Centro de Ciências do Mar do Algarve

Sponges (phylum Porifera) are early-diverging metazoa renowned for establishing complex microbial symbioses. Here we present a global Porifera microbiome survey, set out to establish the ecological and evolutionary drivers of these host-microbe interactions. We show that sponges are a reservoir of exceptional microbial diversity and major contributors to the total microbial diversity of the world's oceans. Little commonality in species composition or structure is evident across the phylum, although symbiont communities are characterized by specialists and generalists rather than opportunists. Core sponge microbiomes are stable and characterized by generalist symbionts exhibiting amensal and/or commensal interactions. Symbionts that are phylogenetically unique to sponges do not disproportionally contribute to the core microbiome, and host phylogeny impacts complexity rather than composition of the symbiont community. Our findings support a model of independent assembly and evolution in symbiont communities across the entire host phylum, with convergent forces resulting in analogous community organization and interactions.

In this review, our current understanding of the species Escherichia coli and its persistence in the open environment is examined. E. coli consists of six different subgroups, which are separable by genomic analyses. Strains within each subgroup occupy various ecological niches, and can be broadly characterized by either commensalistic or different pathogenic behaviour. In relevant cases, genomic islands can be pinpointed that underpin the behaviour. Thus, genomic islands of, on the one hand, broad environmental significance, and, on the other hand, virulence, are highlighted in the context of E. coli survival in its niches. A focus is further placed on experimental studies on the survival of the different types of E. coli in soil, manure and water. Overall, the data suggest that E. coli can persist, for varying periods of time, in such terrestrial and aquatic habitats. In particular, the considerable persistence of the pathogenic E. coli O157:H7 is of importance, as its acid tolerance may be expected to confer a fitness asset in the more acidic environments. In this context, the extent to which E. coli interacts with its human/animal host and the organism's survivability in natural environments are compared. In addition, the effect of the diversity and community structure of the indigenous microbiota on the fate of invading E. coli populations in the open environment is discussed. Such a relationship is of importance to our knowledge of both public and environmental health.

Abstract Enhanced production of high quality and healthy fry is a key target for a successful and competitive expansion of the aquaculture industry. Although large quantities of fish larvae are produced, survival rates are often low or highly variable and growth potential is in most cases not fully exploited, indicating significant gaps in our knowledge concerning optimal nutritional and culture conditions. Understanding the mechanisms that control early development and muscle growth are critical for the identification of time windows in development that introduce growth variation, and improve the viability and quality of juveniles. This literature review of the current state of knowledge aims to provide a framework for a better understanding of fish skeletal muscle ontogeny, and its impact on larval and juvenile quality as broadly defined. It focuses on fundamental biological knowledge relevant to larval phenotype and quality and, in particular, on the factors affecting the development of skeletal muscle. It also discusses the available methodologies to assess growth and larvae/juvenile quality, identifies gaps in knowledge and suggests future research directions. The focus is primarily on the major farmed non‐salmonid fish species in E urope that include gilthead sea bream, E uropean sea bass, turbot, A tlantic cod, S enegalese sole and A tlantic halibut.

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.

Marine protected areas (MPAs) are a global conservation and management tool to enhance the resilience of linked social-ecological systems with the aim of conserving biodiversity and providing ecosystem services for sustainable use. However, MPAs implemented worldwide include a large variety of zoning and management schemes from single to multiple-zoning and from no-take to multiple-use areas. The current IUCN categorisation of MPAs is based on management objectives which many times have a significant mismatch to regulations causing a strong uncertainty when evaluating global MPAs effectiveness. A novel global classification system for MPAs based on regulations of uses as an alternative or complementing the current IUCN system of categories is presented. Scores for uses weighted by their potential impact on biodiversity were built. Each zone within a MPA was scored and an MPA index integrates the zone scores. This system classifies MPAs as well as each MPA zone individually, is globally applicable and unambiguously discriminates the impacts of uses.

International audience

Heinrich Stadials significantly affected tropical precipitation through changes in the interhemispheric temperature gradient as a result of abrupt cooling in the North Atlantic. Here, we focus on changes in South American monsoon precipitation during Heinrich Stadials using a suite of speleothem records covering the last 85 ky B.P. from eastern South America. We document the response of South American monsoon precipitation to episodes of extensive iceberg discharge, which is distinct from the response to the cooling episodes that precede the main phase of ice-rafted detritus deposition. Our results demonstrate that iceberg discharge in the western subtropical North Atlantic led to an abrupt increase in monsoon precipitation over eastern South America. Our findings of an enhanced Southern Hemisphere monsoon, coeval with the iceberg discharge into the North Atlantic, are consistent with the observed abrupt increase in atmospheric methane concentrations during Heinrich Stadials.

