Skip to main content

Geomicrobiologist in lakes (drying and freezing ones), rock licker, hip-hop digger


Our recent paper is out and available in open access in the Depositional Record : Banded Iron Travertines at the Ilia Hot Spring (Greece): An interplay of biotic and abiotic factors leading to a modern Banded Iron Formation analogue?

1 min read

We have a new paper out in @sedimentology journal the Depositional Record. We present a potential modern analogue for investigating the influence of microbes on formation --> Banded Iron Travertines of the Greek Ilia hot spring (link:






New paper out: Lateral variations and vertical structure of the microbial methane cycle in the sediment of Lake Onego (Russia)

1 min read

New paper finally out on our work with @UmrCarrtel on the sedimentary methane cycling in the ice-covered lake Onego : Available in at Inland Waters @SIL_limnology
Lateral variations and vertical structure of the microbial methane cycle in the sediment of Lake Onego (Russia)


we've put up a session at the . Come join us and submit an abstract if you're interested in microbes and their activity in the sediment @EuroGeosciences @limnogeology


My current research projects

6 min read

I am a geomicrobiologist with a geology background, interested in the impact of microbial communities on sedimentary environments. My main playground is lakes and their sediment. Lakes are diverse systems, that host immense potential for paleoclimatic and paleoenvionmental reconstructions. But the processes influencing the deposition, preservation and transformation (early diagenesis) of their sediment are also diverse and complex. Subsurface microbial communities are the main actors in this  environment. Hence, understanding their diversity, structure and activity is fundamental in order to access the full potential of lacustrine sediments as paleoclimatic archives.

We use a panel of classic methods from geology (microfacies analysis, scanning electron microscopy, geochemical characterization of minerals and organic matter) and biology (epifluorescence microscopy, DNA and RNA analysis through gene quantification and sequencing,) to apply cutting edge approach to the field of geomicrobiology.




Ironlake, Lake Fagnano

Lago Fagnano is an iron rich lake that exhibits a unique and anthropogenically undisturbed sedimentary record for the South American region. Within the ironlake project, our goal (together with Ina Neugebauer) is to constrain the modality of formation of iron minerals within iron-rich laminae in order to use iron isotopes as a proxy for climatic reconstructions. The analysis of active microbial communities involved in the iron cycle and their contribution to the formation and dissolution of iron minerals will be investigated to constrain the usage of lago Fagnano’s sediments as climatic archives.



Life under the Ice, Lake Onego

Boreal and sub-boreal lakes are important contributors to greenhouse gases (CO2, CH4) to the atmosphere. However, most global budget are calculated based on icefree periods, while most of these akes are ice-covered during a large part of the year. In collaboration with the Northern Water Problems Institute of Karelia, and a network of western-European universitites, we try to understand what are the parameters influencing microbial communities structural and functional diversity in relation to the methane cycle in the ice-covered Onego lake, in Russia.



 You can read more about this project here


Dead Sea Deep Drilling Project

The DSDDP is an ICDP-funded drilling project that aims at reconstructing the paleoenvironments and paleoseismicity of the Levantine region during the last 250 ka.

Microbes are the only form of life in this hypersaline environments. The unique archives of the deep Dead Sea Basin have revealed that microbial communities differed based on specific sedimentary facies representative of distinct limnological and paleoenvironmental conditions. Our analysis highlights the importance of applying geobiological approach within such pluridisciplinary projects to account for the microbial imprint on paleoclimatic archives.


You can find related publications here


ICDP-SCOPSCO project, Lake Ohrid

I am taking part in the effort of describing and understanding the paleobiologic and paleoclimatic unicity of  Macedonian lake Ohrid, within the ICDP-funded SCOPSCO project. I apply a microbial ecology approach by comparing microbial communities present in deep sedimentary intervals corresponding to distinct climatic stages. Our goal is to gain insights into the way microbial communities assemble in deep sediments.


You can access the ICDP project page here


Greek Travertine, Euboea, Greece

The impact of microbial communities on the geological record has existed since the origin of life. An extraordinary example of this impact is banded iron formation that form today the main iron ore deposits on earth. By applying geochemical and geomicrobiological approach to a iron-rich travertines from a continental hot spring in the Greek Island of Evia, we investigate the processes of formation of iron-rich laminae as potential analogs to BIF deposits.



BaCyGe, Lake Geneva

Microbes also deeply influence biogeochemical cycles in your backyard. Recent discoveries have shown that algal species in lake Geneva have the potential to concentrate metals in their cells by forming carbonate micropearls. I participate in the effort to identify these organisms and the processes leading to such accumulation of metaloids.


 The first publication from this project came out recently in Geobiology




Thomas, C., Ebert, Y., Kiro, Y., Stein, M. and Ariztegui, D.: Microbial sedimentary imprint on the deep Dead Sea sediment, Depos. Rec., 1–21, doi:10.1002/dep2.16, 2016.


