Biodiversity Of Marine Ecosystems Research Articles

DNA metabarcoding as a tool for characterising the spatio-temporal distribution of planktonic larvae in the phylum Echinodermata

AbstractMetabarcoding is revolutionising the analysis of biodiversity in marine ecosystems, especially as it provides a means of detecting and identifying cryptic life stages in field samples. The planktonic larval stage of many species underpins the abundance and distribution of adult populations but is challenging to characterise given the small size of larvae and diffuse distributions in pelagic waters. Yet, planktonic larval dynamics are key to understanding phenomena observed in adult populations, such as the boom-and-bust dynamics exhibited by some echinoderms. Rapid changes in echinoderm population density can have significant effects on local benthic ecosystems. For example, outbreaks of the crown-of-thorns sea star (CoTS) on the Great Barrier Reef (GBR) have led to considerable declines in coral cover. Here, we used a DNA metabarcoding approach to investigate the spatio-temporal distribution and diversity of echinoderm larvae on the GBR, including CoTS. Generalised linear mixed models revealed that echinoderm larval richness, was significantly correlated with temporal variables (i.e. season and year) which is consistent with expected fluctuations in larval output based on adult spawning periodicity. However, neither site-specific differences in echinoderm larval richness, nor correlations between larval composition and environmental, temporal, or spatial variables were found. This study validates the utility of metabarcoding approaches for detecting and characterising echinoderm larvae, including CoTS, which could prove useful to future monitoring efforts. Our findings suggest that metabarcoding can be used to better understand the life history of planktonic larvae, and analyses combining environmental (e.g., temperature, nutrients) and oceanographic (e.g., currents) data could deliver valuable information on the factors influencing their spatio-temporal distributions.

Seasonal distribution patterns and conservation gaps of blue sharks in the Indo‐Western Pacific Ocean

AbstractAimOceanic sharks play an important role in maintaining the stability and biodiversity of marine ecosystems, and yet they are among the most threatened taxa worldwide. Currently, large spatial‐scale distribution patterns and conservation gaps are poorly known for most species since they are challenging to study. To address the problem, we here use an integrated approach with an illustration with the blue shark (Prionace glauca), a common bycatch oceanic species.LocationIndo‐Western Pacific Ocean (IWPO).MethodsWe first collated decades of species occurrences and marine environmental datasets from open‐access sources. We then applied ensembled species distribution models (SDMs) to predict its seasonal distributions and evaluated the model performance using true skill statistic (TSS) and area under the receiver‐operating characteristic curve (AUC). We finally conducted spatial analyses (e.g. bivariate hotspot analyses) to identify conservation gaps/opportunities based on the predicted distribution maps and two additional datasets, namely, marine protected areas (MPAs) and fishing effort.Results(1) Both seasonal SDMs performed well (mean TSS > 0.8, AUC > 0.95), and the results suggested that blue sharks were widely distributed in the IWPO with some seasonal differences in ecological niches and distributions (mainly in the West Indian Ocean and the Northwest Pacific Ocean); (2) large MPAs and shark sanctuaries covered comparable, small portions (4%–9%) of blue shark habitats, but these locations (in MPAs and sanctuaries) varied between seasons; (3) fishery‐shark conflict hotspots also varied between seasons with some located in or close to large MPAs and sanctuaries.Main conclusionsWe provide seasonal (cold vs. warm) distribution maps of blue sharks across the IWPO to advance their conservation and management. We highlight the importance of strengthening management both in and near large MPAs and shark sanctuaries. Our study contributes a feasible integrated approach to reveal seasonal distribution patterns and conservation opportunities for oceanic sharks.

Molecular analyses of carangid fish diets reveal inter-predation, dietary overlap, and the importance of early life stages in trophic ecology.

Carangid fishes are commercially important in fisheries and aquaculture. They are distributed worldwide in both tropical and subtropical marine ecosystems. Their role in food webs is often unclear since their diet cannot be easily identified by traditional gut content analysis. They are suspected to prey on pelagic and benthic species, with clupeiform fishes being important dietary items for some species, though it is unknown whether carangids share food resources or show trophic segregation. Here, we used metabarcoding to overcome traditional challenges of taxonomic approaches to analyze the diet of seven carangid species caught as bycatch in the Brazilian southwest Atlantic sardine fishery. Stomach contents were processed from the following species: Caranx crysos, Caranx latus, Chloroscombrus chrysurus, Hemicaranx amblyrhynchus, Oligoplites saliens, Selene setapinnis, and Trachinotus carolinus. Identified diets were dominated by teleost fishes. The C. latus diet was the most distinct among the seven species, preferentially consuming Engraulis anchoita, but H. amblyrhynchus, O. saliens, and S. setapinnis also showed a trend of predominantly consuming small pelagic fishes. Finally, we found evidence of inter-predation in carangids, especially strong between S. setapinnis and C. crysos, suggesting that consumption of early life stages may result in indirect competition through reduced recruitment in these fishes. These findings provide unprecedented insights into the biodiversity in marine ecosystems, especially the poorly known diet of carangid fishes.

