Curriculum Vitae – Hélène Agogué - LIENSs

Curriculum Vitae – Hélène Agogué
University Studies and Diplomas
1999-2001
Master’s degree in Microbial Ecology, University of Lyon I
“Activity and diversity of bacterial communities in aquatic environment”
Scientific supervisors: Prof. Philippe Lebaron and Prof. Pierre Servais
Oceanographic Institute of Banyuls-sur-Mer
1998-1999
Degree in Biology of populations and ecosystems, University of Brest (IUEM: European
Institute for Marine Studies) Speciality: marine ecosystems
1997-1998
Bachelor’s degree in Biology of populations, University of Brest (UBO: University of
Western Brittany)
1995-1997
Diploma of “Sciences de la vie” received after two years University of Paris 7
Dissertation
2001-2004
PhD degree in Microbial Ecology, University of Lyon I
“Diversity of bacteria of the sea surface microlayer: specificity, adaptation and resistance to
solar radiation” Scientific supervisor : Prof. Philippe LEBARON
Oceanographic Institute of Banyuls-sur-Mer
This PhD thesis was performed within the EU project AIRWIN: “Structure and role of
biological communities involved in the transport and transformation of persistent pollutants at
the marine AIR-Water Interface” (contract EVK3-CT2000-0030).
Postdoctoral Experience
March 2009-present
Post-doctoral research at LIENSs, UMR 6250, CNRS, University of la Rochelle (University
Fellowship) “Role of archaeal and bacterial communities in the nitrogen cycle in the mudflat
of the Perthuis Charentais (France)”
Post-doctoral supervisor: Dr. Christine Dupuy
May 2006-December 2008
Post-doctoral research at the Netherlands Institute for Sea Research, Dept. Biological
Oceanography (Marie Curie Intra European Fellowships, FP6-2004-Mobility): “Prokaryotic
Activity and Phylogeny in Oceanic systems”
Post-doctoral supervisor: Prof Gerhard Herndl
Oct 2004-May 2006
Part-time post-doctoral research at the University of Le Havre, France, Dep. Of Aquatic

Ecotoxicology (temporary teaching and research associate professor).
"Expression and activity of multixenobiotic resistance system in the copepod Eurytemora
affinis"
Post-doctoral supervisors: Prof. François Leboulenger and Dr. Christophe Minier
Teaching
2004-2006
Part-time teacher at the University of Le Havre, sciences and technology section
temporary teaching and research associate professor)
Courses on master program (genetic toxicology, technological risks, microbiology, microbial
ecology, and microbial biotechnology); courses on licence program (ecology and pollution)
April 2000 and 2002
Teaching assistant for the aquatic microbial ecology course (Master), molecular techniques:
Oceanographic Institute of Banyuls-sur-Mer (University of Paris 6).
Jan 2001
Teaching assistant for biological oceanography course (Postgraduate degree), molecular
techniques: Oceanographic Institute of Banyuls-sur-Mer (University of Paris 6)
Research Experience
Jul 1999-Aug 1999
Training course at IFREMER at Brest (French Research Institute for Exploitation of the Sea)
"Bacterial population changes during vacuum storage of refrigerated smoked salmon:
molecular approach to identify spoilage organisms" Scientific supervisors: Prof. Georges
Barbier and Dr. Muriel Bourrain
Jun 1998-Sep 1998
Training course at the Oceanographic Institute of Roscoff “Bacterial diversity of
hydrothermal vents samples by phylogeny methods” Scientific supervisors: Prof. Daniel
Prieur and Dr. Valerie Cilia
Methods
• Microbiology (traditional methods): cellular culture, isolation, collection.
