Isolation and selection of Hemileia Vastatrix antagonists

Organic coffee growing is rapidly increasing in Brazil, and many diseases, especially coffee leaf rust (Hemileia vastatrix), are threatening its production. This study is a first step towards a biocontrol program for coffee rust on organically grown plants. In three organic coffee farms in the state of Minas Gerais, 393 microbial strains including 154 bacterial and 239 fungal strains were isolated from leaves, leaf debris, and soil samples, and in 6 month-old coffee plants, 17 of these isolates reduced both the infection frequency (IF) and the number of H. vastatrix urediniospores produced per leaf (UPL) by more than 70 %. The isolates were identified as eight bacteria isolates, seven Bacillus spp. and one Pseudomonas sp., and nine fungal isolates, four Fusarium spp., two Penicillium spp., one Aspergillus sp., one Acremonium sp. and one Cladosporium sp. Each fungal and bacterial isolate was applied 0, 4, 8, 12 or 16 days before and 0, 4, 8, 12 or 16 days after H. vastatrix inoculation, and the efficiency in reducing both IF and UPL was evaluated. The efficiency was higher and lasted longer when the bacterial isolates were applied before H. vastatrix inoculation. Six Bacillus (B10, B25, B143, B157, B171, B175), two Fusarium (F205, F281), and one Pseudomonas (B286) isolates are potentially efficient as biocontrol agents of H. vastatrix and will be tested using field experiments.     

Effect of cultural practices on the development of arabica coffee berry disease,caused by <Emphasis Type="Italic">Colletotrichum kahawae</Emphasis>

In the high altitude regions of Africa, coffee berry disease (CBD), caused by Colletotrichum kahawae, is the main constraint for arabica coffee (Coffea arabica) production. However, certain agricultural practices can reduce losses caused by the disease and thereby promote optimum production. On small family farms in Cameroon, mixed cropping with fruit trees, intercropping with food crops and maintenance pruning of coffee trees are very widespread agricultural practices that can affect CBD epidemics. Consequently, an epidemiological study was conducted to assess how cultural practices affected the disease in an arabica coffee smallholding in Cameroon. The disease was monitored on a weekly basis over four successive years (2002–2005) on coffee trees in diverse cultural situations. Cultural practices likely to reduce losses due to CBD were identified. The infection rate was significantly lower on coffee trees grown intensively than on coffee trees grown in the traditional manner. Coffee trees located under the shade of fruit trees were significantly less attacked than those located in full sunlight. In addition, berries on the leafless parts of branches, near the main trunk of the coffee tree, were less infected than those on leafy sections. These results show that maintenance pruning, removal of mummified berries, and mixed cropping with shade plants are cultural practices which create environmental conditions that limit CBD development.     

Information networks for disease: commonalities in human management networks and within-host signalling networks

Network models of human epidemics can often be improved by including the effects of behaviour modification in response to information about the approach of epidemics. Similarly, there are opportunities to incorporate the flow of information and its effects in plant disease epidemics in network models at multiple scales. (1) In the case of human management networks for plant disease, each node of a network has four main components: plant communities, microbial communities, human information (among researchers, extension agents, farmers, and other stakeholders), and environmental conditions, along with their interactions. The links between nodes, representing the rate of movement between them, have three parts: the rates for plant materials, the rates for microbes, and the rates for information. Network resilience for information flow is an important goal for such systems. Game theory can provide insights into how human agents decide how to invest their efforts in strengthening information networks, and how policies can support more resilient networks. (2) For the case of within-plant signalling networks, each node has a comparable set of four main components: plant signals (often in the form of phytohormones) and development status, microbial communities and plant disease status, microbial signals (often in the form of quorum sensing molecules), and micro-environmental conditions, along with their interactions. In effect, human information is replaced by plant signals and microbial signals in this second model. The links between nodes have three parts: the rates for microbes, the rates for microbial signals (which may move separately from the microbes, themselves), and the rates for plant signals. Understanding how to enhance adaptive plant signalling networks and microbial signalling networks that support plant productivity, and disrupt microbial signalling networks that contribute to pathogenicity, will be an important step for improved disease management.     