MetaZooGene Atlas and Database: Reference Sequences for Marine Ecosystems.

The MetaZooGene Atlas and Database (MZGdb; https://metazoogene.org/mzgdb/ ) is an open-access data and metadata portal synchronized with the NCBI GenBank and BOLD data repositories. The MZGdb includes sequences for genes used for the classification and identification of marine organisms based on DNA barcoding and metabarcoding. The focus of the MZGdb is biodiversity of marine ecosystems, including phytoplankton and microbes, zooplankton and invertebrates, fish, and other marine vertebrates (pinnipeds, cetaceans, and sea turtles). DNA sequences currently included are mitochondrial cytochrome oxidase I (COI), 12S, and 16S rRNA, and nuclear 18S and 28S rRNA. The MZGdb provides data and mapping tools for assembling and downloading compilations of reference sequence data that are specific to selected genes, taxonomic groups, and/or ocean regions. An additional feature of the MZGdb is the Atlas which summarizes data coverage and proportional completeness based on statistics of species with available sequences versus species commonly found in each ocean region.This chapter is a collaborative effort of the Scientific Committee for Ocean Research (SCOR) Working Group WG157: MetaZooGene: Toward a new global view of marine zooplankton biodiversity based on DNA metabarcoding and reference DNA sequence databases ( https://metazoogene.org ).

Assessment of macrobenthos diversity and a zoning proposal for Seixas coral reefs (northeastern Brazil)

Coral reefs worldwide are under severe threat due to their inherent fragility and urgent need for conservation. The escalating tourism in coral reefs significantly impacts the marine ecosystem's biodiversity and conservation. This study analyzed the diversity and conservation status of macrobenthos in the Seixas coral reef, located in northeastern Brazil, and proposed a zoning plan. We employed monitoring protocols adapted from the Reef Check Program, the Rapid Assessment Protocol for Atlantic and Gulf Reefs, and the Protocol for Monitoring Coastal Benthic Habitats. Species identification was carried out by analyzing 25 transects, each divided into 1 m2 grids, with photos recorded for each grid, totaling 625 photos. Margalef, Shannon-Weaver, Simpson, and Pielou indices were used to analyze species distribution and diversity. The results indicated Dictyotaceae, Sargassaceae, and Corallinaceae as prevalent families. This research offers decision-makers a snapshot of species distribution in the Seixas coral reefs, providing a non-destructive, efficient methodology for assessing environmental impacts on coastal coral reefs.

Temperature Controls eDNA Persistence across Physicochemical Conditions in Seawater.

Environmental DNA (eDNA) quantification and sequencing are emerging techniques for assessing biodiversity in marine ecosystems. Environmental DNA can be transported by ocean currents and may remain at detectable concentrations far from its source depending on how long it persist. Thus, predicting the persistence time of eDNA is crucial to defining the spatial context of the information derived from it. To investigate the physicochemical controls of eDNA persistence, we performed degradation experiments at temperature, pH, and oxygen conditions relevant to the open ocean and the deep sea. The eDNA degradation process was best explained by a model with two phases with different decay rate constants. During the initial phase, eDNA degraded rapidly, and the rate was independent of physicochemical factors. During the second phase, eDNA degraded slowly, and the rate was strongly controlled by temperature, weakly controlled by pH, and not controlled by dissolved oxygen concentration. We demonstrate that marine eDNA can persist at quantifiable concentrations for over 2 weeks at low temperatures (≤10 °C) but for a week or less at ≥20 °C. The relationship between temperature and eDNA persistence is independent of the source species. We propose a general temperature-dependent model to predict the maximum persistence time of eDNA detectable through single-species eDNA quantification methods.

