Dynamics of bacterial blight disease in resistant and susceptible rice varieties

Bacterial blight (X. oryzae pv. oryzae) is a serious disease in rice across the world. To better control the disease, it is important to understand its epidemiology and how key aspects of this (e.g. infection efficiency, and spatial spread) change according to environment (e.g. local site conditions and season), management, and in particular, variety resistance. To explore this, we analysed data on the disease progress on resistant and susceptible varieties of rice grown at four sites in the Philippines across five seasons using a combination of mechanistic modelling and statistical analysis. Disease incidence was generally lower in the resistant variety. However, we found no evidence that the primary infection efficiency was lower in resistant varieties, suggesting that differences were largely due to reduced secondary spread. Despite secondary spread being attributed to splash dispersal which is exacerbated by wind and rain, the wetter sites of Pila and Victoria in south Luzon tended to have lower infection rates than the drier sites in central Luzon. Likewise, we found spread in the dry season can be substantial and should therefore not be ignored. In fact, we found site to be a greater determinant of the number of infection attempts suggesting that other environmental and management factors had greater effect on the disease than climate. Primary infection was characterised by spatially-random observations of disease incidence. As the season progressed, we observed an emerging short-range (1.6 m-4 m) spatial structure suggesting secondary spread was predominantly short-range, particularly where the resistant variety was grown

Rice-Infecting Pseudomonas Genomes Are Highly Accessorized and Harbor Multiple Putative Virulence Mechanisms to Cause Sheath Brown Rot

Sheath rot complex and seed discoloration in rice involve a number of pathogenic bacteria that cannot be associated with distinctive symptoms. These pathogens can easily travel on asymptomatic seeds and therefore represent a threat to rice cropping systems. Among the rice-infecting Pseudomonas, P. fuscovaginae has been associated with sheath brown rot disease in several rice growing areas around the world. The appearance of a similar Pseudomonas population, which here we named P. fuscovaginae-like, represents a perfect opportunity to understand common genomic features that can explain the infection mechanism in rice. We showed that the novel population is indeed closely related to P. fuscovaginae. A comparative genomics approach on eight rice-infecting Pseudomonas revealed heterogeneous genomes and a high number of strain-specific genes. The genomes of P. fuscovaginae-like harbor four secretion systems (Type I, II, III, and VI) and other important pathogenicity machinery that could probably facilitate rice colonization. We identified 123 core secreted proteins, most of which have strong signatures of positive selection suggesting functional adaptation. Transcript accumulation of putative pathogenicity-related genes during rice colonization revealed a concerted virulence mechanism. The study suggests that rice-infecting Pseudomonas causing sheath brown rot are intrinsically diverse and maintain a variable set of metabolic capabilities as a potential strategy to occupy a range of environments.Consortium for International Agricultural Research (CGIAR)Global Rice Science Partnership (GRiSP

Comparative genomic analysis of rice-infecting <i>Pseudomonas</i> secretion apparatus.

<p>Genetic components of T1SS, T2SS, T3SS and T6SS apparatus of <i>P</i>. <i>fuscovaginae-like</i> (<i>Pfv</i>-like) IRRI 6609 was used to compare against 79 closely related <i>Pseudomonas</i> genomes (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139256#pone.0139256.s008" target="_blank">S1 Table</a>). The <i>apr</i>, <i>has</i>, <i>xcp</i>, <i>hxc</i>, <i>gsp</i>, SPI-1, and HSI-1 are previously characterized gene clusters found within each secretion system. Horizontal axis describes the number of species used for comparison. The rows were sorted by amino acid sequence identity with threshold set at 20%. The heat map was visualized in CodaChrome. Homology range values are shown in bottom right.</p

<i>P</i>. <i>fuscovaginae-like</i> (<i>Pfv</i>-like) strains are closely related to <i>P</i>. <i>fuscovaginae</i> (<i>Pfv</i>).

<p><b>A)</b> Average nucleotide identity (ANI) and average amino acid identity (AAI) clustering analysis of the eight rice-infecting <i>Pseudomonas</i> draft genomes. Clustering analysis identified two separated groups involving <i>Pfv</i>-like strains (orange) collected in the Philippines and <i>Pfv</i> strains (blue) collected elsewhere. Values scale is depicted in red, orange, yellow, and white colors in ANI (horizontal) and AAI (vertical) pairwise comparison. Value cut-offs with >95% reflect the possibility of same species grouping. The heatmap was generated in the R package gplots using the heatmap.2 function. <b>B)</b> Phylogenetic reconstruction of rice-infecting <i>Pseudomonas</i> and closely related <i>Pseudomonas</i> species using the concatenated housekeeping <i>rpoB</i> and <i>rpoD</i>. Maximum likelihood was used to infer the phylogenetic relationship with bootstrap of 1000 using the RAxML software [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139256#pone.0139256.ref061" target="_blank">61</a>]. <i>Pfv</i> and <i>Pfv</i>-like are highlighted in blue and orange, respectively.</p

The genome of rice-infecting <i>Pseudomonas</i> harbor high level of structural polymorphism.