Modified plant architecture to enhance crop disease control: genetic control and possible value of upright fruit position in cucumber

Plant architectural features can facilitate disease control by creating unfavourable environments for pathogen growth or limiting pathogen contact with the host. In the case of Phytophthora capsici infection of cucumber (Cucumis sativus), the susceptible fruit typically lie in contact with soil under warm, moist conditions of a full canopy, an ideal location for exposure to inoculum and disease development. We have shown that increased row spacing, trellising and architectural variants that allow for more open canopies, such as shorter vines, reduced branching, or smaller leaves, can modify microclimate as assessed by temperature at the location of developing fruits. However, only trellising reduced infection rates (<3 % infection vs. 22 % for control). A cucumber accession PI308916, with extremely short internodes and resulting upright position of young fruit, also exhibited reduced disease. Fruit of PI308916 were susceptible when inoculated with P. capsici, indicating that reduced infection likely resulted from decreased soil contact. The compact trait is inherited as a single recessive gene, cp. Like many architectural traits, cp may be pleiotropic; PI308916-derived breeding lines were reported to have poor seedling emergence. PI308916 exhibited inconsistent apical hook formation that co-segregated with short internodes in F₂ and backcross generations, and disorganized internodal cortical cell arrangement. The combined phenotypes suggest either pleiotropy or very tight linkage of genes affecting hormone balance or cell division. The narrow chromosome region recently defined by QTL analysis includes candidate gene homologs of meristem related genes modulating cell division or spacing of lateral shoot organs and genes associated with brassinosteroid signaling or cytokinin content.     

Coffee berry disease in Kenya. II. The role of Glomerella cingulata in the Colletotrichum population,colonizing the bark of Coffea arabica

On the maturing bark of cut branches ofCoffea arabica previously sprayed with copper fungicides perithecia ofGlomerella cingulata were easily found after two to ten days of incubation. Without fungicides the number of perithecia was decidedly lower. On prunings left on the ground under the coffee trees for 6 to 24 weeks the perithecia could also be found, but the numbers declined rapidly with time. Perithecia ofG. cingulata could forcibly discharge ascospores under laboratory conditions. Monospore cultures obtained by catching ascospores on agar, invariably belonged to threeColletotrichum types. It was rarely possible to isolate aColletotrichum able to infect green coffee berries. Growthrate, colour of the mycelium, number of conidia producedin vitro and infectivity on green coffee berries, however, differed substantially fromC. coffeanum, the cause of coffee berry disease. In Kenya no evidence has been obtained that ascospores from perithecia on bark could infect wounded or unwounded green coffee berries. Neither has any infection been obtained with ascospores from perithecia grownin vitro. Possible explanations for the difference with previous findings are offered. Based on the data presented in this paper, it is concluded thatG. cingulata is not likely to play a role in the epidemiology of the coffee berry disease in Kenya.     

Proteomic analysis of Colletotrichum kahawae-resistant and susceptible coffee fruit pericarps

Coffee berry disease (CBD) is caused by the fungus Colletotrichum kahawae and is restricted to the African continent, where it generates losses of up to 80 % of coffee production. Weather conditions in certain growing areas at high altitudes in Colombia appear to be very favourable for the development of this disease. Certain genotypes of Coffee arabica are resistant to this pathogen, such as the Timor Hybrid and some Ethiopian accessions. It is important to identify the proteins in these coffee genotypes that are associated with resistance to this fungus. Therefore, we compared the proteomes of two genotypes that are resistant to different isolates of C. kahawae with the proteome of the susceptible coffee genotype Caturra. We optimized the methodology applied for the extraction, cleaning and purification of proteins from the green fruit pericarp at 150 to 170 days after flowering. Through two-dimensional differential gel electrophoresis, proteomic map images were obtained for the resistant and susceptible genotypes. Fifty-two protein spots that were significantly different between the resistant and susceptible genotypes were detected. These protein spots were isolated and sequenced via mass spectrometry. The sequence analysis identified 14 proteins in the Timor Hybrid and 14 in CCC1147 that were associated with resistance and pathogen defence.     

