Experimental parameters defining ultra-low biomass bioaerosol analysis
Investigation of the microbial ecology of terrestrial, aquatic and atmospheric ecosystems requires specific sampling and analytical technologies, owing to vastly different biomass densities typically encountered. In particular, the ultra-low biomass nature of air presents an inherent analytical chal...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , |
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| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2021
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/151955 |
| _version_ | 1811690210597011456 |
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| author | Luhung, Irvan Uchida, Akira LiLim, Serene Boon Yuean Gaultier, Nicolas Eugene Kee, Carmon Lau, Kenny Jia Xu Gusareva, Elena S. Heinle, Cassie Elizabeth Wong, Anthony Premkrishnan, Balakrishnan N. V. Purbojati, Rikky Wenang Acerbi, Enzo Kim, Hie Lim Junqueira, Ana Carolina M. Longford, Sharon Rae Lohar, Sachin R. Yap, Zhei Hwee Panicker, Deepa Koh, Yanqing Kushwaha, Kavita K. Ang, Poh Nee Putra, Alexander Drautz-Moses, Daniela Isabel Schuster, Stephan Christoph |
| author2 | Singapore Centre for Environmental Life Sciences and Engineering |
| author_facet | Singapore Centre for Environmental Life Sciences and Engineering Luhung, Irvan Uchida, Akira LiLim, Serene Boon Yuean Gaultier, Nicolas Eugene Kee, Carmon Lau, Kenny Jia Xu Gusareva, Elena S. Heinle, Cassie Elizabeth Wong, Anthony Premkrishnan, Balakrishnan N. V. Purbojati, Rikky Wenang Acerbi, Enzo Kim, Hie Lim Junqueira, Ana Carolina M. Longford, Sharon Rae Lohar, Sachin R. Yap, Zhei Hwee Panicker, Deepa Koh, Yanqing Kushwaha, Kavita K. Ang, Poh Nee Putra, Alexander Drautz-Moses, Daniela Isabel Schuster, Stephan Christoph |
| author_sort | Luhung, Irvan |
| collection | NTU |
| description | Investigation of the microbial ecology of terrestrial, aquatic and atmospheric ecosystems requires specific sampling and analytical technologies, owing to vastly different biomass densities typically encountered. In particular, the ultra-low biomass nature of air presents an inherent analytical challenge that is confounded by temporal fluctuations in community structure. Our ultra-low biomass pipeline advances the field of bioaerosol research by significantly reducing sampling times from days/weeks/months to minutes/hours, while maintaining the ability to perform species-level identification through direct metagenomic sequencing. The study further addresses all experimental factors contributing to analysis outcome, such as amassment, storage and extraction, as well as factors that impact on nucleic acid analysis. Quantity and quality of nucleic acid extracts from each optimisation step are evaluated using fluorometry, qPCR and sequencing. Both metagenomics and marker gene amplification-based (16S and ITS) sequencing are assessed with regard to their taxonomic resolution and inter-comparability. The pipeline is robust across a wide range of climatic settings, ranging from arctic to desert to tropical environments. Ultimately, the pipeline can be adapted to environmental settings, such as dust and surfaces, which also require ultra-low biomass analytics. |
| first_indexed | 2024-10-01T06:00:23Z |
| format | Journal Article |
| id | ntu-10356/151955 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T06:00:23Z |
| publishDate | 2021 |
| record_format | dspace |
