Annual Review of Phytopathology - Volume 37, 1999

Research endeavors are being affected by issues involving intellectual property (patents, copyrights, and trademarks). The acquisition of rights in intellectual property by universities can result in the transfer of new innovations to the private sector, with the university recouping a share of the profits for support of further scientific research. Intellectual property rights available for new plant cultivars include plant patents, plant variety protection certificates, plant breeder's rights, and utility patents. Under the patent laws, there is no explicit exemption for research use, so researchers are increasingly being required to execute materials transfer agreements to obtain permission to use patented materials, such as techniques, genes, seeds, and cell lines, in laboratory research and in breeding programs. Research scientists must educate themselves on these issues so that they can make informed decisions regarding their research practices and the licensing of their discoveries.

Not until 1973 was it reported that strains of Agrobacterium that cause crown gall disease of grape form a specific group (later characterized as Agrobacterium vitis). Tumorigenic and nontumorigenic A. vitis have since been isolated from infected and symptomless grapes worldwide. Research on the genetic makeup of A. vitis has led to an improved understanding of pathogen biology and bacterial evolution. In addition, the identification of significant gene sequences has facilitated the development of PCR and RFLP-based identification procedures that continue to improve the detection of A. vitis in plants and soil. Current control practices rely on the use of disease-resistant cultivars, cultural practices that minimize plant injury, and the production of pathogen-free vines. Promising future controls include employment of biological control agents and development of crown gall–resistant transgenic grapevines.

The advent of molecular biology in general and the polymerase chain reaction in particular have greatly facilitated genomic analyses of microorganisms, provide enhanced capability to characterize and classify strains, and facilitate research to assess the genetic diversity of populations. The diversity of large populations can be assessed in a relatively efficient manner using rep-PCR-, AFLP-, and AP-PCR/RAPD-based genomic fingerprinting methods, especially when combined with computer-assisted pattern analysis. Genetic diversity maps provide a framework to understand the taxonomy, population structure, and dynamics of phytobacteria and provide a high-resolution framework to devise sensitive, specific, and rapid methods for pathogen detection, plant disease diagnosis, as well as management of disease risk. A variety of PCR-based fingerprinting protocols such as rDNA-based PCR, ITS-PCR, ARDRA, T-RFLPs, and tRNA-PCR have been devised, and numerous innovative approaches using specific primers have been adopted to enhance both the detection and identification of phytobacteria. PCR-based protocols, combined with computer-based analysis, have provided novel fundamental knowledge of the ecology and population dynamics of bacterial pathogens, and present exciting new opportunities for basic and applied studies in plant pathology.

Plant-related inputs provide the resources for nematode communities. Sampling of nematode communities must be on appropriate temporal and spatial scales. Size, feeding types, food or host specificity, and chronology allow over 200 nematode species to coexist in a district. Relationships between nematode functional groups and ecological processes regulating decomposition processes have been found in field experiments. Pulse-labeling experiments have shown root-feeding nematodes to increase the flow of carbon from roots to soil microbial biomass. Soil texture is related to suitability for cropping and affects nematode communities through crop-specific infestations. Nematode diversity tends to be greatest in ecosystems with least disturbance, and bacterial-feeding nematodes make the greatest contribution to the decomposer food web in more intensively managed ecosystems. Indices of the nematode fauna reflect changes in the nematode community; these changes reflect soil and ecological processes. Understanding the role of nematodes in these processes is the key to understanding of the relationship between plants and soil nematode communities.

Positive strand RNA viral genomes are unique in the viral world in serving a dual role as mRNA and replicon. Since the origin of the minus-strand RNA replication intermediate is at the 3′-end of the genome, the 3′-untranslated region (UTR) clearly plays a role in viral RNA replication. The messenger role of this same RNA likely places functional demands on the 3′-UTR to serve roles typical of cellular mRNAs, including the regulation of RNA stability and translation. Current understanding indicates varied roles for positive strand RNA viral 3′-UTRs, with the dominant roles differing between viruses. Three case studies are discussed: turnip yellow mosaic virus RNA, whose 3′ tRNA mimicry is thought to negatively regulate minus strand synthesis; brome mosaic virus, whose 3′-UTR contains a unique promoter element directing minus strand synthesis; and tobacco mosaic virus, whose 3′-UTR contains an enhancer of translational expression.

Polyketides constitute a huge family of structurally diverse natural products including antibiotics, chemotherapeutic compounds, and antiparasitics. Most of the research on polyketide synthesis in bacteria has focused on compounds synthesized by Streptomyces or other actinomycetes; however, plant-associated pseudomonads also produce a variety of compounds via the polyketide pathway including the phytotoxin coronatine, the antibiotic mupirocin, and the antifungal compounds pyoluteorin and 2,4-diacetylphloroglucinol. This review focuses on the mode of action, regulation, biosynthesis, and genetics of these four compounds and the potential use of Pseudomonas-derived polyketide synthases in the generation of novel compounds with unique activities.

