Sediment and bottom water eDNA metabarcoding to support coastal management

Ocean sprawl and climate change exacerbate coastal erosion and flooding, resulting in habitat loss and decreasing biodiversity. To counteract these threats, different coastal defence tools have been developed, with an increasing emphasis on nature-based solutions. However, tracking the impacts of these interventions on marine benthic organisms requires appropriate sampling designs and timely investigation methods due to the dynamic nature of coastal environments. Environmental DNA metabarcoding is a promising, non-invasive, and quick technique to monitor community changes. Here, environmental DNA COI-based metabarcoding data from sediment and bottom water samples were used to characterize benthic communities at three sites along the Emilia-Romagna coast differing in the topology of coastal defence actions (from no defences to groynes and low-crested barriers) and to evaluate the effectiveness of the two sampling matrices in detecting local biodiversity. The findings revealed significant differences in the structure of the benthic communities depending on site, sample type (i.e., sediment versus bottom water), and their interaction. The three sites differ in abiotic characteristic affecting the community composition. Lido di Dante and Riccione showed higher species diversity due to the new type of substrata provided by the hard defence structure, while Foce del Bevano showed the presence of species typical of low impacted areas. Bottom water, hosting more traces of pelagic and nektonic species, showed significantly different species composition compared to sediment samples, suggesting the need to consider both matrices in coastal monitoring

Population genomic structure of the black coral Antipathella subpinnata in Mediterranean Vulnerable Marine Ecosystems

none8siAntipathella subpinnata (Ellis and Solander 1786) is one of the most frequently observed black corals at mesophotic depths (60–200 m) of the Mediterranean Sea, particularly in the northwestern part of the basin, where its populations can reach high densities and create forest-like aggregations, both along the coast and in offshore locations such as seamounts. Similar to other marine underwater forests, black coral gardens host a rich associated fauna and attract numerous species of commercial interest. As such, these corals are targeted by recreational and artisanal fisheries and are vulnerable to human impact due to their arborescent morphology and low growth rates. Genetic connectivity can provide valuable insight into the processes of population maintenance and replenishment following environmental disturbance and is often used as a proxy for population resilience. In our study, a restriction-site associated DNA analysis (2bRAD) was used to evaluate fine-scale population structure of the Mediterranean black coral A. subpinnata, and to understand which populations could serve as a potential source of genetic diversity for adjacent populations. Colonies from two offshore localities (a Ligurian seamount and a Tyrrhenian canyon) and four coastal populations from Liguria and Sicily were sampled and genotyped. Significant genetic differentiation was recorded between coastal and offshore localities. Moreover, offshore localities were genetically distinct from one another, while all coastal populations were characterized by panmixia. This indicates that offshore A. subpinnata gardens are potentially less resilient to human impact (i.e., demersal fishing activities) due to a limited influx of larvae from adjacent habitats. In addition, they are unlikely to supply coral propagules to coastal populations. Overall, this study highlights the vulnerability of Mediterranean A. subpinnata forests, and the importance of enforcing conservation and management measures to achieve Good Environmental Status (GES, EU Marine Strategy Framework Directive) of these valuable marine ecosystems.openTerzin M.; Paletta M.G.; Matterson K.; Coppari M.; Bavestrello G.; Abbiati M.; Bo M.; Costantini F.Terzin, M.; Paletta, M. G.; Matterson, K.; Coppari, M.; Bavestrello, G.; Abbiati, M.; Bo, M.; Costantini, F

Does solar irradiation drive community assembly of vulture plumage microbiotas?

Abstract Background Stereotyped sunning behaviour in birds has been hypothesized to inhibit keratin-degrading bacteria but there is little evidence that solar irradiation affects community assembly and abundance of plumage microbiota. The monophyletic New World vultures (Cathartiformes) are renowned for scavenging vertebrate carrion, spread-wing sunning at roosts, and thermal soaring. Few avian species experience greater exposure to solar irradiation. We used 16S rRNA sequencing to investigate the plumage microbiota of wild individuals of five sympatric species of vultures in Guyana. Results The exceptionally diverse plumage microbiotas (631 genera of Bacteria and Archaea) were numerically dominated by bacterial genera resistant to ultraviolet (UV) light, desiccation, and high ambient temperatures, and genera known for forming desiccation-resistant endospores (phylum Firmicutes, order Clostridiales). The extremophile genera Deinococcus (phylum Deinococcus-Thermus) and Hymenobacter (phylum, Bacteroidetes), rare in vertebrate gut microbiotas, accounted for 9.1% of 2.7 million sequences (CSS normalized and log2 transformed). Five bacterial genera known to exhibit strong keratinolytic capacities in vitro (Bacillus, Enterococcus, Pseudomonas, Staphylococcus, and Streptomyces) were less abundant (totaling 4%) in vulture plumage. Conclusions Bacterial rank-abundance profiles from melanized vulture plumage have no known analog in the integumentary systems of terrestrial vertebrates. The prominence of UV-resistant extremophiles suggests that solar irradiation may play a significant role in the assembly of vulture plumage microbiotas. Our results highlight the need for controlled in vivo experiments to test the effects of UV on microbial communities of avian plumage

Mangrove diversity is more than fringe deep

AbstractMangroves form coastal tropical forests in the intertidal zone and are an important component of shoreline protection. In comparison to other tropical forests, mangrove stands are thought to have relatively low genetic diversity with population genetic structure gradually increasing with distance along a coastline. We conducted genetic analyses of mangrove forests across a range of spatial scales; within a 400 m2 parcel comprising 181 Rhizophora mangle (red mangrove) trees, and across four sites ranging from 6–115 km apart in Honduras. In total, we successfully genotyped 269 R. mangle trees, using a panel of 677 SNPs developed with 2b-RAD methodology. Within the 400 m2 parcel, we found two distinct clusters with high levels of genetic differentiation (FST = 0.355), corresponding to trees primarily located on the seaward fringe and trees growing deeper into the forest. In contrast, there was limited genetic differentiation (FST = 0.027–0.105) across the sites at a larger scale, which had been predominantly sampled along the seaward fringe. Within the 400 m2 parcel, the cluster closest to the seaward fringe exhibited low genetic differentiation (FST = 0.014–0.043) with the other Honduran sites, but the cluster further into the forest was highly differentiated from them (FST = 0.326–0.414). These findings contradict the perception that genetic structure within mangroves forests occurs mainly along a coastline and highlights that there is greater genetic structure at fine spatial scales.</jats:p