Effects of crop management patterns on coffee rust epidemics

The effects of crop management patterns on coffee rust epidemics, caused by Hemileia vastatrix , are not well documented despite large amounts of data acquired in the field on epidemics, and much modelling work done on this disease. One main reason for this gap between epidemiological knowledge and understanding for management resides in the lack of links between many studies and actual production situations in the field. Coffee rust epidemics are based on a seemingly simple infection cycle, but develop polycyclic epidemics in a season and polyetic epidemics over successive seasons. These higher-level processes involve a very large number of environmental variables and, as in any system involving a perennial crop, the physiology of the coffee crop and how it affects crop yield. Crop management is therefore expected to have large effects on coffee rust epidemics because of its immediate effect on the infection cycle, but also because of its cumulative effect on ongoing and successive epidemics. Quantitative examples taken from a survey conducted in Honduras illustrate how crop management, different combinations of shade, coffee tree density, fertilization and pruning may strongly influence coffee rust epidemics through effects on microclimate and plant physiology which, in turn, influence the life cycle of the fungus. We suggest there is a need for novel coffee rust management systems which fully integrate crop management patterns in order to manage the disease in a sustainable way.     

Incidence and etiology of postharvest fungal diseases of loquat fruit (<Emphasis Type="Italic">Eriobotrya japonica</Emphasis> (Thunb.) Lindl. cv. ‘Algerie’) in Alacant province (Spain)

‘Algerie’ is currently the most important loquat cultivar in Spain. The incidence and etiology of postharvest diseases affecting this cultivar were determined under local conditions. Latent and wound pathogens were evaluated for two consecutive seasons on commercially grown loquats from two orchards. Healthy loquats were either surface-disinfected or artificially wounded in the rind and placed in humid chambers at 20 °C for up to 5 weeks. Additionally, decay was assessed on commercially-handled loquats stored at 5 °C for up to 20 weeks. The most frequent disease was caused by Alternaria alternata, followed by Penicillium expansum. These two pathogens were present on fruit assessed for all types of infection. Moreover, decay caused by Botrytis cinerea was abundantly observed on both wounded and cold-stored fruit, while Colletotrichum gloeosporioides was frequently found on surface-disinfected fruit. Other pathogens that were observed causing latent infection to a lesser extent included Pestalotiopsis clavispora and Diplodia seriata. Common isolates were identified by macroscopic and microscopic morphology and/or DNA amplification and sequencing. Pathogenicity of selected isolates was demonstrated by fulfilling Koch’s postulates and disease development was assessed on artificially inoculated loquats stored at either 20 or 5 °C.     

Intercellular invasion of rice roots at the seedling stage by the rice false smut pathogen, <Emphasis Type="Italic">Villosiclava virens</Emphasis>

False smut is a serious disease affecting rice production worldwide. Initial infection of rice seedlings by Villosiclava virens was clarified using axenically cultured chlamydospores to inoculate rice roots. Chlamydospores were found on rice roots at 1 day post inoculation (dpi), and were germinating at 1–4 dpi. At 4 dpi, the infection germ tube had invaded the intercellular space between epidermal rice root cells. Between 5 and 11 dpi, branching and fusion-like structures were observed that may contribute to the establishment of the hyphal network on the root surface.     

