MICROBIAL ECOLOGY OF FOREST ECOSYSTEMS / ECOLOGIE MICROBIENNE DES ECOSYSTEMES FORESTIERS

Research Director (DR2, HDR) [UMR1136 IAM member, UR1138 BEF member, US 1371 ARBRE]

Follow @steph_Uroz
Follow @labexARBRE

CONTACT:

• e-mail: stephane.uroz@inrae.fr
• Phone: +33 (0)3 83 39 40 81
• Fax: +33 (0)3 83 39 40 69

 

BIO: After a Master in Microbial Ecology from the University of Lyon I (2000-2001), I obtained a PhD grant from the French Ministry for Research and Higher Education delivered by the University of Paris XI (Orsay). I performed my PhD thesis  with Yves DESSAUX and Phil OGER as my advisers. My PhD research project was focused on the biological stability of the N-acyl homoserine lactone (quorum sensing signal molecules) based on the hypothesis that these molecules need to be degraded to act as a signal, possibly by bacteria naturally occurring in the soil.  I was lucky to perform my PhD in three places : i) in the ‘Plant Microorganisms Interactions’ lab at the Institute of Plant Sciences (ISV, Gif-sur-Yvette ; adviser : Yves Dessaux) ; ii) in the “Sciences de la Terre” lab at the Normal School (ENS, Lyon ; adviser : Phil Oger) and iii) in the “Institute of Infections and Immunity” at the University of Nottingham (Queen’s Medical Centre, Nottingham; advisers: Paul Williams, Miguel Camara and Siri Ram Chhabra)(European Union Marie Curie programme). The 15th of october 2004, I defended my thesis (Jury: P. SIMONET, S. REVERCHON, D. HAAS, M. DUBOW, Y. DESSAUX, P. OGER).

The 22th of october 2004, I was hired as Junior Research associate (CR2) in the EFPA (Forest, Grassland and Aquatic Environments) Division of the National Institute for Agronomic Reasearch (INRA) and in the INRA center of Nancy, at the interface between two research departments : i) The “Tree microbes interactions” (IAM, UMR1136) department and ii) the “Biogeochemical cycles in forest ecosystems” (BEF, UR1138) department. I am member of the Ecogenomic team in the IAM department and Mineral weathering team in the BEF department. In January 2009, I became Research associate (CR1).

The 24th of februrary 2014, I defended my HDR (Habilitation à diriger des recherches) entitled “Ecology of biotic and abiotic interactions of the forest soil bacterial communities: characterization of the actors, mechanims and related genes” (Jury: C. MOUGEL, P. SIMONET, S. VUILLEMIER, R. MARMEISSE, L. MOULIN, P. LEBLOND, E. GELHAYE, P. OGER and P. FREY-KLETT).

I was appointed INRA Research Director (DR2) in december 2014. From january 2020 to january 2022 I was Head of the Ecogenomics of interactions team.

Since January 2022 I am also Head of the Cluster of Excellence ARBRE (Advanced Research on the Biology of Tree Biology and Forest Ecosystems)(US 1371 INRAE)  with my colleagues Myriam LEGAY and Mathieu PETRISSANS as co-directors.

RESEARCH TOPICS:

My projects aim to decipher the role of microorganisms (mainly bacteria) in forest ecosystem functioning and sustainability as well as the molecular mechanisms and regulations established. To do it, I am linking environmental genomics, microbiology and geochemical/mineralogical analyses. My main interests are related to :

• The relation between soil properties, tree species and soil microbiota. The forests developped on nutrient-poor soils are particularly interesting as they mainly function on their own ressources. They represent a reservoir of bacteria adapated to such conditions and particularly to low nutrient availability. Among bacteria, I am particularly looking the mineral weathering bacteria (functional diversity, genetics, genomics link to biogeochemistry and mineralogy) and their impact on nutrient cycling (geomicrobiology) and plant growth promotion.
• The minerals and rocks as particular microbial habitats : the mineralosphere. Minerals and rocks represent reactive interfaces at both mineralogical and microbiological levels. The microbial communities living in such environment are probably well adapted to low nutrient (K, Mg, Fe, P) availability and low carbon substrates.
• The rhizosphere:mycorrhizosphere : particular places in the soil where complex interactions occur between plant and microorganisms and between microorganisms. I am particularly looking interactions and functions involving quorum sensing, antibiosis and competition.
• The soil fertility (nutrient availability, water availability) as a key parmeter of soil microbiota functioning. I am particularly interested in how nutrient availiability, drought impact the distribution and physiology of soil bacteria, and whether minerals can be used as fertilizers.

COLLABORATIONS:

• On the INRAE Center: My main collaborator is Marie-Pierre TURPAULT (Geochemist and mineralogist). Cintia BLANCO NOUCHE joined the team (01/10/2021) to perform her PhD thesis . I am also involved in several projects related to microbial ecology, interactions between bacteria/fungi, and drought adaptation with  colleagues of the Ecogenomic team (A. DEVEAU, L. AUER, E. MORIN).
• My main local,national and international collaborators: :Phil Oger (CNRS-ENS, Lyon), PE Courty (INRAE, Dijon), Johan H.J. Leveau (Univ. Davis, USA), Wietse de Boer (NIOO-KNAW, Netherlands), Jussi Heinonsalo (Univ. Helsinki, Finland), Jean Armengaud (CEA-Marcoule, Bagnols-sur-Cèze), Cédric Paris (ENSAIA/UL, Vandoeuvre-les-Nancy).

Main projects granted these last years….
Inovative projet granted by The Labex ARBRE (2023-2024) CAIMAN
EC2CO (2023-2024) CAMELEON
EC2CO (2019-2021) Ge2M
Incitative projet granted by The Labex ARBRE (2019-2020) GeM
Multidisciplinary project granted by The Labex ARBRE (2014-2017) INABACT
Young scientist ANR Grant (2012-2015) BACTOWEATHER
EcoFINDERS: Ecological Function and Biodiversity Indicators in European Soils (2011-2014; PI P. Lemanceau)
INRA Metaprogramme Metagenomics (MeM) (2012-2013) METASCREEN
EC2CO ‘Interafaces continentales (2009-2011)
ANR METASOIL (2009-2012)
INRA Projet Innovant (2011-2012)
Région Lorraine ‘Projet Jeune Chercheur’ (2009-2011)
France-Berkeley project (2009-2010)
BRG Project (2007-2009)

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The lab welcomes short stays if related to our research topics, PhD students and Post-doc scientists if their stay is supported by an official grant (i.e., Marie-Curie,…).

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CONGRESS AND WORSHOP ORGANIZATION:

– 21-25 Nov 2022 – Metz, France. International Congress of Ecology and Evolution (SFE²-GfÖ-EEF joint congress) “Ecology and Evolution: new perspectives and societal challenges” Website : https://sfe2gfomeeting.sciencesconf.org/

– 10th december 2019 – Nancy (Lorraine, France): We are co-organizing with the GDR BIM and GE the workshop ‘Journée thématique Transcriptomique complexe‘  Website: https://journees.inra.fr/transcriptomique-complexe/

– 5th to 8th november 2019 – Bussang (France): We co-organized with the LIEC Lab and the AFEM association the IXe Colloque de l’Association Francophone d’Ecologie Microbienne (AFEM2019).  Centre de vacances Azureva. Website : https://colloque.inra.fr/afem2019/

Prices and awards:

Reconnaissance de thèses remarquables par l’Académie d’agriculture en forêt/filière-bois 2022 ‘ Laura PICARD : Génomique de l’altération des minéraux par la souche bactérienne Collimonas pratensis PMB3(1)’

Supervision of Master students:

2022

Maud BEDNARECK-Master 1 -Master Microbiologie (Nancy) Effet de la sècheresse sur la croissance du hêtre et de son microbiote associé (co-supervisor A. DEVEAU)

Clement BEITZ – Master 2 – Master Microbiologie (Nancy) Effet d’un historique de sècheresse sur la structuration taxonomique et fonctionnelle du microbiote du sol de la forêt de Montiers (co-supervisor A. DEVEAU)

2021 

Marie DRAIA – Master 1 – Master Microbiologie (Nancy) Implication du genre bactérien Collimonas dans l’altération des minéraux et caractérisation de gènes impliqués dans la synthèse de sidérophores (co-supervisor L. PICARD)

2019

Antoine SPORTES – Master 2- Master Sciences, Technologies B2i PME (Dijon). Etude d’une interaction multitrophique: Impact d’un champignon mycorhizien à arbuscule et d’une bactérie mobilisatrice de phosphate sur la nutrition phosphatée de la pomme de terre. (co-supervisor P.E. COURTY, INRAE Dijon)

 Amélie JESSU – Master 1 – Master Microbiologie (Nancy) Caractérisation fonctionnelle d’une souche bactérienne de la mycorhizosphère : construction et criblage d’une banque de mutants

2018

 Océane GEISLER – Master 1 – Master Microbiologie (Nancy) Etude des gènes homologues de luxI et luxR impliqués dans le quorum sensing chez Collimonas et caractérisation des N-acyl homosérines lactones produites

 Brice SANCHEZ – Master 1 – Master Microbiologie (Nancy) Caractérisation taxonomique et fonctionnelle des souches bactériennes de la minéralosphère

GROUP ALUMINI

Dr. Laura PICARD (PhD thesis 01/10/2018-12/2021; ‘Genetics and genomics of mineral weathering by Collimonas’ ) — now in post-doc at the Centre CEA de Cadarache
Dr. Océane NICOLITCH (PhD thesis 2014-2017; Now Engineer in Molecular Biology and metagenomic at SUEZ (Le Pecq, Île-de-France)
Dr. Yannick COLIN (Post-doc scientist 2014-2016; microbial diversity in forest soils). Now Lecturer at Université Rouen/Caen (France).
Dr. Marta Torres Béjar (Short stay to work on metagenomics of QS and Quorum quenching; Univ Granada, Spain) now in post-doc at the University of Zurich
Dr. Laura C. Kelly (Active mineralosphere bacterial communities). Now lecturer at Manchester University
Dr. Cendrella Lepleux (Identification of the gene and bacteria involved in mineral weathering; 2009-2012 co-dir. P. Frey-Klett, M-P. Turpault).
Dr. Christelle Collignon (PhD thesis Seasonal effect on mineral weathering ; 2007-2011 dir. J.Ranger, M-P. Turpault and P. Frey-Klett) . Now teacher in high school.
Dr. Panos Ioannidis (Bioinformatic analyses of complex metagenomes; 2010-2011, F. Martin, M. Buée).
Dr. Mathilde Jeanbille (Master 2 thesis 2009/2010) now Post-doc scientist at the Swedeb University of Agriculture Sciences (Uppsala, Sweden)

TEACHING:

Since 2021: Council of the Doctoral School E2M2, University of Lyon 1
Since 2006: Master AEPTF – UE RHIZOSPHERE (M2)
Master MICROBIOLOGIE – UE9.18 (M2) et UE7.05 (M1)

Useful Links:
– for metagenomic analyses: http://metagenomics.nmpdr.org/, http://www.mothur.org/, http://rdp.cme.msu.edu/
-for OTUs and index analyses: http://schloss.micro.umass.edu/wiki/Main_Page ;  http://viceroy.eeb.uconn.edu/EstimateSPages/EstSUsersGuide/EstimateSUsersGuide.htm
– for genomic analyses: http://rast.nmpdr.org/rast.cgi?page=Logout
– for syntheny analyses: http://genome.sfu.ca/cgi-bin/orthoclusterdb/runortho.cgi
– for bibliographic and other analyses: http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed
– for quorum sensing related informations http://www.nottingham.ac.uk/quorum/williams.htm

Journals of interest :
–AEM
– Environmental Microbiology
– FEMS Microbial ecology and letters
– Geomicrobiology J
– GCA
– ISMEJ
– Microbial Ecology
– PNAS
– Soil Biology and Biochemistry
– TRENDS IN MICROBIOLOGY

PROJECT DESCRIPTION

Project 1: Forest soil as a reservoir of microbial biodiversity (specific diversity and functional metagenomic)

Forest soil are characterized by complex microbial communities. To appreciate this diversity, we combine direct or indirect approaches to extract gDNA. The direct approach (DNA extraction for soil samples) is used to analyse fungal and archaeal/bacterial diversity. The indirect approach (density gradient; Nycodenz) is used to focuse only on bacterial diversity.

