Cécile Monard

Chargée de Recherche CNRS

Laboratoire ECOBIO_ UMR 6553 UR1-CNRS

Université de Rennes 1, Campus de Beaulieu, bat 14a

263 Avenue du Général Leclerc


Rennes 35042


Email : cecile [dot] monard [at] univ-rennes [dot] fr

Phone : +33(0)223235419

Office number : 137

I am a soil microbial ecologist studying the role of microorganisms in soil functioning. My research focuses on biotic interactions that control microbial diversity and microbial processes. I am particularly interested in the way earthworms, plant roots or phages are impacting microbial communities and their consequences on biogeochemical cycles and nutrient fluxes.



I am currently involved in four main projects that are shortly presented below:


-ANR Labcom Microscale in collaboration with P. Vandenkoornuyse and the Cellenion company


The ECOBIO laboratory and the company Cellenion created the Joint MICROSCALE Laboratory, in the fields of microbiology and molecular biology, for the analysis of single prokaryotic cells. MICROSCALE is divided into three R&D axes: (i) IsoCell which targets the isolation of single microbial cells from a complex community using the cellenONE systems, (ii) IsoGenes and (iii) IsoTrans, focused on the analysis of genomes and transcriptomes of single microbial cells, respectively. The overall objective of these three axes is to offer a complete system (isolation, preparation of sequencing libraries and bioinformatic analysis) for the study of single microbial cells, creating a conceptual and technological breakthrough for the study of microbial communities, considering the 'meta-omics' tools currently used. Indeed, these 'meta-omics' approaches, while leading to significant advances in the field of microbiology during the last decades, are currently showing their limits. A need for new tools to decipher microbial diversity, and its functions, is therefore emerging. MICROSCALE intends to fulfill this need by transferring single cell sorting systems previously used on eukaryotic cells to prokaryotes, and combining them with molecular analysis and bioinformatics tools. These advances will bring new insights in various fields of research, both fundamental and applied, targeting the microbiota. MICROSCALE will open up new possibilities for generating new data on microbiota and their functioning, increasing major fundamental knowledge in microbiology and microbial ecology.


- miRNA group in collaboration with Abdelhak El Amrani

Plants and microorganisms interact closely in the vicinity of roots that constitutes the rhizosphere. These biotic interactions are intimately part of soil functioning and are involved in the delivery of ecosystem services (e.g. food supply, climate regulation). They are mediated by different signal molecules and, we propose to adress an unexplored way to interact based on microRNAs (miRNAs). Recent research has shown that miRNAs secreted by eukaryotic host can act as an interkingdom signal to impact the recruitment of specific microorganisms. Therefore, the research led within the miRNA group aim to explore the impact of miRNAs secreted by the plant root on the composition and activity of its rhizomicrobiome and the potential selection of beneficial microorganisms. We benefit from several fundings from various collaborations with some bioinformatician of the IRISA lab (MITI CNRS), with the IGEPP lab from the INRAe (PPR Deep Impact), with the Yergeau lab in Laval, Quebec (PhD funding) and with some post-doc reasearcher (European Marie Curie funding).


- Carbophage project

In soil, bacterial communities are involved in the decomposition of soil organic matter, on which rely various processes allowing the delivery of nutrients to plants or the emission of green house gases to the atmosphere. The abundance and the diversity of soil bacteria are partly regulated by their interaction with bacteriophages that are viruses infecting bacteria and that constitute one of the most abundant entities in the biosphere. Phages should thus be some key actors in the dynamic of soil bacteria and we hypothesize that these interactions between phages and bacteria are regulated by changes in the soil water content that regulate the contact between these two entities. To validate this hypothesis, we combine experiments in the lab and on field observation on the SNO Ploemeur-Guidel. This project benefits from a funding from the EC2CO program from the INSU.


