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Contrary to most terrestrial organisms, which release their carbon into the atmosphere after death, carcasses of large marine fish sink and sequester carbon in the deep ocean. Yet, fisheries have extracted a massive amount of this "blue carbon," contributing to additional atmospheric CO2 emissions. Here, we used historical catches and fuel consumption to show that ocean fisheries have released a minimum of 0.73 billion metric tons of CO2 (GtCO2) in the atmosphere since 1950. Globally, 43.5% of the blue carbon extracted by fisheries in the high seas comes from areas that would be economically unprofitable without subsidies. Limiting blue carbon extraction by fisheries, particularly on unprofitable areas, would reduce CO2 emissions by burning less fuel and reactivating a natural carbon pump through the rebuilding of fish stocks and the increase of carcasses deadfall.

The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; "CESTES". Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology.

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This article explores the functional diversity and redundancy in a bacterial metacommunity constituted of three habitats (sediment, water column and fish gut) in a coastal lagoon under anthropogenic pressure. Comprehensive functional gene arrays covering a wide range of ecological processes and stress resistance genes to estimate the functional potential of bacterial communities were used. Then, diversity partitioning was used to characterize functional diversity and redundancy within (α), between (β) and across (γ) habitats. It was showed that all local communities exhibit a highly diversified potential for the realization of key ecological processes and resistance to various environmental conditions, supporting the growing evidence that macro-organisms microbiomes harbour a high functional potential and are integral components of functional gene dynamics in aquatic bacterial metacommunities. Several levels of functional redundancy at different scales of the bacterial metacommunity were observed (within local communities, within habitats and at the metacommunity level). The results suggested a high potential for the realization of spatial ecological insurance within this ecosystem, that is, the functional compensation among microorganisms for the realization and maintenance of key ecological processes, within and across habitats. Finally, the role of macro-organisms as dispersal vectors of microbes and their potential influence on marine metacommunity dynamics were discussed.

Rarity has been a central topic for conservation and evolutionary biologists aiming to determine the species characteristics that cause extinction risk. More recently, beyond the rarity of species, the rarity of functions or functional traits, called functional rarity, has gained momentum in helping to understand the impact of biodiversity decline on ecosystem functioning. However, a conceptual framework for defining and quantifying functional rarity is still lacking. We introduce 12 different forms of functional rarity along gradients of species scarcity and trait distinctiveness. We then highlight the potential key role of functional rarity in the long-term and large-scale maintenance of ecosystem processes, as well as the necessary linkage between functional and evolutionary rarity.

Understanding how ecological assemblages vary in space and time is essential for advancing our knowledge of biodiversity dynamics and ecosystem functioning. Metabarcoding of environmental DNA (eDNA) is an efficient method for documenting biodiversity changes in both marine and terrestrial ecosystems. However, current methods fail to detect and display the biodiversity structure within and between eDNA samples limiting ecological and biogeographical interpretations.We present a spatial matrix factorization method that identifies optimal eDNA sample assemblages—called pools—assuming that taxonomic unit composition is based on a fixed number of unknown sources. These sources, in turn, represent taxonomic units sharing similar habitat properties or characteristics. The method aims to reduce the multi‐taxa composition structure into a low number of dimensions defined by these sources. This method is inspired by admixture analysis in population genetics. Using a marine fish eDNA survey on 263 sampling stations detecting 2888 molecular operational taxonomic units (MOTUs), we apply this method to analyse the biogeography and mixing patterns of fish assemblages at regional and large scales.At large scale, our analysis reveals six primary pools of fish samples characterized by distinct biogeographic patterns, with some mixtures between these pools. We identify pools composed of unique sources, corresponding to distinct and more isolated regions such as the Mediterranean and Scotia Seas. We also identify pools composed of a greater mix of sources, corresponding to geographically connected areas, such as tropical regions. Additionally, we identify the taxa underpinning the formation of each pool. In the regional analysis of Mediterranean eDNA samples, our method successfully identifies different pools, allowing the detection of not only geographic gradients but also human‐induced gradients corresponding to protection levels.Spatial matrix factorization adds a new method in community ecology, where each sample is considered as a mixture of K unobserved sources, to assess the dissimilarity of ecological assemblages revealing environmental and human‐induced gradients. Beyond the study of fish eDNA samples, this method has the potential to shed new light on any biodiversity survey and provide new bioindicators of global change. [ABSTRACT FROM AUTHOR]

