rattle virus (TRV)-based gene silencing in the model plant Nicotiana benthamiana. We used the cell-death phenotype caused by INF1, an oomycete elicitin that induces pattern-triggered immunity, as an indicator. By screening 33 small LRR-RLKs (≤6 LRRs) of unknown function, we identified ELICITIN INSENSITIVE RLK 1 (NbEIR1) as a positive regulator of INF1-induced immunity and oomycete resistance. Nicotiana benthamiana mutants of eir1 generated by CRISPR/Cas9-editing showed significantly compromised immune responses to INF1 and were more vulnerable to the oomycete pathogen Phytophthora capsici. NbEIR1 associates with BRI1-ASSOCIATED RECEPTOR KINASE 1 (NbBAK1) and a downstream component, BRASSINOSTEROID-SIGNALING KINASE 1 (NbBSK1). NbBSK1 also contributes to INF1-induced defense and P. capsici resistance. Upon INF1 treatment, NbEIR1 was released from NbBAK1 and NbBSK1 in vivo. Moreover, the silencing of NbBSK1 compromised the association of NbEIR1 with NbBAK1. We also showed that NbEIR1 regulates flg22-induced immunity and associates with its receptor, FLAGELLIN SENSING 2 (NbFLS2). Collectively, our results suggest that NbEIR1 is a novel regulatory element for BAK1-dependent immunity. NbBSK1-NbEIR1 association is required for maintaining the NbEIR1/NbBAK1 complex in the resting state.

Mycoviruses as a part of the global virome: Diversity, evolutionary links and lifestyle

Knowledge of mycovirus diversity, evolution, horizontal gene transfer and shared ancestry with viruses infecting distantly related hosts, such as plants and arthropods, has increased vastly during the last few years due to advances in the high throughput sequencing methodologies. This also has enabled the discovery of novel mycoviruses with previously unknown genome types, mainly new positive and negative single-stranded RNA mycoviruses ((+) ssRNA and (-) ssRNA) and single-stranded DNA mycoviruses (ssDNA), and has increased our knowledge of double-stranded RNA mycoviruses (dsRNA), which in the past were thought to be the most common viruses infecting fungi. Fungi and oomycetes (Stramenopila) share similar lifestyles and also have similar viromes. Hypothesis about the origin and cross-kingdom transmission events of viruses have been raised and are supported by phylogenetic analysis and by the discovery of natural exchange of viruses between different hosts during virus-fungus coinfection in planta. In this review we make a compilation of the current information on the genome organization, diversity and taxonomy of mycoviruses, discussing their possible origins. Our focus is in recent findings suggesting the expansion of the host range of many viral taxa previously considered to be exclusively fungal, but we also address factors affecting virus transmissibility and coexistence in single fungal or oomycete isolates, as well as the development of synthetic mycoviruses and their use in investigating mycovirus replication cycles and pathogenicity.

Extensive morphological and behavioural diversity among fourteen new and seven described species in Phytophthora Clade 10 and its evolutionary implications

During extensive surveys of global Phytophthora diversity 14 new species detected in natural ecosystems in Chile, Indonesia, USA (Louisiana), Sweden, Ukraine and Vietnam were assigned to Phytophthora major Clade 10 based on a multigene phylogeny of nine nuclear and three mitochondrial gene regions. Clade 10 now comprises three subclades. Subclades 10a and 10b contain species with nonpapillate sporangia, a range of breeding systems and a mainly soil- and waterborne lifestyle. These include the previously described P. afrocarpa, P. gallica and P. intercalaris and eight of the new species: P. ludoviciana, P. procera, P. pseudogallica, P. scandinavica, P. subarctica, P. tenuimura, P. tonkinensis and P. ukrainensis. In contrast, all species in Subclade 10c have papillate sporangia and are self-fertile (or homothallic) with an aerial lifestyle including the known P. boehmeriae, P. gondwanensis, P. kernoviae and P. morindae and the new species P. celebensis, P. chilensis, P. javanensis, P. multiglobulosa, P. pseudochilensis and P. pseudokernoviae. All new Phytophthora species differed from each other and from related species by their unique combinations of morphological characters, breeding systems, cardinal temperatures and growth rates. The biogeography and evolutionary history of Clade 10 are discussed. We propose that the three subclades originated via the early divergence of pre-Gondwanan ancestors > 175 Mya into water- and soilborne and aerially dispersed lineages and subsequently underwent multiple allopatric and sympatric radiations during their global spread. Citation: Jung T, Milenković I, Corcobado T, et al. 2022. Extensive morphological and behavioural diversity among fourteen new and seven described species in Phytophthora Clade 10 and its evolutionary implications. Persoonia 49: 1-57. https://doi.org/10.3767/persoonia.2022.49.01.

Comparative sub-cellular proteome analyses reveals metabolic differentiation and production of effector-like molecules in the dieback phytopathogen Phytophthora cinnamomi

Phytopathogenic oomycetes pose a significant threat to global biodiversity and food security. The proteomes of these oomycetes likely contain important factors that contribute to their pathogenic success, making their discovery crucial for elucidating pathogenicity. Phytophthora cinnamomi is a root pathogen that causes dieback in a wide variety of crops and native vegetation world-wide. Virulence proteins produced by P. cinnamomi are not well defined and a large-scale approach to understand the biochemistry of this pathogen has not been documented. Soluble mycelial, zoospore and secreted proteomes were obtained and label-free quantitative proteomics was used to compare the composition of the three sub-proteomes. A total of 4635 proteins were identified, validating 17.7% of the predicted gene set. The mycelia were abundant in transporters for nutrient acquisition, metabolism and cellular proliferation. The zoospores had less metabolic related ontologies but were abundant in energy generating, motility and signalling associated proteins. Virulence-associated proteins were identified in the secretome such as candidate effector and effector-like proteins, which interfere with the host immune system. These include hydrolases, cell wall degrading enzymes, putative necrosis-inducing proteins and elicitins. The secretome elicited a hypersensitive response on the roots of a model host and thus suggests evidence of effector activity. SIGNIFICANCE: Phytophthora cinnamomi is a phytopathogenic oomycete that causes dieback disease in native vegetation and several horticultural crops such as avocado, pineapple and macadamia. Whilst this pathogen has significance world-wide, its pathogenicity and virulence have not been described in depth. We carried out comparative label-free proteomics of the mycelia, zoospores and secretome of P. cinnamomi. This study highlights the differential metabolism and cellular processes between the sub-proteomes. Proteins associated with metabolism, nutrient transport and cellular proliferation were over represented in the mycelia. The zoospores have a specialised proteome showing increased energy generation geared towards motility. Candidate effectors and effector-like secreted proteins were also identified, which can be exploited for genetic resistance. This demonstrates a better understanding of the biology and pathogenicity of P. cinnamomi infection that can subsequently be used to develop effective methods of disease management.

