Bacteria of the Gallionellaceae family (β-proteobacteria) oxidise dissolved iron at circumneutral pH to fuel their energy metabolism. These bacteria are endemic of microaerobic habitats, where they can outcompete the rapid abiotic oxidation of iron with oxygen. They are thus generally found in the interface areas between the atmosphere and an anoxic iron-rich compartment, such as a resurgence of groundwater. However, in the last five years, several studies have shown the presence of Gallionellaceae at depth in some subsurface environments, at depths where they are generally anoxic. In several of these environments, such as some aquifers in the Armorican basement (Brittany, France), Gallionellaceae even seem to dominate the microbial communities. This suggests (I) that there are deep interface zones in these aquifers between an oxygen-containing compartment and an anoxic iron-rich compartment, and (II) that these interface zones can have a major role in maintaining microbial populations at depth. The objective of this thesis was to explore the diversity and the ecology of Gallionellaceae bacteria in these subsurface environments, for uncover their overall biogeochemical functioning. A multidisciplinary approach was used to achieve this objective, involving metagenomic and hydrogeochemical analyses.