Abstract Aim Meiofaunal communities that inhabit the marine benthos offer unique opportunities to simultaneously study the macroecology of numerous phyla that exhibit different life‐history strategies. Here, we ask: (1) if the macroecology of meiobenthic communities is explained mainly by dispersal constraints or by environmental conditions; and (2) if levels of meiofaunal diversity surpass existing estimates based on morphological taxonomy. Location UK and mainland European coast. Methods Next‐generation sequencing techniques ( NGS ; R oche 454 FLX platform) using 18S nuclear small subunit ribosomal DNA ( rDNA ) gene. Pyrosequences were analysed using A mplicon N oise followed by chimera removal using P erseus . Results Rarefaction curves revealed that sampling saturation was only reached at 15% of sites, highlighting that the bulk of meiofaunal diversity is yet to be discovered. Overall, 1353 OTU s were recovered and assigned to 23 different phyla. The majority of sampled sites had c. 60–70 unique operational taxonomic units ( OTU s) per site, indicating high levels of beta diversity. The environmental parameters that best explained community structure were seawater temperature, geographical distance and sediment size, but most of the variability ( R 2 = 70%–80%) remains unexplained. Main conclusions High percentages of endemic OTU s suggest that meiobenthic community composition is partly niche‐driven, as observed in larger organisms, but also shares macroecological features of microorganisms by showing high levels of cosmopolitanism (albeit on a much smaller scale). Meiobenthic communities exhibited patterns of isolation by distance as well as associations between niche, latitude and temperature, indicating that meiobenthic communities result from a combination of niche assembly and dispersal processes. Conversely, isolation‐by‐distance patterns were not identified in the featured protists, suggesting that animals and protists adhere to radically different macroecological processes, linked to life‐history strategies.

ABSTRACT Changes in water quality significantly shape fish behavior, a crucial index reflecting the growth and welfare status of fish. Given the centrality of this relationship to aquaculture practices, a comprehensive understanding of how water quality dynamics influence fish behavior is imperative. While there have been some summaries of the effects of water quality parameters on fish physiology and growth, few reviews on their effects on fish behavior have been reported yet. This article reviews several water quality parameters which are of great concern in aquaculture from multiple facets of actual production, including physical parameters (water temperature and turbidity), chemical parameters (dissolved oxygen, salinity, pH, and inorganic nitrogen), and chemical pollutants (microplastics and crude oil), which have gained increasing attention from the researchers and aquaculture practitioners over the past decades. Variations in these water quality parameters can exert profound effects on fish physiology, metabolism, internal tissues and organs, and sensory perception, which influences fish behaviors such as swimming, schooling, feeding, predation, anti‐predation, aggression, courtship, as well as adaptive and stress‐related behaviors such as exploration, avoidance response, and anxiety‐like behavior. By synthesizing the behavioral changes caused by specific water quality parameters, this review aims to provide strong support for further water quality‐related research, thereby fostering environments conducive to both fish welfare and aquaculture productivity.

The coastal ocean represents an important global carbon sink and is a focus for interventions to mitigate climate change and meet the Paris Agreement targets while supporting biodiversity and other ecosystem functions. However, the fate of the flux of carbon exported from seaweed forests—the world’s largest coastal vegetated ecosystem—is a key unknown in marine carbon budgets. Here we provide national and global estimates for seaweed-derived particulate carbon export below 200 m depth, which totalled 3–4% of the ocean carbon sink capacity. We characterized export using models of seaweed forest extent, production and decomposition, as well as shelf–open ocean water exchange. On average, 15% of seaweed production is estimated to be exported across the continental shelf, which equates to 56 TgC yr−1 (range: 10–170 TgC yr−1). Using modelled sequestration timescales below 200 m depth, we estimated that each year, 4–44 Tg seaweed-derived carbon could be sequestered for 100 years. Determining the full extent of seaweed carbon sequestration remains challenging, but critical to guide efforts to conserve seaweed forests, which are in decline globally. Our estimate does not include shelf burial and dissolved and refractory carbon pathways; still it highlights a relevant potential contribution of seaweed to natural carbon sinks. Coastal seaweed transported to the open ocean contributes up to 3–4% of the particulate organic carbon sinking into the deeper ocean, according to combined ecological and biogeochemical modelling.

Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g., the development of controlled experimental model systems for holobionts from all major lineages and the modeling of (info)chemical-mediated interactions between organisms. Here we propose that one significant challenge is to bridge cross-disciplinary research on tractable model systems in order to address key ecological and evolutionary questions. This first step is crucial to decipher the main drivers of the dynamics and evolution of holobionts and to account for the holobiont concept in applied areas, such as the conservation, management, and exploitation of marine ecosystems and resources, where practical solutions to predict and mitigate the impact of human activities are more important than ever.

Abstract Aim Marine forests of brown macroalgae create essential habitats for coastal species and support invaluable ecological services. Here, we provide the first global analysis of species richness and endemicity of both the kelp and fucoid biomes. Location Global. Time period Contemporary. Major taxa studied Marine forests of brown macroalgae, formed by kelp (here defined as orders Laminariales, Tilopteridales and Desmarestiales) and fucoid (order Fucales), inhabiting subtidal and intertidal environments. Methods We coupled a large dataset of macroalgal observations (420 species, 1.01 million records) with a high‐resolution dataset of relevant environmental predictors (i.e., light, temperature, salinity, nitrate, wave energy and ice coverage) to develop stacked species distribution models (stacked SDMs) and yield estimates of global species richness and endemicity. Results Temperature and light were the main predictors shaping the distribution of subtidal species, whereas wave energy, temperature and salinity were the main predictors of intertidal species. The highest regional species richness for kelp was found in the north‐east Pacific (maximum 32 species) and for fucoids in south‐east Australia (maximum 53 species), supporting the hypothesis that these regions were the evolutionary sources of global colonization by brown macroalgae. Locations with low species richness coincided between kelp and fucoid, occurring mainly at higher latitudes (e.g., Siberia) and the Baltic Sea, where extensive ice coverage and low‐salinity regimes prevail. Regions of high endemism for both groups were identified in the Galapagos Islands, Antarctica, South Africa and East Russia. Main conclusions We estimated the main environmental drivers and limits shaping the distribution of marine forests of brown macroalgae and mapped biogeographical centres of species richness and endemicity, which largely coincided with the expectation from previous evolutionary hypotheses. The mapped biodiversity patterns can serve as new baselines for planning and prioritizing locations for conservation, management and climate change mitigation strategies, flagging threatened marine forest regions under different climate change scenarios.

Radiometric dating of glacial terminations over the past 640,000 years suggests pacing by Earth's climatic precession, with each glacial-interglacial period spanning four or five cycles of ~20,000 years. However, the lack of firm age estimates for older Pleistocene terminations confounds attempts to test the persistence of precession forcing. We combine an Italian speleothem record anchored by a uranium-lead chronology with North Atlantic ocean data to show that the first two deglaciations of the so-called 100,000-year world are separated by two obliquity cycles, with each termination starting at the same high phase of obliquity, but at opposing phases of precession. An assessment of 11 radiometrically dated terminations spanning the past million years suggests that obliquity exerted a persistent influence on not only their initiation but also their duration.

BACKGROUND: The highly valuable red coral Corallium rubrum is listed in several Mediterranean Conventions for species protection and management since the 1980s. Yet, the lack of data about its Atlantic distribution has hindered its protection there. This culminated in the recent discovery of poaching activities harvesting tens of kg of coral per day from deep rocky reefs off SW Portugal. Red coral was irregularly exploited in Portugal between the 1200s and 1700s, until the fishery collapsed. Its occurrence has not been reported for the last 300 years. RESULTS: Here we provide the first description of an Atlantic red coral assemblage, recently rediscovered dwelling at 60-100 m depth in southern Portugal. We report a very slow growth rate (0.23 mm year-1), comparable to Mediterranean specimens. In comparison with most of the Mediterranean reports, the population reaches much larger sizes, estimated to be over one century old, and has a more complex coral branch architecture that promotes a rich assemblage of associated species, with boreal and Mediterranean affinities. Atlantic red coral is genetically distinct, yet mitochondrial analyses suggest that red corals from the Atlantic may have introgressed the Mediterranean ones after migration via the Algeria current. Our underwater surveys, using advanced mixed-gas diving, retrieved lost fishing gear in all coral sites. Besides illegal harvesting, the use and loss of fishing gears, particularly nets, by local fisheries are likely sources of direct impacts on these benthic assemblages. CONCLUSIONS: We extended the knowledge on the distribution of C. rubrum in the Atlantic, discovered its genetic distinctiveness, and reveal a rich deep-dwelling fauna associated to these coral assemblages. These findings support a barrier role of the Atlantic-Mediterranean transition zone, but reveal also hints of connectivity along its southern margin. The results highlight the genetic and demographic uniqueness of red coral populations from SW Iberia. However, we also report threats to these vulnerable populations by direct and indirect fishing activities and argue that its protection from any mechanically destructive activities is urgent as a precautionary approach. This study advances our understanding of phylogeographic barriers and range edge genetic diversity, and serves as a baseline against which to monitor future human and environmental disturbances to Atlantic C. rubrum.

