Holocene methane pockmarks in the Baltic Sea, Part I: Archaeal community composition based on tetraether lipids and 16S rRNA analysis

Abstract. Methane-rich pockmarks and shallow gas systems are prominent geomorphological features in the Baltic Sea that act as hotspots of microbial activity. Methane pockmarks in the Gdańsk Basin differ in seepage intensity, the efficiency of internal methane biofilters, and the influence of freshwater infiltration. The objective of this research was to examine the effects of methane seepage and submarine groundwater discharge (SGD) on the composition of archaeal communities and the archaeal tetraether lipids (GDGTs) produced by these communities across the examined gas systems. Additionally, the research assessed how these environmental factors affect the use and interpretation of GDGT-based proxies in such environments. The study investigates whether GDGT patterns in these gas systems primarily reflect methane-driven processes (anaerobic oxidation of methane and methanogenesis) or ammonia oxidation, which is a key process in the Baltic Sea. It also evaluates how reliably GDGT indices can be applied in this dynamic environment characterised by strong upward gas flow. The results show elevated GDGT concentrations in pockmark sediments compared with reference non-pockmark sediments; however, GDGT concentrations are variable and depend on whether the flow is active or inactive, reflecting episodic submarine groundwater discharge that coincides with methane release. Overall, GDGT concentrations are much higher at sites with minimal or no SGD. Nevertheless, consistently low Methane Index values (MI < 0.09), together with low GDGT-0/crenarchaeol (< 1) and GDGT-2/cren (< 0.04) ratios, indicate that the iGDGT patterns lack the typical enrichment associated with methane-rich and anaerobic oxidation of methane (AOM) settings, suggesting no strong AOM imprint on the GDGT pool. OH-GDGT% values are consistent with those of Baltic Sea surface sediments. GDGT-based proxies in this system, therefore, primarily reflect ammonia-oxidiser activity rather than methane flux. These findings highlight the complex interplay between SGD and methane fluxes in shaping archaeal communities, GDGT composition, and their sedimentary record. GDGT-based indices must be applied with caution in dynamic shallow gas systems.