The implementation of PCR-based tools for characterisation of organisms has greatly advanced our understanding of the phylogenies and species boundaries in entomopathogenic fungi, especially the widespread taxa Beauveria bassiana and Metarhizium anisopliae. These fungi have received a lot of interest due to their potential as biocontrol agents of pests. However, there is still a lack of knowledge about the fundamental ecology of these fungi in both managed and natural ecosystems, but such information is necessary both for risk assessments prior to release of biocontrol agents in the environment as well as if we wish to understand the distribution of the fungi and their impact on host populations. This latter focus is essential if the fungi are to be included in pest management strategies based on conservation biological control.
A series of unspecific PCR methods have been used to characterise isolates of B. bassiana and M. anisopliae, and many studies have concluded that the fungi contain a lot of genetic diversity. The problem with these methods is that they provide little phylogenetic information of the fungi and the characters can not be used to explicitly compare data between studies. Sequences from specific targets in the DNA provide tools for explicit comparison between isolates across studies. There is now a range of primer sets published along with reference sequences in GenBank to make these comparisons possible. Multi-gene phylogenies have revealed that both B. bassiana and M. anisopliae are complexes of species that contain cryptic taxa or clades. Using merely morphological characteristics will not result in the same degree of taxa identification as will the use of DNA sequence data. Similarly, when using microsatellite markers for population genetic studies of fungal communities, it is necessary to first separate the populations in clades as allele sizes can convert across populations. In the near future, USDA-ARS in Beltsville will launch a web-based platform (MBID, Metarhizium-Beauveria ID) including lists of primers, databases of reference sequences and type isolates of new described species for the reliable identification of taxa for the scientific community. This tool should provide a common framework and nomenclature for scientists and create basis for making comparisons among studies. There should be great potential to learn more about the ecology of the entomopathogenic fungi with the application of these molecular markers. However, designing an appropriate sampling scheme in the environment is absolutely necessary to conduct these ecological studies. The use of isolates from culture collections should be avoided
