Networks and plant disease management: concepts and applications

A network is a natural structure with which to describe many aspects of a plant pathosystem. The article seeks to set out in a nonmathematical way some of the network concepts that promise to be useful in managing plant disease. The field has been stimulated by developments designed to help understand and manage animal and human disease, as well as by technical infrastructures, such as the internet. It overlaps partly with landscape ecology. The study of networks has helped identify likely ways to reduce flow of disease in traded plants, to find the best sites to monitor as warning sites for annually reinvading disease, and to understand the fundamentals of how a pathogen spreads in different structures. A tension between the free flow of goods or species down communication channels and free flow of pathogens down the same pathways is highlighted.

Belowground interactive effects of elevated CO2, plant diversity and earthworms in grassland microcosms

The potential interactive effects of future atmospheric CO2 concentrations and plant diversity loss on the functioning of belowground systems are still poorly understood. Using a microcosm greenhouse approach with assembled grassland plant communities of different diversity (1, 4 and 8 species), we explored the interactive effects between plant species richness and elevated CO2 (ambient and + 200 p.p.m.v. CO2) on earthworms and microbial biomass. We hypothesised that the beneficial effect of increasing plant species richness on earthworm performance and microbial biomass will be modified by elevated CO2 through impacts on belowground organic matter inputs, soil water availability and nitrogen availability. We found higher earthworm biomass in eight species mixtures under elevated CO2, and higher microbial biomass under elevated CO2 in four and eight species mixtures if earthworms were present. The results suggest that plant driven changes in belowground organic matter inputs, soil water availability and nitrogen availability explain the interactive effects of CO2 and plant diversity on the belowground compartment. The interacting mechanisms by which elevated CO2 modified the impact of plant diversity on earthworms and microorganisms are discussed.

Water, irrigation and plant diseases

Irrigation is a major husbandry tool, vital for world food production and security. The purpose of this review is twofold:- firstly drawing attention to the beneficial and deleterious aspects of irrigation resulting from interactions with the microbial world; secondly, forming a basis for encouraging further research and development. Irrigation is for example, a valuable component in the control of some soil borne pathogens such as Streptomyces scabies, the cause of potato common scab and Fusarium cubense, a cause of banana wilt. By contrast, applying irrigation encourages some foliar pathogens and factors such as splash dispersal of propagules and the retention of leaf wetness are important elements in the successful establishment of disease foci. Irrigation applied at low levels in the canopy directly towards the stem bases and root zones of plants also provides means encouraging disease development. Irrigation also offers means for the direct spread of microbes such as water borne moulds, Oomycetes, and plasmodial pathogens coming from populations present in the water supply. The presence of plant disease causing microbes in sources of irrigation has been associated with outbreaks of diseases such as clubroot (Plasmodiophora brassicae). Irrigation can be utilised as a means for applying agrochemicals, fungigation. The developing technologies of water restriction and root zone drying also have an impact on the success of disease causing organisms. This is an emerging technology and its interactions with benign and pathogenic microbes require consideration.

Bacterial evolution by genomic island transfer occurs via DNA transformation in planta

Our understanding of the evolution of microbial pathogens has been advanced by the discovery of "islands" of DNA that differ from core genomes and contain determinants of virulence [1, 2]. The acquisition of genomic islands (GIs) by horizontal gene transfer (HGT) is thought to have played a major role in microbial evolution. There are, however, few practical demonstrations of the acquisition of genes that control virulence, and, significantly, all have been achieved outside the animal or plant host. Loss of a GI from the bean pathogen Pseudomonas syringae pv. phaseolicola (Pph) is driven by exposure to the stress imposed by the plant's resistance response [3]. Here, we show that the complete episomal island, which carries pathogenicity genes including the effector avrPphB, transfers between strains of Pph by transformation in planta and inserts at a specific att site in the genome of the recipient. Our results show that the evolution of bacterial pathogens by HGT may be achieved via transformation, the simplest mechanism of DNA exchange. This process is activated by exposure to plant defenses, when the pathogen is in greatest need of acquiring new genetic traits to alleviate the antimicrobial stress imposed by plant innate immunity [4].

Evidence that nematodes may vector the soft rot-causing enterobacterial phytopathogens

Bacterial soft rot is a globally significant plant disease that causes major losses in the production of many popular crops, such as potato. Little is known about the dispersal and ecology of soft-rot enterobacteria, and few animals have been identified as vectors for these pathogens. This study investigates whether soil-living and bacterial-feeding nematodes could act as vectors for the dispersal of soft-rot enterobacteria to plants. Soft-rot enterobacteria associated with nematodes were quantified and visualized through bacterial enumeration, GFP-tagging, and confocal and electron scanning microscopy. Soft-rot enterobacteria were able to withstand nematode grazing, colonize the gut of Caenorhabditis elegans and subsequently disperse to plant material while remaining virulent. Two nematode species were also isolated from a rotten potato sample obtained from a potato storage facility in Finland. Furthermore, one of these isolates (Pristionchus sp. FIN-1) was shown to be able to disperse soft-rot enterobacteria to plant material. The interaction of nematodes and soft-rot enterobacteria seems to be more mutualistic rather than pathogenic, but more research is needed to explain how soft-rot enterobacteria remain viable inside nematodes.

