Tags:
DNA
Publications
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Anmarkrud, Jarl Andreas; Rosa, Fabricio dos Anjos Santa; Thorbek, Birgitte Lisbeth Graae; Schrøder-Nielsen, Audun; Sviggum, Silvana Melo & Ready, Jonathan Stuart
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(2025).
eDNA Replicates, Polymerase and Amplicon Size Impact Inference of Richness Across Habitats.
Environmental DNA.
7(3).
doi:
10.1002/edn3.70095.
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Environmental DNA-based monitoring has been increasingly used in the last decade to monitor biodiversity in aquatic and terrestrial systems. Molecular-based surveys now allow quick and reliable production of baseline knowledge of species community composition on a large scale, allowing a better understanding of ecosystem function and mitigation of stressors linked to anthropogenic activities. Despite this, technical hurdles often remain, and the impact of replicates, PCR polymerases, and amplicon size on the recovered species richness is still poorly understood. Here, we conducted a large controlled experiment, with bulk samples collected from terrestrial, marine, and freshwater environments to assess the impact of natural and technical replicates, PCR polymerases with different degrees of fidelity or proofreading activity, as well as amplicon size on species richness recovery across habitats. In this study, we consistently found variations in sample species richness depending on PCR polymerase choice. We further demonstrate the dissimilar impacts between natural and technical replicates on species richness recovery and the necessity of increasing natural replications in eDNA-based surveys. We highlight the benefits and limitations of replication strategies, polymerase choice, and amplicon size across terrestrial, marine, and freshwater habitats, and provide recommendations to increase the reliability of future eDNA-based metabarcoding studies.
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Rosa, Fabricio dos Anjos Santa; Gasalla, Maria A.; Queiroz, Anna Karolina Oliveira de; Ribas, Talita Fernanda Augusto; Mauvisseau, Quentin & Boer, Hugo de
[Show all 11 contributors for this article]
(2024).
Molecular analyses of carangid fish diets reveal inter-predation, dietary overlap, and the importance of early life stages in trophic ecology.
Ecology and Evolution.
14(1).
doi:
10.1002/ece3.10817.
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Carangid fishes are commercially important in fisheries and aquaculture. They are distributed worldwide in both tropical and subtropical marine ecosystems. Their role in food webs is often unclear since their diet cannot be easily identified by traditional gut content analysis. They are suspected to prey on pelagic and benthic species, with clupeiform fishes being important dietary items for some species, though it is unknown whether carangids share food resources or show trophic segregation. Here, we used metabarcoding to overcome traditional challenges of taxonomic approaches to analyze the diet of seven carangid species caught as bycatch in the Brazilian southwest Atlantic sardine fishery. Stomach contents were processed from the following species: Caranx crysos, Caranx latus, Chloroscombrus chrysurus, Hemicaranx amblyrhynchus, Oligoplites saliens, Selene setapinnis, and Trachinotus carolinus. Identified diets were dominated by teleost fishes. The C. latus diet was the most distinct among the seven species, preferentially consuming Engraulis anchoita, but H. amblyrhynchus, O. saliens, and S. setapinnis also showed a trend of predominantly consuming small pelagic fishes. Finally, we found evidence of inter-predation in carangids, especially strong between S. setapinnis and C. crysos, suggesting that consumption of early life stages may result in indirect competition through reduced recruitment in these fishes. These findings provide unprecedented insights into the biodiversity in marine ecosystems, especially the poorly known diet of carangid fishes.
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Mueck, Felicitas; Scotti, Francesca; Mauvisseau, Quentin; Thorbek, Birgitte Lisbeth Graae; Wangensteen, Helle & Boer, Hugo de
(2024).
Three-tiered authentication of herbal traditional Chinese medicine ingredients used in women’s health provides progressive qualitative and quantitative insight.
Frontiers in Pharmacology.
15.
doi:
10.3389/fphar.2024.1353434.
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Traditional Chinese Medicine (TCM) herbal products are increasingly used in Europe, but prevalent authentication methods have significant gaps in detection. In this study, three authentication methods were tested in a tiered approach to improve accuracy on a collection of 51 TCM plant ingredients obtained on the European market. We show the relative performance of conventional barcoding, metabarcoding and standardized chromatographic profiling for TCM ingredients used in one of the most diagnosed disease patterns in women, endometriosis. DNA barcoding using marker ITS2 and chromatographic profiling are methods of choice reported by regulatory authorities and relevant national pharmacopeias. HPTLC was shown to be a valuable authentication tool, combined with metabarcoding, which gives an increased resolution on species diversity, despite dealing with highly processed herbal ingredients. Conventional DNA barcoding as a recommended method was shown to be an insufficient tool for authentication of these samples, while DNA metabarcoding yields an insight into biological contaminants. We conclude that a tiered identification strategy can provide progressive qualitative and quantitative insight in an integrative approach for quality control of processed herbal ingredients.
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Bendiksby, Mika; Thorbek, Birgitte Lisbeth Graae; Bjorå, Charlotte Sletten & Halvorsen, Rune
(2023).
Improving procedures for obtaining Sanger sequences from old herbarium specimens.
Bauhinia.
ISSN 0067-4605.
doi:
10.12685/bauhinia.1352.
