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The current study employed diverse statistical and machine learning techniques to investigate the biodiversity and spatial distribution of phytoplankton cysts in the Black Sea. The MaxEnt distribution modeling technique was used to forecast the habitat suitability for the cysts of three potentially toxic microalgal taxa (Lingulodinium polyedra, Polykrikos hartmannii, and Alexandrium spp.). The key variables controlling the habitat suitability of Alexandrium spp. and L. polyedra were nitrates and temperature, while for the P. hartmannii cysts, nitrates and salinity. The region with the highest likelihood of L. polyedra cyst occurrence appears to be in the western coastal and shelf waters, which coincides with the areas where L. polyedra red tides have been documented. The projected habitat suitability of the examined species partially overlapped, perhaps as a result of their cohabitation within the phytoplankton community and shared preferences for specific environmental conditions, demonstrating similar survival strategies. The north-western region of the Black Sea was found to be the most suitable environment for the studied potentially toxic species, presumably posing a greater risk for the onset of blooming events. Two distinct aspects of cysts’ ecology and settlement were observed: the dispersal of cysts concerns their movement within the water column from one place to another prior to settling, while habitat suitability pertains to the particular environment required for their survival, growth, and germination. Therefore, it is crucial to validate the model in order to accurately determine a suitable habitat as well as understand the transportation patterns linked to the particular hydrodynamic properties of the water column and the distinct features of the local environment.

The Black Sea is a vital resource with vast potential to boost the societal value of the Blue Economy for its surrounding countries. Improved knowledge and enhanced infrastructure together with better coordination and alignment of research and innovation efforts are critical for the better management of the deteriorated Black Sea ecosystem to help restore and maintain its resilience and enable sustainable use of natural resources. In 2019, the Black Sea Strategic Research and Innovation Agenda (Black Sea SRIA), was developed by the Black Sea experts, in cooperation with European marine institutes and organizations, with the support of the European Commission. Black Sea SRIA presents the priorities and ecosystem-based management options needed for a healthy, sustainable, and resilient Black Sea. Since 2019, efforts focused on developing concrete actions under the Black Sea SRIA Implementation Plan (IP) to contribute to the national blue economy strategies, better structuring of the relevant funding mechanisms for solution-oriented implementation and the international and regional strategies, supporting the co-funding mechanisms. In this study, we present a transnational process that has led to the development of the IP which utilized a bottom-up, co-design and co-creation-based approach. The SRIA and its IP support better governance of the blue economy principles towards sustainable development and conservation of unique Black Sea ecosystems. The Black Sea SRIA and IP address the fundamental research challenges of the region, promote the blue economy, and also build vital support systems and innovative research infrastructure and capacity together with academia, funding organizations, industry, policy, civil society and local communities. The IP is a long-lasting guide to catalyze new ideas and innovations towards and with the Black Sea community with strong implications for other sea basins.

The red mullet (Mullus barbatus Linnaeus, 1758) is a keynote species for the Bulgarian Black Sea ecosystem and fisheries; nevertheless, existing knowledge on population status is very scarce. The present study was intended to assess the health status and adaptive potential of M. barbatus populations inhabiting the Bulgarian waters of the Black Sea. Our findings revealed that populations of M. barbatus are exposed to a variety of anthropogenic and environmental stressors. The species’ status was assessed using representative genetic, morphological, biochemical and chemical biomarkers from specimens obtained in the research area’s northern and southern regions. Based on mtDNA markers, genetic analysis revealed low haplotype and nucleotide diversity, typically observed in overexploited or “threatened” populations. Examining the morphology of the specimens revealed no discernible pattern of differentiation. Except for aluminium and chrome, metal and PAH concentrations in fish were below the regulatory thresholds. The specimens from the southern region ingested more microplastics than those from the northern region. The majority of specimens collected from the southern region also exhibited elevated levels of oxidative stress and decreased antioxidant defence, which can be interpreted as an early indication that they had reached the limits of their adaptive potential. Further research on the composite effects of the stressogenic environment on the Black Sea biota are critically needed, as well as the introduction of new indicators and thresholds at molecular and cellular levels for adequate monitoring of both the ecological state of the marine environment and its biota.

