Ecological Genomics and Epidemiology

The huge amount of genomic data now becoming available offers both opportunities and challenges for epidemiologists. In this “preview” of likely developments as the field of ecological genomics evolves and merges with epidemiology, we discuss how epidemiology can use new information about genetic sequences and gene expression to form predictions about epidemic features and outcomes and for understanding host resistance and pathogen evolution. DNA sequencing is now complete for some hosts and several pathogens. Microarrays make it possible to measure gene expression simultaneously for thousands of genes. These tools will contribute to plant disease epidemiology by providing information about which resistance or pathogenicity genes are present in individuals and populations, what genes other than those directly involved in resistance and virulence are important in epidemics, the role of the phenotypic status of hosts and pathogens, and the role of the status of the environmental metagenome. Conversely, models of group dynamics supplied by population biology and ecology may be used to interpret gene expression within individual organisms and in populations of organisms. Genomic tools have great potential for improving understanding of resistance gene evolution and the durability of resistance. For example, DNA sequence analysis can be used to evaluate whether an arms race model of co-evolution is supported. Finally, new genomic tools will make it possible to consider the landscape ecology of epidemics in terms of host resistance both as determined by genotype and as expressed in host phenotypes in response to the biotic and abiotic environment. Host phenotype mixtures can be modeled and evaluated, with epidemiological predictions based on phenotypic characteristics such as physiological age and status in terms of induced systemic resistance or systemic acquired resistance.     

Host range ofCercospora piaropi andAcremonium zonatum, potential fungal biocontrol agents for waterhyacinth in Mexico

The host ranges ofCercospora piaropi andAcremonium zonatum, fungi native to Mexico and pathogens of waterhyacinth(Eichhornia crassipes), were evaluated using 31 plant species (some with several cultivars tested) representing 22 families of economic and ecological importance. The results showed that only waterlettuce(Pistia stratiotes), another abundant weed in Mexico, was infected byC. piaropi. The use of those pathogens in the biological control of waterhyacinth would not be expected to affect plants of economic and ecological importance in Mexico.     

Importance of the life cycle in sympatric host race formation and speciation of pathogens

ABSTRACT Numerous morphological species of pathogenic fungi have been shown to actually encompass several genetically isolated lineages, often specialized on different hosts and, thus, constituting host races or sibling species. In this article, we explore theoretically the importance of some aspects of the life cycle on the conditions of sympatric divergence of host races, particularly in fungal plant pathogens. Because the life cycles classically modeled by theoreticians of sympatric speciation correspond to those of free-living animals, sympatric divergence of host races requires the evolution of active assortative mating or of active host preference if mating takes place on the hosts. With some particular life cycles with restricted dispersal between selection on the host and mating, we show that divergence can occur in sympatry and lead to host race formation, or even speciation, by a mere process of specialization, with strong divergent adaptive selection. Neither active assortative mating nor active habitat choice is required in these cases, and this may explain why the phylo-genetic species concept seems more appropriate than the biological species concept in these organisms.     

Bacterial pathogens of Gramineae: systematic review and assessment of quarantine status for the EPPO region1

Bacterial pathogens of Gramineae principally belong to the genera Clavibacter, Erwinia, Pseudomonas and Xanthomonas, the last being the most important. A general survey of these pathogens is given, with details on nomenclature, symptoms, natural host range, geographical distribution and potential quarantine significance for the EPPO region. The status of Xanthomonas campestris pathovars with overlapping broad and narrow host ranges on Gramineae is discussed. It is proposed to adopt a broad concept of X. campestris pv. translucens and evaluate it as a potential quarantine hazard for the EPPO region.     

