About me: I am an aquatic (paleo)ecologist interested in the impact of environmental changes on the phylogenetic diversity and biogeography of micro- and macro-organisms in lakes. In my PhD work, I investigated the long-term dynamics of freshwater plankton - with a focus on cyanobacteria - in relation to anthropogenic-induced eutrophication and climate change.
I use environmental DNA (eDNA)-based approaches coupled with other paleolimnological tools to reconstruct past communities archived in lacustrine sediments. In my current postdoc, I conduct metagenomic (shotgun) and metabarcoding analyses on eDNA in water and sediment samples to describe metazoan diversity and determine the factors driving their distribution in lakes.
I use environmental DNA (eDNA)-based approaches coupled with other paleolimnological tools to reconstruct past communities archived in lacustrine sediments. In my current postdoc, I conduct metagenomic (shotgun) and metabarcoding analyses on eDNA in water and sediment samples to describe metazoan diversity and determine the factors driving their distribution in lakes.
Map of some of the lakes I have sampled in Canada, Switzerland, France, Italy, Romania and Germany.
Summary of current and past projects:
2022 - Workshop on molecular resources available for freshwater macroorganisms
This Working Group funded by the Groupe de Recherche Interuniversitaire en Limnologie (GRIL) aimed at assessing the availability of molecular genetic resources for Canada’s freshwater-dependent macroscopic species and identify data deficiencies where future research should be directed. With a group of >15 scientists from 9 universities, the McGill Genome Centre, and Environment and Climate Change Canada (ECCC), we assessed the availability of barcodes and whole genome assemblies in major sequence repositories and mapped the distribution of archived genetic data across Canada to highlight geographic regions of data deficiencies and help define where future sequencing efforts should be directed to contribute to assess and preserve freshwater biodiversity.
Read the paper here.
This Working Group funded by the Groupe de Recherche Interuniversitaire en Limnologie (GRIL) aimed at assessing the availability of molecular genetic resources for Canada’s freshwater-dependent macroscopic species and identify data deficiencies where future research should be directed. With a group of >15 scientists from 9 universities, the McGill Genome Centre, and Environment and Climate Change Canada (ECCC), we assessed the availability of barcodes and whole genome assemblies in major sequence repositories and mapped the distribution of archived genetic data across Canada to highlight geographic regions of data deficiencies and help define where future sequencing efforts should be directed to contribute to assess and preserve freshwater biodiversity.
Read the paper here.
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2021-2023 PaleoEcoGen Working Group
Our PAGES working group launched in August 2021 aims at improving our understanding of critical transitions in a range of aquatic and terrestrial environments using a key proxy - ancient environmental DNA (eDNA). Visit the working group website for more information and to find out how to get involved!
2021-2023 PaleoEcoGen Working Group
Our PAGES working group launched in August 2021 aims at improving our understanding of critical transitions in a range of aquatic and terrestrial environments using a key proxy - ancient environmental DNA (eDNA). Visit the working group website for more information and to find out how to get involved!
2019-2022 Environmental DNA analysis of Metazoan diversity in Canadian lakes
My main goal during my current postdoctoral fellowship funded by the GRIL (Groupe de Recherche Interuniversitaire en Limnologie) and McGill University is to investigate metazoan diversity across hundreds of Canadian lakes using environmental metagenomics (aka shotgun sequencing). This research project is part of the pan-Canadian LakePulse Network (2017-2019) which conducted a monitoring campaign over 623 lakes across the country with the overarching goal of assessing the health of Canadian lakes. As a method validation first step, I am comparing the diversity of zooplankton detected in water metagenomes (obtained via shotgun sequencing) with taxonomic zooplankton datasets derived from classical microscopy surveys performed in the same lakes. In a next step, we will add metabarcoding of the COI region for eukaryotes to the taxonomic and shotgun sequencing data comparison.
2017-2021 Lac de Joux (Jura Mountains, Switzerland)
The second phase of the Lac de Joux project is a collaboration between sedimentologists, palaeolimnologists, and ecologists that aims at unraveling the impacts of human activities in the watershed on planktonic communities of Lac de Joux (Swiss Jura) over the past 1000 years. We are using both classical paleolimnological proxies and molecular genetics approaches to reconstruct the past dynamics of diverse organisms (cladocerans, bacteria, phytoplankton, chironomids, fish) part of the lake's food web.
