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Povzetek: Diatoms are one of the most important phytoplankton groups in the world’s oceans. There are responsible for up to 40% of the photosynthetic activity in the Ocean, and they play an important role in the silicon and carbon cycles by decoupling carbon from atmospheric interactions through sinking and export. These processes are strongly influenced by the taxonomic composition of diatom assemblages. Traditionally, these have been assessed using microscopy, which in some cases is not reliable or reproducible. Next-generation sequencing enabled us to study diversity in a high-throughput manner and uncover new distribution patterns and diversity. However, phylogenetic markers used for this purpose, such as various 18S rDNA regions, are often insufficient because they cannot distinguish between some taxa. In this work, we demonstrate the performance of the chloroplast-encoded rbcL marker for metabarcoding marine diatoms compared to microscopy and 18S-V9 metabarcoding using a series of monthly samples from the Gulf of Trieste (GoT), northern Adriatic Sea. We demonstrate that rbcL is able to detect more taxa compared to 18S-V9 metabarcoding or microscopy, while the overall structure of the diatom assemblage was comparable to the other two methods with some variations, that were taxon dependent. In total, 6 new genera and 22 new diatom species for the study region were identified. We were able to spot misidentification of genera obtained with microscopy such as Pseudo-nitzschia galaxiae, which was mistaken for Cylindrotheca closterium, as well as genera that were completely overlooked, such as Minidiscus and several genera from the Cymatosiraceae family. Furthermore, on the example of two well-studied genera in the region, namely Chaetoceros and particularly Pseudo-nitzschia, we show how the rbcL method can be used to infer even deeper phylogenetic and ecologically significant differences at the species population level. Despite a very thorough community analysis obtained by rbcL the incompleteness of reference databases was still evident, and we shed light on possible improvements. Our work has further implications for studies dealing with taxa distribution and population structure, as well as carbon and silica flux models and networks.
Ključne besede: rbcL, metabarcoding, monitoring, diatoms, population genetics, Pseudo-nitzschia, Adriatic
Objavljeno v DiRROS: 12.07.2024; Ogledov: 77; Prenosov: 40
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Povzetek: Reliable data and methods for assessing changes in wildlife population size over time are necessary for management and conservation. For most species, assessing abundance is an expensive and labor-intensive task that is not affordable on a frequent basis. We present a novel approach to reconstructing brown bear population dynamics in Slovenia in the period 1998-2019, based on the combination of two CMR non-invasive genetic estimates (in 2007 and 2015) and long-term mortality records, to show how the latter can help the study of population dynamics in combination with point-in-time estimates. The spring (i.e. including newborn cubs) population size estimate was 383 (CI: 336-432) bears in 1998 and 971 (CI: 825-1161) bears in 2019. In this period, the average annual population growth rate was 4.5 %. The predicted population size differed by just 7 % from the non-invasive genetic size estimate after eight years, suggesting that the method is reliable. It can predict the evolution of the population size under different management scenarios and provide information on key parameters, e.g. background mortality and the sex- and age-structure of the population. Our approach can be used for several other wildlife species, but it requires reliable mortality data over time.
Ključne besede: genetic estimates of population size, mortality records, population monitoring, population size, predictive modelling, brown bear
Objavljeno v DiRROS: 28.03.2021; Ogledov: 4403; Prenosov: 2511
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