Project

Back to overview

Molecular evolution and ecology of Foraminifera and related protists

Applicant Pawlowski Jan Wojciech
Number 159709
Funding scheme Project funding (Div. I-III)
Research institution Département de Génétique et Evolution Faculté des Sciences Université de Genève
Institution of higher education University of Geneva - GE
Main discipline Zoology
Start/End 01.04.2015 - 31.03.2018
Approved amount 756'000.00
Show all

All Disciplines (2)

Discipline
Zoology
Genetics

Keywords (9)

DNA Barcoding; Foraminifera; Next Generation Sequencing; Eukaryotes; Ancient DNA; Diversity; Phylogeny; Evolution; Metabarcoding

Lay Summary (French)

Lead
Les foraminifères sont des protistes (eucaryotes unicellulaires) marins largement étudiés en paléontologie, mais dont la diversité actuelle reste encore très mal connue. Dans ce projet, nous utilisons des techniques modernes du séquençage à haut débit afin de mieux comprendre les origines et l’évolution des foraminifères modernes et d’explorer leur diversité.
Lay summary

Contenu et objectifs du travail de recherche

Le projet s’inscrit dans le cadre des études phylogénomiques et métagénomiques dont l’objectif principal est de reconstruire l’histoire évolutive des espèces et d’évaluer leur diversité à partir des données génomiques et transcriptomiques. Nos études précédentes ont permis d’établir la position des foraminifères dans l’arbre du vivant et de définir leurs principaux groupes taxonomiques, ainsi que de découvrir une spectaculaire diversité des foraminifères non-fossilisables. Dans le projet actuel nous allons aborder le phénomène de la diversification des foraminifères en analysant les gènes impliqués dans la morphogenèse et les variations des gènes ribosomiques. Nous allons aussi continuer à explorer la diversité des foraminifères en analysant les données d’ADN environnemental et en complétant notre base des données de référence.

 

Contexte scientifique et social du projet de recherche

Le projet contribuera à la recherche fondamentale de l’évolution et l’écologie des foraminifères et autres protistes. Il contribuera aussi à l’utilisation de ces organismes comme bioindicateurs pour évaluer l’état actuel des écosystèmes aquatiques ainsi que d’étudier leur histoire moderne à travers l’analyse des données paléogénomiques.

 

Direct link to Lay Summary Last update: 01.04.2015

Responsible applicant and co-applicants

Employees

Publications

Publication
SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data
Dufresne Yoann, Lejzerowicz Franck, Perret-Gentil Laure Apotheloz, Pawlowski Jan, Cordier Tristan (2019), SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data, in BMC Bioinformatics, 20(1), 88-88.
Xenophyophores (Rhizaria, Foraminifera) from the Eastern Clarion-Clipperton Zone (equatorial Pacific): the Genus Psammina
Gooday Andrew J., Holzmann Maria, Goineau Aurélie, Kamenskaya Olga, Melnik Vyacheslav F., Pearce Richard B., Weber Alexandra A.-T., Pawlowski Jan (2018), Xenophyophores (Rhizaria, Foraminifera) from the Eastern Clarion-Clipperton Zone (equatorial Pacific): the Genus Psammina, in Protist, 169(6), 926-957.
Five new species and two new genera of xenophyophores (Foraminifera: Rhizaria) from part of the abyssal equatorial Pacific licensed for polymetallic nodule exploration
Gooday Andrew J, Holzmann Maria, Goineau Aurélie, Pearce Richard B, Voltski Ivan, Weber Alexandra A-T, Pawlowski Jan (2018), Five new species and two new genera of xenophyophores (Foraminifera: Rhizaria) from part of the abyssal equatorial Pacific licensed for polymetallic nodule exploration, in Zoological Journal of the Linnean Society, 183(4), 723-748.
New species of the xenophyophore genus Aschemonella (Rhizaria: Foraminifera) from areas of the abyssal eastern Pacific licensed for polymetallic nodule exploration
Gooday Andrew J, Holzmann Maria, Caulle Clemence, Goineau Aurélie, Jones Daniel O B, Kamenskaya Olga, Simon-Lledó Erik, Weber Alexandra A -T, Pawlowski Jan (2018), New species of the xenophyophore genus Aschemonella (Rhizaria: Foraminifera) from areas of the abyssal eastern Pacific licensed for polymetallic nodule exploration, in Zoological Journal of the Linnean Society, 182(3), 479-499.
Cyrea szymborska Gen. Et Sp. Nov., a New Textulariid Foraminifer from the Mediterranean Sea
Hozmann Maria, Sylvain Rigaud, Amini Shahrouz, Voltski Ivan, Pawlowski Jan (2018), Cyrea szymborska Gen. Et Sp. Nov., a New Textulariid Foraminifer from the Mediterranean Sea, in Journal of Foraminiferal Research, 48(2), 156.
Psammophaga fuegia sp. nov., a new monothalamid foraminifera from the Beagle Channel, South America
Gschwend Florian, Majda Aneta, Majewski Wojciech, Pawlowski Jan (2016), Psammophaga fuegia sp. nov., a new monothalamid foraminifera from the Beagle Channel, South America, in Acta Protozoologica, 55, 101.
Worldwide analysis of sedimentary DNA reveals major gaps in taxonomic knowledge of deep-sea benthos
Sinniger Frédéric, Pawlowski Jan, Haki Sarii, Gooday Andrew J (2016), Worldwide analysis of sedimentary DNA reveals major gaps in taxonomic knowledge of deep-sea benthos, in Frontiers in Marine Sciences, 3, 92.

