Our funded research programs address a range of fundamental and applied microbial ecology questions. At Laboratoire Ampère, we have established infrastructure for examining all aspects of environmental microbiology including microbial cultivation, molecular biology and biogeochemical analyses. We have individual, dedicated labs for nucleic acid extraction and manipulation, high throughput sequencing, cultivation of prokaryotes, fungi and viruses, microscopy, and ice, snow, soil, water and plant incubations and gas analysis.

Current Projects

EiCLaR: Enhanced in situ bioremediation for contaminated land remediation

This 6.7 million Euro project funded by the EU and China is composed of 13 EU and 5 Chinese partners. EiCLaR will develop scientific and technical innovations for in situ bioremediation technologies that will be directly developed into industrial processes for the rapid, efficient, cost-effective treatment of a range of environmental pollutants such as chlorinated solvents, heavy metals and pesticides over the next 48 months. These technologies (Electro-Nanobioremediation, Monitored Bioaugmentation, Bioelectrochemical Remediation, and Enhanced Phytoremediation) will enable bioremediation approaches to expand their range of applications to industrial sites that contain complex, high concentration pollutant mixtures. This project will move the proof-of-concepts to industrial commercial processes through laboratory studies to explore the scientific base, scale-up techniques and field demonstrations. EiCLaR’s environmental sustainable and low impact methods will provide partners involved across contaminated land management value chains (researchers, site managers, developers, procurers, service providers, technology providers) with the tools to manage contaminated soil and groundwater, and improve the environmental quality across many sites throughout Europe and China.

(click here to visit EiCLaR website and for list of partners)

(click here to follow us on twitter)

FUNCTION: Arbuscular mycorrhizal fungi interactions in the nitrogen cycle for mitigating nitrous oxide emissions from agroecosystems

Fertilizer use in agriculture has had enormous deleterious environmental consequences. The inefficient use of nitrogen (N) fertilizer in agricultural soils results in the loss of N through nitrate leaching or emission of the greenhouse gas nitrous oxide (N2O), contributing to climate change, ozone depletion and major economic losses. The rate at which anthropogenic-derived N is returned to the atmosphere, including the proportion as N2O, is largely governed by the ecology and biology of the microorganisms involved. Arbuscular mycorrhizal fungi (AMF) are a key group of soil microorganisms that utilize and transfer N to symbiotic plant partners, and have shown potential for reducing N2O emissions. However, these mechanisms have yet to be determined. This 42 months ANR funded project, FUNCTION, will define the role of AMF in the N-cycle via their interaction with microorganism that contribute both direct and indirectly to N2O production in agroecosystems and their involvement in mediating N2O emissions derived from N fertilizer inputs in soil. Ultimately, FUNCTION will determine the extent to which AMF mitigate N2O emissions under different N fertilizer scenarios and the mechanisms responsible. The resulting quantitative data will be used for improving existing N2O modelling approaches that currently do not consider differences in the resulting interactions between AMF and N-cycling microbial groups.

  •  Jennifer Pett-Ridge, Lawrence Livermore National Laboratory, USA

COMICONS: Comammox microorganisms contribute to nitrification in soil

COMICONS is a multidisciplinary programme combining expertise in microbiology, molecular ecology, genomics and biogeochemical modelling of nitrogen (N) dynamics in soil to characterize the physiology, ecological niche(s) of comammox bacteria and their overall contribution to nitrogen cycling processes in soil. Specifically, it aims to determine under what conditions comammox bacteria are active in soil and what sources of N they utilize for growth. Their activity in situ in the soil environment is being characterised together with detailed physiological analysis of novel strains obtained in laboratory culture. Importantly, it aims to model their contribution to N transformations in soil with respect to fertiliser addition, determine their contribution to nitrous oxide emissions in soil, and determine whether they have distinct ecological niche(s) in comparison to other characterized groups of ammonia oxidisers.

Project Partner:

  • Laurent Philippot, AgroEcology, INRAE Dijon 

SARA: Surveillance of emerging pathogens and antibiotic resistances in aquatic ecosystems

Appropriate methods for wastewater-based epidemiology (WBE) and a better understanding of the fate of pathogenic viruses and antibiotic resistant bacteria from the sources to river basins and estuaries are urgently required. Our project will determine the prevalence of pathogenic viruses (including SARS-CoV-2), microbial indicators, antibiotic resistance, and microbial source tracking (MST) markers in wastewater, surface water, coastal sea waters, sediment and bivalve molluscan shellfish (BMS) in catchments located in different climate areas (Sweden, Germany, France, Spain, Portugal, Israel, Mozambique, and Uganda). The project aims are: (i) method harmonization and training of European and African partners, (ii) SARS-CoV-2 detection in raw wastewater as a biomarker of COVID-19 cases, (iii) enteric viruses, antibiotic resistances and MST markers monitoring in aquatic environments, (iv) evaluation of sediments and BMS as integral reservoirs, (v) determination of the impact of climate and extreme weather events, and (vi) microbial risk assessment for water resources. Results and recommendations will be transferred to the scientific community by peer-reviewed papers and conference presentations. International health and environment organisations as well as authorities and waterworks that represent end-users on a global, European and African level will participate in the Stakeholder Forum.

