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Abstract: The study of Antarctic archaeal communities adds information on the biogeography of this group and helps understanding the dynamics of biogenic methane production in such extreme habitats. Molecular methods were combined to methane flux determinations in Martel Inlet, Admiralty Bay, to assess archaeal diversity, to obtain information about contribution of the area to atmospheric methane budget and to detect possible interferences of the Antarctic Brazilian Station Comandante Ferraz (EACF) wastewater discharge on local archaeal communities and methane emissions. Methane fluxes in Martel Inlet ranged from 3.2 to 117.9μmol CH4 m−2 d−1, with an average of 51.3±8.5μmol CH4 m−2 d−1 and a median of 57.6μmol CH4 m−2d−1. However, three negative fluxes averaging −11.3μmol CH4 m−2 d−1 were detected in MacKellar Inlet, indicating that Admiralty Bay can be either a source or sink of atmospheric methane. Denaturing gradient gel electrophoresis (DGGE) showed that archaeal communities at EACF varied with depth and formed a group separated from the reference sites. Granulometric analysis indicated that differences observed may be mostly related to sediment type. However, an influence of wastewater input could not be discarded, since higher methane fluxes were found at CF site, suggesting stimulation of local methanogenesis. DGGE profile of the wastewater sample grouped separated from all other samples, suggesting that methanogenesis stimulation may be due to changes in environmental conditions rather than to the input of allochtonous species from the wastewater. 16S ribosomal DNA clone libraries analysis showed that all wastewater sequences were related to known methanogenic groups belonging to the hydrogenotrophic genera Methanobacterium and Methanobrevibacter and the aceticlastic genus Methanosaeta. EACF and Botany Point sediment clone libraries retrieved only groups of uncultivated Archaea, with predominance of Crenarchaeota representatives (MCG, MG1, MBG-B, MBG-C and MHVG groups). Euryarchaeota sequences found were mostly related to the LDS and RC-V groups, but MBG-D and DHVE-5 were also present. No representatives of cultivated methanogenic groups were found, but coverage estimates suggest that a higher number of clones would have to be analyzed in order to cover the greater archaeal diversity of Martel Inlet sediment. Nevertheless, the analysis of the libraries revealed groups not commonly found by other authors in Antarctic habitats and also indicated the presence of groups of uncultivated archaea previously associated to methane rich environments or to the methane cycle. [Copyright &y& Elsevier]