Aim: Ecological state shifts that alter the structure and function of entire ecosystems are a concerning consequence of human impact. Yet, when, where and why discrete ecological states emerge remains difficult to predict and monitor, especially in high‐diversity systems. We sought to quantify state shifts and their drivers through space and time in the most ecologically complex marine ecosystem: tropical coral reefs. Location: Worldwide. Time Period: 1987–2019. Major Taxa Studied: Coral reef communities. Methods: Using a global dataset of 3375 coral reef surveys, along with 13 time series datasets ranging between 1987 and 2019, we applied a novel double‐dichotomy approach to classify coral reefs into four simplified and discrete states based on the relative contributions of corals versus algae to benthic cover and small‐bodied versus large‐bodied fishes to fish standing stock. We then examined state shifts considering a range of spatial predictors and tested whether states have shifted directionally over time, and the nature of the most common transitions. Results: We show that geographic, environmental and anthropogenic context fundamentally shapes coral reef states at the local scale, which explains disparities among case studies, and stakes out critical baseline expectations for regional management efforts. We also reveal clear multi‐decadal state shifts on coral reefs: over time, systems dominated by reef‐building corals and small‐bodied, planktivorous fishes tend to have been replaced with reefs characterised by algae and larger‐bodied fishes. Main Conclusions: Our results suggest a previously unrecognised transition from systems that harness external subsidies through small‐bodied consumers associated with structurally complex live corals, to herbivore‐dominated systems with stronger bottom‐up dynamics. Overall, the partitioning of complex reef ecosystems into a small suite of discrete ecological states suggests that spatial context‐dependency, shifting baselines and changes in reef functioning are crucial considerations for coral reef management in the 21st century. [ABSTRACT FROM AUTHOR]

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ABSTRACT Aim Location Methods Results Main Conclusions The Mediterranean Sea is one of the most anthropized seas in the world but also a marine biodiversity hotspot with many fish species under threat. The main goal of the study is to test whether on the heavily fished and anthropized Mediterranean coast, the less impacted Corsica and Balearic Islands, can be considered as refugia for threatened and elasmobranch fishes independently of protection by marine reserves.The French Mediterranean coast and three north‐western Mediterranean islands: Corsica and also Mallorca and Minorca from the Balearic archipelago.We performed 187 fish surveys using environmental DNA metabarcoding on three islands and 109 along the continental coast. Of the 78 surveys on islands 22 correspond to no‐take marine reserves and of the 109 continental surveys 26 were carried out within reserves. After eDNA filtration, extraction, amplification, and sequencing we estimated the number of fish species but also the number commercial, threatened and elasmobranch fish species on each sample. We then performed an ANOVA by permutation to test the effect of insularity and protection on these four biodiversity metrics. We also modelled these four biodiversity metrics as a function of protection and human pressure but also environmental, habitat and sampling conditions. We also built species accumulation curves to obtain asymptotes representing the potential regional pools for each species category on both island and continental coasts.We obtained a total of 175,982,610 reads over the 187 eDNA samples that were assigned to 153 fish species including 17 elasmobranch species among which 7 were only detected on islands. We observed a higher total fish richness on continental than island surveys regardless of protection but a higher threatened and elasmobranch fish richness on the island than on continental surveys. We obtained a significant, negative and predominant human gravity impact on the diversity of elasmobranch species. The modelled asymptote reached 148 teleostean fish species on islands and 196 on the continental coastline with a very similar rate of diversity increase with sampling effort but the shape of the species accumulation curves differed markedly for elasmobranchs with a stronger increase in diversity with sampling effort on islands.Our findings highlight that Mediterranean islands can be refugia for sharks and rays but also threatened fishes in this overexploited region. Our results also suggest that reducing or banning trawling activities may play a key role for conserving vulnerable fishes, beyond the benefits of no‐take marine reserves, which appear limited on these large home‐range species. [ABSTRACT FROM AUTHOR]

