Heart rot of Australian pineapples caused by Dickeya zeae

Pineapple plants (hybrid MD2) with bacterial heart rot were detected in a commercial plantation at Glasshouse Mountains, Queensland, in November 2015. The bacterial strain BRIP64263 isolated from infected tissue was shown to be a Gram negative soft-rotting bacterium capable of growth at 41 ºC, and based on its culture properties was provisionally identified as Dickeya. This strain was compared with other putative Dickeya strains affecting banana (BRIP64262) and potato (BRIP29490). Sequence analysis of the recombinase A genes of the pineapple strain placed it in phylotype I of D. zeae, whereas the banana strain was placed in phylotype II. This was confirmed by sequence comparisons for the phosphofructose kinase, RNA polymerase and aconitase genes which showed that the pineapple strain BRIP64263 is distinct from other strains that infect pineapples and other hosts in Australia and overseas. Furthermore, phylogenetic analysis of the replication initiation factor gene showed that strains affecting pineapples were distributed among both phylotypes of D. zeae, indicating multiple acquisitions or opportunistic infections of pineapple from this group of pathogens. The potato isolate, BRIP29490, was shown to be Rahnella aquatica, and is not likely to be pathogenic. It is not known whether the new isolate represents an incursion or whether it has long been associated with pineapples in Australia. Further study is required to determine the epidemiological characteristics of this strain, and what threat it poses to Australian pineapple production

Heart rot of Australian pineapples caused by Dickeya zeae

Pineapple plants (hybrid MD2) with bacterial heart rot were detected in a commercial plantation at Glasshouse Mountains, Queensland, in November 2015. The bacterial strain BRIP64263 isolated from infected tissue was shown to be a Gram negative soft-rotting bacterium capable of growth at 41 ºC, and based on its culture properties was provisionally identified as Dickeya. This strain was compared with other putative Dickeya strains affecting banana (BRIP64262) and potato (BRIP29490). Sequence analysis of the recombinase A genes of the pineapple strain placed it in phylotype I of D. zeae, whereas the banana strain was placed in phylotype II. This was confirmed by sequence comparisons for the phosphofructose kinase, RNA polymerase and aconitase genes which showed that the pineapple strain BRIP64263 is distinct from other strains that infect pineapples and other hosts in Australia and overseas. Furthermore, phylogenetic analysis of the replication initiation factor gene showed that strains affecting pineapples were distributed among both phylotypes of D. zeae, indicating multiple acquisitions or opportunistic infections of pineapple from this group of pathogens. The potato isolate, BRIP29490, was shown to be Rahnella aquatica, and is not likely to be pathogenic. It is not known whether the new isolate represents an incursion or whether it has long been associated with pineapples in Australia. Further study is required to determine the epidemiological characteristics of this strain, and what threat it poses to Australian pineapple production

Draft Genomes of Six Philippine Erwinia mallotivora Isolates: Comparative Genomics and Genome-Wide Analysis of Candidate Secreted Proteins

Erwinia mallotivora is one of the most important bacterial pathogens of papaya and causes bacterial crown rot disease in the Philippines. In this paper, we present the draft genome sequences of six Philippine E. mallotivora isolates to provide insights into the genes involved in host–pathogen interactions and compare their genomes to other Erwinia species. The genomes were sequenced using Illumina Miseq platform. The draft whole-genome assemblies of the E. mallotivora isolates are composed of 36–64 contigs with N50 value ranging from 285 to 332 kbp and cover 96.2–100% of the estimated genome size. Structural genome annotation of these assemblies has predicted 4489–4749 protein-coding genes. Comparative genomic analysis using orthologous gene sets led to the identification of conserved genes within the genus and species-specific gene orthologous groups, which collectively provide a baseline for functional genomic studies to determine genes affecting virulence and host specificity. Secreted proteins of E. mallotivora were also predicted and characterized to unravel putative genes involved in plant–pathogen interactions. This study provides the first draft whole-genome sequences of Philippine isolates of E. mallotivora, thus expanding the genomic knowledge for this species in comparison with other members of the genus Erwinia

Draft Genomes of Six Philippine Erwinia mallotivora Isolates: Comparative Genomics and Genome-Wide Analysis of Candidate Secreted Proteins

Erwinia mallotivora is one of the most important bacterial pathogens of papaya and causes bacterial crown rot disease in the Philippines. In this paper, we present the draft genome sequences of six Philippine E. mallotivora isolates to provide insights into the genes involved in host–pathogen interactions and compare their genomes to other Erwinia species. The genomes were sequenced using Illumina Miseq platform. The draft whole-genome assemblies of the E. mallotivora isolates are composed of 36–64 contigs with N50 value ranging from 285 to 332 kbp and cover 96.2–100% of the estimated genome size. Structural genome annotation of these assemblies has predicted 4489–4749 protein-coding genes. Comparative genomic analysis using orthologous gene sets led to the identification of conserved genes within the genus and species-specific gene orthologous groups, which collectively provide a baseline for functional genomic studies to determine genes affecting virulence and host specificity. Secreted proteins of E. mallotivora were also predicted and characterized to unravel putative genes involved in plant–pathogen interactions. This study provides the first draft whole-genome sequences of Philippine isolates of E. mallotivora, thus expanding the genomic knowledge for this species in comparison with other members of the genus Erwinia

Phylotypes of the potato bacterial wilt pathogen in the Philippines and their relationship to pathogen aggressiveness

