Using rpb1 as a marker gene to assess tillage effects on assemblages of arbuscular mycorrhizal fungi

Due to the potential of arbuscular mycorrhizal fungi (AMF, Glomeromycota) to improve plant growth and soil quality, the influence of agricultural practice on their diversity continues to be an important research question. Up to now studies of community diversity in AMF have exclusively been based on nuclear ribosomal gene regions, which in AMF show high intra-organism polymorphism, seriously complicating interpretation of these data. We designed specific PCR primers for 454 sequencing for a region of the rpb1 gene, and established a new reference dataset comprising all major AMF lineages. This gene is monomorphic within fungal isolates but shows an excellent barcode gap between species. We used these new markers to analyze the influence of tillage regimes on AMF communities in a field experiment. The PCR primers showed a specificity of 99.94%. We found evidence of significant shifts of the AMF communities caused by soil management and for increased patchiness among non-tilled plots. Tillage effects on different AMF taxa are more complex than previously thought and provide indications about their ability to adapt to agricultural management practices and their life history strategies. The high resolving power of high-throughput sequencing highlights the need for quantitative measurements to efficiently detect these effects.