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Background  Knowledge of the natural occurrence and community structure of entomopathogenic fungi is important to understand their ecological role. Species of the genus  Metarhizium  are widespread in soils and have recently been reported to associate with plant roots, but the species  M. flavoviride  has so far received little attention and intra-specific diversity among isolate collections has never been assessed. In the present study  M. flavoviride  was found to be abundant among  Metarhizium  spp. isolates obtained from roots and root-associated soil of winter wheat, winter oilseed rape and neighboring uncultivated pastures at three geographically separated locations in Denmark. The objective was therefore to evaluate molecular diversity and resolve the potential population structure of  M. flavoviride .    Results  Of the 132  Metarhizium  isolates obtained, morphological data and DNA sequencing revealed that 118 belonged to  M. flavoviride , 13 to  M. brunneum  and one to  M. majus . Further characterization of intraspecific variability within  M. flavoviride  was done by using amplified fragment length polymorphisms (AFLP) to evaluate diversity and potential crop and/or locality associations. A high level of diversity among the  M. flavoviride  isolates was observed, indicating that the isolates were not of the same clonal origin, and that certain haplotypes were shared with  M. flavoviride  isolates from other countries. However, no population structure in the form of significant haplotype groupings or habitat associations could be determined among the 118 analyzed  M. flavoviride  isolates.    Conclusions  This study represents the first in-depth analysis of the molecular diversity within a large isolate collection of the species  M. flavoviride . The AFLP analysis confirmed a high level of intra-specific diversity within the species and lack of apparent association patterns with crop or location indicates limited ecological specialization. The relatively infrequent isolation of  M. flavoviride  directly from crop roots suggests low dependence of root association for the species.    Electronic supplementary material  The online version of this article (doi:10.1186/s12866-015-0589-z) contains supplementary material, which is available to authorized users.

Diversity within the entomopathogenic fungal species Metarhizium flavoviride associated with agricultural crops in Denmark