[Induced biosynthesis of fengycin and surfactin in a strain of Bacillus amyloliquefaciens with oomyceticidal activity on zoospores of Phytophthora capsici]

A potential alternative to the use of chemical products with oomyceticidal action for the control of Phytophthora capsici in vegetables is the use of antimicrobial metabolites, biosynthesized in Bacillus species. The objective of this study was to induce the biosynthesis of lipopeptides in Bacillus amyloliquefaciens KX953161.1 by using glutamic acid, iron, cellulose, chitin, or inactive Colletotrichum spp. cells. The in vitro oomyceticidal effect of the bacterial lipopeptides on zoospores of Phytophthora capsici was evaluated. The lipopeptides identified and quantified in the crude extracts by high performance thin layer chromatography (HPTLC) were fengycin and surfactin. The bacterial culture with inactive fungal cells yielded the greatest biosynthesis of lipopeptides, at 1847.02± 11.8 and 2563.45± 18.4 μg/ml of fengycin and surfactin, respectively and the treatments that obtained lower production of these lipopeptides, were those to which iron and cellulose were added with 608.05 ± 22.6 and 903.74± 22.1; 563.31± 11.9 and 936.96± 41.1 μg/ml for fengicin and surfactin, respectively. The lipopeptide extracted showed 100% germination inhibition on zoospores of P. capsici, revealing encystment, malformations in the germ tube and cellular degradation. Lipopeptides have the potential to control P. capsici; however, the biosynthesis of these lipopeptides requires further study to determine their biological mode of action and optimize lipopeptide performance and profile.

Variance of allele balance calculated from low coverage sequencing data infers departure from a diploid state

Background

Polyploidy and heterokaryosis are common and consequential genetic phenomena that increase the number of haplotypes in an organism and complicate whole-genome sequence analysis. Allele balance has been used to infer polyploidy and heterokaryosis in diverse organisms using read sets sequenced to greater than 50× whole-genome coverage. However, sequencing to adequate depth is costly if applied to multiple individuals or large genomes.

Results

We developed VCFvariance.pl to utilize the variance of allele balance to infer polyploidy and/or heterokaryosis at low sequence coverage. This analysis requires as little as 10× whole-genome coverage and reduces the allele balance profile down to a single value, which can be used to determine if an individual has two or more haplotypes. This approach was validated using simulated, synthetic, and authentic read sets from the oomycete species Bremia lactucae and Phytophthora infestans, the fungal species Saccharomyces cerevisiae, and the plant species Arabidopsis arenosa. This approach was deployed to determine that nine of 21 genotyped European race-type isolates of Bremia lactucae were inconsistent with diploidy and therefore likely heterokaryotic.

Conclusions

Variance of allele balance is a reliable metric to detect departures from a diploid state, including polyploidy, heterokaryosis, a mixed sample, or chromosomal copy number variation. Deploying this strategy is computationally inexpensive, can reduce the cost of sequencing by up to 80%, and used to test any organism.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-022-04685-z.

Biomonitoring of Fungal and Oomycete Plant Pathogens by Using Metabarcoding

Fungal and oomycete plant pathogens are responsible for the devastation of various ecosystems such as forest and crop species worldwide. In an effort to protect such natural resources for food, lumber, etc., early detection of non-indigenous phytopathogenic fungi in new areas is a key approach in managing threats at their source of introduction. A workflow was developed using high-throughput sequencing (HTS), more specifically metabarcoding, a method for rapid and higher throughput species screening near high-risk areas, and over larger geographical spaces. Biomonitoring of fungal and oomycete entities of plant pathogens (e.g., airborne spores) regained from environmental samples and their processing by metabarcoding is thoroughly described here. The amplicon-based approach goes from DNA and sequencing library preparation using custom-designed polymerase chain reaction (PCR) fusion primers that target the internal transcribed spacer 1 (ITS1) from fungi and oomycetes and extends to multiplex HTS with the Ion Torrent platform. In addition, a brief and simplified overview of the bioinformatics analysis pipeline and other available tools required to process amplicon sequences is also included. The raw data obtained and processed enable users to select a bioinformatics pipeline in order to directly perform biodiversity, presence/absence, geographical distribution, and abundance analyses through the tools suggested, which allows for accelerated identification of phytopathogens of interest.

Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation

The genus Phytophthora comprises many economically and ecologically important plant pathogens. Hybrid species have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a wider host range and display enhanced vigour compared to their progenitors. Phytophthora hybrids therefore pose a serious threat to agriculture as well as to natural ecosystems. Early and correct identification of hybrids is therefore essential for adequate plant protection but this is hampered by the limitations of morphological and traditional molecular methods. Identification of hybrids is also important in evolutionary studies as the positioning of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we have combined genotyping-by-sequencing (GBS) and genome size estimation on a genus-wide collection of 614 Phytophthora isolates. Analyses based on locus- and allele counts and especially on the combination of species-specific loci and genome size estimations allowed us to confirm and characterize 27 previously described hybrid species and discover 16 new hybrid species. Our method was also valuable for species identification at an unprecedented resolution and further allowed correct naming of misidentified isolates. We used both a concatenation- and a coalescent-based phylogenomic method to construct a reliable phylogeny using the GBS data of 140 non-hybrid Phytophthora isolates. Hybrid species were subsequently connected to their progenitors in this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations.

Genome of the destructive oomycete Phytophthora cinnamomi provides insights into its pathogenicity and adaptive potential

BACKGROUND

Phytophthora cinnamomi is an oomycete pathogen of global relevance. It is considered as one of the most invasive species, which has caused irreversible damage to natural ecosystems and horticultural crops. There is currently a lack of a high-quality reference genome for this species despite several attempts that have been made towards sequencing its genome. The lack of a good quality genome sequence has been a setback for various genetic and genomic research to be done on this species. As a consequence, little is known regarding its genome characteristics and how these contribute to its pathogenicity and invasiveness.

RESULTS

In this work we generated a high-quality genome sequence and annotation for P. cinnamomi using a combination of Oxford Nanopore and Illumina sequencing technologies. The annotation was done using RNA-Seq data as supporting gene evidence. The final assembly consisted of 133 scaffolds, with an estimated genome size of 109.7 Mb, N50 of 1.18 Mb, and BUSCO completeness score of 97.5%. Genome partitioning analysis revealed that P. cinnamomi has a two-speed genome characteristic, similar to that of other oomycetes and fungal plant pathogens. In planta gene expression analysis revealed up-regulation of pathogenicity-related genes, suggesting their important roles during infection and host degradation.

CONCLUSION

This study has provided a high-quality reference genome and annotation for P. cinnamomi. This is among the best assembled genomes for any Phytophthora species assembled to date and thus resulted in improved identification and characterization of pathogenicity-related genes, some of which were undetected in previous versions of genome assemblies. Phytophthora cinnamomi harbours a large number of effector genes which are located in the gene-poor regions of the genome. This unique genomic partitioning provides P. cinnamomi with a high level of adaptability and could contribute to its success as a highly invasive species. Finally, the genome sequence, its annotation and the pathogenicity effectors identified in this study will serve as an important resource that will enable future studies to better understand and mitigate the impact of this important pathogen.

AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data

Our assembly-free linkage analysis pipeline (AFLAP) identifies segregating markers as k-mers in the raw reads without using a reference genome assembly for calling variants and provides genotype tables for the construction of unbiased, high-density genetic maps without a genome assembly. AFLAP is validated and contrasted to a conventional workflow using simulated data. AFLAP is applied to whole genome sequencing and genotype-by-sequencing data of F1, F2, and recombinant inbred populations of two different plant species, producing genetic maps that are concordant with genome assemblies. The AFLAP-based genetic map for Bremia lactucae enables the production of a chromosome-scale genome assembly.

