Development of a quantitative colorimetric LAMP assay for fast and targeted molecular detection of the invasive lionfish Pterois miles from environmental DNA

The Mediterranean basin has faced an increased influx of invasive species since the Suez Canal expansion in 2015. The invasive lionfish species, Pterois miles, has rapidly established new populations in the Eastern Mediterranean Sea, impacting local fish biodiversity. Here, we have developed a new, fast (< 35 min) molecular approach to detect and quantify P. miles environmental DNA (eDNA) in combination with a portable device for field-based analysis. Using a species-specific real-time colorimetric loop-mediated isothermal amplification (qcLAMP) for the cytochrome oxidase subunit 1 (COI) gene, we demonstrate a high sensitivity with a limit of detection of 0.002 ng DNA per reaction, equivalent to only 50 copies of the COI gene. The assay is specific to the target in the presence of closely related and co-occurring species, and it is quantitative over five orders of magnitude. We validated the assay using aquarium water samples and further demonstrated its utility on natural eDNA samples collected from locations around the island of Crete where P. miles had been sighted. P. miles was indeed detected in three out of nine locations, two nature reserves and a closed bay. Lack of detection in the remaining locations suggests that populations are still at a low density. We also demonstrate the feasibility of P. miles eDNA qualitative detection directly from the filter used to collect eDNA-containing particles, completely omitting DNA extraction. Overall, we present a new approach for fast and targeted eDNA quantification. The developed LAMP assay together, with the quantitative real-time colorimetric detection approach, open new possibilities for monitoring invasive P. miles in the field

Diversity of zooxanthellae from corals and sea anemones after long-term aquarium culture

Aquarium systems allow technically sophisticated experiments that promise new opportunities to answer urgent questions about reef coral biology, for instance assessing the responses to decreasing environmental pH and/or increased temperatures. Over recent years, long-term culture and (predominantly asexual) propagation of corals has become possible in such systems. At present however, only limited data are available that clarify whether or not responses of the coral holobiont are dominated by the acclimatization to life in captivity or continue to reflect, for example, taxonomic differences seen in nature. We studied the diversity of the symbiotic algae in corals and sea anemones after long-term aquaculture by analysis of their small subunit (SSU) ribosomal DNA gene. A field sample of Acropora clathrata from the Arabian Gulf which was used as a control contained clade C zooxanthellae. The aquarium corals also harboured clade C symbionts, but sequencing of the SSU DNA suggested that the analysed animals host different subclades. A prevalence of clade C is also found among corals from the Indo-Pacific region, the origin of most of the aquarium samples. An individual of the temperate sea anemone Anemonia sulcata (viridis) contained clade A symbionts, similar to those found in nature, even after nearly 10 years of co-culture with sea anemones (Entacmaea quadricolor) and corals hosting clade C symbionts. The results indicate that the specific host–symbiont association occurring in nature appears to persist over >2 years timescales in captivity, with no mixing of symbionts between hosts maintained in the same aquarium or apparent selection of stress-tolerant symbiont strains such as clade D

Unveiling biogeographical patterns in the worldwide distributed Ceratitis capitata (medfly) using population genomics and microbiome composition

