TEAM 2 : MICROBIAL ECOLOGY - FLUXES, INTERACTIONS and FUNCTIONNAL DIVERSITY

Monique Acquaviva (IE CNRS)	Badr Al Ali (PhD student)	Jean-Claude Bertrand (Prof.)	Patricia Bonin (DR2; Coordinator team 2)	Philippe Cuny (Assistant Prof.)	Michel Denis (DR1 CNRS)
Marc Garel (IE CNRS)	Gérald Grégori (CR2 CNRS)	Sophie Guasco (AJTR CNRS)	Cédric JAVANAUD (PhD student)	Dominique Lefèvre (CR1 CNRS)	Danielle Marty (CR1 CNRS)
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Lounis Mebarek (PhD student)	Valérie Michotey (Assistant Prof.)	Agathe Talarmin (Doctorante)	Christian Tamburini (CR1 CNRS)	Anne Robert (PhD student)	Melilotus Thyssen (Post-doc)
France van Wambeke (DR2 CNRS)	Yosmina Tapilatu (PhD student)

Fields of study:

Our works aim for a better understanding of the microorganisms role in the organic matter transformation and mineralization processes. The global objective is the quantification of microbial processes during the organic matter biodegradation and the study of the microbial community responsible of this biodegradation.
This objective requires a integrative approach, from the ecosystem to the cellular and even molecular levels.

Our works are particularly focused on:
- ectoenzymatic hydrolysis of organic biopolymers (aminopeptidase, phosphatase, lipase activities…),
- bacterial production fluxes,
- nutrients biological fluxes resulting from mineralization processes and bacterial production fluxes O2 and CO2 (heterotrophic respiration), N2O (nitrogen cycle), CH4 (methanogenesis),
- biodegradation efficiency related to the distribution of the bacterial production fluxes, bacterial biomass and mineralization,
- study of the processes,
- microbial population diversity,
- proportion of active bacteria, able or not to grow,
- proportion of microbial population able to perform the studied function,
- bacterial species in place in term of taxonomy, relative abundance and function .

Hence, several levels of investigation are considered. Our particular interests are:

-modification of structural parameters of the bacterial, phytoplanctonic and zooplanctonic compartments,
-physiological status (viability, metabolic activities,..) of the individual inside the the community,
- dynamics and specific structure of the bacterial community,
-relationship between the structure and function of the microbial communities involved in the organic matter degradation.

Several activities can be distinguished into the team 2: microbiology, analysis and molecular biology:

Projects :

- PROOF-SINPAS: SINking PArticle Simulation (coord.: A. Bianchi et C. Tamburini)
- PROOF-PECHE (Production et Exportation du carbone : Contrôle par les organismes HEterotrophes a petite echelle de temps) coord.: M. Goutx et V. Andersen.
- PROOF-UVECO: Mediterranean Sea. Induction of microbial communities responses and dissolved organic matter transformations by UltraViolet radiation in marine ECOsytems (Coord.: R. Sempéré et F. Joux).
- PROOF-BIOSOPE (BIogeochemistry and Optics SOuth Pacific Experiment)
- PROOF-KEOPS (Kerguelen : Etude comparée de l’Océan et du Plateau en Surface et sub-surface.) Coord.: S. Blain.
- PROOF-MELISSA (MEditerranée LImitationS SAisonnières) Coord.: C. Migon.
- CIMOM (Caractérisation individuelle des microorganismes marins) Coord.: Michel Denis
- COST denitrification : network of european people working on denitrification  process
- CYMIS (Flux cytometry in situ)
- MATBIOPOL: Coord.: Pierre Caumette Rôle des tapis microbien dans les processus de biorémédiation
- PROOF-DOREMI (DOublement de la pression partielle en CO2 sur le REseau MIcroplanctonique). Coord.:Michel Denis

Selected ublications (from 2001) :

- Aries E, Doumenq P, Artaud J, Acquaviva M., Bertrand J.C. Effects of petroleum hydrocarbons on the phospholipid fatty acid composition of a consortium composed of marine hydrocarbon-degrading bacteria Organis Geochemistry, sous presse (13p).

- Aristegui J., Denis M., Almunia J. and Montero M.F. Water-column remineralisation in the Indian sector of the Southern Ocean during early spring. Deep-Sea Res. II (in press)
- Bonin P., Rontani J-F. et Bordenave L. 2001 Metabolic differences between attached and free-living marine bacteria : inadequacy of liquid cultures for describing in situ bacterial activity. FEMS Microbiol. Lett. 194 : 111-119.
- Bonin P., Tamburini C. & Michotey V. 2001. Determination of the bacterial processes wich sources of Nitrous oxide production in marine samples. Acceptée dans Water Research.

- Christaki U., Giannakourou A., Van Wambeke F, Grégori G. (2001) Nanoflagellate predation on auto- and heterotrophic picoplankton in the oligotrophic Mediterranean Sea. Journal of Plankton research, 23: 1297-1310
- Dadoui., Lamy F., Rabouille C., Ruiz Pino D., AndersenV., Bianchi M., Garcon V. (2001) An intergated biological pump model from the euphotic zone to the sediment: a 1-D application in the Northeast tropical Atlantic. Deep-Sea Research II 48: 2345-2381.
- Grégori G., Citterio S., Ghiani A., Labra M., Sgorbati S., Brown S. & Denis M. 2001. Resolution of viable and membrane-compromised bacteria in freshwater and marine waters based on analytical flow cytometry and nucleic acid double staining. Appl. Environ. Microbiol. 67: 4662-4670.

