Species delimitation is central to understanding biodiversity and its conservation, yet genetic divergence among sister lineages is often insufficient to demonstrate reproductive isolation or to resolve speciation unambiguously. This limitation is especially pronounced in marine invertebrates such as corals. Their slowly evolving genomes, cryptic diversity, and complex reproductive traits can obscure species boundaries. These challenges also characterize the Paramuricea-species complex occurring in the Iberian-Atlantic, whose members, including those studied here, commonly dominate deep coral forests. Within this complex, sympatrically occurring yellow and purple morphs exhibit little mitochondrial differentiation, despite evidence of partial genetic structuring. By characterizing gametogenesis, spawning time, and early life-history stages, we reveal pronounced prezygotic barriers between the yellow (broadcast spawning) and purple (surface-brooding) morphs, including consistent multi-year temporal separation and strongly contrasting fertilization environments. These differences extend into embryonic development, larval morphology, behavior, and settlement dynamics and reflect divergent dispersal strategies. Overall, our results provide direct biological evidence that the two morphs represent independent evolutionary lineages, supporting their recognition as distinct species. This model system represents a contemporary example of ecological speciation and may serve as a powerful model for future research on the genetic coupling between reproductive modes and life-history traits.

Larval settlement is a critical bottleneck in coral life cycles, yet mechanistic understanding is largely derived from tropical scleractinians, however lacking for non-tropical octocorals. Tropical crustose coralline algae (CCA) and their associated microbiome are known to be a major trigger for settlement processes. We investigated settlement drivers in a temperate octocoral ( Paramuricea sp.) to assess whether similar processes operate in temperate and cold-water coral forests: (1) In a choice experiment larvae were exposed to different types of substrates. Settlement occurred exclusively on substrates naturally colonized by crustose coralline algae (CCA), independent of rock lithology, indicating that biogenic surface properties, rather than mineral composition, govern settlement. Substrate covered with Lithophyllaceae -associated CCA induced settlement across depth ranges, whereas other CCA taxa and bare fragments did not. (2) Experimental exposure to the bacterial metabolite cycloprodigiosin (CYPRO) triggered settlement behaviour in up to 44% of the exposed larvae, suggesting chemical cues as primary inducers. (3) Spatial analyses of settlement patterns revealed that attachment rarely occurred directly on CCA surfaces. Instead, larvae settled near CCA and within millimetre-scale crevices and depressions. Small-scale heterogeneity suggests that microtopographic features act as secondary filters after chemical induction. These findings indicate that key elements of settlement regulation might be shared between tropical reefs and temperate coral forests highlighting the joint importance of CCA communities and structural complexity for recruitment and conservation.

Marine ecosystem engineers such as corals, seaweeds, and seagrasses are foundational to coastal ecosystems, yet are declining at unprecedented rates due to accelerating climate and anthropogenic pressures. Microbiome-based approaches have attracted attention as a promising avenue to enhance the resilience and recovery of these organisms. Over the past decade, diverse marine probiotic microbes have been isolated and shown to positively influence key host life functions, including growth, development, reproduction, responses to environmental stressors, and pathogen defence. However, current research remains confined to laboratory settings, with few practical field applications tested or utilised, likely driven by practical and technological challenges and lacking communication between science and policy. To help close this gap, we propose a set of risk and success assessment criteria for microbiome-assisted restoration. This framework is built around four pillars: (1) ensuring environmental compatibility of candidate probiotics, (2) establishing scientific validation for their mechanisms of action, (3) securing legal clarity before application, and (4) implementing mandatory in situ monitoring to evaluate ecological outcomes. By integrating these pillars into a cycle of risk assessment, monitoring, and adaptive management, microbiome-assisted restoration could progress from an experimental concept to a practical application complementing existing conservation tools, strengthening the resilience of these ecosystems.