Martignier, A., Pacton, M., Filella, M., Jaquet, J.-M., Barja, F., Pollok, K., Langenhorst, F., Lavigne, S., Guagliardo, P., Kilburn, M., Thomas, C., Martini, R., Ariztegui, D. and Ariztegui, R. M. D.: Intracellular amorphous carbonates uncover a new biomineralization process in eukaryotes, Geobiology, 1–14, doi:10.1111/gbi.12213, 2016.



Thomas, C., Ionescu, D. and Ariztegui, D.: Impact of paleoclimate on the distribution of microbial communities in the subsurface sediment of the Dead Sea, Geobiology, 13(6), 546–561, doi:10.1111/gbi.12151, 2015.


Ariztegui, D., Thomas, C. and Vuillemin, A.: Present and future of subsurface biosphere studies in lacustrine sediments through scientific drilling, Int. J. Earth Sci., 104(6), 1655–1665, 2015.



 Thomas, C., Ionescu, D., Ariztegui, D. and Party,  the D. S.: Archaeal populations in two distinct sedimentary facies of the subsurface of the Dead Sea, Mar. Genomics, 17, 53–62, doi:10.1016/j.margen.2014.09.001, 2014a.


Recent communications

Thomas C., Perga M.-E., Frossard V., Pasche N., Hofmann H., Ariztegui D., Dubois N., Belkina N. & Lyautey E.(2017) Vertical structure and horizontal variations in the cycling of methan in the sediment of Lake Onego, Russia. In EGU General Assembly Conference 2017, Vienna, Austria (Poster)


Lyautey E, Ariztegui D, Bouffard D, Dubois N, Frossard V, Tofield-Pasche N, Perga M-E & Thomas C. (2016) and the Life Under the Ice scientific team: Microbial Ecology and Biogeochemical Cycling in the Seasonally-Covered Lake Onego, Russia. In Goldschmidt 2016 conference, Yokohama, Japan. (Oral)


Thomas, C., Ariztegui, D., Frossard V., Lyautey E., Perga M.-E. & Life Under Ice Scientific Team. (2016, April). Life under ice: Investigating microbial-related biogeochemical cycles in the seasonally-covered Great Lake Onego, Russia. In EGU General Assembly Conference Abstracts (Vol. 18, p. 17868). (Poster)


Thomas, C., Levy, E. J., Antler, G., Grossi, V., Sivan, O., Yechieli, Y., Gavrieli, I., Turchyn,  a V, Stein, M., Ariztegui, D. and the DSDDP Scientific Team (2014) Organic Proxy Disturbance in the Dead Sea Basin at the Beginning of the Holocene. In AGU fall Meeting, 2014, San Francisco, USA. (Poster)


Thomas, C., Ionescu, D., Ariztegui D., and the DSDDP Scientific team (August 2014)

The Dead Sea subsurface biosphere: Identifying specific microbial assemblages and their metabolic potential in an extreme environment. In International Sedimentology Congress, Geneva, Switzerland. (Oral)


just started a postdoc @unige_en on Fe-cycling microbes and and their impact on lake archives used for paleoclimatic studies. So Excited!
I'll be part of the Limnogeology and Geomicrobiology team at the Earth Sciences department of the University of Geneva.


New paper out by Martignier et al., in Geobiology : discovery of a new biomineralization process by algae in lake Geneva --> Intracellular amorphous Barium and Strontium rich calcium carbonates


Bathyarchaeota could be methanogens!

2 min read

A recent metagenome study by Evans et al., (2015) has detected the presence of a divergent mcrA gene sequence in Bathyarchaeota (formerly Miscellaneous Crenaorchaeotal group).

This has very strong implications such as : 

-not only members of the Euryachaeota phylum are able to perform methanogenesis 

-a version of mcrA existed in the Bathyarchaota and Euryarchaeota common ancestor

-new primers should be used to take into account the divergent Bathyarchaota mcrA gene to analysie methanogenesis, in the marine realm, and also in lacustrine ecosystems.

-these Bathyarchaeota can do a lot of amazing things (see Lloyd et al., 2013 & Meng et al., 2014)

here is the paper :

and here is a nice overview of the story : (where the figure below comes from)


Evans et al., (2015) Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics Science  350 (6259), 434-438. [DOI:10.1126/science.aac7745]
Lloyd, K. G., (2015) Beyond known methanogens Science : 350 (6259), 384. [DOI:10.1126/science.aad4066]

Lloyd, K. G., Schreiber, L., Petersen, D. G., Kjeldsen, K. U., Lever, M. A., Steen, A. D., ... & Jørgensen, B. B. (2013). Predominant archaea in marine sediments degrade detrital proteins. Nature, 496(7444), 215-218.

Meng, J., Xu, J., Qin, D., He, Y., Xiao, X., & Wang, F. (2014). Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses. The ISME journal, 8(3), 650-659.




Starting of a new project as a Postdoc @INRA lab. i'll be based at the University of Savoy Mont-Blanc to work on lake and lake methane cycle.


Last day @UNIGEnews working on @icdpDrilling material from lake . Next: Postdoc @Univ_Savoie lab for lake geobiology


Aux Lyonnais engagés, citoyens, responsables, innovants :
merci @ArmMax @LaPaillasaône allez hop à la Doua..