The colonization of land by plants appears to have coincided with the appearance of mycorrhiza-like fungi. Over evolutionary time, fungi have maintained their prominent role in the formation of mycorrhizal associations. In addition, however, they have been able to occupy other terrestrial niches of which the decomposition of recalcitrant organic matter is perhaps the most remarkable. This implies that, in contrast to that of aquatic organic matter decomposition, bacteria have not been able to monopolize decomposition processes in terrestrial ecosystems. The emergence of fungi in terrestrial ecosystems must have had a strong impact on the evolution of terrestrial bacteria. On the one hand, potential decomposition niches, e.g. lignin degradation, have been lost for bacteria, whereas on the other hand the presence of fungi has itself created new bacterial niches. Confrontation between bacteria and fungi is ongoing, and from studying contemporary interactions, we can learn about the impact that fungi presently have, and have had in the past, on the ecology and evolution of terrestrial bacteria. In the first part of this review, the focus is on niche differentiation between soil bacteria and fungi involved in the decomposition of plant-derived organic matter. Bacteria and fungi are seen to compete for simple plant-derived substrates and have developed antagonistic strategies. For more recalcitrant organic substrates, e.g. cellulose and lignin, both competitive and mutualistic strategies appear to have evolved. In the second part of the review, bacterial niches with respect to the utilization of fungal-derived substrates are considered. Here, several lines of development can be recognized, ranging from mutualistic exudate-consuming bacteria that are associated with fungal surfaces to endosymbiotic and mycophagous bacteria. In some cases, there are indications of fungal specific selection in fungus-associated bacteria, and possible mechanisms for such selection are discussed.

Living in a fungal world: impact of fungi on soil bacterial niche development⋆

Plant diseases need to be controlled to maintain the quality and abundance of food, feed, and fiber produced by growers around the world. Different approaches may be used to prevent, mitigate or control plant diseases. Beyond good agronomic and horticultural practices, growers often rely heavily on chemical fertilizers and pesticides. Such inputs to agriculture have contributed significantly to the spectacular improvements in crop productivity and quality over the past 100 years. However, the environmental pollution caused by excessive use and misuse of agrochemicals, as well as fear-mongering by some opponents of pesticides, has led to considerable changes in people’s attitudes towards the use of pesticides in agriculture. Today, there are strict regulations on chemical pesticide use, and there is political pressure to remove the most hazardous chemicals from the market. Additionally, the spread of plant diseases in natural ecosystems may preclude successful application of chemicals, because of the scale to which such applications might have to be applied. Consequently, some pest management researchers have focused their efforts on developing alternative inputs to synthetic chemicals for controlling pests and diseases. Among these alternatives are those referred to as biological controls.

/pdf/biological-control-of-plant-pathogens-2035vipjmu.pdf

Biological Control of Plant Pathogens

Certain strains of fluorescent pseudomonads are important biological components of agricultural soils that are suppressive to diseases caused by pathogenic fungi on crop plants. The biocontrol abilities of such strains depend essentially on aggressive root colonization, induction of systemic resistance in the plant, and the production of diffusible or volatile antifungal antibiotics. Evidence that these compounds are produced in situ is based on their chemical extraction from the rhizosphere and on the expression of antibiotic biosynthetic genes in the producer strains colonizing plant roots. Well-characterized antibiotics with biocontrol properties include phenazines, 2,4-diacetylphloroglucinol, pyoluteorin, pyrrolnitrin, lipopeptides, and hydrogen cyanide. In vitro, optimal production of these compounds occurs at high cell densities and during conditions of restricted growth, involving (i) a number of transcriptional regulators, which are mostly pathway-specific, and (ii) the GacS/GacA two-component system, which globally exerts a positive effect on the production of extracellular metabolites at a posttranscriptional level. Small untranslated RNAs have important roles in the GacS/GacA signal transduction pathway. One challenge in future biocontrol research involves development of new strategies to overcome the broad toxicity and lack of antifungal specificity displayed by most biocontrol antibiotics studied so far.

Regulation of antibiotic production in root-colonizing pseudomonas spp. and relevance for biological control of plant disease

The genus Verticillium encompasses phytopathogenic species that cause vascular wilts of plants. In this review, we focus on Verticillium dahliae, placing emphasis on the controversy surrounding the elevation of a long-spored variant as a new species, recent advances in the analysis of compatible and incompatible interactions, highlighted by the use of strains expressing fluorescent proteins, and the genetic diversity among Verticillium spp. A synthesis of the approaches to explore genetic diversity, gene flow, and the potential for cryptic recombination is provided. Control of Verticillium wilt has relied on a panoply of chemical and nonchemical strategies, but is beset with environmental or site-specific efficacy problems. Host resistance remains the most logical choice, but is unavailable in most crops. The genetic basis of resistance to Verticillium wilt is unknown in most crops, as are the subcellular signaling mechanisms associated with Ve-mediated, race-specific resistance. Increased understanding in each of these areas promises to facilitate management of Verticillium wilts across a broad range of crops.