The metagenomic DNA is then used for monogenic metagenomics studies (Buée et al., 2009; Lepleux et al., 2012; Uroz et al., 2010, 2012, 2014, 2016), for massive metagenomics (Uroz et al., 2013), microarrays (Colin et al., Scient. Rep. 2017) or construction of fosmid libraries (Torres et al., 2017).

Through these different approaches, we are characterizing how the different environmental and anthropic factors structure archaea, bacteria and fungi in forest environments.

A large part of these aspects has been synthesized in a review article published in Soil Biology and Biochemistry ‘Ecology of the forest microbiome: Highlights of temperate and boreal ecosystems‘.

Project 2: Ecology of the mineral weathering bacteria in forest soils

To date no functional genes related to mineral weathering by heterotrophic soil bacterial communities have been identified. To elucidate this process, we developed a cultivation-dependent approach to highlight the functional potentials of the soil bacteria using different bioassays measuring the ability to solubilize inorganic phosphorous, mobilize iron or weather biotite. Our works are mainly based on the analysis of to acidic forest site in central France (Breuil-Chenue), in little Britany (Fougères) or in the Meuse region (Montiers).

a- Relationship bacterial diversity and functional ability
We focused our analysis on various ecological niches such as the mycorrhizal roots (mycorrhizosphere)(Calvaruso et al., 2010; Uroz et al., 2007), the hyphosphere, the rhizosphere, the surrounding bulk soil and the soil minerals (mineralosphere) (Uroz et al, Geomicrobiology J. 2012; Lepleux et al., 2012; Colin et al., 2017) looking at the relative distribution of the bacterial communities in these niches.

b- Specific case of the Collimonas
Our works highlighted that the collimonads mainly isolated in poor nutrients or pristine environments such as dune, acidic soil, rock surfaces were very efficient to weather minerals, suggesting an oligotrophc lifestyle (Uroz et al., 2009, 2014; Leveau et al., 2010).

c- Seasonal effect on the mineral weathering bacterial communities
We compared the rhizosphere bacterial communities to those of the bulk soil under beech and spruce stands  and during seasons (spring, summer, autumn and winter). We showed that the functional and taxonomic structures of the mineral weathering bacterial communities  varied significantly with the tree species as well as with season. The weathering efficacy of the rhizosphere isolates was significantly higher for the autumn isolates compared to the isolates sampled in the other seasons under the beech stand and in summer compared to the other seasons under spruce. These results suggest that seasonal differences do occur in forest soil bacterial communities and that evergreen and deciduous trees do not follow the same dynamic (Collignon et al., 2011).

d- Impact of the nutrient availability on the structuration of the mineral weathering bacterial communities
A good example to test this impact in the field remains the mineral amendment (liming) practice on tree plantation or natural forest. During the last years, we have studies the impact of such amendment on the long-term in a beech plantation of the experimental site of Fougère (site managed by C. Nys and A. Legout) and then on the short-term using a small-scale plantation in the experimentala site of Breuil-Chenue (site managed by J. Ranger and A. Legout).
Using a cultivation dependent approach, we highlighted that 33 years after amendment, the amended plot was chararcterized by low concentrations of some nutritive cations and by the enrichment of efficient mineral weathering bacterial communities compared to the control plot (non amended). Our results highlights that on the long-term, one pulse of amendment can create ‘secondary deficiencies’ (Uroz et al., SBB 2011; Lepleux et al., 2013).
Using a microcosm approach we have manipulated the soil properties to deterrmine how these changes impact the taxonomic and functional diversity of the soil bacteria (Nicolitch et al., 2019)

e) Soil type effect
We are considering the links between the soil properties and the distribution of the microbial communities. The choice of the experimental sites is critical as we are interested in functional aspects in the relation to pedogenesis and plants species. In this context, we are especially interested in natural toposequences or chronosequences. One of our project (France-Berkeley, Coll. JHJ Leveau) was developed on the ecological staircase of Mendocino. This natural site is characterized by a same mineral parental material varying in age. In other words, this site presents similar soil with different level of weathering. Using a combination of cultivation-dependent and -independent approaches, we highlighted the relations existing between the soil parameters and the taxonomic and functional diversity of the bacterial communities along the Mendocino terraces (Uroz et al., SBB 2014). We have also investigated how such conditions affect the fungal communities. A second project (Labex project INABACT) is focusing on the natural toposequence of Montiers which is characterized by a succession 3 soil types on a short gradient of 1.5 km and a homogenous land cover dominated by beech trees (Nicolitch et al. 2016, 2017; Colin et al. 2017).

Project 3: Investigation of the molecular mechanisms used by mineral weathering bacteria

a) Genomic characterization of effective mineral weathering bacterial strains
To investigate molecular mechanisms used by heterotrophic bacteria to weather minerals, we sequenced the genome of  three model bacterial strains: i) Caballeronia mineralivorans (i.e. Burkholderia mineralivorans) PML1(12), ii) Collimonas sp. PMB3(1) and iii) Pseudomonas sp. PML3(3). We used a suite of sequencing methods (454, Illumina short and 20kb fragments and Nanopore MinION). The genomes of these model strains have been assembled. The first draft version of the strain PML1(12)  is presented in Uroz and Oger (Genome annoucement 2015) and the final version is deposited on MAGE under private access. The analysis of the physiological and genomic properties allowed to the proposition of a new species name for PML1(12), which is now Caballeronia mineralivorans sp. (Uroz and Oger, System Appl Microbiol 2017).The genome of PMB3(1) was also mined (Picard et al., 2020). At last the genome of the strain PML3(3) was assembled using a hybrid assembly of Nanopore and Illumina data. We are currently mining these genomes to highlight the specific functions carried by these effective mineral weathering bacterial strains.

b) Elucidation of the molecular mechanisms used by bacteria to interact and to weather minerals
To investigate molecular mechanisms used by heterotrophic bacteria to weather bacteria, we combined a suite of genomic and genetic tools (transcriptomic, proteomic and genesis of random mutant libraries and targeted mutagenesis) to evidence candidate genes and determine their function. The use of a combination of transcriptomics and proteomics allowed to evidence the functions activated or repressed in presence/absence of the mineral on the strain Caballeronia mineralivorans PML1(12) (Uroz et al. 2020). Molecular analyses permitted to better understand the diversity of mechanisms used by bacteria to weather minerals (Picard et al. 2021). The work performed evidenced the role of GMC oxidoreductase in the mineral weathering process by Collimonas. The role of siderophore was also evidenced, but only in buffered condition (PIcard et al. 2022; Blanco-Nouche et al 2023). Investigation of the quorum sensing regulation system of the strain Collimonas pratensis PMB3(1) permitted to identify the genetic bases, the molecules produced and the functio regulated (Uroz et al., FEMS 2022). Noticeably, QS regulation appeared involved in metabolic adjustement and especially of the GMC activity. The link between mineral properties, solution chemistry and carbon substrate was evidenced by combining microbiology, mineral, geochemistry and various mutants (Picard et al., 2023). These new findings provide us a clearer understanding of the mechanisms and genes involved in mineral weathering by bacteria and on their diversity (Uroz et al. 2022).

Project 4: Impact of bacteria on the nutrient cycling (Microcosm approach)

One of our goal is to determine the impact of the soil bacterial communities on the minerals and to determine their relative contribution in the mineral weathering process.

a. Interactions bacteria/plants:

Previous experiments developed in the team (Calvaruso et al., 2006) have demonstrated the impact mineral weathering bacteria on tree nutrition and mineral weathering. The strain PML1(12) of B. glathei significantly improved pine growth when the seedlings were supplied with a nutrient solution which did not contain the nutrients present in the biotite. No improvement of pine growth was observed when the seedlings were supplied with all the nutrients necessary for pine growth. We therefore propose that the growth-promoting effect of B. glathei PML1(12) mainly resulted from the improved plant nutrition via increased mineral weathering.

b. Interactions bacteria/plants/mycorrhizal fungi:

More recently, we tested the impact of inoculation of efficient mineral weathering in microcosms containing pine seedling associated or not with two ectomycorrhizal fungi: Laccaria bicolor and Scleroderma citrinum (Koele et al., 2009). In vitro assays have demonstrated that the two fungal strains used in our experiments were not efficient to weather minerals. Notably, co-inoculating the mycorrhizal fungus S. citrinum and the efficient mineral-weathering B. glathei bacterial strain PML1(12) in microcosms significantly improved the Mg budget. Similarly, co-inoculating S. citrinum with the Collimonas sp. bacterial strain PMB3(1) significantly improved the pine biomass compared to non-inoculated pine plants.

 

2023

77- Picard, L., Blanco Nouche, C., Cochet, C., Turpault, M-P., Uroz, S.* Mineral weathering by Collimonas pratensis PMB3(1) as a function of mineral properties, solution chemistry and carbon substrate. NPJ Material Degradation (In press).

76- Zhang,Y., Zhao, Q., Uroz, S., Gao, T., Li, J., He, F., Rosazlina, R., Martin, F., Xu, L. The cultivation regimes of Morchella sextelata trigger shifts in the community assemblage and ecological traits of soil bacteria. Frontiers in Microbiology (In press).

75- Blanco Nouche, C., Paris, C., Dhalleine, T., Oger, P., Turpault, M-P.,  Uroz, S*. The Non-ribosomal peptide synthetase-Independent Siderophore (NIS) Rhizobactin produced by Caballeronia mineralivorans PML1(12) confers the ability to weather minerals. Applied and Environmental Microbiology (In press).

74- Mieszkin, S., Trouche, B., Ancousture, J., Raouf, Y., Uroz, S., Alain, K. Scleromaebacter humisilvae gen., nov., sp. nov. isolated from an oak forest soil. International Journal of Systematic and Evolutionary Microbiology, 73 (3), 005793.

