Last update 20/02/2015
Research Director (DR2)
- e-mail: firstname.lastname@example.org
- Phone: +33 (0)3 83 39 40 81
- Fax: +33 (0)3 83 39 40 69
Bio: I received my PhD in Microbial Ecology from University of Paris XI, Orsay in 2004 with Yves DESSAUX and Phil OGER as my advisers. My research was focused on the stability of the quorum sensing signal molecules, especially the N-acyl homoserine lactone class based on the hypothesis that these molecules need to be degraded to act as a signal, possibly by bacteria naturally occuring in the soil. To verify this hypothesis, I have combined classical microbiology, molecular tools, genetic, biochemistry and chemistry. I performed my PhD in three places : Interactions Plant Microorganisms at Institut of Plant Sciences (ISV, Gif-sur-Yvette ; adviser : Yves Dessaux) ; Lab of “Sciences de la Terre” at Normal School (ENS, Lyon ; adviser : Phil Oger) and Institute of Infections and Immunity at 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).
In october 2004, I was hired as Junior Research associate (CR2) in the EFPA department of the National Institute of Agronomic Reasearch (INRA), at the interface between two labs, “Tree microbes interactions” (IAM) and the “Biogeochemical cycles in forest ecosystems” (BEF). I am member of th Ecogenomic and mineral weathering teams. 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 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.
My main research associates are Marie-Pierre TURPAULT (INRA-BeF), Marc BUEE (INRA-IaM), Francis MARTIN (INRA-IaM), and Emmanuelle MORIN (INRA-IaM). One Post-doctoral colleague Yannick COLIN recently joined the group to work on the microbial diversity in forest soils. The group was reinforced by one PhD student: Océane NICOLITCH (relation between soil fertility and the bacterial communities; Co-dir. with M-P. TURPAULT).
Miss Marta Torres Béjar (Short stay to work on metagenomics of QS and Quorum quenching; Univ Granada, Spain)
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 (Seasonal effect on mineral weathering ; 2007-2011 dir. J.Ranger, M-P. Turpault and P. Frey-Klett) PhD defense in 2011.
Dr. Panos Ioannidis (Bioinformatic analyses of complex metagenomes; 2010-2011, F. Martin, M. Buée).
My current projects, integrated in a more global questioning related to forest ecosystem functioning and sustainability, are:
- Forest soil as a reservoir of microbial biodiversity (specific diversity by monogenic metagenomics, global approach by massive metagenomics and functional metagenomics)
- Forest soil as a reservoir of mineral weathering bacteria (functional diversity, genetics, genomics link to biogeochemistry and mineralogy)
- Impact of nutrient availability / soil type /tree species on microbial communities
- Impact of the microorganisms on the nutrient cycle (geomicrobiology)
- Interactions microbe-microbe (quorum sensing signals)
Multidisciplinary project granted by The Labex ARBRE (2014-2017)
Young scientist ANR Grant ‘ Bactoweather’ (2012-2015)
INRA Metaprogramme Metagenomics (MeM) ‘ MetaScreen’ (2012-2013)
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)
-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 :
Project 1: Forest soil as a reservoir of microbial biodiversity (specific diversity and 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 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), for massive metagenomics (Ioannidis et al., 2011) or construction of fosmid libraries.
Project 2: 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) and in little Britany (Fougères).
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) 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).
We also considered soil chronosequences and soil successions which vary in their nutrient availability characteristics. One of our analysis was developed on ecological staircase of Mendocino. RThis 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.
e) Genomic and genetic characterization of effective mineral weathering bacteria
To investigate molecular mechanisms used by heterotrophic bacteria to weather bacteria, we combined a suite of genomic and genetic tools (genome, transcriptome, mutant libraries) mainly on two model bacterial strains: Burkholderia glathei PML1(12) and Collimonas sp. PMB3(1).
Project 3: 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.
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. Sci Rep. 2017 Aug 29;7(1):9604. doi: 10.1038/s41598-017-07639-1.
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
54 – Uroz, S.* and Oger, P. Caballeronia mineralivorans sp. nov., isolated from oak-Scleroderma citrinum mycorrhizosphere. Systematic and Applied Microbiology. In press.
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.
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. In press (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).
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)0>