• Molecular techniques: Nucleic acid extraction, PCR, RT-PCR, cloning, Denaturing
Gradient Gel Electrophoresis (DGGE), Single Strand Conformation Polymorphism
(SSCP), Restriction Fragment Length Polymorphism (RFLP)
• Immunochemical studies: western blot, slot blot
• Cellular techniques: fluorescent physiological state markers (CTC...), bacterial
enumeration by different techniques (Acridine Orange, DAPI, cytometry),
fluorescence imaging (laser scanning confocal microscopy)
• Analytical tools: Flow cytometry and cells sorting analysis (FacsCalibur, Becton
Dickinson), epifluorescence microscopy and image analysis, phylogeny analysis
(Blast analysis, Bioedit, Phylowin, Clustal and NjPlot software)

Publications
2009 De Corte D., T. Yokokawa, M. M. Varela, H. Agogué and G. J. Herndl. 2009. Spatial
distribution of Bacteria and Archaea and amoA gene copy numbers throughout the water
column of the Eastern Mediterranean Sea. The ISME Journal. 3:147-158.
(Abstract:http://www.nature.com/ismej/journal/ vaop/ncurrent/abs/ismej200894a.html)
2008 H. Agogué, M. Brink, J. Dinasquet and G. J. Herndl. Major gradients in putitatively
nitrifying and non-nitrifying Archaea in the deep North Atlantic. Nature. 456:788-791.
(Abstract: http://www.nature.com/nature/journal/v456/n7223/abs/nature07535.html)
2008 Herndl G. J., H. Agogué, F. Baltar, T. Reinthaler, E. Sintes and M. M. Varela.
Regulation of aquatic microbial processes: the ‘microbial loop’ of the sunlit surface waters
and the dark ocean dissected. Contribution to the SAME-10 Special Issue. Aquatic Microbial
Ecology. 53:69-81. (PDF: http://www.int-res.com/articles/ame_oa/a053p059.pdf)
2008 Urios L., H. Agogué, L. Intertaglia, F. Lesongeur and P. Lebaron. Melitea salexigens
gen. nov., sp. nov., a member of the class Gammaproteobacteria from the Mediterranean Sea.
International Journal of Systematic and Evolutionary Microbiology. 58:2479-2483.
(Abstract: http://ijs.sgmjournals.org/cgi/content/abstract/58/11/2479)
2006 Urios L., H. Agogué, F. Lesongeur, E. Stackbrandt and P. Lebaron. Balneola vulgaris
gen. nov., a new member of the Cytophaga-Flavobacterium-Bacteroides phylum from the
Mediterranean Sea in Banyuls sur Mer, France. International Journal of Systematic and
Evolutionary Microbiology. 56:1883-1887.
(Abstract: http://ijs.sgmjournals.org/cgi/content/abstract/56/8/1883)
2006 Joux F., H. Agogué, I. Obernosterer, C. Dupuy, T. Reinthaler, G. J. Herndl and P.
Lebaron. Microbial community structure in the sea surface microlayer at two contrasting
coastal sites in the Northwestern Mediterranean Sea. Aquatic Microbial Ecology. 42:91-104.
(Abstract: http://www.int-res.com/abstracts/ame/v42/n1/p91-104)
2005 Agogué H., E.O. Casamayor, M. Bourrain, I. Obernosterer, F. Joux, G. J. Herndl and
P. Lebaron. A survey on bacteria inhabiting the sea surface microlayer of coastal ecosystems.
FEMS Microbial Ecology. 54: 269-280. (Abstract: doi:10.1016/j.femsec.2005.04.002)
2005 Agogué H., F. Joux, I. Obernosterer and P. Lebaron. Resistance of marine
bacterioneuston to solar radiation. Applied and Environmental Microbiology. 71(9):5282-
5289. (PDF: http://aem.asm .org/cgi/reprint/71/9/5282)
2004 Agogué H., E. O. Casamayor, F. Joux, I. Obernosterer, C. Dupuy, F. Lantoine, P.
Catala, M. G. Weinbauer, T. Rheinthaler, G. J. Herndl and P. Lebaron. Comparison of
samplers for the biological characterization of the sea surface microlayer. Limnology and
Oceanography: Methods. 2: 213-225.