Seagrass seedlings are key to meadow recovery under global change, as they enable recolonization of degraded areas and provide genetic variability needed for adaptation. While invasive macroalgae increasingly threaten seagrass communities, elevated CO2 has been proposed to enhance seagrass performance and potentially buffer other stressors. Here, we conducted a mesocosm experiment to test the combined effects of two invasive macroalgae (Lophocladia trichoclados and Caulerpa cylindracea) and elevated CO2 on Posidonia oceanica seedlings. CO2 enrichment increased carbohydrate reserves in rhizomes and induced subtle shifts in root-associated microbiomes. In contrast, invasive macroalgae had consistently negative effects on seedling development and physiology and strongly altered both above- and belowground microbial communities. Despite its potential to stimulate seagrass productivity, elevated CO2 did not mitigate the detrimental impacts of invasive macroalgae. These findings indicate that future CO2 conditions may not offset invasion-driven stress at the recruitment stage, highlighting the need for targeted management efforts to limit macroalgal proliferation and support seagrass meadow regeneration.

Despite successful preservation efforts, macroalgal diversity remains under-represented in global biobanks. A major limitation is the extreme morphological diversity of seaweed thalli, which hinders standardized isolation and phenotyping and often requires taxon-specific protocols. Here we present SAMMBA (Seaweed Automatable Microplate Microscopy for Breeding Approaches), an end-to-end pipeline for the high-throughput isolation, phenotyping and storage of macroalgal propagules in 384-well plates. By optimizing live-cell manipulation for chlorophyll autofluorescence (CAF) imaging and segmentation, multiple unialgal propagules can be isolated by dilution-based workflows. In a single plate, we obtained 68 singlet gametophyte fragments of Laminaria ochroleuca (17.7%) and 60 meiospores of Phyllariopsis purpurascens (31.25%). We demonstrated taxonomic and morphological versatility by isolating 60 unialgal cultures from three distinct Rhodophyta morphotypes (filamentous, crustose and foliose) and 10 strains of Ulva sp., also in a single plate. Furthermore, CAF-based area increase over 30 days enabled high-precision estimates of specific growth rates, yielding 0.130 +/- 0.006 and 0.117 +/- 0.01 day- 1 for male and female L. ochroleuca gametophytes, respectively (n = 768; p = 1.27e-53). This precision substantially increases experimental reproducibility and statistical power compared to conventional methods, supporting high-throughput recovery of unialgal strains without motorized platforms, while remaining fully compatible with automation. SAMMBA expands operational capacity for strain discovery and phenotyping, providing a scalable foundation for phenomics, domestication workflows, and standardized macroalgal biobanking. We outline how the platform can benefit multiple areas of phycological research and facilitate the development of improved strains that can support aquaculture and restoration efforts.

The widespread decline of coral-dominated ecosystems has highlighted the urgent need for active habitat restoration. Coral restoration using sexually produced individuals instead of clonal fragments is essential to reduce impacts on donor populations and promote genetic diversity, which is vital for adaptability to environmental changes. However, for most coral species critical knowledge of reproduction and larval ecology for ex situ sexual propagation is lacking. To address this gap, this study presents the first report of spawning of the octocoral Eunicella verrucosa in the North-East Atlantic and describes larval development and settlement. The annual reproductive timing in South-West Portugal was determined from samples collected as fisheries bycatch from the same habitat and monitored for comparison across distinct durations and conditions. The species exhibited split spawning (three major events approximately every two weeks) over about one month (mid-September–mid-October). Spawning patterns can suggest lunar periodicity but shifted between colonies kept in distinct conditions. Oocytes were positively buoyant and developed into swimming larvae after three days. Settlement trials using substrates such as natural rock, crustose coralline algae (CCA), and gorgonian skeleton, showed larvae started testing the substrates about two weeks after spawning, with settlement activity continuing over up to three months. Fully developed recruits were observed after one month, with sclerite production starting before tentacle development. The observation of new larval settlement up to three months indicates a prolonged competency period. This study provides crucial data for coral restoration efforts using ex-situ sexual propagation of a vulnerable species.

