Isolation source matters: sclerotia and ectomycorrhizal roots provide different views of genetic diversity in <i>Cenococcum geophilum</i>

<i>Cenococcum geophilum</i> forms sclerotia and ectomycorrhizas with host plants in forest soils. We demonstrated the differences in genetic diversity of <i>C. geophilum</i> between cultured isolates from sclerotia and those from ectomycorrhizal roots in the same 73 soil samples based on glyceraldehyde-3-phosphate dehydrogenase (<i>GAPDH</i>) gene sequences and newly developed microsatellite markers. Based on <i>GAPDH</i> sequences, 759 cultured isolates (553 from sclerotia and 206 from ectomycorrhizas) were classified into 107 “genotypes” with sequence variation of up to 8.6%. The total number of <i>GAPDH</i> genotypes per soil sample ranged from 1 to 9, but genotypes that were shared between sclerotia and ectomycorrhizas were uncommon (0–3 per soil sample). More than 50% of <i>GAPDH</i> genotypes were unique to one source in most soil samples. Unique <i>GAPDH</i> genotypes were detected from either scleotia or ectomycorrhizal roots in most of the soil samples. Multilocus analysis using nine microsatellite markers provided additional resolution to differentiate fungal individuals and supported the results of <i>GAPDH</i> genotyping. The results indicated that sampling both sclerotia and ectomycorrhizal roots maximizes the detection of diversity at the soil core scale. On the other hand, when all isolates were viewed together, 82 <i>GAPDH</i> genotypes were unique to sclerotia whereas only 6 <i>GAPDH</i> genotypes were unique to ectomycorrhizas. Rarefaction analysis indicated that <i>GAPDH</i> genotypic diversity is significantly higher in sclerotia than ectomycorrhizal roots and the diversity within sclerotia is nearly the same as that of both sclerotia and ectomycorrhizas together. These findings suggest that sampling sclerotia alone is likely to detect the majority of <i>GAPDH</i> genotypes in <i>Cenococcum</i> at the regional scale. When deciding whether to sample sclerotia, ectomycorrhizas, or both types of tissues from <i>Cenococcum</i>, it is critical to consider the spatial scale and also the main questions and hypotheses of the study.