Outbreaks of epizootic ulcerative syndrome in Kerala, India following episodes of flooding

Large-scale fish mortality was observed in flood-affected fish farms across several parts of Kerala following heavy rainfall in August 2018 and 2019-nearly 53% above the normal monsoon rain that the region receives. The affected fish had severe haemorrhages and ulcers, typical of the highly infectious disease epizootic ulcerative syndrome (EUS) caused by the water mould Aphanomyces invadans. In freshwater, snakeheads Channa spp. and in brackish water mullet (Mugilidae) and pearl spot (Etroplus suratensis) were severely affected. EUS was observed in 4 freshwater fishes for the first time: dotted sawfin barb Pethia punctata (Cyprinidae), Malabar leaffish Pristolepis malabarica (Pristolepididae), mahecola barb Puntius mahecola (Cyprinidae) and giant snakehead Channa pseudomarulius (Channidae). Histology and molecular diagnosis confirmed the cause of mortality to be EUS. Fungal hyphae were also observed in deeply ulcerated fish, revealed by lactophenol cotton blue staining. The severity of the EUS outbreak was linked to the sudden change in water quality associated with the flood, such as lower water temperature, and decreases in pH, total alkalinity and total hardness.

Control of damping-off in tomato seedlings exerted by Serratia spp. strains and identification of inhibitory bacterial volatiles in vitro

Serratia marcescens can be a plant growth promoting bacteria (PGPB) and an opportunistic human and plant pathogen. We have identified and characterized strains of related species of Serratia and evaluated their biological control of damping-off of tomato seeds caused by Pythium cryptoirregulare. Serratia ureilytica, S. bockelmannii and S. nevei were identified by phylogenetic analysis of partial gyrB gene sequence and average nucleotide identity (ANI). Tomato seeds inoculated with S. ureilytica ILBB 145 showed higher germination percentage and reduced damping-off in greenhouse experiment resembling a commercial operation, and volatiles produced by this strain caused the nearly complete inhibition in vitro of P. cryptoirregulare. Analysis of volatile organic compounds (VOCs) showed that ILBB 145 produced dimethyl disulfide (DMDS), which can partially account for this inhibition. Serratia bockelmannii ILBB 162 performance against damping-off was intermediate and the inhibition of P. cryptoirregulare in vitro was lower and explained by volatile and diffusible metabolites. Both strains augmented DMDS production in the presence of P. cryptoirregulare, suggesting this compound may play a role in the context of interspecific competition. Serratia nevei ILBB 219 showed the lowest inhibition of P. cryptoirregulare in vitro, no DMDS production, and no biocontrol in planta. Draft genomes of the three strains were annotated and individual genes and biosynthesis gene clusters were identified in relation with the observed phenotypes. We report S. ureilytica - a low risk species- with activity as a biological control agent and DMDS produced by this bacterial species putatively involved in seed and seedling protection against P. cryptoirregulare.

The In Vitro Effect of Ozone Therapy Against Equine Pythium insidiosum

The goal of the present study was to characterize the antimicrobial action of different ozone (O₃) presentations against Pythium insidiosum isolated from horses. In experiment 1, P. insidiosum was treated with ozonated distilled water, ozonated sunflower oils with distinct peroxide indexes or O₃ gas (72 μg O₃ mL^-1). In experiment 2, samples were exposed one or three times to oxygen (O₂) or O₃ gas (72 μg O₃ mL^-1; 30 min/day). In experiment 3, P. insidiosum was treated with different concentrations of O₃ gas (Ø, 32, 52, or 72 μg O₃ mL^-1) for three days (30 min/day). In experiment 4, samples were exposed to O₂ or O₃ gas (72 μg O₃ mL^-1) for 05, 15, or 30 minutes during three days. Posteriorly, all samples were cultured for two weeks, and the pathogen growth area was measured until D14. Samples with absence of growth on D14 were recultured to assess the germicidal or germistatic action of the treatment. In experiment 1, only ozonized sunflower oil with a high peroxide index had germicidal action against the pathogen. In experiment 2, samples exposed three times to O₃ gas were inactivated. In experiment 3, the O₃ therapy had germicidal action against P. insidiosum independently of the gas concentration (P > .1). In experiment 4, O₃ treatments ≥15 minutes suppressed the pathogen development, whereas samples exposed to O₃ gas for 5 minutes had progressive growth (P < .01). In conclusion, ozonated sunflower oil with a high peroxide index and multiple exposures to O₃ gas mixtures were able to inactivate P. insidiosum isolated from horses.

The chaperone Lhs1 contributes to the virulence of the fish-pathogenic oomycete Aphanomyces invadans

Oomycetes are fungal-like eukaryotes and many of them are pathogens that threaten natural ecosystems and cause huge financial losses for the aqua- and agriculture industry. Amongst them, Aphanomyces invadans causes Epizootic Ulcerative Syndrome (EUS) in fish which can be responsible for up to 100% mortality in aquaculture. As other eukaryotic pathogens, in order to establish and promote an infection, A. invadans secretes proteins, which are predicted to overcome host defence mechanisms and interfere with other processes inside the host. We investigated the role of Lhs1 which is part of an ER-resident complex that generally promotes the translocation of proteins from the cytoplasm into the ER for further processing and secretion. Interestingly, proteomic studies reveal that only a subset of virulence factors are affected by the silencing of AiLhs1 in A. invadans indicating various secretion pathways for different proteins. Importantly, changes in the secretome upon silencing of AiLhs1 significantly reduces the virulence of A. invadans in the infection model Galleriamellonella. Furthermore, we show that AiLhs1 is important for the production of zoospores and their cluster formation. This renders proteins required for protein ER translocation as interesting targets for the potential development of alternative disease control strategies in agri- and aquaculture.

Saprolegnia parasitica zoospore activity and host survival indicates isolate variation in host preference

The ubiquitous freshwater pathogen Saprolegnia parasitica has long been considered a true generalist, capable of infecting a wide range of fish species. It remains unclear, however, whether different isolates of this pathogen, obtained from distinct geographic locations and host species, display differences in host preference. To assess this, the current study examined the induced zoospore encystment responses of four S. parasitica isolates towards the skin of four fish species. While three of the isolates displayed 'specialist' responses, one appeared to be more of a 'generalist'. In vivo challenge infections involving salmon and sea trout with the 'generalist' (salmon isolate EA001) and a 'specialist' (sea trout isolate EA016) pathogen, however, did not support the in vitro findings, with no apparent host preference reflected in infection outcomes. Survival of sea trout and salmon though was significantly different following a challenge infection with the sea trout (EA016) isolate. These results indicate that while S. parasitica isolates can be considered true generalists, they may target hosts to which they have been more frequently exposed (potential local adaptation). Understanding host preference of this pathogen could aid our understanding of infection epidemics and help with the development of fish management procedures.