An Isolate of Alternaria alternata That Is Pathogenic to Both Tangerines and Rough Lemon and Produces Two Host-Selective Toxins, ACT- and ACR-Toxins

ABSTRACT Two different pathotypes of Alternaria alternata cause Alternaria brown spot of tangerines and Alternaria leaf spot of rough lemon. The former produces the host-selective ACT-toxin and the latter produces ACR-toxin. Both pathogens induce similar symptoms on leaves or young fruits of their respective hosts, but the host ranges of these pathogens are distinct and one pathogen can be easily distinguished from another by comparing host ranges. We isolated strain BC3-5-1-OS2A from a leaf spot on rough lemon in Florida, and this isolate is pathogenic on both cv. Iyokan tangor and rough lemon and also produces both ACT-toxin and ACR-toxin. Isolate BC3-5-1-OS2A carries both genomic regions, one of which was known only to be present in ACT-toxin producers and the other was known to exist only in ACR-toxin producers. Each of the genomic regions is present on distinct small chromosomes, one of 1.05 Mb and the other of 2.0 Mb. Alternaria species have no known sexual or parasexual cycle in nature and populations of A. alternata on citrus are clonal. Therefore, the ability to produce both toxins was not likely acquired through meiotic or mitotic recombination. We hypothesize that a dispensable chromosome carrying the gene cluster controlling biosynthesis of one of the host-selective toxins was transferred horizontally and rearranged by duplication or translocation in another isolate of the fungus carrying genes for biosynthesis of the other host-selective toxin.     

Citrus Black Rot is Caused by Phylogenetically Distinct Lineages of Alternaria alternata

ABSTRACT Phylogenetic analysis revealed that isolates of Alternaria alternata causing black rot of citrus were associated with six well-supported evolutionary lineages. Isolates recovered from brown spot lesions on Minneola tangelo, leaf spot lesions on rough lemon, and healthy citrus tissue and noncitrus hosts were related closely to isolates from black-rotted fruit. Phylogenies estimated independently from DNA sequence data from an endopolygalacturonase gene (endoPG) and two anonymous regions of the genome (OPA1-3 and OPA2-1) had similar topologies, and phylogenetic analysis was performed on the combined data set. In the combined phylogeny, isolates from diverse ecological niches on citrus and noncitrus hosts were distributed in eight clades. Isolates from all lineages, regardless of ecological or host association, caused black rot in fruit inoculation assays, demonstrating that small-spored Alternaria isolates associated with different ecological niches on citrus and other plant hosts are potential black rot pathogens. These data also indicated that the fungi associated with black-rotted fruit do not form a natural evolutionary group distinct from other Alternaria pathogens and saprophytes associated with citrus. The use of the name A. citri to describe fungi associated with citrus black rot is not justified and it is proposed that citrus black rot fungi be referred to as A. alternata.     

Aggressiveness and its role in the adaptation of plant pathogens

Aggressiveness, the quantitative component of pathogenicity, and its role in the adaptation of plant pathogens are still insufficiently investigated. Using mainly examples of biotrophic and necrotrophic fungal pathogens of cereals and Phytophthora infestans on potato, the empirical knowledge on the nature of aggressiveness components and their evolution in response to host and environment is reviewed. Means of measuring aggressiveness components are considered, as well as the sources of environmental variance in these traits. The adaptive potential of aggressiveness components is evaluated by reviewing evidence for their heritability, as well as for constraints on their evolution, including differential interactions between host and pathogen genotypes and trade-offs between components of pathogenicity. Adaptations of pathogen aggressiveness components to host and environment are analysed, showing that: (i) selection for aggressiveness in pathogen populations can be mediated by climatic parameters; (ii) global population changes or remarkable population structures may be explained by variation in aggressiveness; and (iii) selection for quantitative traits can influence pathogen evolution in agricultural pathosystems and can result in differential adaptation to host cultivars, sometimes leading to erosion of quantitative resistance. Possible links with concepts in evolutionary ecology are suggested.     

