DNA Barcoding; Ancient DNA; Metabarcoding; Diversity; Eukaryotes; Evolution; Next Generation Sequencing; Foraminifera; Phylogeny
Barrenechea Angeles Inès, Lejzerowicz Franck, Cordier Tristan, Scheplitz Janin, Kucera Michal, Ariztegui Daniel, Pawlowski Jan, Morard Raphaël (2020), Planktonic foraminifera eDNA signature deposited on the seafloor remains preserved after burial in marine sediments, in
Scientific Reports, 10(1), 20351-20351.
Pawłowska Joanna, Wollenburg Jutta E., Zajączkowski Marek, Pawlowski Jan (2020), Planktonic foraminifera genomic variations reflect paleoceanographic changes in the Arctic: evidence from sedimentary ancient DNA, in
Scientific Reports, 10(1), 15102-15102.
Pawlowski Jan, Apothéloz‐Perret‐Gentil Laure, Altermatt Florian (2020), Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring, in
Molecular Ecology, 29(22), 4258-4264.
Mauffrey Florian, Cordier Tristan, Apothéloz‐Perret‐Gentil Laure, Cermakova Kristina, Merzi Thomas, Delefosse Matthieu, Blanc Philippe, Pawlowski Jan (2020), Benthic monitoring of oil and gas offshore platforms in the North Sea using environmental DNA metabarcoding, in
Molecular Ecology, mec.15698-mec.15698.
Frontalini Fabrizio, Cordier Tristan, Balassi Eszter, Armynot du Chatelet Eric, Cermakova Kristina, Apothéloz-Perret-Gentil Laure, Martins Maria Virginia Alves, Bucci Carla, Scantamburlo Enrico, Treglia Mauro, Bonamin Vladimiro, Pawlowski Jan (2020), Benthic foraminiferal metabarcoding and morphology-based assessment around three offshore gas platforms: Congruence and complementarity, in
Environment International, 144, 106049-106049.
Siemensma Ferry, Holzmann Maria, Apothéloz-Perret-Gentil Laure, Clauß Steffen, Voelcker Eckhard, Bettighofer Wolfgang, Roshan Samira Khanipour, Walden Susanne, Dumack Kenneth, Pawlowski Jan (2020), Broad sampling of monothalamids (Rhizaria, Foraminifera) gives further insight into diversity of non-marine Foraminifera, in
European Journal of Protistology, 125744-125744.
Gooday Andrew J., Durden Jennifer M., Holzmann Maria, Pawlowski Jan, Smith Craig R. (2020), Xenophyophores (Rhizaria, Foraminifera), including four new species and two new genera, from the western Clarion-Clipperton Zone (abyssal equatorial Pacific), in
European Journal of Protistology, 75, 125715-125715.
Cordier Tristan, Alonso‐Sáez Laura, Apothéloz‐Perret‐Gentil Laure, Aylagas Eva, Bohan David A., Bouchez Agnès, Chariton Anthony, Creer Simon, Frühe Larissa, Keck François, Keeley Nigel, Laroche Olivier, Leese Florian, Pochon Xavier, Stoeck Thorsten, Pawlowski Jan, Lanzén Anders (2020), Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap, in
Molecular Ecology, mec.15472-mec.15472.
Pawłowska Joanna, Pawlowski Jan, Zajączkowski Marek (2020), Dataset of foraminiferal sedimentary DNA (sedDNA) sequences from Svalbard, in
Data in Brief, 30, 105553-105553.
Blackman Rosetta C., Bruder Andreas, Burdon Francis J., Convey Peter, Funk W. Chris, Jähnig Sonja C., Kishe Mary Alphonce, Moretti Marcelo S., Natugonza Vianny, Pawlowski Jan, Stubbington Rachel, Zhang Xiaowei, Seehausen Ole, Altermatt Florian (2020), A meeting framework for inclusive and sustainable science, in
Nature Ecology & Evolution, 4(5), 668-671.
Frühe Larissa, Cordier Tristan, Dully Verena, Breiner Hans‐Werner, Lentendu Guillaume, Pawlowski Jan, Martins Catarina, Wilding Thomas A., Stoeck Thorsten (2020), Supervised machine learning is superior to indicator value inference in monitoring the environmental impacts of salmon aquaculture using eDNA metabarcodes, in
Molecular Ecology, mec.15434-mec.15434.
Pawłowska Joanna, Łącka Magdalena, Kucharska Małgorzata, Pawlowski Jan, Zajączkowski Marek (2020), Multiproxy evidence of the Neoglacial expansion of Atlantic Water to eastern Svalbard, in
Climate of the Past, 16(2), 487-501.
Burkett Ashley, Rathburn Anthony, Pratt Robert Brandon, Holzmann Maria (2020), Insights into the ecology of epibenthic calcareous foraminifera from a colonization study at 4000 m (Station M) in the NE Pacific Ocean, in
Deep Sea Research Part II: Topical Studies in Oceanography, 173, 104709-104709.