This study was conducted to investigate genetic and some morphometric and meristic characteristics of garfish Belone belone from Nesebar in the Bulgarian Black Sea coast. Twelve morphometric characters were measured, and six meristic characters were counted for each individual. Based on both sexes’ morphological and meristic analyses, no statistically significant sexual differences were observed. Additionally, DNA barcoding was done. The fragment of the cytochrome oxidase subunit I (COI) gene of mitochondrial DNA was sequenced to supplement the species identification and population diversity study. Two haplotypes were found out of 39 sequences, indicating a low level of haplotype diversity (0.146±0.072). Nucleotide diversity was also found to be low (0.00023±0.00011). The Nesebar population of B. belone requires conservation efforts, due to the highly decreased mtDNA genetic diversity.

During a survey of the marine benthic diatom flora on the coasts off Livingston Island (South Shetland Islands, Maritime Antarctic Region), two Halamphora species that could not be identified based on the currently available literature, were observed. Detailed light and scanning electron microscopy observations and thorough comparison with similar taxa in the literature revealed that both taxa should be described as new species. The first taxon, Halamphora kenderoviana sp. nov., was most likely misidentified in past Antarctic studies, and included within the range of another taxon, Halamphora coffeaeformis. Analysis of literature data showed that the second new taxon, Halamphora moncheviana sp. nov., has been previously reported from the Antarctic Continent (but as an unidentified species). The new taxa are compared with similar Halamphora taxa worldwide. Data on their ecology and distribution are also provided.

Background and aims – Despite a long research history, knowledge of Antarctic marine benthic diatoms is fragmentary. This study reports on marine benthic diatoms from South Bay, Livingston Island, focusing on diatoms living on hard substrata, and species distribution across different coastal habitats.Material and methods – Samples were collected from tidal pools (19), intertidal cobbles (9), artificial substrata installed at various depths (10), coastal rocks (2), and bottom sediments at depths > 20 m (2). Species identifications and community analyses were done using LM with additional information obtained using SEM. nMDS based on diatom abundance data was applied to display differences between the samples by habitat/substratum type and sampling month. The significance of the habitat/substratum type and sampling month on diatom communities was checked with PERMANOVA. Similarity/dissimilarity within and between sample groups and their contributing species were explored with SIMPER.Key results – In total, 133 diatom taxa were recorded, of which 110 are benthic. A large number of taxa could not be certainly identified. Taxonomic remarks and ecology and distribution data for some rarely reported species with convoluted taxonomic and nomenclatural histories are given. One new combination is proposed. Diatom communities were influenced by the habitat/substratum type, but not by seasonality. Significant differences existed between communities in tidal pools and those on cobbles, artificial substrata, and sediments, and between those on sediments and artificial substrata. Navicula aff. perminuta dominated on cobbles and often on artificial substrata. Species forming mucilage tubes, tree-like colonies, and chains of cells embedded in mucilage were restricted to tidal pools.Conclusion – Benthic diatom communities from South Bay are highly diverse and species show distinct distributions in the coastal habitats, but the scarce studies and often confusing nomenclature history of the taxa make their identification challenging, and potentially common species for the region remain unknown.

The present study examined the genetic diversity and spatial distribution of turbot (Scophthalmus maximus), an economically important species on the Bulgarian Black Sea coast. Maximum entropy (MaxEnt) modeling software Version 3.4.4. was utilized to develop a habitat suitability model for S. maximus in the Bulgarian Black Sea region. Data collected via demersal and pelagic surveys and genetic sampling from 2017 to 2021 were utilized to link species occurrence localities with selected abiotic factors. Our findings showed that the species’ habitat preferences are strongly influenced by temperature and dissolved oxygen, and projections based on simplified climatic scenarios indicated potential distribution shifts and a substantial reduction in reproduction habitats in the northern region. The assessment of genetic diversity was based on mtDNA COIII sequencing; MtDNA revealed a low level of polymorphism in all analyzed populations. The extensive fishing pressure may have increased the likelihood of genetic and population bottlenecks and a consequent decline in genetic diversity in the Shabla, Nesebar, and Tsarevo populations. The Tajima’s D values for the latter indicated that turbot underwent a bottleneck followed by rapid population expansion. Our findings are essential for the conservation and effective management of S. maximus stocks in the region.