Host matrix has major impact on the morphology of <Emphasis Type="Italic">Pseudoperonospora cubensis</Emphasis>

Oomycetes contain some of the economically most important pathogens of flowering plants. Most have a rather narrow host range, often being restricted to single host species. In downy mildews and other obligate biotrophic plant parasites, like powdery mildews and rusts, delimitating species on grounds of morphological characteristics is often hardly possible and thus often based on only subtle differences. This has led to the widespread application of a broad species concept for these organisms. Consequently, despite the fact that morphological differences were reported for Pseudoperonospora cubensis from different host species, the corresponding new pathogen species were not accepted as being independent, and the host range of Pseudoperonospora cubensis is reported to encompass more than 50 host species in the Cucurbitaceae in temperate to tropical climates. However, recent studies have reported narrow host ranges for other downy mildew genera and advocated a narrow species concept. Here, we report successful colonisation of five different tribes of the Cucurbitaceae by a strain of Pseudoperonospora cubensis and demonstrate that the host matrix has a major impact on the morphology of the pathogen. On the basis of five morphological criteria significant differences could be found for all hosts. These differences were more pronounced in phylogenetically unrelated than in related hosts. Our results provide evidence for a broad host range of Pseudoperonospora cubensis and demonstrate that species delimitation based on morphological characters is not feasible in Pseudoperonospora on Cucurbitaceae. Also in other biotrophic plant pathogens, the situation could be similar, thus necessitating thorough morphological, molecular phylogenetic and cross inoculation experiments for species recognition.     

Stepwise Evolution of Races in Fusarium oxysporum f. sp. ciceris Inferred from Fingerprinting with Repetitive DNA Sequences

ABSTRACT Plant pathogens often exhibit variation in virulence, the ability to cause disease on host plants with specific resistance, evident from the diversity of races observed within pathogen species. The evolution of races in asexual fungal pathogens has been hypothesized to occur in a stepwise fashion, in which mutations to virulence accumulate sequentially in clonal lineages, resulting in races capable of overcoming multiple host plant resistance genes or multiple resistant cultivars. In this study, we demonstrate a simple stepwise pattern of race evolution in Fusarium oxysporum f. sp. ciceris, the fungus that causes Fusarium wilt of chickpeas. The inferred intraspecific phylogeny of races in this fungus, based on DNA fingerprinting with repetitive sequences, shows that each of the eight races forms a monophyletic lineage. By mapping virulence to each differential cultivar (used for defining races) onto the inferred phylogeny, we show that virulence has been acquired in a simple stepwise pattern, with few parallel gains or losses. Such a clear pattern of stepwise evolution of races, to our knowledge, has not been demonstrated previously for other pathogens based on analyses of field populations. We speculate that in other systems the stepwise pattern is obscured by parallel gains or losses of virulence caused by higher mutation rates and selection by widespread deployment of resistant cultivars. Although chickpea cultivars resistant to Fusarium wilt are available, their deployment has not been extensive and the stepwise acquisition of virulence is still clearly evident.     

Host Range of Tropical and Sub-tropical Isolates of Polymyxa graminis

The host range of Polymyxa graminis isolates originating from peanut clump-infested areas in India (Andhra Pradesh and Rajasthan), Pakistan and Senegal was studied on monocotyledonous and dicotyledonous cultivated species, using known quantities of sporosori as inoculum. Profuse multiplication occurred only on some graminaceous species, but the various isolates showed different host specificity. All the isolates produced high infection on sorghum and pearl millet, and all but one isolate from Rajasthan infected maize. Wheat, rye and barley were susceptible to some of the tested isolates. The isolates from Rajasthan and Pakistan produced moderate to severe infection on at least one of these species. On rice, groundnut and sugar beet, only traces of infection by some isolates were detected, whereas no infection was observed on mustard and sunflower. Differences of susceptibility in Pennisetum spp. and Sorghum spp. were demonstrated. The variations in host specificity among isolates from peanut clump-infested areas may result from an adaptation of P. graminis populations to various biotopes. The implications of these results for the management of peanut clump disease are discussed. A comparison of the host ranges of isolates of P. graminis and P. betae from temperate areas demonstrated that distinct types of Polymyxa might be identified based on their relative ability to multiply on susceptible species. Nevertheless, overlapping in the host ranges among the different Polymyxa types, characterised by distinct ecological and genomic features, raises doubts about the host range as a classification criterion for the Polymyxa genus.     