Habitat model forecasts suggest potential redistribution of marine predators in the southern Indian Ocean

AbstractAimClimate change will likely lead to a significant redistribution of biodiversity in marine ecosystems. We examine the potential redistribution of a community of marine predators by comparing current and future habitat distribution projections. We examine relative changes among species, indicative of potential future community‐level changes and consider potential consequences of these changes for conservation and management.LocationSouthern Indian Ocean.MethodsWe used tracking data from 14 species (10 seabirds, 3 seals and 1 cetacean, totalling 538 tracks) to model the habitat selection of predators around the Prince Edward Islands. Using random forest classifiers, we modelled habitat selection as a response to a static environmental covariate and nine dynamic environmental covariates obtained from eight IPCC‐class climate models. To project the potential distribution of the predators in 2071–2100, we used climate model outputs assuming two greenhouse gas emission scenarios: RCP 4.5 and RCP 8.5.ResultsAnalogous climates are projected to predominantly shift to the southeast and southwest. Species’ potential range shifts varied in direction and magnitude, but overall shifted slightly to the southwest. Despite the variable shifts among species, current species co‐occurrence patterns and future projections were statistically similar. Our projections show that at least some important habitats will shift out of national waters and marine protected areas by 2100, but important habitat area will increase in the Convention on the Conservation of Antarctic Marine Living Resources Area. Predicted areas of common use among predators decreased north of the islands and increased to the south, suggesting that multiple predator species may use southerly habitats more intensively in the future. Consequently, Southern Ocean management authorities could implement conservation actions to partially offset these shifts.Main conclusionsOverall, we predict that marine predator biodiversity in the southern Indian Ocean will be redistributed, with ecological, conservation and management implications.

EDNA captures depth partitioning in a kelp forest ecosystem.

Environmental DNA (eDNA) metabarcoding is an increasingly important tool for surveying biodiversity in marine ecosystems. However, the scale of temporal and spatial variability in eDNA signatures, and how this variation may impact eDNA-based marine biodiversity assessments, remains uncertain. To address this question, we systematically examined variation in vertebrate eDNA signatures across depth (0 m to 10 m) and horizontal space (nearshore kelp forest and surf zone) over three successive days in Southern California. Across a broad range of teleost fish and elasmobranchs, results showed significant variation in species richness and community assemblages between surface and depth, reflecting microhabitat depth preferences of common Southern California nearshore rocky reef taxa. Community assemblages between nearshore and surf zone sampling stations at the same depth also differed significantly, consistent with known habitat preferences. Additionally, assemblages also varied across three sampling days, but 69% of habitat preferences remained consistent. Results highlight the sensitivity of eDNA in capturing fine-scale vertical, horizontal, and temporal variation in marine vertebrate communities, demonstrating the ability of eDNA to capture a highly localized snapshot of marine biodiversity in dynamic coastal environments.

Robots Versus Humans: Automated Annotation Accurately Quantifies Essential Ocean Variables of Rocky Intertidal Functional Groups and Habitat State

Standardized methods for effectively and rapidly monitoring changes in the biodiversity of marine ecosystems are critical to assess status and trends in ways that are comparable between locations and over time. In intertidal and subtidal habitats, estimates of fractional cover and abundance of organisms are typically obtained with traditional quadrat-based methods, and collection of photoquadrat imagery is a standard practice. However, visual analysis of quadrats, either in the field or from photographs, can be very time-consuming. Cutting-edge machine learning tools are now being used to annotate species records from photoquadrat imagery automatically, significantly reducing processing time of image collections. However, it is not always clear whether information is lost, and if so to what degree, using automated approaches. In this study, we compared results from visual quadrats versus automated photoquadrat assessments of macroalgae and sessile organisms on rocky shores across the American continent, from Patagonia (Argentina), Galapagos Islands (Ecuador), Gorgona Island (Colombian Pacific), and the northeast coast of the United States (Gulf of Maine) using the automated software CoralNet. Photoquadrat imagery was collected at the same time as visual surveys following a protocol implemented across the Americas by the Marine Biodiversity Observation Network (MBON) Pole to Pole of the Americas program. Our results show that photoquadrat machine learning annotations can estimate percent cover levels of intertidal benthic cover categories and functional groups (algae, bare substrate, and invertebrate cover) nearly identical to those from visual quadrat analysis. We found no statistical differences of cover estimations of dominant groups in photoquadrat images annotated by humans and those processed in CoralNet (binomial generalized linear mixed model or GLMM). Differences between these analyses were not significant, resulting in a Bray-Curtis average distance of 0.13 (sd 0.11) for the full label set, and 0.12 (sd 0.14) for functional groups. This is the first time that CoralNet automated annotation software has been used to monitor “Invertebrate Abundance and Distribution” and “Macroalgal Canopy Cover and Composition” Essential Ocean Variables (EOVs) in intertidal habitats. We recommend its use for rapid, continuous surveys over expanded geographical scales and monitoring of intertidal areas globally.