- SILVESTER - SoIL BiodiVErSiTy forEst Revitalization, in collaboration with Céline Roose-Amsaleg and the ECOTREE company

ECOBIO and ECOTREE are working together to gain a better understanding of the effects of pre- and probiotic treatments on soil microorganisms and the consequences for the development of newly planted trees. ECOTREE aims to reforest areas previously degraded by agricultural use or intensive forest management. We are seeking to identify practices likely to improve tree development (growth, yield, stress resistance, etc.) based on the induction of beneficial soil microbial diversity and/or functions. The project includes in situ field monitoring by analysing several bio-physico-chemical properties of the soil. It will also be based on laboratory experiments involving the incubation of soil microcosms to identify the mechanisms that are finely regulated by the addition of pre- and probiotics. Microbial and earthworm diversity will be explored in the new planted forest soils. At the same time, indicators of soil functioning (enzymatic activity and quantification of functional genes) will be measured.



PhD people and Alumni

Since my beginning at the CNRS, I participated in the supervision of several PhD students whose projects involved soil microbial communities submitted to biotic or abiotic interactions.


- 2020-2023: Solène Mauger

Microorganisms play key roles in various ecosystems but many of their functions and interactions remain undefined. To investigate the ecological relevance of microbial communities, new molecular tools are being developed. Among them, single-cell omics assessing genetic diversity at the population and community level and linking each individual cell to its functions is gaining interest in microbial ecology. By giving access to a bigger range of ecological scales (from individual to community) than culture-based approaches and meta-omics, single-cell omics can contribute to microorganisms genomes and functions identification but also to the testing of concepts in ecology. Solene PhD project is thus to develop the use of single cell omics for prokaryotes using the CellenOne device and to apply this method to answer relevant questions in microbial ecology.


- 2019-2023: Harriet Middleton

The importance of microorganisms in plant development, nutrition and stress resistance is consensus and has led to a more holistic approach of plant-microbe interactions, under the holobiont concept. The structure of plant microbiota is often described as host-driven, especially in the rhizosphere, where microbial communities are shaped by diverse rhizodeposits. Gradually, this anthropogenic vision is fading and being replaced by the idea that plants and microorganisms co-shape the plant microbiota. Through co-evolution, plants and microbes have developed cross-kingdom communication channels. We propose that microRNAs are crucial mediators of plant-microbe interactions and microbiota shaping in the rhizosphere. Moreover, we suggest, as an alternative to generally unsuccessful strategies based on microbial inoculants, microRNAs as a promising tool for novel holobiont engineering.


- 2016-2019: Eve Hellequin

Modern agriculture is undergoing important changes toward agroecological practices that rely on biodiversity and ecological processes. In agrosystems, the organic matter is the key of the soil fertility and an important reserve of carbon. Organic fertilization by crop residues is therefore an agricultural practice that improves the organic matter content in soil. Soil microorganisms have an important role in the organic carbon (orgC) dynamic because they are key players of its mineralization and are involved in the nutrients recycling. Thus, the use of agricultural biostimulant (BS) intended to enhance this microbial function is proposed as an alternative solution to improve indirectly plant growth while reducing chemical inputs. This thesis aimed to i) identify the effect of soil biostimulant on heterotrophic microbial communities, the orgC mineralization and the nutrient releases, ii) evaluate its genericity by testing different experimental conditions and iii) identify the environmental filters that control both the microbial communities and the mineralization function. We showed that the orgC dynamic was different according to contrasted physico-chemical and biological characteristics of different soils. We showed that plants can also influence the orgC dynamic by returning litter to the soil and through its root effect on the bacterial and fungal communities. Unlike plants, the amount of orgC provided by the two tested BS was negligible. However, we evaluated the effect of one BS as at least similar or even higher than those of plant on active bacterial and fungal abundances, richness and diversity. Among the two BS tested we showed that one enhanced the orgC mineralization by recruiting indigenous soil bacterial and fungal decomposers and that the other did not affect the orgC mineralization but activated indigenous soil plant-growth-promoting bacteria as well as soil bacterial and fungal decomposers. Furthermore, our study call for new normative methodological and integrative approach by monitoring simultaneously several descriptors for advancing our knowledge on BS action on microbial soil functioning.