Coffee berry disease in Kenya. I. Colletotrichum spp. colonizing the bark of Coffea arabica

Several species ofColletotrichum occur in maturing bark ofCoffea arabica branches in Kenya. TheColletotrichum population inhabits the bark tissue external to the developing phellogens in the cortex. TheColletotrichum species are unable to invade green bark tissue, where the phellogen has not yet been differentiated, while colonization ceases on the phelloderm of the true bark. Only one of theColletotrichum species discussed in this paper,C. coffeanum, can infect green coffee berries. Shortly after the initiation of the first phellogen in the cortex the parasite is in a small area in the bark. It cannot be found in bark tissues where more phellogens have been formed and where the colour of the bark has changed from yellow-green to brown or black. From the bark ofC. liberica trees, grown in Kenya, andC. arabica cv. ’lsBourbon’, grown in greenhouses in the Netherlands one of the saprophytic components of theColletotrichum population could be isolated. It was impossible to induce ddie-back symptoms or mere infection by inoculation of green internodes even after wounding of live branches ofC. arabica with any of theColletotrichum components colonizing the bark. It is suggested that die-back systems of coffee in Kenya are primarily caused by unfavourable growing conditions.     

Suppression of Fusarium wilt of spinach with compost amendments

The effect of different organic composts on the suppression of wilt disease of spinach caused by Fusarium oxysporum f. sp. spinaciae was evaluated in a continuous cropping system in both containers and in microplot field trials. Test soils infested with the pathogen were amended with wheatbran, wheatbran and sawdust, coffee grounds, chicken manure, or mixture of different composts with and without 5% (w/w) crab shell powder either once (5%, w/w) or continuously (2.5%) into the test soils infested with the pathogen. In the container trials, the soil amended with composts became suppressive to disease development on the second and third cropping. The suppressive effect was notable in the soil amended with the mixture of compost with and without crab shell powder. The coffee compost lowered soil pH but became suppressive to the disease after modifying the soil pH. In the field trial using the mixture of the different composts containing 5% crab shell powder, a combination of 5% before the first cropping and 2.5% every second cropping gave stable disease control and promoted plant growth. After compost amendment, populations of fungi, bacteria and actinomycetes as measured by dilution plate counting and the total microbial activity as evaluated by fluorescein diacetate hydrolysis increased and population of the pathogen gradually decreased. These phenomena were especially notable in soils amended with the mixture of different composts. These results indicate that diversity in the organic materials promotes higher microbial activity and population in the soil thereby enhancing disease suppressiveness.     

Anthracnose on almond in Australia:disease progress and inoculum sources of Colletotrichum acutatum

Anthracnose, caused by Colletotrichum acutatum, is an important disease of almond and has caused significant economic losses in California, Israel and Australia. Anthracnose development was monitored for three growing seasons in an almond orchard in South Australia on two almond cultivars, Price and Nonpareil, with up to 80 % of fruit affected in 2004. Lesions, typical of anthracnose, formed on young developing fruit and symptoms continued to appear until the fruit were ca 20 mm long, after which no further lesions developed. Symptoms were observed on leaves, woody tissue showed signs of dieback, but blossom blight was not observed. Maximum disease incidenceperfor, man and Relative Area Under the Disease Progress Curve (RAUDPC) were significantly larger for Price than Nonpareil for each season, but differences in the apparent rates of infection for both cultivars were insignificant for the three growing seasons. The apparent rates of infection were correlated with rainfall and daily temperature for the three years combined but there was no correlation between maximum disease incidence or RAUDPC and these environmental parameters. Considerably more mummified fruit remained on the trees of cv. Price than Nonpareil each year; however, there was no correlation between the number of mummified fruit in one season and maximum disease incidence, RAUDPC or apparent rate of infection, in the following season. C. acutatum was recovered from mummified fruit, peduncles and bark, from both Price and Nonpareil, every month throughout a year-long sampling period. C. acutatum was also recovered from asymptomatic leaves, fruit, bark, buds and blossom, however, less frequently and at lower rates than from mummified fruit and peduncles. Recovery was consistently greater from Price than from Nonpareil for all tissues.     

