Comparative analysis of bottom trawl and nanopore sequencing in fish biodiversity assessment: The sylt outer reef example.

The assessment of fish diversity is crucial for effective conservation and management strategies, especially in ecologically sensitive regions such as marine protected areas. This study contrasts the effectiveness of environmental DNA (eDNA) metabarcoding analysis employing Nanopore technology with compare beam trawl surveys at the Sylt Outer Reef, a Natura 2000 site in the North Sea, Germany. Out of the 17 fish species caught in a bottom trawl (using a 3m beam trawl), 14 were also identified through eDNA extracted from water samples. The three species not detected in the eDNA results were absent because they lacked representation in public DNA databases. The eDNA method detected twice as many fish species as the beam trawl, totalling 36 species, of which 14 were also detected by the trawl. Additionally, the selection of primers (Mifish) facilitated the identification of one marine mammal species, the harbour porpoise. In conclusion, the findings underscore the potential of eDNA coupled with MinION sequencing (Long read technology) as a robust tool for biodiversity assessment, surpassing traditional methods in detecting species richness.

Occurrence of the pugnose pipefish Bryx dunckeri in the Sargasso Sea.

Juvenile specimens of the pugnose pipefish, Bryx dunckeri, were collected during a multipurpose research survey conducted within the Sargasso Sea Subtropical Convergence Zone, extending the known distribution range of this species to include open ocean areas of the Western North Atlantic. Novel spatial data are of scientific interest as information on the distribution, population structure, and population size of this species is limited. Additionally, we present detailed photographs and morphological data on the collected specimens. The results are discussed in relation to the dispersal abilities and population structure in syngnathids.

Environmental enrichment during early rearing provokes epigenetic changes in the brain of a salmonid fish.

Environmental enrichment is used to increase structural complexity of captive rearing systems and has been shown to provoke a wide range of effects in the kept animals. Here we studied the effects of enrichment on DNA methylation patterns at the whole-genome level in the brain of rainbow trout reared in an aquaculture setting. We investigated the epigenetic effects between different types of enrichment (natural substrate vs. artificial substrate vs. barren) in three developmental stages (egg vs. alevin vs. fry) and as enrichment was discontinued at the fingerling stage by means of the Methylation-Sensitive Amplified Polymorphism (MSAP) technique. While enrichment did not affect growth in body size, we found enrichment to affected global DNA methylation in the brain at the egg and alevin stage, i.e., the period during development where the animals are in close physical contact with the substrate. At these stages, trout reared on the two substrates differed more from the control than the substrates differed from each other. Only minor differences between rearing environments were detected following emergence at the fry stage. When enrichment was discontinued during the rearing of fingerlings, no differences in DNA methylation patterns were observed between the rearing environments. Our results provide further evidence on the effects of enrichment in the captive rearing of fish and show that enrichment can even modulate epigenetic patterns. The effect on the epigenome may be causal for the previously reported effects of enrichment on gene expression, behaviour and brain development.

Metamorphosis and transition between developmental stages in European eel (Anguilla anguilla, L.) involve epigenetic changes in DNA methylation patterns.

The life history of the European eel (Anguilla anguilla, L.) is characterized by a series of metamorphoses and transitions that provoke drastic morphological changes. Most of these changes go along with the catadromous life cycle in eels, involving extensive physiologically adaptations. In this study it was investigated whether these drastic changes have an epigenetic basis by analyzing global methylation patterns in liver, gill and brain tissue from glass eels caught at the British coast as well as yellow and silver eels from River Rhine using methylation-sensitive amplified polymorphisms (MSAP). Analysis of molecular variance (AMOVA) on MSAP data derived from liver tissue revealed only minor differences in methylation patterns between glass, yellow and silver eels, reflecting uniform functioning of the liver throughout the investigated lifespan. In brain and gill tissue, however, marked differences in methylation patterns were found. Principal coordinates analysis (PCoA) revealed yellow eels being partially clustered with silver eels and a more distinct cluster of glass eels based on the methylation patterns in the brain. According to results found in the gills, glass eels were more similar to silver eels whereas yellow eels were found to be clustered separately. From these results it can be concluded that epigenetic changes in gill tissue most likely reflect and are linked with adaptation towards salt- and freshwater conditions. The observed differences in brain methylation patterns, however, might be linked to morphological and physiological changes during metamorphosis and transitions within the life history of European eels potentially affecting subsequent differential gene expression patterns required for such changes.