Seagrass Meadows Provide a Significant Resource in Support of Avifauna

Seagrass meadows are known to be rich in fauna, with complex food webs that provide trophic subsidy to species and habitats way beyond the extent of their distribution. Birds are an often-overlooked part of marine ecosystems; not only are they crucial to the health of marine ecosystems, but their populations are also supported by the productivity and biodiversity of marine ecosystems. The links of birds to specific habitat types such as seagrass meadows are largely not considered except in the context of direct herbivorous consumption. Here, we examine the linkages between seagrass and birds and propose a conceptual framework for how seagrasses may support bird populations beyond their distribution in both direct and indirect pathways. We present evidence that seagrass meadows are globally foraged for fish and invertebrates by coastal birds. They are also targeted by herbivorous wildfowl and potentially benefit birds further afield indirectly as a result of their support for offshore marine fish species at critical times in their life cycle (e.g., Atlantic Cod and King George Whiting). Evidence from the literature indicates that seagrass does provide support for birds, but reveals a field of research requiring much gap filling as studies are globally sparse, mechanistically limited, and small in spatial and temporal scales.

Ecoacoustics as a novel tool for assessing pond restoration success: Results of a pilot study

Abstract Ecoacoustics is increasingly being used to monitor species populations and to estimate biodiversity in marine ecosystems, but the underwater soundscapes of freshwater environments remain largely unexplored in this respect. Few studies exist concerning the acoustic diversity of ponds, but because aquatic plants and many arthropods such as Coleoptera and Hemiptera are known to produce sound, there is potential to use ecoacoustic techniques to monitor changes in biodiversity and conservation value. This pilot study compares the underwater soundscapes of recently restored open‐canopy ponds and unmanaged highly terrestrialized ponds situated in an arable agricultural landscape of North Norfolk, UK, in order to assess the benefits of farmland pond restoration. Daytime sound recordings were made for 10 min in each pond and analysed primarily for arthropod stridulations. In addition, six commonly used acoustic indices were calculated to assess the soundscape biodiversity between the unmanaged and the restored ponds. The stridulations of three diving beetle species (Dytiscidae) were recorded in tank studies to assess the potential for individual species recognition from underwater sound capture. Sound‐type richness and abundance, as estimated by visually and aurally identifying arthropod stridulation from spectrograms, were significantly higher in the restored open‐canopy ponds compared with the unmanaged terrestrialized ponds. In addition, the acoustic indices ‘acoustic complexity’ and ‘biodiversity index’ were significantly higher in restored open‐canopy ponds than in unmanaged terrestrialized ponds. The three dytiscid water beetle species recorded in a tank were found to produce distinctive and recognizable sounds, indicating potential to create an audio reference library that could be used for automatic acoustic monitoring of freshwater arthropods. Pond soundscapes are rich in biological information and this study suggests that, with further development, automated passive ecoacoustic monitoring could be an effective non‐invasive technique for assessing pond conservation value and pond restoration and management success.

Validating environmental DNA metabarcoding for marine fishes in diverse ecosystems using a public aquarium

AbstractEnvironmental DNA metabarcoding has been widely touted as a powerful tool for monitoring biodiversity in marine ecosystems. However, this method still requires thorough validation and standardization before it can be widely applied for ecological monitoring. The potential utility of environmental DNA metabarcoding is greatest in systems with high levels of diversity, yet environmental DNA metabarcoding has typically been validated in closed systems with relatively low levels of diversity. Additionally, the use of a multiple marker approach has been minimally explored under controlled, closed systems in the literature. Using a pilot study, we assess the ability of eDNA metabarcoding to capture biodiversity in a highly diverse closed system at the Ripley's Aquarium of Canada in Toronto, Ontario. Our pilot study highlights several key knowledge gaps that must be addressed before metabarcoding can be employed for widespread use in ecological monitoring. We found that environmental DNA metabarcoding recovered just over 50% of target species and 80% of target genera within a closed marine system containing 107 species and 44 genera using previously published markers for COI, 12S, and 16S. Additionally, COI and 12S were found to identify fewer target species than 16S, with COI generating the most off‐target identifications, but maximum detection success was achievable by combining all three markers. We discuss numerous key limitations which currently present barriers to the application of eDNA metabarcoding for studying highly diverse marine systems. These include marker selection, data validation and confidence, and the complexity of abundant and diverse novel systems. This study highlights important, yet incompletely resolved, challenges of environmental DNA metabarcoding for the detection of marine fishes in a diverse closed system environment using a multiple marker approach.