Further observations on the use of fungicides to control Peronosclerospora sacchari (T. Miyake) Shirai and K. Hara in sugarcane in Papua New Guinea

Abstract

Many biologists perceive organisms as constantly evolving and therefore consider the host plant ranges of biological control agents as labile. Host plant ranges are thus likely to undergo adaptive change should environmental conditions change, for example following successful biological control. As a consequence, the introduction of biological control agents against weeds is considered by many to be an inherently unsafe practice with non‐target plants at risk of attack. However, despite the introduction of over 600 insect species from one geographic region to another for biological weed control during this century, there are relatively few documented cases of changes in host plant range. Purported instances are discussed in relation to behavioural and genetic concepts. It is concluded that apparent additions to the host range can, in all of the cases examined, be explained in terms of established behavioural concepts of pre‐adaptation, threshold change resulting from host deprivation, and effects of experience (learning). The inappropriateness of the often‐used term host shift’ to describe these cases is demonstrated, and it is concluded that evidence from biological weed control contradicts some aspects of ecological and evolutionary theory.     

Seeing the forest for the trees: Use of phages to treat bacterial tree diseases

Trees and woody plants can be attacked by many pests and pathogens either individually or as polymicrobial infections. In particular, infections caused by tree-specific bacterial pathogens have become more common during the last decade, causing serious concern for important tree and woody plant species in horticulture, urban environments, and forests. For example, Xylella and Pseudomonas bacteria are causing significant economic and ecological devastation throughout Europe in olive, cherry, and other stone fruits, mainly because of lack of efficient control methods and the emergence of bacterial resistance to traditional antimicrobial compounds such as copper and antibiotics. Hence, there is an urgent need for innovative approaches to tackle bacterial plant diseases. One way to achieve this could be through the application of biological control, which offers a more environmentally friendly and targeted approach for pathogen management. This review will explore recent advances in use of pathogen-specific viruses, bacteriophages (or phages), for the biocontrol of bacterial tree diseases. Phages are an important component of plant microbiomes and are increasingly studied in plant pathogen control due to their highly specific host ranges and ability to selectively kill only the target pathogenic bacteria. However, their use still poses several challenges and limitations, especially in terms of managing the bacterial diseases of long-lived trees. A particular insight will be given into phage research focusing on controlling Pseudomonas syringae pathovars, Erwinia amylovora, Xanthomonas species, Ralstonia solanacearum, and Agrobacterium tumefaciens. Recent milestones, current challenges, and future avenues for phage therapy in the management of tree diseases are discussed.     

Evolutionary analysis of herbivorous insects in natural and agricultural environments

Herbivorous insects offer a remarkable example of the biological diversity that formed the foundation for Darwin's theory of evolution by natural selection. The ability of insects to evolve resistance rapidly to insecticides and host‐plant resistance present a continual challenge for pest management. This paper considers the manner in which genetic constraints, host‐plant availability and trade‐offs affect the evolution of herbivorous insects in natural and agricultural environments, and the extent to which lessons learned from studying natural systems may be applied to improve insect resistance management in agricultural systems. Studies on the genetic architecture of adaptation by herbivores to host plants and to insecticides are reviewed. The genetic basis of resistance is an important component of simulation models that predict the evolution of resistance. These models often assume monogenic resistance, but available data suggest that this assumption may be overly narrow and that modeling of resistance as oligogenic or polygenic may be more appropriate. As omics (e.g. genomics and proteomics) technologies become more accessible, a better understanding of the genetic basis of resistance will be possible. Trade‐offs often accompany adaptations by herbivores. Trade‐offs arise when the benefit of a trait, such as the ability to feed on a novel host plant or to survive in the presence of an insecticide, is counterbalanced by fitness costs that decrease fitness in the absence of the selective agent. For resistance to insecticides, and resistance to insecticidal transgenic crops in particular, fitness costs may act as an evolutionary constraint and delay or prevent the evolution of resistance. An important observation is that certain ecological factors such as host plants and entomopathogens can magnify fitness costs, which is termed ecological negative cross‐resistance. The application of omics technologies may allow for more efficient identification of factors that will impose ecological negative cross‐resistance, thereby bolstering insect resistance management. Copyright © 2009 Society of Chemical Industry     

