Genetics

Experts

Silvia G. Acinas

  • Institute of Marine Science (ICM)-CSIC
  • sacinas@icm.csic.es

Outside the Working Group:

Isabel Ferrera

  • Institute of Marine Science (ICM)-CSIC/Spanish Institute of Oceanography (IEO)-Malaga
  • iferrera@icm.csic.es

Josep M. Gasol

  • Institute of Marine Science (ICM)-CSIC
  • pepgasol@icm.csic.es

Ramon Massana

  • Institute of Marine Science (ICM)-CSIC
  • ramonm@icm.csic.es

Stephane Pesant

  • MARUM; Center for Marine Environmental Sciences
  • spesant@marum.de

Pablo Sánchez

  • Institute of Marine Science (ICM)-CSIC
  • pablosanchez@icm.csic.es

Marta Sebastián

  • Institute of Marine Science (ICM)-CSIC;
  • Institute of Oceanography and Global Change (IOCAG)
  • msebastian@icm.csic.es

Shinichi Sunagawa

  • ETH Zurich and Swiss Institute of Bioinformatics
  • ssunagawa@ethz.ch

Laurence Garczarek

  • CNRS Station Biologique de Roscoff
  • garczare@sb-roscoff.fr

Relevant Documents

*In bold is shown the scientist and collaborators involved within this WG.

Relevant documents regarding sampling protocols for collecting plankton biomass from marine samples and implemented already in two global oceanographic cruises: Tara Oceans and Malaspina.

1. Tara Oceans´s paper providing details of sampling during their expedition.

Stéphane Pesant , Fabrice Not, Marc Picheral, Stefanie Kandels-Lewis,Noan Le Bescot, Gabriel Gorsky, Daniele Ludicone, Eric Karsenti, Sabrina Speich,Romain Troublé, Céline Dimier, Sarah Searson & Tara Oceans Consortium Coordinators; Silvia G. Acinas, Peer Bork, Emmanuel Boss, Chris Bowler, Colomban De Vargas, Michael Follows, Gabriel Gorsky, Nigel Grimsley, Pascal Hingamp, Daniele Iudicone, OlivierJaillon, Stefanie Kandels-Lewis, Lee Karp-Boss, Eric Karsenti, Uros Krzic, Fabrice Not, Hiroyuki Ogata, Stéphane Pesant, Jeroen Raes, Emmanuel G. Reynaud, Christian Sardet, Mike Sieracki, Sabrina Speich, Lars Stemmann, Matthew B. Sullivan, Shinichi Sunagawa, Didier Velayoudon, Jean Weissenbach, Patrick Wincker. 2015. Open science resources for the discovery and analysis of Tara Oceans data. Scientific Data. 2:150023. doi: 10.1038/sdata.2015.23.

2. Tara Oceans´s paper proving details about protocols of genetic sequencing analyses.

Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, Eric Pelletier, Gaëlle Samson, Mark Wessner, Genoscope Technical Team, Silvia G. Acinas, Marta Royo-Llonch, Francisco M. Cornejo- Castillo, Ramiro Logares, Beatriz Fernández-Gómez, Guy Cochrane, Clara Amid, Petra Ten Hoopen, Colomban De Vargas, Nigel Grimsley, Elodie Desgranges, Hiroyuki Ogata, Nicole Poulton, Michael E. Sieracki, Ramunas Stepanauskas, Matthew B. Sullivan, Jennifer R. Brum, Melissa B. Duhaime, Bonnie T. Poulos, Bonnie L. Hurwitz, Tara Oceans Consortium Coordinators, Stéphane Pesant, Eric Karsenti, Patrick Wincker. 2017. Marine plankton from viruses to metazoans: nucleotide sequences from the Tara Oceans expedition (2009-2013). Scientific Data. 2017 Aug 1;4:170093. doi: 10.1038/sdata.2017.93.

3. Documents about protocols sampling using on Malaspina expedition. Malaspina protocols are very similar to Tara Oceans regarding the plankton sampling strategy.

  • Arrieta JM, Acinas SG, Massana R, Vaqué D. 2012. Concentración de biomasa de picoeucariotas, bacterias y virus marinos para la extracción de ácidos nucleicos. Pag. 521-532. Ed (Moreno-Ostos, E). Expedición de Circunnavegacion Malaspina 2010: Cambio Global y Exploración de la Biodiversidad del Océano Global. Libro Blanco de métodos y técnicas de trabajo Oceanográfico. Publicaciones CSIC.
  • Vaqué D. Lara E, Sá E-L, Acinas SG. 2012. Obtención de muestras para la determinación de la composición vírica. Pag. 543-551. Ed (Moreno-Ostos, E). Expedición de Circunnavegacion Malaspina 2010: Cambio Global y Exploración de la Biodiversidad del Océano Global. Libro Blanco de métodos y técnicas de trabajo Oceanográfico. Publicaciones CSIC.