Turbot (Scophthalmus maximus L., 1758) is a valuable commercial fish species classified as endangered. The conservation and sustainability of the turbot populations require knowledge of the population’s genetic structure and constant monitoring of its biodiversity. The present study was performed to evaluate the population structure of turbot along the Bulgarian Black Sea coast using seven pairs of microsatellites, two mitochondrial DNA (COIII and CR) and 23 morphological (15 morphometric and 8 meristic) markers. A total of 72 specimens at three locations were genotyped and 59 alleles were identified. The observed number of alleles of microsatellites was more than the effective number of alleles. The overall mean values of observed (Ho) and expected heterogeneity (He) were 0.638 and 0.685. A high rate of migration between turbot populations (overall mean of Nm = 17.484), with the maximum value (19.498) between Shabla and Nesebar locations, was observed. This result corresponded to the low level of genetic differentiation amongst these populations (overall mean Fst = 0.014), but there was no correlation between genetic and geographical distance. A high level of genetic diversity in the populations was also observed. The average Garza-Williamson M index value for all populations was low (0.359), suggesting a reduction in genetic variation due to a founder effect or a genetic bottleneck. Concerning mitochondrial DNA, a total number of 17 haplotypes for COIII and 41 haplotypes for CR were identified. The mitochondrial DNA control region showed patterns with high haplotype diversity and very low nucleotide diversity, indicating a significant number of closely-related haplotypes and suggesting that this population may have undergone a recent expansion. Tajima’s D test and Fu’s FS test suggested recent population growth. Pairwise Fst values were very low. The admixture and lack of genetic structuring found pointed to the populations analysed probably belonging to the same genetic unit. Therefore, a proper understanding and a sound knowledge of the level and distribution of genetic diversity in turbot is an important prerequisite for successful sustainable development and conservation strategies to preserve their evolutionary potential.

Abstract Background The Black Sea is the largest brackish water body in the world, although it is connected to the Mediterranean Sea and presents an upper water layer similar to some regions of the former, albeit with lower salinity and temperature. Despite its well-known hydrology and physicochemical features, this enormous water mass remains poorly studied at the microbial genomics level. Results We have sampled its different water masses and analyzed the microbiome by shotgun and genome-resolved metagenomics, generating a large number of metagenome-assembled genomes (MAGs) from them. We found various similarities with previously described Black Sea metagenomic datasets, that show remarkable stability in its microbiome. Our datasets are also comparable to other marine anoxic water columns like the Cariaco Basin. The oxic zone resembles to standard marine (e.g. Mediterranean) photic zones, with Cyanobacteria (Synechococcus but a conspicuously absent Prochlorococcus), and photoheterotrophs domination (largely again with marine relatives). The chemocline presents very different characteristics from the oxic surface with many examples of chemolithotrophic metabolism (Thioglobus) and facultatively anaerobic microbes. The euxinic anaerobic zone presents, as expected, features in common with the bottom of meromictic lakes with a massive dominance of sulfate reduction as energy-generating metabolism, a few (but detectable) methanogenesis marker genes, and a large number of “dark matter” streamlined genomes of largely unpredictable ecology. Conclusions The Black Sea oxic zone presents many similarities to the global ocean while the redoxcline and euxinic water masses have similarities to other similar aquatic environments of marine (Cariaco Basin or other Black Sea regions) or freshwater (meromictic monimolimnion strata) origin. The MAG collection represents very well the different types of metabolisms expected in this kind of environment. We are adding critical information about this unique and important ecosystem and its microbiome.

