Data from: Application of ancient DNA to the reconstruction of past microbial assemblages and for the detection of toxic cyanobacteria in subtropical freshwater ecosystems

Ancient DNA (aDNA) analysis of lake sediments is a promising tool for detecting shifts in past microbial assemblages in response to changing environmental conditions. We examined sediment core samples from subtropical, freshwater Laguna Blanca (Uruguay), which has been severely affected by cultural eutrophication since 1960 and where cyanobacterial blooms, particularly those of the saxitoxin-producer Cylindrospermopsis raciborskii, have been reported since the 1990s. Samples corresponding to ~1846, 1852, 2000 and 2007 A.D. were selected to perform Denaturing Gradient Gel Electrophoresis (DGGE) analysis of the 16S-23S rRNA intergenic transcribed spacer (ribosomal ITS) to compare their prokaryotic assemblage composition. Each stratum showed different ITS patterns, but the composition of 21st Century samples was clearly different than those of mid-19th Century. This compositional change was correlated to shifts in sediment organic matter and chlorophyll a content, which were significantly higher in recent samples. The presence of saxitoxin-producing cyanobacteria was addressed by quantitative real time PCR of the sxtU gene involved in toxin biosynthesis. This gene was present only in recent samples, for which clone libraries and ITS sequencing indicated the presence of Cyanobacteria. Phylogenetic analyses identified C. raciborskii only in the 2000 sample, shortly after several years when blooms were recorded in the lake. These data suggest the utility of aDNA for the reconstruction of microbial assemblage shifts in subtropical lakes, at least on centennial scales. The application of aDNA analysis to genes involved in cyanotoxin synthesis extends the applicability of molecular techniques in paleolimnological studies to include key microbial community characteristics of great scientific and social interest.湖泊沉积物古代DNA（aDNA）分析是检测过往微生物群落响应环境变化发生演替的颇具应用潜力的分析手段。本研究针对乌拉圭亚热带淡水湖拉古纳布兰卡（Laguna Blanca）的沉积物岩芯样本展开分析，该湖自1960年以来受人为富营养化影响严重，且自1990年代起便有蓝藻水华暴发的记录，其中尤以产石房蛤毒素的柱孢藻（Cylindrospermopsis raciborskii）为典型。研究选取对应公元1846年、1852年、2000年及2007年的沉积物样本，针对16S-23S rRNA基因间转录间隔区（ribosomal ITS）开展变性梯度凝胶电泳（Denaturing Gradient Gel Electrophoresis，DGGE）分析，以对比各样本的原核生物群落组成。结果显示，各沉积层的ITS图谱均存在差异，且21世纪样本的群落组成与19世纪中期样本的差异尤为显著。此类群落组成变化与沉积物有机质及叶绿素a含量的变化显著相关，且近年样本的上述指标含量显著更高。本研究通过针对参与毒素生物合成的sxtU基因开展定量实时PCR，检测产石房蛤毒素蓝藻的存在情况：该基因仅在近年样本中检出，针对这些样本构建的克隆文库及ITS测序结果也证实了蓝藻的存在。系统发育分析仅在2000年的样本中检测到柱孢藻（Cylindrospermopsis raciborskii），该时间点恰好在该湖记录到蓝藻水华暴发的数年之后。上述数据表明，古代DNA（aDNA）可用于重建亚热带湖泊的微生物群落演替，至少在百年尺度上具备可行性。将古代DNA（aDNA）分析应用于蓝藻毒素合成相关基因的研究，可将分子技术在古湖沼学研究中的适用范围拓展至兼具重要科学与社会价值的关键微生物群落特征领域。