Marine megafauna has always elicited contrasting feelings. In the past, large marine animals were often depicted as fantastic mythological creatures and dangerous monsters, while also arousing human curiosity. Marine megafauna has been a valuable resource to exploit, leading to the collapse of populations and local extinctions. In addition, some species have been perceived as competitors of fishers for marine resources and were often actively culled. Since the 1970s, there has been a change in the perception and use of megafauna. The growth of marine tourism, increasingly oriented towards the observation of wildlife, has driven a shift from extractive to non-extractive use, supporting the conservation of at least some species of marine megafauna. In this paper, we review and compare the changes in the perception and use of three megafaunal groups, cetaceans, elasmobranchs and groupers, with a special focus on European cultures. We highlight the main drivers and the timing of these changes, compare different taxonomic groups and species, and highlight the implications for management and conservation. One of the main drivers of the shift in perception, shared by all the three groups of megafauna, has been a general increase in curiosity towards wildlife, stimulated inter alia by documentaries (from the early 1970s onwards), and also promoted by easy access to scuba diving. At the same time, environmental campaigns have been developed to raise public awareness regarding marine wildlife, especially cetaceans, a process greatly facilitated by the rise of Internet and the World Wide Web. Currently, all the three groups (cetaceans, elasmobranchs and groupers) may represent valuable resources for ecotourism. Strikingly, the economic value of live specimens may exceed their value for human consumption. A further change in perception involving all the three groups is related to a growing understanding and appreciation of their key ecological role. The shift from extractive to non-extractive use has the potential for promoting species conservation and local economic growth. However, the change in use may not benefit the original stakeholders (e.g. fishers or whalers) and there may therefore be a case for providing compensation for disadvantaged stakeholders. Moreover, it is increasingly clear that even non-extractive use may have a negative impact on marine megafauna, therefore regulations are needed.

Seagrasses structure some of the world’s key coastal ecosystems presently in decline due to human activities and global change. The ability to cope with environmental changes and the possibilities for shifts in distribution range depend largely on their evolvability and dispersal potential. As large-scale data usually show strong genetic structure for seagrasses, finer-grained work is needed to understand the local processes of dispersal, recruitment and colonization that could explain the apparent lack of exchange across large distances. We aimed to assess the fine-grained genetic structure of one of the most important and widely distributed seagrasses, Zostera marina, from seven meadows in Brittany, France. Both classic population genetics and network analysis confirmed a pattern of spatial segregation of polymorphism at both regional and local scales. One location exhibiting exclusively the variety ‘angustifolia’ did not appear more differentiated than the others, but instead showed a central position in the network analysis, confirming the status of this variety as an ecotype. This phenotypic diversity and the high allelic richness at nine microsatellites (2.33–9.67 alleles/locus) compared to levels previously reported across the distribution range, points to Brittany as a centre of diversity for Z. marina at both genetic and phenotypic levels. Despite dispersal potential of several 100 m, a significant pattern of genetic differentiation, even at fine-grained scale, revealed ‘genetic patchiness’. Meadows seem to be composed of a mosaic of clones with distinct origins in space and time, a result that calls into question the accuracy of the concept of populations for such partially clonal species.

Abstract Increasing oceanic uptake of CO 2 is predicted to drive ecological change as both a resource (i.e. CO 2 enrichment on primary producers) and stressor (i.e. lower pH on consumers). We use the natural ecological complexity of a CO 2 vent (i.e. a seagrass system) to assess the potential validity of conceptual models developed from laboratory and mesocosm research. Our observations suggest that the stressor-effect of CO 2 enrichment combined with its resource-effect drives simplified food web structure of lower trophic diversity and shorter length. The transfer of CO 2 enrichment from plants to herbivores through consumption (apparent resource-effect) was not compensated by predation, because carnivores failed to contain herbivore outbreaks. Instead, these higher-order consumers collapsed (apparent stressor-effect on carnivores) suggesting limited trophic propagation to predator populations. The dominance of primary producers and their lower-order consumers along with the loss of carnivores reflects the duality of intensifying ocean acidification acting both as resource-effect (i.e. bottom-up control) and stressor-effect (i.e. top-down control) to simplify community and trophic structure and function. This shifting balance between the propagation of resource enrichment and its consumption across trophic levels provides new insights into how the trophic dynamics might stabilize against or propagate future environmental change.

