Microbiology of shallow subsurface aquifer and carbonate rocks studied by culture-dependent and culture-independent methods. Preliminary results on an underground laboratory, the LSBB, Rustrel, France

¹ Aix-Marseille Université, CEREGE, Centre St Charles, Case 67, 3 place Victor Hugo, 13331 Marseille, France
² Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288 Marseille Cedex 09, France
³ INRA, UMR 1163 Biodiversité et Biotechnologie Fongiques, Marseille, France
⁴ LSBB, University of Nice, University of Avignon, CNRS, Aix-Marseille University, La grande combe, 84000 Rustrel, France
⁵ UMR EMMAH Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes, INRA/Université d'Avignon et des Pays de Vaucluse, 33 rue Louis Pasteur, 84000 Avignon, France

^a Corresponding author: gregoire.gales@univ-amu.fr

Abstract

We investigated the microbiology of a shallow subsurface site, the LSBB, located near Avignon. This site lies in carbonate rocks, belonging to the Urgonian facies. Rock, concrete and water samples were collected and directly transferred to the laboratory. Studies of microorganisms as pure cultures are the only way to get their real physiological properties. Nevertheless, microbiologists cannot cultivate and isolate the majority of microorganisms for several reasons, one being our lack of understanding of their minimal needs. Molecular studies, e.g. extraction and sequencing of the total nucleic acids present in an environment provide phylogenetic and metabolic information on uncultivated microorganisms. We performed aerobic and anaerobic culture with various electron acceptors and donors, searching for heterotrophic, methanogenic, sulphate- nitrate- and FeIII- reducing Prokaryotes. We also performed DNA extractions and PCR amplification of ribosomal RNA genes, to test if our protocols were adapted to this environment. Our results show that the LSBB galleries are colonized by a low diversity microbiote, with a strong influence of anthropogenic activities. Further studies will link the microorganisms biodiversity and the petrophysic properties of rocks.