A simple method for high molecular-weight genomic DNA extraction suitable for long-read sequencing from spores of an obligate biotroph oomycete

Long-read sequencing technologies are having a major impact on our approaches to studying non-model organisms and microbial communities. By significantly reducing the cost and facilitating the genome assembly pipelines, any laboratory can now develop its own genomics program regardless of the complexity of the genome studied. The most crucial current challenge is to develop efficient protocols for extracting genomic DNA (gDNA) with high quality and integrity adapted to the organism of interest. This can be particularly complex for obligate pathogens that must maintain intimate interactions inside infected host tissues. Here we propose a simple and cost-effective method for high molecular weight gDNA extraction from spores of Plasmopara halstedii, an obligate biotroph oomycete pathogen responsible for downy mildew in sunflower. We optimized the yield, the quality and the integrity of the extracted gDNA by fine-tuning three critical parameters, the grinding, the lysis temperature and the lysis duration. We obtained gDNA with a fragment size distribution reaching a peak ranging from 79 to 145 kb. More than half of the extracted gDNA consisted of DNA fragments larger than 42 kb, with 23% of fragments larger than 100 kb. We then demonstrated the relevance of this protocol for long-read sequencing using PacBio RSII technology. With this protocol, we were able to obtain a mean read length of 9.3 kb, a max read length of 71 kb and an N50 of 13.3 kb. The development of such DNA extraction protocols is an essential prerequisite for fully exploiting technologies requiring high molecular weight gDNA (e.g. long-read sequencing or optical mapping). These technological advances will help generate data to answer questions such as the role of newly duplicated gene clusters, repeated regions, genomic structural variations or to define number of chromosomes that still remains undefined in many species of pathogenic fungi and oomycetes.

Pythiosis in cats in northeastern Brazil

The epidemiological, clinical and anatomopathological aspects of pythiosis in cats in northeastern Brazil are described. From January 2000 to December 2018 the Laboratory of Animal Pathology of the Federal University of Campina Grande received 1928 tissue samples of cats, three of which were diagnosed as pythiosis. Grossly, the cats showed a multinodular mass in the oral cavity associated with facial deformity (case 1), a large multinodular mass thickening the jejunum wall (case 2), and an ulcerated nodule in the skin at the base of the tail (case 3). Histologically, pyogranulomatous inflammation and necrosis, with intralesional predominantly negatively stained hyphae, were observed in all cases. Immunohistochemistry for Pythium insidiosum revealed strong immunolabelling of the hyphae. The diagnosis of pythiosis was based on the epidemiological, clinical and anatomopathological findings, and was confirmed by immunohistochemistry. Although uncommon in cats, pythiosis should be readily considered as a differential diagnosis of chronic pyogranulomatous infections of the gastrointestinal tract and skin, especially in endemic areas, where the disease is often diagnosed in other animal species.

Oomycete small RNAs bind to the plant RNA-induced silencing complex for virulence

The exchange of small RNAs (sRNAs) between hosts and pathogens can lead to gene silencing in the recipient organism, a mechanism termed cross-kingdom RNAi (ck-RNAi). While fungal sRNAs promoting virulence are established, the significance of ck-RNAi in distinct plant pathogens is not clear. Here, we describe that sRNAs of the pathogen Hyaloperonospora arabidopsidis, which represents the kingdom of oomycetes and is phylogenetically distant from fungi, employ the host plant’s Argonaute (AGO)/RNA-induced silencing complex for virulence. To demonstrate H. arabidopsidis sRNA (HpasRNA) functionality in ck-RNAi, we designed a novel CRISPR endoribonuclease Csy4/GUS reporter that enabled in situ visualization of HpasRNA-induced target suppression in Arabidopsis. The significant role of HpasRNAs together with AtAGO1 in virulence was revealed in plant atago1 mutants and by transgenic Arabidopsis expressing a short-tandem-target-mimic to block HpasRNAs, that both exhibited enhanced resistance. HpasRNA-targeted plant genes contributed to host immunity, as Arabidopsis gene knockout mutants displayed quantitatively enhanced susceptibility.

Severe meningoencephalitis secondary to calvarial invasion of Lagenidium giganteum forma caninum in a dog

Background:

The oomycete Lagenidiumgiganteum forma caninum is an uncommon cause of severe dermal and subcutaneous infections in dogs with possible vascular invasion and other fatal sequelae. Infection within the central nervous system of affected dogs has not been previously reported.

Case Description:

A 6-year-old spayed female mixed-breed dog was evaluated at a referral institution with a 2-month history of suspected fungal infection in the region of the right mandibular lymph node that was refractory to surgical resection and empiric medical therapy. Physical examination identified a 6-cm fluctuant subcutaneous mass caudoventral to the ramus of the right mandible and a second firm mass in the region of the right caudal maxilla. Lesional punch biopsies were submitted for fungal culture and polymerase chain reaction (PCR), which subsequently identified L. giganteum forma caninum infection. Initial treatment consisted of anti-inflammatory doses of prednisone and hyperbaric oxygen therapy. Four weeks following initial evaluation, the patient was presented with progressive neurological signs consistent with a forebrain lesion. Magnetic resonance imaging revealed soft-tissue, contrast-enhancing lesions ventral to the calvarium adjacent to the site of original surgical resection and throughout the brain. Humane euthanasia was elected, and postmortem examination was consistent with the extension of local disease from the right masseter muscle into the right ventral calvarium. Postmortem DNA sequencing confirmed the identity of the organism as L. giganteum forma caninum.

Conclusion:

This is the first reported case of intracranial lagenidiosis in the dog. PCR distinguished this species from other Lagenidium species and from oomycetes of other genera, such as Pythiuminsidiosum and Paralagenidium karlingii. Regional extension of cutaneous lagenidiosis should therefore be considered in cases with concurrent or spontaneous neurologic disease.

The high-affinity phosphodiesterase PcPdeH is involved in the polarized growth and pathogenicity of Phytophthora capsici

The cAMP signaling pathway has been shown to be important in controlling morphological changes and pathogenicity in plant pathogens. In the present study, we identified PcPdeH, a gene encoding a high-affinity phosphodiesterase (PDE), which is a key regulator of the cAMP signaling pathway. To elucidate the function of PcPdeH, PcPdeH-knockout mutants were obtained using a type II CRISPR/Cas9 system in Phytophthora capsici. The knockout transformants of PcPdeH showed vegetative growth defects and abnormal cyst germination. Infection assays indicated that compared with the wild type, PcPdeH-knockout mutants showed significantly reduced virulence on pepper and tobacco leaves and exhibited increased (1.5-2-fold) cAMP levels relative to the wild-type and CK strains. Based on these phenotypic features, we propose that PcPdeH is crucial for vegetative growth, cyst germination and pathogenicity in P. capsici.

High mortality in Bufo gargarizans eggs associated with an undescribed Saprolegnia ferax strain in the Republic of Korea

Pathogenic water molds have a significant impact on many species, especially amphibians. The genus Saprolegnia is a pathogenic oomycete restricted to aquatic and moist habitats, and its presence is strongly linked to the abundance of amphibians and fishes. We investigated the influence of Saprolegnia presence on egg mortality and egg occurrence under varying environmental conditions in the Asiatic toad Bufo gargarizans at 27 breeding sites in the Republic of Korea. We then assessed the impact of Saprolegnia on the presence of B. gargarizans at the 27 sites surveyed weekly during the B. gargarizans breeding season for 3 consecutive years. We used molecular tools to identify the water molds as belonging to an undescribed S. ferax strain. We demonstrated that the presence of S. ferax was positively associated with higher water conductivity and ponds. In addition, while S. ferax prevalence was associated with a reduction in B. gargarizans breeding activity and breeding success, we could not determine its impact on the subsequent breeding seasons. Our study highlights the potential negative effects of Saprolegnia on amphibian reproduction, although additional research is necessary to determine the relationship between Saprolegnia, its hosts and the impacts of habitat loss on amphibians.

