Osmotolerance is a driver of microbial carbon processes in the Elbe estuary.

Estuaries are blue carbon loci, storing and exchanging carbon between aquatic, atmospheric, and terrestrial environments. Estuarine particles facilitate the transformation and transport of organic matter. The fate of particulate organic matter in estuaries is driven by structural changes in polymers that modify buoyancy, determining the proportions of sinking and suspended particles. In the open ocean and coastal ecosystems, the microbial composition and function of sinking and suspended particles differ, impacting carbon remineralization and sedimentation rates. We leverage 190 metagenomes and 73 metatranscriptomes to assess free-living, sinking, and suspended particle-associated microbial composition and function across the Elbe estuary. The salinity gradient in the Elbe estuary is the primary driver of microbiome composition and function. Transparent exopolymer particles (TEP) production was localized to freshwater, with seemingly no TEP-associated organisms detected above 20 practical salinity units (PSU). We observed differences in the function of free-living and particle-associated microbial communities, with diazotrophs enriched on particles. We observed that sinking particles may better support methanogenesis, and suspended particles showed signs of continued primary and secondary production. From this, we conclude that activities such as dredging, which resuspend sediment, will exacerbate carbon turnover and greenhouse gas emissions, and reduced dredging may lower greenhouse gas (GHG) emissions in the Elbe estuary. Many of these GHG linking processes are inhibited by salinity due to the osmosensitivity of methanogens and methanotrophs along the estuary. Changes in sea level and precipitation rates will likely directly interact with activities such as dredging, with as yet uncertain impacts on microbial carbon processing and storage. IMPORTANCE: Estuaries, lower river areas that merge into oceans, play a large role in Earth's carbon cycle. Estuaries store carbon and manage greenhouse gases, exchanging carbon between land, water, and the air. As carbon travels down estuaries, it is processed by free-living and particle-associated microbes. We explore the relationship between environmental conditions and present and expressed genes. Based on gene profiles, methane concentrations in the water column may be related to the abundance of sinking particles, while suspended particles are linked to growth and energy acquisition. Therefore, the balance of suspended vs. sinking particles is important in highly turbid estuaries, like the Elbe estuary, where urban activities affect greenhouse gas emissions and salinity intrusions. Dredging often tips the balance toward sinking particles and therefore increased greenhouse gas emissions. Our study thereby informs future policy decisions and the impact these decisions will have on our future climate.