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.

本研究以DNA与cDNA为模板，对18S rRNA基因开展高通量焦磷酸测序（high-throughput pyrosequencing），以此评估两个采样时间点（植株生长47天的t1时刻与104天的t2时刻）下，四个玉米品种（包含两个转基因（genetically modified，GM）品种）的土壤真菌群落。研究未检测到不同玉米品种相关的土壤真菌群落存在显著差异。但在采样时间与靶向核酸类型（DNA与RNA）维度上，观测到了明显差异。基于DNA方法检测得到的丰度最高的土壤真菌，未必即为最具“活性”的真菌（即通过rRNA测序得到的类群）。基于操作分类单元（Operational Taxonomic Units，OTU）的有无分析结果显示，t1时刻的cDNA来源群落组成与t2时刻的DNA来源群落组成相对相似。本研究获取到了大量属于丛枝菌根真菌与担子菌门的真菌序列，尤其在RNA水平上，这表明这类重要且具有潜在益生功能的真菌，既不受玉米品种的影响，也不受转基因性状（Bt毒素合成）的影响。本研究结果表明，尽管同一时间点下DNA与cDNA来源的土壤真菌群落可能差异显著，但RNA组成或可较强地预测真菌群落随时间的动态变化。