Tom Delmont Environmental Microbial Genomics Group

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Laboratoire Ampere
Ecole Centrale de Lyon . France
(33) 472 18 65 14

Education | Research Interests | Publications | Curriculum Vitae

  Tom Delmont  
  Tom O. Delmont

Marine Biological Laboratory
Josephine Paul Bay center
Woods Hole, USA



Email address:


Cell phone: (001) 508-524-8115
Office phone: (001) 508-289-7774



2003-2006      BS Microbiology, University of Pau, France.
2006-2008      MSE Microbiology and Biotechnologies, University of Pau, France. Valedictorian
2008-2011      Ph. D. Environmental Microbiology, Ecole Centrale de Lyon (Engineering School), University of Lyon, Ecully, France. Advisor: Timothy M. Vogel.
2012              Postdoctoral position in Environmental Microbiology, Ecole Centrale de Lyon (Engineering School), University of Lyon, Ecully, France. Advisor: Timothy M. Vogel.
2013              Postdoctoral position at the Marine Biological Laboratory (Josephine Paul Bay Center), Woods Hole, USA. Advisor: Anton F. Post.

2007-2008      Masters stipend University of Pau, Pau, France
2008-2011      Doctoral student stipend (Rhone-Alpes Region), Ecully, France
2012              University of Lyon, Ecully, France
2013-2015      Marine Biological Laboratory, Woods Hole, MA, USA

2008              Rhone-Alps Region Doctoral Fellowship
2013              US National Science Foundation (NSF) postdoctoral fellowship


During my PhD at the University of Lyon from October 2008 to December 2011, I was in charge of the METASOIL project funded by the French National Research Agency. This project played an important role in the creation of an international consortium (Terragenome) and in the sequencing and assembly of an entire soil metagenome. The selected soil was located in the ParkGrass experiment of the oldest experimental station in the world (Rothamsted, Harpenden, UK), and my principal objectives were i) to stimulate the accessibility of the metagenome by improving DNA extraction methods and ii) to use a novel strategy to characterize microbial communities from this reference soil.

Thus, I created a global DNA fractionation strategy to access distinct diversities from the same soil and this original method was able to improve by about 80% the detected diversity of the Park Grass soil metagenome (Delmont et al., 2011, AEM). Afterwards, I applied this strategy to characterize microbial communities from this soil using a NGS sequencing technology. More than 12 million sequences were generated. Datasets were annotated to study the functional potential of these communities (Delmont, et al., 2011, ISMEj). Finally, these datasets were compared to metagenomes corresponding to other environments to emphasize environmental microbial peculiarities and democratize metagenomics in the microbiology field (Delmont et al., 2011).

However, it appears that assembly efficiency was highly limited using classical metagenomic approaches (direct extraction of DNA form the environment prior deep sequencing of its related metagenome). To stimulate the reconstruction of genetic structures from soil metagenomes, I proposed an alternative metagenomic strategy: to sequence a complex metagenome one evenness at a time by stressing communities under controlled extreme conditions (e.g. mercury, heavy metals, salt or ethanol enrichment). Using this strategy, we were able to reconstruct 17 novel genomes from simplified metagenomes extracted from the Park Grass soil that represent 0.05% of the original metagenome (Delmont et al., submitted in PNAS). This approach represents a considerable opportunity to reconstruct genomes from complex microbial communities and can be applied to other environments.

After four years learning about soil microorganisms’ peculiarities while developing new approaches applied to metagenomics, I decided to explore different horizons of the microbial world while using different tools. I was particularly interested in extreme environments but also in biogeochemical cycling and the role of microbial life on Earth climate. Consequently, I integrated the Marine Biological Laboratory (MBL) through a project led by Anton F. Post (MBL) and Kevin R. Arrigo (Stanford) and focusing on the cycle of Phaeocystis Antarctica. This photosynthetic algae plays important roles in polar ecology (bloom formation, impact on prokaryote diversity) and biogeochemistry (carbon fixation, dimethylsulfoniopropionate production) and appears to be stimulated by global warming through ice melting and the release of iron. I am exploiting distinct tools (satellite data, genomics, metagenomics, transcriptomics, physiology parameters, photosynthesis activity, oligoelement requirements) to study the diversity, activity and constraints of this organism in culture experiments, and in situ during bloom events in the Ross Sea and Amundsen Bay. One of the major objectives of the project is to understand the factors that are co-limiting the bloom. I will subsequently focus on the response of Phaeocystis Antarctic during light and iron shifts as these parameters are hypothesized to control the bloom intensity and duration.



Delmont TO., Robe P, Cecillon S, Clark I.M., Constancias F, Simonet P, Hirsch P.R., Vogel TM. 2011. Accessing Microbial Diversity for Soil Metagenomic Studies. Appl Environ Microbiol. 77:1315–1324.

Delmont TO., Malandain, C., Prestat, E., Larose, C. Monier, JM., Simonet P, Vogel TM. 2011. Metagenomic mining for microbiologists. ISME Journal doi:10.1038/ismej.2011.61.

Monier JM, Demanèche S, Delmont TO, Mathieu A, Vogel TM, Simonet P. 2011. Metagenomic exploration of antibiotic resistance in soil. Curr Opin Microbiol. 14:229-35. Review.

Delmont, T. O., L. Franqueville, S. Jacquiod, P. Simonet and T. M. Vogel. 2011. Soil Metagenomic Exploration of the Rare Biosphere. In De Bruijn, F. J. (ed.), Handbook of Molecular Microbial Ecology, Volume I: Metagenomics and Complementary Approaches, First Edition. Wiley-Blackwell.

Delmont TO, Robe P, Clark I, Simonet P, Vogel TM. 2011. Metagenomic comparison of direct and indirect soil DNA extraction approaches.J Microbiol Methods. 86:397-400.

Delmont TO, Prestat E, Keegan KP, Faubladier M, Robe P, Clark IM, Pelletier E, Hirsch PR, Meyer F, Gilbert JA, Le Paslier D, Simonet P, Vogel TM. 2012. Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME journal. 6:1677-87.

Delmont TO, Simonet P. and Vogel TM. 2012. Decrypting microbial communities and performing global comparisons in the ‘omic era. ISME journal. 6:1625-8.

Delmont TO, Simonet P, Vogel TM. 2013. Mastering methodological pitfalls for surviving the metagenomic jungle. BioEssays. 35-744-54.

Mathieu A, Delmont TO, Vogel TM, Robe P, Nalin R, Simonet P. 2013. Life on human surfaces: skin metagenomics. PLoS One. 8:e65288.


Soil metagenomic: how to access the diversity?
BAGECO 2009 (Uppsala):


Perturbing complex microbial communities for metagenomic discoveries one designed evenness at the time. October 2011. 3rd annual Argonne soil metagenomics workshop.

Caractérisation, comparaison et assemblage des communautés microbiennes d’un sol de prairie par une approche métagénomique. Colloque Génomique Environnementale Lyon 2011.Organisation RTP-GE de l’INEE-CNRS et Réseau Ecologie Microbienne de l’INRA.

Exploring the soil metagenome one designed evenness at the time. Seminar February 2012 at Rutgers, New Brunswick (

Soil metagenomics: can we access the diversity?
ISME 13 Seattle (USA) August 2010

Global metagenomic comparisons : a functional confrontation of pieces of the microbial word puzzle
Soil metagenomic conference, Braunschweig (Germany), December 2010

Earth Microbiome Project  and Global metagenomic comparisons
First Earth microbiome project conference, Shenzhen (China), June 2011


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