Marine Protected Areas (MPAs) are a cornerstone of marine conservation efforts, with the potential to protect biodiversity and provide socioeconomic benefits. We quantified the effect of MPAs on fishing outcomes, economic activities, and material living standards in 24 coastal villages of Tanzania over two decades. We accessed original data from a study conducted in 2003 that found no effect of MPAs 3–8 years after their creation. Eighteen years later, we replicated the survey and used a Before‐After Control‐Intervention design to quantify the effect of MPAs. We found that villages near MPAs experienced a 50% higher improvement in living standards compared to those further from MPAs. This benefit is not related to higher fishing outcomes but to a diversification of economic sectors. Our findings highlight a decoupling between fish catches and economic benefits, revealing that socio‐economic outcomes can be observed for MPAs whose ecosystems' productivity has declined. [ABSTRACT FROM AUTHOR]

Evidence of large‐scale biodiversity degradation in marine ecosystems has been reported worldwide, yet most research has focused on few species of interest or on limited spatiotemporal scales. Here we assessed the spatial and temporal changes in the taxonomic and functional composition of fish communities in European seas over the last 25 years (1994–2019). We then explored how these community changes were linked to environmental gradients and fishing pressure. We show that the spatial variation in fish species composition is more than two times higher than the temporal variation, with a marked spatial continuum in taxonomic composition and a more homogenous pattern in functional composition. The regions warming the fastest are experiencing an increasing dominance and total abundance of r‐strategy fish species (lower age of maturity). Conversely, regions warming more slowly show an increasing dominance and total abundance of K‐strategy species (high trophic level and late reproduction). Among the considered environmental variables, sea surface temperature, surface salinity and chlorophyll‐a most consistently influenced communities' spatial patterns, while bottom temperature and oxygen had the most consistent influence on temporal patterns. Changes in communities' functional composition were more closely related to environmental conditions than taxonomic changes. Our study demonstrates the importance of integrating community‐level species traits across multi‐decadal scales and across a large region to better capture and understand ecosystem‐wide responses and provides a different lens on community dynamics that could be used to support sustainable fisheries management. [ABSTRACT FROM AUTHOR]

While extinction risk categorization is fundamental for building robust conservation planning for marine fishes, empirical data on occurrence and vulnerability to disturbances are still lacking for most marine teleost fish species, preventing the assessment of their International Union for the Conservation of Nature (IUCN) status. In this article, we predicted the IUCN status of marine fishes based on two machine learning algorithms, trained with available species occurrences, biological traits, taxonomy, and human uses. We found that extinction risk for marine fish species is higher than initially estimated by the IUCN, increasing from 2.5% to 12.7%. Species predicted as Threatened were mainly characterized by a small geographic range, a relatively large body size, and a low growth rate. Hotspots of predicted Threatened species peaked mainly in the South China Sea, the Philippine Sea, the Celebes Sea, the west coast Australia and North America. We also explored the consequences of including these predicted species' IUCN status in the prioritization of marine protected areas through conservation planning. We found a marked increase in prioritization ranks for subpolar and polar regions despite their low species richness. We suggest to integrate multifactorial ensemble learning to assess species extinction risk and offer a more complete view of endangered taxonomic groups to ultimately reach global conservation targets like the extending coverage of protected areas where species are the most vulnerable. Empirical data on occurrences and vulnerability are still lacking for most marine teleost fish species, preventing assessment of their IUCN extinction risk status. This study uses machine learning with occurrence data, species biological traits, taxonomy and human usage to infer a 12.8% extinction risk for marine fish species, surpassing existing estimates. [ABSTRACT FROM AUTHOR]