Summary• Sequencing of the 5 ′ end of the large ribosomal subunit (LSU rDNA) and quantitative polymerase chain reaction (qPCR) were combined to assess the impact of four annual Medicago species ( Medicago laciniata , Medicago murex , Medicago polymorpha and Medicago truncatula ) on the genetic diversity of arbuscular mycorrhizal (AM) fungi, and on the relative abundance of representative AM fungal genotypes, in a silty-thin clay soil (Mas d'Imbert, France).• Two hundred and forty-six Glomeromycete LSU rDNA sequences from the four plant species and the bulk soil were analysed. The high bootstrap values of the phylogenetic tree obtained allowed the delineation of 12 operational taxonomic units (OTUs), all belonging to Glomus .• Specific primers targeting Glomeromycetes and major OTUs were applied to quantify their abundance by qPCR. Glomeromycetes and targeted OTUs were significantly more abundant in the root tissues than in the bulk soil, and the frequencies of three of them differed significantly in the root tissues of the different plant species.• These differences indicate that, despite the absence of strict host specificity in mycorrhizal symbiosis, there was a preferential association between some AM fungal and plant genotypes.

Mycorrhizae result from symbiotic associations between soil fungi and the roots of most plants. Mycorrhizae are considered to be classic examples of mutualistic symbioses. The basis for this mutualism relies on the supply of carbon to the fungus by the host plant and, in return, on the supply of mineral nutrients and water to the plant and on the plant's protection against soil-borne diseases by the fungus (41). Among mycorrhizal symbioses, arbuscular mycorrhizae (AM) are the most widespread. AM are recorded in 80% of land plants and are generated by the association of plant roots and fungal populations belonging to the Glomeromycota phylum (37, 41), which includes around 160 species (23,45). AM are ancient; the first fossil evidence of this symbiosis dates back 400 million years (33). Several authors have proposed that AM have contributed to the colonization of early land plants (32,38).AM are generally assumed to be nonspecific associations, since Glomeromycota are able to colonize roots of several host plants and are themselves colonized by different AM fungal species (12,14,35,44). Despite this lack of host specificity, the diversity of AM fungi has been shown to affect the plant community composition under field conditions (43), and the genetic structure of the AM fungal community was shown to differ significantly according to the plant species

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