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- Capo, Eric, et al.
(författare)
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Droplet digital PCR applied to environmental DNA, a promising method to estimate fish population abundance from humic-rich aquatic ecosystems
- 2021
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Ingår i: Environmental DNA. - : John Wiley & Sons. - 2637-4943. ; 3:2, s. 343-352
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Tidskriftsartikel (refereegranskat)abstract
- Measures of environmental DNA (eDNA) concentrations in water samples have the potential to be both a cost-efficient and a nondestructive method to estimate fish population abundance. However, the inherent temporal and spatial variability in abiotic and biotic conditions in aquatic systems have been suggested to be a major obstacle to determine relationships between fish eDNA concentrations and fish population abundance. Moreover, once water samples are collected, methodological biases are common, which introduces additional sources of variation to potential relationships between eDNA concentrations and fish population abundance. Here, we evaluate the performance of applying the droplet digital PCR (ddPCR) method to estimate fish population abundance in experimental enclosures. Using large-scale enclosure ecosystems that contain populations of nine-spined stickleback (Pungitius pungitius), we compared the concentrations of fish eDNA (COI mitochondrial region, 134 bp) obtained with the ddPCR method with high precision estimates of fish population abundance (i.e., number of individuals) and biomass. To evaluate the effects of contrasted concentrations of humic substances (potential PCR inhibitors) on the performance of ddPCR assays, we manipulated natural dissolved organic carbon (DOC) concentrations (range 4–11 mg/L) in the enclosures. Additionally, water temperature (+2°C) was manipulated in half of the enclosures. Results showed positive relationships between eDNA concentration and fish abundance and biomass estimates although unexplained variation remained. Still and importantly, fish eDNA estimates from high DOC enclosures were not lowered by potential inhibitory effects with our procedure. Finally, water temperature (although only 2°C difference) was neither detected as a significant factor influencing fish eDNA estimates. Altogether, our work highlights that ddPCR-based eDNA is a promising method for future quantification of fish population abundance in natural systems.
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| 2. |
- Capo, Eric, et al.
(författare)
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Lake sedimentary dna research on past terrestrial and aquatic biodiversity: Overview and recommendations
- 2021
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Ingår i: Quaternary. - : MDPI. - 2571-550X. ; 4:1
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Forskningsöversikt (refereegranskat)abstract
- The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.
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| 3. |
- Kanbar, Hussein Jaafar, et al.
(författare)
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Tracking mineral and geochemical characteristics of Holocene lake sediments : the case of Hotagen, west-central Sweden
- 2021
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Ingår i: Journal of Soils and Sediments. - : Springer. - 1439-0108 .- 1614-7480. ; 21:9, s. 3150-3168
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Intact lake sediments reflect the development of terrestrial ecosystems. This development can be understood by decoding mineral and geochemical information of sedimentary archives. Therefore, we characterized a Holocene lake sediment core and revealed bulk to micro-scale variations via a combination of geochemical techniques and statistical methods.Methods: A 2.3 m sediment core was collected from Hotagen, a lake in west-central Sweden; a sediment sample was collected every 5 cm. A part of each sediment sample was kept untreated (named bulk) and another part was size-fractionated into < 4, 4–16, 16–64, and > 64 µm subsamples. Characterization was then made with respect to grain size distribution (GSD), physico-chemical parameters, geochemical properties, organic composition, and mineralogy. The sediments were investigated at bulk, micro-, and elemental scales using powder X-ray diffraction (XRD), diffuse reflectance infrared Fourier transform spectroscopy (DRIFT), and scanning electron microscopy coupled to energy-dispersive X-ray spectroscopy (SEM–EDX).Results: The deepest sediment was identified as glacial till dating back to the Late Pleistocene. The bulk sediments showed a clear distinction between 0–195 cm (unit 1, U1) and 200–225 cm (unit 2, U2) depths. Quartz and feldspar minerals decreased and organic matter and clay minerals increased from the till towards the lower limit of U1. The development in the sedimentary properties marked the transformation of the terrestrial ecosystem from glacier-covered land to vegetated areas. This development was also well reflected by the appearance of X-ray amorphous materials and the formation of distinct organo-mineral aggregates; chlorite was the predominant clay mineral in these aggregates. The geochemical variation between U2 and U1 sediments was further established by resolving the DRIFT spectral components through multivariate curve resolution alternating least square (MCR-ALS). The U1 sediments settled over a period of ~ 7500 years and showed comparable mineral, geochemical, and organic composition. However, the size-fractionated sediments, mainly < 4 µm, showed diverse mineral and geochemical composition. Indeed, these sediments were distinct by containing relatively higher amounts of X-ray amorphous materials and clay minerals, the latter had variable Na, Mg, and K contents.Conclusion: The combined use of geochemical and statistical approaches used in this study followed the mineral and geochemical development of sediments that had settled during the Late Pleistocene and Early Holocene Epochs. Finally, the U2 sediments marked the terrestrial ecosystem development that occurred during the late glaciation, deglaciation, and post-glaciation periods. Graphical abstract: [Figure not available: see fulltext.]
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