Friends and foes: streptomycetes as modulators of plant disease and symbiosis

The ecological role of soil streptomycetes within the plant root environment is currently gaining increased attention. This review describes our recent advances in elucidating the complex interactions between streptomycetes, plants, pathogenic and symbiotic microorganisms. Streptomycetes play diverse roles in plant-associated microbial communities. Some act as biocontrol agents, inhibiting plant interactions with pathogenic organisms. Owing to the antagonistic properties of streptomycetes, they exert a selective pressure on soil microbes, which may not always be for plant benefit. Others promote the formation of symbioses between plant roots and microbes, and this is in part due to their direct positive influence on the symbiotic partner, expressed as, e.g., promotion of hyphal elongation of symbiotic fungi. Recently, streptomycetes have been identified as modulators of plant defence. By repressing plant responses to pathogens they facilitate root colonisation with pathogenic fungi. In contrast, other strains induce local and systemic resistance against pathogens or enhance plant growth. In conclusion, while streptomycetes have a clear potential of acting as biocontrol agents, care has to be taken to avoid strains that select for virulent pathogens or enhance disease development. We argue towards the use of an integrated screening approach in the search for efficient biocontrol agents, including assays on in vitro antagonism, plant growth, and disease suppression.     

Antibiotic production by bacterial biocontrol agents

Interest in biological control of plant pathogens has been stimulated in recent years by trends in agriculture towards greater sustainability and public concern about the use of hazardous pesticides. There is now unequivocal evidence that antibiotics play a key role in the suppression of various soilborne plant pathogens by antagonistic microorganisms. The significance of antibiotics in biocontrol, and more generally in microbial interactions, often has been questioned because of the indirect nature of the supporting evidence and the perceived constraints to antibiotic production in rhizosphere environments. Reporter gene systems and bio-analytical techniques have clearly demonstrated that antibiotics are produced in the spermosphere and rhizosphere of a variety of host plants. Several abiotic factors such as oxygen, temperature, specific carbon and nitrogen sources, and microelements have been identified to influence antibiotic production by bacteria biocontrol agents. Among the biotic factors that may play a determinative role in antibiotic production are the plant host, the pathogen, the indigenous microflora, and the cell density of the producing strain. This review presents recent advances in our understanding of antibiotic production by bacterial biocontrol agents and their role in microbial interactions. This revised version was published online in August 2006 with corrections to the Cover Date.     

Molecular and biochemical aspects of rhizobacterial ecology with emphasis on biological control

The rhizosphere is the narrow zone of soil surrounding the root that is subject to influence by the root. Rhizobacteria are plant-associated bacteria that are able to colonize and persist on roots. An understanding of the ecology of a microorganism is a fundamental requirement for the introduction of a microbial inoculant into the open environment. This is particularly true for biological control of root pathogens in the rhizosphere, where one is actively seeking to alter the ecological balance so as to favour growth of the host plant and to curtail the development of pathogens. Some strains of plant growth-promoting rhizobacteria can effectively colonize plant roots and protect plants from diseases caused by a variety of root pathogens and growth promotion of plants through direct stimulation of growth hormone. Such beneficial or plant health-promoting strains are emerging as promising biocontrol agents. They are suitable as soil inoculants either individually or in combination and may be compatible with current chemical pesticides. Considerable progress has been achieved using molecular genetic techniques to elucidate the important microbial factors or genetic traits involved in the suppression of fungal root diseases. Strategies utilizing molecular genetic techniques have been developed to complement the ongoing research ranging from the characterization and genetic improvement of a selected biocontrol agent to the measurement of its persistence and dispersal. Finally, biocontrol is considered as part of a disease control strategy like integrated pest management which offers a successful approach for the deployment of both agro-chemicals and biocontrol agents.     

Traits of fluorescent Pseudomonas spp. involved in suppression of plant root pathogens.

