Comparison of different PCR primers on detecting arbuscular mycorrhizal communities inside plant roots

Communities of arbuscular mycorrhizal fungi (AMF) colonizing roots have been increasingly investigated by molecular approaches with AMF-specific PCR primers. However, it is difficult to compare the species diversity and species compositions of AMF communities across various studies due to the PCR primers used differently, and also little is known if significant difference of community compositions is characterized by different primers. We aim to compare the difference of efficiency of four primers for AMF.

We chose four commonly used AMF-specific primer combinations (NS31-AM1, AMLl-AML2, NS31-AML2 and SSUmCf-LSUmBr), and used 18S rDNA clone libraries to describe the AMF diversity and community.

Our results showed that the specificity and coverage varied among the tested primers, different primer combinations would yield distinct patterns of species diversity and composition of AMF community. SSUmCf-LSUmBr had the best specificity and coverage in amplifying AMF sequences, followed by NS31-AML2 and NS31-AM1, and AML1-AML2 showed the lowest specificity towards AMF sequences.

SSUmCf-LSUmBr is not the optimal primer pair for AMF community study in current stage due to limited reference sequences and large DNA size. As an alternative, NS31-AML2 is more suitable in AMF community study, because its target rDNA region could well match the increasingly used virtual taxonomy database (http://maarjam. botany.ut.ee) and also its suitable DNA size could be efficiently used in high-throughput sequencing.