Reference : Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from...
Scientific journals : Article
Life sciences : Environmental sciences & ecology
Systems Biomedicine
http://hdl.handle.net/10993/44832
Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams
English
Busi, Susheel Bhanu* mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology >]
Pramateftaki, Paraskevi* mailto [Ecole Polytechnique Fédérale de Lausanne - EPFL > Stream Biofilm and Ecosystems Research]
Brandani, Jade mailto [Ecole Polytechnique Fédérale de Lausanne - EPFL > Stream Biofilm and Ecosystems Research]
Fodelianakis, Stilianos mailto [Ecole Polytechnique Fédérale de Lausanne - EPFL > Stream Biofilm and Ecosystems Research]
Peter, Hannes mailto [Ecole Polytechnique Fédérale de Lausanne - EPFL > Stream Biofilm and Ecosystems Research]
Halder, Rashi mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Scientific Central Services >]
Wilmes, Paul mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology >]
Battin, Tom mailto [Ecole Polytechnique Fédérale de Lausanne - EPFL > Stream Biofilm and Ecosystems Research]
* These authors have contributed equally to this work.
27-Oct-2020
PeerJ
PeerJ
Yes (verified by ORBilu)
International
2167-8359
San Francisco
CA
[en] Biofilms ; Streams ; Alpine streams ; Glacier fed streams ; Glaciers ; Metagenomics ; Biomolecular extraction
[en] Glacier-fed streams (GFS) are harsh ecosystems dominated by microbial life organized in benthic biofilms, yet the biodiversity and ecosystem functions provided by these communities remain under-appreciated. To better understand the microbial processes and communities contributing to GFS ecosystems, it is necessary to leverage high throughput sequencing. Low biomass and high inorganic particle load in GFS sediment samples may affect nucleic acid extraction efficiency using extraction methods tailored to other extreme environments such as deep-sea sediments. Here, we benchmarked the utility and efficacy of four extraction protocols, including an up-scaled phenol-chloroform protocol. We found that established protocols for comparable sample types consistently failed to yield sufficient high-quality DNA, delineating the extreme character of GFS. The methods differed in the success of downstream applications such as library preparation and sequencing. An adapted phenol-chloroform-based extraction method resulted in higher yields and better recovered the expected taxonomic profile and abundance of reconstructed genomes when compared to commercially-available methods. Affordable and straight-forward, this method consistently recapitulated the abundance and genomes of a mock community, including eukaryotes. Moreover, by increasing the amount of input sediment, the protocol is readily adjustable to the microbial load of the processed samples without compromising protocol efficiency. Our study provides a first systematic and extensive analysis of the different options for extraction of nucleic acids from glacier-fed streams for high-throughput sequencing applications, which may be applied to other extreme environments.
University of Luxembourg: High Performance Computing - ULHPC
Swiss National Foundation
R-AGR-3458-10-R
Researchers ; Professionals ; Students ; General public
http://hdl.handle.net/10993/44832
10.7717/peerj.9973
https://peerj.com/articles/9973/
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
Cite this article
Busi SB, Pramateftaki P, Brandani J, Fodelianakis S, Peter H, Halder R, Wilmes P, Battin TJ. 2020. Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams. PeerJ 8:e9973 https://doi.org/10.7717/peerj.9973

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