Bioremediation potential of Sargassum sp. biomass to tackle pollution in coastal ecosystems: Circular economy approach.

During the past years, the ecological integrity and biodiversity of marine ecosystems have been highly threatened due to the controlled or uncontrolled release of high concentrations of pollutants generated through anthropogenic activities. The occurrence of environmentally related hazardous pollutants, such as toxic elements, and recalcitrant compounds in various environmental matrices has raised increasing concern. Different technologies have been developed for efficient removal and complete mitigation or degradation of these toxic elements from the aquatic environment. Among them, biosorption and bioaccumulation by renewable and biodegradable sources are of supreme interest and have not been reviewed much. For instance, the invasive seaweed Sargassum sp. has been spotted as a cost-effective natural material to capture targeted pollutants from the coastal ecosystem, which is currently becoming a pressing problem, around the globe, due to its unusual proliferation near tropical shores. This review is an effort to cover the left behind gap to present the multifunctional potentialities of Sargassum sp. biomass. Herein, salient information is given to highlight the potential of Sargassum sp. biomass for environmental decontamination with particular focus to coastal ecosystems. Bioremediation mechanisms, challenges of implementation and factors involved in adsorption and absorption of pollutants by seaweeds are also discussed in this review. Against this background, a circular economy perspective is given for the integrated use of the algal raw material. The up-taken pollutants can be recovered and reintegrated into the value chain of industrial processes, while residual biomass is refined to obtain added-value products as bioactive compounds with potential applications for biofuel, agriculture, cosmetics, nutraceutical, pharmaceutical industries among others, to make the most of renewable resources.

A Facilitation Cascade Enhances Local Biodiversity in Seagrass Beds

Invertebrate diversity can be a key driver of ecosystem functioning, yet understanding what factors influence local biodiversity remains uncertain. In many marine and terrestrial systems, facilitation cascades where primary foundation and/or autogenic ecosystem engineering species promote the settlement and survival of a secondary foundation/engineering species have been shown to enhance local biodiversity and ecosystem functioning. We experimentally tested if a facilitation cascade occurs among eelgrass (Zostera marina), pen clams (Atrina rigida), and community diversity in temperate seagrass beds in North Carolina, U.S.A., and if this sequence of direct positive interactions created feedbacks that affected various metrics of seagrass ecosystem function and structure. Using a combination of surveys and transplant experiments, we found that pen clam density and survivorship was significantly greater in seagrass beds, indicating that eelgrass facilitates pen clams. Pen clams in turn enhanced local diversity and increased both the abundance and species richness of organisms (specifically, macroalgae and fouling invertebrate fauna)—the effect of which scaled with increasing clam density. However, we failed to detect an impact of pen clams on other seagrass functions and hypothesize that functioning may more likely be enhanced in scenarios where secondary foundation species specifically increase the diversity of key functional groups such as epiphyte grazers and/or when bivalves are infaunal rather than epifaunal. Our findings add to the growing amount of literature that demonstrates that secondary foundation species are important drivers of local biodiversity in marine ecosystems. Further experimentation is needed that directly examines (i) the role of functional versus overall diversity on seagrass functions and (ii) the relative importance of life-history strategy in determining when and where engineering bivalves increase biodiversity and/or functioning of seagrass beds.

Discovering novel enzymes from marine ecosystems: a metagenomic approach

Abstract There exists a massive pool of biodiversity in marine ecosystems. This biodiversity is an excellent source for acquiring an inventory of enzymes that can be used for a variety of biotech applications. This diversity has, to date, not been fully exploited. One major reason being the difficulties that arise in culturing many microorganisms in the laboratory, as opposed to natural conditions. However, advents of newer omics techniques, such as metagenomics have greatly enhanced the opportunity for sustainable resource management. It is in this context that metagenomics is rapidly emerging as an alternative approach to conventional microbial screening. Metagenomics allows for exhaustive screening of microbial genomes in their natural environments. In this review, an overview of work that uses genomic strategies to examine the biotechnological potential of the marine reservoir was explored. These genomic strategies include homology-driven screening of enormous amounts of sequence data and activity-based functional screening of genomic and metagenomic libraries. Finally, the review concludes with an overview of some of the potential challenges and future prospects of metagenomics in bioprospecting novel biocatalysts and bioactive compounds from marine sources.

