Literature DB >> 35727544

A Metabarcoding Protocol to Analyze Coastal Planktic Communities Collected by Desalination Plant Filters: From Sampling to Bioinformatic Exploratory Analyses.

Matteo Cecchetto1,2, Andrea Di Cesare3, Ester Eckert3, Isabella Moro4, Diego Fontaneto3, Stefano Schiaparelli5,6.   

Abstract

The temporal dynamics of coastal planktic communities can be disclosed through DNA metabarcoding on the filters of reverse-osmosis desalination plants. Here, we describe the steps that are necessary to process the filters in order to create the subsamples used for DNA extraction and the bioinformatic pipeline to perform the first exploratory analyses on this kind of dataset.
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Bioinformatic protocol; Coastal plankton; DNA metabarcoding; Desalination plant; Monitoring

Mesh：

Year:  2022        PMID： 35727544     DOI： 10.1007/978-1-0716-2313-8_8

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  11 in total

1.  Search and clustering orders of magnitude faster than BLAST.

Authors:  Robert C Edgar
Journal:  Bioinformatics       Date:  2010-08-12       Impact factor: 6.937

2.  Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities.

Authors:  Patrick D Schloss; Sarah L Westcott; Thomas Ryabin; Justine R Hall; Martin Hartmann; Emily B Hollister; Ryan A Lesniewski; Brian B Oakley; Donovan H Parks; Courtney J Robinson; Jason W Sahl; Blaz Stres; Gerhard G Thallinger; David J Van Horn; Carolyn F Weber
Journal:  Appl Environ Microbiol       Date:  2009-10-02       Impact factor: 4.792

3.  obitools: a unix-inspired software package for DNA metabarcoding.

Authors:  Frédéric Boyer; Céline Mercier; Aurélie Bonin; Yvan Le Bras; Pierre Taberlet; Eric Coissac
Journal:  Mol Ecol Resour       Date:  2015-05-26       Impact factor: 7.090

4.  Time series are critical to understand microbial plankton diversity and ecology.

Authors:  David Moreira; Purificación López-García
Journal:  Mol Ecol       Date:  2019-03       Impact factor: 6.185

5.  Antarctic coastal nanoplankton dynamics revealed by metabarcoding of desalination plant filters: Detection of short-term events and implications for routine monitoring.

Authors:  Matteo Cecchetto; Andrea Di Cesare; Ester Eckert; Giulia Fassio; Diego Fontaneto; Isabella Moro; Marco Oliverio; Katia Sciuto; Giovanni Tassistro; Luigi Vezzulli; Stefano Schiaparelli
Journal:  Sci Total Environ       Date:  2020-11-19       Impact factor: 7.963

6.  VSEARCH: a versatile open source tool for metagenomics.

Authors:  Torbjørn Rognes; Tomáš Flouri; Ben Nichols; Christopher Quince; Frédéric Mahé
Journal:  PeerJ       Date:  2016-10-18       Impact factor: 2.984

7.  Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia.

Authors:  Luisa W Hugerth; Emilie E L Muller; Yue O O Hu; Laura A M Lebrun; Hugo Roume; Daniel Lundin; Paul Wilmes; Anders F Andersson
Journal:  PLoS One       Date:  2014-04-22       Impact factor: 3.240

8.  phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.

Authors:  Paul J McMurdie; Susan Holmes
Journal:  PLoS One       Date:  2013-04-22       Impact factor: 3.240

9.  The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy.

Authors:  Laure Guillou; Dipankar Bachar; Stéphane Audic; David Bass; Cédric Berney; Lucie Bittner; Christophe Boutte; Gaétan Burgaud; Colomban de Vargas; Johan Decelle; Javier Del Campo; John R Dolan; Micah Dunthorn; Bente Edvardsen; Maria Holzmann; Wiebe H C F Kooistra; Enrique Lara; Noan Le Bescot; Ramiro Logares; Frédéric Mahé; Ramon Massana; Marina Montresor; Raphael Morard; Fabrice Not; Jan Pawlowski; Ian Probert; Anne-Laure Sauvadet; Raffaele Siano; Thorsten Stoeck; Daniel Vaulot; Pascal Zimmermann; Richard Christen
Journal:  Nucleic Acids Res       Date:  2012-11-27       Impact factor: 16.971

10.  Waste not, want not: why rarefying microbiome data is inadmissible.

Authors:  Paul J McMurdie; Susan Holmes
Journal:  PLoS Comput Biol       Date:  2014-04-03       Impact factor: 4.475
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