2022

73- Uroz, S*, Geisler, O., Fauchery, L., Rodrigues, A.M.S., Morin, E., LAMI, R., Leveau, JHJ, Oger, P. Genomic and transcriptomic characterization of the Collimonas quorum sensing genes and regulon. FEMS Microbial Ecology. (IF=4.19) https://doi.org/10.1093/femsec/fiac100

72- Uroz, S*, Picard, L., Turpault, M-P. Recent progress in understanding the ecology and molecular genetics of soil mineral weathering bacteria. Trends in Microbiology. 30(9)882-897 (IF=17) doi.org/10.1016/j.tim.2022.01.019

71- Picard, L., Paris, C., Dhalleine, T., Morin, E., Turpault, M-P., Oger, P., Uroz, S.* The mineral weathering ability of Collimonas pratensis PMB3(1) involves a Malleobactin-mediated iron acquisition system. Environmental Microbiology.24 (2), 784-802 (IF=5.49)

2021

70- Mieszkin, S. *, Pouder, E., Uroz, S., Simon-Colin, C., Alain, K. Acidisoma silvae sp. nov. and Acidisoma cellulosilytica sp. nov., two acidophilic bacteria isolated from decaying wood, hydrolyzing cellulose and producing poly-β-hydroxybutyrate. Microorganisms. 9 (10), 2053 (IF=4.16)

69-Colin, Y., Turpault, M-P., Fauchery L., Buée, M., Uroz, S.* Forest plant cover and mineral type determine the diversity and composition of mineral-colonizing fungal communities. European Journal of Soil Biology. 105, 103334 (IF=2.84)

68-Thomas F.*, Le Duff, N., Wu, TD., Cébron, A., Uroz, S., Riera, P., Leroux, C., Tanguy, G., Legeay, E., Guerquin-Kern, J-L. Isotopic tracing reveals single-cell assimilation of a macroalgal polysaccharide by a few marine Flavobacteria and Gammaproteobacteria. ISME Journal. 15 (10), 3062-3075 doi.org/10.1038/s41396-021-00987-x (IF=10.30)

67-Mieszkina,S*, Richet P., Bach, B, Lambrot, C, Augusto, L., Buée, M., Uroz, S. Oak decaying wood harbors taxonomically and functionally different bacterial communities in sapwood and heartwood. Soil Biology and Biochemistry. 155, 108160 (IF=7.61)

66- Picard, L., Turpault, M-P., Oger, P., Uroz, S.* Identification of a novel type of glucose dehydrogenase involved in the mineral weathering ability of Collimonas pratensis strain PMB3(1). FEMS Microbial Ecology. 29; 97(1):fiaa232. doi: 10.1093/femsec/fiaa232. (IF=4.19)

2020

65- Picard, L., Oger, P., Turpault, M-P., Uroz, S.* Draft genome of Collimonas pratensis strain PMB3(1), an effective mineral weathering and chitin hydrolyzing bacterial strain. Microbiology Resource Announcements. 9 (37).(IF=0.88)

64- Uroz, S.*, Picard, L., Turpault, M-P., Auer, L., Armengaud, J., Oger, P. Dual transcriptomics and proteomics analyses of the early stage of interaction between Caballeronia mineralivorans PML1(12) and mineral. Environmental Microbiology. 22 (9), 3838-3862. (IF=5)

2019

63- Nicolitch, O., Feucherolles, M., Churin, J-L., Fauchery, L., Turpault, M-P., Uroz, S.* A microcosm approach highlights the response of soil mineral weathering bacterial communities to an increase of K and Mg availability. Scientific Report. 9 (1), 1-13. (IF=4)

62- Uroz, S.*, Courty, P.E., Oger, P. Plant symbionts are engineers of the plant-associated microbiome. Trends in Plant Sciences. 24 (10), 905-916. (IF=14)

61- Splivallo, R., Vahdatzadeh, M., Maciá-Vicente, J.G., Molinier, V., Peter, M., Egli, S., Uroz, S., Paolocci, F., Deveau, F. Orchard conditions and fruiting body characteristics drive the microbiome of the black truffle Tuber aestivum. Frontiers in Microbiology 10, 1437 (IF=4.25)

60- Uroz, S.* and Oger, P. Corrigendum to “Caballeronia mineralivorans sp. nov., isolated from oak-Scleroderma citrinum mycorrhizosphere” [Syst. Appl. Microbiol. 40 (2017) 345-351]. Systematic and Applied Microbiology. 42(3):423-424. doi: 10.1016/j.syapm.2019.03.001. (IF=2.8)

59- Plassart, P., Chemidlin Prévost-Bouré,N., Uroz, S., Dequiedt, S., Stone, D.,  Creamer, R., Griffiths, R., Bailey, M., Ranjard, L.,  Lemanceau, P. Soil parameters, land use, and geographical distance drive soil bacterial communities along a European transect. Scientific Report. 24;9(1):605. doi: 10.1038/s41598-018-36867-2. (IF=4)

2018

58- Maharaj, NN, Miyao, EM, Davis, RM, Uroz, S, Leveau, JHJ* Impact of soil chemistry, nutrient supplements, and fungicides on the health and yield of field-grown processing tomatoes. European Journal of Plant Pathology, 152 (4), 855-868 (IF=1.74)

57- P. E. Courty, M. Buée, J J.T. Tech, D. Brulé, Y. Colin, J.H.J. Leveau, S. Uroz* Impact of soil pedogenesis on the diversity and composition of fungal communities across the California soil chronosequence of Mendocino. Mycorrhiza. 28 (4), 343-356 (IF=3.047)

2017

56- Colin Y, Nicolitch O, Van Nostrand JD, Zhou JZ, Turpault MP, Uroz S.* Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence. Scientific Report.  29;7(1):9604. doi: 10.1038/s41598-017-07639-1. (IF=4.259)

55- Nicolitch, O, Colin, Y, Turpault, MP, Fauchery, L, Uroz S*. Tree roots select specific bacterial communities in the subsurface critical zone. Soil Biology and Biochemistry 115, 109-123 (IF=4.857)

54 – Uroz, S.* and Oger, P. Caballeronia mineralivorans sp. nov., isolated from oak-Scleroderma citrinum mycorrhizosphere. Systematic and Applied Microbiology. 40 (6), 345-351 (IF=3.931)

53 -Martin FM*, Uroz S, Barker DG. Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria. Science. 2017 May 26;356(6340). pii: eaad4501. doi: 10.1126/science.aad4501.(IF=37.205)

52- Torres, M., Uroz, S., Salto, R., Fauchery, L., Quesada, E., Llamas Company, I.* HqiA, a novel quorum-quenching enzyme which expands the AHL lactonase family. Scientific Reports. 7 (1), 943 (IF=5.5)

51-Crampon,M.,  Cebron, A.,  koltalo, F., Uroz, S., Lederf, F., Bodilis, J.* Low effect of phenanthrene bioaccessibility on its biodegradation in diffusely contaminated soil. Environmental Pollution. In press (IF=4.84)

50- Colin, Y., Nicolitch, O., Turpault, M-P., Uroz, S.* Mineral type and tree species determine the functional and taxonomic structure of forest soil bacterial communities. Applied and Environmental Microbiology. 83(5). pii: e02684-16. doi: 10.1128/AEM.02684-16. (IF=3.8)

49- Elly Morriën, S. Emilia Hannula, Basten Snoek, Nico R. Helmsing, Anton Johan Zweers, Mattias de Hollander, Raquel Lujan Soto, Marie-Lara Bouffaud, Marc Buee, Wim Dimmers, Henk Duyts, Stefan Geisen, Mariangela Girlanda, Robert Griffiths, Helene-Bracht Jorgensen, John Jensen, Pierre Plassart, Dirk Redecker, Rudiger M. Schmelz, Olaf Schmidt, Bruce C. Thomson, Emilie Tisserant, Stéphane Uroz, Anne Winding, Mark Bailey, Michael Bonkowski, Jack Faber, Francis Martin, Philippe Lemanceau, Wietse de Boer, Johannes van Veen, and Wim van der Putten. Soil networks become more connected and take up more carbon as nature restoration progresses. Nature Communication. 8:14349. doi: 10.1038/ncomms14349. (IF=11.3)

48- Krieger, C., Calvaruso, C., Morlot, C., Uroz, S., Salsi, L., Turpault, M-P.*. Identification, distribution and quantification of biominerals in a deciduous forest. Geobiology. 15 (2), 296-310  (IF=3.5).

2016

47- Nicolitch, O., Colin, Y., Turpault, M-P., Uroz, S.* Soil type determines the distribution of nutrient mobilizing bacterial communities in the rhizosphere of beech trees. Soil Biology and Biochemistry. 103, 429-445 (IF=4.4)

46-Uroz, S.*, Buée, M., Deveau, A., Mieszkyn, S., Martin, F. Ecology of the forets microbiome: Highlights of temperate and boreal ecosystems. Soil Biology and Biochemistry. 103, 471-488 (IF=4.4)

45- Uroz S.*, Oger P. , Tisserand E. , Cébron A., Turpault M-P., Buée M., De Boer W., Leveau J.H.J., and P. Frey-Klett. Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities. Scientific Reports. 6: 27756. doi:  10.1038/srep27756  (IF=5.5)

44-Kelly, LC., Collin, Y., Tupault, M-P. and Uroz, S.* Mineral type and solution chemistry affect the structure and composition of actively growing bacterial communities as revealed by bromodeoxyuridine immunocapture and 16S rRNA pyrosequencing. Microbial Ecology. Volume 72, Issue 2, pp 428–442. (IF=2.973)

43- Deveau, A.*, Antony-Babu, S., Le Tacon, F., Robin, C., Frey-Klett, P. and Uroz, S. Temporal changes of bacterial communities in the Tuber melanosporum ectomycorrhizosphere during ascocarp development. Mycorrhiza. Volume 26, Issue 5, pp 389–399 (IF=3.459)

42- Jeanbille, M., Buée, M., Bach, C., Cébron, A., Frey-Klett, P, Turpault, M-P., Uroz, S.* Soil parameters drive the structure, diversity and functions of the bacterial communities across a temperate beech forest soil sequence. Microbial Ecology. Volume 71, Issue 2, pp 482–493 (IF=2.973)

41. F Martin*, S Uroz*  Microbial environmental genomics (MEG) Humana Press. Methods in Molecular Biology Volume 1399 2016

2015

40-Uroz, S.*, Kelly, L.C., Turpault, M-P., Lepleux, C., and P. Frey-Klett. The Mineralosphere concept: mineralogical control of bacterial communities. Trends in Microbiology. Volume 23, 751–762. (IF=9.186)

39-Uroz S.* and Oger P. (2015) Burkholderia sp. strain PML1(12), an ectomycorrhizosphere-inhabiting bacterium with effective mineral weathering ability. Genome announcement. DOI 10.1128/genomeA.00798-15 Genome Announc.  vol. 3 no. 4 e00798-15 (IF=)

38-Thomson, B.C., Tisserant, E., Plassart, P., Uroz, S., Griffiths, R.I., Hannula, E., Buée, M., Mougel, C., Ranjard, L., van Veen, J.A., Martin, F., Bailey, M.J., Lemanceau, P. Soil conditions and land use intensification effects on soil microbial communities across a range of European field sites. Soil Biology and Biochemistry (IF=4.4). Volume 88, 403–413.

2014

37- Uroz, S.*, Tech, J.J., Sawaya, N.A., Frey-Klett, P., and J.H.J. Leveau. Structure and function of bacterial communities in ageing soils: Insights from the Mendocino ecological staircase. Soil Biology and Biochemistry. Volume 69, 265–274 (IF=4.4).