Efficacy of miltefosine therapy against subcutaneous experimental pythiosis in rabbits

We evaluated the in vitro activity of miltefosine against 29 Pythium spp. and the in vivo therapeutic response of 2mg/kg/day of miltefosine given orally to rabbit with pythiosis induced experimentally. The MICs (in μg/mL) of miltefosine was medium-dependent and ranged from 0.5 to 2 and 32-64 on RPMI 1640 and Mueller Hinton broth, respectively. The treatment with miltefosine demonstrated significantly lower subcutaneous lesion areas compared to the control group but was not sufficient for the complete remission of the lesions. This study indicates that miltefosine has limited efficacy against pythiosis and furthers in vitro and in vivo studies are necessary to determine the possible potential of this drug in the treatment of pythiosis.

N-acetyltransferase AAC(3)-I confers gentamicin resistance to Phytophthora palmivora and Phytophthora infestans

Background

Oomycetes are pathogens of mammals, fish, insects and plants, and the potato late blight agent Phytophthora infestans and the oil palm and cocoa infecting pathogen Phytophthora palmivora cause economically impacting diseases on a wide range of crop plants. Increasing genomic and transcriptomic resources and recent advances in oomycete biology demand new strategies for genetic modification of oomycetes. Most oomycete transformation procedures rely on geneticin-based selection of transgenic strains.

Results

We established N-acetyltransferase AAC(3)-I as a gentamicin-based selectable marker for oomycete transformation without interference with existing geneticin resistance. Strains carrying gentamicin resistance are fully infectious in plants. We further demonstrate the usefulness of this new antibiotic selection to super-transform well-characterized, already fluorescently-labelled P. palmivora strains and provide a comprehensive protocol for maintenance and zoospore electro-transformation of Phytophthora strains to aid in plant-pathogen research.

Conclusions

N-acetyltransferase AAC(3)-I is functional in Phytophthora oomycetes. In addition, the substrate specificity of the AAC(3)-I enzyme allows for re-transformation of geneticin-resistant strains. Our findings and resources widen the possibilities to study oomycete cell biology and plant-oomycete interactions.

in phytotelmata

The oomycete genus Lagenidium, which includes the mosquito biocontrol agent L. giganteum, is composed of animal pathogens, yet is phylogenetically closely related to the well characterized plant pathogens Phytophthora and Pythium spp. These phylogenetic affinities were further supported by the identification of canonical oomycete effectors in the L. giganteum transcriptome. In this study, culture-independent, metabarcoding analyses aimed at detecting L. giganteum in bromeliad phytotelmata (a proven mosquito breeding ground) microbiomes were performed. Two independent and complementary microbial detection strategies based on the amplification of cox1 DNA barcodes were used and produced globally concordant outcomes revealing that two distinct Lagenidium phylotypes are present in phytotelmata. A total of 23,869 high quality reads were generated from four phytotelmata, with 52%, and 11.5% of these reads taxonomically associated to oomycetes, and Lagenidium spp., respectively. Newly designed Lagenidium-specific cox1 primers combined with cloning/Sanger sequencing produced only Lagenidium spp. sequences, with a majority of variants clustering with L. giganteum. High throughput sequencing based on a Single Molecule Real Time (SMRT) approach combined with broad range cox1 oomycete primers confirmed the presence of L. giganteum in phytotelmata, but indicated that a potentially novel Lagenidium phylotype (closely related to L. humanum) may represent one of the most prevalent oomycetes in these environments (along with Pythium spp.). Phylogenetic analyses demonstrated that all detected Lagenidium phylotype cox1 sequences clustered in a strongly supported, monophyletic clade that included both L. giganteum and L. humanum. Therefore, Lagenidium spp. are present in phytotelmata microbiomes. This observation provides a basis to investigate potential relationships between Lagenidium spp. and phytotelma-forming plants, and reveals phytotelmata as sources for the identification of novel Lagenidium isolates with potential as biocontrol agents against vector mosquitoes.

Aspergillus terreus obtained from mangrove exhibits antagonistic activities against Pythium aphanidermatum-induced damping-off of cucumber

A study was conducted to investigate the potential of Aspergillus terreus obtained from Avicennia marina mangrove roots in inhibiting Pythium aphanidermatum and damping-off disease of cucumber. Aspergillus terreus exhibited in vitro inhibition of Pythium aphanidermatum growth. Electron microscope examination revealed that the antagonistic fungal isolate resulted in shrinking and groves in Pythium hypha. When Aspergillus terreus culture filtrate was added to Pythium aphanidermatum, it resulted in a significant increase (by 73%) in electrolyte leakage from Pythium hypha compared to the control, as well as significant reduction (by 71%) in oospore production. The Aspergillus terreus culture was also found to produce a cellulase enzyme, which is suggested to be involved in the antagonism against Pythium aphanidermatum. Adding Aspergillus terreus to soil infested with Pythium aphanidermatum significantly reduced percent mortality in cucumber seedlings by 70%. Aspergillus terreus, when applied alone on cucumber seedlings, did not show any suppressive effects on cucumber growth (length and fresh and dry weight). This appears to be the first report of isolation from mangrove of Aspergillus terreus with antagonistic activity against Pythium aphanidermatum-induced damping-off of cucumber. The study indicates that fungal isolates obtained from marine environments may serve as potential biocontrol agents against some plant pathogens.

Spatially resolved transcriptomics reveals plant host responses to pathogens

BACKGROUND

Thorough understanding of complex model systems requires the characterisation of processes in different cell types of an organism. This can be achieved with high-throughput spatial transcriptomics at a large scale. However, for plant model systems this is still challenging as suitable transcriptomics methods are sparsely available. Here we present GaST-seq (Grid-assisted, Spatial Transcriptome sequencing), an easy to adopt, micro-scale spatial-transcriptomics workflow that allows to study expression profiles across small areas of plant tissue at a fraction of the cost of existing sequencing-based methods.

RESULTS

We compare the GaST-seq method with widely used library preparation methods (Illumina TruSeq). In spatial experiments we show that the GaST-seq method is sensitive enough to identify expression differences across a plant organ. We further assess the spatial transcriptome response of Arabidopsis thaliana leaves exposed to the bacterial molecule flagellin-22, and show that with eukaryotic (Albugo laibachii) infection both host and pathogen spatial transcriptomes are obtained.

CONCLUSION

We show that our method can be used to identify known, rapidly flagellin-22 elicited genes, plant immune response pathways to bacterial attack and spatial expression patterns of genes associated with these pathways.

Epizootic ulcerative syndrome - First report of evidence from South Africa's largest and premier conservation area, the Kruger National Park

This study reports on the first evidence of genomic material of the causative agent for epizootic ulcerative syndrome (EUS), Aphanomyces invadans, from fish in the Limpopo River system and the Kruger National Park, South Africa. Fourteen fish species were collected from various depressions in the floodplains of the Limpopo and Luvuvhu Rivers in the Makuleke Wetlands during 2015 and 2017. A single individual of Clarias gariepinus was found to have a suspected epizootic ulcerative syndrome (EUS) lesion. Samples were collected and evidence of A. invadans DNA in the samples was found through PCR and amplicon sequencing. The spread of EUS into this premier conservation area is of concern as it could potentially spread across borders and into other naïve river systems with important conservation statuses.