Aquaculture is the fastest-growing sector in food production worldwide. For decades, research on animal physiology, nutrition, and behavior established the foundations of best practices in land-based fish rearing and disease control. Current DNA sequencing, bioinformatics, and data science technologies now allow deep investigations of host-associated microbiomes in a tractable fashion. Adequate use of these technologies can illuminate microbiome dynamics and aid the engineering of microbiome-based solutions to disease prevention in an unprecedented manner. This review examines molecular studies of bacterial diversity, function, and host immunitymodulation at early stages of fish development, where microbial infections cause important economic losses. We uncover host colonization and virulence factors within a synthetic assemblage of fish pathogens using high-end comparative genomics and address the use of probiotics and paraprobiotics as applicable disease-prevention strategies in fish larval and juvenile rearing. We finally propose guidelines for future microbiome research of presumed relevance to fish larviculture.

Marine sponges are early-branching, filter-feeding metazoans that usually host complex microbiomes comprised of several, currently uncultivatable symbiotic lineages. Here, we use a low-carbon based strategy to cultivate low-abundance bacteria from Spongia officinalis. This approach favoured the growth of Alphaproteobacteria strains in the genera Anderseniella, Erythrobacter, Labrenzia, Loktanella, Ruegeria, Sphingorhabdus, Tateyamaria and Pseudovibrio, besides two likely new genera in the Rhodobacteraceae family. Mapping of complete genomes against the metagenomes of S. officinalis, seawater, and sediments confirmed the rare status of all the above-mentioned lineages in the marine realm. Remarkably, this community of low-abundance Alphaproteobacteria possesses several genomic attributes common to dominant, presently uncultivatable sponge symbionts, potentially contributing to host fitness through detoxification mechanisms (e.g. heavy metal and metabolic waste removal, degradation of aromatic compounds), provision of essential vitamins (e.g. B6 and B12 biosynthesis), nutritional exchange (especially regarding the processing of organic sulphur and nitrogen) and chemical defence (e.g. polyketide and terpenoid biosynthesis). None of the studied taxa displayed signs of genome reduction, indicative of obligate mutualism. Instead, versatile nutrient metabolisms along with motility, chemotaxis, and tight-adherence capacities - also known to confer environmental hardiness - were inferred, underlying dual host-associated and free-living life strategies adopted by these diverse sponge-associated Alphaproteobacteria.

Globally, there are a large and growing number of researchers using biotelemetry as a tool to study aquatic animals. In Europe, this community lacks a formal network structure. The aim of this study is to review the use of acoustic telemetry in Europe and document the contribution of cross-boundary studies and inter-research group collaborations. Based on this, we explore the potential benefits and challenges of a network approach to identify future priorities and best practices for aquatic biotelemetry research in Europe. Over the past decade, there was an approximately sevenfold increase in the number of acoustic telemetry studies published on marine and diadromous species in Europe compared to a sixfold increase globally. Over 90% of these studies were conducted on fishes and undertaken in coastal areas, estuaries, or rivers. 75% of these studies were conducted by researchers based in one of five nations (Norway, UK, France, Portugal, and Spain) and, even though 34% were based on collaborations between scientists from several countries, there was only one study with an acoustic receiver array that extended beyond the borders of a single country. In recent years, acoustic telemetry in European waters has evolved from studying behavioural aspects of animals (82.2%), into more holistic approaches addressing management-related issues (10%), tagging methods and effects (5%), and technology and data analysis development (2.8%). Despite the increasing number of publications and species tracked, there is a prominent lack of planned and structured acoustic telemetry collaborations in Europe. A formal pan-European network structure would promote the development of (1) a research platform that could benefit the acoustic telemetry community through capacity building, (2) a centralized database, and (3) key deployment sites and studies on priority species requiring research in Europe. A network may increase efficiency, expand the scope of research that can be undertaken, promote European science integration, enhance the opportunities and success of acquiring research funding and, ultimately, foster regional and transatlantic collaborations. It may also help address research priorities such as the large-scale societal challenges arising from climate change impacts and assist the EU’s Marine Strategy Framework Directive via identification of good environmental status of endangered or commercially important species.