Phylogenetic and population genetic methods that compare nucleic acid variation are being used to identify species and populations of pathogenic fungi and determine how they reproduce in nature. These studies show that asexual or sexual reproductive morphology does not necessarily correlate with clonal or recombining reproductive behavior, and that fungi with all types of reproductive morphologies and behaviors can be accommodated by a phylogenetic species concept. Although approximately one fifth of described fungi have been thought to be asexual and clonal, recent studies have shown that they are also recombining. Whether a particular pathogen reproduces clonally or by recombination depends on factors relating to its biology and its distribution in space and time. Knowing the identity of species and populations and their reproductive modes, while taking a broad view of pathogen behavior in space and time, should enhance the ability of pathologists to control pathogens and even predict their behavior.

The completion of the entire genome sequence of the free-living nematode, Caenorhabditis elegans is a tremendous milestone in modern biology. Not only will scientists be poring over data mined from this resource, but techniques and methodologies developed along the way have changed the way we can approach biological questions. The completion of the C. elegans genomic sequence will be of particular importance to scientists working on parasitic nematodes. In many cases, these nematode species present intractable challenges to those interested in their biology and genetics. The data already compared from parasites to the C. elegans database reveals a wealth of opportunities for parasite biologists. It is likely that many of the same genes will be present in parasites and that these genes will have similar functions. Additional information regarding differences between free-living and parasitic species will provide insight into the evolution and nature of parasitism. Finally, genetic and genomic approaches to the study of parasitic nematodes now have a clearly marked path to follow.

Numerous significant changes have been made in the taxonomy of both the anamorphs and teleomorphs of the Septoria group of leaf spot pathogens on small grain cereals during the past 30 years. The pathogens fall into two related but distinct groups, with anamorphic genera now placed in Septoria and Stagonospora of the Sphaeropsidales. Each of these genera has distinct teleomorphs in the Loculoascomycetes in Mycosphaerella and Phaeosphaeria. These reclassifications were based largely on fungal morphology and host pathogenicity as originally characterized. Recent studies have investigated the phylogenetic relationships among these species using the techniques of molecular genetics, and have related molecular characteristics to taxonomy based on classical morphology. A clearer understanding of the taxonomy of this group will enhance our ability to diagnose and manage these important cereal pathogens.

One of the best and longest-studied defense response of plants to infection is the induced accumulation of antimicrobial, low-molecular-weight secondary metabolites known as phytoalexins. Since the phytoalexin hypothesis was first proposed in 1940, a role for these compounds in defense has been revealed through several experimental approaches. Support has come, for example, through studies on the rate of phytoalexins in relation to cessation of pathogen development, quantification of phytoalexins at the infection site, and relationship of pathogen virulence to the phytoalexin tolerance. Evidence in support of phytoalexins in resistance as well some recent advances in phytoalexin biosynthesis are reviewed. Criteria for evaluating a role for phytoalexins in disease resistance are also discussed.

The critical role of iron in plant host-parasite relationships has been elucidated in diseases as different as the soft rot and fire blight incited by Erwinia chrysanthemi and E. amylovora, respectively. As in animal infections, the role of iron and its ligands in the virulence of plant pathogens seems to be more subtle than might be expected, and is intimately related to the life cycle of the pathogen within its host. This review discusses how iron, because of its unique position in biological systems, controls the activities of these plant pathogens. Molecular studies illustrating the key question of iron acquisition and homeostasis during pathogenesis are described. The production of siderophores by pathogens not only represents a powerful strategy to acquire iron from host tissues but may also act as a protective agent against iron toxicity. The need of the host to bind and possibly sequester the metal during pathogenesis is another central issue. Possible modes of iron competition between plant host and pathogen are considered.

Over the past 20 years, the interaction between the biotrophic fungal pathogen Cladosporium fulvum and tomato has developed into a versatile experimental system for molecular plant pathology and resistance breeding. This interaction provided the resources for cloning of fungal avirulence genes for the first time and interesting clues on recognition of their extracellular products by tomato, as well as mechanisms employed by the fungus to circumvent this recognition. A wealth of information has become available on the structure and genomic organization of Cf resistance genes. The occurrence of many clustered Cf homologues allows the generation of new genes with additional recognitional specificities by reshuffling. It is anticipated that potentially all proteins secreted by C. fulvum are recognized by one or more individuals in a population of tomato genotypes, a hypothesis that has been experimentally confirmed. The future challenge will be to elucidate the mechanisms of perception of avirulence factors and the subsequent signaling eventually leading to activation of host defense responses.