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First evidence of genomic material of Aphanomyces invadans from the Limpopo River.

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Incidental discovery of A. invadans on Clarias gariepinus in the Makuleke Wetlands.

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Little information known about the distribution of EUS in northern South Africa.

Genetic toolkits of the red alga Pyropia tenera against the three most common diseases in Pyropia farms

Disease outbreaks devastate Pyropia aquaculture farms every year. The three most common and serious diseases are Olpidiopsis-blight and red-rot disease caused by oomycete pathogens and green-spot disease caused by the PyroV1 virus. We hypothesized that a basic genetic profile of molecular defenses will be revealed by comparing and analyzing the genetic response of Pyropia tenera against the above three pathogens. RNAs isolated from infected thalli were hybridized onto an oligochip containing 15,115 primers designed from P. tenera expressed sequence tags (EST)s. Microarray profiles of the three diseases were compared and interpreted together with histochemical observation. Massive amounts of reactive oxygen species accumulated in P. tenera cells exposed to oomycete pathogens. Heat shock genes and serine proteases were the most highly up-regulated genes in all infection experiments. Genes involved in RNA metabolism, ribosomal proteins and antioxidant metabolism were also highly up-regulated. Genetic profiles of P. tenera in response to pathogens were most similar between the two biotrophic pathogens, Olpidiopsis pyropiae and PyroV1 virus. A group of plant resistance genes were specifically regulated against each pathogen. Our results suggested that disease response in P. tenera consists of a general constitutive defense and a genetic toolkit against specific pathogens.

Phytopythium and Pythium Species (Oomycota) Isolated from Freshwater Environments of Korea

Oomycetes are widely distributed in various environments, including desert and polar regions. Depending upon different habits and hosts, they have evolved with both saprophytic and pathogenic nutritional modes. Freshwater ecosystem is one of the most important habitats for members of oomycetes. Most studies on oomycete diversity, however, have been biased mostly towards terrestrial phytopathogenic species, rather than aquatic species, although their roles as saprophytes and parasites are essential for freshwater ecosystems. In this study, we isolated oomycete strains from soil sediment, algae, and decaying plant debris in freshwater streams of Korea. The strains were identified based on cultural and morphological characteristics, as well as molecular phylogenetic analyses of ITS rDNA, cox1, and cox2 mtDNA sequences. As a result, we discovered eight oomycete species previously unknown in Korea, namely Phytopythium chamaehyphon, Phytopythium litorale, Phytopythium vexans, Pythium diclinum, Pythium heterothallicum, Pythium inflatum, Pythium intermedium, and Pythium oopapillum. Diversity and ecology of freshwater oomycetes in Korea are poorly understood. This study could contribute to understand their distribution and ecological function in freshwater ecosystem.

Diversity and evolution of chitin synthases in oomycetes (Straminipila: Oomycota)

The oomycetes are filamentous eukaryotic microorganisms, distinct from true fungi, many of which act as crop or fish pathogens that cause devastating losses in agriculture and aquaculture. Chitin is present in all true fungi, but it occurs in only small amounts in some Saprolegniomycetes and it is absent in Peronosporomycetes. However, the growth of several oomycetes is severely impacted by competitive chitin synthase (CHS) inhibitors. Here, we shed light on the diversity, evolution and function of oomycete CHS proteins. We show by phylogenetic analysis of 93 putative CHSs from 48 highly diverse oomycetes, including the early diverging Eurychasma dicksonii, that all available oomycete genomes contain at least one putative CHS gene. All gene products contain conserved CHS motifs essential for enzymatic activity and form two Peronosporomycete-specific and six Saprolegniale-specific clades. Proteins of all clades, except one, contain an N-terminal microtubule interacting and trafficking (MIT) domain as predicted by protein domain databases or manual analysis, which is supported by homology modelling and comparison of conserved structural features from sequence logos. We identified at least three groups of CHSs conserved among all oomycete lineages and used phylogenetic reconciliation analysis to infer the dynamic evolution of CHSs in oomycetes. The evolutionary aspects of CHS diversity in modern-day oomycetes are discussed. In addition, we observed hyphal tip rupture in Phytophthora infestans upon treatment with the CHS inhibitor nikkomycin Z. Combining data on phylogeny, gene expression, and response to CHS inhibitors, we propose the association of different CHS clades with certain developmental stages.

Data on whole genome sequencing of the oomycete Pythium insidiosum strain CBS 101555 from a horse with pythiosis in Brazil

Objectives

The oomycete Pythium insidiosum infects humans and animals worldwide, and causes the life-threatening condition, called pythosis. Most patients lose infected organs or die from the disease. Comparative genomic analyses of different P. insidiosum strains could provide new insights into its pathobiology, and can lead to discovery of an effective treatment method. Several draft genomes of P. insidiosum are publicly available: three from Asia (Thailand), and one each from North (the United States) and Central (Costa Rica) Americas. We report another draft genome of P. insidiosum isolated from South America (Brazil), to serve as a resource for comprehensive genomic studies.

Data description

In this study, we report genome sequence of the P. insidiosum strain CBS 101555, isolated from a horse with pythiosis in Brazil. One paired-end (180-bp insert) library of processed genomic DNA was prepared for Illumina HiSeq 2500-based sequencing. Assembly of raw reads provided genome size of 48.9 Mb, comprising 60,602 contigs. A total of 23,254 genes were predicted and classified into 18,305 homologous gene clusters. Compared with the reference genome (the P. insidiosum strain Pi-S), 1,475,337 sequence variants (SNPs and INDELs) were identified in the organism. The genome sequence data has been deposited in DDBJ under the accession numbers BCFP01000001–BCFP01060602.

A time-course investigation of resistance to the carboxylic acid amide mandipropamid in field populations of Plasmopara viticola treated with anti-resistance strategies

BACKGROUND

Despite anti-resistance strategies being recommended to reduce selection pressure on insensitive strains, no information is available on fungal population dynamics following their application in real field conditions. In this study, the effects on Plasmopara viticola populations of two identical spray programs, differing only in including or not the carboxylic acid amide (CAA) mandipropamid in mixture and in alternation with an anti-resistance partner, were compared in terms of downy mildew control efficacy and mandipropamid sensitivity in two commercial vineyards for four seasons.

RESULTS

Both programs effectively and similarly protected grapevine from downy mildew, despite different starting sensitivity levels of the P. viticola populations. In the vineyard where resistant strains were initially present, the frequency of mutations associated with resistance (G1105S/V) fluctuated within seasons in both programs and a shift towards sensitivity occurred after 3 years of the mandipropamid-free program. Where sensitivity was initially present, no changes occurred in the mandipropamid-free program and resistant strains were selected in the mandipropamid program in high disease pressure conditions.

CONCLUSION

The anti-resistance strategy including mandipropamid in mixture showed a good field performance, but did not completely prevent an increase in the frequency of insensitive strains. This supports the need for appropriate planning to determine which mixtures should be used in the field. © 2018 Society of Chemical Industry.