<p>Global comparison of eight rice-infecting <i>Pseudomonas</i> draft genomes using BLASTn. The inner most ring corresponds to the genomic position at IRRI 6609. The second and third rings indicate G+C content and G+C skew, respectively. The rest of the rings indicate presence and absence portions of the eight rice-infecting <i>Pseudomonas</i> draft genomes against IRRI 6609. Solid colors represent genomic regions with hits while white spaced represent gaps. <i>P</i>. <i>fuscovaginae</i> (<i>Pfv</i>) and <i>P</i>. <i>fuscovaginae</i>-like (<i>Pfv</i>-like) strains are depicted. Sequence identity is related to color intensity. Also included are locations of four intact prophage insertions found in <i>Pfv</i>-like IRRI 6609 (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139256#pone.0139256.s004" target="_blank">S4 Fig</a>). The global alignment was visualized using BRIG [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139256#pone.0139256.ref043" target="_blank">43</a>].</p

Nucleotide identity and percentage of orthologous genes obtained in rice-infecting <i>Pseudomonas</i> draft genomes compared to IRRI 6609

<p>^a Identity based on BLASTn results</p><p>Nucleotide identity and percentage of orthologous genes obtained in rice-infecting <i>Pseudomonas</i> draft genomes compared to IRRI 6609</p

Infection caused by <i>P</i>. <i>fuscovaginae</i>-like strain IRRI 7007 in <i>O</i>. <i>sativa</i> cv. Azucena.

<p><b>A)</b> Plants were inoculated at 45 days after transplanting using toothpick method. <b>B)</b> Symptom development along the sheath showing brown necrotic lesions. <b>C)</b> Discolored inner sheath. <b>D)</b> Poorly emerged panicles with brown to dark brown grains. <b>E)</b> Emerged panicles with discolored grains and progressive necrotic stripes at maturity stage.</p

The pan-genome of rice-infecting <i>Pseudomonas</i> reveals high proportion of strain-specific genes.

<p><b>A)</b> Distribution of the 12,351 orthologous gene clusters according to strain-specific genes (only in one genome = 1), dispensable genes (in more than one genome = 2 ≥ x ≤ 7), and core genes (in all genomes = 8). <b>B</b>) Orthologous gene distribution in the <i>P</i>. <i>fuscovaginae</i> (blue) and <i>P</i>. <i>fuscovaginae</i>-like (orange) genomes depicting number of core, dispensable, and strain-specific gene clusters.</p

The core secretome of rice-infecting <i>Pseudomonas</i> has signatures of positive selection.

<p>Distribution of Ka/Ks ratio for 123 protein-coding genes, calculated with Yn00 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139256#pone.0139256.ref059" target="_blank">59</a>] method on rice-infecting <i>Pseudomonas</i>-all (black, <i>P</i>-all, n = 8), <i>P</i>. <i>fuscovaginae</i> (blue, <i>Pfv</i>, n = 5), and <i>P</i>. <i>fuscovaginae</i>-like (orange, <i>Pfv</i>-like, n = 3) datasets. All secreted protein selected on this graph have <i>p</i>-values ≤ 0.01.</p

The core secretome of rice-infecting <i>Pseudomonas</i> harbor unique genes.

<p>Conservation of core secreted proteins from rice-infecting <i>Pseudomonas</i> was evaluated in 79 closely related <i>Pseudomonas</i> genomes (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139256#pone.0139256.s008" target="_blank">S1 Table</a>). Columns were sorted by averaging the amino acid identity to identify conserved and species-specific proteins using threshold of 20%. Secreted proteins are also classified in: conserved in all <i>Pseudomonas</i>, non-conserved in all <i>Pseudomonas</i>, and <i>Pfv-</i> and <i>Pfv</i>-like-specific. Horizontal axis describes the number of species used for comparison. The heat map was visualized in CodaChrome [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139256#pone.0139256.ref040" target="_blank">40</a>]. Homology range values are shown in bottom right.</p