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...
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Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8052325/ http://www.ncbi.nlm.nih.gov/pubmed/33863892 https://doi.org/10.1038/s41522-021-00209-4 |
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ftpubmed:oai:pubmedcentral.nih.gov:8052325 2023-05-15T15:06:07+02:00 Experimental parameters defining ultra-low biomass bioaerosol analysis Luhung, Irvan Uchida, Akira Lim, Serene B. Y. Gaultier, Nicolas E. Kee, Carmon Lau, Kenny J. X. Gusareva, Elena S. Heinle, Cassie E. Wong, Anthony Premkrishnan, Balakrishnan N. V. Purbojati, Rikky W. Acerbi, Enzo Kim, Hie Lim Junqueira, Ana C. M. Longford, Sharon Lohar, Sachin R. Yap, Zhei Hwee Panicker, Deepa Koh, Yanqing Kushwaha, Kavita K. Ang, Poh Nee Putra, Alexander Drautz-Moses, Daniela I. Schuster, Stephan C. 2021-04-16 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8052325/ http://www.ncbi.nlm.nih.gov/pubmed/33863892 https://doi.org/10.1038/s41522-021-00209-4 en eng Nature Publishing Group UK http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8052325/ http://www.ncbi.nlm.nih.gov/pubmed/33863892 http://dx.doi.org/10.1038/s41522-021-00209-4 © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/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/ (https://creativecommons.org/licenses/by/4.0/) . CC-BY NPJ Biofilms Microbiomes Article Text 2021 ftpubmed https://doi.org/10.1038/s41522-021-00209-4 2021-05-09T00:25:51Z 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. Text Arctic PubMed Central (PMC) Arctic npj Biofilms and Microbiomes 7 1 |
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Article Luhung, Irvan Uchida, Akira Lim, Serene B. Y. Gaultier, Nicolas E. Kee, Carmon Lau, Kenny J. X. Gusareva, Elena S. Heinle, Cassie E. Wong, Anthony Premkrishnan, Balakrishnan N. V. Purbojati, Rikky W. Acerbi, Enzo Kim, Hie Lim Junqueira, Ana C. M. Longford, Sharon Lohar, Sachin R. Yap, Zhei Hwee Panicker, Deepa Koh, Yanqing Kushwaha, Kavita K. Ang, Poh Nee Putra, Alexander Drautz-Moses, Daniela I. Schuster, Stephan C. Experimental parameters defining ultra-low biomass bioaerosol analysis |
topic_facet |
Article |
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. |
format |
Text |
author |
Luhung, Irvan Uchida, Akira Lim, Serene B. Y. Gaultier, Nicolas E. Kee, Carmon Lau, Kenny J. X. Gusareva, Elena S. Heinle, Cassie E. Wong, Anthony Premkrishnan, Balakrishnan N. V. Purbojati, Rikky W. Acerbi, Enzo Kim, Hie Lim Junqueira, Ana C. M. Longford, Sharon Lohar, Sachin R. Yap, Zhei Hwee Panicker, Deepa Koh, Yanqing Kushwaha, Kavita K. Ang, Poh Nee Putra, Alexander Drautz-Moses, Daniela I. Schuster, Stephan C. |
author_facet |
Luhung, Irvan Uchida, Akira Lim, Serene B. Y. Gaultier, Nicolas E. Kee, Carmon Lau, Kenny J. X. Gusareva, Elena S. Heinle, Cassie E. Wong, Anthony Premkrishnan, Balakrishnan N. V. Purbojati, Rikky W. Acerbi, Enzo Kim, Hie Lim Junqueira, Ana C. M. Longford, Sharon Lohar, Sachin R. Yap, Zhei Hwee Panicker, Deepa Koh, Yanqing Kushwaha, Kavita K. Ang, Poh Nee Putra, Alexander Drautz-Moses, Daniela I. Schuster, Stephan C. |
author_sort |
Luhung, Irvan |
title |
Experimental parameters defining ultra-low biomass bioaerosol analysis |
title_short |
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_sort |
experimental parameters defining ultra-low biomass bioaerosol analysis |
publisher |
Nature Publishing Group UK |
publishDate |
2021 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8052325/ http://www.ncbi.nlm.nih.gov/pubmed/33863892 https://doi.org/10.1038/s41522-021-00209-4 |
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Arctic |
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Arctic |
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Arctic |
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Arctic |
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NPJ Biofilms Microbiomes |
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8052325/ http://www.ncbi.nlm.nih.gov/pubmed/33863892 http://dx.doi.org/10.1038/s41522-021-00209-4 |
op_rights |
© The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/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/ (https://creativecommons.org/licenses/by/4.0/) . |
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CC-BY |
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https://doi.org/10.1038/s41522-021-00209-4 |
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