Certain members of the fluorescent pseudomonad group have been shown to be potential agents for the biocontrol of plant root diseases. The major problems with the commercialization of these beneficial strains are that few wild-type strains contain all the desired characteristics for this process and the performance of strains in different soil and climatic conditions is not reproducible. Consequently, prior to selection and/or improvement of suitable strains for biocontrol purposes, it is necessary to understand the important traits required for this purpose. The production of fluorescent siderophores (iron-binding compounds) and antibiotic compounds has been recognized as important for the inhibition of plant root pathogens. Efficient root colonization is also a prerequisite for successful biocontrol strains. This review discusses some of the characteristics of fluorescent pseudomonads that have been suggested to be important for biocontrol. The genetic organization and regulation of these processes is also examined. This information is necessary for attempts aimed at the improvement of strains based on deregulating pathways or introducing traits from one strain to another. The release of genetically engineered organisms into the environment is governed by regulations, and this aspect is summarized. The commercialization of fluorescent pseudomonads for the biological control of plant root diseases remains an exciting possibility. The understanding of the relevant characteristics will facilitate this process by enabling the direct selection and/or construction of strains which will perform under a variety of environmental conditions.     

Use of molecular techniques to elucidate the mechanisms of action of fungal biocontrol agents: a review

Biological control of fungal plant pathogens appears as an attractive and realistic approach, and numerous microorganisms have been identified as biocontrol agents. There have been many efforts to understand the mechanisms of action of fungal biocontrol agents. Microbiological, microscopic, and biochemical techniques applied over many years have shed light on these mechanisms without fully demonstrating them. More recently, the development of molecular techniques has yielded innovative alternative tools for understanding and demonstrating the mechanisms underlying biocontrol properties. To date, more than 70 publications describe the use of molecular techniques for this purpose. They describe work exploiting targeted or non-targeted gene isolation, gene expression profiling, gene inactivation and/or overexpression, the study of regulatory factors. This work has shed considerable light on mechanisms underlying biocontrol properties. It has also fully demonstrated a number of targeted action mechanisms of some biocontrol agents. This review describes the techniques used in such studies, with their potential and limitations. It should provide a guide for researchers wanting to study the molecular basis of the biocontrol in diverse biocontrol agents.     

Third-party mutualists have contrasting effects on host invasion under the enemy-release and biotic-resistance hypotheses

Plants engage in complex multipartite interactions with mutualists and antagonists, but these interactions are rarely included in studies that explore plant invasiveness. When considered in isolation, we know that beneficial microbes can enhance an exotic plant’s invasive ability and that herbivorous insects often decrease an exotic plant’s likeliness of success. However, the effect of these partners on plant fitness has not been well characterized when all three species coevolve. We use computational evolutionary modeling of a trait-based system to test how microbes and herbivores simultaneously coevolving with an invading plant affect the invaders’ probability of becoming established. Specifically, we designed a model that explores how a beneficial microbe would influence the outcome of an interaction between a plant and herbivore. To model novel interactions, we included a phenotypic trait shared by each species. Making this trait continuous and selectable allows us to explore how trait similarities between coevolving plants, herbivores and microbes affect fitness. Using this model, we answer the following questions: (1) Can a beneficial plant-microbe interaction influence the evolutionary outcome of antagonistic interactions between plants and herbivores? (2) How does the initial trait similarity between interacting organisms affect the likelihood of plant survival in novel locations? (3) Does the effect of tripartite interactions on the invasion success of a plant depend on whether organisms interact through trait similarity [Enemy Release Hypothesis (ERH)] or dissimilarity (Biotic Resistance Hypothesis)? We found that it was much more difficult for plants to invade under the ERH but that beneficial microbes increase the probability of plant survival in a novel range under both hypotheses. To our knowledge, this model is the first to use tripartite interactions to explore novel species introductions. It represents a step towards gaining a better understanding of the factors influencing establishment of exotic species to prevent future invasions.     

Effects of actinobacteria on plant disease suppression and growth promotion

Biological control and plant growth promotion by plant beneficial microbes has been viewed as an alternative to the use of chemical pesticides and fertilizers. Bacteria and fungi that are naturally associated with plants and have a beneficial effect on plant growth by the alleviation of biotic and abiotic stresses were isolated and developed into biocontrol (BCA) and plant growth-promoting agents (PGPA). Actinobacteria are a group of important plant-associated spore-forming bacteria, which have been studied for their biocontrol, plant growth promotion, and interaction with plants. This review summarizes the effects of actinobacteria as BCA, PGPA, and its beneficial associations with plants.     