Posidonia oceanica forms extensive seagrass meadows in the Mediterranean Sea, providing key ecosystem services. However, these meadows decline due to anthropogenic pressures like anchoring and coastal development. Transplantation-based restoration has been explored for decades, yet the role of the plant-associated microbiome in restoration success remains largely unknown. 16 S rRNA gene amplicon sequencing was used to investigate how different transplantation methods and donor origins influence the bacterial communities of P. oceanica cuttings two years post-transplantation. We tested three transplantation methods, iron staples, coconut fiber mats, and BESE elements, and compared them with control meadows and donor populations from two different origins: naturally uprooted storm-fragments and intermatte cuttings manually harvested from established meadows. Our results show that transplantation methods strongly shape bacterial communities in seagrass roots. Iron staples promoted microbial assemblages most similar to natural meadows, likely due to direct sediment contact enhancing recruitment of key functional bacterial orders such as Chromatiales and Desulfobacterales. In contrast, BESE elements and coconut fiber mats displayed dissimilar bacterial communities compared to control meadows, likely due to material composition and physical separation between the cuttings and the sediment. Donor origin had only subtle effects on bacterial communities’ structure, although intermatte cuttings showed higher abundances of Candidatus Thiodiazotropha, a genus thought to be involved sulfur oxidation and nitrogen fixation. Our results demonstrate that transplantation methods strongly influence root-associated bacterial communities. Limited sediment contact in elevated substrates delayed the establishment of key functional bacteria, highlighting the importance of direct interaction with the sediment microbial pool. These results imply that restoration strategies should prioritize methods enhancing sediment–root interactions to support microbial recovery. Incorporating microbiome considerations, such as optimized substrates or microbial inoculation, could improve the resilience and long-term success of P. oceanica restoration.

Since 2011, holopelagic Sargassum has been accumulating in a region of the tropical Atlantic now referred to as the Great Atlantic Sargassum Belt (GASB). Among the hypothesized contributors to these accumulations are the increased inputs of nitrogen (N) and phosphorus (P) in the tropical Atlantic Ocean. Little is known about the effects of N and P additions on Sargassum physiology and its microbiome. We studied the effects of N, P, and NP additions on the growth, photosynthetic efficiency, and microbiome composition of Sargassum fluitans III in a six‐day experiment on the Caribbean Island of Curaçao. Sargassum fluitans III took up most nitrate and phosphate within 3 days with respective uptake rates of 0.343 and 0.0399 μmol · g −1 DW · h −1 . F v/ F m decreased in the control after 6 days but remained constant in nutrient treatments. Growth rates did not differ significantly among treatments, but a trend in higher growth rates in the NP treatment was discerned, suggesting a possible NP co‐limitation. The relative abundance of epiphytic Cyanobacteria such as Schizothrix and bacteria such as Lentilitoribacter increased under N and P addition, while heterotrophic Rhodobacteraceae decreased in abundance. Microeukaryotic communities responded with varying changes in alpha diversity, possibly steered by increased photosynthesis and growth of S. fluitans III or bacterial interactions. The physiological response to N and P and rapid change of the microbiome demonstrates that the studied S. fluitans III can quickly benefit from increased nutrient concentrations, which might contribute to its growth success in the GASB.

Global blue carbon assessments are hindered by a lack of data from understudied seagrass regions, such as those of Western Africa. This study reports the first in situ records of organic carbon (OC) stocks and burial rates for seagrass beds at Arguin Island, Banc d'Arguin (Mauritania), Western Africa, measured in intertidal Zostera noltei and subtidal Cymodocea nodosa meadows. The major blue carbon sources in seagrass meadows since 1900 were assessed using sedimentary environmental DNA (eDNA) and chronostratigraphy. The OC stocks in the top 50 cm of the sediment cores were not significantly different between the beds of the two seagrass species and averaged 27.8 ± 7.14 Mg C ha−1, which is 5 times higher than that in adjacent unvegetated sediments. The OC sequestration rate for the past 100 years was 10.3 ± 1.4 g C m−2 year−1 in C. nodosa sediments and 12.3 ± 5.9 g C m−2 year−1 in Z. noltei sediments. Sedimentary eDNA analysis revealed that the major OC source within the C. nodosa and Z. noltei sediments has been the seagrass species itself, with low contributions from allochthonous eDNA reads. Carbon sources in Z. noltei meadows were more diverse than those in C. nodosa meadows. In bare sediment, diatoms were the major carbon source. The present study demonstrates the potential of sedimentary eDNA to reveal the major sources of organic matter in blue carbon ecosystems, improving our understanding of the provenance of sedimentary OC and thus carbon cycling processes. Additionally, it provides new OC stock and sequestration rate measurements from a region of the world that remains underrepresented in global blue carbon assessments.