Comparative genomics of downy mildews reveals potential adaptations to biotrophy

BACKGROUND

Spinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen. P. effusa is highly variable and 15 new races have been recognized in the past 30 years.

RESULTS

We virulence phenotyped, sequenced, and assembled two isolates of P. effusa from the Salinas Valley, California, U.S.A. that were identified as race 13 and 14. These assemblies are high quality in comparison to assemblies of other downy mildews having low total scaffold count (784 & 880), high contig N50s (48 kb & 52 kb), high BUSCO completion and low BUSCO duplication scores and share many syntenic blocks with Phytophthora species. Comparative analysis of four downy mildew and three Phytophthora species revealed parallel absences of genes encoding conserved domains linked to transporters, pathogenesis, and carbohydrate activity in the biotrophic species. Downy mildews surveyed that have lost the ability to produce zoospores have a common loss of flagella/motor and calcium domain encoding genes. Our phylogenomic data support multiple origins of downy mildews from hemibiotrophic progenitors and suggest that common gene losses in these downy mildews may be of genes involved in the necrotrophic stages of Phytophthora spp.

CONCLUSIONS

We present a high-quality draft genome of Peronospora effusa that will serve as a reference for Peronospora spp. We identified several Pfam domains as under-represented in the downy mildews consistent with the loss of zoosporegenesis and necrotrophy. Phylogenomics provides further support for a polyphyletic origin of downy mildews.

Multilocus sequence typing reveals clonality in Saprolegnia parasitica outbreaks

The molecular epidemiology of fish pathogen Saprolegnia parasitica is still largely unknown. We developed a multilocus sequence typing scheme based on seven housekeeping genes to characterize 77 S. parasitica strains isolated from different fish host species at different times and from different geographic areas in Switzerland between 2015 and 2017. Ten different diploid sequence types (DSTs) were identified. The majority (52%) of outbreaks in Switzerland seemed to be caused by one genotype, namely DST3, which was recovered from farm-raised and wild-caught fish in all the geographic areas and river basins included in the study. DST3 was also recovered from the rivers Bienne (eastern France) and Doubs, where the episodes of massive mortality due to saprolegniosis started in 2009. Another genotype (DST7) showed, to a lesser extent, a distribution across different river basins, while eight DSTs were unique to a defined geographic area or river basin. The occurrence of sporadic DSTs indicates a certain degree of diversity within S. parasitica in the environment. The wide distribution of DST3 suggests that a clonal population may have spread in eastern France and Switzerland across geographic barriers, with strong implications for the management of both captive and wild fish populations.

Stable predictive markers for Phytophthora sojae avirulence genes that impair infection of soybean uncovered by whole genome sequencing of 31 isolates

BACKGROUND

The interaction between oomycete plant pathogen Phytophthora sojae and soybean is characterized by the presence of avirulence (Avr) genes in P. sojae, which encode for effectors that trigger immune responses and resistance in soybean via corresponding resistance genes (Rps). A recent survey highlighted a rapid diversification of P. sojae Avr genes in soybean fields and the need to deploy new Rps genes. However, the full genetic diversity of P. sojae isolates remains complex and dynamic and is mostly characterized on the basis of phenotypic associations with differential soybean lines.

RESULTS

We sequenced the genomes of 31 isolates of P. sojae, representing a large spectrum of the pathotypes found in soybean fields, and compared all the genetic variations associated with seven Avr genes (1a, 1b, 1c, 1d, 1k, 3a, 6) and how the derived haplotypes matched reported phenotypes in 217 interactions. We discovered new variants, copy number variations and some discrepancies with the virulence of previously described isolates with Avr genes, notably with Avr1b and Avr1c. In addition, genomic signatures revealed 11.5% potentially erroneous phenotypes. When these interactions were re-phenotyped, and the Avr genes re-sequenced over time and analyzed for expression, our results showed that genomic signatures alone accurately predicted 99.5% of the interactions.

CONCLUSIONS

This comprehensive genomic analysis of seven Avr genes of P. sojae in a population of 31 isolates highlights that genomic signatures can be used as accurate predictors of phenotypes for compatibility with Rps genes in soybean. Our findings also show that spontaneous mutations, often speculated as a source of aberrant phenotypes, did not occur within the confines of our experiments and further suggest that epigenesis or gene silencing do not account alone for previous discordance between genotypes and phenotypes. Furthermore, on the basis of newly identified virulence patterns within Avr1c, our results offer an explanation why Rps1c has failed more rapidly in the field than the reported information on virulence pathotypes.

Oomycete parasites in freshwater copepods of Patagonia: effects on survival and recruitment

Copepods are hosts to various oomycete parasite species, but the effects of pathogens on copepod populations have rarely been studied. This study aimed to characterize oomycete infection in the freshwater copepod Parabroteas sarsi in a temporary pond in Patagonia (Argentina). A complete hydroperiod was monitored, evaluating environmental variables as influencing factors in the oomycete infections. Laboratory experiments were performed to evaluate the susceptibility of infected copepods to consumption by predators. Although 5 species of copepods were present in the pond, only ovigerous P. sarsi females were parasitized by oomycetes. Two species of oomycetes were always found together: Aphanomyces ovidestruens and Pythium flevoense. Infections were detected at water temperatures >20°C, with a positive relationship between temperature and parasite prevalence. Infection occurred after a decrease in large filter-feeder densities. The pathogens were not lethal to P. sarsi females in the short-term, but did produce mortality of entire egg sacs, thus negatively impacting subsequent recruitment. Mean prevalence of infection in females was 53%, reaching 83% in December. Females have the capacity to release an infected egg sac and generate a new one in a few days. This infection does not affect the susceptibility of P. sarsi to the predator Notonecta vereertbruggheni. The decrease in female abundance registered towards the end of the hydroperiod could be related to a combination of factors that may have a differential effect on female survival, such as increasing temperature, the energy cost of egg sac development and carrying and oomycete infection.

Assessment of intra-specific variability in Saprolegnia parasitica populations of aquaculture facilities in British Columbia, Canada

Among the Saprolegnia species found in aquaculture facilities, S. parasitica is recognized as the primary fish pathogen and remains an ongoing concern in fish health management. Until recently, these pathogens were kept in check by use of malachite green; due to its toxicity, this chemical has now been banned from use in many countries. It is difficult to predict and control S. parasitica outbreaks in freshwater systems and there is a need to understand the population genetic structure of this pathogen. Genetic characterization of this species in aquaculture systems would provide information to track introductions and determine possible sources of inoculum. Degenerate PCR primers containing short sequence repeats were used to create microsatellite-associated genetic markers (random amplified microsatellites) for the comparison of S. parasitica isolates collected primarily from commercial Atlantic salmon aquaculture systems in British Columbia, Canada, over a 15 mo period to describe their spatial and temporal variability. The frequencies of amplified products were compared and the population genetic diversity was measured using Nei's genetic distance and Shannon's information index, while the species population structure was evaluated by phylogenetic analysis. S. parasitica was detected in all facilities sampled. Genetic diversity was low but not clonal, most likely due to repeated introduction events and a low level of sexual recombination over time. A better understanding of pathogen population structure will assist the development of effective preventative measures and targeted treatments for disease outbreaks.

