Tracking fungal community responses to maize plants by DNA- and RNA-based pyrosequencing

We assessed soil fungal communities at two sampling times (t1=47 days and t2=104 days of plant age) associated with four maize cultivars, including two genetically modified (GM) cultivars by high-throughput pyrosequencing of the 18S rRNA gene using DNA and cDNA as template. We detected no significant differences in soil fungal communities associated with plant cultivars. However, clear differences were observed in relation to sampling time and the nucleic pool targeted (DNA versus RNA). The most abundant soil fungi, as recovered by DNA-based methods, did not necessary represent the most “active” fungi (as recovered via rRNA). However, cDNA derived community compositions at t1 were relatively similar to DNA derived communities at t2, based on presence/absence measures of OTUs. We recovered large proportions of fungal sequences belonging to arbuscular mycorrhizal fungi and Basidiomycota, especially at the RNA level, suggesting that these important and potentially beneficial fungi are not affected by the plant cultivars nor by GM traits (Bt toxin production). Our results suggest that even though DNA and cDNA derived soil fungal communities can be very different at a given time, RNA composition may have a strong predictive power of fungal community development through time.