Hallmann Christian, Nettersheim Benjamin J., Brocks Jochen J., Schwelm Arne, Hope Janet M., Not Fabrice, Lomas Michael, Schmidt Christiane, Schiebel Ralf, Nowack Eva C. M., De Deckker Patrick, Pawlowski Jan, Bowser Samuel S., Bobrovskiy Ilya, Zonneveld Karin, Kucera Michal, Stuhr Marleen (2020), Reply to: Sources of C30 steroid biomarkers in Neoproterozoic–Cambrian rocks and oils, in
Nature Ecology & Evolution, 4(1), 37-39.
Makiola Andreas, Compson Zacchaeus G., Baird Donald J., Barnes Matthew A., Boerlijst Sam P., Bouchez Agnès, Brennan Georgina, Bush Alex, Canard Elsa, Cordier Tristan, Creer Simon, Curry R. Allen, David Patrice, Dumbrell Alex J., Gravel Dominique, Hajibabaei Mehrdad, Hayden Brian, van der Hoorn Berry, Jarne Philippe, Jones J. Iwan, Karimi Battle, Keck Francois, Kelly Martyn, Knot Ineke E., et al. (2020), Key Questions for Next-Generation Biomonitoring, in
Frontiers in Environmental Science, 7, 197.
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.
Cordier Tristan, Barrenechea Inès, Lejzerowicz Franck, Reo Emanuela, Pawlowski Jan (2019), Benthic foraminiferal DNA metabarcodes significantly vary along a gradient from abyssal to hadal depths and between each side of the Kuril-Kamchatka trench, in
Progress in Oceanography, 178, 102175-102175.
Hayward Bruce W., Holzmann Maria., Tsuchiya Masashi (2019), Combined Molecular and Morphological Taxonomy of the Beccarii/T3 Group of the Foraminiferal Genus Ammonia, in
Journal of Foraminiferal Research, 49(4), 367-389.
Levin Lisa A., Bett Brian J., Gates Andrew R., Heimbach Patrick, Howe Bruce M., Janssen Felix, McCurdy Andrea, Ruhl Henry A., Snelgrove Paul, Stocks Karen I., Bailey David, Baumann-Pickering Simone, Beaverson Chris, Benfield Mark C., Booth David J., Carreiro-Silva Marina, Colaço Ana, Eblé Marie C., Fowler Ashley M., Gjerde Kristina M., Jones Daniel O. B., Katsumata K., Kelley Deborah, Le Bris Nadine, et al. (2019), Global Observing Needs in the Deep Ocean, in
Frontiers in Marine Science, 6, 241.
Cordier Tristan, Lanzén Anders, Apothéloz-Perret-Gentil Laure, Stoeck Thorsten, Pawlowski Jan (2019), Embracing Environmental Genomics and Machine Learning for Routine Biomonitoring, in
Trends in Microbiology, 27(5), 387-397.
Zinger Lucie, Bonin Aurélie, Alsos Inger G., Bálint Miklós, Bik Holly, Boyer Frédéric, Chariton Anthony A., Creer Simon, Coissac Eric, Deagle Bruce E., De Barba Marta, Dickie Ian A., Dumbrell Alex J., Ficetola Gentile Francesco, Fierer Noah, Fumagalli Luca, Gilbert M. Thomas P., Jarman Simon, Jumpponen Ari, Kauserud Håvard, Orlando Ludovic, Pansu Johan, Pawlowski Jan, Tedersoo Leho, et al. (2019), DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions, in
Molecular Ecology, 28(8), 1857-1862.
Nettersheim Benjamin J., Brocks Jochen J., Schwelm Arne, Hope Janet M., Not Fabrice, Lomas Michael, Schmidt Christiane, Schiebel Ralf, Nowack Eva C. M., De Deckker Patrick, Pawlowski Jan, Bowser Samuel S., Bobrovskiy Ilya, Zonneveld Karin, Kucera Michal, Stuhr Marleen, Hallmann Christian (2019), Putative sponge biomarkers in unicellular Rhizaria question an early rise of animals, in
Nature Ecology & Evolution, 3(4), 577-581.
Cordier Tristan, Frontalini Fabrizio, Cermakova Kristina, Apothéloz-Perret-Gentil Laure, Treglia Mauro, Scantamburlo Enrico, Bonamin Vladimiro, Pawlowski Jan (2019), Multi-marker eDNA metabarcoding survey to assess the environmental impact of three offshore gas platforms in the North Adriatic Sea (Italy), in
Marine Environmental Research, 146, 24-34.
He Xiaoping, Sutherland Terri F., Pawlowski Jan, Abbott Cathryn L. (2019), Responses of foraminifera communities to aquaculture‐derived organic enrichment as revealed by environmental DNA metabarcoding, in
Molecular Ecology, 28(5), 1138-1153.
Adl Sina M., Bass David, Lane Christopher E., Lukeš Julius, Schoch Conrad L., Smirnov Alexey, Agatha Sabine, Berney Cedric, Brown Matthew W., Burki Fabien, Cárdenas Paco, Čepička Ivan, Chistyakova Lyudmila, Campo Javier, Dunthorn Micah, Edvardsen Bente, Eglit Yana, Guillou Laure, Hampl Vladimír, Heiss Aaron A., Hoppenrath Mona, James Timothy Y., Karnkowska Anna, Karpov Sergey, et al. (2019), Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes, in
Journal of Eukaryotic Microbiology, 66(1), 4-119.
