Innate Resistance and Phosphite Treatment Affect Both the Pathogen's and Host's Transcriptomes in the Tanoak-Phytophthora ramorum Pathosystem

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.

Assembly and analysis of the genome of Notholithocarpus densiflorus

Tanoak (Notholithocarpus densiflorus) is an evergreen tree in the Fagaceae family found in California and southern Oregon. Historically, tanoak acorns were an important food source for Native American tribes, and the bark was used extensively in the leather tanning process. Long considered a disjunct relictual element of the Asian stone oaks (Lithocarpus spp.), phylogenetic analysis has determined that the tanoak is an example of convergent evolution. Tanoaks are deeply divergent from oaks (Quercus) of the Pacific Northwest and comprise a new genus with a single species. These trees are highly susceptible to "sudden oak death" (SOD), a plant pathogen (Phytophthora ramorum) that has caused widespread deaths of tanoaks. In this study, we set out to assemble the genome and perform comparative studies among a number of individuals that demonstrated varying levels of susceptibility to SOD. First, we sequenced and de novo assembled a draft reference genome of N. densiflorus using cobarcoded library processing methods and an MGI DNBSEQ-G400 sequencer. To increase the contiguity of the final assembly, we also sequenced Oxford Nanopore long reads to 30× coverage. To our knowledge, the draft genome reported here is one of the more contiguous and complete genomes of a tree species published to date, with a contig N50 of ∼1.2 Mb, a scaffold N50 of ∼2.1 Mb, and a complete gene score of 95.5% through BUSCO analysis. In addition, we sequenced 11 genetically distinct individuals and mapped these onto the draft reference genome, enabling the discovery of almost 25 million single nucleotide polymorphisms and ∼4.4 million small insertions and deletions. Finally, using cobarcoded data, we were able to generate a complete haplotype coverage of all 11 genomes.

Evidence of Phosphite Tolerance in Phytophthora cinnamomi from New Zealand Avocado Orchards

There is a limited number of chemical control agents for managing Phytophthora root and collar rot diseases of avocado internationally; of these, phosphite is one of the most effective. To determine whether prolonged phosphite use in New Zealand avocado orchards has led to decreased sensitivity of Phytophthora cinnamomi to phosphite, 57 isolates were collected from phosphite-treated and -untreated avocado orchards and screened for tolerance using a mycelial growth inhibition assay. The inhibitory effect of phosphite on mycelial growth was tested in vitro using six concentrations of phosphite. Based on changes in mycelial growth using optical density measurements to calculate the effective concentration to reduce growth by 50% (EC₅₀) estimates, three phosphite-susceptible (EC₅₀ range = 18.71 to 29.26 µg/ml) and three tolerant (EC₅₀ range = 81.85 to 123.89 µg/ml) isolates were selected. The effects of phosphite on the colonization of lupin (Lupinus angustifolius) seedling roots and sporangia and zoospore production of three susceptible and three tolerant isolates were determined. The three tolerant isolates colonized lupin roots more extensively than the three susceptible isolates in the presence of phosphite at 5 and 10 g/liter. The tolerant isolates were able to asymptomatically colonize further above the lesion margin in the lupin treated with phosphite at 5 g/liter relative to the phosphite-susceptible isolates but no isolates were completely resistant to phosphite. The tolerant isolates produced more sporangia and, consequently, zoospores in the presence of phosphite than the susceptible isolates. The detection of phosphite tolerance by P. cinnamomi in planta and in vivo is concerning for the future efficacy of phosphite to manage Phytophthora diseases.

Comparative transcriptomic responses of European and Japanese larches to infection by Phytophthora ramorum

BACKGROUND AND OBJECTIVES

Phytophthora ramorum severely affects both European larch (EL) and Japanese larch (JL) trees as indicated by high levels of mortality particularly in the UK. Field observations suggested that EL is less severely affected and so may be less susceptible to P. ramorum than JL; however, controlled inoculations have produced inconsistent or non-statistically significant differences. The present study aimed to compare RNA transcript accumulation profiles in EL and JL in response to inoculation with P. ramorum to improve our understanding of their defence responses.

METHODOLOGY

RNA-sequencing was carried out on bark tissues following the inoculation with P. ramorum of potted saplings in both EL and JL carried out under controlled environment conditions, with sampling at 1, 3, 10, and 25 days post inoculation in infected and control plants.

