Fine-scale differences in eukaryotic communities inside and outside salmon aquaculture cages revealed by eDNA metabarcoding

North Atlantic deep-sea benthic biodiversity unveiled through sponge natural sampler DNA

The deep-sea remains the biggest challenge to biodiversity exploration, and anthropogenic disturbances extend well into this realm, calling for urgent management strategies. One of the most diverse, productive, and vulnerable ecosystems in the deep sea are sponge grounds. Currently, environmental DNA (eDNA) metabarcoding is revolutionising the field of biodiversity monitoring, yet complex deep-sea benthic ecosystems remain challenging to assess even with these novel technologies. Here, we evaluate the effectiveness of whole-community metabarcoding to characterise metazoan diversity in sponge grounds across the North Atlantic by leveraging the natural eDNA sampling properties of deep-sea sponges themselves. We sampled 97 sponge tissues from four species across four North-Atlantic biogeographic regions in the deep sea and screened them using the universal COI barcode region. We recovered unprecedented levels of taxonomic diversity per unit effort, especially across the phyla Chordata, Cnidaria, Echinodermata and Porifera, with at least 406 metazoan species found in our study area. These assemblages identify strong spatial patterns in relation to both latitude and depth, and detect emblematic species currently employed as indicators for these vulnerable habitats. The remarkable performance of this approach in different species of sponges, in different biogeographic regions and across the whole animal kingdom, illustrates the vast potential of natural samplers as high-resolution biomonitoring solutions for highly diverse and vulnerable deep-sea ecosystems.

Effects of livestock on arthropod biodiversity in Iberian holm oak savannas revealed by metabarcoding

Increasing food production while avoiding negative impacts on biodiversity constitutes one of the main challenges of our time. Traditional silvopastoral systems like Iberian oak savannas ("dehesas") set an example, where free-range livestock has been reared for centuries while preserving a high natural value. Nevertheless, factors decreasing productivity need to be addressed, one being acorn losses provoked by pest insects. An increased and focalized grazing by livestock on infested acorns would kill the larvae inside and decrease pest numbers, but increased livestock densities could have undesired side effects on ground arthropod communities as a whole. We designed an experimental setup including areas under trees with livestock exclosures of different ages (short-term: 1-year exclusion, long-term: 10-year exclusion), along with controls (continuous grazing), using DNA metabarcoding (mitochondrial markers COI and 16S) to rapidly assess arthropod communities' composition. Livestock removal quickly increased grass cover and arthropod taxonomic richness and diversity, which was already higher in short-term (1-year exclosures) than beneath the canopies of control trees. Interestingly, arthropod diversity was not highest at long-term exclosures (≥10 years), although their community composition was the most distinct. Also, regardless of treatment, we found that functional diversity strongly correlated with the vegetation structure, being higher at trees beneath which there was higher grass cover and taller herbs. Overall, the taxonomic diversity peak at short term exclosures would support the intermediate disturbance hypothesis, which relates it with the higher microhabitat heterogeneity at moderately disturbed areas. Thus, we propose a rotatory livestock management in dehesas: plots with increased grazing should co-exist with temporal short-term exclosures. Ideally, a few long-term excluded areas should be also kept for the singularity of their arthropod communities. This strategy would make possible the combination of biological pest control and arthropod conservation in Iberian dehesas.

Molecular quantification of parasitic sea louse larvae depends on species and life stage

Sea lice cause substantial economic and environmental harm to Norway's aquaculture industry and wild salmonid populations. Rapid, accurate quantification of lice larval densities in coastal waters remains the greatest bottleneck for providing empirical data on infestation risk within wild salmon habitats and aquaculture production regions. We evaluated the capability of droplet digital PCR (ddPCR) as an absolute quantification method for the planktonic stages of two parasitic louse species, Lepeophtheirus salmonis (Krøyer) and Caligus elongatus (von Nordman). Results demonstrated linear relationships between the DNA quantity measured and the number of spiked larvae for both species and life stages. However, L. salmonis contained a significantly greater number of DNA copies than C. elongatus individuals and for C. elongatus, nauplii displayed a significantly higher number of DNA copies than copepodids. Our results suggest that ddPCR can effectively enumerate louse larvae, but interpreting ddPCR results differ between the two louse species. Obtaining larval abundance estimates from marine plankton samples will depend on the nauplii to copepodid ratio for C. elongatus, but not for L. salmonis.