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.
Cordier Tristan, Forster Dominik, Dufresne Yoann, Martins Catarina I. M., Stoeck Thorsten, Pawlowski Jan (2018), Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring, in
Molecular Ecology Resources, 18(6), 1381-1391.
Pawlowski Jan, Kelly-Quinn Mary, Altermatt Florian, Apothéloz-Perret-Gentil Laure, Beja Pedro, Boggero Angela, Borja Angel, Bouchez Agnès, Cordier Tristan, Domaizon Isabelle, Feio Maria Joao, Filipe Ana Filipa, Fornaroli Riccardo, Graf Wolfram, Herder Jelger, van der Hoorn Berry, Iwan Jones J., Sagova-Mareckova Marketa, Moritz Christian, Barquín Jose, Piggott Jeremy J., Pinna Maurizio, Rimet Frederic, Rinkevich Buki, et al. (2018), The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems, in
Science of The Total Environment, 637-638, 1295-1310.
Majda Aneta, Majewski Wojciech, Mamos Tomasz, Grabowski Michał, Godoi Maria Angelica, Pawłowski Jan (2018), Variable dispersal histories across the Drake Passage: The case of coastal benthic Foraminifera, in
Marine Micropaleontology, 140, 81-94.
| Author |
Cordier, Tristan |
| Publication date |
12.07.2019 |
| Persistent Identifier (PID) |
https://doi.org/10.1016/j.pocean.2019.102175 |
| Repository |
NCBI
|
| Abstract |
Environmental genomics data from sediment samples collected during the KuramBio II (Kuril Kamchatka Biodiversity Studies II) expedition on RV Sonne in 2016
Eukaryotic metabarcodes for benthic monitoring
| Author |
Cordier , Tristan |
| Publication date |
21.02.2018 |
| Persistent Identifier (PID) |
doi: 10.1111/1755-0998.12926 |
| Repository |
NCBI
|
| Abstract |
The study compares the performance of five barcoding genes for ecological quality status inference in marine environments. The genes include one bacterial, one foraminiferal and three eukaryotes ones,
Eukaryotic metabarcodes from North Adriatic
| Author |
Cordier, Tristan |
| Persistent Identifier (PID) |
doi: 10.1016/j.marenvres.2018.12.009 |
| Repository |
NCBI
|
| Abstract |
Multi-marker eDNA metabarcoding survey around offshore gas platforms in the North Adriatic Sea
North Sea sediment DNA metabarcodes
| Author |
Cordier, Tristan |
| Persistent Identifier (PID) |
doi: 10.1111/mec.15698 |
| Repository |
NCBI
|
| Abstract |
This study aimed at evaluating the potential of metabarcoding to replace morphological identification for assessing the impact of oil drilling platform activities on sediments community.
The evolutionary and ecological studies of microbial eukaryotes, or protists, have been completely transformed by accumulation of genomic and metagenomic data readily obtained from diverse biological and environmental material. The evolutionary history of protists has been profoundly revised by phylogenomics, while environmental genomics brought to light the immense diversity of the microeukaryotic biome and enhanced its ecological importance. Yet, unraveling the evolutionary and ecological information from extremely complex eukaryotic genomes and metagenomes is not always straightforward, and the transformation of this information into practical applications can be sometimes problematic.Here, we address some of the challenges raised by the deluge of high-throughput sequencing (HTS) data, focusing on molecular evolution and ecology of foraminifera and related protists. The project continues a long-term research that has been conducted by our group on protist phylogeny, taxonomy, and molecular ecology. The project is based on our extensive expertise in the field, the large databases accumulated over the years, and in-house built pipelines for their analyses. It also benefits of a large network of collaborations that facilitates the access to samples, assists in their processing and analyzing the obtained data.The project comprises two complementary parts. In the first part, we will use single-cell DNA and RNA-seq approaches in order to (1) complement the foraminiferal barcoding database, (2) revise the evolutionary relationships and identify foraminiferal mitochondrial genes, (3) assess the importance of intra-genomic variations, and (4) evaluate the role of bacterial microbiomes in the metabolism of foraminifera and their close relatives. In the second part, we will use environmental genomics in order to (5) assess the patterns of deep-sea benthic diversity, (6) expand the use of fossil eukaryotic DNA as paleoenvironmental proxy, and (7) search for species and genes that could be used as biosensors of environmental impacts. To facilitate the latter tasks, (8) we will develop bioinformatic tools for rapid and accurate analysis of environmental HTS data, focusing on machine learning and ecological network analyses applied to biomonitoring.The project has significance for both fundamental and applied science. Foraminifera are highly diversified both taxonomically and ecologically, and therefore represent a key model to improve our understanding of the origin and evolution of single-cell eukaryotes. The ubiquity, sensitivity and adaptability of foraminifera prompt their use as a proxy to infer global biodiversity patterns and to reconstruct paleoenvironments and paleoclimates using DNA preserved in the sediment. Finally, we will develop a novel category of DNA-based sensors to assess the environmental impacts of industrial activities.