寄生荔枝蒂蛀虫卵的斑螟分索赤眼蜂过寄生驯化培育

针对寄生荔枝蒂蛀虫卵的斑螟分索赤眼蜂Trichogrammatoidea hypsipylae Nagaraja不能正常羽化出蜂问题,室内以米蛾Corcyra cephalonia（stainton）卵为寄主,分别以1：3、1：5、1：10（对照）的蜂卵比接蜂培养,经过35代过寄生连代繁殖驯化,其36代（F36）成蜂个体大小显著小于对照组。与对照组相比,成蜂体长、体宽分别减小28．89％、16．08％（1：3处理）和27．43％、20．56％（1：5处理）。经蜂卵1：3、1：5接蜂连代繁殖驯化后的F36斑螟分索赤眼蜂对荔枝蒂蛀虫卵的寄生率分别为44％和55％,与对照差异不显著,但能顺利从荔枝蒂蛀虫卵内羽化出蜂,羽化率分别为31．8％、25．5％,对照则无羽化出蜂。表明通过过寄生驯化培育可以改变斑螟分索赤眼蜂的个体大小,并有望使其在荔枝园内建立稳定种群,达到持续控制荔枝蒂蛀虫的目的。     

Evolution of gene-for-gene systems in metapopulations: the effect of spatial scale of host and pathogen dispersal

The concept of gene-for-gene coevolution is a major model for research on disease resistance in crop plants. However, few theoretical or empirical studies have examined such systems in natural situations, and as a consequence, there is little knowledge of how spatial effects are likely to influence the evolution of host resistance and pathogen virulence in gene-for-gene interactions. In this work, a simulation approach was used to investigate the epidemiological and genetic consequences of varying host and pathogen dispersal in metapopulation situations. The results demonstrate clear impacts of dispersal distance on the total number of host and pathogen genotypes that are maintained, as well as on genetic variation at individual host resistance and pathogen virulence loci. Several other important results also emerged from this study. In contrast to the predictions of many earlier nonspatial models, so-called 'super-races' of pathogens do not always evolve and dominate, indicating that it is not necessary to assume costs of resistance or virulence to maintain high levels of polymorphism in biologically realistic situations. The rate of evolution of both resistance and virulence depend on the scale of dispersal, with greater mixing (as a function of dispersal scale) resulting in a faster approach to a dynamic endpoint. The model in this paper also predicts that, despite the greater total genotypic diversity of pathogens across the metapopulation, variation in host resistance will generally be greater than variation in pathogen virulence within local populations.     

Recent outbreaks of rust diseases and the importance of basic biological research for controlling rusts

Rust fungi are obligate plant parasites belonging to the order Pucciniales; they comprise about 7,800 species throughout the world. Some species seriously damage crops, vegetables, fruits and trees. Of these species, wheat stem rust (Puccinia graminis f. sp. tritici), Asian soybean rust (Phakopsora pachyrhizi) and myrtle rust (Puccinia psidii) have recently become major concerns worldwide, and this review, discusses recent rust disease outbreaks of Asian soybean rust and myrtle rust. Both rusts have very wide host ranges. Asian soybean rust has spread from its original region of distribution (eastern Asia) to many areas of soybean cultivation around the world. Myrtle rust is a new disease in areas where host plants were first introduced and has spread to other parts of the world including the areas where the host plants are indigenous. New diseases of economically important plants can occur by host shifts from wild host plants or host jumps from phylogenetically unrelated plant species. Recent advances in molecular phylogenetic studies have contributed to a revision of rust taxonomy. Molecular phylogenetic analyses, together with precise morphological observations and inoculation experiments, have identified taxonomic groups among populations that are morphologically very similar. Systematic, ecological and other basic biological studies of rust fungi in both cultivated and wild host plants are very important for developing methods to control rust diseases. Recent changes in the International Code of Botanical Nomenclature will surely affect the systematics of rust fungi.     