36- Hervé, V., Le Roux, X., Uroz, S., Gelhaye, E. and P. Frey‐Klett. Diversity and structure of bacterial communities associated with Phanerochaete chrysosporium during wood decay.  Environmental Microbiology. 16, 2238–2252 (IF=5.756)

35- Antony-Babu, S., Deveau, A.*, van Nostrand, J., Zhou, J., Le Tacon, F., Frey-Klett, P. and Uroz, S. Black truffle-associated bacterial communities during the development and maturation of Tuber melanosporum ascocarps and putative functional roles. Environmental Microbiology. 16, 2831–2847 (IF=5.756)

2013

34-Antony-Babu, S., Murat, C., Deveau, A., Le Tacon, F., Frey-Klett, P., Uroz, S.* An improved method compatible with metagenomic analyses to extract genomic DNA from soils in Tuber melanosporum orchards. Journal of Applied Microbiology. 5:163-170. (IF=2.337)

33-Lepleux, C., Uroz, S.*, Collignon, C., Churin J-L., Turpault, M.-P. and Frey-Klett, P. A short-term mineral amendment impacts the mineral weathering bacterial communities in an acidic forest soil. Research in Microbiology. 164:729-739 (IF=2.76)

32- Bontemps C, Toussaint M, Revol PV, Hotel L, Jeanbille M, Uroz S, Turpault MP, Blaudez D, Leblond P. Taxonomic and functional diversity of Streptomyces in a forest soil. FEMS Microbiology Letter. 342:157-167. (IF=2.044)

31- Uroz, S.*, Courty P.E., Pierrat J.C., Peter, M., Buée M., Turpault M.P., Garbaye J. , and Frey-Klett, P. Functional profiling and distribution of the forest soil bacterial communities along the soil mycorrhizosphere continuum. Microbial Ecology. 66:404-415. (IF=2.912)

30- Uroz, S.*, Ioannidis, P., Lengelle, J., Cébron, A., Morin, E., Buée, M., Martin, F. Functional assays and metagenomic analyses reveals differences between the microbial communities inhabiting the soil horizons of a Norway spruce plantation. Plos ONE. 8:e55929. (IF=4.092)

29- Calvaruso, C.*, Turpault, M-P., Frey-Klett, P., Uroz, S., Pierret, M-C., Kies, A. Effect of Scots pine roots associated or not with Burkholderia glathei PML1(12) on apatite dissolution rate. Geochimica and Cosmochimica Acta. 106 :287-306. (IF=4.259)

2012

28-Lepleux, C., Turpault, M-P., Oger, P., Frey-Klett, P., Uroz, S.*(2012) Abundance of Beta-Proteobacteria on mineral surfaces correlates with mineral weathering in forest soils. Applied Environmental Microbiology.78:7114-7119 (IF=3.83)

27-Uroz, S.*, Oger, P.M., Morin, E.. and Frey-Klett, P. (2012) Distinct ectomycorrhizospheres share similar bacterial communities composition as revealed by pyrosequencing-based analysis of 16S rRNA genes. Applied Environmental Microbiology. 78:3020-3024 (IF=3.83)

26-Uroz, S.*, Turpault, M.P., Delaruelle, C., Mareschal, L., Pierrat, J-C. and Frey-Klett, P. (2012) Minerals affect the specific diversity of forest soil bacterial communities. Geomicrobiology  Journal.29:88-98 (IF=2.017)

2011

25- Uroz, S.*, Turpault, M-P., Van Scholl, L., Palin, B. and Frey-Klett P.(2011) Long term impact of mineral amendment on the distribution of the mineral weathering associated bacterial communities from the beech Scleroderma citrinum ectomycorrhizosphere. Soil Biol & Biochem. 43 :2275-2282. (IF : 3.5)

24- Collignon, C., Uroz, S.*, Turpault, M-P. and Frey-Klett P. (2011) Seasons differently impact the structure of mineral weathering bacterial communities in beech and spruce stands. Soil Biol & Biochem. 43 :2012-2022. (IF : 3.5)

23- Uroz, S.*, and Frey-Klett, P.(2011) Linking diversity to function: highlight on the mineral weathering bacteria. Central European Journal of Biology. 6:817-820. (IF=1)

22- Uroz, S.*, Oger, P., Lepleux, C., Collignon, C., Frey-Klett, P. and Turpault, M-P. (2011)Bacterial weathering and its contribution to nutrient cycling in temperate forest ecosystems. Research in Microbiology . 162 :820-831 .(IF=2.76)

2010

21- Cusano A.M., Burlinson, P., Deveau, A., Vion, P., Uroz S., Preston G.M. and Frey-Klett P. (2010) Pseudomonas fluorescens BBc6R8 type III secretion mutants no longer promote ectomycorrhizal symbiosis.  Environmental Microbiology Reports. 3:203–210 (IF=3.076)

20- Calvaruso C., Turpault M-P., Leclerc E., Ranger J., Garbaye J., Uroz S.∗, and Frey-Klett P. (2010) Forest trees influence distribution of the mineral weathering bacterial communities from the Scleroderma citrinum mycorrhizosphere. Appl. Environ Microbiol. 76:4780-4787(IF=3.77)

19- Courty, P.E., Buée, M., Diedhiou, A.G., Frey-Klett, P., Le Tacon, F., Rineau, F., Turpault, M-P., Uroz, S. and Garbaye, J. (2010) The role of ectomycorrhizal communities in forest ecosystem processes: new perspectives and emerging concepts. Soil Biol & Biochem. 42: 679-698 (IF : 3.24)

18- Uroz, S.*, Buée, M., Murat, C., Frey-Klett, P. and Martin, F. (2010) Pyrosequencing highlights the contrasted bacterial diversity in forest soil. Environmental Microbiology Reports. 2: 281-288. (IF=3.076) (PDF)

2009

17- Buée, M., Reich, M., Murat, C., Morin, E., Nilsson, R.H., Uroz, S. and Martin, F. (2009) 454-pyrosequencing analyses of forest soil reveal an unexpectedly high fungal diversity. New Phytologist. 184:449-456(IF : 5.2)(PDF)

16- Uroz, S.*, Calvaruso, C., Turpault, M.P., de Boer, W., Leveau J.H. and Frey-Klett, P. (2009) Novel bacteria harbouring efficient mineral-weathering ability, a widespread functional trait of the genus Collimonas. Soil Biol & Biochem. 41 : 2178-2186 (IF : 2.9)

15- Leveau, J.H.J., Uroz, S. and de Boer, W. (2009) The bacterial genus Collimonas: mycophagy, weathering, and other adaptive solutions to life in oligotrophic environments. Environmental Microbiology. 12:281-292 (IF : 4.9)(PDF)

14- Calvaruso, C., Turpault, MP, Uroz, S., Leclerc, E., Kies, A and Frey-Klett, P. (2009) Ectomycorrhizal fungus Laccaria bicolor S238N contributes to tree mineral nutrition in vitro by increasing root nutrient uptake : a budgeting approach. Plant and Soil. 328:145-154. (IF : 2.4)

13- Uroz, S.*, Calvaruso, C., Turpault, MP and Frey-Klett, P. (2009) The microbial weathering of soil minerals: Ecology, actors and mechanisms. Trends in Microbiology. 17:378-387. (IF:7.9)(PDF)

12- Koele, N., Turpault, M-P, Hildebrand, E.E., Uroz, S., and Frey-Klett, P. (2009) Interactions between mycorrhizal fungi and mycorrhizosphere bacteria during mineral weathering: budget analysis and bacterial quantification. Soil Biol & Biochem. 41: 1935-1942. (IF : 2.9)

11- Uroz, S.*, Dessaux, Y., and Oger P. (2009) Quorum sensing and quorum quenching : the yin and yang of bacterial communication. ChemBioChem 10 : 205-216. (IF : 3.5)(PDF)

2008

10- Rineau, F., Courty, PE, Uroz, S., Buée, M. and Garbaye J. (2008) Simple microplate assays to measure iron mobilization and oxalate secretion by ectomycorrhizal tree roots. Soil Biol & Biochem. 40:2460-2463. (IF : 2.9)

9- Uroz, S.* and Heinonsalo, J. (2008) Inactivation of N-acyl homoserine lactone quorum sensing molecules by forest soil fungi. FEMS Microbiol. Ecol. 65 : 271-278. (IF : 3)

8- Uroz, S., Oger, P., Chapelle,E., Adeline M-T., Faure, D., and Dessaux, Y. (2008) “In Rhodococcus, the qsdA encoded-enzyme defines a novel class of large spectrum quorum-quenching lactonases”. Appl. Environ Microbiol. 74 :1357-1366. (IF : 4)

2007

7- Uroz, S.*, Calvaruso, C., Turpault, M.P., Pierrat, J.C., Mustin, C. and Frey-Klett, P. (2007) Mycorrhizosphere effect on the genotypic and metabolic diversity of the soil bacterial communities involved in mineral weathering in a forest soil. Appl. Environ Microbiol. 73 :3019-3027. (IF : 4)

6- Uroz, S., Chhabra, S. R., Camara, M., Williams, P., Oger, P. and Dessaux. Y. (2007) N-acyl homoserine lactones are degraded via an amidolytic activity in Comamonas sp. strain D1. Archives in Microbiol. 187: 249-256. (IF : 2.3)

2005

5- Uroz, S., Chhabra, S. R., Camara, M., Williams, P., Oger, P. and Dessaux. Y. (2005) N-Acylhomoserine lactone quorum-sensing molecules are modified and degraded by Rhodococcus erythropolis W2 by both amidolytic and novel oxidoreductase activities. Microbiology. 151: 3313-3322. (IF : 3.1)

4- Delalande, L., Faure., D., Raffoux, A., Uroz, S., D’angelo-Picard, C., Elasri, M., Carlier, A., Berruyer, R., Petit, A.,. Williams P. and Dessaux., Y. (2005) Plant-, temperature- and pH-dependent stability of hexanoyl-homoserine lactone, a mediator of quorum-sensing regulation. FEMS Microbiol. Ecol. 52:13-20. (IF : 3)

2004

3- D’Angelo-Picard, C., Faure, D., Carlier, A., Uroz, S., Raffoux, A., Fray, R. and Dessaux, Y. (2004) Dynamics of bacterial signal populations in the rhizosphere of tobacco plants producing – or not – the quorum-sensing molecule hexanoyl-homoserine lactone and 3-oxo-hexanoyl-homoserine lactone. FEMS Microbiol. Ecol. 51: 19-29. (IF : 3)

2003

2- Carlier, A. Uroz, S., Smadja, B., Fray, R., Latour, X., Dessaux, Y. and D. Faure. (2003) The Ti plasmid of Agrobacterium tumefaciens harbors an attM paralogous gene, aiiB, also encoding N-acyl homoserine lactonase activity. Appl. Environ Microbiol. 69:4989-4993. (IF : 4)

1- Uroz, S., D’Angelo, C., Carlier, A., Elasri, M., Sicot, C., Petit, A., Oger, P., Faure, D. and Dessaux, Y. (2003) Novel bacteria degrading N-acyl homoserine lactones and their use as quenchers of quorum-sensing regulated functions of plant pathogenic bacteria. Microbiology. 149: 1981-1989. (IF : 3.1) (PDF)

OTHER PUBLICATIONS AND BOOK CHAPTERS:

A1- Uroz, S. (2000) Etude de la stabilité biologique des N-acyl homoserine lactones ” – Diplôme d’Etude Approfondie. Université Claude Bernard, Lyon I.

A2-Uroz, S. (2004) Dégradation des N-acyl homoserine lactones, médiateurs de la régulation quorum sensing : les organismes, les mécanismes, les applications potentielles “. Thèse de doctorat (CNRS de Gif-sur-yvette et ” Laboratoire de sciences de la Terre “, Ecole Normale Supérieure de Lyon), Université Paris XI, Orsay (PhD thesis).

A3-D’Angelo-Picard, C., Uroz, S., Nalin, R., Dessaux, Y. et Faure, D. (2005) Diversité génétique bactérienne liée à l’émission et la transformation du signal quorum-sensing dans la rhizosphère, in Les Actes du BRG n°5, Un dialogue pour la diversité génétique, pp119-135, Bureau des Ressources Génétiques (éditeur), Bialec (Nancy).

A4-Uroz, S.*, Calvaruso, C., Turpault, M-P et Frey-Klett, P. (2006) Altération microbienne des minéraux :Quelle importance, quels acteurs et quels mécanismes ? BIOFUTUR Vol. 25/268 :37-41.

A5- Uroz, S.*, Calvaruso, C., Turpault, M-P et Frey-Klett, P. (2007) Altération microbienne des minéraux :quelle importance, quels acteurs et quels mécanismes ? Mensuel INRA N°128 : 23-24.

A6- Ranger J., Gelhaye D., Bienaimé S., Bonnaud P., Calmet J.P., Calvaruso C., Foret M., Gerard F., Jaffrain J., Mareschal L., Moukoumi J., Nourrisson G., Pollier B., Saint-André L., Sicard C., Turpault M.P., Zeller B., Buée M., Frey-Klett P., Le Tacon F., Uroz S., Maurice J.P., Chaussod R., Lejon D., Ranjard L., Berthelin J., Béguiristain T., Boudot J.P., Kulhankova A., Mallouhi N., Munier-Lamy C., Delvaux B., Titeux H., Trum F. (2007) Effet de la substitution d’essence sur le fonctionnement et la durabilité des écosystèmes forestiers: l’apport des travaux pluridisciplinaires menés en forêt de Breuil Chenue Morvan. Bourgogne Nature.