Genetic Diversity of Xylella fastidiosa Strains from Costa Rica, São Paulo, Brazil, and United States

ABSTRACT The diversity of 42 Xylella fastidiosa strains from Costa Rica, S?o Paulo, Brazil, and the United States were analyzed using the sequence of the 16S rRNA gene by variable number of tandem repeat (VNTR) fragment analysis and by restriction fragment length polymorphisms (RFLP) of a specific polymerase chain reaction (PCR)-amplification product using enzyme CfoI. Limited variability in the sequence of the 16S rRNA gene was observed and, although the separation was not absolute, most strains from Costa Rica clustered with strains from the United States and not with strains from S?o Paulo. The PCR-RFLP produced different patterns of DNA bands. The same pattern was shared by strains from Costa Rica, the United States, and two coffee strains from S?o Paulo, but a different pattern was observed in six coffee and orange strains from Brazil. In all, 32 amplification products were scored in the VNTR fragment analysis. The total variation observed among the X. fastidiosa strains had significant (P < 0.001) contributions from both geography and host origin as inferred by Nei's values of genetic diversity and WINAMOVA statistics. The strains from Costa Rica were isolated from diseased grapevines, coffee, and sweet orange and these strains grouped together and could be distinguished from strains from grapevine from the United States or from either coffee or sweet orange from S?o Paulo. The strains tested from Costa Rica are most likely of local origin, although the possibility that they have been introduced along with horticultural crops cannot be excluded. In either case, they are examples of independent selection of strains of X. fastidiosa affecting coffee and sweet orange. Greater genetic similarity was observed between strains from Costa Rica and the United States than with those from S?o Paulo.     

A general model of plant-virus disease infection incorporating vector aggregation

In plant-virus disease epidemiology, dynamical models have invariably incorporated a bilinear inoculation rate that is directly proportional to both the abundance of healthy (susceptible) hosts and the abundance of infective vectors. Similarly, the acquisition rate is usually assumed to be directly proportional to the abundance of nonviruliferous vectors and that of infectious hosts. These bilinear assumptions have been questioned for certain human diseases, and infection rates that incorporate power parameters of the variables have been proposed. Here, infection rates for plant-virus diseases that are of a more general form than the familiar bilinear terms are examined. For such diseases, the power parameter can be regarded as a measure of the spatial aggregation of the vectors or as a coefficient of interference between them, depending on the context.
Field data of cassava mosaic virus disease (CMD) incidence were examined. When vector population density and disease incidence were high, disease progress curves over the first 6 months from planting could not be explained using models with bilinear infection rates. Incorporation of the new infection terms allowed the range of observed disease progress curve types to be described. New evidence of a mutually beneficial interaction between the viruses causing CMD and the whitefly vector, Bemisia tabaci , has shown that spatial aggregation of the vectors is an inevitable consequence of infection, particularly with a severe virus strain or a sensitive host. Virus infection increases both vector fecundity and the density of vectors on diseased plants. It is postulated that this enhances disease spread by causing an increased emigration rate of infective vectors to other crops. Paradoxically, within the infected crop, vector aggregation reduces the effective contact rate between vector and host and therefore the predicted disease incidence is less than when a bilinear contact rate is used.     

Evidence of cork barrier formation as a resistance mechanism to berry disease (Colletotrichum coffeanum) in arabica coffee

The histology of resistance to coffee berry disease (CBD) was studied in artificially inoculated berries and hypocotyls of 6-week old seedlings of a number of varieties ofCoffea arabica L. In resistant varieties a phellogen was quickly formed some cell layers below the site of infection and progress of the fungal invasion was effectively blocked by a complete barrier of suberized cells. Such barriers were absent or incompletely developed in CBD susceptible varieties. A highly significant correlation (r=0.87) was found between the frequencies of complete barrier formation in berries and in hypocotyls of young seedlings, while both were also highly correlated to observed mature plant resistance (r>-0.93). Resistance to CBD in arabica coffee may to an important extent be based on the formation of cork barriers. These cork barriers confine the pathogen to the small volume of tissue external to the barrier so that its growth is severely restricted. Such a resistance mechanism is likely to be stable (race-nonspecific). The almost identical response to infection observed in berries and hypocotyls provides further evidence that plants with resistance to CBD can be reliably preselected by the hypocotyl inoculation test.     