Collaboration

Group / person Country
Types of collaboration
Dr. Jutta Wollenburg, AWI, Bremerhaven Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Dr. Andrew Gooday, National Oceanographic Center, Southampton Great Britain and Northern Ireland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr. Sylvain Rigaud, University of Geneva Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr. Michael Kaminski, King Fahd University Saudi Arabia (Asia)
- in-depth/constructive exchanges on approaches, methods or results
Prof. Lisa Levin, Scripps Oceanographic Institution, San Diego United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Tomas Cedhagen, University of Aarhus Denmark (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr. Marek Zajaczkowski, Institute Oceanology, Polish Academy of Sciences, Sopot Poland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Dr. P. Martinez Arbizu DZMB-Forschungsinstitut Senckenberg, Wilhelmshaven Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Dr. Thomas Wilding, SAMS, Oban Great Britain and Northern Ireland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Edward Mitchell, University of Neuchâtel Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Dr. Xavier Pochon, Cawthron Institute New Zealand (Oceania)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr. Fabrizio Frontalini, University of Urbino Italy (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Dr. Angelika Brandt, Zoological Museum, University of Hamburg Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Prof. Ludovic Orlando, Centre for Geogenetics, Natural History Museum of Denmark Denmark (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr. Witold Szczucinski, Department of Paleontology, UAM, Poznan, Poland Poland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr. Colomban de Vargas, Station Biologique de Roscoff France (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr. Wojciech Majewski, Institut of Paleobiology, Polish Academy of Sciences, Warszawa Poland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr. Sigal Abramovich, University of Beer Sheva Israel (Asia)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr Samuel Bowser, Wadworth Center, Albany, NY United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Michal Kucera, Universität Bremen Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Swiss Conference of Organismic Biology Talk given at a conference High-throughput biomonitoring of marine ecosystems with eDNA: supervised machine learning for the building of robust predictive models 15.02.2018 Neuchâtel, Switzerland Cordier Tristan;
7th International Barcode of Life Conference Talk given at a conference Ecobarcoding: taxonomy-free approach for high-throughput environmental DNA-based biomonitoring 20.11.2017 Kruger Parc, South Africa Pawlowski Jan Wojciech;
DNAqua-Net conference Talk given at a conference Biomonitoring with eDNA: should we care about taxonomy? 27.09.2017 Sarajevo, Bosnia-Hercegovina Pawlowski Jan Wojciech; Cordier Tristan;
The Batsheva de Rotshild Workshop on live foraminifera as a new model system for monitoring and reconstructing marine environments Talk given at a conference Foraminiferal DNA metabarcoding applied to benthic monitoring: promises and challenges 11.09.2017 Eilat, Israel Kuznetcov Ivan; Pawlowski Jan Wojciech;
7th Congress of European Microbiologists (FEMS) Poster Predicting the ecological quality status of marine environments from eDNA metabarcoding: comparing learning algorithms 09.07.2017 Valencia, Spain Cordier Tristan;
15th International Congress of Protistology Talk given at a conference Single cell high-throughput sequencing unveils different patterns of intragenomic polymorphism in ribosomal RNA genes of Foraminifera 03.07.2017 Prague, Czech Republic Pawlowski Jan Wojciech;
International Workshop on Environmental Genomics Talk given at a conference Predicting benthic ecological status from eDNA metabarcoding data using supervised machine learning 08.06.2017 St Johns, Canada Pawlowski Jan Wojciech;
Revolutionizing Next-Generation Sequencing Talk given at a conference Marine biomonitoring: predicting biotic indices from eDNA metabarcoding data using supervised machine learning. 20.03.2017 Antwerp, Belgium Cordier Tristan;
DNAqua- Net kick-off conference Talk given at a conference Taxonomy-free approach: Predicting biotic indices from eDNA metabarcoding data using supervised machine learning 07.03.2017 Essen, Germany Pawlowski Jan Wojciech; Cordier Tristan;
VII European Congress of Protistology Talk given at a conference Protist metabarcoding and its applications 08.09.2016 Seville, Spain Pawlowski Jan Wojciech;
Ecotox seminar Individual talk Environmental DNA monitoring: promises and challenges 22.03.2016 Lausanne, Switzerland Pawlowski Jan Wojciech;
6th International Barcode of Life Conference Talk given at a conference Inferring biotic indices from molecular data 20.08.2015 Guelph, Canada Pawlowski Jan Wojciech;
Eawag seminar Individual talk Environmental monitoring in NGS era 08.05.2015 Zürich, Switzerland Pawlowski Jan Wojciech;