A7-Dessaux, Y., A. Cirou, S. Uroz, E. Chapelle, X. Latour, & D. Faure (2007) Quorum sensing as a target for novel biocontrol strategies directed at Pectobacterium. Proceedings of the XIII international congress on molecular plant microbe interactions. Sorrento, Italie.

A8- Uroz, S.*, Calvaruso, C., Turpault, M-P et Frey-Klett, P. (2008) Altération microbienne des minéraux :quelle importance, quels acteurs et quels mécanismes ? Bulletin de l’INRA.

A9-Calvaruso C., Turpault M.-P, Frey-Klett P., Uroz S., Kies A., Leclerc E. (2008) Mobilization and acquisition of nutrients from apatite and biotite by Scots pine roots associated or not with a mycorrhizosphere bacterial strain. Proceedings of the 5th International Symposium of Interactions of Soil Minerals with Organic Components and Microorganisms. J. Soil Sci. Plt Nutr. 8, 178-179.

A10- Oger, P. and Uroz, S. (2010) Screening for N-AHSL-based-signalling interfering enzymes. Molecular Methods in Metagenomics- Book chapter 668:203-217.

A11-Cirou A., UrozS., Chapelle E., Latour X., Orange N., Faure D., Dessaux Y. Quorum sensing as a target for novel biocontrol strategies directed at Pectobacterium (2010), pp 121-132. In Recent developments in disease management, Plant Pathology in the 21st Century. U. Gisi, I. Chet & M.L. Gullino (eds), Springer-Verlag (Berlin Heidelberg).

A12- Uroz*, S., Marmeisse, R., Buée, M., Dessaux, Y., Faure, D. and Geremia, R. (2011) De la diversité à la fonction des sols peu anthropisés. Dossier de Métagénomique. Biofutur 319:39-43.

A13- Lepleux C, Uroz S, Frey-Klett P, Turpault MP. (2011) Caractérisation taxonomique et fonctionnelle des communautés bactériennes associées à la surface des minéraux dans les sols forestiers pauvres en nutriments : méthodologies et concepts. Publications de l’Ecole Doctorale RP2E, Nancy, France, vol.1.

A14. Tisserant E, Plassart P, Buée M, Lengelle J, Payen T, Murat C, Uroz S*, Lemanceau P and F. Martin Developing and Standardizing Tools and Procedures for Assessment of Soil Biodiversity. Newsletter of the European Society for Soil Conservation (ESSC) sous presse.

A15. Tisserant E, Plassart P, Buée M, Lengelle J, Payen T, Murat C, Uroz S*, Lemanceau P and F. Martin Developing and Standardizing Tools and Procedures for Assessment of Soil Biodiversity. Quick win. ECOFINDER consortium. Final Report Summary – ECOFINDERS (Ecological Function and Biodiversity Indicators in European Soils) (Project reference: 264465)

A16. Uroz, S.*, Bispo, A., Buée, M., Cébron, A., Cortet, J., Decaens, T., Hedde, M., Peres, G., Vennetier, M., Villenave, C. (2015) Aperçu des avancées dans le domaine de la biologie des sols forestiers. Revue forestière française. N°4, p. 467 DOI : 10.4267/2042/56560

A17. Uroz, S., Bispo, A., Buée, M., Cébron, A., Cortet, J., Decaens, T., Hedde, M., Peres, G., Vennetier, M., Villenave, C. (2015) Highlights on progress in forest soil biology. Revue forestière française. RFF -LXVI- Hors série – 2014 .

A18. Torres, M., Uroz, S., Quesada, E., Llamas, I. (2015) Screening of the quorum quenching activity in a metagenomic library from a hypersaline-soil sample taken in Rambla Salada (Murcia, Spain) Book of abstracts, 26 (Santigao de compostella)

A19. Uroz, S. and Oger, P.  (2016) Screening for N-AHSL-based-signalling interfering enzymes. Molecular Methods in Metagenomics- Book chapter 2nd edition. In press.

A20. Uroz, S., Cébron, A., Deveau, A., Martin, F. (2016) Microbiote: les plantes aussi!  Pour la Science. n°469, 74-79.

>A21. Fauchery, L, Uroz, S, Buée, M, Kohler, A* (2018) Purification of Fungal High Molecular Weight Genomic DNA from Environmental Samples. Fungal Genomics, 21-35

A22.Uroz, S. Cebron, A., Deveau, A., Martin, F. (2018) Le charme discret…. de la racine. Hors-série Pour la Science n°101.

A23. John T Van Stan II, Cindy E Morris, Kyaw Aung, Yakov Kuzyakov, Donát Magyar, Eria A Rebollar, Mitja Remus-Emsermann, Stéphane Uroz, Philippe Vandenkoornhuyse  (2020) Precipitation Partitioning—Hydrologic Highways Between Microbial Communities of the Plant Microbiome? Precipitation Partitioning by Vegetation. p. 229-252 Springer, Cham

A24. Uroz, S. and Oger, P.  (2023) High-Throughput Screening of Fosmid Libraries for Increased Identification of Novel N-Acyl Homoserine Lactone Degrading Enzymes. Microbial Environmental Genomics (MEG), 227-240

A25. Uroz, S. and Martin, F.  (2023) Preface of the book. Microbial Environmental Genomics (MEG).

National and international congress and workshop participations

2023
– FEMS 11th Congress of European Microbiologists(Hamburg, Germany) Blanco-Nouche, C., Paris, C., Dhalleine, T. ,  Oger, P., Turpault, MP, Uroz, S.. Decreasing biotite particle size increases siderophore-mediated weathering of biotite mineral by Caballeronia mineralivorans strain PML1(12) (Poster)

– FEMS 11th Congress of European Microbiologists (Hamburg, Germany) Picard, L., Blanco-Nouche, C., Paris, C., Dhalleine, T., Cochet, C.,  Oger, P., Turpault, MP, Uroz, S.  Mineral weathering by heterotrophic bacteria as a function of mineral properties, solution chemistry and carbon substrate (Poster)

– Aussois 2023 16èmes Rencontres Plantes Bactéries.  Blanco Nouche, C.,Paris, C., Dhalleine, T., Morin, E., Turpault, M-P., Oger, P., Uroz, S. The NRPS-Independent Siderophore (NIS) Rhizobactin produced by the strain Caballeronia mineralivorans PML1(12) confers the ability to weather minerals (Oral)

2022
– Séminaire invité. Colloque scientifique du Labex ARBRE (25 Novembre 2022). Uroz S. and colleagues. “Nutrient availability and mineral properties condition the distribution and functioning of the mineral weathering bacteria ” (Oral)

– Webminaire invité. University of Hohenheim (Ellen Kandeler group; 17 Janvier 2022). Uroz S. and colleagues. “Ecology, Molecular mechanisms and Genomics of Mineral Weathering Bacteria” (Oral)

2021

– Webminaire invité. UMR Eco&sols (17 juin 2021). Uroz S. and colleagues. “Ecologie, génomique et mécanismes moléculaires de l’altération des minéraux” (Oral)

2020

Inauguration du dispositif exclusion de pluie (Montiers; 16 Septembre 2020). Uroz S. and colleagues. “Sol et micro-organismes dans un contexte de changements globaux ”

2019

Colloque AFEM09 (Bussang, France)(Organization by IAM and LIEC)

– Sophie Mieszkin, Perrine Richet , Catherine Lambrot, Cyrille Bach , Laurent Augusto , Marc Buée , Stéphane Uroz. Diversité taxonomique et fonctionnelle des communautés bactériennes colonisant le duramen et l’aubier du chêne sessile (Quercus petraea) en decomposition (Poster)
– Laura Picard, Marie-Pierre Turpault, Phil Oger, Stéphane Uroz. Mécanismes moléculaires impliqués dans la dissolution des minéraux chez la souche modèle PMB3(1) de Collimonas isolée de la mycorhizosphère de Scleroderma citrinum associé au chêne. (poster)
– François Thomas, Nolwen Le Duff, Pascal Riera, Aurélie Cébron, Cédric Leroux, Gwenn Tanguy, Stéphane Uroz, Ting-Di WU, Jean-Luc Guerquin-Kern. Exploration par marquage isotopique de la diversité des bactéries marines dégradant l’alginate des macroalgues
– Stéphane Uroz, Phil Oger, Laura Picard, Jean Armangaud, Marie-Pierre Turpault. Caractérisation transcriptomique et protéomique des déterminants moléculaires de l’altération des minéraux utilisés par la souche PML1(12) de Caballeronia mineralivorans (Poster)
– Laure Fauchery, Igor Grigoriev, Stéphane Uroz, Marc Buée, Annegret Kohler, Francis Martin. Optimisation des méthodes de purification de l’ADN fongique de haute qualité pour le séquençage.(Poster)
– Antoine Sportes, Raphael Boussageon, Diederik van Tuinen, Daniel Wipf, Claude Plassard, Stéphane Uroz, Pierre-Emmanuel Courty. Coopération entre des bactéries solubilisatrices de phosphate et le champignon mycorhizien à arbuscule Rhizophagus irregularis dans la nutrition phosphatée de la pomme de terre (Poster)

– Franco-Indian Workshop in Functional Metagenomics – from ecosystem processes to biotechnology. (5 to 8 February, Lyon/ IFCPAR/CEFIPRA/CNRS/UL-funded) Uroz,S., Colin, Y., Nicolitch, O., Turpault, M-P. Functional characterization of the soil microbiome in relation with soil properties.(Invited talk).

2018

– Séminaire invité. Laboratoire d’Ecologie Microbienne (LEM) et (MAP)(Lyon). Uroz, S., Nicolitch, O., Colin, Y., Turpault, M-P. Impact de la disponibilité en nutriments et des interfaces minérales sur la diversité, la fonction et le fonctionnement des communautés bactériennes des sols forestiers.( invited talk).

– International Workshop on INRA’s Metaprograms 2018. Sophie Bozonnet, Roland Marmeisse, Diego Morgavi, Marion Leclerc, Stephane Uroz, Alain Brauman, Guillermina Hernandez-Raquet, Muriel Mercier-Bonin, Claire Dumon, Elisabeth Laville, Sandra Pizzut-Serin, Sophie Duquesne, Sandrine Laguerre, Simon Ladevèze, Lisa Ufarté, Alexandre David, Gregory Arnal, Adèle Lazuka, Laurence Tarquis, Marie-Pierre Duviau, Joël Doré, Patricia Luis, Laetitia Bernard, and Gabrielle Potocki-Veronese*.  High-throughput functional exploration of microbial diversity (METASCREEN)( talk).

2017

– 14th Symposium on Bacterial Genetics and Ecology (BAGECO) 4–8 June 2017 • Aberdeen/Scotland : Uroz, S., Colin, Y., Nicolitch,O., Van Nostrand, J.D., Zhou, J.Z., Turpault, M-P. Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence (Poster). Nicolitch, O., Colin, Y., Turpault, M-P., Fauchery, L. and Uroz, S. Exploration of the functional and taxonomic diversity of the bacterial communities occurring in the bedrock/root interface of beech trees (Poster).