Modelling disease spread and control in networks: implications for plant sciences

Networks are ubiquitous in natural, technological and social systems. They are of increasing relevance for improved understanding and control of infectious diseases of plants, animals and humans, given the interconnectedness of today's world. Recent modelling work on disease development in complex networks shows: the relative rapidity of pathogen spread in scale-free compared with random networks, unless there is high local clustering; the theoretical absence of an epidemic threshold in scale-free networks of infinite size, which implies that diseases with low infection rates can spread in them, but the emergence of a threshold when realistic features are added to networks (e.g. finite size, household structure or deactivation of links); and the influence on epidemic dynamics of asymmetrical interactions. Models suggest that control of pathogens spreading in scale-free networks should focus on highly connected individuals rather than on mass random immunization. A growing number of empirical applications of network theory in human medicine and animal disease ecology confirm the potential of the approach, and suggest that network thinking could also benefit plant epidemiology and forest pathology, particularly in human-modified pathosystems linked by commercial transport of plant and disease propagules. Potential consequences for the study and management of plant and tree diseases are discussed.

Plant–pathogen interactions: disease resistance in modern agriculture

The growing human population will require a significant increase in agricultural production. This challenge is made more difficult by the fact that changes in the climatic and environmental conditions under which crops are grown have resulted in the appearance of new diseases, whereas genetic changes within the pathogen have resulted in the loss of previously effective sources of resistance. To help meet this challenge, advanced genetic and statistical methods of analysis have been used to identify new resistance genes through global screens, and studies of plant-pathogen interactions have been undertaken to uncover the mechanisms by which disease resistance is achieved. The informed deployment of major, race-specific and partial, race-nonspecific resistance, either by conventional breeding or transgenic approaches, will enable the production of crop varieties with effective resistance without impacting on other agronomically important crop traits. Here, we review these recent advances and progress towards the ultimate goal of developing disease-resistant crops.

Early changes in apoplast composition associated with defence and disease in interactions between Phaseolus vulgaris and the halo blight pathogen Pseudomonas syringae pv. phaseolicola

The apoplast is the arena in which endophytic pathogens such as Pseudomonas syringae grow and interact with plant cells. Using metabolomic and ion analysis techniques, this study shows how the composition of Phaseolus vulgaris leaf apoplastic fluid changes during the first six hours of compatible and incompatible interactions with two strains of Pseudomonas syringae pv. phaseolicola (Pph) that differ in the presence of the genomic island PPHGI-1. Leaf inoculation with the avirulent island-carrying strain Pph 1302A elicited effector-triggered immunity (ETI) and resulted in specific changes in apoplast composition, including increases in conductivity, pH, citrate, γ-aminobutyrate (GABA) and K+, that are linked to the onset of plant defence responses. Other apoplastic changes, including increases in Ca2+, Fe2/3+ Mg2+, sucrose, β-cyanoalanine and several amino acids, occurred to a relatively similar extent in interactions with both Pph 1302A and the virulent, island-less strain Pph RJ3. Metabolic footprinting experiments established that Pph preferentially metabolizes malate, glucose and glutamate, but excludes certain other abundant apoplastic metabolites, including citrate and GABA, until preferred metabolites are depleted. These results demonstrate that Pph is well-adapted to the leaf apoplast metabolic environment and that loss of PPHGI-1 enables Pph to avoid changes in apoplast composition linked to plant defences.

The role of uncomposted materials, composts, manures, and compost extracts in reducing pest and disease incidence and severity in sustainable temperate agricultural and horticultural crop production - A review

This review evaluates evidence of the impact of uncomposted plant residues, composts, manures, and liquid preparations made from composts (compost extracts and teas) on pest and disease incidence and severity in agricultural and horticultural crop production. Most reports on pest control using such organic amendments relate to tropical or and climates. The majority of recent work on the use of organic amendments for prevention and control of diseases relates to container-produced plants, particularly ornamentals. However, there is growing interest in the potential for using composts to prevent and control diseases in temperate agricultural and horticultural field crops and information concerning their use and effectiveness is slowly increasing. The impact of uncomposted plant residues, composts, manures, and compost extracts/teas on pests and diseases is discussed in relation to sustainable temperate field and protected cropping systems. The factors affecting efficacy or such organic amendments in preventing and controlling pests and disease are examined and the mechanisms through which control is achieved are described.