Coastal coral habitats face growing threats from extreme weather events such as marine heatwaves and storms. The impact of these stressors compromises important ecosystem services that contribute to human well-being. While the effects of hurricanes on tropical coral reefs are well documented, studies assessing the impacts of similar disturbances on temperate and cold-water coral communities are lacking. This study investigates a gorgonian mass mortality event following 2 winter storms-Emma and Felix-along the southern Portuguese coast in 2018. A total of 439 stranded gorgonians, primarily Leptogorgia sarmentosa (Esper, 1791), were collected over 4 d, with 81.1% comprising detached colonies and 18.9% comprising broken branches. This corresponds to an approximate removal of 1572.5 m2 (181.1-3260.0 m2) of living gorgonian cover area based on average densities found at surrounding sites (<30 m). Differences in species composition and size suggest that L. sarmentosa is more vulnerable to storm-induced detachment than other co-occurring gorgonians. This is likely due to higher drag forces resulting from the colonies' planar and densely branched morphology, although differences in species depth distribution may also play a role. Colony sizes varied across sampling dates, generally aligning with wave height during the storms. Overall, our results suggest that storm-induced wave forces caused significant biomass loss. This finding highlights the severe impact extreme storms can have on shallow-water coral populations and underscores the urgent need to assess the long-term consequences of these events, especially given the projected increase in their frequency and severity under future climate change scenarios.

The central role played by microbes as driving forces of biogeochemical cycles, as well as the second genome of most organisms, has reinforced the necessity to study this unseen majority. Their relationships with Marine Animal Forests (MAFs) have been proven essential for maintaining these ecosystems in the face of ongoing climate change, driving key processes such as nutrient cycling, pathogen control, and resistance and resilience to anthropogenic perturbations. In MAFs, diverse microorganisms – viruses, archaea, bacteria, fungi, and protists - have been shown to occupy different compartments and act as symbionts, parasites, or pathogens, depending on the environmental conditions. They are also vulnerable to change, which can result in impacts on the MAF functioning. In this chapter, we present omics techniques that can be used for a better understanding of the distribution, ecological roles, and interactions between MAFs and their associated microbiomes. The chapter explores themes ranging from sampling design and field procedures to analysis, aiming to provide a set of tools that can be used in a standardized manner to facilitate comparative studies and contribute to the protection, management, and restoration of these ecosystems.

Temperate coral gardens are dense coral formations, which support rich marine species diversity, enabling benthic-pelagic coupling. Over the past decades, coral gardens have been increasingly threatened by bottom fishing, oil and gas exploitation, and climate change. Microbiome research bears great potential for assisted resilience in targeted conservation and restoration approaches. Yet, fundamental parameters of the coral garden microbiome remain poorly understood. Here, we provide a first broad record of bacterial communities associated with NE Atlantic coral garden corals and their community changes as response to human maintenance in conservation research. Octocorals (10 species), scleractinians (2 species) and one black coral species, were opportunistically collected from fisheries bycatch at 60–480 m depth around Cape St. Vincent (SW Portugal). Metabarcoding of the 16S-rRNA gene using third-generation sequencing revealed a high microbial host-specificity in the wild-collected coral species analyzed, and supported the importance of bacterial families Endozoicomonadaceae (mean relative abundance ± SE; 28.3 ± 10.5%), Spirochaetaceae (8.2 ± 5.8%) and Spongiibacteraceae (4.6 ± 1.8%). Endozoicomonadaceae were particularly dominant in the octocoral order Malacalcyonacea (67.7 ± 14.5%). The low microbial alpha diversity and limited interspecies differences among the Malacalcyonacea species suggest a conserved microbiome within this group, as compared to orders Scleralcyonacea, Antipatharia, and Scleractinia. Microbial responses to ex-situ maintenance of two branching octocoral species, Eunicella verrucosa and Paramuricea cf. grayi (Order Malacalcyonacea), were investigated (1) over 45 days under standardized aquaria conditions in the research station (Ramalhete Marine Station, CCMAR) and (2) over long-term captivity in two public aquaria, Oceanário de Lisboa and Zoomarine. Eunicella verrucosa displayed a stronger microbial community shift to short-term captivity (45 days), in contrast to greater microbiome stability in P. cf. grayi. However, long-term captivity in public aquaria led to microbiome shifts in both species. The strong host specificity of microbial diversity and its response to maintenance indicate that conservation and restoration of coral gardens require taxon-specific strategies.