– FEMS 7th Congress of European Microbiologists (Valencia, Spain) 9-13 juillet 2017.A novel quorum-quenching enzyme identified in a hypersaline soil.  Torres, M., Uroz, S., Salto, R., Fauchery, L., Llamas, I. (Poster)

– Journées H2020 INSPIRATION – ANR – SOLS: Quels besoins en R&D pour une gestion durable des sols et une utilisation durable du territoire ? (16 et 17 janvier 2017 à Paris). Stephane Uroz, Bilan sur Bactoweather: Caractérisation des communautés bactériennes de la minéralosphère et des gènes bactériens impliqués dans l’altération des minéraux en sol forestier (Invited talk).

2016

– 3rd Thünen Symposium on Soil Metagenomics. “From gene predictions to systems ecology” (14-16th of december, Braunschweig, Germany) Stephane Uroz, Yannick Colin, Océane Nicolitch, Marie-Pierre Turpault, Joy van Nostrand, Jizhong Zhou. Taxonomic and functional shifts of beech rhizosphere microbiome along a natural soil toposequence (Poster). Yannick Colin, Océane Nicolitch, Marie-Pierre Turpault, Stéphane Uroz. Short-term effects of minerals on the structure and weathering potential of soil bacterial communities under different tree stands (Poster).

– Launch of the Global Soil Biodiversity Atlas in France (Académie d’agriculture (AAF); Paris, 28 November). Uroz S. Exploration of the biodiversity and functions of the forest microbiome: a focus on temperate ecosystems. (Invited talk).

– Journée du Labex ARBRE (Champenoux, France, 18 october) Uroz, S., Turpault, M-P., Nicolitch, O., Colin, Y., Buée, M., Churin, J-L., Deveau, A., Bontemps, C., Leblond, P., Aigle, B., Angeli, N., Derrien, D., Besserer, A., .impact of nutrient availability on the diversity, function and functioning of the forest soil bacterial communities: insights from the soil succession of the forest experimental site of montiers (Talk)

– 16th International Symposium on Microbial Ecology (Montreal, Canada). Deveau, A., Splivallo, R., Palin, B., Nicolitch, O., Kohler, A., Uroz, S. Black truffles as a model in microbial ecology to analyse fungal-bacterial interactions (Talk).

2015

– Summer school ‘Functions of microbial communities in soils: Biotic interactions‘ (August 31 – September 11 2015, HMGU Campus Neuherberg, Germany) Uroz, S. Mineral weathering in forest soils: focus on the bacterial communities (Oral).

– Journée Doc-PostDoc du Labex ARBRE (Champenoux, France, 16 november) Impact of nutrient availability on the structure of the rhizospheric bacterial communities: Insights from the Montiers soil sequence.Nicolitch, O., Colin, Y., Turpault, M.P., Uroz, S. (Oral). Mineral composition determines the bacterial community structure and mineral weathering in forest soils. Colin, Y., Nicolitch, O., Turpault, M.P., Uroz, S. (Oral).

– 7em colloque AFEM (Anglet, France; 3-6 november) Impact of nutrient availability on the structure of the forest bacterial communities : Insights from the Montiers soil succession. Nicolitch, O., Colin, Y., Turpault, M.P., Uroz, S. (Oral)

– Rhizosphere 4 congress (Maastricht, The Netherlands; 21-25 june 2015). Forest tree species shape their soil microbiome. Uroz S., Oger P., Tisserand E., Cébron A., Turpault M-P., Höppener-Ogawa S., Buée M., De Boer W, Leveau JHJ, and P. Frey-Klett (Poster). Effect of soil type on the beech fine root distribution M-P.Turpault, C. Calvaruso, S. Uroz, P-O. Redon, G. Kirchen. (Poster)

–Colloque ‘Expérimentation sur le site de Montiers’ (Champenoux, France) 20 mars 2015. Relation entre le type de sol et la structure taxonomique et fonctionnelle des communautés bactériennes,  S. Uroz et al. (Oral)

–International Symposium on Quorum Sensing Inhibition (Santiago de Compostela, Galicia, Spain) 3-5 juin 2015. Screening of the quorum quenching activity in a metagenomic library from a hypersaline-soil sample taken in Rambla Salada (Murcia, Spain).  Torres,M., Uroz, S., Llamas, I. (Oral)

2014
– RED NACIONAL DE MICROORGANISMOS EXTREMÓFILOS. (Alicante, Spain)2014. Búsqueda de genes implicados en la comunicación bacteriana mediante un estudio metagenómico. Torres,M., Uroz, S., Quesada, E., Llamas, I. (Oral)
– First Global Soil Biodiversity Conference (Dijon, France)  2-5 décembre 2014. Forest tree species shape their soil microbiome. Uroz S., Oger P., Tisserand E., Cébron A., Turpault M-P., Höppener-Ogawa S., Buée M., De Boer W, Leveau JHJ, and P. Frey-Klett (Poster); Impact of soil type on the structure of the microbial communities: Insights from the Montiers-sur-Saulx soil succession. Nicolitch, O., Jeanbille, M., Buée M., Colin Y., Turpault M-P., Frey-Klett P. and Uroz S. (Poster)
-workshop “Bioinformatique pour la Génomique Environnementale”, Lyon, 27-28 mai 2014 Uroz S., Oger P, Leveau J.H., Frey-Klett P., Turpault M-P. Impact of biotic and abiotic soil parameters on the distribution of forest soil bacterial communities (Poster)
– Third EcoFINDERS Meeting (Manchester, UK)  WP3 workshop ”Strategies and tools for sampling, DNA extraction, DNA sequencing and bioinformatics’, (Nancy, France) Tisserant E, Plassart P, Buée M, Terrat S, Lengelle J, Dequiedt S, Chemidlin N, Regnier T, Faivre C, Payen T, Murat C, Uroz, S, Ranjard L, Lemanceau P, and Martin F. (Talk)
– International Mycology Conference, Bangkok, Session « Fungal-Bacterial Interaction », (3- 8 aout 2014). Deveau , Splivallo, R., Kirchoff N., Nicolitch O., Bontemps C., Antony-Babu S., Le Tacon F., Frey-Klett P., Kohler A., Uroz S. The Black Truffle : more than a niche for bacteria ? (Invited talk)

2013
– 12th Symposium on Bacterial Genetics and Ecology (BAGECO, Ljubljana, Slovénie) Hervé V., Le Roux X., Uroz S., Gelhaye E. and Frey-Klett, P. The white-rot fungus Phanerochaete chrysosporium structures the diversity of the associated bacterial community during wood decay. (Poster).

– ATELIER Labex ARBRE (Nancy): Montage de projet de recherche Uroz, S., Duplessis, S. ‘Retour d’expérience sur une ANR JC’

– Colloque de restitution du programme SYSTRUF (France). Robin, C., Le Tacon, F., Plain, C., Zeller, B., Hossann, C., Bréchet, C., Antony-Babu, S., Deveau, A., Uroz, S. La nutrition de la truffe, un lien à l’arbre et au sol. (Oral). Deveau, A., Antony-Babu, S., Robin, C., Le Tacon, F., Uroz, S., Frey-Klett, P. Les bactéries, des partenaires méconnus de la truffe. (Oral)

Herve V., Le Roux X., Ketter E., Pierrat J.C., Uroz S., Gelhaye E. & Frey-Klett P. 2013. Differential impacts of wood and of the white-rot fungusPhanerochaete chrysosporiumon the taxonomic and functional diversities of bacterial communities during wood decay. InConférences Jacques Monod “Bacterial-fungal interactions: a federative field for fundamental and applied microbiology”, Roscoff, France [oral presentation].

– Summer school organized by the LIEC (Nancy, France) Uroz, S. Mineral weathering in forest soil : Focus on the bacterial communities and their relationship with nutrient availability (Oral invité).

– Goldschmidt (Florence, Italie) Kelly, LC., Uroz, S. and Turpault, M-P. Characterisation of Active Forest Soil Bacteria during Mineral Weathering (Oral)

-Journées REGEFOR (Nancy, France) Uroz, S., Bispo A., Buée M., Cébron A., Cortet J., Decaens T., Hedde M., Peres G., Vennetier M., Villenave C. Les avancées dans le domaine de la biologie des sols forestiers. (invited talk)

– MEM days (Meta’omics of the microbial ecosystems; Paris). Uroz, S., , Buée, M., Cébron, A., W. de Boer, Frey-Klett, P., Ioannidis, P., Lengelle, J., Lepleux, C., Leveau, J., Martin, F., Oger, P., Pierrat, J-C., and Turpault, M-P. Contribution of metagenomics to the study of mineral weathering bacterial communities in forest soils. (invited talk)

– ICOM7 (New Delhi, India) Aurélie Deveau., Sanjay Antony-Babu, Stéphane Uroz., François Le Tacon, Pascale Frey-Klett.Do bacterial communities associated with the black truffle contribute to the life cycle of the ectomycorrhizal fungus ? (Talk)

2012

– Ecole Thématique Expert Génomique Environnementale (ETEGE)(Aussois, France) Lepleux, C., Uroz, S., Turpault, MP., Oger, P., Frey-Klett, P. Caractérisation taxonomique et fonctionnelle des communautés bactériennes associées à la surface des minéraux : Combinaison d’approches non-cultivable et cultivable. (Poster)

– 14th ISME congress, (Coppenague, Danemark), Antony-Babu, A., Deveau, A., Uroz, S., van Nostrand, J., Zhou, J., Le Tacon, F., Frey-Klett, P. Bacterial diversity associated with the black truffle Tuber melanosporum along its biological cycle. (Talk) Lepleux, C., Turpault, MP., Oger, P., Frey-Klett, P., Uroz, S. Combination of culture-independent and dependent approach reveals positive correlation between abundance of Beta-proteobacteria and mineral weathering in nutrient-poor forest soil. (Poster)

2011

Colloque Génomique Environnementale (Lyon, France) Uroz, S., Buée, M, Frey-Klett, P., Ioannidis, P.,Lepleux, C., Deveau, A., Cébron, A., Turpault, M-P., Morin, E., Murat, C. Oger, P., Martin, F. Exploration du microbiome des sols forestiers: de la diversité fonctionnelle au fond métagénomique. (Talk)

Goldschmit 2011 (Prague, Czech Republic) Turpault, M-P., Uroz, S. , Calvaruso, C., Collignon, C., Mareschal, L., Frey-Klett, P., Lepleux, C. Life as the Catalist of Mineral Weathering in Acidic Forest Ecosystem.(Talk)

1st EcoFINDERS WP3 workshop ”Strategies and tools for sampling, DNA extraction, DNA sequencing and bioinformatics’, (Nancy, France) Uroz S, Buée, M., Martin, F., Coince, A., Murat, C., Morin, E., Tisserand, E. Metagenomics of the forest soil microbiome : from diversity to function (Talk)

26th Fungal Genetics Conference  (Azilomar, USA) Deveau A, Burlinson P, Cusano A, Diedhiou A, Uroz S, Sarniguet A, Preston G and Frey-Klett P. Ectomycorrhizal fungi and their bacterial associates:  what’s new about the mechanisms of their interactions? (Talk)

Ecology of soil microorganisms: Microbes  as important drivers of the soil processes (Prague, Czech Republic) C. Lepleux, S. Uroz, M-P Turpault, P. Frey-Klett. Taxonomic and functional characterization of the mineral associated bacterial communities in forest soil. (Poster)// Uroz, S., Turpault, M-P., Frey-Klett, P., Calvaruso, C., Collignon, C., Lepleux, C., Oger, P., Leveau, J., and W. de Boer. MINERAL WEATHERING BY FOREST SOIL BACTERIAL COMMUNITIES: FROM FUNCTION TO DIVERSITY (Poster)

2010

13th ISME congress, (Seattle, USA) : Uroz, S., Turpault, M-P., Frey-Klett, P., Calvaruso, C., Collignon, C., Lepleux, C., Oger, P., Leveau, J., and W. de Boer. MINERAL WEATHERING BY FOREST SOIL BACTERIAL COMMUNITIES: FROM FUNCTION TO DIVERSITY (Talk)

