Some species of seagrasses (e.g., Zostera marina and Posidonia oceanica) have declined in the Mediterranean, at least locally. Others are progressing, helped by sea warming, such as Cymodocea nodosa and the non-native Halophila stipulacea. The decline of one seagrass can favor another seagrass. All in all, the decline of seagrasses could be less extensive and less general than claimed by some authors. Natural recolonization (cuttings and seedlings) has been more rapid and more widespread than was thought in the 20th century; however, it is sometimes insufficient, which justifies transplanting operations. Many techniques have been proposed to restore Mediterranean seagrass meadows. However, setting aside the short-term failure or half-success of experimental operations, long-term monitoring has usually been lacking, suggesting that possible failures were considered not worthy of a scientific paper. Many transplanting operations (e.g., P. oceanica) have been carried out at sites where the species had never previously been present. Replacing the natural ecosystem (e.g., sandy bottoms, sublittoral reefs) with P. oceanica is obviously inappropriate in most cases. This presupposes ignorance of the fact that the diversity of ecosystems is one of the bases of the biodiversity concept. In order to prevent the possibility of seagrass transplanting from being misused as a pretext for further destruction, a guide for the proper conduct of transplanting is proposed.

The temperate Northwest Pacific brown alga Rugulopteryx okamurae (Dictyotales, Phaeophyceae) was first discovered in 2002 in the Mediterranean Sea in the Thau coastal lagoon (Occitania, France) and then again in 2015 along the southern side of the Strait of Gibraltar, where it was assigned with invasive status. We report here on the first occurrence of the species in the Northwest Mediterranean Sea in Calanques National Park (Marseille, France) in 2018. By 2020, a large population had developed, extending over 9.5 km of coastline, including highly protected no-take zones. The seafood trade, with R. okamurae used as packing material for sea urchin Paracentrotus lividus shipments from Thau Lagoon, could be the vector of its introduction into the Marseille area. As observed in the Strait of Gibraltar, R. okamurae is spreading rapidly along the Marseille coasts, suggesting an invasive pathway. The subtidal reefs are densely carpeted with R. okamurae, which overgrows most native algal species. Fragments of the alga are continuously detached by wave actions and currents, sedimenting on the seabed and potentially clogging fishing nets, and thus, impacting artisanal fishing or washing up on the beaches, where they rot and raise concern among local populations.

The direct and indirect impact of fish farms, shellfish aquaculture, and extensive forms of aquaculture such as seeding of juvenile sea urchins, on macrophytes (seaweeds and seagrasses), is reviewed in Mediterranean benthic ecosystems. Fish farms constitute a source of organic matter and nutrients (food and fecal pellets) that causes the extirpation of Posidonia oceanica seagrass meadows beneath and near to farm facilities. In addition to direct effects, the nitrogen enrichment of macrophytes tissues increases the grazing pressure by herbivorous fishes and sea urchins. In some cases, the impact can continue to increase several years after the cessation of farming activities. Natural restoration of extirpated seagrass meadows is generally unlikely at the human time scale. Shellfish aquaculture is the cause of the main flow of introduced macrophytes in the Mediterranean; the main vector is the importation of oyster spat from Japan and Korea. North-eastern Pacific seaweeds are now the dominant biotic component of some Mediterranean lagoons (e.g., Thau, Mar Piccolo, and Venice lagoons). In addition to direct effects, mussel aquaculture can constitute a source of larvae that flow with currents, the adults of which can overwhelm seaweed forests (e.g., Carpodesmia mediterranea). Shellfish aquaculture is also a source of fecal pellets, resulting in changes in bottom macrophytes, and a vector of diseases of metazoans, the extirpation of which may change the functioning of recipient macrophyte ecosystems. The edible sea urchin Paracentrotus lividus is sometimes erroneously considered as in decline due to over-harvesting. However, its abundance in the second half of the 20th century was probably a consequence of human impact (overfishing of its predatory fish, organic pollution. This man-induced proliferation resulted in the extirpation of seaweed forests (e.g., Carpodesmia spp., Treptacantha spp. – formerly Cystoseira spp. – Sargassum spp.; many species are endemic), which play a key role in Mediterranean coastal ecosystems. Therefore, the attempts to restore sea urchin abundance, via seeding of juveniles from hatcheries, has further artificialized the habitats rather than contributing to the restoration of natural ecosystems. Good practices guidelines are proposed aimed at minimizing the impact of aquaculture on macrophytes.

