The Black Sea is the largest meromictic sea with a reservoir of anoxic water extending from 100 to 1000 m depth. These deeper layers are characterised by a poorly understood fluorescence signal called “deep red fluorescence”, a chlorophyll a- (Chl a) like signal found in deep dark oceanic waters. In two cruises, we repeatedly found up to 103 cells ml−1 of picocyanobacteria at 750 m depth in these waters and isolated two phycoerythrin-rich Synechococcus sp. strains (BS55D and BS56D). Tests on BS56D revealed its high adaptability, involving the accumulation of Chl a in anoxic/dark conditions and its capacity to photosynthesise when re-exposed to light. Whole-genome sequencing of the two strains showed the presence of genes that confirms the putative ability of our strains to survive in harsh mesopelagic environments. This discovery provides new evidence to support early speculations associating the “deep red fluorescence” signal to viable picocyanobacteria populations in the deep oxygen-depleted oceans, suggesting a reconsideration of the ecological role of a viable stock of Synechococcus in dark deep waters.

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.

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<p>                The quality of the Black Sea ecosystem is partly but importantly dependent on the survival and sustainability of the top predator populations. It is difficult to foresee all consequences for the regional biodiversity if cetaceans disappear as it had happened with the Mediterranean monk seals in the past. During 7 days, between 30 September and 7 October, 2019, a joint oceanographical survey was made with a multipurpose R/V Mare Nigrum in offshore as well as deep sea locations, within the Romanian (RO), Bulgarian (BG) and western Turkish (TK) national waters of the Black Sea in the frame of ANEMONE project. The total track line was around 700 nautical miles and the sampled area covered 9754,58 km<sup>2</sup>. Observations were made of cetaceans and floating litter, following line transect sampling method, with a single platform (2 observers, on the left and right of the vessel bridge) over 380.44 km of transects. A total of 54 cetacean sightings and 81 floating litter items were recorded. All the three species, short-beaked common dolphin (<em>Delphinus delphis</em> ssp. <em>ponticus</em>), Black Sea bottlenose dolphin (<em>Tursiops truncatus</em> ssp. <em>ponticus</em>), and Black Sea harbour porpoise (<em>Phocoena phocoena </em>ssp. <em>relicta</em>), were registered with a similar density (individuals/km<sup>2</sup>), 0.012 for RO sector and 0.013 for BG-TK sector. The number of debris varied between 1 and 24 items, reaching 5.26± 5.93 items on average. Among the transects, 53% contained less than 5 items and only 13% were with more than 10 items. Based on these results, the average density of floating macro-litter in BG waters was found 2.43 ± 2.4 items/km<sup>2</sup>, 1.73 ± 1.24 items/km<sup>2 </sup>in the RO waters and 2.43±2.17 items/km<sup>2</sup> in TR waters. This study was the first to make a joint and continuous survey effort for both cetaceans and litter simultaneously in the Black Sea.</p><p><strong>Key words:</strong>  Black Sea, cetaceans, marine litter, joint cruise, ANEMONE project.</p>

The ultimate goal of modern operational oceanography are end user oriented products with high scientific quality. Beneficiaries are the governmental services, coast and offshore based enterprises and research institutions that make use of the products generated by operational oceanography. Direct users are coastal managers, shipping, search and rescue, oil spill combat, offshore industry, ports, fishing, tourism, and recreation industry. Indirect beneficiaries, through climate forecasting based on ocean observations, are food, energy, water and medical suppliers. Availability of updated information on the actual state as well as forecast of marine environment is essential for the success and safety of maritime operations in the offshore industry. Various systems for the collection and presentation of marine data for the needs of different users have been developed and put in operation in the Black Sea. The systems are located both along the coast and in the open sea and the information they provide is used by both the maritime industry and the widest range of users. The Black Sea Monitoring and Forecasting Center in the frame of the Copernicus Marine Service is providing regular and systematic information about the physical state of the ocean, marine ecosystem and wave conditions in the Black Sea area, assimilating observations, keeping efficient operations, advanced technology and high quality modeling products. Combining and optimizing in situ, remote sensing, modeling and forecasting into a Black Sea observing system is a task that has to be solved, and that will allow to get a more complete and comprehensive picture of the state of the marine environment as well as to forecast future changes of physical and biogeochemical state of the Black Sea and the Black Sea ecosystem.

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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.

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 (mostly) temperature. In spite of its well-known hydrology and physico chemistry, 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 classic and genome-resolved metagenomics generating a large number of metagenome-assembled genomes (MAGs) from them. The oxic zone presents many similarities to the global ocean while the euxinic water mass has similarities to other similar aquatic environments of marine or freshwater (meromictic monimolimnion strata) origin. The MAG collection represents very well the different types of metabolisms expected in this kind of environments and includes Cyanobacteria (Synechococcus), photoheterotrophs (largely with marine relatives), facultative/microaerophilic microbes again largely marine, chemolithotrophs (N and S oxidizers) and a large number of anaerobes, mostly sulfate reducers but also a few methanogens and a large number of 'dark matter' streamlined genomes of largely unpredictable ecology. Conclusions: The Black Sea presents a mixture of similarities to other water bodies. The photic zone has many microbes in common with that of the Mediterranean with the relevant exception of the absence of Prochlorococcus. The chemocline already presents very different characteristics with many examples of chemolithotrophic metabolism (Thioglobus) and facultatively anaerobic microbes. Finally 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 and a small but detectable methanogenesis.We are adding critical information about this unique and important ecosystem and its microbiome.