Our funded research programs address a range of fundamental and applied microbial ecology questions. At our laboratories 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 Include...

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)

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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)

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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.

ABS: Atmospheric Biogenic Sugars

Primary biogenic organic aerosol (PBOA) is little studied although it forms up to 30% of the organic fraction of atmospheric PM (in Europe in summer average) and presents important properties for atmospheric particles (PM), both for cloud formation and for health impacts. Despite its importance, this fraction is currently not considered in atmospheric chemistry models. The central hypothesis of the project is that an important part of these species is closely related to living matter (bacteria and fungi), and that the coupling of chemical and microbiological measurements can lead to a better understanding of their sources and emission processes to the atmosphere, as well as of the interactions between chemistry and microbiology in situ. We will consider the variability and sources of this chemical fraction in atmosphere samples collected mainly in Europe but also in tropical areas (e.g. 1500 samples), in the seasonal alpine snowpack and in an alpine ice core corresponding to a 150-year record (Col du Dome, Mont Blanc). The snowpack work will include both in situ and mesocosm studies to understand the biological processes involving these carbohydrates in cold snow, including potential changes in the chemical profiles of sugars in the deposits. The synergy of the approach in the 3 domains will reinforce these advances with a unique view of the importance of atmospheric PBAO emissions and concentrations, coupling with living matter, and their historical evolution in the European atmosphere. ABS should reinforce the strong need to take into account these primary biogenic emissions in atmospheric chemistry models. The advances in the knowledge of the emission sources by ABS will open the door to the quantification of the specific processes involved for further emissions inventories. The established proof of concept of using these species in ice cores as tracers of the evolution of particulate biogenic composition will allow applications to other glaciological records, in mid latitudes and polar ice.

Other partners:

  • Coordinator: Institut des Géosciences de l’Environnement (IGE), Grenoble
  • Environnements, Dynamiques et Territoires de Montagne (EDyTEM), Chambéry

ENVOSNOW: Evolutionary drivers of snow microbial communities

Microorganisms form the basis of life on earth and inhabit all ecological niches, including terrestrial snowpacks. Snowpacks cover large expanses of the Earth’s land surface, up to 63 million km2 in the Northern hemisphere winter and constitute habitats for diverse microbial communities including algae, prokaryotes 3 and fungi. Given the unique environmental characteristics of snowpacks including: strong temperature gradients and transient nutrient inputs, microbial communities living within them are subjected to multiple environmental stressors that might impact community dynamics and adaptation both on short-term and long-term scales. In order to determine the impact of changing ecosystem properties on snowpack microbial communities, longer time series are needed that integrate different types of data (physical, chemical and biological). This requires the development of new tools that can be used remotely to increase spatial and temporal measurements, in addition to the integration of different scientific fields such as molecular biology, chemistry, engineering, remote sensing, physics and data modelling. With EVOSNOW, we propose to link temporal changes in snowpack physical characteristics to the evolution of snowpack microbial communities and chemistry by developing a new tool based on LIDAR technology. This snow LIDAR will autonomously monitor the geometry of the snowpack over an area of 0.1-1 km2 over an entire winter season. The technological innovation will produce detailed information on snow surface properties, accumulation or erosion, as well as derived metrics such as 3D models of the stratigraphy, internal structure of the snowpack, and potentially albedo as well as the age of the individual snow layers. The overarching goal of this project is to link to the evolution of microbial communities to the age data and physical properties of snowpacks generated from LIDAR measurements.

Project partners:

  • Institut des Géosciences de l’Environnement, Grenoble, France
  • Department of Geosciences, University of Oslo, Norway

FBF: Investigating the diversity and distribution of fungal viruses in soil

Fungi make key contributions to biogeochemical cycling and plant productivity, yet they can fall prey to viruses that limit their growth and, thereby, their impacts on soil ecosystem function. We know very little about the diversity and distribution of fungal viruses in nature, which precludes an understanding of the effects of viral infection on fungal ecology. This project will leverage expertise in soil viromics and root-associated arbuscular mycorrhizal fungi to investigate fungal viruses in Mediterranean grasslands, which store 30% of global terrestrial carbon. A better understanding of mycovirus diversity and distribution will facilitate exploration of their fundamental control on fungal abundance and plant productivity, leading to potential applied, sustainable mechanisms for controlling AMF-mediated plant growth.

  • Partner: Christina Hazard
  • Partner: Joanne Emerson, University of California, Davis
    • PhD Student: Anneliek ter Horst, University of California, Davis

ACTIONr: Research action network for reducing reactive nitrogen losses from agricultural ecosystems

Globally, 50-70% of the N fertilizer applied to cropping systems is lost as nitrate and N-oxides, raising agricultural production costs and contributing to pollution and climate change. These losses are directly linked to the nitrification process catalysed by soil nitrifying microbes. The mitigation of reactive nitrogen (Nr) loss via nitrification inhibitors (NIs) is a promising solution for increasing N use efficiency (NUE) in agriculture. ACTIONr aims to unravel the scientific excellence and innovation potential through a European network of excellence on establishing novel tools and pathways for optimized NUE, reducing the continued acceleration of the N cycle, and decreasing the environmental footprint of Nr.

