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Sequence-Based Characterization of Microalgal Microbiomes: Impact of DNA Extraction Protocol on Yield and Community Composition

Line Roager Orcid Logo, Eva C. Sonnenschein Orcid Logo, Lone Gram Orcid Logo

Microbiology Spectrum, Volume: 11, Issue: 2

Swansea University Author: Eva C. Sonnenschein Orcid Logo

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DOI (Published version): 10.1128/spectrum.03408-22

Abstract

The bacterial communities associated with microalgae are vital for the growth and health of the host, and engineering algal microbiomes can enhance the fitness of the algae. Characterization of these microbiomes mostly relies on sequencing of DNA, which can be extracted with an array of protocols th...

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Published in: Microbiology Spectrum
ISSN: 2165-0497
Published: American Society for Microbiology 2023
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URI: https://cronfa.swan.ac.uk/Record/cronfa63855
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spelling v2 63855 2023-07-11 Sequence-Based Characterization of Microalgal Microbiomes: Impact of DNA Extraction Protocol on Yield and Community Composition f6a4027578a15ea3e6453a54b849c686 0000-0001-6959-5100 Eva C. Sonnenschein Eva C. Sonnenschein true false 2023-07-11 SBI The bacterial communities associated with microalgae are vital for the growth and health of the host, and engineering algal microbiomes can enhance the fitness of the algae. Characterization of these microbiomes mostly relies on sequencing of DNA, which can be extracted with an array of protocols that potentially impact DNA quantity and quality and thus potentially affect subsequent analyses of microbiome composition. Here, we extracted DNA from Isochrysis galbana, Tetraselmis suecica, and Conticribra weissflogii microbiomes using four different protocols. DNA yield and quality was greatly impacted by the choice of extraction protocol, whereas microbiome composition determined by 16S rRNA gene amplicon sequencing was only impacted to a minor degree, with microalgal host species being the main determinant of microbiome composition. The I. galbana microbiome was dominated by the genus Alteromonas, whereas the microbiome associated with T. suecica was dominated by Marinobacteraceae and Rhodobacteraceae family members. While these two families were also prevalent in the microbiome associated with C. weissflogii, Flavobacteriaceae and Cryomorphaceae were also highly dominant. Phenol-chloroform extraction resulted in higher DNA quality and quantity compared to commercial kits; however, because they have other advantages such as high throughput and low toxicity, commercial kits can be employed to great benefit for the characterization of microalgal microbiomes. Journal Article Microbiology Spectrum 11 2 American Society for Microbiology 2165-0497 DNA extraction, microalgae, microbiome analyses, phycosphere 13 4 2023 2023-04-13 10.1128/spectrum.03408-22 http://dx.doi.org/10.1128/spectrum.03408-22 COLLEGE NANME Biosciences COLLEGE CODE SBI Swansea University Another institution paid the OA fee This research was supported by the Novo Nordisk Foundation (grant no. NNF20OC0064249). 2023-08-09T14:41:36.3042176 2023-07-11T11:20:27.8038115 Faculty of Science and Engineering School of Biosciences, Geography and Physics - Biosciences Line Roager 0000-0002-7033-7309 1 Eva C. Sonnenschein 0000-0001-6959-5100 2 Lone Gram 0000-0002-1076-5723 3 63855__28220__f0800c98813d45f5951190047d5a5a53.pdf 63855.VOR.pdf 2023-07-31T16:32:19.5887763 Output 2352056 application/pdf Version of Record true © 2023 Roager et al. Distributed under the terms of a Creative Commons Attribution 4.0 License (CC BY 4.0). true eng https://creativecommons.org/licenses/by/4.0/
title Sequence-Based Characterization of Microalgal Microbiomes: Impact of DNA Extraction Protocol on Yield and Community Composition
spellingShingle Sequence-Based Characterization of Microalgal Microbiomes: Impact of DNA Extraction Protocol on Yield and Community Composition
Eva C. Sonnenschein
title_short Sequence-Based Characterization of Microalgal Microbiomes: Impact of DNA Extraction Protocol on Yield and Community Composition
title_full Sequence-Based Characterization of Microalgal Microbiomes: Impact of DNA Extraction Protocol on Yield and Community Composition
title_fullStr Sequence-Based Characterization of Microalgal Microbiomes: Impact of DNA Extraction Protocol on Yield and Community Composition
title_full_unstemmed Sequence-Based Characterization of Microalgal Microbiomes: Impact of DNA Extraction Protocol on Yield and Community Composition
title_sort Sequence-Based Characterization of Microalgal Microbiomes: Impact of DNA Extraction Protocol on Yield and Community Composition
author_id_str_mv f6a4027578a15ea3e6453a54b849c686
author_id_fullname_str_mv f6a4027578a15ea3e6453a54b849c686_***_Eva C. Sonnenschein
author Eva C. Sonnenschein
author2 Line Roager
Eva C. Sonnenschein
Lone Gram
format Journal article
container_title Microbiology Spectrum
container_volume 11
container_issue 2
publishDate 2023
institution Swansea University
issn 2165-0497
doi_str_mv 10.1128/spectrum.03408-22
publisher American Society for Microbiology
college_str Faculty of Science and Engineering
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hierarchy_top_id facultyofscienceandengineering
hierarchy_top_title Faculty of Science and Engineering
hierarchy_parent_id facultyofscienceandengineering
hierarchy_parent_title Faculty of Science and Engineering
department_str School of Biosciences, Geography and Physics - Biosciences{{{_:::_}}}Faculty of Science and Engineering{{{_:::_}}}School of Biosciences, Geography and Physics - Biosciences
url http://dx.doi.org/10.1128/spectrum.03408-22
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description The bacterial communities associated with microalgae are vital for the growth and health of the host, and engineering algal microbiomes can enhance the fitness of the algae. Characterization of these microbiomes mostly relies on sequencing of DNA, which can be extracted with an array of protocols that potentially impact DNA quantity and quality and thus potentially affect subsequent analyses of microbiome composition. Here, we extracted DNA from Isochrysis galbana, Tetraselmis suecica, and Conticribra weissflogii microbiomes using four different protocols. DNA yield and quality was greatly impacted by the choice of extraction protocol, whereas microbiome composition determined by 16S rRNA gene amplicon sequencing was only impacted to a minor degree, with microalgal host species being the main determinant of microbiome composition. The I. galbana microbiome was dominated by the genus Alteromonas, whereas the microbiome associated with T. suecica was dominated by Marinobacteraceae and Rhodobacteraceae family members. While these two families were also prevalent in the microbiome associated with C. weissflogii, Flavobacteriaceae and Cryomorphaceae were also highly dominant. Phenol-chloroform extraction resulted in higher DNA quality and quantity compared to commercial kits; however, because they have other advantages such as high throughput and low toxicity, commercial kits can be employed to great benefit for the characterization of microalgal microbiomes.
published_date 2023-04-13T14:41:36Z
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