Some Problems Posed by the Heterodera avenae Complex1

Cyst nematodes are sedentary parasites with limited host ranges and co-evolution with circumscribed host groups is believed to result in species complexes. A scheme for this process is given. The Heterodera avenae group is such a complex parasitising cereals and grasses. Although the group includes ten nominal species, only H. mani, H. avenae and H. avenae pathotype 3 present taxonomic problems of immediate relevance in agriculture. Application of a multivariate technique, principal co-ordinate analysis, to second-stage juvenile characters indicates that H. avercae pathotype 3 is as distinct from H. avenae as H. arenaria, an accepted species in the H. avenae group. In contrast there are difficulties with juvenile and cyst morphology in distinguishing H. mani from H. avenae.     

Direct and host‐mediated interactions between Fusarium pathogens and herbivorous arthropods in cereals

Fusarium head blight and fusarium ear rot diseases of cereal crops are significant global problems, causing yield and grain quality losses and accumulation of harmful mycotoxins. Safety limits have been set by the European Commission for several Fusarium‐produced mycotoxins; mitigating the risk of breaching these limits is of great importance to crop producers as part of an integrated approach to disease management. This review examines current knowledge regarding the role of arthropods in disease epidemiology. In the field, diseased host plants are likely to interact with arthropods that may substantially impact the disease by influencing spread or condition of the shared host. For example, disease progress by Fusarium graminearum can be doubled if wheat plants are aphid‐infested. Arthropods have been implicated in disease epidemiology in several cases and the evidence ranges from observed correlations between arthropod infestation and increased disease severity and mycotoxin accumulation, to experimental evidence for arthropod infestation causing heightened pathogen prevalence in hosts. Fusarium pathogens differ in spore production and impact on host volatile chemistry, which influences their suitability for arthropod dispersal. Herbivores may allow secondary fungal infection after wounding a plant or they may alter host susceptibility by inducing changes in plant defence pathways. Post‐harvest, during storage, arthropods may also interact with Fusarium pathogens, with instances of fungivory and altered behaviour by arthropods towards volatile chemicals from infected grain. Host‐mediated indirect pathogen–arthropod interactions are discussed alongside a comprehensive review of evidence for direct interactions where arthropods act as vectors for inoculum.     

Pathogens and their products affecting weedy plants

There are many natural enemies of weedy plants; among them are plant pathogens. Plant pathogens are capable of affecting plants, in part because of the phytotoxins they produce. Phytoloxins of weedy pathogens are produced in culture media by most of the phytopathogenic fungi of weeds that we have studied. In most cases the phytotoxin(s) usually belongs to a family of related compounds produced by the pathogen. Phytotoxin production in the medium can be optimized by placement of the host extract into the medium. Lethal activity is usually observed in the concentration range of 10^-3-10^-6M. The concept of using these molecules, or derivatives thereof, or related compounds as herbicides, should be explored.     

Host range and molecular phylogenies of the soft rot enterobacterial genera pectobacterium and dickeya

ABSTRACT Pectobacterium and Dickeya spp. are related broad-host-range entero-bacterial pathogens of angiosperms. A review of the literature shows that these genera each cause disease in species from at least 35% of angiosperm plant orders. The known host ranges of these pathogens partially overlap and, together, these two genera are pathogens of species from 50% of angiosperm plant orders. Notably, there are no reported hosts for either genus in the eudicots clade and no reported Dickeya hosts in the magnoliids or eurosids II clades, although Pectobacterium spp. are pathogens of at least one plant species in the magnoliids and at least one in each of the three eurosids II plant orders. In addition, Dickeya but not Pectobacterium spp. have been reported on a host in the rosids clade and, unlike Pectobacterium spp., have been reported on many Poales species. Natural disease among nonangiosperms has not been reported for either genus. Phylogenetic analyses of sequences concatenated from regions of seven housekeeping genes (acnA, gapA, icdA, mdh, mtlD, pgi, and proA) from representatives of these genera demonstrated that Dickeya spp. and the related tree pathogens, the genus Brenneria, are more diverse than Pectobacterium spp. and that the Pectobacterium strains can be divided into at least five distinct clades, three of which contain strains from multiple host plants.