Other partners:

  • Coordinator: University of Thessaly, Greece
  • University of Vienna, Austria

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CONSERVE: Controlling nitrification in soil by exploiting virus ecology

Microorganisms have a central role in soil biogeochemical processes. While we have substantial knowledge of the diversity and functional role of different prokaryotic groups, we are only beginning to recognise the scale of soil virus diversity. Importantly, the impacts of virus-host interactions on biogeochemical cycles are unknown. In marine systems, 40% of prokaryotes are lysed each day, releasing 150 Gt carbon per year. However, there is no knowledge about the impact of top-down control by viruses on soil populations nor the scale of the viral shunt of nutrients. It is likely that viruses have a major impact on microbial diversity and nutrient cycling, with consequences for ecosystem processes.

This research programme aims to understand the diversity and impact of viruses interacting with microbial hosts that are involved in the critical biogeochemical process of nitrification. Input of N via fertilisers now exceeds that entering through natural processes and fertiliser input will increase with a growing global population. A key microbially-mediated process of fertiliser loss is nitrification, whereby ammonia is oxidised to nitrate via nitrite. While ammonium is retained in the soil, nitrate is highly mobile and nitrification leads to an estimated loss of 67% of applied fertiliser and an economic cost of $15.9 billion. In CONSERVE, we will focus on understanding the diversity, activity and ecological impact of viruses infecting archaea and bacteria that have a central role in the process of nitrification.

ICEBIO: Center for glacial biome doctoral network

Glaciers and ice sheets were long believed to be sterile environments, but just like other large ecosystems (e.g. tropical forests, tundra), they are now widely recognized as one of the Earth’s biomes, teeming with life. Active algae, fungi, bacteria and viruses dominate the glacial environment and they have the ability to change the physical and chemical characteristics of the ice and snow, with global effects. For instance, increasing ice melt rates are observed due to growth of pigmented algae on glacier surfaces and substantial amounts of methane from subglacial habitats are added to the global greenhouse gas budget. Despite their global influence, many of the microbiological processes within the cryosphere remain poorly quantified. A deeper understanding of such processes are relevant to researchers interested in the possibility of life on icy extraterrestrial bodies, the survival and proliferation of life forms on our early Earth (e.g. during the part of the Proterozoic era known as Snowball Earth), and the positive and negative feedbacks that the cryosphere may have on global warming. The microbial communities living in association with icy environments may also harbor unique metabolic pathways, providing novel opportunities in biotechnology.

ICEBIO is a Doctoral Network that will train the next generation of glacier microbiology and biogeochemistry experts. The training and research programme is made up of seven interlinked Work Packages (WP). WP1 to WP4 are research work packages at the cutting edge of glacial microbiology and biogeochemistry and these will be supported by three overarching WPs (WP5-7) associated with the management, training, and dissemination of results. ICEBIO will deliver a detailed framework and database of the functional diversity and potential of the glacier biome, not only serving to dramatically advance our understanding of a threatened biome, but also laying out potential for use in economic and environmental services.

Partners: Catherine LaroseTim Vogel

Other partners: 

  • Coordinator: Aarhus University, Denmark
  • University of Innsbruck, Austria
  • Helmholtz Zentrum Potsdam, Germany
  • Norges Arktiske University, Norway
  • Hydreka SAS, France
  • GMBH Institute for Hygiene and Microbiology, Germany 

ViBNI: Pipeline for development of virus-mediated biological nitrification inhibition

Transformation of reactive nitrogen (N) in the environment is the most anthropogenically impacted elemental biogeochemical cycle on Earth. Input of N via fertilizers and deposition of atmospheric N now exceeds that entering naturally through nitrogen fixation with major environmental impacts on terrestrial and aquatic systems. Existing strategies to increase N fertilizer use efficiency include inhibiting microorganisms that perform nitrification (nitrifiers) and transformation of fertilizer N with synthetic nitrification inhibitors (NI). These approaches require knowledge of mechanisms of interaction and importantly the potential impact of NIs on non-target microorganisms. A novel, highly-targeted approach to controlling microbially-mediated processes is the use of bacteria-targeting viruses (bacteriophages or ‘phages’) that infect specific populations. Viruses infect every living organism and affect microbially-mediated biogeochemical fluxes by killing active cells via lysis. As virus-host interactions are highly specific, there is major potential for using viruses to naturally target individual microbial processes within diverse microbial communities and circumventing indirect effects on non-target populations. ViBNI will evaluate the potential of using highly-targeted ‘soil phage therapy’ for mitigating environmental impacts of fertilizer N transformation.

Microbial Ecology
Université Claude Bernard Lyon 1
Université de Lyon
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Bioengineering Department
Laboratoire Ampère
Ecole Central de Lyon
Université de Lyon
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69134 Ecully cedex

Institute of Environmental Geosciences
Université Grenoble Alps
CS 40700
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