Seagrass meadows are among the most productive ecosystems on Earth and function as biodiversity hotspots in coastal seas. They provide nursery grounds for juvenile fish, refuge and food for invertebrates, stabilise sediments, protect coastlines from erosion, sequester carbon, cycle nutrients and even buffer ocean acidification. Globally, these underwater grasslands are estimated to support around 20 percent of the world’s largest fisheries. Along the Black Sea coast, seagrass beds cover roughly 917 hectares, and the waters off Burgas and Sarafovo alone account for 52 percent of Bulgaria’s total seagrass area, making the region a national stronghold for these habitats.

Foros Bay itself is a morphologically complex, shallow embayment in the innermost part of Burgas Bay, featuring low-lying coastal plains, sandy barriers and sheltered lagoon-type environments. Both persistent seagrass meadows and unvegetated seabed areas, some of which were previously covered by seagrass, create a natural gradient for measuring biodiversity gains and losses. The bay is designated under the European Union’s Natura 2000 network for its high conservation value and is recognised as a regional biodiversity hotspot. Long-term monitoring indicates that the dominant seagrass species is Zostera noltei, which supports a diverse array of metazoan life, from bivalves and gastropods to crustaceans and fish, including the broadnosed pipefish, the nerophis pipefish and the seahorse Hippocampus guttulatus.

The bay also faces mounting human pressure. Urban expansion of Burgas City, home to roughly 200,000 people, the operation of a major oil refinery and an adjacent commercial port have elevated nutrient and contaminant loads, reducing light availability, water quality and the natural recovery capacity of the seagrass. These cumulative impacts make Foros Bay an ideal natural laboratory for testing how coastal habitats respond to stress and for evaluating Nature-based Solution interventions aimed at boosting ecological resilience.

Conventional survey methods, such as trawling, grab sampling and visual counts, often fail to capture the full scope of community composition and spatial variability in seagrass ecosystems. They are logistically constrained, frequently limited to specific species or developmental stages, and can miss rare, cryptic or elusive organisms entirely. eDNA metabarcoding sidesteps many of these limitations by detecting the genetic material that organisms release into the environment through tissue shedding, excretion and decomposition. Because of its exceptional sensitivity, the technique can identify rare species, early life stages such as larvae and eggs, and taxa that would otherwise require direct capture.

In June 2025, SCUBA divers collected ten two-litre water samples: five directly above Zostera beds and five from neighbouring bare sand areas. Each sample was filtered through sterile 0.22-micrometre cartridge filters, which were sealed and frozen at minus 30 degrees Celsius until processing. Genomic DNA was extracted from the filters, and two genetic markers were amplified and sequenced: the 12S mitochondrial region, which targets fish, and the 18S rDNA V4 region, which captures a broader sweep of metazoan life. Sequencing was performed on an Illumina MiSeq i100 platform, and the resulting data were processed through a bioinformatic pipeline that included quality trimming, error modelling, chimera removal and the inference of amplicon sequence variants, or ASVs. Taxonomic assignment relied on the PR2 reference database for 18S data and a custom database of 637 sequences representing 117 fish species reported from the Black Sea for the 12S data.

The results were striking. For the 18S marker, more than one million paired-end reads were acquired, and quality filtering yielded over 768,000 non-chimeric merged reads corresponding to 1,448 ASVs. Of these, 55 ASVs were assigned to Metazoa, representing 48 distinct taxa. Metazoan taxa had greater read counts in seagrass stations compared to bare sand. Species richness and Shannon diversity were moderately higher in seagrass, with mean values of 23.40 and 2.23 respectively, compared to 17.80 and 1.70 in bare sand. Simpson diversity and Pielou’s evenness were also considerably elevated in seagrass, at 0.83 and 0.71, versus 0.74 and 0.59 in bare sand. However, none of these individual disparities reached statistical significance, a reminder that small sample sizes and natural variability can obscure even biologically meaningful patterns.

Community-level analyses told a different and more compelling story. Non-metric multidimensional scaling revealed partial separation of metazoan communities between the two habitats, and permutational multivariate analysis of variance, or PERMANOVA, showed that habitat type had a statistically significant effect on community composition, explaining approximately 24.8 percent of the total variation. Similarity percentage and indicator species analyses showed that this difference was driven by a specific subset of taxa strongly linked to seagrass, including mussels, serpulid worms, the polychaete Pectinaria koreni, caenogastropods, and the colonial tunicate Botryllus schlosseri, which together accounted for 95 percent of the dissimilarity between habitats. Detection probability for metazoan taxa was approximately 38 percent lower in bare sand compared with seagrass, according to a binomial generalised linear model. Yet multivariate dispersion analysis revealed no significant difference in within-habitat compositional variability between the two habitat types, suggesting that seagrass enhances the presence and abundance of benthic taxa with pronounced environmental preferences rather than restructuring entire communities.

The fish story was equally revealing but followed a different logic. For the 12S marker, nearly 2.8 million paired-end reads were acquired, yielding 2.47 million non-chimeric merged reads and 3,651 ASVs, of which 15 were assigned to fish taxa encompassing nine species. Four species were found exclusively in seagrass stations: the broadnosed pipefish, garfish, sand goby and Mediterranean horse mackerel. Conversely, the black goby, stellate sturgeon and chub mackerel were found only in bare sand environments. Two additional species, the round goby and European anchovy, appeared in both habitat types. At the community level, however, fish assemblages showed no significant differences between habitats in composition, variability or detection frequency, likely reflecting the high mobility of many coastal fish species and their frequent movement between habitat types.

The presence of commercially important species such as European anchovy, garfish and horse mackerel in seagrass habitats underscores the significance of Zostera beds for coastal fisheries from both ecological and economic perspectives. The detection of the stellate sturgeon, an endangered species, in bare sand areas highlights the value of eDNA in uncovering species that may be missed by traditional approaches. The round goby and anchovy, found in both environments, signal functional connectivity between seagrass and bare sand, reinforcing the need to preserve habitat heterogeneity across coastal mosaics. The authors caution that eDNA metabarcoding still faces constraints, including inadequate regional reference databases and limited taxonomic resolution of the marker regions, which led some ASVs to be assigned only at higher taxonomic levels or to subtropical species whose local presence is questionable. As sequencing technology advances and database coverage expands, eDNA metabarcoding may evolve into a standardised and efficient approach for ecosystem monitoring. For now, the study demonstrates that seagrass meadows can enhance species richness and diversity without consistently stabilising community composition, and that losing these habitats could have a disproportionate impact on benthic biodiversity and ecosystem functioning across the Black Sea coast.

Subject of Research: Environmental DNA metabarcoding reveals how Black Sea seagrass meadows shape biodiversity in Foros Bay, Bulgaria

Article Title: Biodiversity in seagrass meadows in contrast to adjacent bare sand habitats of Foros Bay (Bulgarian Black Sea coast) assessed using environmental DNA (eDNA) metabarcoding

Article References: Dzhembekova, N., Ivanova, P., Zlateva, I., Valchev, N., & Prodanov, B. (2026). Biodiversity in seagrass meadows in contrast to adjacent bare sand habitats of Foros Bay (Bulgarian Black Sea coast) assessed using environmental DNA (eDNA) metabarcoding. Nature Conservation, 63, 259-274. https://doi.org/10.3897/natureconservation.63.187493

Image Credits: AI Generated

DOI: 10.3897/natureconservation.63.187493

Keywords: Biodiversity, seagrass, meadows, contrast, adjacent, bare, sand, habitats, Foros, Bulgarian, Black, coast