Self-organised

Title Date Place
Workshop on application of genomic tools for biomonitoring of marine environment: from technology to legal and socio-economic aspects 04.04.2016 Genève, Switzerland

Knowledge transfer events

Active participation

Title Type of contribution Date Place Persons involved
Et si la vie venait d’ailleurs? Talk 10.01.2018 Genève, Switzerland Pawlowski Jan Wojciech;


Communication with the public

Communication Title Media Place Year
Print (books, brochures, leaflets) Arbre de la vie Western Switzerland International 2017

Use-inspired outputs


Start-ups

Name Year

Associated projects

Number Title Start Funding scheme
179125 Molecular evolution and ecology of Foraminifera and related protists 01.05.2018 Project funding (Div. I-III)
150817 High-throughput sequencing for research on evolution and ecology of microeukaryotes 01.12.2013 R'EQUIP
140766 Molecular evolution and ecology of Foraminifera and related protists 01.04.2012 Project funding (Div. I-III)

Abstract

Over the last few years the research on molecular evolution and ecology of protists have greatly benefited from the development of high-throughput next-generation sequencing (NGS) technologies. The deluge of sequence data allowed refining the phylogenomic tree of eukaryotes and revealed a new dimension of eukaryotic diversity based on in-depth environmental surveys. However, this progress of phylogenomic and metagenomic studies driven by the new sequencing technologies did not contribute equally to the knowledge of all groups of protists.The present project focuses on the genetically most undersampled super-group of eukaryotes: the Rhizaria and its flagship taxon, the Foraminifera. The project is a continuation of the long-term research on molecular evolution of foraminifera and other protists conducted by the applicant since several years. In our previous studies we have pioneered the use of NGS tools to explore protist evolutionary history and diversity, raising several important questions concerning the origin of foraminifera, their spectacular diversification, widespread occurrence, and ecological role. In this project we will further address these questions from genomic and metagenomic perspectives.The project is divided into three parts, including (1) phylogenomic analyses, (2) genetic variability, and (3) environmental diversity assessment. In the first part, we will use NGS to fuel genomic and transcriptomic databases focusing on the foraminiferal mitochondrial genome and the genes involved in process of skeletonization and biomineralization. In the second part, we will develop the NGS-based single-cell barcoding approach in order to tackle the issue of ribosomal RNA genes variability and its possible origins. The third part will comprise the development of mathematical and computational tools for NGS diversity data analyses and their various applications, notably for the establishment of biotic indices of present and past environmental changes. Our project will contribute substantially to the knowledge of foraminifera. It will promote the revision of their classification, prompt their use as ecological indicators, and introduce non-fossilized taxa as paleoceanographic proxies. Importantly, the project will also have a broader impact on the study of other protists. On the one hand, it will contribute to the development of innovative approaches such as the single-cell multiplexed NGS barcoding as well as algorithms for rapid, accurate and robust analysis of NGS diversity data. On the other hand, it will open new avenues for the investigation of important biological processes such as hybridization that have not yet been deeply explored in protists. Moreover, by surveying the environmental diversity of the whole eukaryotic domain, this project is bound to discover numerous groups of protists likely to become the future gold standards for environmental biomonitoring.
-