RESULTS

All of the inoculated trees rapidly developed lesions but no statistically significant differences were found in lesion lengths between EL and JL. RNA-Sequencing comparing control and inoculate saplings identified key differences in differentially expressed genes (DEGs) between the two larch species. European larch had rapid induction of defence genes within 24 hours of infection followed by sustained expression until 25 days after inoculation. Results in JL were more varied; upregulation was stronger but more transient and represented fewer defence pathways. Gene enrichment analyses highlighted differences in jasmonate signalling and regulation including NPR1 upregulation in EL only, and specific aspects of secondary metabolism. Some DEGs were represented by multiple responsive copies including lipoxygenase, chalcone synthase and nucleotide-binding, leucine-rich-repeat genes.

CONCLUSION

The variations between EL and JL in responsive DEGs of interest as potentially related to differences seen in the field and should be considered in the selection of trees for planting and future breeding.

Alcaligenes faecalis Juj3 alleviates Plasmodiophora brassicae stress to cabbage via promoting growth and inducing resistance

Clubroot is a devastating disease threatening global cruciferous vegetable production caused by Plasmodiophora brassicae (Pb). We have evaluated the positive effects of the Alcaligenes faecalis Juj3 on cabbage growth promotion and Pb stress alleviation through pot and field experiments. The Juj3 strain was isolated from a healthy cabbage rhizosphere with growth-promoting characteristics and was identified as A. faecalis based on morphological traits and phylogeny. Seed germination assays revealed that Juj3 inoculation enhances cabbage bud shoot and root growth. In pot experiments, inoculation with Juj3 fermentation powder at cabbage sowing dates significantly improved the seedling biomass. Combining seed treatments with root irrigation after transplanting considerably reduced the clubroot disease index and resulted in appreciable biocontrol efficacy (83.7%). Gene expression analyses of cabbage after Juj3 inoculation showed that PR2 and EIN3 expression were significantly up-regulated. Physiologically, Juj3 inoculation enhanced cabbage chlorophyll content and root activity in a normal environment. Irrespective of whether plants were under normal environment or Pb stresses, Juj3 improved photosynthesis. Field trial analyses revealed that Juj3 exhibits satisfactory biocontrol efficacy in cabbage (51.4%) and Chinese cabbage (37.7%). Moreover, Juj3 could also enhance cabbage and Chinese cabbage biomass to improve the yield quality. These findings pave the way for future use of A. faecalis as biocontrol agents for clubroot and reveal the great potential of the rhizobacterium for plant growth-promoting applications in agriculture and horticulture.

Natural Biostimulants Elicit Plant Immune System in an Integrated Management Strategy of the Postharvest Green Mold of Orange Fruits Incited by Penicillium digitatum

This study was aimed at testing the integrated use of a natural biostimulant based on seaweed (Ascophyllum nodosum) and plant (alfalfa and sugarcane) extracts and reduced dosages of the conventional synthetic fungicide Imazalil (IMZ) to manage postharvest rots of orange fruits. The following aspects were investigated: (i) the effectiveness of postharvest treatment with natural biostimulant alone or in mixture with IMZ at a reduced dose against green mold caused by Penicillium digitatum; (ii) the differential expression of defense genes in orange fruits treated with the natural biostimulant both alone and in combination with a reduced dose of IMZ; (iii) the persistence of the inhibitory activity of both biostimulant and the mixture biostimulant/IMZ against green mold; and (iv) the residue level of fungicide in citrus peel when applied alone or in combination with the biostimulant. Treatments with the chemical plant resistance-inducer potassium phosphite, alone or with a reduced dose of IMZ, were included for comparison. The mixture of natural biostimulant and IMZ at a low dose consistently reduced the incidence and severity of fruit green mold and induced a significant increase of the expression level of β-1,3-glucanase-, peroxidase (PEROX)-, and phenylalanine ammonia-lyase (PAL)-encoding genes in fruit peel, suggesting that the natural biostimulant elicits a long-lasting resistance of citrus fruits to infections by P. digitatum. Interestingly, the residual concentration of IMZ in fruits treated with the biostimulant/fungicide mixture was significantly lower than that of IMZ in fruits treated only with the fungicide at the same dose and by far below the threshold values set by the European Union. This study laid the foundations for (i) conceiving a practical and more eco-friendly alternative to the conventional postharvest management of green mold of citrus fruits, based almost exclusively on the use of synthetic fungicide IMZ, alone or mixed with potassium phosphite and (ii) providing a better insight into the mechanisms of disease resistance induction by biostimulants.