Groundwater flow impacts on microbial communities and biogeochemistry in seafloor pockmarks

Biogeochemical processes and microbial community structure were investigated in sediment cores from three pockmarks in Hanko, Finland, in the northern Baltic Sea, and compared to groundwater and seawater measurements. Three studied pockmarks varied with the rate of submarine groundwater discharge (SGD). Based on e.g., chloride and DIC concentrations from sediment porewaters, pockmark D had the strongest groundwater influence, while in pockmark E SGD had ceased and therefore this pockmark resembled typical Baltic Sea water and sediment. The pockmark B was the intermediate representative of SGD. The inactive pockmark E had orders of magnitude higher methane concentrations compared to the active pockmarks, but interestingly, this did not reflect on the copy numbers of methanogenesis marker gene (mcrA) results, as pockmark B had equal methanogenesis gene pool as the pockmark E. Sulfate reducer numbers measured with dsrB marker gene was highest in pockmark E sample but also many orders of magnitude higher in other pockmark sediments compared to seawater and groundwater, where the sulfate reducer numbers were only negligible. Reactive transport modeling (RTM) established that the porewater systems in pockmarks D and B were dominated by groundwater advection pushing reactants for biogeochemical reaction into a narrow zone at sediment surface. The advection reduced the organic matter accumulation which results in absence of sulfate-methane transition zone in these pockmarks and concentrates the microbial activity to these habitats. Microbial community structure revealed with phylogenetic marker gene amplicon sequencing reflects the groundwater in active pockmarks, as notable populations of ammonia-oxidizing archaea and nitrifying bacteria in pockmarks are mainly originating from groundwater. RTM also estimated low rates of sulfate consumption and low rates of methane, ammonium and DIC in the active pockmarks.