Soil metagenomics, (Brunswick, Germany), .Ioannidis P., Uroz S., Buée M., Morin E. and Martin F. Comparative metagenomics of mineral and organic layers of a forest soil (Poster)

Journée de Microbiologie de l’INRA (Poitiers, France),Collignon, C., Uroz, S., Turpault, M-P. and Frey-Klett, P. Seasons differently impact on the structure of mineral weathering bacterial communities in a forest soil (Talk) // Uroz, S.,  Turpault, M-P., Frey-Klett, P., Calvaruso, C., Colligon, C., Lepleux, C., Höppener-Ogawa, S., Oger, P., Leveau, J., Buée, M.,  Martin, F., Murat, C., Pierrat J-C. and W. de Boer. Highlight of the bacterial communities involved in mineral weathering and in the  fertility of forest soils (Poster) // Lepleux, C., Uroz, S., Turpault, M-P., Oger, P.and Frey-Klett, P. Taxonomic and functional characterization of the mineral associated bacterial communities : pyrosequencing FLX 454 Titanium approach (Poster)

Rencontres de Phytopathologie, (Aussois, France). P. Frey-Klett, A. Deveau, A. Diedhiou, A. Cusano, B. Palin, M. Barret, S. Uroz, J. Garbaye, A. Sarniguet. The ectomycorhizal complex, a reference model for the study of fungal-bacterial interactions. (Talk)

9th International Mycological Congress, (Edinburgh, UK),  Buée, M., Reich, M., Murat, C., Morin, E., Nilsson, R.H., Uroz, S. and Martin, F. Fungal diversity in soil forest: next-generation sequencing sheds light in the black-box. (Talk).//P FREY-KLETT, A CUSANO, P BURLINSON, A DEVEAU, A DIEDHIOU, G PRESTON , S. UROZ et al. The Ectomycorrhizal Complex, a Reference Model for the Study of Fungal-Bacterial Interactions. (Talk)

2009

8th PGPR workshop, Portland (Oregon, USA), P. Frey-Klett, A. Deveau, A. Diedhiou, A. Cusano, M. Barret, S. Uroz, J. Garbaye, A. Sarniguet . Mycorrhiza helper bacteria : a particular PGPR group with multiple facets (Talk).

22nd New Phytologist Symposium, (Versaille, France), Cusano A.M., Deveau A., Burlinso P., Palin B., Uroz S., Sarniguet A., Hogan D., Preston G., Frey-Klett P., Role of the bacterial Type III Secretion System (T3SS) in the interactions between bacteria and ectomycorrhizal fungi. « Effectors in Plant-Microbe interactions »(poster).

2008

GDR ComEvol « Interactions biotiques dans les communautés : théories et modèles . (Versaille, France), Frey-Klett, P., Uroz, S., Garbaye, J., Turpault, M-P., Pierrat, J-C., Calvaruso, C. and Collignon, C. Structure de la diversité taxonomique et fonctionnelle des communautés bactériennes dans le sol et la rhizosphère des arbres en forêt. (Talk)

10ème Journées d’Ecologie Fonctionnelle, (La Grande Motte, France) Frey-Klett P., Uroz S., Garbaye J., Turpault M-P., Pierrat J-C., Calvaruso C., Collignon C. Structure de la diversité taxonomique et fonctionnelle des communautés bactériennes dans le sol et la rhizosphère des arbres en forêt. (Talk).

Workshop of Geomycology, (Uppsala, Sweden). Uroz, S., Calvaruso, C., Turpault, M-P., Frey-Klett, P. Mineral weathering in forest soils :  what are the respective roles  of bacteria and fungi? (Invited Talk)

2007

Rhizosphere congress Second edition, (Montepelier, France), Uroz, S., Calvaruso, C., Turpault, M-P., Pierrat, J.C., Mustin, C. and Frey-Klett, P. Mineral weathering by mycorrhizosphere  bacteria: Linking roots to rocks (Talk)// Koele, N., Turpault, M-P., Hildebrand, E.E., Uroz, S., Frey-Klett, P. Interactions between mycorrhizal fungi and mycorrhizosphere bacteria during mineral weathering: Budget analysis and bacterial quantification. (Talk)// Dessaux, Y., Cirou, A., Uroz, S. Chapelle, E., Latour, X., and Faure, D. Quorum sensing as a target for novel biocontrol strategies directed at Pectobacterium. (Talk)// Calvaruso C., Turpault M.P., Uroz S., Leclerc E., Frey-Klett P. Does rhizospheric activity explain forest ecosystem sustainability?(poster)

The 4th meeting on multitrophic interactions in soil, (Dijon, France). Frey-Klett P., Deveau A., Tarkka M., Uroz S., Palin B., Pierrat J.-C., Martin F., Garbaye J. Interactions between bacteria and ectomycorrhizal fungi: what’s new? (Talk)

MPMI, (Sorento, Italy). Uroz S. and Heinonsalo, J. Degradation of N-acyl homoserine lactone quorum sensing signal molecules by forest root-associated fungi.  (Poster)

Workshop of metagenomics MicroEnGenIII (Lyon, France), Uroz, S., Tupault, M-P. and Frey-Klett, P. Mineral weathering by mycorrhizosphere bacteria: Linking roots to rocks. (Invited Talk)

Colloque d’Ecologie Microbienne (AFEM), (La grande Motte, France), Stéphane Uroz, Christophe Calvaruso, Marie-Pierre Turpault, Christian Mustin,  Jean-Claude Pierrat et Pascale Frey-Klett. Altération des minéraux par les bactéries mycorhizosphèriques : Une connexion entre les minéraux du sol et les racines (Talk).

XIIème International congress on molecular plant microbe interactions (Sorento, Italy), Dessaux, Y., Cirou, A., Uroz, S. Chapelle, E., Latour, X., and Faure, D. Quorum sensing as a target for novel biocontrol strategies directed at Pectobacterium. (Talk)

PhD and HDR viva

2023

– Romain JOUAN (PhD Thesis), December, 7th  ‘The fitness landscape of the soil bacteria Caballeronia insecticola and Sinorhizobium meliloti in diverse natural and synthetic environments’, Gif-sur-Yvettes, France
Mme Gabriella PESSI, Chercheuse, University of Zurich, Rapporteur
M. Stéphane UROZ, Directeur de Recherche, INRAe/Univ.de Lorraine/, Rapporteur
Mme Marta TORRES BEJAR, Chercheuse, University of Zurich, Examinatrice
M. Pascal RATET, Directeur de Recherche, CNRS – Université Paris-Saclay, Président
Mme Tania TIMTCHENKO, DR2, CNRS/Univ Paris-Saclay, Co-Dir. de thèse
M. Peter MERGAERT, DR2, CNRS/Univ Paris-Saclay, Co-Dir. de thèse

2022

– Zélia BONTEMPS (PhD Thesis), December, 13th  ‘Dynamique de la diversité microbienne dans la grotte de Lascaux’, Lyon, France
M. Patrick DI MARTINO, Professeur, Univ. de Cergy-Pontoise, Rapporteur
M. Stéphane UROZ, Directeur de Recherche, Univ.de Lorraine/INRAe, Rapporteur
Mme Emmanuelle GERARD, Ingénieure de Recherche, Univ. Paris Cité, Examinatrice
Mme Veronica RODRIGUEZ-NAVA, Professeure, Univ. Lyon 1, Examinatrice
M. Yvan MOËNNE-LOCCOZ, Professeur, Univ. Lyon 1, Directeur de thèse
Mme Mylène HUGONI, Maitre de conférence, Univ. Lyon 1, Co-Directrice de thèse

– Matthieu BARRET (HDR) – Januray, 12th – ‘Processus impliqués dans l’assemblage et la dynamique du microbiote des semences’ Angers, France
Mme Marie-Anne BARNY (Directeur de Recherche, INRAE, Dijon) Rapporteur
M. Loïc RAJJOU (Professeur AgroParisTech) Rapporteur
M. Stéphane Uroz (Directeur de Recherche, INRAE, Nancy) Rapporteur
M. Marie-Agnès JACQUES (Directrice de Recherche, INRAE Angers-Nantes) Examinatrice
M. Philippe SIMONEAU (Professeur des Universités Université d’Angers) Examinateur

2021

-Charlotte AMY – (PhD Thesis), December, 17th ‘Optimiser la nutrition azotée et phosphorée du colza pour une production durable via l’utilisation de biointrants améliorant le fonctionnement du phytobiome’
M. Alain MOLLIER, Chargé de Recherche, UMR INRAe ISPA (Rapporteur)
Mme Claude PLASSARD, Directrice de Recherche, UMR INRAe Eco&Sols (Rapporteur)
M. Stéphane UROZ, Directeur de Recherche, UMR1136 IAM (Examinateur)
Mme Marie-Pascale PRUD’HOMME, Professeure, UMR INRAe Université de
Caen (Examinateur)
M. Jean-Christophe AVICE, Professeur, UMR INRAe UMR INRAe Université de
Caen (Directeur de thèse)
Mme Karine LAVAL, Directrice de Recherche, Unité Aghyle, UniLaSalle (Directrice de thèse)

-Laura PICARD – (PhD Thesis), December, 6th ‘Génomique de l’altération des minéraux par la souche bactérienne Collimonas pratensis PMB3(1)’
Mr Lionel MOULIN, Directeur de recherche, IRD (Rapporteur)
Mme Florence WISNIEWSKI-DYE, Professeure, Univ Lyon (Rapportice)
Mr Stephane VUILLEUMIER, Professeur, Univ Strasbourg (Président)
Mr Patrick BILLARD, Maitre de conférence, Univ Lorraine (Examinateur)
Mme Marie-Pierre TURPAULT, Directrice de Recherche INRAE (Co-directrice de thèse)
Mr. Stéphane UROZ, Directeur de recherche INRAE, Univ de Lorraine (directeur de thèse)

-Claire RICONO – (PhD Thesis), November, 25th ‘Effets des pratiques agricoles biologiques en contexte bocager sur le microbiote du blé et ses fonctions associées’
Mr. Stéphane UROZ, Directeur de recherche, Univ de Lorraine (Rapporteur)
Mme Mélanie ROY, Maître de conférences, Univ Toulouse (Rapportice)
Hélène FREVILLE Chercheur, INRAE (Examinatrice)
Edith LE CADRE Professeure, Agrocampus Ouest (Présidente)
Philippe VANDENKOORNHUYSE, Professeur, Univ de Rennes (Directreur de thèse)
Cendrine MONY, Maître de conférences, Univ Rennes (Co-Directrice de thèse)

2020

– Rosa PADILLA – (PhD Thesis) June, 29th ‘Spécificités écologiques d’Agrobacterium fabrum :rôle des gènes spécifiques dans l’interaction avec la plante’ Lyon, France (directed by Isabelle KERZAON and Xavier NESME)
Mme Geneviève CHIAPUSIO, Maître de Conférences, Université de Savoie Mont-Blanc (Rapportrice)
Mr. Ali RHOUMA , Professeur, PRIMA Foundation (Rapporteur)
Mme Lisa SANCHEZ , Ingénieur de Recherche, Université de Reims (Rapportrice)
Mr Gilles COMTE, Professeur, Université Lyon 1 (Président du jury)
Mr Stephane UROZ, Directeur de Recherche, Université de Lorraine (Examinateur)
Mme Florence WISNIEWSKI-DYE , Professeure, Université Lyon 1 (Examinatrice)
Mme Isabelle KERZAON, Ma.tre de Conférences, Université Lyon 1 (Directrice de thèse)
Mr Xavier NESME, Ingénieur de Recherche, Université Lyon 1 (Co-Directrice de thèse)

