Environmental Science Department, Barnard College, NY, NY, 10027, New York, USA.
Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Sci Rep. 2019 Jul 17;9(1):10370. doi: 10.1038/s41598-019-46663-1.
Determining the carbon sources for active microbial populations in the subsurface is a challenging but highly informative component of subsurface microbial ecology. This work developed a method to provide ecological insights into groundwater microbial communities by characterizing community RNA through its radiocarbon and ribosomal RNA (rRNA) signatures. RNA was chosen as the biomolecule of interest because rRNA constitutes the majority of RNA in prokaryotes, represents recently active organisms, and yields detailed taxonomic information. The method was applied to a groundwater filter collected from a shallow alluvial aquifer in Colorado. RNA was extracted, radiometrically dated, and the 16S rRNA was analyzed by RNA-Seq. The RNA had a radiocarbon signature (ΔC) of -193.4 ± 5.6‰. Comparison of the RNA radiocarbon signature to those of potential carbon pools in the aquifer indicated that at least 51% of the RNA was derived from autotrophy, in close agreement with the RNA-Seq data, which documented the prevalence of autotrophic taxa, such as Thiobacillus and Gallionellaceae. Overall, this hybrid method for RNA analysis provided cultivation-independent information on the in-situ carbon sources of active subsurface microbes and reinforced the importance of autotrophy and the preferential utilization of dissolved over sedimentary organic matter in alluvial aquifers.
确定地下活跃微生物种群的碳源是地下微生物生态学中具有挑战性但信息量很大的组成部分。本研究通过对微生物群落 RNA 的放射性碳和核糖体 RNA（rRNA）特征进行分析，开发了一种方法来深入了解地下水微生物群落的生态特征。选择 RNA 作为感兴趣的生物分子，是因为 rRNA 构成了原核生物中 RNA 的大部分，代表了最近活跃的生物体，并提供了详细的分类信息。该方法应用于从科罗拉多州浅层冲积含水层中采集的地下水过滤器。提取 RNA 后，进行放射性测年，并通过 RNA-Seq 对 16S rRNA 进行分析。RNA 的放射性碳特征（ΔC）为-193.4 ± 5.6‰。将 RNA 的放射性碳特征与含水层中潜在碳库的特征进行比较表明，至少有 51%的 RNA 来自自养生物，这与 RNA-Seq 数据非常吻合，该数据记录了自养生物类群（如硫杆菌和泉古菌科）的普遍存在。总的来说，这种用于 RNA 分析的混合方法提供了关于地下活跃微生物原位碳源的培养独立信息，并强调了自养作用和对冲积含水层中溶解态有机物质优先利用的重要性。
