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Publications (6 of 6) Show all publications
Capo, E., Spong, G., Koizumi, S., Puts, I., Olajos, F., Königsson, H., . . . Byström, P. (2021). Droplet digital PCR applied to environmental DNA, a promising method to estimate fish population abundance from humic-rich aquatic ecosystems. Environmental DNA, 3(2), 343-352
Open this publication in new window or tab >>Droplet digital PCR applied to environmental DNA, a promising method to estimate fish population abundance from humic-rich aquatic ecosystems
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2021 (English)In: Environmental DNA, E-ISSN 2637-4943, Vol. 3, no 2, p. 343-352Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
John Wiley & Sons, 2021
Keywords
ddPCR, environmental DNA, fish population estimates, nine-spined sticklebacks, species-specific detection
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:umu:diva-183699 (URN)10.1002/edn3.115 (DOI)2-s2.0-85106016581 (Scopus ID)
Funder
Swedish Research Council Formas, CTS16:84Swedish Research Council Formas, CTS18:812Knut and Alice Wallenberg Foundation, 2016.0083
Available from: 2021-05-31 Created: 2021-05-31 Last updated: 2024-02-13Bibliographically approved
Capo, E., Giguet-Covex, C., Rouillard, A., Nota, K., Heintzman, P. D., Vuillemin, A., . . . Parducci, L. (2021). Lake sedimentary dna research on past terrestrial and aquatic biodiversity: Overview and recommendations. Quaternary, 4(1), Article ID 6.
Open this publication in new window or tab >>Lake sedimentary dna research on past terrestrial and aquatic biodiversity: Overview and recommendations
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2021 (English)In: Quaternary, E-ISSN 2571-550X, Vol. 4, no 1, article id 6Article, review/survey (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
MDPI, 2021
Keywords
Biodiversity, Lake sediments, Metabarcoding, Metagenomics, Paleoecology, Paleogenetics, Paleogenomics, Paleolimnology, Sedimentary ancient DNA, Sedimentary DNA
National Category
Geochemistry
Identifiers
urn:nbn:se:umu:diva-182945 (URN)10.3390/quat4010006 (DOI)000633093700001 ()2-s2.0-85104594727 (Scopus ID)
Available from: 2021-05-11 Created: 2021-05-11 Last updated: 2024-02-13Bibliographically approved
Kanbar, H. J., Tran Le, T., Olajos, F., Englund, G. & Holmboe, M. (2021). Tracking mineral and geochemical characteristics of Holocene lake sediments: the case of Hotagen, west-central Sweden. Journal of Soils and Sediments, 21(9), 3150-3168
Open this publication in new window or tab >>Tracking mineral and geochemical characteristics of Holocene lake sediments: the case of Hotagen, west-central Sweden
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2021 (English)In: Journal of Soils and Sediments, ISSN 1439-0108, E-ISSN 1614-7480, Vol. 21, no 9, p. 3150-3168Article in journal (Refereed) Published
Abstract [en]

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.]

Place, publisher, year, edition, pages
Springer, 2021
Keywords
DRIFT, Ecosystem development, Post-glaciation, Sediment core, Size fraction, XRD
National Category
Geochemistry Geology
Identifiers
urn:nbn:se:umu:diva-186576 (URN)10.1007/s11368-021-03012-y (DOI)000679014900001 ()2-s2.0-85111312144 (Scopus ID)
Available from: 2021-08-12 Created: 2021-08-12 Last updated: 2022-01-12Bibliographically approved
Kanbar, H. J., Olajos, F., Englund, G. & Holmboe, M. (2020). Geochemical identification of potential DNA-hotspots and DNA-infrared fingerprints in lake sediments. Applied Geochemistry, 122, Article ID 104728.
Open this publication in new window or tab >>Geochemical identification of potential DNA-hotspots and DNA-infrared fingerprints in lake sediments
2020 (English)In: Applied Geochemistry, ISSN 0883-2927, E-ISSN 1872-9134, Vol. 122, article id 104728Article in journal (Refereed) Published
Abstract [en]