AimBiogenic structural complexity increases mobile animal richness and abundance at local, regional and global scales, yet animal taxa vary in their response to complexity. When these taxa also vary functionally, habitat structures favouring certain taxa may have consequences for ecosystem function. We characterised global patterns of epifaunal invertebrates in eelgrass (Zostera marina) beds that varied in structural and genetic composition.LocationNorth America, Europe and Asia.Time Period2014.Major Taxa StudiedPeracarid crustaceans and gastropod molluscs.MethodsWe sampled epifaunal invertebrate communities in 49 eelgrass beds across 37 degrees latitude in two ocean basins concurrently with measurements of eelgrass genetic diversity, structural complexity and other abiotic and biotic environmental variables. We examined how species richness, abundance and community composition varied with latitude and environmental predictors using a random forest approach. We also examined how functional trait composition varied along with community structure.ResultsTotal species richness decreased with latitude, but this was accompanied by a taxonomic shift in dominance from peracarid crustaceans to gastropods, which exhibited different sets of functional traits. Greater eelgrass genetic diversity was strongly correlated with both richness and abundance of peracarids, but less so for gastropods.Main ConclusionsOur results add to a growing body of literature that suggests genetic variation in plant traits influences their associated faunal assemblages via habitat structure. Because peracarids and gastropods exhibited distinct functional traits, our results suggest a tentative indirect link between broad-scale variation in plant genetic diversity and ecosystem function.

Caulerpa J.V. Lamouroux is a genus of green macroalgae belonging to the family Caulerpaceae in the order Bryopsidales. The genus comprises 104 currently accepted species, of which 51 have been recorded from Pacific Islands. Among these islands, French Polynesia is found in the middle of the South Pacific Ocean and includes five archipelagos (i.e., the Austral, Gambier, Marquesas, Society, and Tuamotu Islands) where seaweed inventories have reported a total of 16 Caulerpa species so far based on morphology. Here, based on a sampling covering the five archipelagos of French Polynesia, we attempt to (i) verify the taxonomy of Caulerpa species present in these regions based on phylogeny, (ii) describe in more detail the specific diversity between the five archipelagos, and (iii) provide a morphological identification tool for these species. We successfully obtained 134 new tufA sequences for phylogenetic analyses, which corresponded to 13 species. We propose to resurrect C. pickeringii Harvey & Bailey for representatives of C. webbiana var. pickeringii and classify it in the Caulerpa subgenus Araucarioideae. We also transfer C. seuratii to C. pickeringii based on genetic results. A new morphological identification key is provided as well as an updated distribution of Caulerpa species across French Polynesia.

In the marine environment, seaweeds (i.e. marine macroalgae) provide a wide range of ecological services and economic benefits. Like land plants, seaweeds do not provide these services in isolation, rather they rely on their associated microbial communities, which together with the host form the seaweed holobiont. However, there is a poor understanding of the mechanisms shaping these complex seaweed-microbe interactions, and of the evolutionary processes underlying these interactions. Here, we identify the current research challenges and opportunities in the field of seaweed holobiont biology. We argue that identifying the key microbial partners, knowing how they are recruited, and understanding their specific function and their relevance across all seaweed life history stages are among the knowledge gaps that are particularly important to address, especially in the context of the environmental challenges threatening seaweeds. We further discuss future approaches to study seaweed holobionts, and how we can apply the holobiont concept to natural or engineered seaweed ecosystems.