Isolation and Characterization of Antagonistic Bacillus Strains Capable to Degrade Ethylenethiourea

In this study, more than 150 bacteria showing antagonistic properties against bacterial and fungal pathogens of the tomato plant were isolated and characterized. The most efficient agents against these phytopathogenic microorganisms belong to the genus Bacillus: the best biocontrol isolates were representatives of Bacillus subtilis, B. mojavensis and B. amyloliquefaciens species. They intensively produced fengycin or/and surfactin depsipeptide antibiotics and also proved to be excellent protease secretors. It was proved, that the selected strains were able to use ethylenethiourea (ETU) as sole nitrogen source. These antagonistic and ETU-degrading Bacillus strains can be applied as biocontrol and also as bioremediation agents.     

The function of terpene natural products in the natural world

As the largest class of natural products, terpenes have a variety of roles in mediating antagonistic and beneficial interactions among organisms. They defend many species of plants, animals and microorganisms against predators, pathogens and competitors, and they are involved in conveying messages to conspecifics and mutualists regarding the presence of food, mates and enemies. Despite the diversity of terpenes known, it is striking how phylogenetically distant organisms have come to use similar structures for common purposes. New natural roles undoubtedly remain to be discovered for this large class of compounds, given that such a small percentage of terpenes has been investigated so far.     

Biological Control of Oomycete Soilborne Diseases Caused by Phytophthora capsici,Phytophthora infestans,and Phytophthora nicotianae in Solanaceous Crops

Oomycete pathogens that belong to the genus Phytophthora cause devastating diseases in solanaceous crops such as pepper, potato, and tobacco, resulting in crop production losses worldwide. Although the application of fungicides efficiently controls these diseases, it has been shown to trigger negative side effects such as environmental pollution, phytotoxicity, and fungicide resistance in plant pathogens. Therefore, biological control of Phytophthora-induced diseases was proposed as an environmentally sound alternative to conventional chemical control. In this review, progress on biological control of the soilborne oomycete plant pathogens, Phytophthora capsici, Phytophthora infestans, and Phytophthora nicotianae, infecting pepper, potato, and tobacco is described. Bacterial (e.g., Acinetobacter, Bacillus, Chryseobacterium, Paenibacillus, Pseudomonas, and Streptomyces) and fungal (e.g., Trichoderma and arbuscular mycorrhizal fungi) agents, and yeasts (e.g., Aureobasidium, Curvibasidium, and Metschnikowia) have been reported as successful biocontrol agents of Phytophthora pathogens. These microorganisms antagonize Phytophthora spp. via antimicrobial compounds with inhibitory activities against mycelial growth, sporulation, and zoospore germination. They also trigger plant immunity-inducing systemic resistance via several pathways, resulting in enhanced defense responses in their hosts. Along with plant protection, some of the microorganisms promote plant growth, thereby enhancing their beneficial relations with host plants. Although the beneficial effects of the biocontrol microorganisms are acceptable, single applications of antagonistic microorganisms tend to lack consistent efficacy compared with chemical analogues. Therefore, strategies to improve the biocontrol performance of these prominent antagonists are also discussed in this review.     

Natural solution to antibiotic resistance: bacteriophages ‘The Living Drugs’

Antibiotics have been a panacea in animal husbandry as well as in human therapy for decades. The huge amount of antibiotics used to induce the growth and protect the health of farm animals has lead to the evolution of bacteria that are resistant to the drug’s effects. Today, many researchers are working with bacteriophages (phages) as an alternative to antibiotics in the control of pathogens for human therapy as well as prevention, biocontrol, and therapy in animal agriculture. Phage therapy and biocontrol have yet to fulfill their promise or potential, largely due to several key obstacles to their performance. Several suggestions are shared in order to point a direction for overcoming common obstacles in applied phage technology. The key to successful use of phages in modern scientific, farm, food processing and clinical applications is to understand the common obstacles as well as best practices and to develop answers that work in harmony with nature.     