Since 2011, massive new strandings of holopelagic Sargassum have been reported on the coasts of the Caribbean, northern Brazil, Guiana, and West Africa, causing severe economic and ecological damage. Three common morphotypes (S. fluitans III, S. natans I, and S. natans VIII) were identified as responsible for these catastrophic events, with dominance shifts between them over time. However, the taxonomic status of these holopelagic Sargassum morphotypes remains unclear. Using an integrative taxonomy framework, combining a morphological study and molecular analyses, this study aimed to clarify their taxonomic status. Morphological analyses of 54 characters revealed no intermediate form between the three morphotypes, with the overall shape, nature of the axis, and size and shape of blades and vesicles being the most discriminating. An analysis of mitochondrial (IGS, cox2, cox3, mt16S rRNA, and nad6) and plastid (rbcL) markers confirmed the genetic divergence among the three morphotypes, with a lower level of divergence between the two S. natans morphotypes. Without additional molecular characterization, these morphotypes cannot be classified as three distinct species. However, due to their distinct morphological characteristics and sympatry within drifting aggregations, a revision of holopelagic species names is proposed, with Sargassum fluitans var. fluitans (for S. fluitans III), Sargassum natans var. natans (for S. natans I), and S. natans var. wingei (for S. natans VIII). This revision provides necessary clarity on the species involved in inundations of the tropical Atlantic.

Biodiversity means the variety of life, encompassing levels of complexity from within species to across ecosystems. Biodiversity therefore includes several dimensions: evolutionary scale (genetic, species, higher taxonomic levels and phylogenetic diversity), functional scale, organizational scale (patch, ecosystem, landscape/seascape diversity), spatial scale (from sample to local, regional and global richness) and heterogeneity diversity. Biodiversity can therefore be measured in different and complementary ways, thus involving the use of at least 200 different metrics, which can suggest different and contrasting conclusions. It is worth emphasizing that species richness may be the least appropriate metric, despite its popular acceptance. There is a growing tendency for stakeholders, managers, government officials, environmentalists, scientists, politicians and the media to focus, as concerns threats to biodiversity, on species richness and climate change. However, focusing on climate warming can mask other stressors that, today, and perhaps for decades to come, may have more impact on ecosystems than global warming. In the Mediterranean Sea, the overall impact of Non-Indigenous Species (NISs) and overfishing on species diversity, ecosystem diversity and ecosystem functioning exceeds to a greater or lesser degree the direct impact of warming. Drastically altered functioning patterns, and even new ecosystems are spreading throughout the Mediterranean Sea. This trend is likely to become more pronounced over the next decades. Ecosystem goods and services are also being profoundly altered, generally towards a decline, as illustrated by the overgrazed barren grounds of the eastern basin, which no longer support fisheries, by the impact of the Caulerpa meadows on the scuba diving business and the economic value of the fisheries of the western basin, by the brackish lagoon ecosystems and by the blooms of the introduced comb jelly Mnemiopsis leidyi in the Black Sea, before the arrival of its predator Beroe ovata. Here, we draw attention to the fact that, at this moment and probably also in the future, the huge flow of NISs and overfishing constitute worrying issues, although largely ignored by stakeholders and political authorities. Take care: Un train peut en cacher un autre (one train can hide another; i.e. one danger may hide other unsuspected dangers), that is to say the impact of warming may contribute to hiding other effects, of at least equal gravity, such as biological invasions and overfishing.