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Query: "keywords" (amplicon sequencing) .

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1.
Phytoplankton diversity in the Northern Adriatic Sea : insights and inconsistencies from microscopy and metabarcoding
Giorgia Montali, Francesca Neri, Elisa Banchi, Federica Cerino, Timotej Turk Dermastia, Janja Francé, Patricija Mozetič, 2026, original scientific article

Abstract: Phytoplankton plays a fundamental role in marine ecosystems and is widely used to assess environmental change. In this study, light microscopy and DNA metabarcoding approaches were used to investigate phytoplankton communities at three long-term monitoring sites in the northern Adriatic Sea. By combining the two approaches, more than 500 species were recorded. Metabarcoding detected substantially higher diversity, particularly among small and fragile organisms that are difficult to identify under a microscope, whereas microscopy was better for identifying larger species with distinctive morphology. Because species contain different amounts of genetic material, DNA data can overestimate or underestimate their true contribution to the community. Indeed, after applying correction factors that account for these differences, the DNA-based estimates became more consistent with the microscopy results for several phytoplankton groups. The differences among the samples were influenced more by the approach used than by the sampling location. Overall, combining these two approaches provides an accurate and robust picture of phytoplankton communities. In this way, it is possible to improve the reliability of marine biodiversity assessments and to support better environmental monitoring and management in coastal seas.
Keywords: phytoplankton, diversity, environmental DNA, Long-Term Ecological Research, amplicon sequencing, North Adriatic Sea
Published in DiRROS: 25.03.2026; Views: 364; Downloads: 282
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2.
Inter-comparison of marine microbiome sampling protocols
Francisco Pascoal, Maria Paola Tomasino, Roberta Piredda, Grazia Marina Quero, Luís Torgo, Julie Poulain, Tinkara Tinta, Timotej Turk Dermastia, 2023, original scientific article

Abstract: Research on marine microbial communities is growing, but studies are hard to compare because of variation in seawater sampling protocols. To help researchers in the inter-comparison of studies that use different seawater sampling methodologies, as well as to help them design future sampling campaigns, we developed the EuroMarine Open Science Exploration initiative (EMOSE). Within the EMOSE framework, we sampled thousands of liters of seawater from a single station in the NW Mediterranean Sea (Service d'Observation du Laboratoire Arago [SOLA], Banyuls-sur-Mer), during one single day. The resulting dataset includes multiple seawater processing approaches, encompassing different material-type kinds of filters (cartridge membrane and flat membrane), three different size fractionations (>0.22 µm, 0.22–3 µm, 3–20 µm and >20 µm), and a number of different seawater volumes ranging from 1 L up to 1000 L. We show that the volume of seawater that is filtered does not have a significant effect on prokaryotic and protist diversity, independently of the sequencing strategy. However, there was a clear difference in alpha and beta diversity between size fractions and between these and “whole water” (with no pre-fractionation). Overall, we recommend care when merging data from datasets that use filters of different pore size, but we consider that the type of filter and volume should not act as confounding variables for the tested sequencing strategies. To the best of our knowledge, this is the first time a publicly available dataset effectively allows for the clarification of the impact of marine microbiome methodological options across a wide range of protocols, including large-scale variations in sampled volume.
Keywords: marine microbiome, standardized sampling, inter-comparison, amplicon sequencing, microbial diversity, seawater sampling
Published in DiRROS: 12.07.2024; Views: 1541; Downloads: 1110
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