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Archaeal community composition in Holocene methane pockmarks of the Gdańsk Basin (Baltic Sea; Poland): insights from tetraether lipids and 16S rRNA analysis
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DOI：10.5194/bg-23-4485-2026.png)
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Abstract
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Abstract. Methane pockmarks and shallow gas systems are prominent geomorphological features in the Baltic Sea that act as hotspots of microbial activity. In the Gdańsk Basin; pockmarks vary in gas-seepage intensity and in the extent of freshened porewater discharge; both of which influence the archaeal community structure and the composition of internal methane biofilters. The objective of this study was to examine the effects of methane seepage and freshened porewater on the composition of archaeal communities and on the isoprenoid glycerol dialkyl glycerol tetraethers (iGDGTs); membrane lipids synthesised by these communities; across the gas systems examined. Additionally; the effects of these environmental factors on the use and interpretation of iGDGT-based proxies under conditions of gas and water seepage were assessed. The study investigates whether iGDGT patterns in these Baltic gas systems reflect methane-driven processes; including anaerobic oxidation of methane (AOM) and methanogenesis; porewater freshening; or pelagic contributions from ammonia-oxidising archaea (AOA). The results show elevated iGDGT concentrations in pockmark cores compared with reference non-pockmark cores; however; the summed iGDGT concentration varies by site. Overall; iGDGT concentrations are much higher at sites with reduced seabed pockmark activity and weak porewater freshening. Nevertheless; consistently low Methane Index values (MI < 0.09); together with low GDGT-0 / crenarchaeol (< 1) and low GDGT-2 / cren (< 0.04) ratios; indicate that the iGDGT pool lacks the typical enrichment in GDGT-1 to -3 associated with AOM; suggesting no AOM imprint on the iGDGT pool. However; 16S rRNA analysis revealed that the anaerobic methanotrophic archaeal lineages (ANME) consist of ANME-2b and ANME-3. A strong positive correlation between OH-GDGTs and crenarchaeol; together with the consistency of OH-GDGT% values with those previously reported for Baltic Sea surface sediments; suggests a thaumarchaeal source of iGDGTs in the studied pockmark and reference cores. The Branched and Isoprenoid Tetraether (BIT) index values suggest marine archaeal GDGT production. In this system; iGDGT-based proxies primarily reflect a strong pelagic presence of AOA; as indicated by the dominance of crenarchaeol. This suggests that; despite the local presence of methanogenic and ANME-related archaeal groups; methane-related AOM does not influence the iGDGT signal due to the archaeal community structure. These findings highlight the complex interplay between freshened porewater and gas seepage in shaping archaeal communities; and the role of ammonia-oxidising Nitrososphaeria in controlling iGDGT composition and the sedimentary record.
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