Plankton cyst abundance and distribution is controlled by multiple factors. The stress linked to the fluctuations and variations of the environmental conditions in the water column is a major vector of encystment and intraspecific variability is an important adaptive strategy. The present study aims to disclose a link between the spatial distribution and abundance of different cyst morphotypes of Scrippsiella acuminata complex in surface sediments collected in the Black Sea at 34 sites and selected environmental variables. With this purpose, a basin scale data set was analyzed for patterns of intraspecific spatial heterogeneity. Redundancy analysis (RDA) was implemented to identify explanatory environmental variables associated with the cyst morphotypes abundance. Environmental multiyear data were used to ensure better approximation of a model that links environmental gradients with cyst abundance. Our results show that all S. acuminata cysts morphotypes are significantly correlated to one or a combination of the environmental variables, i.e., salinity, temperature and nutrients (nitrates and phosphates). The geographical distribution of Scrippsiella blooms in the Black Sea indicates that the interplay between the planktonic and benthic habitat of the dinoflagellate gives to S. acuminata the advantage to dominate in the plankton communities.

One of the assets, assigned to the phytoplankton resting stages, is that of serving as the “memory” of the aquatic ecosystems and preserved biodiversity in the course of time. However, an accurate cyst identification proves to be a more difficult and extremely challenging process, even today. In order to gain a better taxonomic coverage of cyst assemblages in the Black Sea, an integrated approach of the classical morphological identification with metabarcoding methods (MySeq sequencing of V7-V9 regions of the 18S rDNA) was applied on thirteen surface sediment samples collected from different sites. A total number of 112 dinoflagellate taxa was detected at the species level and ascribed to 51 genera. In general, it is the molecular analysis that yields a higher number of taxa as compared to those obtained through the morphological taxonomy (66 taxa based on the DNA sequences versus 56 morphologically-identified taxa). Besides, it should be pointed out that the integrated dataset includes 14 potentially toxic dinoflagellate species. Discerned, subsequently, was a good dataset consistency for ten species, followed by some discrepancies as to a number of taxa, identified with one of the methods only, due to specific methodological biases. On the whole, it could be concluded that the combination of morphological and molecular methods is likely to increase the potential for a more reliable taxonomic assessment of phytoplankton diversity in marine sediments which, in turn, proves conclusively the utmost importance of the integrated approach.

Numerous potentially toxic plankton species commonly occur in the Black Sea, and phycotoxins have been reported. However, the taxonomy, phycotoxin profiles, and distribution of harmful microalgae in the basin are still understudied. An integrated microscopic (light microscopy) and molecular (18S rRNA gene metabarcoding and qPCR) approach complemented with toxin analysis was applied at 41 stations in the northwestern part of the Black Sea for better taxonomic coverage and toxin profiling in natural populations. The combined dataset included 20 potentially toxic species, some of which (Dinophysis acuminata, Dinophysis acuta, Gonyaulax spinifera, and Karlodinium veneficum) were detected in over 95% of the stations. In parallel, pectenotoxins (PTX-2 as a major toxin) were registered in all samples, and yessotoxins were present at most of the sampling points. PTX-1 and PTX-13, as well as some YTX variants, were recorded for the first time in the basin. A positive correlation was found between the cell abundance of Dinophysis acuta and pectenotoxins, and between Lingulodinium polyedra and Protoceratium reticulatum and yessotoxins. Toxic microalgae and toxin variant abundance and spatial distribution was associated with environmental parameters. Despite the low levels of the identified phycotoxins and their low oral toxicity, chronic toxic exposure could represent an ecosystem and human health hazard.

Picocyanobacteria of the genus Synechococcus are major contributors to global primary production and nutrient cycles due to their oxygenic photoautotrophy, their abundance, and the extensive distribution made possible by their wide-ranging biochemical capabilities. The recent recovery and isolation of strains from the deep euxinic waters of the Black Sea encouraged us to expand our analysis of their adaptability also beyond the photic zone of aquatic environments. To this end, we quantified the total abundance and distribution of Synechococcus along the whole vertical profile of the Black Sea by flow cytometry, and analyzed the data obtained in light of key environmental factors. Furthermore, we designed phylotype-specific primers using the genomes of two new epipelagic coastal strains – first described here – and of two previously described mesopelagic strains, analyzed their presence/abundance by qPCR, and tested this parameter also in metagenomes from two stations at different depths. Together, whole genome sequencing, metagenomics and qPCR techniques provide us with a higher resolution of Synechococcus dynamics in the Black Sea. Both phylotypes analyzed are abundant and successful in epipelagic coastal waters; but while the newly described epipelagic strains are specifically adapted to this environment, the strains previously isolated in mesopelagic waters are able, in low numbers, to withstand the aphotic and oxygen depleted conditions of deep layers. This heterogeneity allows different Synechococcus phylotypes to occupy different niches and underscores the importance of a more detailed characterization of the abundance, distribution, and dynamics of individual populations of these picocyanobacteria.