Three hundred seventy-two Ralstonia solanacearum isolates were collected from potato fields, in the Philippines, and characterized based on phylotypes, distribution and aggressiveness to host plants. Two major genetic group were identified: Phylotype I (Asiaticum), which were predominant in the southern region (Bukidnon), and Phylotype II (Americanum), found mainly in the northern region (Benguet). Phylotypes I and II were both pathogenic to tomato and potato host plants, but Phylotype I induced significantly earlier wilting symptoms to tomato and potato than Phylotype II (P = 0.03 – <0.01). No correlation was found between elevation and phylotype distribution (coefficient = 0.03–0.22). Based on the current taxonomic classification of R. solanacearum species complex, R. pseudosolanacearum and R. solanacearum cause potato bacterial wilt in the Philippines. Implications for quarantine regulations and breeding programs are discussed

Phylotypes of the potato bacterial wilt pathogen in the Philippines and their relationship to pathogen aggressiveness

Three hundred seventy-two Ralstonia solanacearum isolates were collected from potato fields, in the Philippines, and characterized based on phylotypes, distribution and aggressiveness to host plants. Two major genetic group were identified: Phylotype I (Asiaticum), which were predominant in the southern region (Bukidnon), and Phylotype II (Americanum), found mainly in the northern region (Benguet). Phylotypes I and II were both pathogenic to tomato and potato host plants, but Phylotype I induced significantly earlier wilting symptoms to tomato and potato than Phylotype II (P = 0.03 – <0.01). No correlation was found between elevation and phylotype distribution (coefficient = 0.03–0.22). Based on the current taxonomic classification of R. solanacearum species complex, R. pseudosolanacearum and R. solanacearum cause potato bacterial wilt in the Philippines. Implications for quarantine regulations and breeding programs are discussed

Evaluation of inoculation techniques to screen for bacterial crown rot resistance in different breeding lines of carica papaya

Bacterial crown rot (BCR) is considered as the most destructive disease of papaya in the Philippines. The use of resistant cultivars with acceptable horticultural traits remains the most effective and economical strategy to manage the disease. This study was conducted to develop a rapid and effective inoculation technique that could be used to screen for BCR resistance in a papaya breeding program. Furthermore, papaya breeding lines and germplasm collections were evaluated using the inoculation technique to identify promising materials that can either be released as commercial cultivars or used as parental lines. Different isolates of Erwinia mallotivora collected from Luzon and Mindanao, Philippines were tested for patogenicity in papaya seedlings cv. ‘Solo’. The most aggressive and virulent isolate was identified and used in the evaluation of various inoculation techniques. The leaf abrasion technique proved to be the most effective of the five inoculation techniques that were assessed, namely: a) stem injection, b) pricking, c) leaf clipping, d) drenching and e) leaf abrasion. This technique was able to differentiate levels of resistance/susceptibility of the different breeding lines and cultivars. Fifty-nine of the eighty parentals/ inbreds/lines that exhibited resistance in the field with high BCR incidence were further evaluated using the leaf abrasion technique in the screenhouse. Of these, nine parental lines, six inbred lines and five accessions exhibited resistance to BCR. These materials are now being grown in the field for horticultural trait evaluation. © 2017, Edizioni ETS. All rights reserved

Guide to understanding and managing bacterial diseases affecting Australian vegetable crops

Bacterial diseases cause significant impacts to vegetable production nationally. Disease outbreaks are sporadic and influenced substantially by weather conditions. This guide provides information on the most common bacterial diseases in Australian vegetables, how to identify them and what management is available for their control. Bacterial diseases can affect all production systems from open field to high-tech protected cropping. This disease guide covers bacteria already present in Australia. There are many other bacterial diseases present overseas which could enter Australia. It is important to be aware of these diseases and send samples for diagnoses if you suspect a new disease has arrived. For more information on exotic diseases please visit the Plant Health Australia website https://www.planthealthaustralia.com.au/)

A metagenomic investigation of phytoplasma diversity in Australian vegetable growing regions

In this study, metagenomic sequence data was used to investigate the phytoplasma taxonomic diversity in vegetable-growing regions across Australia. Metagenomic sequencing was performed on 195 phytoplasma-positive samples, originating either from historic collections (n=46) or during collection efforts between January 2015 and June 2022 (n=149). The sampled hosts were classified as crop (n=155), weed (n=24), ornamental (n=7), native plant (n=6), and insect (n=3) species. Most samples came from Queensland (n=78), followed by Western Australia (n=46), the Northern Territory (n=32), New South Wales (n=17), and Victoria (n=10). Of the 195 draft phytoplasma genomes, 178 met our genome criteria for comparison using an average nucleotide identity approach. Ten distinct phytoplasma species were identified and could be classified within the 16SrII, 16SrXII (PCR only), 16SrXXV, and 16SrXXXVIII phytoplasma groups, which have all previously been recorded in Australia. The most commonly detected phytoplasma taxa in this study were species and subspecies classified within the 16SrII group (n=153), followed by strains within the 16SrXXXVIII group (‘Ca. Phytoplasma stylosanthis’; n=6). Several geographic- and host-range expansions were reported, as well as mixed phytoplasma infections of 16SrII taxa and ‘Ca. Phytoplasma stylosanthis’. Additionally, six previously unrecorded 16SrII taxa were identified, including five putative subspecies of ‘Ca. Phytoplasma australasiaticum’ and a new putative 16SrII species. PCR and sequencing of the 16S rRNA gene was a suitable triage tool for preliminary phytoplasma detection. Metagenomic sequencing, however, allowed for higher-resolution identification of the phytoplasmas, including mixed infections, than was afforded by only direct Sanger sequencing of the 16S rRNA gene. Since the metagenomic approach theoretically obtains sequences of all organisms in a sample, this approach was useful to confirm the host family, genus, and/or species. In addition to improving our understanding of the phytoplasma species that affect crop production in Australia, the study also significantly expands the genomic sequence data available in public sequence repositories to contribute to phytoplasma molecular epidemiology studies, revision of taxonomy, and improved diagnostics