/pdf/diversity-pathogenicity-and-management-of-verticillium-fv3gg7mppu.pdf

Diversity, Pathogenicity, and Management of Verticillium Species

Plant roots communicate with microbes in a sophisticated manner through chemical communication within the rhizosphere, thereby leading to biofilm formation of beneficial microbes and, in the case of plant growth-promoting rhizomicrobes / -bacteria (PGPR), resulting in priming of defense or induced resistance in the plant host. The knowledge of plant-plant and plant-microbe interactions have been greatly extended over recent years; however, the chemical communication leading to priming is far from being well understood. Furthermore, linkage between below- and above-ground plant physiological processes adds to the complexity. In metabolomics studies, the main aim is to profile and annotate all exo- and endo-metabolites in a biological system that drive and participate in physiological processes. Recent advances in this field has enabled researchers to analyze hundreds of compounds in one sample over a short time period. Here, from a metabolomics viewpoint, we review the interactions within the rhizosphere and subsequent above-ground ‘signalomics’, and emphasize the contributions that mass spectrometric-based metabolomic approaches can bring to the study of plant-beneficial – and priming events.

/pdf/the-chemistry-of-plant-microbe-interactions-in-the-3oajtrgm2k.pdf

The Chemistry of Plant-Microbe Interactions in the Rhizosphere and the Potential for Metabolomics to Reveal Signaling Related to Defense Priming and Induced Systemic Resistance.

Bull, C. T., Shetty, K. G., and Subbarao, K. V. 2002. Interactions between myxobacteria, plant pathogenic fungi, and biocontrol agents. Plant Dis. 86:889-896. Myxobacteria are soil dwelling gram-negative gliding bacteria that form fruiting bodies containing myxospores. Although myxobacteria produce a wide range of antibiotics and lytic enzymes that assist in their ability to prey on other microorganisms, their role in agriculture has received little attention. Myxococcus spp. were isolated from soils in organic and conventionally managed strawberry production and transplant fields in the absence of soil fumigation. Fumigation with methyl bromide and chloropicrin virtually eliminated these organisms from soil. However, soil fumigation had no effect on the frequency of isolation of Myxococcus spp. from strawberry roots. Six Myxococcus spp. were tested in vitro against eight soilborne plant pathogenic fungi (Cylindrocarpon spp., Fusarium oxysporum f. sp. apii, Phytophthora capsici, Pythium ultimum, Rhizoctonia spp., Sclerotinia minor, Verticillium albo-atrum, and V. dahliae) and against two fungal biological control agents (Gliocladium virens and Trichoderma viride). Phytophthora capsici, Pythium ultimum, Rhizoctonia spp., S. minor, and T. viride were completely inhibited by all of the Myxococcus spp. tested. F. oxysporum f. sp. apii was the least sensitive to the myxobacteria, and no inhibition occurred with some Myxococcus spp. Inhibition of the other fungi tested was variable. Myxococcus coralloides inhibited nearly all the fungi tested. The ability of bacterial biological control agents to produce antibiotics and other secondary metabolites determined whether or not they were lysed by myxobacteria. Secondary metabolite production regulated by gacS protected Pseudomonas fluorescens strain CHA0 from lysis by myxobacteria. More specifically, phenazine antibiotics produced by Pseudomonas aureofaciens strain 30-84 protected it from lysis.

https://apsjournals.apsnet.org/doi/pdfplus/10.1094/PDIS.2002.86.8.889

Interactions Between Myxobacteria, Plant Pathogenic Fungi, and Biocontrol Agents.

Broccoli is resistant to Verticillium dahliae infection and does not express wilt symptoms. Incorporation of broccoli residues reduces soil populations of V. dahliae. The effects of broccoli residue were tested on the colonization of roots by V. dahliae, plant growth response, and disease incidence of both broccoli and cauliflower in soils with different levels of V. dahliae inoculum and with or without fresh broccoli residue amendments. The three soils included a low-Verticillium soil, a high-Verticillium soil, and a broccoli-rotation soil (soil from a field after two broccoli crops) with an average of 13, 38, and below-detectable levels of microsclerotia per g of soil, respectively. Cauliflower plants in broccoli-amended high-Verticillium soil had significantly (P </= 0.05) lower wilt incidence and severity than did plants in unamended soil. An immunohistochemical staining assay utilizing a monoclonal antibody specific to V. dahliae was used to determine colonization of the root cortex. Despite the absence of wilt symptoms, broccoli roots were colonized by V. dahliae. In high-Verticillium soil, the broccoli residue amendment caused a marked reduction in colonization rate of V. dahliae per unit of inoculum on both cauliflower and broccoli roots. In addition to its detrimental effects on the viability of microsclerotia in soil, broccoli residue may also have an inhibitory effect on the root-colonizing potential of surviving microsclerotia.

https://apsjournals.apsnet.org/doi/pdfplus/10.1094/PHYTO.2000.90.3.305

Mechanism of broccoli-mediated verticillium wilt reduction in cauliflower.

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Interactions Between Myxobacteria, Plant Pathogenic Fungi, and Biocontrol Agents.

Mechanism of broccoli-mediated verticillium wilt reduction in cauliflower.