Halioticida noduliformans infection in eggs of lobster (Homarus gammarus) reveals its generalist parasitic strategy in marine invertebrates

A parasite exhibiting Oomycete-like morphology and pathogenesis was isolated from discoloured eggs of the European lobster (Homarus gammarus) and later found in gill tissues of adults. Group-specific Oomycete primers were designed to amplify the 18S ribosomal small subunit (SSU), which initially identified the organism as the same as the 'Haliphthoros' sp. NJM 0034 strain (AB178865.1) previously isolated from abalone (imported from South Australia to Japan). However, in accordance with other published SSU-based phylogenies, the NJM 0034 isolate did not group with other known Haliphthoros species in our Maximum Likelihood and Bayesian phylogenies. Instead, the strain formed an orphan lineage, diverging before the separation of the Saprolegniales and Pythiales. Based upon 28S large subunit (LSU) phylogeny, our own isolate and the previously unidentified 0034 strain are both identical to the abalone pathogen Halioticida noduliformans. The genus shares morphological similarities with Haliphthoros and Halocrusticida and forms a clade with these in LSU phylogenies. Here, we confirm the first recorded occurrence of H. noduliformans in European lobsters and associate its presence with pathology of the egg mass, likely leading to reduced fecundity.

identifies a new class of oomycete effector associated with host adaptation

Background

Oomycetes are a group of filamentous eukaryotic microorganisms that have colonized all terrestrial and oceanic ecosystems, and they include prominent plant pathogens. The Aphanomyces genus is unique in its ability to infect both plant and animal species, and as such exemplifies oomycete versatility in adapting to different hosts and environments. Dissecting the underpinnings of oomycete diversity provides insights into their specificity and pathogenic mechanisms.

Results

By carrying out genomic analyses of the plant pathogen A. euteiches and the crustacean pathogen A. astaci, we show that host specialization is correlated with specialized secretomes that are adapted to the deconstruction of the plant cell wall in A. euteiches and protein degradation in A. astaci. The A. euteiches genome is characterized by a large repertoire of small secreted protein (SSP)-encoding genes that are highly induced during plant infection, and are not detected in other oomycetes. Functional analysis revealed an SSP from A. euteiches containing a predicted nuclear-localization signal which shuttles to the plant nucleus and increases plant susceptibility to infection.

Conclusion

Collectively, our results show that Aphanomyces host adaptation is associated with evolution of specialized secretomes and identify SSPs as a new class of putative oomycete effectors.

Electronic supplementary material

The online version of this article (10.1186/s12915-018-0508-5) contains supplementary material, which is available to authorized users.

Illuminating Phytophthora Biology with Fluorescent Protein Tags

Phytophthora species cause diseases that threaten agricultural, ornamental, and forest plants worldwide. Explorations of the biology of these pathogens have been aided by the availability of genome sequences, but much work remains to decipher the roles of their proteins. Insight into protein function can be obtained by visualizing them within cells, which has been facilitated by recent improvements in fluorescent protein and microscope technologies. Here, we describe strategies to permit investigators to generate strains of Phytophthora that express fluorescently tagged proteins and study their localization during growth in artificial media and during plant infection.

Effects of Phytophthora ramorum on volatile organic compound emissions of Rhododendron using gas chromatography-mass spectrometry

Phytophthora ramorum is an invasive and devastating plant pathogen that causes sudden oak death in coastal forests in the western United States and ramorum blight in nursery ornamentals and native plants in various landscapes. As a broad host-range quarantine pest that can be asymptomatic in some hosts, P. ramorum presents significant challenges for regulatory efforts to detect and contain it, particularly in commercial nurseries. As part of a program to develop new detection methods for cryptic infections in nursery stock, we compared volatile emissions of P. ramorum-inoculated and noninoculated Rhododendron plants using three gas chromatography-mass spectrometry methods. The first used a branch enclosure combined with headspace sorptive extraction to measure plant volatiles in situ. Seventy-eight compounds were found in the general Rhododendron profile. The volatile profile of inoculated but asymptomatic plants (121 days post-inoculation) was distinguishable from the profile of the noninoculated controls. Three compounds were less abundant in inoculated Rhododendron plants relative to noninoculated and mock-inoculated control plants. A second method employed stir bar sorptive extraction to measure volatiles in vitro from leaf extractions in methanol; 114 volatiles were found in the overall profile with 30 compounds less abundant and one compound more abundant in inoculated Rhododendron plants relative to mock-inoculated plants. At 128 days post-inoculation, plants were asymptomatic and similar in appearance to the noninoculated controls, but their chemical profiles were different. In a third technique, volatiles from water runoff from the soil of potted healthy and inoculated Rhododendron plants were compared. Runoff from the inoculated plants contained four unique volatile compounds that never appeared in the runoff from mock-inoculated plants. These three volatile detection techniques could lead to innovative approaches that augment detection and diagnosis of P. ramorum and oomycete pathogens in nurseries and other settings. Graphical abstract Detection of volatile signatures may aid in discriminating healthy vs. infected but asymptomatic plants in nursery and greenhouse facilities.

Rethinking the evolution of eukaryotic metabolism: novel cellular partitioning of enzymes in stramenopiles links serine biosynthesis to glycolysis in mitochondria

Background

An important feature of eukaryotic evolution is metabolic compartmentalization, in which certain pathways are restricted to the cytosol or specific organelles. Glycolysis in eukaryotes is described as a cytosolic process. The universality of this canon has been challenged by recent genome data that suggest that some glycolytic enzymes made by stramenopiles bear mitochondrial targeting peptides.

Results

Mining of oomycete, diatom, and brown algal genomes indicates that stramenopiles encode two forms of enzymes for the second half of glycolysis, one with and the other without mitochondrial targeting peptides. The predicted mitochondrial targeting was confirmed by using fluorescent tags to localize phosphoglycerate kinase, phosphoglycerate mutase, and pyruvate kinase in Phytophthora infestans, the oomycete that causes potato blight. A genome-wide search for other enzymes with atypical mitochondrial locations identified phosphoglycerate dehydrogenase, phosphoserine aminotransferase, and phosphoserine phosphatase, which form a pathway for generating serine from the glycolytic intermediate 3-phosphoglycerate. Fluorescent tags confirmed the delivery of these serine biosynthetic enzymes to P. infestans mitochondria. A cytosolic form of this serine biosynthetic pathway, which occurs in most eukaryotes, is missing from oomycetes and most other stramenopiles. The glycolysis and serine metabolism pathways of oomycetes appear to be mosaics of enzymes with different ancestries. While some of the noncanonical oomycete mitochondrial enzymes have the closest affinity in phylogenetic analyses with proteins from other stramenopiles, others cluster with bacterial, plant, or animal proteins. The genes encoding the mitochondrial phosphoglycerate kinase and serine-forming enzymes are physically linked on oomycete chromosomes, which suggests a shared origin.

Conclusions

Stramenopile metabolism appears to have been shaped through the acquisition of genes by descent and lateral or endosymbiotic gene transfer, along with the targeting of the proteins to locations that are novel compared to other eukaryotes. Colocalization of the glycolytic and serine biosynthesis enzymes in mitochondria is apparently necessary since they share a common intermediate. The results indicate that descriptions of metabolism in textbooks do not cover the full diversity of eukaryotic biology.

Electronic supplementary material

The online version of this article (10.1186/s12862-017-1087-8) contains supplementary material, which is available to authorized users.