- 2015-2018: Kevin Hoeffner

Litter decomposition is a key process in soil functioning that contributes to many ecosystem services. In temperate climates, earthworms interacting with soil microorganisms contribute significantly to this process. However, knowledge about earthworms most often targets the three ecological categories in which they are defined: epigeics, endogeics and anecics. Anecics are very common in temperate soils, constitute the major part of the earthworm biomass and are involved in the litter decomposition. Several studies have observed behavioral, morphological and physiological traits that distinguish two subcategories within anecics: epi-anecics and strict anecics. The first objective of this thesis was to verify if this distinction had a reality in the context of the litter decomposition process. Under controlled conditions, we evaluated (i) the role of the main anecic earthworm species in the decomposition process, (ii) the impact of these species on microorganism communities and (iii) soil enzymatic activities and (vi) the impact of interactions between anecic species on the decomposition process. Taking into account their major roles in various soil processes, based on field observations, the second objective of this thesis was to define the assembly of earthworm communities in grassland, The results obtained confirmed the distinction between epi and strict-anecic earthworms: only epic-anecics contribute to the litter decomposition process, which is correlated to the average individual biomass of each species. This contribution involved a greater stimulation of soil enzymatic activities, regardless of the species considered. In contrast to bacteria, soil fungal communities depend on the epi-anecic earthworm species with which they interact. This work also highlights that the abundance, biomass and diversity of earthworm communities in grassland soils are regulated by different environmental filters, including landscape diversity. This thesis highlights that the two ecological subcategories within the anecic category have different roles in the litter decomposition process and therefore contribute to ecosystem services provided by the soil in a differentiated way.


- 2014-2017: Kevin Potard

Volatile Organic Compounds (VOCs) are trace carbonaceous gases emitted in low concentrations from the continental and marine surfaces to the atmosphere. Highly reactive, these compounds are involved in atmospheric chemistry and are at the heart of many current environmental issues such as climate change related to greenhouse gases, air quality and feedback on the functioning of ecosystems. Terrestrial plant cover was previously identified as the main source of VOCs of biogenic origin. But recent studies suggest that soils could be major sources of VOCs. However, in agricultural anthropogenic landscapes, soils are subject to various and varied uses and management and are likely to modify qualitatively and quantitatively the patterns of VOC emissions. Paradoxically, agrosystem soils have been the subject of few inventories of their VOC emissions (compared to NOx and CH4). The scarcity of knowledge on the contribution of agrosystems soils in VOC emissions motivated this work of thesis in which three objectives were pursued : i) inventory the spectra and quantify the VOCs fluxes emitted by soils in agricultural landscapes (ii) to determine the role of soil microorganisms in emissions and (iii) to identify the abiotic determinants controlling VOC emissions by soils. The integrative and interdisciplinary approach implemented in this thesis work has made it possible to increase knowledge about biogenic VOC emissions by soils and suggests that VOC emissions by soils are not negligible. Their key position in terms of issues (chemical, ecological, agronomic, sanitary) requires to be of greater interest and to take them into account in future scenarios of global changes (climate and land uses), especially with regard to emerging practices of soil management in connection with the ecological transition initiated in agriculture. Similarly, the consideration of VOCs emissions in the biogeochemical cycles of carbon and that of nitrogen to better understand the functioning of ecosystems is also of importance.



