After soybean plants have matured in the field, many organisms begin to grow and colonize these plants. Rainy weather often promotes growth of and colonization by these organisms. The longer that plants have been sitting in a field after they are mature, the more likely that they will be colonized by all types of organisms.
Some of the organisms that are colonizing the soybean plants at this stage are soybean pathogens. The soybean pathogens that are best at colonizing these dead soybean plants generally are also good saprophytes, which means that they are able to grow and obtain nutrients from dead organic matter.
When samples of soybean plants that have been mature for several weeks are submitted to a diagnostic lab, this can present a major challenge for diagnosticians. The challenge is not in finding plant pathogens. In fact, this can be very easy, as they may be all over the plants. The challenge is figuring out which, if any, of these plant pathogens caused a disease on the plant when it was still alive.
Common soybean pathogens that can be found almost every year on soybean plants that have been dead for several weeks include species of Diaporthe (causal agents of stem canker and pod and stem blight), species of Colletotrichum (causal agents of anthracnose), Macrophomina phaseolina (causal agent of charcoal rot), species of Fusarium (many of the Fusarium species found at this stage may not be pathogens of soybean, but some found may include those that cause Fusarium root rot), and species of Alternaria (a well-known group of plant pathogens, but generally not considered a major pathogen of soybean).
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Unfortunately, there are not really any adequate methods available to determine if the pathogens that can be readily found on soybean plants that have been mature for weeks actually caused a disease or if they had any impact on plant growth or yield. The most accurate diagnoses often occur when plants are submitted when they are dying, not after they are dead.
When this occurs, making a correct determination about the relationship between observed symptoms and observed plant pathogens will be much more likely.