What can we learn from population genomics studies of Curtobacterium flaccumfaciens pv. flaccumfaciens, the cause of tan spot on mungbean?

The bacterium Curtobacterium flaccumfaciens pv. flaccumfaciens (Cff) is the cause of tan spot (in some regions known as ‘wilt’) on mungbean (Vigna radiata) and other legumes worldwide. The pathogen was first reported in mungbean paddocks in Queensland in 1984, and subsequently in New South Wales in 1986, causing yield losses of up to 25% in hot and dry seasons. No chemical control is available, and disease management relies on pathogen exclusion, through the use of clean seed, and deployment of moderately susceptible varieties. Breeding programs are currently working to incorporate better resistance into new mungbean varieties. The success of breeding programs depends on a thorough understanding of the genetic diversity and evolution of the pathogen population(s). This project was designed to elucidate the genotypic diversity of Cff population(s) and investigate sources of inoculum that contribute to tan spot epidemics in the northern grains region (Queensland and northern New South Wales). Whole genome re-sequencing of 100 Cff isolates detected moderate genotypic diversity, with a narrower genetic background compared to the global Cff population. One highly adapted clonal lineage was found to dominate the population with a frequency of 45%. This study showcases how population genomics studies can be used to test hypotheses relating to disease epidemiology and provide useful information for resistance breeding programs. The results provide insights on Cff population structure and epidemiology, and have direct application for breeding programs by providing a set of Cff isolates that represent the genetic diversity of the pathogen population(s) in the northern grains region

A broad look at charcoal rot in the Northern Region broadacre crops through soil sampling and in-crop surveys

Macrophomina phaseolina (Tassi) Goid. is a generalist soil-born pathogen, which is endemic to Australia. The pathogen has a broad host-range of both monocot and dicot plant species which include numerous weed and crop plant species (1, 2). The disease is most commonly identified with summer crops, e.g. soybean, sorghum, sunflower, maize and mungbean (3) and occurs most often when hot, dry conditions occur during the growing season. Current estimates predict that north-eastern Australia will become hotter and dryer as a result of climate change (4, 5). Thus, it is likely that conditions favouring the development of this disease will become more common in the future. However, to date, no work has been done to determine the extent of the pathogen’s presence in Australian soils, in-paddock spatial variability, or the occurrence of the disease as correlated with pathogen presence and population levels. In this paper, we present findings from soil sampling and end-of-season disease assessments in sorghum paddocks across northern New South Wales (NNSW), south eastern Queensland (SEQ) and central Queensland (CQ) during the 2016/17 and 2017/18 summer cropping seasons

Australia: A Continent Without Native Powdery Mildews? The First Comprehensive Catalog Indicates Recent Introductions and Multiple Host Range Expansion Events, and Leads to the Re-discovery of Salmonomyces as a New Lineage of the Erysiphales

In contrast to Eurasia and North America, powdery mildews (Ascomycota, Erysiphales) are understudied in Australia. There are over 900 species known globally, with fewer than currently 60 recorded from Australia. Some of the Australian records are doubtful as the identifications were presumptive, being based on host plant-pathogen lists from overseas. The goal of this study was to provide the first comprehensive catalog of all powdery mildew species present in Australia. The project resulted in (i) an up-to-date list of all the taxa that have been identified in Australia based on published DNA barcode sequences prior to this study; (ii) the precise identification of 117 specimens freshly collected from across the country; and (iii) the precise identification of 30 herbarium specimens collected between 1975 and 2013. This study confirmed 42 species representing 10 genera, including two genera and 13 species recorded for the first time in Australia. In Eurasia and North America, the number of powdery mildew species is much higher. Phylogenetic analyses of powdery mildews collected from Acalypha spp. resulted in the transfer of Erysiphe acalyphae to Salmonomyces, a resurrected genus. Salmonomyces acalyphae comb. nov. represents a newly discovered lineage of the Erysiphales. Another taxonomic change is the transfer of Oidium ixodiae to Golovinomyces. Powdery mildew infections have been confirmed on 13 native Australian plant species in the genera Acacia, Acalypha, Cephalotus, Convolvulus, Eucalyptus, Hardenbergia, Ixodia, Jagera, Senecio, and Trema. Most of the causal agents were polyphagous species that infect many other host plants both overseas and in Australia. All powdery mildews infecting native plants in Australia were phylogenetically closely related to species known overseas. The data indicate that Australia is a continent without native powdery mildews, and most, if not all, species have been introduced since the European colonization of the continent

First report of resistance to DMI fungicides in Australian populations of the wheat pathogen Zymoseptoria tritici

