How to do disease ecology

Abstract Plant disease ecologists rely on a wide array of technical skills to diagnose and study plant disease. Disease intensity can be measured as the prevalence of disease across a host population or the severity of disease in individual plants. Sampling plans must consider both precision and accuracy. Plant diseases are diagnosed through the combination of symptoms in the host and signs of the pathogen itself. Pathogens can be detected in plants or in the environment using cultural methods by growing pathogens in medium (including dilution plating), through serological approaches that use antibodies to detect the pathogen, or through a variety of DNA-based molecular approaches. PCR is used to amplify standard organismal barcodes such as the ribosomal RNA internal transcribed spacer region (ITS); the DNA sequence of the ITS uniquely identifies many fungal pathogens to species or genus and is used to distinguish among fungi. Alternatively, pathogen-specific primers are used to detect pathogens and sometimes to quantify them through real-time PCR. Disease severity is measured by assessing the amount of plant tissue affected by the pathogen, and a range of methods is available to aid precision and accuracy. Impact on the host can be quantified via experimental or observational studies. Disease progress over time is synthesized from repeated measurements of disease prevalence in a population using the area under the disease progress curve.