Relevant papers using amplicon Tags of specific gene markers (16S rRNA for prokaryotes and 18S RNA for picocyanobacteria) or metagenomics on marine samples.


Extracting DNA after filtration of marine samples allowed to us to analyze total microbial diversity or specific taxa or functional groups by two different strategies :

  1. Amplifying using PCR specific molecular phylogenetic markers such as the ribosomal genes 16S rRNA and 18S rRNA for prokaryotes and protists respectively.

This is called amplicons tags: 16S iTAGs and 18S iTAGs. Nowadays, people use Illumina sequencing platforms to analyze microbial and functional diversity. See selected papers on people from our WG or contacted related to microbial diversity in marine samples.

Note: I have selected only some papers that are using amplicon 16S or 18S Tags sequencing from marine global studies since there are hundreds of them.

1.1. Global diversity of marine bacteria and archaea by analyzing 16S iTAGs from diffferent global marine sampling iniciatives.

From International Census of Marine Microbes (ICOMM):

  • Jean-François Ghiglione, Pierre E. Galand, Thomas Pommier, Carlos Pedrós-Alió, Elizabeth W. Maas, Kevin Bakker, Stefan Bertilson, David L. Kirchman, Connie Lovejoy, Patricia L. Yager, and Alison E. Murray. Pole-to-pole biogeography of surface and deep marine bacterial communities. PNAS 2012. www.pnas.org/cgi/doi/10.1073/pnas.1208160109
  • Zinger L, Amaral-Zettler LA, Fuhrman JA, Horner-Devine MC, Huse SM, et al. 2011. Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems. PLoS ONE 6(9): e24570. doi:10.1371/journal.pone.0024570.

From Tara Oceans Expedition: (see below, diversity was done based on extraction the 16S genes directly from metagenomes: miTAGs rather than amplify 16S iTAGs, although this is done now and currently under analyses)

From Malaspina 2010 Expedition:

  • Mestre M, Ruiz-González C, Logares R, Duarte CM, Gasol JM, Sala MM. 2018. Sinking particles promote vertical connectivity in the ocean microbiome. Proc Natl Acad Sci U S A. 2018 Jul 17;115(29):E6799-E6807. doi: 10.1073/pnas.1802470115. Epub 2018 Jul 2.
  • Salazar G, Cornejo-Castillo FM, Benítez-Barrios V, Fraile-Nuez E, Álvarez-Salgado XA, Duarte CM, Gasol JM, Acinas SG. 2016. Global diversity and Biogeography of deep-sea pelagic prokaryotes. ISME J. doi: 10.1038/ismej.2015.137. Epub 2015 Aug 7.

1.2. Global diversity of marine protist by analyzing 18S iTAGs.

From Tara Oceans Expedition:

  • Colomban de Vargas, Stéphane Audic, Nicolas Henry, Johan Decelle, Frédéric Mahé, Ramiro Logares, Enrique Lara, Cédric Berney,Noan Le Bescot, Ian Probert,Margaux Carmichael,Julie Poulain, Sarah Romac, Sébastien Colin, Jean- Marc Aury, Lucie Bittner,Samuel Chaffron, Micah Dunthorn, Stefan Engelen, Olga Flegontova, Lionel Guidi, Aleš Horák, Olivier Jaillon, Gipsi Lima-Mendez, Julius Lukeš,Shruti Malviya,Raphael Morard, Matthieu Mulot, Eleonora Scalco, Raffaele Siano,Flora Vincent, Adriana Zingone, Céline Dimier,Marc Picheral,Sarah Searson,Stefanie Kandels-Lewis,Tara Oceans Coordinators, Silvia G. Acinas, Peer Bork, Chris Bowler, Gabriel Gorsky, Nigel Grimsley,Pascal Hingamp, Daniele Iudicone, Fabrice Not,Hiroyuki Ogata, Stephane Pesant, Jeroen Raes, Michael E. Sieracki,Sabrina Speich,Lars Stemmann, Shinichi Sunagawa, Jean Weissenbach,Patrick Wincker, Eric Karsenti. 2015. Eukaryotic plankton diversity in the sunlit global ocean. Science. 348(6237):1261605. doi: 10.1126/science.1261605.

From Malaspina 2010 Expedition:

  • Massimo C. Pernice, Caterina R. Giner, Ramiro Logares, Julia Perera, Silvia G. Acinas, Carlos M. Duarte, Josep M. Gasol and Ramon Massana. 2015. Large variability of bathypelagic microeukaryotic communities across the world's oceans. ISME J. DOI: 10.1038/ismej.2015.170a.