K. Hoeffner, K. R. Butt, C. Monard, J. Frazao, G. Pérès, D. Cluzeau. 2022. Two distinct ecological behaviours within anecic earthworm species in temperate climates. European Journal of Soil Biology, 113 (2022) 103446

L. J. Marchand, F. Hennion, M. Tarayre, M-C. Martin, B. R. Martins, C. Monard. 2022. Fellfields of the Kerguelen Islands harbour specific soil microbiomes and rhizomicrobiomes of an endemic plant facing necrosis. Frontiers in Soil Science, 2: 995716

T. Kalachova, B. Jindřichová, L. Burketová, C. Monard, M. Blouin, S. Jacquiod, E. Ruelland, R. Puga-Freitas. 2022. Controlled natural selection of soil microbiome through plant-soil feedback confers resistance to a foliar pathogen. Plant and Soil, in press

S. Mauger, C. Monard, C. Thion, P. Vandenkoornhuyse. 2022. Contribution of single-cell omics to microbial ecology. Trends in Ecology and Evolution, 37(1): 67-78



E. Hellequin, F. Binet, O. Klarzynski, S. Hallin, J. Juhanson, V. Daburon, C. Monard. 2021. Shaping of soil microbial communities by plants does not translate into specific legacy effects on organic carbon mineralization. Soil Biology and Biochemistry 163 (2021) 108449

C. Monard, J-P. Caudal, D. Cluzeau, J-L. Le Garrec, E. Hellequin, K. Hoeffner, G. Humbert, V. Jung, C. Le Lann, A. Nicolai. 2021. Short-Term Temporal Dynamics of VOC Emissions by Soil Systems in Different Biotopes. Frontiers in Environmental Sciences, 9: 650701

K. Hoeffner, M. Santonja, C. Monard, L. Barbe, M. Lemoing, D. Cluzeau. 2021. Soil properties, grassland management, and landscape diversity drive the assembly of earthworm communities in temperate grasslands. Pedosphere, 31 (3): 375-383

Middleton, H., Yergeau, É., Monard, C., Combier, J.-P., El Amrani, A., 2021. Rhizospheric plant–microbe interactions: miRNAs as a key mediator. Trends in Plant Science, 26(2): 132-141

A. Cavé-Radet, S. Correa-Garcia, C. Monard, A. El Amrani, A. Salmon, M. Ainouche, E. Yergeau. 2021. Phenanthrene contamination and ploidy level affect the rhizosphere bacterial communities of Spartina spp. FEMS Microbiology Ecology, 96 (10) fiaa156.



E. Hellequin, C. Monard, M. Chorin, N. Le Bris, V. Daburon, O. Klarzynski, F. Binet. 2020. Responses of active soil microorganisms facing to a soil biostimulant input compared to plant legacy effect. Scientific Reports, 10:13727

A. Nicolai, M. Guernion, S. Guillocheau, K. Hoeffner, P. Le Gouar, N. Ménard, C. Piscart, D. Vallet, M.E.T Hervé, E. Benezeth, H. Chedanne, J. Blémus, P. Vernon, D. Cylly, H. Hotte, G. Loïs, B. Mai, G. Perez, T. Ouisse, C. Monard, C. Wiegand C, J.-P. Caudal, A. Butet, M. Dahirel, L. Barbe, M. Balbi, V. Briand, M. Bormans, M. Charrier, G. Bouger, V. Jung, C. Le Lann, A. Pannard, J. Petillon, Y. Rantier, D. Marguerie, K. Tougeron, P. Devogel, S. Dugravot, T. Dubos, M. Garrin, M. Carnet, C. Gouraud, A. Chambet, J. Esnault, M. Poupelin, E. Welk, A. Bütof, G.F. Dubois, G. Humbert, O. Marie-Réau, O. Norvez, G. Richard, B. Froger, C. Rochais, M. Potthoff, K. Ayati, A. Bellido, A. Rissel, M. Santonja, J.-O. Farcy, E. Collias, L. Sene, D. Cluzeau, R. Supper. 2020. Transdisciplinary bioblitz: Rapid biotic and abiotic inventory allows studying environmental changes over 60 years at the Biological Field Station of Paimpont (Brittany, France) and opens new interdisciplinary research opportunities. Biodiversity Data Journal, 8: e50451