Differential expression of molecular rust resistance components have distinctive profiles in <Emphasis Type="Italic">Coffea arabica</Emphasis> - <Emphasis Type="Italic">Hemileia vastatrix</Emphasis> interactions

Countering the economic hurdle caused by coffee leaf rust disease is most appealing at this time as it has posed a major threat to coffee production around the world. Establishing differential expression profiles at different times following pathogen invasion in both innate and acquired immunities unlocks the molecular components of resistance and susceptibility. Suppression subtractive hybridization (SSH) was used to identify genes differentially over-expressed and repressed during incompatible and compatible interactions between Coffea arabica and Hemileia vastatrix. From 433 clones of expressed sequence tags (ESTs) sequenced, 352 were annotated and categorized of which the proportion of genes expressed during compatible interaction were relatively smaller. The result showed upregulation and downregulation of various genes at 12 and 24 h after pathogen inoculation in both interactions. The use of four different databases in searching for gene homology resulted in different number of similar sequences. BLASTx against EMBL-EBI (European Molecular Biology Laboratory-European Bioinformatics Institute) database being with the maximum (100%) hits for all the annotated sequences. RT-qPCR analysis of seven resistance-signaling genes showed similar expression patterns for most of the genes in both interactions, indicating these genes are involved in basal (non-specific) defense during which immune reactions are similar. Using SSH, we identified different types of resistance related genes that could be used for further studies towards resistant cultivar development. The potential role of some of the resistance related proteins found were also discussed.     

Yield Reduction in Wheat in Relation to Leaf Disease From Yellow (tan) Spot and Septoria Nodorum Blotch

Yellow or tan spot (caused by Pyrenophora tritici-repentis) and septoria nodorum blotch (caused by Phaeosphaeria nodorum) occur together and are a constraint to wheat yields in Australia. Recently, higher crop yields and lower fungicide costs have made fungicides an attractive management tool against these diseases. Yield-loss under different rates of progress of yellow spot and septoria nodorum blotch was examined in four experiments over three years to define the relationship between disease severity and yield. In these experiments, differences in disease were first promoted by inoculations either with P. tritici-repentis-infected stubble or aqueous spore suspensions of P. nodorum. Disease progress was further manipulated with foliar application of fungicide. The pattern of disease development varied in each year under the influence of different rainfall patterns. The inoculation and fungicide treatments produced differences in disease levels after flag leaf emergence. The infection of yellow spot or septoria nodorum blotch caused similar losses in grain yield, ranging from 18% to 31%. The infection by either disease on the flag or penultimate leaf provided a good indication of yield-loss. Disease severity on flag leaves during the milk stage of the crop or an integration of disease as area under the disease progress curve on the flag leaves based on thermal time explained more than 80% variance in yield in a simple regression model. The data provided information towards the development of disease management strategies for the control of septoria nodorum blotch and yellow spot.     

Variation in pathogen aggressiveness within a metapopulation of the Cakile maritima–Alternaria brassicicola host–pathogen association

Variation in aggressiveness and its consequences for disease epidemiology were studied in the Cakile maritima–Alternaria brassicicola host–pathogen association. Variability in pathogen growth rates and spore production in vitro , as well as disease severity and lesion growth rate on C. maritima in glasshouse inoculation trials, were investigated . Substantial variation was found in growth rates among individual A. brassicicola isolates, as well as among pathogen populations. A significant trade-off also existed between growth and spore production, such that faster-growing isolates produced fewer spores per unit area. While there was little evidence for a link between growth in vitro and either disease severity or lesion development among fast- vs slow-growth isolate classes at the individual isolate level, the results suggest that variation in pathogen fitness components associated with aggressiveness may influence disease dynamics in nature. An analysis using an independent data set of disease prevalence in the associated host populations found a significant positive relationship between the average growth rate of pathogen populations in vitro and disease progress over the growing season in wild host populations. Trade-offs such as those demonstrated between growth rate and spore production may contribute to the maintenance of variation in quantitatively based host–pathogen interactions.