McGill University
Postdoctoral fellow candidate
Supervisor: Irene Gregory-Eaves
Melania Cristescu
Start: 2019-09-16
End: 2023-05-31
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Project

Metagenomic analysis of metazoan diversity across Canadian lakes
Global changes threaten lake ecosystems and facilitate invasions by non-native species, which may greatly modify ecosystems and reduce services derived from lakes. Environmental DNA (eDNA) approaches are broadly used to assess biodiversity trends in aquatic environments. Environmental metagenomics (shotgun sequencing of an environmental sample) has recently emerged as a powerful approach to recover taxonomic and genetic diversity of whole taxonomic groups of plants and animals from water and sediment. The main goals of my project are to 1- determine the effectiveness of metagenomes of water samples in detecting metazoan diversity, and 2- determine how diversity derived from metagenomes compares with metabarcoding and morphologically-identified datasets. In a first step, I will validate the approach using datasets of zooplankton and rotifers and in a second step, I will extend the study to other groups of aquatic metazoans (e.g. fish and molluscs). This project is part of the LakePulse Network, a pan-Canadian initiative that aims at assessing the health of lakes across the country.

Keywords

Environmental DNA, biodiversity, environmental metagenomics, paleogenetics, climate change

Publications

1- Early human impact on lake cyanobacteria revealed by a Holocene record of sedimentary ancient DNA
Nwosu, Ebuka Canisius, Achim Brauer, Marie-Eve Monchamp, Sylvia Pinkerneil, Alexander Bartholomäus, Martin Theuerkauf, Jens-Peter Schmidt, Kathleen R. Stoof-Leichsenring, Theresa Wietelmann, Jerome Kaiser, Dirk Wagner, Susanne Liebner
2023 Communications Biology

2- Investigating the effects of anthropogenic stressors on lake biota using sedimentary DNA
Barouillet, Cécilia, Marie‐Eve Monchamp, Stefan Bertilsson, Katie Brasell, Isabelle Domaizon, Laura S. Epp, Anan Ibrahim, Hebah Mejbel, Ebuka Canisius Nwosu, John K. Pearman, Maïlys Picard, Georgia Thomson‐Laing, Narumi Tsugeki, Jordan Von Eggers, Irene Gregory‐Eaves, Frances Pick, Susanna A. Wood, Eric Capo
2022 Freshwater Biology

3- Comparative analysis of zooplankton diversity in freshwaters: What can we gain from metagenomic analysis?
Monchamp, Marie‐Ève, David A. Walsh, Rebecca E. Garner, Susanne A. Kraemer, Beatrix E. Beisner, Melania E. Cristescu, Irene Gregory‐Eaves
2022 Environmental DNA

4- Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations
Capo, Eric, Charline Giguet-Covex, Alexandra Rouillard, Kevin Nota, Peter D. Heintzman, Aurèle Vuillemin, Daniel Ariztegui, Fabien Arnaud, Simon Belle, Stefan Bertilsson, Christian Bigler, Richard Bindler, Antony G. Brown, Charlotte L. Clarke, Sarah E. Crump, Didier Debroas, Göran Englund, Gentile Francesco Ficetola, Rebecca E. Garner, Joanna Gauthier, Irene Gregory-Eaves, Liv Heinecke, Ulrike Herzschuh, Anan Ibrahim, Veljo Kisand, Kurt H. Kjær, Youri Lammers, Joanne Littlefair, Erwan Messager, Marie-Eve Monchamp, Fredrik Olajos, William Orsi, Mikkel W. Pedersen, Dilli P. Rijal, Johan Rydberg, Trisha Spanbauer, Kathleen R. Stoof-Leichsenring, Pierre Taberlet, Liisi Talas, Camille Thomas, David A. Walsh, Yucheng Wang, Eske Willerslev, Anne van Woerkom, Heike H. Zimmermann, Marco J. L. Coolen, Laura S. Epp, Isabelle Domaizon, Inger G. Alsos, Laura Parducci
2021 Quaternary

