Combining real-time PCR and next-generation DNA sequencing to provide quantitative comparisons of fungal aerosol populations
Combining real-time PCR and next-generation DNA sequencing to provide quantitative comparisons of fungal aerosol populations
复制标题
DOI：
10.1016/j.atmosenv.2013.11.036
复制
发表时间：
2014-02-01
影响因子：
5
通讯作者：
Peccia, Jordan
中科院分区：
文献类型：
--
作者：
Dannemiller, Karen C.;Lang-Yona, Naama;Peccia, Jordan
我们研究了真菌群落与PM10质量的Rehobaly，以色列室外空气样品收集在春季和秋季。通过对真菌核糖体RNA编码基因的内转录间隔区（ITS）进行454焦磷酸测序来描述真菌群落。为了更定量地比较人类中的真菌暴露，通过将特定分类群的相对丰度值乘以样品的总真菌孢子浓度（源自通用真菌qPCR）将这些值转换为绝对浓度。接下来，基于测序的链格孢、枝孢状枝孢、黑附球菌和青霉/曲霉属的绝对浓度。与A. alternata、互花米草C. cladosporioides、枝孢真杆菌E.黑曲霉（Penicillium/Aspergillus spp.）来自同一个春季和秋季的气溶胶样本。这些比较的结果表明，焦磷酸测序产生的绝对浓度值与分类群特异性qPCR产生的浓度值密切相关（对于所有四个物种，p < 0.005，所有R > 0.70）。浓度较高的物种的相关系数较大。我们的微生物气溶胶种群分析表明，真菌多样性（真菌操作分类单位的数量）是较高的春季相比，秋季（p = 0.02），和主坐标分析显示出明显的季节性差异分类群分布（ANOSIM p = 0.004）。在含有过敏性和/或致病性物种的属中，链格孢属、曲霉属、镰刀菌属和枝孢属的绝对浓度在秋季较大，而隐球菌属、青霉属和细格孢属的浓度在春季较大。焦磷酸测序真菌种群相对丰度数据到绝对浓度的转换可以改进下一代基于DNA测序的定量气溶胶暴露评估。(C)2013爱思唯尔有限公司保留所有权利。
We examined fungal communities associated with the PM10 mass of Rehovot, Israel outdoor air samples collected in the spring and fall seasons. Fungal communities were described by 454 pyrosequencing of the internal transcribed spacer (ITS) region of the fungal ribosomal RNA encoding gene. To allow for a more quantitative comparison of fungal exposure in humans, the relative abundance values of specific taxa were transformed to absolute concentrations through multiplying these values by the sample's total fungal spore concentration (derived from universal fungal qPCR). Next, the sequencing-based absolute concentrations for Alternaria alternata, Cladosporium cladosporioides, Epicoccum nigrum, and Penicillium/ Aspergillus spp. were compared to taxon-specific qPCR concentrations for A. alternata, C. cladosporioides, E. nigrum, and Penicillium/Aspergillus spp. derived from the same spring and fall aerosol samples. Results of these comparisons showed that the absolute concentration values generated from pyrosequencing were strongly associated with the concentration values derived from taxon-specific qPCR (for all four species, p < 0.005, all R > 0.70). The correlation coefficients were greater for species present in higher concentrations. Our microbial aerosol population analyses demonstrated that fungal diversity (number of fungal operational taxonomic units) was higher in the spring compared to the fall (p = 0.02), and principal coordinate analysis showed distinct seasonal differences in taxa distribution (ANOSIM p = 0.004). Among genera containing allergenic and/or pathogenic species, the absolute concentrations of Alternaria, Aspergillus, Fusarium, and Cladosporium were greater in the fall, while Cryptococcus, Penicillium, and Ulocladium concentrations were greater in the spring. The transformation of pyrosequencing fungal population relative abundance data to absolute concentrations can improve next-generation DNA sequencing-based quantitative aerosol exposure assessment. (C) 2013 Elsevier Ltd. All rights reserved.