Non-indigenous species often rely on trophic plasticity to adjust to available food sources and even to avoid interspecific competition while overcoming environmental constraints during the establishment phase and, eventually, as they become invasive. The Atlantic blue crab Callinectes sapidus Rathbun, 1896 is expanding quickly in southwestern Europe and northwestern Africa, raising concerns about its impacts. Its feeding ecology in non-native areas is poorly understood, so this study aimed to 1) unveil the diet and feeding strategy used by the Atlantic blue crab in a highly invaded European estuary, 2) evaluate if their invasiveness was facilitated by an invasion meltdown process concerning trophic facilitation, and 3) determine its trophic position. Metagenomic analyses of gut content and stable isotopes showed that the species relied on opportunistic and carnivorous feeding traits and preyed mainly on native animal species, such as fish, shrimps, and oysters. We did not observe evidence of a widespread invasion meltdown process through trophic facilitation mediated by other invaders. The Atlantic blue crab’s trophic niche overlapped with two native crab species, particularly the European green crab Carcinus maenas (Linnaeus, 1758), while it’s high trophic position (4.3 ± 0.5) reflected the reliance on animal prey. These evidence suggests that trophic plasticity likely contributed to the invasiveness of the Atlantic blue crab because of its ability to exploit readily available prey. The Atlantic blue crab metapopulation is expanding and increasing over a vast region, and unfortunately a series of cascading effects throughout the food web can still be expected, as observed elsewhere.

Caulerpa is a genus of green macroalgae that lives in tropical and subtropical coastal waters. It is an intriguing organism because, despite having plant-like structures, it is one giant cell – which, next to multiple nuclei, chloroplasts, and mitochondria, also contains endo- and epiphytic bacteria. The role of these bacteria is unknown, but they might impact the growth and development of the host, adaptation to environmental parameters, and, hence, the ecological success of these algae. We hypothesised that increased sulphide concentrations would trigger a significant shift in the microbial community composition associated with C. prolifera rhizoids, favouring sulphide-oxidizing bacteria. To test this hypothesis, we conducted a mesocosm experiment incubating C. prolifera in sediments with different sulphide concentrations and analysed the algal photosynthesis, growth, and microbiome composition. While photosynthesis was not affected, the Caulerpa weight-based growth rate decreased linearly with increasing sulphide concentration. To analyse the microbiome, we extracted DNA and RNA from the fronds, rhizoids, and the accompanying sediments and performed 16S amplicon sequencing. The microbiome of the fronds was unaffected in both the DNA and RNA samples. However, an increase in sulphide concentration coincided with a decrease in the relative abundance of sulphate-reducing bacteria associated with Caulerpa rhizoids, particularly from the family Desulfocapsaceae. In the RNA samples, potential sulphide oxidisers of the rhizoid-associated members of the Beggiatoaceae were detected. Our results suggest that the rhizobiome of Caulerpa plays a significant role in its adaptation to sulphide-rich environments, offering new insights into the complex interactions within marine holobionts.

Seagrass meadows provide essential ecosystem services but have been strongly declining over the past. Due to their incapability to recover effectively naturally, assisted restoration is used. This study aimed to test textile fabrics from natural derivatives to serve as carrier substrates for seagrass transplantation. The use of biotextile fabrics should enable seagrasses to better withstand hydrodynamic forces, especially in high-energy areas and during autumn and winter storms in the initial phase of restoration, thereby increasing restoration success. Here, the biodegradation behavior of three natural textiles was assessed in different configurations. Coir, sisal, and jute meshes were fixed on the top and bottom of a coir nonwoven mat, forming a so-called "sandwich structure." Specimens were buried in the Ria Formosa Lagoon, Portugal, and retrieved weekly within the first months of burial and subsequently monthly over a total period of 3 months. Weight, tensile strength, and oxygen consumption rate were used as descriptors for biodegradation and tested after each retrieval. The results obtained in this study were discussed in the context of the application of the tested materials on Zostera marina transplants. Due to experimental errors, these results are solely used for discussion purposes in a conservative manner. Based on the three descriptors, coir mesh was the least degraded by the end of the experiment. Yet, it is vital to analyze the microbiome in a study site to understand the biodegradation process and based on that select a textile material. Coir fibers appear to be a good choice in highly biologically active areas to prolong the degradation process, whereas in areas with less activity sisal could be sufficient and even beneficial through the release of compounds that foster vegetations induced by degradation.