5- Trade‐offs between reducing complex terminology and producing accurate interpretations from environmental DNA: Comment on “Environmental DNA: What's behind the term?” by Pawlowski et al., (2020)
Rodriguez‐Ezpeleta, Naiara, Olivier Morissette, Colin W. Bean, Shivakumara Manu, Pritam Banerjee, Anaïs Lacoursière‐Roussel, Kingsly C. Beng, S. Elizabeth Alter, Fabian Roger, Luke E. Holman, Kathryn A. Stewart, Michael T. Monaghan, Quentin Mauvisseau, Luca Mirimin, Owen S. Wangensteen, Caterina M. Antognazza, Sarah J. Helyar, Hugo Boer, Marie‐Eve Monchamp, Reindert Nijland, Cathryn L. Abbott, Hideyuki Doi, Matthew A. Barnes, Matthieu Leray, Pascal I. Hablützel, Kristy Deiner
2021 Molecular Ecology

6- Paleoecological evidence for a multi-trophic regime shift in a perialpine lake (Lake Joux, Switzerland)
Monchamp, Marie-Ève, Rosalie Bruel, Victor Frossard, Suzanne McGowan, Marlène Lavrieux, Moritz Muschick, Marie-Élodie Perga, Nathalie Dubois
2021 Anthropocene

7- PaleoEcoGen: Unlocking the power of ancient environmental DNA to understand past ecological trends

2021 Past Global Changes Magazine

8- High dispersal levels and lake warming are emergent drivers of cyanobacterial community assembly in peri-Alpine lakes
Monchamp, Marie-Eve, Piet Spaak, Francesco Pomati
2019 Scientific Reports

9- Using DNA from formaldehyde-preserved Daphnia to reconstruct past populations
Turko, Patrick, Justyna Wolinska, Christoph Tellenbach, Marcin Krzysztof Dziuba, Marie-Eve Monchamp, Piet Spaak
2019 Hydrobiologia

10- Long Term Diversity and Distribution of Non-photosynthetic Cyanobacteria in Peri-Alpine Lakes
Monchamp, Marie-Eve, Piet Spaak, Francesco Pomati
2019 Frontiers in Microbiology

11- Homogenization of lake cyanobacterial communities over a century of climate change and eutrophication
Monchamp, Marie-Eve, Piet Spaak, Isabelle Domaizon, Nathalie Dubois, Damien Bouffard, Francesco Pomati
2017 Nature Ecology & Evolution

12- Sedimentary and egg-bank DNA from 3 European lakes reveal concurrent changes in the composition and diversity of cyanobacterial and Daphnia communities
Monchamp, Marie-Eve, Ioana Enache, Patrick Turko, Francesco Pomati, Geta Rîşnoveanu, Piet Spaak
2017 Hydrobiologia

13- Nitrogen Forms Influence Microcystin Concentration and Composition via Changes in Cyanobacterial Community Structure
Marie-Eve Monchamp, Frances R. Pick, Beatrix E. Beisner, Roxane Maranger
2014 PLoS ONE

14- Sedimentary DNA Reveals Cyanobacterial Community Diversity over 200 Years in Two Perialpine Lakes
Monchamp, Marie-Eve, Jean-Claude Walser, Francesco Pomati, Piet Spaak,
2016 Applied and Environmental Microbiology

15- Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential
Capo, Eric, Marie‐Eve Monchamp, Marco J. L. Coolen, Isabelle Domaizon, Linda Armbrecht, Stefan Bertilsson
2022 Environmental Microbiology

16- Century-Long Homogenization of Algal Communities Is Accelerated by Nutrient Enrichment and Climate Warming in Lakes and Reservoirs of the North Temperate Zone
Huo, Shouliang, Hanxiao Zhang, Marie-Eve Monchamp, Rong Wang, Nanyan Weng, Jingtian Zhang, Hong Zhang, Fengchang Wu
2022 Environmental Science & Technology

17- Comparing microscopy and DNA metabarcoding techniques for identifying cyanobacteria assemblages across hundreds of lakes
MacKeigan, Paul W., Rebecca E. Garner, Marie-Ève Monchamp, David A. Walsh, Vera E. Onana, Susanne A. Kraemer, Frances R. Pick, Beatrix E. Beisner, Michael D. Agbeti, Naíla Barbosa da Costa, B. Jesse Shapiro, Irene Gregory-Eaves
2022 Harmful Algae