- Marty D, Bonin P, Michotey V, Bianchi M. (2001) Bacterial biogas production in coastal systems affected by freshwater inputs. Continental Shelf Research, 21:2105-2115
- Tamburini, C., Garcin, J. Ragot, M., Bianchi A. (2002). Biopolymer hydrolysis and bacterial production under ambient hydrostatic pressure through a 2000 m water column in the NW Mediterranean. Deep-Sea Res. II, 49: 2109-2123.

- Tamburini C., Garcin J. & Bianchi A. (2003). Role of deep-sea bacteria in organic matter mineralization and adaptation to hydrostatic pressure conditions in the NW Mediterranean Sea. Aquatic Microbial Ecology, 32 (3): 209-218.

- Van Wambeke F, Christaki U, Giannakourou A, Moutin T, Souvemerzoglou K. (2002) Longitudinal and vertical trends of bacterial limitation by phosphorus and carbon in the Mediterranean Sea. Microbial Ecology, 43:119-133.
- Van Wambeke F., Heussner, H., Diaz, F., Raimbault, P., Conan P. (2002) Small-scale variability in the coupling/uncoupling of bacteria, phytoplankton and organic carbon fluxes along the continental margin of the Gulf of Lions, Northwestern Mediterranean Sea. Journal of Marine Systems 33-34:411-429.
- Karayanni H, Christaki U, Van Wambeke F, Dalby A, 2004. Evaluation of double formalin-Lugol’s fixation in assessing number and biomasses of ciliates: an example of estimations at mesoscale in NE Atlantic. Journal of Microbiological Methods, 56:349-358.
- Christaki U, Van Wambeke F, Bianchi M, 2004. Heterotrophic bacterial growth and substrate utilization in the oligotrophic Eastern Mediterranean (Aegean Sea). Mediterranean Marine Science, 4(1):23-39.
- Van Wambeke F, Lefèvre D, Prieur L, Sempéré R, Bianchi M, Oubelkheir K, Bruyant F, 2004. Distribution of microbial biomass, production, respiration, dissolved organic carbon and factors controlling bacterial production across a geostrophic front (Almeria-Oran, SW Mediterranean Sea). Marine Ecology Progress Series, 269: 1-15

Collaborations :

French collaboration
Laboratoire d’Ecologie Moléculaire-Microbiologie, Université de Pau et des pays de l’Adour , Studies of hydrocarbon bioremediation by microbial maps, Pierre Caumette

OSU Villefranche sur Mer, Attached bacteria on coccolithophoridae and carbonates dissolution sinking throughout the water column, Jean-Pierre Gattuso

Laboratoire de Chimie Bactérienne, Marseille. Vincent Méjean 
Laboratoire d’Ecologie Microbienne Faculté des Sciences de St Jérome Marseille U3. Technical formation in molecular biology (DGGE), Sylvie Neble 

Laboratoire de Microbiologie, IMEP, Université d’Aix-Marseille III, Anaerobic biodegradation of hydrocarbon substrats, Agnès Hirschler 

International collaboration
Germany
Biotanical institute . University of Cologne. Bothe Hermann Allemagne Member

England
University of Dundee (UK) Department of biological Science, Rodney Herbert: Study of maps bacteria degrading hydrocarbons

Australy
CSIRO (Brian Griffiths) et University of Tasmania (Clive Crossley et Peter Sedwick) Hobart: data analysis of ANTARES 4 (1999) et SAZ V6 (1998) cruises

Canada
ISMER Rimouski, Pr. Serge Demers : PhD co-supervisor (Christophe Vasseur)

Chili
Laboratoire PROFC Conception (Laura Farias ) : FONDECYT project

Spain
Institut de Ciences del Mar, CSIC, Barcelona (Spain). (Dolors Vaqué, Pep Gasol) : Spatial and temporal variations of seawater microbes in NW Mediterranean Sea
Universidade de Santiago de Compostela Dr. Cepeda Catalina : competitive and quantitative PCR

Denmark
Marine Biological Laboratory , University of Copenhagen, Andrea Wieland : biogeochemical fluxes into microbial maps of Camargue (France)

Israel
Mose shilo Minerva centre for marine Biogeochemistry, the Hebrew University of Jerusalem, Yehuda Cohen : Microbial diversity of denitrication in microbial maps mesocosm

Italy
Universita di Milano Bicocca, Pr Sergio Sgorbati : bacterial viability study 
Universita di Roma La Sapienza, Pr Alfredo Colosimo
CNR Messina , Dr. Laura Giuliano : Deep Hypersaline Anoxic Basins microbiology (BioDeep project), microbial bioluminescence.

The Netherlands 

NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, Texel, Gerhard Herndl. NWO project: ARCHIMEDES (Activity, Rates, Carbon use and HIgh-pressure Microbial Ecology of the DEep Sea).

Tunisy
INSTM, Tunis, Tunisie
Faculté des Sciences de Sfax, Pr. Sami Maalej : étude de la survie de Aeromonas hydrophila en milieu marin

U. S. A.
University of Wyoming, Laramie, Paul Johnson : Pathogenic bacteria detection by flux cytometry.
University of Delaware, Lewes DE (USA), David Kirchman : Microbial diversity, FISH, MAR-FISH methods, sinking particles simulation (SINPAS project)
Stony Brook University, NY (USA), Cindy Lee : Particle fluxes in NW Mediterranean Sea (MedFlux)