Experimental parameters defining ultra-low biomass bioaerosol analysis
Abstract 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 analyt...
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Nature Portfolio
2021
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oai:doaj.org-article:b0ea86173c334bafac820e2b1267137a2021-12-02T14:27:54ZExperimental parameters defining ultra-low biomass bioaerosol analysis10.1038/s41522-021-00209-42055-5008https://doaj.org/article/b0ea86173c334bafac820e2b1267137a2021-04-01T00:00:00Zhttps://doi.org/10.1038/s41522-021-00209-4https://doaj.org/toc/2055-5008Abstract 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.Irvan LuhungAkira UchidaSerene B. Y. LimNicolas E. GaultierCarmon KeeKenny J. X. LauElena S. GusarevaCassie E. HeinleAnthony WongBalakrishnan N. V. PremkrishnanRikky W. PurbojatiEnzo AcerbiHie Lim KimAna C. M. JunqueiraSharon LongfordSachin R. LoharZhei Hwee YapDeepa PanickerYanqing KohKavita K. KushwahaPoh Nee AngAlexander PutraDaniela I. Drautz-MosesStephan C. SchusterNature PortfolioarticleMicrobial ecologyQR100-130ENnpj Biofilms and Microbiomes, Vol 7, Iss 1, Pp 1-11 (2021) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Microbial ecology QR100-130 |
| spellingShingle |
Microbial ecology QR100-130 Irvan Luhung Akira Uchida Serene B. Y. Lim Nicolas E. Gaultier Carmon Kee Kenny J. X. Lau Elena S. Gusareva Cassie E. Heinle Anthony Wong Balakrishnan N. V. Premkrishnan Rikky W. Purbojati Enzo Acerbi Hie Lim Kim Ana C. M. Junqueira Sharon Longford Sachin R. Lohar Zhei Hwee Yap Deepa Panicker Yanqing Koh Kavita K. Kushwaha Poh Nee Ang Alexander Putra Daniela I. Drautz-Moses Stephan C. Schuster Experimental parameters defining ultra-low biomass bioaerosol analysis |
| description |
Abstract 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 |
article |
| author |
Irvan Luhung Akira Uchida Serene B. Y. Lim Nicolas E. Gaultier Carmon Kee Kenny J. X. Lau Elena S. Gusareva Cassie E. Heinle Anthony Wong Balakrishnan N. V. Premkrishnan Rikky W. Purbojati Enzo Acerbi Hie Lim Kim Ana C. M. Junqueira Sharon Longford Sachin R. Lohar Zhei Hwee Yap Deepa Panicker Yanqing Koh Kavita K. Kushwaha Poh Nee Ang Alexander Putra Daniela I. Drautz-Moses Stephan C. Schuster |
| author_facet |
Irvan Luhung Akira Uchida Serene B. Y. Lim Nicolas E. Gaultier Carmon Kee Kenny J. X. Lau Elena S. Gusareva Cassie E. Heinle Anthony Wong Balakrishnan N. V. Premkrishnan Rikky W. Purbojati Enzo Acerbi Hie Lim Kim Ana C. M. Junqueira Sharon Longford Sachin R. Lohar Zhei Hwee Yap Deepa Panicker Yanqing Koh Kavita K. Kushwaha Poh Nee Ang Alexander Putra Daniela I. Drautz-Moses Stephan C. Schuster |
| author_sort |
Irvan Luhung |
| 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 Portfolio |
| publishDate |
2021 |
| url |
https://doaj.org/article/b0ea86173c334bafac820e2b1267137a |
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