The erosion of demethylation inhibitor (DMI) fungicides effectiveness over time in Europe has been attributed to mutation sites in the 14α-demethylase encoded by the nuclear gene CYP51 (Cools and Fraaije 2013). These mutations first appeared in Europe in the 1990s, became widespread over the next 20 years, and were also recently reported in North America (Estep et al. 2015; Lucas et al. 2015). Zymoseptoria tritici has been present and causing disease on wheat (Triticum aestivum) in Australia for many decades and the use of fungicides for its control has become more common over the past 15 years. However, no significant changes in the field performance of fungicides have been noted by growers. To investigate possible undetected changes, we sequenced the CYP51 gene of 18 isolates cultured from wheat leaves collected in a commercial field on 1 July 2012 at Inverleigh, Victoria (–38.086743° S; 143.935783° E), and 3 isolates cultured from wheat leaves collected from trial plots on 22 August 2002 at Wagga Wagga,NSW (–35.044544° S; 147.316318° E). The nucleotide sequence of Z. tritici strain ST1 eburicol 14 alpha-demethylase (CYP51) gene (GenBank Accession No. AY730587.1) was used to design a set of three forward and three reverse sequencing primers across the known mutations. The sequence reads were assembled into contigs and checked for complete sequence. To generate an alignment of mature protein sequences, the mature protein sequence of ST1 (CYP51) gene was downloaded from NCBI to use as a reference. CYP51 nucleotide sequences were translated into amino acid sequences using all six possible frame shifts. These were aligned to the mature protein sequence of ST1 (CYP51) to identify the correct frame-shift sequence, enable the removal of intron sequences, and finally generate an amino acid alignment. Nucleotide and amino acid sequences are deposited in GenBank with Accession Nos. KT201543 to KT201563. Sixteen of the isolates from Victoria were carrying the Y137F mutation, one isolate carried the L50S-Y461S mutation, and one the L50S-S188N-N513K. The three isolates from NSW collected in 2002 contained no mutations compared with the reference accession. Fungicide sensitivities for propiconazole were determined at 50% effective concentrations (EC50) using rates of 100, 30, 10, 3, 1, 0.3, 0.1, 0.03, 0.01, 0.003, and 0.001 mg/liter, and the resistance factor (RF) of each isolate was calculated as fold change in the EC50 compared with that of the wild-type strains as per Cools et al. (2011), four replicates per isolate were performed. Results of the phenotypic assay of a subset of nine isolates (four Y137F mutants, one L50S-Y461S, one L50S-S188N-N513K, and three Wild-type) confirmed the elevated EC50 values for the mutations known to cause reduced sensitivity. The Y137F and L50S-Y461S mutants showed EC50 values of 1.08 and 1.03 mg/liter and RF levels in the range of 3.07 and 2.93. respectively, while the wild-type and L50S-S188N-N513K mutant had EC50 of 0.352 and 0.367 mg/liter, respectively. The EC50 values observed for the isolates appear higher than those found by Cools et al. (2011); however, the RF values are lower for both mutations. Further exploration of CYP51 mutations occurring in Z. tritici within the Australian cropping regions will be necessary to establish how widespread the Y137F and L50S-Y461S mutants are, and if others such as the S524T or the V136A, which are associated with higher levels of resistance to DMIs, are also present

Implications of bacterial contaminated seed lots and endophytic colonization by Pseudomonas fuscovaginae on rice establishment

The economic impact of seedborne bacterial diseases on rice production provides a major motivation for research on seed health. This paper reports on the endophytic growth of a rifampicin-marked strain of the seedborne rice pathogen Pseudomonas fuscovaginae. The bacterium was found in most tested seeds indicating that, even without visible discolouration, seed transmission is possible. Crushed discoloured seeds contained more bacterial cells than did non-crushed discoloured seeds. These bacteria were released during seed soaking, contaminating clean seed and lowering seed germination. Cells of a rifampicin-resistant strain of P. fuscovaginae, which had been inoculated onto rice seeds, were subsequently recovered from different growth stages and from different rice tissues, thereby indicating endophytic colonization. These results have implications for seedling establishment, as symptomless seeds do not assure disease-free seeds, and the presence of seedborne bacteria results in poor germination and poor seedling establishment. Elimination of seedborne bacteria by soaking in sodium hypochlorite can increase seed germination. This could be used in developing control strategies, and, if practised regularly, reduce entry of seedborne disease- causing organisms into crops, resulting in lower disease pressure

Australia: A Continent Without Native Powdery Mildews? The First Comprehensive Catalog Indicates Recent Introductions and Multiple Host Range Expansion Events, and Leads to the Re-discovery of Salmonomyces as a New Lineage of the Erysiphales

In contrast to Eurasia and North America, powdery mildews (Ascomycota, Erysiphales) are understudied in Australia. There are over 900 species known globally, with fewer than currently 60 recorded from Australia. Some of the Australian records are doubtful as the identifications were presumptive, being based on host plant-pathogen lists from overseas. The goal of this study was to provide the first comprehensive catalog of all powdery mildew species present in Australia. The project resulted in (i) an up-to-date list of all the taxa that have been identified in Australia based on published DNA barcode sequences prior to this study; (ii) the precise identification of 117 specimens freshly collected from across the country; and (iii) the precise identification of 30 herbarium specimens collected between 1975 and 2013. This study confirmed 42 species representing 10 genera, including two genera and 13 species recorded for the first time in Australia. In Eurasia and North America, the number of powdery mildew species is much higher. Phylogenetic analyses of powdery mildews collected from Acalypha spp. resulted in the transfer of Erysiphe acalyphae to Salmonomyces, a resurrected genus. Salmonomyces acalyphae comb. nov. represents a newly discovered lineage of the Erysiphales. Another taxonomic change is the transfer of Oidium ixodiae to Golovinomyces. Powdery mildew infections have been confirmed on 13 native Australian plant species in the genera Acacia, Acalypha, Cephalotus, Convolvulus, Eucalyptus, Hardenbergia, Ixodia, Jagera, Senecio, and Trema. Most of the causal agents were polyphagous species that infect many other host plants both overseas and in Australia. All powdery mildews infecting native plants in Australia were phylogenetically closely related to species known overseas. The data indicate that Australia is a continent without native powdery mildews, and most, if not all, species have been introduced since the European colonization of the continent