(PDF: http://www.aslo.org/lomethods/free/2004/0213.pdf)
2001 Servais, P., H. Agogué, C. Courties, F. Joux and P. Lebaron. Are the actively respiring
cells (CTC+) those responsible for bacterial production in aquatic environments? FEMS
Microbiology Ecology.35:171-179. (Abstract: doi:10.1016/S0168-6496(01)00089-7)

2001 Lebaron, P., P. Servais, H. Agogué, C. Courties and F. Joux. Does the high nucleic
acid content of individual bacterial cells allow us to discriminate between active cells and
inactive cells in aquatic systems? Applied and Environmental Microbiology. 67:1775-
1782. (PDF: http://aem.asm.org/cgi/reprint/67/4/1775)
Meetings and Workshops
International Census of Marine Microbes 454 Users Spring Meeting, Woods Hole, USA,
April 2009. “Bacterial assemblages composition in the North Atlantic Ocean revealed by
massively parallel tag sequencing”. H. Agogué, D. Lamy, P. R. Neal, M. L. Sogin and G. J.
Herndl. (Invited talk)
ASLO (American Society of Limnology and Oceanography) meeting, Nice, France, Jan
2009. "Bacterial and archaeal dynamics in function and phylogeny in the North Atlantic deep
waters: Linking large-scale circulation patterns to microbial oceanography". H. Agogué, M.
Brink, J. Dinasquet and G. J. Herndl (Talk)
ISME 12 (12th International Symposium on Microbial Ecology), Cairns, Australie, Aug
2008. "Pronounced latitudinal and vertical gradients in putitatively nitrifying versus nonnitrifying
Archaea in the dark realm of the North Atlantic". H. Agogué, M. Brink and G. J.
Herndl (Poster)
EurOceans workshop (Shedding light on the dark ocean: Breaking paradigms in
biogeochemistry, diversity and plankton metabolism in the meso- and bathypelagic realm)
Noordwijkerhout, The Netherlands, Feb 2008. "Are there fundamental differences in the
diversity patterns (richness, evenness) between surface and deep ocean ?". H. Agogué and G.
J. Herndl (Talk)
SAME 10 (10th Symposium on Aquatic Microbial Ecology), Faro, Portugal, Sept 2007
"Distinct archaeaplankton assemblages characterize the meso- and bathypelagic zones of the
eastern North Atlantic basin". H. Agogué, M. Brink, W-D. Lienhart and G. J. Herndl (Poster)
2nd CeBiTec Symposium. The Future of Genome Research in the Light of Ultrafast
Sequencing Technologies. Bielefeld, Germany, July 2007
BAGECO 9 (9th symposium on Bacterial Genetics and Ecology), Wernigerode,
Germany, June 2007 "Bacterial and archaeal diversity in the meso- and bathypelagic waters
of the eastern North Atlantic basin". H. Agogué, M. Brink, J-M. Arrieta and G. J. Herndl
(Poster)
Discussion meeting on “Sequencing the seas – accessing unknown microbial function”
(sponsored by Natural Environment Research Council and Natural Science Foundation),
London, UK
EGU (European Geosciences Union) General Assembly, Vienna, Austria, Apr 2007
"Bacterial and archaeal diversity in the meso- and bathypelagic waters of the eastern North
Atlantic basin". H. Agogué, M. Brink, J-M. Arrieta and G. J. Herndl (Poster)

38th CIESM (Mediterranean Science Commission) congress, Istanbul, Turkey, Apr
2007 "Bacterial and archaeal diversity in the meso- and bathypelagic waters of the eastern
North Atlantic basin". H. Agogué, M. Brink, J-M. Arrieta and G. J. Herndl (Talk)
9th International Conference On Copepoda, Hammamet, Tunisia, Jul 2005
"Expression and activity of multixenobiotic resistance system in the copepod Eurytemora
affinis". H. Agogué, G. Maillet, K. Cailleaud, J. Forget-Leray and C. Minier (Poster)
Workshop of the European project AIRWIN at Banyuls-sur-Mer, France, Jan 2004
"Screening for resistance to solar radiation of marine bacteria isolated from the sea surface
microlayer and from underlying waters" (Talk)
Annual workshop of the European project AIRWIN at Toulouse, France, Jan 2003
"Isolation, identification and characterization of bacterial strains isolated from the sea surface
microlayer and from underlying waters" (Talk)
National meeting of Microbial Ecology at Carry le Rouet, France, May 2003
“Taxonomic and physiological characterizations of bacterial communities of the sea surface
microlayer” H. Agogué, M. Bourrain, F. Joux and P. Lebaron (Poster)
Seminar for Journées des doctorants du CSM (Centre des Sciences de la Mer) at
Banyuls-sur-Mer, France, Nov 2002 “Bacterial species located at the sea surface microlayer
: isolation, taxonomic characterization and physiological study” (Talk)
National meeting of Functional Ecology at La Londe-Les-Maures, France , Mar 2001
“Activity and diversity of bacterial populations in aquatic environment” H. Agogué, P.
