Aim β diversity and its linkages with ecosystem functioning remain poorly documented. This impedes our capacity to predict biodiversity changes and how they affect ecosystem functioning at scales relevant for conservation. Here, we address the functional implications of ongoing seafloor changes by characterizing at regional scale the taxonomic and functional α and β diversities of benthic habitats currently threatened by biotic homogenization. Location Western Europe. Methods Combining a trait‐based approach to benthic community monitoring data covering a 7‐year period and 500 km of coast, we explored the mechanisms governing community assembly in habitats associated with two types of foundation species, intertidal seagrass and subtidal maerl beds, compared to bare sediment at similar tidal level. We assessed their spatial and temporal variability and linked these mechanisms to their repercussions at regional scale through analyses of taxonomic and functional β diversity. Results Foundation species locally promote taxonomic and functional diversity. Maerl fine‐scale heterogeneity promotes niche diversity and leads to high functional redundancy for the whole subtidal compartment, providing insurance for seafloor functioning. Seagrass high diversity seems more reliant on transient species and is associated with redundancy of only a few functions. Maintaining the seascapes in which seagrass are embedded seems essential to ensure their long‐term functioning. At regional scale, the locally poorer bare sediment harbour similar functional richness as biogenic habitats because of higher within‐habitat β diversity. Main conclusions Our study reinforces the conservation value of biogenic habitats but highlights that different mechanisms underlie their local diversity, which has implications for the vulnerabilities of their associated communities. Accounting for β diversity at regional scale also stressed a potential underrated conservation value of bare sediment for benthic ecosystem functioning. Coupling trait‐based approaches to monitoring data can help link broad‐scale β diversity to its underlying drivers, bringing local mechanistic understanding closer to the scales at which biodiversity loss and management actions occur.

Biological invasions are one of the main global threats to biodiversity in terrestrial, freshwater and marine ecosystems worldwide, requiring effective inventorying and monitoring programs. Here, we present an updated list of non-indigenous species in French marine and transitional waters. Focused on eukaryote pluricellular species found throughout the three metropolitan French marine regions (Western Mediterranean Sea, Bay of Biscay and the Northern Seas), a total of 342 non-indigenous, including 42 cryptogenic, species are listed as having been introduced since the 13th century. The majority of the species originated from the temperate Northern Pacific. They mainly arrived through both ballast and hull fouling and also are associated with shellfish farming activities. Most of them have been introduced since the 1970s, a time when maritime and aquaculture trade intensified. Despite important human-aided opportunities for species transfer between the three marine regions (for instance, via recreational boating or aquaculture transfers), only a third of these NIS are common to all regions, as expected due to their environmental specificities.