2019

– Tania FORT – (PhD Thesis) December, 10th ‘Fonctions, transmission et émission du microbiote de la canopée’ – Bordeaux, France (directed by C. Vacher)
Mme. Anne-Marie DELORT, Institut de Chimie de Clermont-Ferrand, Rapporteuse
M. Stéphane Uroz, INRA Nancy, Rapporteur
Mme. Patricia Luis, Université de Lyon 1, Rapporteuse
Mme. Annabel Porté, INRA Bordeaux, Présidente
Mme. Corinne Vacher, INRA Bordeaux Directrice de thèse

– Adriana M. GARCIA LEMOS – (PhD Thesis) November, 19th ‘Belowground microbial interactions in Abies nordmanniana : The hidden world underneaththe Christmas tree’. – Copenhague, Danemark (directed by Dr. Ole Nybroe)
Mme Birgit JENSEN, University of Copenhaguen, Présidente de jury
M. Jacob BAELUM, Plant Health at Chr. Hansen, Danemark, Rapporteur interne
M. Stéphane UROZ, INRA, Champenoux, France, Rapporteur externe

– Florian LEMMEL – (PhD Thesis) January, 14th ‘Diversités taxonomique et fonctionnelle des communautés microbiennes en lien avec le cycle du carbone dans un gradient de sols multi-contaminés’ – Vandoeuvre-Les-Nancy, France (dirigé par Dr. A Cébron)
M. Josselin BODILIS, Université de Rouen, France, Rapporteur
M. Naoise NUNAN, CNRS, Paris, France, Rapporteur
Mme. Françoise BINET, CNRS, Renne, France, Examinatrice
M. Stéphane UROZ, INRA, Champenoux, France, Président
Mme. Aurélie CEBRON, CNRS, Vandoeuvre-Les-Nancy, France, Directrice de thèse
Mme. Florence MAUNOURY-DANGER, Univ.de Lorraine, Metz, France, Directrice de thèse
Mme. Corine LEYVAL, CNRS, Vandoeuvre-Les-Nancy, France, Co-Directrice de thèse

2018

– Anne TOURNEROCHE- (PhD Thesis) 29th of November ‘Bacterial-fungal interactions within the endo microbiota of brown algae: implication of quorum sensing in the metabolic crosstalk’ – MUSEUM NATIONAL D’HISTOIRE NATURELLE, Paris, France
M. Gérald CULIOLI, Université de Toulon, France Rapporteur
M. Florian WEINBERGER, Helmholtz-Zentrum für Ozeanforschung Kiel / GEOMAR, Kiel, Germany, Rapporteur
Mme Catherine LEBLANC, CNRS, Roscoff, France Examinateur
M. Stéphane UROZ, INRA, Nancy, France Examinateur
Mme Soizic PRADO, Museum National d’Histoire Naturelle, Paris, France, Directeur de thèse
M. Raphael LAMI, Sorbonne Université, banyuls, France, Directeur de thèse

– Andréa CHANE- (PhD Thesis) 10th of July ‘Regulation, expression in situ et biostimulation de l’activité quorum-quenching d’un agent de biocontrôle : Rhodococcus erythropolis’ – Evreux, France
Mme Sylvie REVERCHON, INSA, Lyon, France Rapporteur
M. Stéphane UROZ, INRA, Nancy, France Rapporteur
M. Philippe LEMANCEAU, INRA, Dijon, France Examinateur
Mme Laura EGEL FN3PT/RD3PT, Arras, Examinateur
M. Xavier LATOUR, Université de Rouen, Evreux, France, Directeur de thèse

– Ilonka C. ENGELHARDT- (PhD Thesis) 29th of June ‘Impact of precipitation patterns on the plant-microbial response to rewetting’ – Dijon, France
M. Graeme NICOL, CNRS, Lyon, France Rapporteur
M. Johannes ROUSK, Université de Lund, Lund, Sweden Rapporteur
M. David WENDEHENNE, Université de Bourgogne, Dijon, France Examinateur
M. Stéphane UROZ, INRA, Nancy, France Examinateur
M. Romain BARNARD, INRA, Dijon, France Directeur de thèse

– Patricia LUIS (HDR) – 16th of May- ‘Impact du milieu et des changements environnementaux sur la diversité fonctionnelle des microorganismes eucaryotes’ Villeurbanne, France
M. Pierre-Alain Maron (Directeur de Recherche, INRA, Dijon) Rapporteur
M. Eric Record (Directeur de Recherche, INRA, Aix-Marseille) Rapporteur
M. Stéphane Uroz (Directeur de Recherche, INRA, Nancy) Rapporteur
M. Christophe Bruel (Professeur, Université Claude Bernard, Lyon1) Examinateur
Mme Martina Peter (Chercheur, WSL, Suisse) Examinateur
Mme Corinne Vacher (Directrice de Recherche, INRA, Bordeaux) Examinateur

– Guillaume SCHWOB -(PhD Thesis) 19th of March ‘Rôle écologique de la sporulation in-planta dans les symbioses actinorhiziennes : Cas de la symbiose Alnus – Frankia’- Villeurbanne, France
M. UROZ Stéphane Directeur de Recherche, UL/INRA Nancy, Rapporteur
M. LATA Jean-Christophe Maître de Conférences, Sorbonne Université, Rapporteur
M. CLEMENT Jean-Christophe, Professeur des Universités, Université de Savoie, Examinateur
Mme. PIOLA Florence, Maître de Conférences, Université de Lyon, Examinatrice
Mme. BROCHIER-ARMANET Céline Professeure des Universités, Université de Lyon Examinatrice
Mme. FERNANDEZ Maria, Professeure des Universités, Université de Lyon Directrice
Mme. HERRERA-BELAROUSSI Aude, Maître de Conférences, Université de Lyon Co-directrice

2017

–Océane NICOLITCH (PhD Thesis) – 21th of December’ Impact de la Disponibilité en Nutriments Inorganiques sur la Structure Fonctionnelle et Taxonomique des Communautés Bactériennes des Sols Forestiers’, Champenoux, France
– Pr. Pierre LEBLOND, Professeur, Université de Lorraine (Président)
– Dr. Claude PLASSARD, Directeur de Recherche INRA Montpellier (Rapporteur)
– Dr. Christophe MOUGEL, Directeur de Recherche INRA Rennes (Rapporteur)
– Dr. Claire PRIGENT-COMBARET, Directeur de Recherche CNRS Lyon (Examinateur)
– Dr. Philippe OGER, Directeur de Recherche CNRS Lyon (Examinateur)
– Dr. Marie-Pierre TURPAULT, Directeur de Recherche INRA Nancy
– Dr.  Stéphane UROZ, Directeur de Recherche, INRA Nancy

–Bastien WILD (PhD thesis) – 22th of february- ‘Changements microstructuraux et diversité microbienne associés à l’altération des silicates : influence sur les cinétiques de dissolution du laboratoire au terrain’ Strasbourg, France
– Dr. Gwenaël IMFELD CR CNRS, Université de Strasbourg
– Dr. Karim Benzerara DR CNRS, Univ.Pierre et Marie Curie, Paris (Rapporteur)
– Dr. Stéphane Uroz DR INRA, Université de Lorraine (Rapporteur)
– Dr. Damien Daval CR CNRS, Université de Strasbourg
– Dr. Alejandro Fernandez-Martinez, CR CNRS, Université Grenoble Alpes
– Dr. Stéphane Gin, DR CEA, Commissariat à l’énergie atomique, Marcoule

2013

– Stephen SUMMERS (PhD Thesis) 2th of July ‘The bacterial ecology and function from a sub-surface critical zone’. Open university, Uk
M. J Colin Murrell (external examiner)
M. Toni Gladding (internal examiner)
M. Stephane Uroz (external examiner)

– Clémentine LEPINAY (PhD Thesis) 15th of May ‘Etude des interactions plantes microbes et microbes-microbes au sein de la rhizosphère, sous un aspect coûts-bénéfices, dans un contexte de variation environnementale’. Dijon, France
M. Jean-Claude Cleyet-Marel, INRA, Montpelier, Rapporteur
M. Christophe Robin, INRA, Nancy, Rapporteur.
M. Dirk Redecker,INRA, Dijon, Examinateur
M. Stéphane Uroz, INRA, Nancy, Examinateur
M. Christophe MOUGEL, INRA, Dijon, Directeur de thèse

2012

–Cendrella LEPLEUX (PhD thesis) 3th of December ‘ Alteration bactérienne des mineraux dans les écosystemes forestiers pauvres en nutriments: analyse des communautes bactériennes et identification des mécanismes impliqués’, Nancy, France
Pr. Pierre Leblond Professeur Université de Lorraine de Nancy, Président du jury
Dr. Christophe Mougel Directeur de recherche INRA de Dijon, Rapporteur
Dr. Alain Sarniguet Directeur de recherche INRA de Rennes, Rapporteur
Dr. Pascal Simonet Directeur de recherche CNRS de Lyon, Examinateur
Pr. Stéphane Vuilleumier, Professeur à l’Université de Strasbourg, Examinateur
Dr. Marie-Pierre Turpault, Directeur de recherche INRA de Nancy, Examinateur
Dr. Pascale Frey-Klett, Directeur de recherche INRA de Nancy, Directrice de thèse
Dr. Stéphane Uroz, Chargé de recherche INRA de Nancy, Co-directeur de thèse
Dr. Laura C. Kelly, Chercheur Post-doctoral INRA de Nancy, Chercheur invité

2011

–Christelle COLLIGNON (PhD thesis) 8th of November ‘Evolution saisonnière de l’altération des minéraux dans un sol forestier acide : couplage d’approches minéralogiques, géochimiques et microbiologiques dans la rhizosphère et le sol global’, Nancy, France
– Pr. Guillaume ECHEVARRIA, Professeur, INPL / INRA ENSAIA, Président
– Dr. Sophie CORNU, Directeur de recherche INRA Aix-en-Provence , Rapporteur
– Dr. Philippe HINSINGER, Directeur de recherche INRA de Montpellier, Rapporteur
– Dr. Alain SARNIGUET, Directeur de recherche INRA de Rennes, Examinateur
– Dr. Christophe CALVARUSO, Chercheur post-doctorant, invité
– Dr. Marie-Pierre TURPAULT, Directeur de recherche INRA de Nancy, Examinateur
– Dr. Stéphane UROZ, Chargé de recherche INRA de Nancy, Co-directeur de thèse

2010

– Clarisse BALLAND BOLOU BI (PhD Thesis) 15th of April ‘Caractérisation expérimentale des relations entre les bactéries des sols, les phyllosilicates et les solutions : Modélisation et Rôle des Paramètres Environnementaux’ Nancy, France
– Dr. Guilhem BOURRIE, Directeur de Recherche, INRA Rapporteur
– Dr. Oleg POKROVSKY, Chargé de Recherche HDR, CNRS Rapporteur
– Dr. Sylvie DOUSSET, Professeur, Université Henri Poincaré Président
– Dr. Joseph DUFEY, Professeur, Université catholique de Louvain-la-Neuve Examinateur
– Dr. Frédéric GERARD, Chargé de Recherche HDR, INRA Examinateur
– Dr. Stéphane UROZ, Chargé de Recherche, INRA Examinateur
– Dr. Corinne LEYVAL, Directeur de Recherche, CNRS Directrice de thèse
– Dr. Anne POSZWA, Maître de Conférences, Université Henri Poincaré Co-directrice de thèse

Master and L3 jury

Lucile Hubert (Licence 3; CMI UNiv Lorraine) UNDERSTANDING THE CHANGES THAT OCCUR IN THE SOIL WHEN B. AMBIFARIA IS APPLIED AS A SEED COAT BIOPESTICIDE. Internship mentor : Prof. Eshwar Mahenthiraligam