Resting stages are common for the life cycle of some phytoplankton species, including blooming and potentially toxic species. The “seed bank” accumulated in the sediments can initiate blooms in the water column and could be an early warning signal of harmful algal blooms (HABs). In order to identify the phytoplankton cyst assemblages, thirteen surface sediment samples were collected from different sites in the Black Sea. The diversity of the resting stages was assessed using high-throughput sequencing metabarcoding (V7-9 hypervariable region of the 18S rDNA). One hundred and eighty microalgal species were identified with high level of similarity to the reference sequences. Dinoflagellates were dominated by Biecheleria, Gymnodinium and Karlodinium. Within diatoms, Skeletonema, Chaetoceros and Thalassiosira were the most abundant genera. Sixteen of the detected operational taxonomic units (OTUs) were assigned to harmful microalgae (12 dinoflagellates species, 1 diatom, 1 haptophyte and 2 raphidophytes). No pattern of microalgal sequences depth distribution was discriminated. The results show that DNA metabarcoding has a great potential for assessment of the phytoplankton diversity in environmental sediments.

Marine environmental monitoring has tended to focus on site-specific methods of investigation. These traditional methods have low spatial and temporal resolution and are relatively labour intensive per unit area/time that they cover. To implement the Marine Strategy Framework Directive (MSFD), European Member States are required to improve marine monitoring and design monitoring networks. This can be achieved by developing and testing innovative and cost-effective monitoring systems, as well as indicators of environmental status. Here, we present several recently developed methodologies and technologies to improve marine biodiversity indicators and monitoring methods. The innovative tools are discussed concerning the technologies presently utilized as well as the advantages and disadvantages of their use in routine monitoring. In particular, the present analysis focuses on: (i) molecular approaches, including microarray, Real Time quantitative PCR (qPCR), and metagenetic (metabarcoding) tools; (ii) optical (remote) sensing and acoustic methods; and (iii) in situ monitoring instruments. We also discuss their applications in marine monitoring within the MSFD through the analysis of case studies in order to evaluate their potential utilization in future routine marine monitoring. We show that these recently-developed technologies can present clear advantages in accuracy, efficiency and cost.

Currently, no tool is available that precisely identifies and quantifies all 48 species of Pseudo-nitzschia simultaneously. In the present study, we used massively parallel sequencing-based technology with genus-specific Pseudo-nitzschia primers to investigate the distribution and population dynamics of the genus in Tokyo Bay, Japan. Furthermore, we attempted to quantify the abundance of each species using both relative abundance data detected in the massively parallel sequencing-based survey, and cell count data, obtained by light microscopy. Several species of Pseudo-nitzschia were detected continuously from July 10 to September 9, 2016 in the sampling location. Cell densities ranged from 2-300 cells mL-1 (sample no.=10). Fourteen operational taxonomic units (OTUs) attributable to Pseudonitzschia were detected, and 99.9% of sequences detected by massively parallel sequencing belonged to the genus. Each of the most abundant OTUs comprised a single species, and were identified, in decreasing order of abundance, as P. multistriata (Takano) Takano, P. pungens (Grunow ex Cleve) Hasle, P. fraudulenta (Cleve) Hasle, P. multiseries (Hasle) Hasle, and P. galaxiae Lundholm & Moestrup. Species identification was possible in 9 of the 14 OTUs detected, of which several were detected in Tokyo Bay for the first time. The cell abundance ranges of the five most abundant species were estimated as 1,976-246,395, 0.03-52,999, 5-42,820, 4-24,617, and 0.03-1,007 cells L-1, respectively. The detection limit was 0.03 cells L-1. [ABSTRACT FROM AUTHOR]