Genome analyses of an aggressive and invasive lineage of the Irish potato famine pathogen.

Pest and pathogen losses jeopardise global food security and ever since the 19(th) century Irish famine, potato late blight has exemplified this threat. The causal oomycete pathogen, Phytophthora infestans, undergoes major population shifts in agricultural systems via the successive emergence and migration of asexual lineages. The phenotypic and genotypic bases of these selective sweeps are largely unknown but management strategies need to adapt to reflect the changing pathogen population. Here, we used molecular markers to document the emergence of a lineage, termed 13_A2, in the European P. infestans population, and its rapid displacement of other lineages to exceed 75% of the pathogen population across Great Britain in less than three years. We show that isolates of the 13_A2 lineage are among the most aggressive on cultivated potatoes, outcompete other aggressive lineages in the field, and overcome previously effective forms of plant host resistance. Genome analyses of a 13_A2 isolate revealed extensive genetic and expression polymorphisms particularly in effector genes. Copy number variations, gene gains and losses, amino-acid replacements and changes in expression patterns of disease effector genes within the 13_A2 isolate likely contribute to enhanced virulence and aggressiveness to drive this population displacement. Importantly, 13_A2 isolates carry intact and in planta induced Avrblb1, Avrblb2 and Avrvnt1 effector genes that trigger resistance in potato lines carrying the corresponding R immune receptor genes Rpi-blb1, Rpi-blb2, and Rpi-vnt1.1. These findings point towards a strategy for deploying genetic resistance to mitigate the impact of the 13_A2 lineage and illustrate how pathogen population monitoring, combined with genome analysis, informs the management of devastating disease epidemics.

Biocontrol agents promote growth of potato pathogens, depending on environmental conditions.

There is a pressing need to understand and optimize biological control so as to avoid over-reliance on the synthetic chemical pesticides that can damage environmental and human health. This study focused on interactions between a novel biocontrol-strain, Bacillus sp. JC12GB43, and potato-pathogenic Phytophthora and Fusarium species. In assays carried out in vitro and on the potato tuber, the bacterium was capable of near-complete inhibition of pathogens. This Bacillus was sufficiently xerotolerant (water activity limit for growth = 0.928) to out-perform Phytophthora infestans (~0.960) and challenge Fusarium coeruleum (~0.847) and Fusarium sambucinum (~0.860) towards the lower limits of their growth windows. Under some conditions, however, strain JC12GB43 stimulated proliferation of the pathogens: for instance, Fusarium coeruleum growth-rate was increased under chaotropic conditions in vitro (132 mM urea) by >100% and on tubers (2-M glycerol) by up to 570%. Culture-based assays involving macromolecule-stabilizing (kosmotropic) compatible solutes provided proof-of-principle that the Bacillus may provide kosmotropic metabolites to the plant pathogen under conditions that destabilize macromolecular systems of the fungal cell. Whilst unprecedented, this finding is consistent with earlier reports that fungi can utilize metabolites derived from bacterial cells. Unless the antimicrobial activities of candidate biocontrol strains are assayed over a full range of field-relevant parameters, biocontrol agents may promote plant pathogen infections and thereby reduce crop yields. These findings indicate that biocontrol activity, therefore, ought to be regarded as a mode-of-behaviour (dependent on prevailing conditions) rather than an inherent property of a bacterial strain.

Draft genome sequences of seven isolates of Phytophthora ramorum EU2 from Northern Ireland.

Here we present draft-quality genome sequence assemblies for the oomycete Phytophthora ramorum genetic lineage EU2. We sequenced genomes of seven isolates collected in Northern Ireland between 2010 and 2012. Multiple genome sequences from P. ramorum EU2 will be valuable for identifying genetic variation within the clonal lineage that can be useful for tracking its spread.

The effect of foliar application of phosphonate formulations on the susceptibility of potato tubers to late blight.

Foliar sprays of potato plants with phosphonic acid (partially neutralised with potassium hydroxide to pH 6.4) substantially reduced infection of the tubers by Phytophthora infestans, the cause of late blight, in glasshouse and field experiments over a 4-year period. Healthy tubers of blight-susceptible cultivars removed from treated plants and artificially inoculated by spraying with sporangial/zoospore suspensions of P infestans did not develop disease symptoms, demonstrating that the phosphonate applications had directly reduced the susceptibility of tubers to infection, probably as a result of translocation into tuber tissue. In contrast, foliar application of fosetyl-aluminium did not significantly reduce tuber blight development following inoculation. Five to six sprays of partially neutralised phosphonic acid (2 kg ha-1) applied at 10-14 day intervals resulted in the least tuber infection, but such a treatment regime may not be economic. In trials where the effect of timing and rate of application of 2-4 kg phosphonic acid ha-1 was examined, a single treatment of 4 kg ha-1 applied mid- or late-season proved the most effective. A spray programme in which one or two applications of phosphonic acid are combined with use of a non-systemic or systemic fungicide to enhance foliar protection offers the possibility of controlling both foliage and tuber blight and could have a major impact in reducing overwinter survival of P infestans in tubers.