S. Jacquiod, R. Puga-Freitas, A. Spor, A. Mounier, C. Monard, C. Mougel, L. Philippot, M. Blouin. 2020. A core microbiota of the plant-earthworm interaction conserved across soils. Soil Biology and Biochemistry 114 (2020) 107754

C. Monard, L. Jeanneau, J.-L. Le Garrec, N. Le Bris, F. Binet. 2020. Short-term effect of pig slurry and its digestate application on biochemical properties of soils and emissions of volatile organic compounds. Applied Soil Ecology 147 (2020) 103376



K. Hoeffner,  C. Monard, D. Cluzeau, M. Santonja. 2019. Response of temperate anecic earthworm individual biomass to species interactions. Applied Soil Ecology 144: 8-12.

K. Hoeffner, M. Santonja, D. Cluzeau, C. Monard. 2019. Epi-anecic rather than strict-anecic earthworms enhance soil enzymatic activities. Soil Biology and Biochemistry 132: 93-100.



E. Hellequin, C. Monard, A. Quaiser, M. Henriot, O. Klarzynski, F. Binet. 2018. Specific recruitment of soil bacteria and fungi decomposers following a biostimulant application increased crop residues mineralization. PloS One, 13 (12).

K. Hoeffner, C. Monard, M. Santonja, D. Cluzeau. 2018. Feeding behaviour of epi-anecic earthworm species and their impacts on soil microbial communities. Soil Biology and Biochemistry 125:1-9.




K. Potard, C. Monard, J.-L. Le Garrec, J.-P. Caudal, N. Le Bris, F. Binet. 2017. Organic amendment practices as possible drivers of biogenic Volatile Organic Compounds emitted by soils in agrosystems. Agriculture, Ecosystems and Environment, 250: 25-36.



C. Monard, S. Gantner, S. Bertilsson, S. Hallin, J. Stenlid. 2016. Habitat generalists and specialists in microbial communities across a terrestrial−freshwater gradient. Scientific Reports, 6: 37719



C. Monard, S. Gantner, J. Stenlid. 2013. Utilising ITS1 and ITS2 to study environmental fungal diversity using pyrosequencing. FEMS Microbiology Ecology, 84 (1): 165-175.



C. Monard, F. Martin-Laurent, O. Lima, M. Devers-Lamrani, F. Binet. 2012. Estimating the biodegradation of pesticides in soils by monitoring pesticide-degrading gene expression. Biodegradation, 24 (2): 203-213.

C. Monard, C. Mchergui, N. Nunan, F. Martin-Laurent, L. Vieublé-Gonod. 2012. Impact of the soil matric potential on the fine-scale spatial distribution and activity of specific microbial degrader communities. FEMS Microbiology Ecology, 81 (3): 673-683



C. Monard, P. Vandenkoornhuyse, B. Le Bot, F. Binet. 2011. Relationship between bacterial diversity and function under biotic control: the soil pesticide degraders as a case study. ISME Journal, 5 (6): 1048-1056



C. Monard, N. Nunan, G. Bardoux, L. Vieublé-Gonod. 2010. A miniaturised method to quantify microbial mineralisation of 13C-labelled organic compounds in small soil samples. Soil Biology and Biochemistry, 42 (9): 1640-1642

C. Monard, F. Martin-Laurent, M. Devers-Lamrani, O. Lima, P. Vandenkoornhuyse, F. Binet. 2010. atz gene expressions during atrazine degradation in the soil drilosphere. Molecular Ecology, 19 (4): 749-759



C. Monard, F. Binet, P. Vandenkoornhuyse. 2008. Short-term response of soil bacteria to carbon enrichment in different soil microsites. Applied and Environmental Microbiology, 74 (17): 5589-5592

C. Monard, F. Martin-Laurent, C. Vecchiato, A-J. Francez, P. Vandenkoornhuyse, F. Binet. 2008. Combined effect of bioaugmentation and bioturbation on atrazine degradation in soil. Soil Biology and Biochemistry, 40 (9): 2253-2259