Endophytes, bacterial, fungal or viral, colonize plants often without causing visible symptoms. More important, they may benefit host plants in many ways, most notably by preventing diseases caused by normally virulent pathogens. Craigella tomatoes (Lycopersicon esculentum Mill.) can be infected with Verticillium dahliae Kleb., either race 1 (Vd1) or a non-host isolate Dvd-E6 resulting in susceptibility or tolerance, respectively. The present study sought to determine whether Dvd-E6 is endophytic and can protect tomato against Vd1. The total amount of Verticillium in stems and roots was determined by quantitative PCR; the relative amounts of Vd1 and Dvd-E6 were assessed by restriction fragment polymorphism. When Dvd-E6 infects before or together with Vd1, Vd1 is excluded almost completely from the root but, when Vd1 infects first, Dvd-E6 can compete on an equal basis. Previous studies suggested that Dvd-E6 suppresses symptom-related genes, raising the possibility that Dvd-E6 simultaneously induces tolerance to Vd1. This does not seem to be entirely the case since the minimal symptoms following Vd1 infection of Dvd-E6 tolerant Craigella result, at least in part, from restricted Vd1 colonization. Furthermore, when Vd1 and Dvd-E6 are cultured on PDA plates alone or together, the growth rates are similar and neither is inhibitory to the other. Dvd-E6 does not outgrow or inhibit Vd1, in vitro. The protective effect apparently requires interplay between Dvd-E6 and the plant. Expression analyses of tomato genes involved in resistance and defence support this interpretation.

Although the hypersensitive reaction in foliar plant diseases has been extensively described, little is clear regarding plant defense strategies in vascular wilt diseases affecting numerous economically important crops and trees. We have examined global genetic responses to Verticillium wilt in tomato (Lycopersicon esculentum Mill.) plants differing in Ve1 resistance alleles. Unexpectedly, mRNA analyses in the susceptible plant (Ve1-) based on the microarrays revealed a very heroic but unsuccessful systemic response involving many known plant defense genes. In contrast, the response is surprisingly low in plants expressing the Ve1+ R-gene and successfully resisting the pathogen. Similarly, whole-cell protein analyses, based on 2D gel electrophoresis and mass spectrometry, demonstrate large systemic increases in a variety of known plant defense proteins in the stems of susceptible plants but only modest changes in the resistant plant. Taken together, the results indicate that the large systemic increases in plant defense proteins do not protect the susceptible plant. Indeed, since a number of the highly elevated proteins are known to participate in the plant hypersensitive response as well as natural senescence, the results suggest that some or all of the disease symptoms, including ultimate plant death, actually may be the result of this exaggerated plant response.

Relatively little is known about the molecular mechanisms utilized by plants to defend themselves against fungal vascular pathogens. Based on DNA microarray analyses, in past studies we used a model tomato‐Verticillium pathosystem to compare the global expression of genes in compatible and incompatible interactions. While very significant patterns of mRNA changes were defined, how these are translated at the protein level remained unclear. In the present study, 2D gel electrophoresis and proteomic analyses were applied to evaluate the actual changes in protein levels. Whole cell protein was extracted simultaneously with RNA to permit parallel comparisons of both mRNA and proteins from the same samples. Proteins representing 13 of the most intense changes were identified using mass spectrometry. Three were products of commonly identified pathogenesis related genes, three were peroxidase related and two were osmotin related proteins, all products of genes commonly reported to be involved in genetic responses to stress or pathogens. The levels of induction relative to other cellular proteins were particularly striking, an observation which underlines the plant's heroic systemic response to a vascular disease such as Verticillium wilt.

An endophyte is a microorganism, usually bacterium or fungus, which lives within the internal tissue of a host plant, causing no apparent harm. Some characteristics of an endophyte include ability to promote plant growth and to confer plant tolerance to biotic and abiotic stresses. Endophytic bacteria spread across many phyla including the Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. Endophytic bacteria are recruited by hosts and they get attached to the surface and eventually find their way into the internal tissues where they spread to the intercellular spaces of host plants. These bacteria have been isolated and characterized from different plants. Currently, culture-independent methods such as sequencing of the 16S rRNA gene or metalogenomics are used for identification and characterization of endophytes. The mechanisms by which the endophyte-induced plant protection is brought about can be through direct and/or indirect methods. The direct strategy antagonizes phytopathogens by the production of chemical substances while the indirect mechanisms improve resistance of hosts to pathogens. Global gene expression studies on some common endophytic bacteria implicated these direct and indirect strategies of bacterial-induced protection. More research should be geared towards how the economic importance of endophytic bacteria could be utilized to enhance global food security.

Plants are affected by a number of severe conditions including damages caused by phytopathogens, which ultimately reduce productivity. Overtime, plants have evolved different mechanisms for defence against and resistance to invading pathogens, such as bacteria, viruses and fungi in different pathosystems. Defence mechanisms in plants could either be innate or artificial. Innate defence is said to occur when plants are naturally able to limit the development of a specific pathogen or the damage it may cause based on properties inherent in the plant without human intervention. This defence strategy could be divided into pre-existing and induced defence mechanisms. The pre-existing defence strategy comprises defence gardgets endogenously present in the plant even before pathogen colonization. It include the use of superficial structures (such as thick walled tissues, waxes and cuticle), biochemical substances (such as inhibitors released by plant into its environment) and defence through lack of essential factors (such as lack of host receptors and sensitive sites for toxins). The induced defence mechanism only becomes active in response to pathogen attack. It consists of defence through the formation of structures (such as cytoplasmic and cellular defence structures) and through biochemical reactions or the production of certain substances (such as pathogenesis related proteins and phenolics). Proper understanding of plant defence mechanisms against pathogens is important in developing new and improved disease resistant varieties.