Effects of arbuscular mycorrhizal fungi and a non-pathogenic<Emphasis Type="Italic"> Fusarium oxysporum</Emphasis> on<Emphasis Type="Italic"> Meloidogyne incognita</Emphasis> infestation of tomato

Arbuscular mycorrhizal (AM) fungi and non-pathogenic strains of soil-borne pathogens have been shown to control plant parasitic nematodes. As AM fungi and non-pathogenic fungi improve plant health by different mechanisms, combination of two such partners with complementary mechanisms might increase overall control efficacy and, therefore, provide an environmentally safe alternative to nematicide application. Experiments were conducted to study possible interactions between the AM fungus Glomus coronatum and the non-pathogenic Fusarium oxysporum strain Fo162 in the control of Meloidogyne incognita on tomato. Pre-inoculation of tomato plants with G. coronatum or Fo162 stimulated plant growth and reduced M. incognita infestation. Combined application of the AM fungus and Fo162 enhanced mycorrhization of tomato roots but did not increase overall nematode control or plant growth. A higher number of nematodes per gall was found for mycorrhizal than non-mycorrhizal plants. In synergisms between biocontrol agents, differences in their antagonistic mechanisms seem to be less important than their effects on different growth stages of the pathogen.     

Ecological,practical, and political inputs into selection of weed targets: What makes a good biological control target?

The topic of ecological, practical, and political considerations in the selection of weed targets for biological control has been widely discussed during the past two decades, mostly from the perspective of insect herbivores. For conceptual and practical purposes, plant pathogens have been treated in these discussions as if they are a subset of inoculative biocontrol agents, with little said about the inherent differences between pathogens and insects as biocontrol agents or the selection of weed targets for control by the inundative, bioherbicide strategy. Herein, I attempt to address the question of what makes a good biological control target for plant pathogens used as inoculative as well as inundative agents, basing my analysis on examples from the past three decades. Despite the small number of examples available for this analysis, the following generalizations can be made: (1) Weeds with robust capacity for vegetative regeneration are more difficult to control with pathogens than those that lack this trait. (2) A plant’s growth habit is not a reliable guide for target selection; weeds that have been successfully controlled include annual and biennial herbs, perennial shrubs, perennial vines, and trees, while numerous failures have been reported irrespective of the target’s growth habit or reproductive mode. (3) It is more challenging to control species with genetic heterogeneity and capacity for introgression than genetically homogeneous and reproductively conserved species. (4) Matching the target host’s susceptibility with the candidate pathogen’s virulence is of utmost importance for biocontrol success since host–pathogen interactions at the species and subspecies levels are often governed by single-gene differences (e.g., varietal specificity). (5) Practical and political considerations are central to the selection of targets for control with pathogens. (6) Demand from influential stakeholders for control and/or for a nonchemical or economically sustainable control typically drives the initiative as well as the continuance of biocontrol projects to their completion. (7) In the case of inundative, bioherbicide agents, the continuity and ultimate implementation of a project will be dictated by the prospects of economic returns from developing and using a pathogen. (8) The stakeholders’ perceptions of the effectiveness of a biocontrol program can be unpredictable, leading to conflicting views of “success.” In the final analysis, a good weed target for control by a pathogen is one that has strong stakeholder backing and the list of available pathogens for the target suggests a possibility of acceptable control at a cost that is competitive with those of other control options. While this conclusion is also applicable to target selection for insect biocontrol agents, it is more relevant for pathogens because of limited funding and personnel available for development of pathogens and the added cost and technological complexity of implementing bioherbicides compared to classical biocontrols.     

In vitro antagonism of an actinobacterial Kitasatospora isolate against the plant pathogen Phytophthora citricola as elucidated with ultrahigh resolution mass spectrometry

