Since its beginnings, the traditional microbiology has depended on artificial culture media for the study of microorganisms. They must be able not only to reproduce in the media but also to be pure without contamination with other microorganisms. Some microorganisms have been directly observed by staining or because of their manifestations in the environment. The diagnosis of the causal agent of plant diseases is very important for its management and control, so misdiagnosis affects the control actions of primary causal agent. In addition, the diagnosis of plant viral pathogens is important because these diseases occur frequently. It may be due to constant mutations producing new variants, but it could be also due to the erroneous identification . At the present time there are some plant diseases where the causal agent is unknown or the disease symptoms are associated to different pathogens or abiotic agents.
To study some of these microorganisms, lenses have been used for direct observation since 1670, such as Robert Hooke and van Leeuwenhoek Antonius did to see the first structures like hyphae of plant pathogenic fungi, algae, protozoa and some bacterial cells. Today, the detection and identification of new pathogens can be accomplished through a number of traditional and modern techniques. Traditionally, it is done testing a susceptible host or through a set of tests for the characterization of the plant pathogen. This is also possible using molecular techniques such as polymerase chain reaction (PCR) or nucleic acid hybridization. In this sense metagenomics provide a new rationale and effective methodology to identifying the primary causative agents. The study of uncultured microbes may carry out by metagenomics, which gives a broad sight for the investigation of microorganism origins and function in the environment.
Molecular techniques has revealed that more than one pathogen or pathogen isolation may be involved in a plant disease symptom, other contribution is the identification of some pathogens involved in a plant disease which were not identified until today. Plant pathogen genomics offer new knowledge about infection mechanisms, host-plant interactions, new molecular targets for fungicides, bactericides and so on. The Phytopathology in the omics era book has been designed as a text book for a plant pathology bachelor or master degree course, as intent to present in simple terms the most recent advances on the omic sciences, and their applications on plant pathology. Our purpose is present to farmers, students, professors and researchers involved on this agriculture area, a review of plant pathogen genomics, proteomics, transcriptomics and metabolomics. We wish that this kind of scientific knowledge may contribute to a better understanding of plant pathogens, plant disease and plant disease management.