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Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits

PREMISE: Within a broader study on leaf fossilization in freshwater environments, a long‐term study on the development and microbiome composition of biofilms on the foliage of aquatic plants has been initiated to understand how microbes and biofilms contribute to leaf decay and preservation. Here, w...

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Autores principales: Janssen, Kathrin, Low, Shook Ling, Wang, Yan, Mu, Qi‐Yong, Bierbaum, Gabriele, Gee, Carole T.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8419396/
https://www.ncbi.nlm.nih.gov/pubmed/34504737
http://dx.doi.org/10.1002/aps3.11444
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author Janssen, Kathrin
Low, Shook Ling
Wang, Yan
Mu, Qi‐Yong
Bierbaum, Gabriele
Gee, Carole T.
author_facet Janssen, Kathrin
Low, Shook Ling
Wang, Yan
Mu, Qi‐Yong
Bierbaum, Gabriele
Gee, Carole T.
author_sort Janssen, Kathrin
collection PubMed
description PREMISE: Within a broader study on leaf fossilization in freshwater environments, a long‐term study on the development and microbiome composition of biofilms on the foliage of aquatic plants has been initiated to understand how microbes and biofilms contribute to leaf decay and preservation. Here, water lily leaves are employed as a study model to investigate the relationship between bacterial microbiomes, biodegradation, and fossilization. We compare four DNA extraction kits to reduce biases in interpretation and to identify the most suitable kit for the extraction of DNA from bacteria associated with biofilms on decaying water lily leaves for 16S rRNA amplicon analysis. METHODS: We extracted surface‐associated DNA from Nymphaea leaves in early stages of decay at two water depth levels using four commercially available kits to identify the most suitable protocol for bacterial extraction, applying a mock microbial community standard to enable a reliable comparison of the kits. RESULTS: Kit 4, the FastDNA Spin Kit for Soil, resulted in high DNA concentrations with better quality and yielded the most accurate depiction of the mock community. Comparison of the leaves at two water depths showed no significant differences in community composition. DISCUSSION: The success of Kit 4 may be attributed to its use of bead beating with a homogenizer, which was more efficient in the lysis of Gram‐positive bacteria than the manual vortexing protocols used by the other kits. Our results show that microbial composition on leaves during early decay remains comparable and may change only in later stages of decomposition.
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spelling pubmed-84193962021-09-08 Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits Janssen, Kathrin Low, Shook Ling Wang, Yan Mu, Qi‐Yong Bierbaum, Gabriele Gee, Carole T. Appl Plant Sci Application Article PREMISE: Within a broader study on leaf fossilization in freshwater environments, a long‐term study on the development and microbiome composition of biofilms on the foliage of aquatic plants has been initiated to understand how microbes and biofilms contribute to leaf decay and preservation. Here, water lily leaves are employed as a study model to investigate the relationship between bacterial microbiomes, biodegradation, and fossilization. We compare four DNA extraction kits to reduce biases in interpretation and to identify the most suitable kit for the extraction of DNA from bacteria associated with biofilms on decaying water lily leaves for 16S rRNA amplicon analysis. METHODS: We extracted surface‐associated DNA from Nymphaea leaves in early stages of decay at two water depth levels using four commercially available kits to identify the most suitable protocol for bacterial extraction, applying a mock microbial community standard to enable a reliable comparison of the kits. RESULTS: Kit 4, the FastDNA Spin Kit for Soil, resulted in high DNA concentrations with better quality and yielded the most accurate depiction of the mock community. Comparison of the leaves at two water depths showed no significant differences in community composition. DISCUSSION: The success of Kit 4 may be attributed to its use of bead beating with a homogenizer, which was more efficient in the lysis of Gram‐positive bacteria than the manual vortexing protocols used by the other kits. Our results show that microbial composition on leaves during early decay remains comparable and may change only in later stages of decomposition. John Wiley and Sons Inc. 2021-08-28 /pmc/articles/PMC8419396/ /pubmed/34504737 http://dx.doi.org/10.1002/aps3.11444 Text en © 2021 The Authors. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ (https://creativecommons.org/licenses/by-nc-nd/4.0/) License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.
spellingShingle Application Article
Janssen, Kathrin
Low, Shook Ling
Wang, Yan
Mu, Qi‐Yong
Bierbaum, Gabriele
Gee, Carole T.
Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits
title Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits
title_full Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits
title_fullStr Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits
title_full_unstemmed Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits
title_short Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits
title_sort elucidating biofilm diversity on water lily leaves through 16s rrna amplicon analysis: comparison of four dna extraction kits
topic Application Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8419396/
https://www.ncbi.nlm.nih.gov/pubmed/34504737
http://dx.doi.org/10.1002/aps3.11444
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