Dispersal capacity and diet breadth modify the response of wild bees to habitat loss

Habitat loss poses a major threat to biodiversity, and species-specific extinction risks are inextricably linked to life-history characteristics. This relationship is still poorly documented for many functionally important taxa, and at larger continental scales. With data from five replicated field studies from three countries, we examined how species richness of wild bees varies with habitat patch size. We hypothesized that the form of this relationship is affected by body size, degree of host plant specialization and sociality. Across all species, we found a positive species–area slope (z ¼ 0.19), and species traits modified this relationship. Large-bodied generalists had a lower z value than small generalists. Contrary to predictions, small specialists had similar or slightly lower z value compared with large specialists, and small generalists also tended to be more strongly affected by habitat loss as compared with small specialists. Social bees were negatively affected by habitat loss (z ¼ 0.11) irrespective of body size. We conclude that habitat loss leads to clear shifts in the species composition of wild bee communities.

A capture–recapture approach for screening using two diagnostic tests with availability of disease status for the test positives only

The article considers screening human populations with two screening tests. If any of the two tests is positive, then full evaluation of the disease status is undertaken; however, if both diagnostic tests are negative, then disease status remains unknown. This procedure leads to a data constellation in which, for each disease status, the 2 × 2 table associated with the two diagnostic tests used in screening has exactly one empty, unknown cell. To estimate the unobserved cell counts, previous approaches assume independence of the two diagnostic tests and use specific models, including the special mixture model of Walter or unconstrained capture–recapture estimates. Often, as is also demonstrated in this article by means of a simple test, the independence of the two screening tests is not supported by the data. Two new estimators are suggested that allow associations of the screening test, although the form of association must be assumed to be homogeneous over disease status. These estimators are modifications of the simple capture–recapture estimator and easy to construct. The estimators are investigated for several screening studies with fully evaluated disease status in which the superior behavior of the new estimators compared to the previous conventional ones can be shown. Finally, the performance of the new estimators is compared with maximum likelihood estimators, which are more difficult to obtain in these models. The results indicate the loss of efficiency as minor.

Economic impact of Turnip mosaic virus, Cauliflower mosaic virus and Beet mosaic virus in three Kenyan vegetables

Screenhouse experiments conducted in Kenya showed that inoculation of cabbage seedlings with Turnip mosaic virus (TuMV), either alone, or in combination with Cauliflower mosaic virus (CaMV), reduced the number and weight of marketable harvested heads. When viruses were inoculated simultaneously, 25% of cabbage heads were non-marketable, representing 20-fold loss compared with control. By contrast, inoculation with CaMV alone had insignificant effects on cabbage yield. This suggests that TuMV is the more detrimental of these pathogens, and its management should be a priority. Early exposure to TuMV produced cabbages that were 50% lighter than non-infected plants, but later infection was less damaging suggesting that controlling virus infection at the seedling stage is more important. TuMV was far less damaging to kale than it was to cabbage; although high proportions of TuMV-inoculated kale plants showed symptoms (> 90%), the marketability and quality of leaves were not significantly reduced, and no clear relationship existed between timing of infection and subsequent crop losses. Early inoculation of Swiss chard with Beet mosaic virus (BtMV) significantly impaired leaf quality (similar to 50% reduction in marketable leaf production), but the impact of disease was greatest in plants that had been inoculated at maturity, where average leaf losses were two and a half times those recorded in virus-free plants. Disease-management of BtMV in Swiss chard is important, therefore, not only at the seedling stage, but particularly when plants are transplanted from nursery to field.

Contrasting success in the restoration of plant and phytophagous beetle assemblages of species-rich mesotrophic grasslands

Over the last 60 years changes to the management of species-rich mesotrophic grasslands have resulted in the large-scale loss and degradation of this habitat across Europe. Restoration of such grasslands on agriculturally improved pastures provides a potentially valuable approach to the conservation of these threatened areas. Over a four-year period a replicated block design was used to test the effects of seed addition (green hay spreading and brush harvest collection) and soil disturbance on the restoration of phytophagous beetle and plant communities. Patterns of increasing restoration success, particularly where hay spreading and soil disturbance were used in combination, were identified for the phytophagous beetles. In the case of the plants, however, initial differences in restoration success in response to these same treatments were not followed by subsequent temporal changes in plant community similarity to target mesotrophic grassland. It is possible that the long-term consequences of the management treatments would not be the establishment of beetle and plant communities characteristic of the targets for restoration. Restoration management to enhance plant establishment using hay spreading and soil disturbance techniques would, however, still increase community similarity in both taxa to that of species-rich mesotrophic grasslands, and so raise their conservation value.