| spelling | ntu-10356/1519552021-10-30T20:12:12Z Experimental parameters defining ultra-low biomass bioaerosol analysis Luhung, Irvan Uchida, Akira LiLim, Serene Boon Yuean Gaultier, Nicolas Eugene Kee, Carmon Lau, Kenny Jia Xu Gusareva, Elena S. Heinle, Cassie Elizabeth Wong, Anthony Premkrishnan, Balakrishnan N. V. Purbojati, Rikky Wenang Acerbi, Enzo Kim, Hie Lim Junqueira, Ana Carolina M. Longford, Sharon Rae Lohar, Sachin R. Yap, Zhei Hwee Panicker, Deepa Koh, Yanqing Kushwaha, Kavita K. Ang, Poh Nee Putra, Alexander Drautz-Moses, Daniela Isabel Schuster, Stephan Christoph Singapore Centre for Environmental Life Sciences and Engineering Science::Biological sciences Environmental Microbiology Next-generation Sequencing Investigation of the microbial ecology of terrestrial, aquatic and atmospheric ecosystems requires specific sampling and analytical technologies, owing to vastly different biomass densities typically encountered. In particular, the ultra-low biomass nature of air presents an inherent analytical challenge that is confounded by temporal fluctuations in community structure. Our ultra-low biomass pipeline advances the field of bioaerosol research by significantly reducing sampling times from days/weeks/months to minutes/hours, while maintaining the ability to perform species-level identification through direct metagenomic sequencing. The study further addresses all experimental factors contributing to analysis outcome, such as amassment, storage and extraction, as well as factors that impact on nucleic acid analysis. Quantity and quality of nucleic acid extracts from each optimisation step are evaluated using fluorometry, qPCR and sequencing. Both metagenomics and marker gene amplification-based (16S and ITS) sequencing are assessed with regard to their taxonomic resolution and inter-comparability. The pipeline is robust across a wide range of climatic settings, ranging from arctic to desert to tropical environments. Ultimately, the pipeline can be adapted to environmental settings, such as dust and surfaces, which also require ultra-low biomass analytics. Ministry of Education (MOE) Published version The work was supported by Singapore Ministry of Education Academic Research Fund Tier 3 grant (grant MOE2013-T3-1-013). 2021-10-26T04:47:58Z 2021-10-26T04:47:58Z 2021 Journal Article Luhung, I., Uchida, A., LiLim, S. B. Y., Gaultier, N. E., Kee, C., Lau, K. J. X., Gusareva, E. S., Heinle, C. E., Wong, A., Premkrishnan, B. N. V., Purbojati, R. W., Acerbi, E., Kim, H. L., Junqueira, A. C. M., Longford, S. R., Lohar, S. R., Yap, Z. H., Panicker, D., Koh, Y., ...Schuster, S. C. (2021). Experimental parameters defining ultra-low biomass bioaerosol analysis. Npj Biofilms and Microbiomes, 7(1), 37-. https://dx.doi.org/10.1038/s41522-021-00209-4 2055-5008 https://hdl.handle.net/10356/151955 10.1038/s41522-021-00209-4 33863892 2-s2.0-85104470712 1 7 37 en MOE2013-T3-1-013 npj Biofilms and Microbiomes © 2021 The Author(s). Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. application/pdf |
| spellingShingle | Science::Biological sciences Environmental Microbiology Next-generation Sequencing Luhung, Irvan Uchida, Akira LiLim, Serene Boon Yuean Gaultier, Nicolas Eugene Kee, Carmon Lau, Kenny Jia Xu Gusareva, Elena S. Heinle, Cassie Elizabeth Wong, Anthony Premkrishnan, Balakrishnan N. V. Purbojati, Rikky Wenang Acerbi, Enzo Kim, Hie Lim Junqueira, Ana Carolina M. Longford, Sharon Rae Lohar, Sachin R. Yap, Zhei Hwee Panicker, Deepa Koh, Yanqing Kushwaha, Kavita K. Ang, Poh Nee Putra, Alexander Drautz-Moses, Daniela Isabel Schuster, Stephan Christoph Experimental parameters defining ultra-low biomass bioaerosol analysis |
| title | Experimental parameters defining ultra-low biomass bioaerosol analysis |
| title_full | Experimental parameters defining ultra-low biomass bioaerosol analysis |
| title_fullStr | Experimental parameters defining ultra-low biomass bioaerosol analysis |
| title_full_unstemmed | Experimental parameters defining ultra-low biomass bioaerosol analysis |
| title_short | Experimental parameters defining ultra-low biomass bioaerosol analysis |
| title_sort | experimental parameters defining ultra low biomass bioaerosol analysis |
| topic | Science::Biological sciences Environmental Microbiology Next-generation Sequencing |
| url | https://hdl.handle.net/10356/151955 |
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