Population changes in Phytophthora infestans in Taiwan associated with the appearance of resistance to metalaxyl.

In recent years, late blight, caused by Phytophthora infestans (Mont) De Bary, has increased in severity in many parts of the world, and this has been associated with migrations which have introduced new, arguably more aggressive, populations of the pathogen. In Taiwan, late blight has been endemic on outdoor tomato crops grown in the highlands since the early 1900s, but recent epidemics have been more damaging. To ascertain the present status of the Taiwanese population of P infestans, 139 isolates of the pathogen collected and maintained by the Asian Vegetable Research and Development Center (AVRDC) were characterized using mating type, metalaxyl sensitivity, allozyme genotype, mitochondrial haplotype and RFLP fingerprinting. Up to 1997, all isolates were found to belong to the old clonal lineage of P infestans (US-1 and variants), but in isolates from 1998 a new genotype appeared, and by 2000 this had apparently completely displaced the old population. This new genotype was an A1 mating type and has the dilocus allozyme genotype 100/100/111, 100/100 for the loci coding for glucose-6-phosphate isomerase and peptidase, respectively. These characters, together with RG57 fingerprinting, indicated that these isolates belonged to the US-11 clonal lineage, a minority (11%) being a previously unreported variant of US-11. Whereas metalaxyl-resistant isolates were not detected in the old population, 96% of the new genotypes proved resistant, with the remainder being intermediate in sensitivity. It may be inferred from this sudden, marked change in the characteristics of the Taiwanese P infestans that a new population of the pathogen was introduced around 1997-98 and that this may well have already been metalaxyl-resistant when it arrived, although a role for in situ selection cannot be excluded.

European Union policy on pesticides: implications for agriculture in Ireland.

European Community (EC) legislation has limited the availability of pesticide active substances used in effective plant protection products. The Pesticide Authorisation Directive 91/414/EEC introduced the principle of risk assessment for approval of pesticide active substances. This principle was modified by the introduction of Regulation (EC) 1107/2009, which applies hazard, the intrinsic toxicity of the active substance, rather than risk, the potential for hazard to occur, as the approval criterion. Potential impacts of EC pesticide legislation on agriculture in Ireland are summarised. While these will significantly impact on pesticide availability in the medium to long term, regulations associated with water quality (Water Framework Directive 2000/60/EC and Drinking Water Directive 1998/83/EC) have the potential to restrict pesticide use more immediately, as concerns regarding public health and economic costs associated with removing pesticides from water increase. This rationale will further reduce the availability of effective pesticide active substances, directly affecting crop protection and increasing pesticide resistance within pest and disease populations. In addition, water quality requirements may also impact on important active substances used in plant protection in Ireland. The future challenge for agriculture in Ireland is to sustain production and profitability using reduced pesticide inputs within a framework of integrated pest management.

Genome-wide sequencing of Phytophthora lateralis reveals genetic variation among isolates from Lawson cypress (Chamaecyparis lawsoniana) in Northern Ireland.

Phytophthora lateralis is a fungus-like (oomycete) pathogen of trees in the family Cupressaceae, including Chamaecyparis lawsoniana (Lawson cypress or Port Orford cedar). Known in North America since the 1920s, presumably having been accidentally introduced from its assumed East Asian centre of origin, until recently, this pathogen has not been identified causing disease in Europe except for a few isolated outbreaks. However, since 2010, there have been several reports of infection of C. lawsoniana by P. lateralis in the United Kingdom, including Northern Ireland. We sequenced the genomes of four isolates of P. lateralis from two sites in Northern Ireland in 2011. Comparison with the closely related tree and shrub pathogen P. ramorum (cause of ramorum disease of larch and other species in the UK) shows that P. lateralis shares 91.47% nucleotide sequence identity over the core conserved compartments of the genome. The genomes of the four Northern Ireland isolates are almost identical, but we identified several single-nucleotide polymorphisms (SNPs) that distinguish between isolates, thereby presenting potential molecular markers of use for tracking routes of spread and in epidemiological studies. Our data reveal very low rates of heterozygosity (compared with P. ramorum), consistent with inbreeding within this P. lateralis population.