The roles of endolithic fungi in bioerosion and disease in marine ecosystems. II. Potential facultatively parasitic anamorphic ascomycetes can cause disease in corals and molluscs

ABSTRACTAnamorphic ascomycetes have been implicated as causative agents of diseases in tissues and skeletons of hard corals, in tissues of soft corals (sea fans) and in tissues and shells of molluscs. Opportunist marine fungal pathogens, such as Aspergillus sydowii, are important components of marine mycoplankton and are ubiquitous in the open oceans, intertidal zones and marine sediments. These fungi can cause infection in or at least can be associated with animals which live in these ecosystems. A. sydowii can produce toxins which inhibit photosynthesis in and the growth of coral zooxanthellae. The prevalence of many documented infections has increased in frequency and severity in recent decades with the changing impacts of physical and chemical factors, such as temperature, acidity and eutrophication. Changes in these factors are thought to cause significant loss of biodiversity in marine ecosystems on a global scale in general, and especially in coral reefs and shallow bays.

THERAPEUTICAL IMPORTANCE OF HYPNEA MUSCIFORMIS (WULFEN) J.V. LAMOUROUX :

Red algae are rich in protein, crude lipid and fibre content and therefore ideal as food in terms of nutritional and biochemical point of view. Currently, red algae have gained importance due to their nutritional composition and various bioactive compounds they produce to accustom to the biodiversity of marine ecosystem. Biologically unique compounds of algal include carrageenan, sulpholipids, and pigments such as phycocyanin. Seaweeds are low in fats but contain vitamins and bioactive compounds such as flavonoids, terpenoids and sulphated polysaccharides, which are potential natural antioxidants not found in the terrestrial plants. Hypnea, a common seaweed distributed widely along the tropical and subtropical shores Nutraceutical value of Hypnea musciformis includes nutrients, vitamin, ash and large amount of sodium and potassium electrolytes. There were reports that they possess potent antitumour and antimicrobial activity.

Microfouling communities from pelagic and benthic marine plastic debris sampled across Mediterranean coastal waters

The present study used scanning electron microscopy to characterize the organisms colonizing marine plastic debris collected from pelagic and benthic habitats across Mediterranean coastal waters of Greece, Italy and Spain. A total of 42 fragments of plastic were collected during the COMSOM experimental cruise, 16 from the seafloor and 26 from surface waters. The results showed that diatoms were the most abundant organisms on both pelagic and benthic plastics. The diatom Ceratoneis closterium , frequently observed on surface plastics (73%), is a harmful microalgae associated with mucilage events in the Mediterranean. The abundance of marine plastic in coastal and oceanic waters may provide new habitats that offer an easy substrate for these invasive organisms. Furthermore, the colonization of these new environments might reduce the success of life strategies, or drive the organisms out of their essential habitat by dispersion and rafting phenomena. The results of the present work highlight the need to increase our knowledge of the consequences of colonization of plastics introduced into the marine environment, and the need to raise awareness of the potential impacts of debris accumulation on biodiversity of marine ecosystems.

Biodiversity in marine ecosystems – European developments towards robust assessments

Biodiversity in marine ecosystems – European developments towards robust assessments

Biodiversity in Marine Ecosystems—European Developments toward Robust Assessments

Sustainability of marine ecosystems and their services are dependent on marine biodiversity, which is threatened worldwide. Biodiversity protection is a major target of the EU Marine Strategy Framework Directive, requiring assessment of the status of biodiversity on the level of species, habitats, and ecosystems including genetic diversity and the role of biodiversity in food web functioning and structure. This paper provides a summary of the development of new indicators and refinement of existing ones in order to address some of the observed gaps in indicator availability for marine biodiversity assessments considering genetic, species, habitat, and ecosystem levels. Promising new indicators are available addressing genetic diversity of microbial and benthic communities. Novel indicators to assess biodiversity and food webs associated with habitats formed by keystone species (such as macroalgae) as well as to map benthic habitats (such as biogenic reefs) using high resolution habitat characterization were developed. We also discuss the advances made on indicators for detecting impacts of non-native invasive species and assessing the structure and functioning of marine food-webs. The latter are based on indicators showing the effects of fishing on trophic level and size distribution of fish and elasmobranch communities well as phytoplankton and zooplankton community structure as food web indicators. New and refined indicators are ranked based on quality criteria). Their applicability for various EU and global biodiversity assessments and the need for further development of new indicators and refinement of the existing ones is discussed.