Many soil microorganisms antagonistic to soil borne plant pathogens are well known for their ability to control diseases in situ. A variety of substances, like lytic enzymes, siderophores and antibiotics, produced by these organisms have the potential to protect roots against pathogens. Understanding the ecology and a functional assessment of antagonistic microbial communities in soil requires in-depth knowledge of the mechanisms involved in these interactions, a challenging task in complex systems if low-resolution methods are applied. We propose an information-rich strategy of general relevance, composed of adequate preconcentration in conjunction with ultrahigh resolution ion cyclotron resonance Fourier transform mass spectrometry (ICR-FT/MS) and nuclear magnetic resonance (NMR) spectroscopy to identify any bioactive substances in complex systems. This approach is demonstrated on the specific example of substance identification considered responsible for in vitro antagonism of an actinobacterial antagonist isolated from European beech (Fagus sylvatica) rhizosphere soil against the oomycetous root rot pathogen Phytophthora citricola. The isolate belonging to the genus Kitasatospora exhibited strong antibiosis against the oomycete in vitro. The bioactive substance was observed to exhibit a molar mass of 281.1699 g/mol in positive electrospray ionization mass spectra, and the high mass accuracy of the ICR-FT/MS measurements allowed a precise assignment of a molecular formula that was found identical to the macrolide polyketide cycloheximide C(15)H(23)NO(4)+H(+); its identity was then unequivocally confirmed by the information-rich atomic signature of proton NMR spectroscopy. In conclusion, the combination of the near orthogonal methods (pre)fractionation, ultrahigh-resolution ICR-FT mass spectrometry (yielding molecular and MS(n) fragment signatures) and nuclear magnetic resonance spectroscopy (providing atomic signatures) has been found capable of identifying a biocontrol active compound of Kitasatospora active against Phytophthora citricola expediently, quickly, and accurately. This straightforward approach is of general applicability to elucidate biocontrol mechanisms in any complex system with improved efficiency.     

Fungal chitinases and their biological role in the antagonism onto nematode eggs. A review

Chitin, the most abundant aminopolysaccharide in nature, is a rigid and resistant structural component that contributes to the mechanical strength of chitin-containing organisms. Chemically, it is a linear cationic heteropolysaccharide composed of N-acetyl-D-glucosamine and D-glucosamine units. The enzymatic degradation of chitin is performed by a chitinolytic system with synergistic and consecutive action. Diverse organisms (containing chitin or not) produce a great variety of chitinolytic enzymes with different specificities and catalytic properties. Their physiological roles involve nutrition, parasitism, chitin recycling, morphogenesis, and/or defense. Microorganisms, as the main environmental chitin degraders, constitute a very important natural source of chitinolytic enzymes. Nowadays, the most used method for pest and plant diseases control is the utilization of chemical agents, causative of significant environmental pollution. Social concern has generated the search for alternative control systems (i.e., biological control), which contribute to the generation of sustainable agricultural development. Interactions among the different organisms are the natural bases of biological control. Interest in chitinolytic enzymes in the field of biological control has arisen due to their possible involvement in antagonistic activity against pathogenic chitin-containing organisms. The absence of chitin in plants and vertebrate animals allows the consideration of safe and selective “target” molecules for control of chitin-containing pathogenic organisms. Fungi show appropriate characteristics as potential biological control agents of insects, fungi, and nematodes due to the production of fungal enzymes with antagonistic action. The antagonistic interactions between fungi and plant nematode parasites are among the most studied experimental models because of the high economic relevance. Fungi which target nematodes are known as nematophagous fungi. The nematode egg is the only structural element where the presence of chitin has been demonstrated. In spite of being one of the most resistant biological structures, eggs are susceptible to being attacked by egg-parasitic fungi. A combination of physical and chemical phenomena result in their complete destruction. The contribution of fungal chitinases to the in vitro rupture of the eggshell confirms their role as a pathogenic factor. Chitinases have been produced by traditional fermentation methods, which have been improved by optimizing the culture conditions for industrial processes. Although wild-type microorganisms constitute an alternative source of chitinolytic enzymes, the advances in molecular biology are allowing the genetic transformation of fungi to obtain strains with high capability as biocontrol agents. Simultaneously, a better understanding of rhizosphere interactions, additional to the discovery of new molecular biology tools, will allow the choosing of better alternatives for the biological control of nematodes in order to achieve an integrated management of the soil ecosystem.     