In this study (Monchamp et al., 2021), we found that, despite of centuries of growing human pressure since the first human settlements in the catchment, Lake Joux communities remained rather stable between ca. 1000 and 1950 CE. The sediments of Lake Joux revealed a simultaneous major turnover in the mid-twentieth century in all biotic communities. This transition qualifies as a true regime shift and is a consequence of the rapid eutrophication of Lake Joux which started mid-twentieth century. Further, despite seven decades of re-oligotrophication of the lake, communities have not returned to their pre-disturbance composition. Our study highlights that human-driven changes in lake ecosystems may lead to regime shifts that are not easily reversible through management strategies.
The second phase of the Lac de Joux project is a collaboration between sedimentologists, palaeolimnologists, and ecologists that aims at unraveling the impacts of human activities in the watershed on planktonic communities of Lac de Joux (Swiss Jura) over the past 1000 years. We are using both classical paleolimnological proxies and molecular genetics approaches to reconstruct the past dynamics of diverse organisms (cladocerans, bacteria, phytoplankton, chironomids, fish) part of the lake's food web.
In this study (Monchamp et al., 2021), we found that, despite of centuries of growing human pressure since the first human settlements in the catchment, Lake Joux communities remained rather stable between ca. 1000 and 1950 CE. The sediments of Lake Joux revealed a simultaneous major turnover in the mid-twentieth century in all biotic communities. This transition qualifies as a true regime shift and is a consequence of the rapid eutrophication of Lake Joux which started mid-twentieth century. Further, despite seven decades of re-oligotrophication of the lake, communities have not returned to their pre-disturbance composition. Our study highlights that human-driven changes in lake ecosystems may lead to regime shifts that are not easily reversible through management strategies.
2013-2017 CyanoArchive (Swiss -- Romanian collaboration, PhD thesis)
As part of this collaborative project at Eawag, the Swiss Federal Institute of Aquatic Science and Technology, I investigate the phylogenetic diversity of cyanobacteria communities and the dynamics of toxic/non-toxic cyanobacteria in several lakes located both in the Danube Delta (Romania) and in the plains located around the European Alps (Switzerland, Italy, France).
We extracted DNA from sediment cores collected in multiple lakes and sequenced the cyanobacteria 16S rRNA genes to uncover their past diversity over decades to several centuries. We identified climate warming as an important driver that contributed to shaping cyanobacteria diversity in the peri-Alpine lakes over the twentieth century. Eutrophication caused by increased lake water pollution by phosphorus and nitrogen loadings was also an important driver of change in both cyanobacteria and cladocera (Daphnia) communities.
The figure on the right shows the temporal change of Daphnia populations reconstructed from resting eggs preserved inside ephippia in the sediment cores collected in three lakes: Gorgova (Danube Delta, Romania), Greifensee, and Halwillersee (Switzerland). At the start of the main period of eutrophication, D. galeata became more dominant before Daphnia longispina was replaced by the more resistant hybrid D. longispina x D. galeata in the two Swiss lakes. (From Monchamp et al., 2019)
2013-2017 CyanoArchive (Swiss -- Romanian collaboration, PhD thesis)
As part of this collaborative project at Eawag, the Swiss Federal Institute of Aquatic Science and Technology, I investigate the phylogenetic diversity of cyanobacteria communities and the dynamics of toxic/non-toxic cyanobacteria in several lakes located both in the Danube Delta (Romania) and in the plains located around the European Alps (Switzerland, Italy, France).
We extracted DNA from sediment cores collected in multiple lakes and sequenced the cyanobacteria 16S rRNA genes to uncover their past diversity over decades to several centuries. We identified climate warming as an important driver that contributed to shaping cyanobacteria diversity in the peri-Alpine lakes over the twentieth century. Eutrophication caused by increased lake water pollution by phosphorus and nitrogen loadings was also an important driver of change in both cyanobacteria and cladocera (Daphnia) communities.
The figure on the right shows the temporal change of Daphnia populations reconstructed from resting eggs preserved inside ephippia in the sediment cores collected in three lakes: Gorgova (Danube Delta, Romania), Greifensee, and Halwillersee (Switzerland). At the start of the main period of eutrophication, D. galeata became more dominant before Daphnia longispina was replaced by the more resistant hybrid D. longispina x D. galeata in the two Swiss lakes. (From Monchamp et al., 2019)