Bubbles evolving from active gas seeps can be traced by hydroacoustic imaging up to 1000 m high in the Black Sea water column. Although methane concentrations are not distinguishable between the water column above the deep seep and reference sites, atmospheric noble gas measurements clearly show the constant input of gases (mainly methane) via seepage into the Black Sea. Archaea (ANME-1, ANME-2) and methanotrophic bacteria detected with specific 16S rRNA-targeted oligonucleotide probes are related to active gas seeps in the oxic and anoxic water column. It is suggested that methane seeps have a much greater influence on the Black Sea methane budget than previously acknowledged and that ANME-1 and ANME-2 are injected via gas bubbles from the sediment into the anoxic water column mediating methane oxidation. Our results show further that only minor amounts of methane evolving from Black Sea gas seeps reach the atmosphere due to the very effective microbial barrier. Hence only major thermodynamically and/or tectonically triggered gas hydrate dissociation has the potential to induce rapid climate changes as suggested by the "clathrate gun hypothesis."