Other Partners:

  • Coordinator: DVGW-Technologiezentrum Wasser (TZW), Mikrobiologie und Molekularbiologie (Germany)
  • Universitat de Barcelona (UB), Departament de Genètica, Microbiologia i Estadística (Spain)
  • Ministry of Health (PHLTA), National Public Health Laboratory (Israel)
  • European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency (SFA), BiologyDepartment (Sweden)
  • Universidade Lisboa, Instituto Superior Tecnico (IST), Laboratorio Analises (Portugal)
  • Mbarara University of Science and Technology (MUST), Department of Community Health
  • Eduardo Mondlane University (EMU), Engineering Faculty (Mozambique)

CONTACT: Consequences of antimicrobials and antiparasitics administration in fish farming for aquatic ecosystems

Aquaculture is an important source for food, nutrition, income and livelihoods for millions of people around the globe. Intensive fish farming is often associated with pathogen outbreaks and therefore high amounts of veterinary drugs are used worldwide. As in many other environments, mostly application of antimicrobials triggers the development of (multi)resistant microbiota. This process might be fostered by co-selection as a consequence of the additional use of antiparasitics. Usage of antimicrobials in aquaculture does not only affect the cultured fish species, but – to a so far unknown extent – also aquatic ecosystems connected to fish farms including microbiota from water and sediment as well as its eukaryotes. Effects include increases in the number of (multi)resistant microbes, as well as complete shifts in microbial community structure and function. This dysbiosis might have pronounced consequences for the functioning of aquatic ecosystems. Thus in the frame of this project we want to study consequences of antimicrobial/-parastic application in aquaculture for the cultured fish species as well as for the aquatic environments. To consider the variability of aquaculture practices worldwide four showcases representing typical systems from the tropics, the Mediterranean and the temperate zone will be studied including freshwater and marine environments. For one showcase, a targeted mitigation approach to reduce the impact on aquatic ecosystems will be tested.

Other Partners:

  • Coordinator: Helmholtz Zentrum Muenchen – German Research Center for Environmental Health (GmbH), Research Unit Comparative, Microbiome Analysis (Germany)
  • University of Campinas, Analytical Chemistry (Brazil)
  • Technical University of Denmark, Health Technology (Denmark)
  • Israel Oceanographic & Limnological Research, The National Center for Mariculture, Microbiology and Water Quality (Israel)

ARISTO: The European industry - academia network for revising and advancing the assessment of the soil microbial toxicity of pesticides

The EU boasts one of the most strictest systems in the world for authorising and controlling the use of pesticides. The aim is to minimise the impact of pesticides on human health and the environment. The EU-funded ARISTO project is bringing together academia and industry to research the environmental off-target effects of pesticides. It will improve knowledge on the development of advanced tools and procedures for the comprehensive assessment of toxicity of pesticides on soil organisms. The project will offer doctorate fellows a training programme aimed at developing advanced experimental lab and field tests to assess the toxicity of pesticides on natural soil. It will also develop a toxicity assessment to identify the response of soil microbial networks to pesticides.

(click here to visit ARISTO website and for list of partners)  

IN-SPACE: An integrated network to measure seasonal processes in Arctic habitats via novel experiments

The purpose of this project is to conduct a comprehensive census of microbial biodiversity, functional diversity and activity in a range of proglacial and glacial habitats within snow and snow/ice and snow/tundra transition zones and couple these to changes in their chemical and physical environment. By collecting new data on the spatial-temporal variation of snow, the snow/ice and snow/soil transition zones, we will improve our understanding of impact of snowpack characteristics on energy balance and chemical reactions and determine the rate, timing and release of fresh water during snow melt. These have all been identified as gaps in knowledge related to identified in the SESS report 2018 (SIOS report for stakeholders). The project builds on a collaboration between scientists from Germany, the UK, Norway, France, Italy and Poland. Together, the team members will contribute an essential cross-disciplinary perspective to this emerging field of research, with individual specializations in snow physics, chemistry, biogeochemistry, glaciology, hydrology, and microbiology.


  • James A Bradley, Queen Mary University of London, UK
  • Liane G. Benning, GFZ, Germany
  • Bartlomiej Luks, IG PAS, Poland
  • Jean-Charles Gallet, NPI, Norway
  • Andrea Spolaor, CNR, Italy

MicroLife2: Microorganisms living in the Arctic

The Arctic is an area of growing strategic importance for European policy. As a consequence, there is an increasing need to estimate the impact that environmental change will have on the Arctic and our planet. Among the most critical, yet under-studied components of the Arctic cryosphere is seasonal snow. Next to the ocean, snow is the second largest interface between the atmosphere and the Earth’s surface during winter. Since snow on the land surface is thermodynamically unstable, it is in constant evolution due to metamorphism, whose rate is a function of temperature and the temperature gradient in the snow pack. As a result, snow, especially seasonal snow, is very sensitive to climate conditions and undergoes continuous modification in a changing environment. Despite the crucial role of snow for climatic, hydrological and biological processes, there are relatively few regular measurements of even the most basic snow parameters (e.g. snow thickness, snow density, temperature, snow hardness, the presence of ice layers) from the Arctic region in general and from Svalbard in particular. Even less is known about the biodiversity of the microbial communities inhabiting the snowpack and their biogeochemical processes in comparison with the rest of the terrestrial biosphere. In order determine the impact of climate change on terrestrial ecosystems, longer time series are needed that integrate different types of data (physical, chemical and biological). Many samples need to be collected, including precipitation sampling. The seasonal variability of snow also needs to be assessed in term of properties and length of the period between senescence and freezing (before/after the snow comes). With MicroLife2, we are proposing to provide such time series data through yearly sampling of snow in collaboration with NPI and onsite research staff. Using these samples, we will address a series of questions related to microbial ecology as well as adaptation to change. The knowledge of the relative importance of colonization processes, post-depositional selection, wintertime activity and microbial redistribution within snow packs is of crucial importance to understand biological activity in Arctic systems. Microorganisms in Arctic environments are still the unknown variable in the climate change equation.

Environmental Microbial Genomics
Laboratoire Ampère
Ecole Central de Lyon
Université de Lyon
36 avenue Guy de Collongue
69134 Ecully cedex

© 2021 Environmental Microbial Genomics Group​