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Optimized DNA extraction and metagenomic sequencing of airborne microbial communities

Nature Protocols volume 10, pages 768–779 (2015)Cite this article

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Abstract

Metagenomic sequencing has been widely used for the study of microbial communities from various environments such as soil, ocean, sediment and fresh water. Nonetheless, metagenomic sequencing of microbial communities in the air remains technically challenging, partly owing to the limited mass of collectable atmospheric particulate matter and the low biological content it contains. Here we present an optimized protocol for extracting up to tens of nanograms of airborne microbial genomic DNA from collected particulate matter. With an improved sequencing library preparation protocol, this quantity is sufficient for downstream applications, such as metagenomic sequencing for sampling various genes from the airborne microbial community. The described protocol takes ∼12 h of bench time over 2–3 d, and it can be performed with standard molecular biology equipment in the laboratory. A modified version of this protocol may also be used for genomic DNA extraction from other environmental samples of limited mass or low biological content.

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Figure 1: Workflow for particulate matter sample pretreatment.
Figure 2: Experimental setup for particulate matter collection and sample pretreatment.
Figure 3: Quality assessment of extracted genomic DNA and validation of the quality of prepared sequencing libraries.

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Acknowledgements

We thank M. Kayani, C. Liu and C. Cao for helpful discussions and for help taking the experimental setup photos. This work was supported in part by funding from the Ministry of Science and Technology of China (973 grant no. 2015CB553402), the National Natural Science Foundation of China (grant nos. 31470532, 21190054, 21221004), the Tsinghua University-Peking University Center for Life Sciences (CLS), a Tsinghua-Janssen Scholarship and research grant and the Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases.

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Authors and Affiliations

  1. School of Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, China

    Wenjun Jiang, Peng Liang & Ting F Zhu

  2. State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, Tsinghua University, Beijing, China

    Buying Wang & Jingkun Jiang

  3. Center of Biomedical Analysis, School of Life Sciences, Tsinghua University, Beijing, China.

    Jianhuo Fang, Jidong Lang & Geng Tian

Authors
  1. Wenjun Jiang
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  2. Peng Liang
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  3. Buying Wang
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  6. Geng Tian
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  7. Jingkun Jiang
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  8. Ting F Zhu
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Contributions

W.J., P.L., B.W., J.F. and J.L., with inputs from T.F.Z., J.J. and G.T., performed the experiments and analyzed the data. T.F.Z. conceived and organized the study. W.J. and T.F.Z., with inputs from the other coauthors, wrote the paper.

Corresponding author

Correspondence to Ting F Zhu.

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The authors declare no competing financial interests.

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Jiang, W., Liang, P., Wang, B. et al. Optimized DNA extraction and metagenomic sequencing of airborne microbial communities. Nat Protoc 10, 768–779 (2015). https://doi.org/10.1038/nprot.2015.046

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