DNA preserved in sedimentary materials can be used to study past ecosystem changes, such as species' colonization and extinction. It is believed that minerals, especially clay minerals, enhance the preservation of DNA. However, the role of minerals, as well as organic matter, on DNA sorption in heterogeneous sediments is still not clear. In this study, we examined the effect of mineral and organic matter on DNA binding in lake sediments. Bulk and size-fractionated sediments (0–4, 4–16, 16–64, and >64 μm), having different mineral and organic composition, were used to test DNA sorption; similar experiments were also run after the removal of sedimentary organic matter. Additionally, diffuse reflectance infrared spectroscopy (DRIFT) was used to determine the chemical changes caused by DNA sorption and subsequently produce a DNA-infrared (IR) fingerprint. Clay minerals were the main minerals to sorb DNA in the different samples. Moreover, mica promoted DNA sorption in all size fractions, while chlorite promoted DNA sorption in size fractions greater than 16 μm; clay-mineral and organo-mineral complexes caused a preference of certain clay minerals over others. Sedimentary organic matter affected DNA sorption by covering as well as by amplifying potential DNA binding sites, yet DNA sorption did not change significantly. DNA sorption showed IR spectral modifications mainly at ~1640, 1416, and 1231 cm−1. Interestingly, the DNA-IR fingerprint in the heterogeneous sediments was evident by those peaks after spectral subtraction. Finally, we proposed a simple model, based on sediment geochemistry, that can be used to determine potential DNA-hotspots in sediments.

Place, publisher, year, edition, pages
Elsevier, 2020
Keywords
DNA sorption, Sediment grain size, Mineralogy, Clay minerals, Organic matter
National Category
Geochemistry
Identifiers
urn:nbn:se:umu:diva-177774 (URN)10.1016/j.apgeochem.2020.104728 (DOI)000587914200017 ()2-s2.0-85089741678 (Scopus ID)
Funder
The Kempe Foundations, JCK-1821
Available from: 2020-12-22 Created: 2020-12-22 Last updated: 2023-03-23Bibliographically approved
Englund, G., Öhlund, G., Olajos, F., Finstad, A., Bellard, C. & Hugueny, B. (2020). Holocene extinctions of a top predator: effects of time, habitat area and habitat subdivision. Journal of Animal Ecology, 89(5), 1202-1215
Open this publication in new window or tab >>Holocene extinctions of a top predator: effects of time, habitat area and habitat subdivision
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2020 (English)In: Journal of Animal Ecology, ISSN 0021-8790, E-ISSN 1365-2656, Vol. 89, no 5, p. 1202-1215Article in journal (Refereed) Published
Abstract [en]

Loss of habitat and changes in the spatial configuration of habitats are major drivers of species extinctions, but the responses to these drivers differ between organisms. To advance theory on how extinction risk from different types of habitat alteration relates to species-specific traits, there is a need for studies of the long-term extinction dynamic of individual species. The goal of this study was to quantify how habitat area and the spatial configuration of habitats affect extinction rate of an aquatic top predator, the northern pike Esox lucius L. We recorded the presence/absence of northern pike in 398 isolated habitat fragments, each one consisting of a number of interconnected lakes. Time since isolation of the habitat fragments, caused by cut-off from the main dispersal source in the Baltic Sea, varied between 0 and 10,000 years. Using survival regression, we analysed how pike population survival was affected by time since isolation, habitat size and habitat subdivision. The approach builds on the assumptions that pike colonized all fragments before isolation and that current absences result from extinctions. We verified these assumptions by testing (a) if pike was present in the region throughout the entire time period when the lakes formed and (b) if pike typically colonize lakes that are formed today. We also addressed the likelihood that unrecorded anthropogenic introductions could bias our estimates of extinction rate. Our results supported the interpretation that current patterns of presence/absence in our study system are shaped by extinctions. Further, we found that time since isolation and fragment area had strong effects on pike population survival. In contrast, spatial habitat subdivision (i.e. if a fragment contained few large lakes or many small lakes) and other environmental covariates describing climate and productivity were unrelated to pike survival. Over all, extinction rate was high in young fragments and decreased sharply with increasing fragment age. Our study demonstrates how the link between extinction rate and habitat size and spatial structure can be quantified. More similar studies may help us find generalizations that can guide management of habitat size and connectivity.

