Rutgers University, Department of Environmental Sciences, 14 College Farm Rd., New Brunswick, NJ 08901, United States.
Rutgers University, Department of Environmental Sciences, 14 College Farm Rd., New Brunswick, NJ 08901, United States.
Sci Total Environ. 2018 Apr 15;621:939-947. doi: 10.1016/j.scitotenv.2017.10.154. Epub 2017 Nov 1.
A limited number of studies have been conducted to analyze ribosomal RNA (rRNA, present in the ribosome) in bioaerosol samples to identify currently or potentially active airborne microbes, although its genomic counterpart, the rRNA gene (on the chromosome) has been frequently targeted for airborne microbial community analysis. A knowledge gap still exists regarding whether the bioaerosol rRNA abundances are affected by the bioaerosol collection process. We investigated the effect of air sampling stress on the measurement and characterization of 16S rRNA for bioaerosols in the laboratory and field experiments using quantitative polymerase chain reaction (qPCR) and high-throughput sequencing techniques. In a laboratory study, known quantities of freshly grown Escherichia coli cells were spiked onto the filter of a Button Aerosol Sampler and into liquids of BioSampler and SpinCon air samplers and then exposed to sampling stress when the samplers were operated for 2h. We found that the recovered cellular 16S rRNA abundance as determined by qPCR was dependent on sampler type. Further, two devices (Button Aerosol Sampler and BioSampler) that exhibited markedly different efficiency in preserving 16S rRNA were employed in an outdoor environment to collect bioaerosols simultaneously on eight days in two different seasons. The abundance of 16S rRNA in the outdoor air sample (1.3×10-4.9×10copies/m) was about two orders of magnitude higher than that of 16S rRNA gene (6.9×10-1.5×10copies/m). The 16S rRNA sequences revealed a different bacterial community compared with 16S rRNA gene-based results across all samples, and this difference depended on the sampling device. In addition, a number of bacterial taxa exhibited higher abundance in the 16S rRNA gene sequences than in 16S rRNA sequences, which suggests the potential activities of certain microbes in airborne phase. Overall, this study highlights the importance of sampling device selection when analyzing RNA in bioaerosols.
已有少量研究分析生物气溶胶样本中的核糖体 RNA（rRNA，存在于核糖体中），以鉴定当前或潜在的空气中微生物，但rRNA 基因（在染色体上）的基因组对应物已被频繁用于空气中微生物群落分析。目前仍然存在一个知识空白，即生物气溶胶 rRNA 的丰度是否受到生物气溶胶收集过程的影响。我们使用定量聚合酶链反应（qPCR）和高通量测序技术，在实验室和现场实验中研究了空气采样压力对生物气溶胶 16S rRNA 测量和特征描述的影响。在实验室研究中，将已知数量的新鲜大肠杆菌细胞接种到 Button 气溶胶采样器的滤器上，并接种到 BioSampler 和 SpinCon 空气采样器的液体中，然后在采样器运行 2 小时时暴露于采样压力下。我们发现，qPCR 测定的回收细胞 16S rRNA 丰度取决于采样器类型。此外，在户外环境中，同时在两个不同季节的八天内，使用两种在保存 16S rRNA 方面表现出明显不同效率的设备（Button 气溶胶采样器和 BioSampler）收集生物气溶胶。户外空气样本中 16S rRNA 的丰度（1.3×10-4.9×10copies/m）比 16S rRNA 基因（6.9×10-1.5×10copies/m）高两个数量级。所有样本的 16S rRNA 序列显示出与基于 16S rRNA 基因的结果不同的细菌群落，这种差异取决于采样设备。此外，一些细菌类群在 16S rRNA 基因序列中的丰度高于 16S rRNA 序列中的丰度，这表明某些微生物在空气中具有潜在的活性。总体而言，这项研究强调了在分析生物气溶胶中的 RNA 时选择采样设备的重要性。
