eDNA, Microbiomes, Photogrammetry and Hormones Assessment Techniques in Cetaceans

This study evaluates methodological approaches for marine vertebrate eDNA metabarcoding. We compared DNA extraction methods, tested polymerases with different proofreading capacities, and developed MVeM, an open-source bioinformatics pipeline for reliable taxonomic assignment. Direct extraction from intact filters yielded higher DNA concentrations and ASV richness, while polymerase performance varied between cetaceans and fish. Overall, combining optimised laboratory methods with a robust bioinformatics workflow provides an accessible and reliable framework for marine vertebrate biodiversity monitoring.

This study explores how exhaled breath samples can be used to assess the respiratory health of wild cetaceans. By analysing the respiratory microbiome of short-finned pilot whales (Globicephala macrorhynchus) and common dolphins (Delphinus delphis) using both short-read and long-read DNA sequencing, we compared the performance of the two approaches. PacBio provided greater microbial diversity, higher taxonomic resolution, and improved detection of potential pathogens. Our findings reveal distinct respiratory microbiomes between species and confirm that exhaled breath condensate is a powerful, non-invasive tool for monitoring the health of cetaceans.

This study examines the application of environmental DNA and DNA metabarcoding to evaluate cetacean communities and their potential prey along the northern coast of Mainland Portugal. Over four seasonal campaigns, we collected seawater samples and analysed them using Next-Generation Sequencing, identifying five cetacean species. Molecular detections largely aligned with visual monitoring, confirming year-round presence. Notably, the detection of fin whales (Balaenoptera physalus) was significant, as no prior scientific records exist for the area. We also found evidence of predator-prey overlap, suggesting the coastal area serves as a feeding ground.​​​​​​​​​

This study examines how analysing the breath of short-finned pilot whales (Globicephala macrorhynchus) can aid in assessing their respiratory health. Since respiratory diseases are a major threat to cetaceans, we examined the microbes in exhaled breath samples from whales off Madeira Island. By sequencing DNA, we identified key bacterial groups and compared two different genetic markers to determine which method best captures microbial diversity. Our findings also highlight how social interactions may influence respiratory microbiomes and confirm that breath samples can serve as valuable health indicators for wild cetaceans.