Fungal (-like) biocontrol organisms in tomato disease control

The worldwide important crop tomato is attacked by various pathogens, for which management is still primarily reliant on fungicides despite increasing concerns and constraints on their use. Other approaches are investigated, including the use of biocontrol organisms to manage tomato diseases. In this review we discuss and compare the interaction of major biocontrol fungi (BCF) with tomato, including the endophytic arbuscular mycorrhizal fungi and Piriformospora indica, the free-living opportunistic symbionts Trichoderma spp. and non-pathogenic Fusarium oxysporum, as well as the oomycete Pythium oligandrum. We cover recent advances that have been made in unraveling biocontrol modes of action against the most important tomato pathogens, encompassing direct effects of the BCF on pathogens and their indirect effects through the plant, with a main focus on induced systemic resistance. It is an exciting era for the study of biocontrol tripartite interactions, with the emergence of next-generation sequencing tools and the higher pace at which new genomes are being sequenced nowadays, as was recently also achieved for tomato. In addition, plant pathology and biocontrol research domains are increasingly reaching out to each other, because of the parallels that we are only beginning to discover between the interactions of beneficial and detrimental micro-organisms with a plant. Considering the enormous technological possibilities at hand today, this seems a timely opportunity to review the most recent advances in this field and to anticipate to what is ahead of us, discussing breakthroughs expected in our understanding of biocontrol interactions and remaining hurdles on the way to reach them.     

Ecology and biological control application of multicoloured Asian ladybird, Harmonia axyridis: A review

The ecology of and biological control by multicoloured Asian ladybird beetle, Harmonia axyridis (Pallas) are reviewed. Our emphasis is on assembling and interpreting information on general characteristics, invasion and establishment, sexual activity, foraging and predation, development, survival and reproduction, predator-predator interactions, natural enemies, biocontrol, non-target effects and status of H. axyridis as a pest of fruits. Colonization of H. axyridis for aphid biocontrol in the USA have been successful in terms of its establishment, but its abundance is turning out to be a nuisance to humans. Its harmful non-target impact on beneficial organisms, humans and native species is becoming a debatable issue. The question on its present position, whether it is a biocontrol agent or pest, is a critical issue and discussed. Inferences from the empirical data are made and new avenues for future research are suggested.     

Microbiology is the basis of sustainable agriculture: an opinion

Agricultural microbiology is presented as a synthetic research field responsible for knowledge transfer from general microbiology and microbial ecology to the agricultural biotechnologies. The major goal of agricultural microbiology is a comprehensive analysis of symbiotic micro‐organisms (bacteria, fungi) interacting with agriculturally important plants and animals: here we have focussed on plants. In plants, interactions with micro‐organisms are diverse, ranging from two‐partite symbioses (e.g. legume–rhizobia N₂‐fixing nodular symbioses or arbuscular mycorrhiza) to multipartite endophytic and epiphytic (root‐associated, phyllosphere) communities. Two‐partite symbioses provide the clearest models for addressing genetic cooperation between partners, resulting in the formation of super‐organism genetic systems, which are responsible for host productivity. Analysis of these systems has now been extended considerably by using the approaches of metagenomics, which allow the dissection of taxonomic/population structures and the metabolic/ecological functions of microbial communities, which have resulted from the adaptation of free‐living, soil microflora in the endosymbiotic niches. Both beneficial (nutritional, defensive, regulatory) and antagonistic (biocontrol) functions expressed by symbiotic microbes towards their hosts are the potential subjects of effective agronomic use. A fundamental knowledge of the genetics, molecular biology, ecology and evolution of symbiotic interactions could enable the development of microbe‐based sustainable agriculture. This could achieve: (a) an improvement of major adaptive functions and productivity in crop plants by manipulating their microbial cohabitants; (b) partial or even full substitution of ecologically hazardous agrochemicals (mineral fertilizers, pesticides) by microbial preparations; (c) a decrease in the cost and an improvement of the quality of agricultural products.     

Immunity against extracellular pathogens

Summary Eukaryotic cells live in a relatively comfortable equilibrium with a wide variety of microbes. However, while many of the cohabiting microorganisms are harmless or even beneficial to the eukaryotic host, a number of prokaryotes have evolved the capacity to invade and replicate within host cells, thereby becoming potentially pathogenic. To be able to cope with potential pathogens, most organisms have developed several host defense mechanisms. First, microbes can be internalized and destroyed by a number of cell types of an innate immune system in a rather aspecific manner. Second, more complex organisms possess additionally an adaptive immune system that is capable of eliminating hazardous microbes in a highly specific manner. This review describes recent progress in our understanding of how pathogens interact with cells of the immune system, resulting in activation of the immune system or, for certain microorganisms, in the evasion of host defense reactions.