2. Doing metagenomics; meaning sequencing all genes of microbial communities without previous PCR amplification step and then extracting the taxonomic or functional genes of interest. I have selected only some papers that are using specific gene markers extracted from metagenomes to analyze:

2.1. Total diversity of bacterial extracting the 16S rRNA fragments from metagenomes (16S miTAGs).

About the method of extracting the 16S rRNA genes directly from metagenomes (16S miTAGs).

  • Ramiro Logares, Shinichi Sunagawa, Guillem Salazar, Francisco M. Cornejo-Castillo, Isabel Ferrera, Hugo Sarmento, Pascal Hingamp, Hiroyuki Ogata, Colomban de Vargas, Gipsi Lima-Mendez, Jeroen Raes, Julie Poulain, Olivier Jaillon, Patrick Wincker, Stefanie Kandels-Lewis, Eric Karsenti, Peer Bork and Silvia G. Acinas. 2014. Metagenomic 16S rDNA Illumina-Tags as a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities. Environ Microbiol. 9:2659-71.

This approach was applied to infer bacterial and archaeal diversity in Tara Oceans dataset.

  • Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima- Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S; Tara Oceans coordinators, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E*, Raes J*, Acinas SG*, Bork P*. 2015. Structure and Function of the Global Ocean Microbiome. Science. 348(6237):1261359. doi: 10.1126/science.1261359. (*lP leading and corresponding author).

2.2. Diversity of picocyanobacteria using petB gene or other functional gene markers related to pigment types genes such as (cpcBA, mpeBA, and mpeW)

  • Grébert T, Doré H, Partensky F, Farrant GK, Boss ES, Picheral M, Guidi L, Pesant S, Scanlan DJ, Wincker P, Acinas SG, Kehoe DM, Garczarek L. 2018. Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria. Proc Natl Acad Sci U S A. 2018 Feb 12. doi: 10.1073/pnas.1717069115.
  • Gregory K. Farrant, Hugo Doré, Francisco M. Cornejo-Castillo, Fréderic Partensky, Morgane Ratin, Martin Ostrowski, Francesca Pitt, Patrick Wincker, David J. Scanlan, Daniele Ludicone, Silvia G. Acinas and Laurence Garczarek. 2016. Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria. Proc Natl Acad Sci U S A. 113 (24): 3365-74

2.3. Bacterial functional groups related to photoheterotrophs: using the proteorodopsin (PR) gene and the bacterioclorophll a (pufM) as gene markers.

  • Daniel K. Olson, Susumu Yoshizawa, Dominique Boeuf, Wataru Iwasaki, Edward F. DeLong. 2018. Proteorhodopsin variability and distribution in the North Pacific Subtropical Gyre. The ISME Journal12:1047–1060.
  • Isabel Ferrera, Carles M. Borrego, Guillem Salazar and Josep M. Gasol.2013.Marked seasonality of aerobic anoxygenic phototrophic bacteria in the coastal NW Mediterranean Sea as revealed by cell abundance, pigment concentration and pyrosequencing of pufM gene . Environmental Microbiology. doi:10.1111/1462- 2920.12278.
  • E. D. Graham, J. F. Heidelberg and B. J. Tully.2018. Potential for primary productivity in a globally-distributed bacterial phototroph. The ISME Journal, 12:1861–1866.

2.4.Functional groups that have phoX gene to uptake inorganic phosphorous and used as P-starvation gene marker.

  • Marta Sebastian and James W Ammerman. 2009. The alkaline phosphatase PhoX is more widely distributed in marine bacteria than the classical PhoA. The ISME Journal 3, 563–572

Reviews and Reports:

  • A global Census of Marine Microbes. ASM report 2010.
  • Ferrera I, Sebastian M, Acinas SG, Gasol JM. Prokaryotic functional gene diversity in the sunlit ocean: Stumbling in the darkness. 2015. Current Opinion in Microbiology. 25: 33-39.
  • Carlos Pedrós-Alió. The rare Bacterial Biosphere. 2012. Annu. Rev. Mar. Sci. 2012. 4:449–66
  • Lucie Zinger, Angelique Gobet and Thomas Pommier. Two decades of describing the unseen majority of aquatic microbial diversity. 2012. Molecular Ecology, 21, 1878–1896

Chapter of book:

  • Carles Pedrós-Alió, Silvia G. Acinas, Ramiro Logares and Ramon Massana. 2018. Marine Microbial Diversity as Seen by High Throughput Sequencing. In Microbial Ecology of the Oceans, 3rd Edition Josep M. Gasol (Editor), David L. Kirchman (Editor). ISBN: 978-1-119-10718-7