Invasive species are among the most important, growing threats to food security and agricultural systems. The Mediterranean medfly, Ceratitis capitata, is one of the most damaging representatives of a group of rapidly expanding species in the family Tephritidae, due to their wide host range and high invasiveness potential. Here, we used restriction site-associated DNA sequencing (RADseq) to investigate the popu-lation genomic structure and phylogeographical history of medflies collected from six sampling sites, including Africa (South Africa), the Mediterranean (Spain, Greece), Latin America (Guatemala, Brazil) and Australia. A total of 1907 single nucleotide pol-ymorphisms (SNPs) were used to identify two genetic clusters separating native and introduced ranges, consistent with previous findings. In the introduced range, all indi-viduals were assigned to one genetic cluster except for those in Brazil, which showed introgression of an additional genetic cluster that also appeared in South Africa, and which could not be previously identified using microsatellite markers. Moreover, we assessed the microbial composition variations in medfly populations from selected sampling sites using amplicon sequencing of the 16S ribosomal RNA (V4 region). Microbiome composition and structure were highly similar across geographical re-gions and host plants, and only the Brazilian specimens showed increased diversity levels and a unique composition of its microbiome compared to other sampling sites. The unique SNP patterns and microbiome features in the Brazilian specimens could point to a direct migration route from Africa with subsequent adaptation of the micro-biota to the specific conditions present in Brazil. These findings significantly improve our understanding of the evolutionary history of the global medfly invasions and their adaptation to newly colonized environments.M.B.A. was supported by the National Agency for Research and Development (ANID), fellowship programme Doctorado en el extranjero/2014 and Postdoctorado en el extranjero/2019 –74200143. S.E. was supported by an EMBO grant (ASTF-42-2010) and a CSIRO Julius Career Award (R- 91040-11). S.T. received funding from the grant PID2020-117115GA-100 funded by MCIN/AEI/10.13039/50110001103Peer reviewe

Technologies for Ocean Sensing project developments in imaging and sensing

International audienceThe TechOceanS project is developing new remote ocean sensing technology supporting wider ocean measurement and a drive to net zero. The project will deliver 5 new sensor classes for biogeochemistry, biology and ecosystems addressing 10 of 19 EOVs, 31 of 73 subvariables, 6 of 9 MSFD targets together with microplastics and a range of biotoxins and contaminants. It will also develop a new image processing workflow for extracting EOVs (9) and MSFD (6) and litter measurements from images. These innovations concentrate on key capability gaps in ocean observing from non-ship systems with a focus on low-cost per measurement through minimised instrument and deployment costs. This paper gives a brief overview of the technologies, and were possible, because of progress or protection of intellectual property, details of our approaches and early results

Technologies for Ocean Sensing project developments in imaging and sensing

The TechOceanS project is developing new remote ocean sensing technology supporting wider ocean measurement and a drive to net zero. The project will deliver 5 new sensor classes for biogeochemistry, biology and ecosystems addressing 10 of 19 EOVs, 31 of 73 subvariables, 6 of 9 MSFD targets together with microplastics and a range of biotoxins and contaminants. It will also develop a new image processing workflow for extracting EOVs (9) and MSFD (6) and litter measurements from images. These innovations concentrate on key capability gaps in ocean observing from non-ship systems with a focus on low-cost per measurement through minimised instrument and deployment costs. This paper gives a brief overview of the technologies, and were possible, because of progress or protection of intellectual property, details of our approaches and early results

Technologies for Ocean Sensing project developments in imaging and sensing

International audienceThe TechOceanS project is developing new remote ocean sensing technology supporting wider ocean measurement and a drive to net zero. The project will deliver 5 new sensor classes for biogeochemistry, biology and ecosystems addressing 10 of 19 EOVs, 31 of 73 subvariables, 6 of 9 MSFD targets together with microplastics and a range of biotoxins and contaminants. It will also develop a new image processing workflow for extracting EOVs (9) and MSFD (6) and litter measurements from images. These innovations concentrate on key capability gaps in ocean observing from non-ship systems with a focus on low-cost per measurement through minimised instrument and deployment costs. This paper gives a brief overview of the technologies, and were possible, because of progress or protection of intellectual property, details of our approaches and early results

Technologies for ocean sensing project developments in imaging and sensing

The TechOceanS project is developing new remote ocean sensing technology supporting wider ocean measurement and a drive to net zero. The project will deliver 5 new sensor classes for biogeochemistry, biology and ecosystems addressing 10 of 19 EOVs, 31 of 73 subvariables, 6 of 9 MSFD targets together with microplastics and a range of biotoxins and contaminants. It will also develop a new image processing workflow for extracting EOVs (9) and MSFD (6) and litter measurements from images. These innovations concentrate on key capability gaps in ocean observing from non-ship systems with a focus on low-cost per measurement through minimised instrument and deployment costs. This paper gives a brief overview of the technologies, and were possible, because of progress or protection of intellectual property, details of our approaches and early results.</p