Place, publisher, year, edition, pages
John Wiley & Sons, 2020
Keywords
aquatic ecosystems, connectivity, extinction, fragmentation, habitat age, habitat area
National Category
Zoology Ecology Environmental Sciences
Identifiers
urn:nbn:se:umu:diva-168983 (URN)10.1111/1365-2656.13174 (DOI)000512817300001 ()31943165 (PubMedID)2-s2.0-85079448005 (Scopus ID)
Available from: 2020-03-27 Created: 2020-03-27 Last updated: 2023-03-24Bibliographically approved
Olajos, F., Bokma, F., Bartels, P., Myrstener, E., Rydberg, J., Öhlund, G., . . . Englund, G. (2018). Estimating species colonization dates using DNA in lake sediment. Methods in Ecology and Evolution, 9(3), 535-543
Open this publication in new window or tab >>Estimating species colonization dates using DNA in lake sediment
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2018 (English)In: Methods in Ecology and Evolution, E-ISSN 2041-210X, Vol. 9, no 3, p. 535-543Article in journal (Refereed) Published
Abstract [en]
  1. Detection of DNA in lake sediments holds promise as a tool to study processes like extinction, colonization, adaptation and evolutionary divergence. However, low concentrations make sediment DNA difficult to detect, leading to high false negative rates. Additionally, contamination could potentially lead to high false positive rates. Careful laboratory procedures can reduce false positive and negative rates, but should not be assumed to completely eliminate them. Therefore, methods are needed that identify potential false positive and negative results, and use this information to judge the plausibility of different interpretations of DNA data from natural archives.
  2. We developed a Bayesian algorithm to infer the colonization history of a species using records of DNA from lake-sediment cores, explicitly labelling some observations as false positive or false negative. We illustrate the method by analysing DNA of whitefish (Coregonus lavaretus L.) from sediment cores covering the past 10,000 years from two central Swedish lakes. We provide the algorithm as an R-script, and the data from this study as example input files.
  3. In one lake, Stora Lögdasjön, where connectivity with the proto-Baltic Sea and the degree of whitefish ecotype differentiation suggested colonization immediately after deglaciation, DNA was indeed successfully recovered and amplified throughout the post-glacial sediment. For this lake, we found no loss of detection probability over time, but a high false negative rate. In the other lake, Hotagen, where connectivity and ecotype differentiation suggested colonization long after deglaciation, DNA was amplified only in the upper part of the sediment, and colonization was estimated at 2,200 bp based on the assumption that successful amplicons represent whitefish presence. Here the earliest amplification represents a false positive with a posterior probability of 41%, which increases the uncertainty in the estimated time of colonization.
  4. Complementing careful laboratory procedures aimed at preventing contamination, our method estimates contamination rates from the data. By combining these results with estimates of false negative rates, our models facilitate unbiased interpretation of data from natural DNA archives.
Place, publisher, year, edition, pages
British Ecological Society, 2018
Keywords
ancient DNA, colonization, Coregonus lavaretus, detection probability, divergence, environmental DNA, lake sediment, population age
National Category
Environmental Sciences
Identifiers
urn:nbn:se:umu:diva-143248 (URN)10.1111/2041-210X.12890 (DOI)000426867600010 ()2-s2.0-85030156606 (Scopus ID)
Funder
Swedish Research Council, 2013-5110
Available from: 2017-12-19 Created: 2017-12-19 Last updated: 2024-05-20Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-2001-5077

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