Begomoviruses have circular single-stranded DNA genomes, cause many diseases of dicotyledons in areas with warm climates and are transmitted by whiteflies of the Bemisia tabaci complex. Their genomic and antigenic variation represents geography-related lineages that have little relation to host range. Genomic variation resulting from mutation is amplified by acquisition of extra DNA components, pseudo-recombination and recombination, both intraspecific and interspecific. Recombination, especially interspecific recombination, seems the key mechanism for generating novel virus forms, for enhancing biological fitness of pseudo-recombinants derived from closely related species and for maintaining the flow of genetic material among different geminiviruses occurring in the same geographical region. Recent begomovirus epidemics reflect favorable conjunctions of plant, vector, and viral (e.g. emergence of a novel recombinant virus) factors. Such epidemics typically result in co-infection of plants with different begomoviruses, leading to the appearance of further variants, especially recombinants. In their patterns of variation and evolution, begomoviruses differ greatly from plant viruses with RNA genomes.

Research on impacts of climate change on plant diseases has been limited, with most work concentrating on the effects of a single atmospheric constituent or meteorological variable on the host, pathogen, or the interaction of the two under controlled conditions. Results indicate that climate change could alter stages and rates of development of the pathogen, modify host resistance, and result in changes in the physiology of host-pathogen interactions. The most likely consequences are shifts in the geographical distribution of host and pathogen and altered crop losses, caused in part by changes in the efficacy of control strategies. Recent developments in experimental and modeling techniques offer considerable promise for developing an improved capability for climate change impact assessment and mitigation. Compared with major technological, environmental, and socioeconomic changes affecting agricultural production during the next century, climate change may be less important; it will, however, add another layer of complexity and uncertainty onto a system that is already exceedingly difficult to manage on a sustainable basis. Intensified research on climate change–related issues could result in improved understanding and management of plant diseases in the face of current and future climate extremes.

Broad spectrum biological control of diseases caused by soilborne plant pathogens such as Pythium, Phytophthora, and Rhizoctonia solani requires the introduction into or presence of edaphic sources of organic nutrients in soil for sustenance of biocontrol agents. The decomposition level of organic matter critically affects the composition of bacterial taxa as well as the populations and activities of biocontrol agents. Competition, antibiosis, parasitism, and systemic induced resistance are all affected. Highly stabilized sources of Sphagnum peat consistently fail to support sustained biological control, even when inoculated with biocontrol agents. Composts, on the other hand, can serve as an ideal food base for biocontrol agents and offer an opportunity to introduce and establish specific biocontrol agents into soils, which in turn leads to sustained biological control based on the activities of microbial communities.

Melanins are darkly pigmented polymers that protect organisms against environmental stress. Even when not directly involved in pathogenesis, fungal melanin is likely required by melanizing phytopathogens for survival in the environment. However, some phytopathogenic fungi that produce melanized appressoria for host invasion require appressorial melanogenesis for pathogenicity. Much less is known about the role melanins play in pathogenesis during infection by other phytopathogens that do not rely on appressoria for host penetration. Here we focus on one such phytopathogenic fungus, Gaeumannomyces graminis var. tritici, the etiologic agent of the devastating root disease of cereals, take-all. This fungus is lightly pigmented in culture, but requires melanin biosynthesis for pathogenesis, perhaps to produce melanized, ectotrophic macrohyphae on roots. However, the constitutively melanized, asexual Phialophora anamorph of G. graminis var. tritici is nonpathogenic. In addition, melanization of G. graminis var. graminis is not required to produce root disease on its rice host. Explanations for these apparent contradictions are suggested, as are other functions for the melanins of phytopathogenic fungi.

Beneficial plant-associated microbes can profoundly influence plant health by suppressing disease, enhancing nutrient uptake, fixing atmospheric nitrogen, and promoting plant growth. Host variation, among cultivars or plant genotypes, for response to beneficial microorganisms suggests that plant genes play a role in supporting these interactions. Such host variation can be found among diverse groups of microorganisms including rhizobia, mycorrhizal fungi, and microbial biocontrol agents. Discrete variation among plant genotypes for interaction with beneficial microbes has led to the discovery of single genes that specify compatible interactions. Continuous variation for interaction phenotypes such as disease suppression, plant growth, or nutrient uptake have led to hypotheses, and in some cases genetic descriptions, of multigenic control of these interactions. Future research into the role of plant genes involved in hosting beneficial plant-associated microbes will provide greater insight into this relatively unexplored area of biology and should provide new tools to improve plant health in agriculture.