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Metagenomic survey of bacterial diversity in the atmosphere of Mexico City using different sampling methods

机译：使用不同采样方法对墨西哥城大气中细菌多样性的元基因组学调查

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摘要

The identification of airborne bacteria has traditionally been performed by retrieval in culture media, but the bacterial diversity in the air is underestimated using this method because many bacteria are not readily cultured. Advances in DNA sequencing technology have produced a broad knowledge of genomics and metagenomics, which can greatly improve our ability to identify and study the diversity of airborne bacteria. However, researchers are facing several challenges, particularly the efficient retrieval of low density microorganisms from the air and the lack of standardized protocols for sample collection and processing. In this study, we tested three methods for sampling bioaerosols - a Durham-type spore trap (Durham), a seven-day recording volumetric spore trap (HST), and a high-throughput 'Jet' spore and particle sampler (Jet) - and recovered metagenomic DNA for 16S rDNA sequencing. Samples were simultaneously collected with the three devices during one week, and the sequencing libraries were analyzed. A simple and efficient method for collecting bioaerosols and extracting good quality DNA for high-throughput sequencing was standardized. The Durham sampler collected preferentially Cyanobacteria, the HST Actinobacteria, Proteobacteria and Firmicutes, and the Jet mainly Proteobacteria and Firmicutes. The HST sampler collected the largest amount of airborne bacterial diversity. More experiments are necessary to select the right sampler, depending on study objectives, which may require monitoring and collecting specific airborne bacteria. (C) 2017 Elsevier Ltd. All rights reserved.
机译：传统上，通过在培养基中进行提取来鉴定空气中的细菌，但是由于许多细菌不容易培养，因此使用这种方法会低估空气中的细菌多样性。 DNA测序技术的进步已经产生了广泛的基因组学和宏基因组学知识，可以大大提高我们识别和研究空气传播细菌多样性的能力。然而，研究人员面临着一些挑战，特别是从空气中有效地回收低密度微生物，以及缺乏用于样品收集和处理的标准化方案。在这项研究中，我们测试了三种采样生物气溶胶的方法-杜伦型孢子阱（Durham），七天记录体积孢子阱（HST）和高通量“喷射”孢子和颗粒采样器（Jet）-并回收宏基因组DNA用于16S rDNA测序。在一周内用三种设备同时收集样品，并对测序文库进行分析。标准化了一种简单高效的方法，用于收集生物气溶胶和提取高质量DNA以进行高通量测序。达勒姆采样器优先收集蓝细菌，HST放线菌，变形杆菌和Firmicutes，而Jet则主要收集变形杆菌和Firmicutes。 HST采样器收集了最大数量的空气传播细菌多样性。根据研究目标，需要更多的实验来选择合适的采样器，这可能需要监视和收集特定的空气传播细菌。 （C）2017 Elsevier Ltd.保留所有权利。

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  • 来源
    《Environmental pollution》 |2018年第4期|20-29|共10页
  • 作者

    Serrano-Silva N.; Calderon-Ezquerro M. C.;

  • 作者单位

    Univ Nacl Autonoma Mexico, Dept Ciencias Ambientales, Ctr Ciencias Atmosfera, Circuito Exterior S-N, Mexico City 04510, DF, Mexico;

    Univ Nacl Autonoma Mexico, Dept Ciencias Ambientales, Ctr Ciencias Atmosfera, Circuito Exterior S-N, Mexico City 04510, DF, Mexico;

  • 收录信息 美国《科学引文索引》(SCI);美国《工程索引》(EI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

    Airborne bacteria; Microbial diversity; Urban air; High-throughput sequencing; Bioaerosol samplers;

    机译：空气传播细菌;微生物多样性;城市空气;高通量测序;生物气溶胶采样器;

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