Servais and P. Lebaron (Poster)
Contributed Talks and Poster Presentations
ISME 12 (12th International Symposium on Microbial Ecology), Cairns, Australie, Aug
2008 "Archaeal diversity in the meso- and bathypelagic waters of the subtropical north
Atlantic Ocean". A. M. Schmitz, H. Agogué, M. Brink and G. J. Herndl (Poster)
ISME 12 (12th International Symposium on Microbial Ecology), Cairns, Australie, Aug
2008 "Distribution and diversity of archaeal and bacterial ammonia monooxygenase genes in
the subtropical north Atlantic Ocean". A. Hunting, H. Agogué, J. van Bleijswijk, M. Brink
and G. J. Herndl (Poster)
Meeting of the Scientific Advisory Committee of the Int. Census of Marine Microbes,
Amsterdam, 2008 "454 sequence analysis of the Bacteria of North Atlantic Deep Waters". H.
Agogué, G. J. Herndl (Talk)
SAME 10 (10th Symposium on Aquatic Microbial Ecology), Faro, Portugal, Sept 2007
"Characterization of bacterial isolates from the meso- and bathypelagic realm of the
(sub)tropical North Atlantic". D. De Corte, H. Agogué, M. Brink and G. J. Herndl (Poster)

Workshop on bioinformatic and microbial diversity, Institut Pasteur/Société Française
de Microbiologie, Paris, France, March 2007. “Creation of a marine bacterial collection in
the Oceanological Observatory of Banyuls-sur-Mer“ L. Urios, L. Intertaglia, H. Agogué, F.
Joux and P. Lebaron (Talk)
22nd International Meeting on Organic Geochemistry, Sevilla, Spain, Sep 2005
“Exploration of lipid classes and their molecular composition of cultured marine bacteria:
progresses and paradigms towards bacterial proxy improvements” L. Méjanelle, L. Pinturier,
C. Treignier, H. Agogué, P. Lebaron and M. Goutx (Talk)
13th Annual Meeting of the Society for Environmental Toxicology & Chemistry
(SETAC Europe), Hamburg, Germany, April 2003 “Degradation kinetics of nonylphenol
and phenanthrene in the sea surface microlayer” N. Garcia-Flor, L. Ortiz, C. Guitart, J. M.
Bayona, J. Albageis, H. Agogué and P. Lebaron (Talk)
8th Symposium on Aquatic Microbial Ecology (SAME), Taormina, Italy, Oct 2002
“Structure of the microbial food webs at the air-water interface” H. Agogué, F. Joux, E.
Casamayor, P. Lebaron, G. Herndl, M. Weinbauer and T. Reinthaler (Talk)
Workshop on anaerobic microbiology, Société Française de Microbiologie, Lyon,
France, April 2000 “Bacterial population shifts during vacuum storage of cold-smoked
salmon. Application of a molecular approach to describe communities of facultative
anaerobes“ M. Bourrain, H. Agogué, F. Leroi, J. J. Joffraud, F. Chevalier and G. Barbier
(Talk)