Does ecological restoration align prokaryotic community structure with natural references across European coastal wetlands?

Abstract Coastal wetlands are crucial for biodiversity and act as critical buffers for carbon sequestration and atmospheric greenhouse gases (GHG) concentrations, yet their degradation often turns them into GHG sources. Restoration is widely implemented to recover these services, but it remains unclear whether interventions successfully reestablish the microbial functional diversity underpinning biogeochemical cycles. We tested the hypothesis that restoration aligns prokaryotic community structure with natural references, analyzing, a European gradient of coastal wetlands, comparing well-preserved, altered, and restored sites in water and sediment. Using 16SrRNA-metabarcoding and IndVal-Analysis, we characterized community assembly identifying diagnostic functional consortia. Results revealed a marked difference in water and sediment recovery after restoration. Bacterioplankton communities rapidly converge to natural references, while sediment microbiome displayed significant “ecological memory”. Restored wetlands show sediment communities structurally distinct from well-preserved, retaining alteration-associated guilds decades. Results support the initial hypothesis: restoration processes in coastal wetlands can re-establish communities and metabolisms resembling well-preserved conditions in the water in the short term, while sediments retain microbial communities and metabolisms inherited from altered conditions for a long time. Future strategies must integrate active sediment interventions using molecular bioindicators to validate not only the landscape appearance, but the effective reactivation of ecosystem processes and microbiota-related services.