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Because DNA degrades over time, extracting DNA of sufficient quality for sequencing is presumed to be more difficult from older than younger herbarium specimens. Although massive parallel sequencing techniques have clear advantages when it comes to sequencing ancient DNA, Sanger sequencing is still in frequent use, prompting us to test and improve its application on herbarium specimens. During molecular phylogenetic investigations of the subfamily Lamioideae (Lamiaceae) and subgroups, we extracted DNA from 651 herbarium specimens collected between 1826 and 2006 using regular mini-prep methods. The aim was to obtain DNA of sufficient quality for Sanger sequencing of various plastid and nuclear genetic markers. Here, we report successful Sanger sequencing of the commonly used plastid marker, rps16, as a conservative measure of DNA quality, and logistic regression to investigate the relationship between age of the material and DNA quality. Our result indicates that the upper age limit for obtaining DNA suitable for Sanger sequencing from herbarium specimens using regular mini-prep DNA extraction methods has not been reached. After simple modifications to the regular DNA mini-prep and PCR procedures, at least one genetic marker was successfully sequenced for about 90 % of the specimens tested, the oldest being 168 years old. Jointly, despite the technique's drawbacks, these results demonstrate a high success rate of Sanger sequencing of herbarium specimens.
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Raclariu-Manolică, Ancuţa Cristina; Anmarkrud, Jarl Andreas; Kierczak, Marcin; Rafati, Nima; Thorbek, Birgitte Lisbeth Graae & Schrøder-Nielsen, Audun
[Show all 7 contributors for this article]
(2021).
DNA Metabarcoding for Quality Control of Basil, Oregano, and Paprika.
Frontiers in Plant Science.
doi:
10.3389/fpls.2021.665618.
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Herbs and spices are some of the most vulnerable products in terms of fraud and adulteration in the food sector. Although standard analytical methods are accurate for quality control of specific lead or marker compounds, they cannot accurately assess the entire species composition of many marketed products. Complementary analytical approaches are thus often used for comprehensive screening of herbs and spices. In this study we evaluate DNA metabarcoding for the identification and authentication of 62 products, containing basil, oregano, and paprika collected from different retailers and importers in Norway. Our results show varying degrees of discrepancy between the constituent species and those listed on the product labels, despite high product authenticity. We suggest the false positives result from the sensitivity of DNA metabarcoding and filtering thresholds should be integrated into protocols to reduce false positives. Our results highlight how integrating DNA metabarcoding into the toolbox of analytical methods for quality control of fresh and/or processed plant-based food can improve product quality.
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Schure, Anneke ter; Anusree, Ajitha Kumari Sethu KumaranPil; Thorbek, Birgitte Lisbeth Graae; Shankar, Maradani Bhavani; Puri, Rajindra & Ravikanth, Gudasalamani
[Show all 8 contributors for this article]
(2020).
eDNA metabarcoding reveals dietary niche overlap among herbivores in an Indian wildlife sanctuary.
Environmental DNA.
p. 1–16.
doi:
10.1002/edn3.168.
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As many ecosystems are under increasing pressure from invasive species, habitat degradation, overgrazing and overharvesting, pollution, and climate change, dietary niche monitoring is gaining importance. The Malai Mahadeshwara Wildlife Sanctuary (MMH) in southern India is home to several long‐standing ethnic and tribal groups and supports a considerable number of domestic herbivores (cattle, goats and water buffalo) as well as a range of wildlife (including several species of deer, bonnet macaque, and Asian elephant). We reconstructed dietary niche partitioning of the herbivores occurring in MMH using eDNA metabarcoding to quantify diet richness, composition, and overlap. In total, we distinguish 134 diet items (molecular operational taxonomic units), covering 31 plant families. Overall, our results indicate 35% overlap in domestic and wild herbivore diet items. The greatest overlap is found for the dietary niches of cattle and sambar deer (Pianka's niche overlap index: 0.68), and the dietary niche of cattle also overlaps considerably with those of Indian hare (0.65) and Asian elephant (0.46). This suggests that these herbivores may compete for these food plants in the case of limited availability, which could lead to exclusion of some herbivore species. Particular concern should go to bonnet macaque and Asian elephant as their below average dietary richness could make them vulnerable to changes in their environment. With increasing pressures on local wildlife from a range of different factors, DNA metabarcoding of fecal samples is a non‐invasive method for monitoring changes in animal diets, providing valuable information for the management of biodiversity in mosaic natural and anthropogenic landscapes.
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Kistenich, Sonja; Halvorsen, Rune; Schrøder-Nielsen, Audun; Thorbek, Birgitte Lisbeth Graae; Timdal, Einar & Bendiksby, Mika
(2019).
DNA Sequencing Historical Lichen Specimens.
Frontiers in Ecology and Evolution.
7.
doi:
10.3389/fevo.2019.00005.
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Biological specimens in natural history collections worldwide are increasingly being used in biogeographical, environmental, and taxonomic studies. For their meaningful use, correct species identification is crucial. For example, clarifying if a species is new to science requires an overview of what has already been described. This includes comparisons with existing authoritative specimens (types). Most type specimens are rather old and their DNA expected to be degraded to various extents. Comparative DNA sequence analysis is in regular use in taxonomic research of today and is essential for identifying and delimiting species. In this study, we focus on lichenized fungi (lichens), in which many species groups are highly inconspicuous and impossible to identify to species based on morphology alone. Our aim was to test the non-mutually exclusive hypotheses that DNA quality of lichens depends on (1) time since collection, (2) taxonomic affinity, and/or (3) habitat/ecology. We included two species from each of four different lichen genera (i.e., Cladonia, Nephroma, Peltigera, and Ramalina), each species pair with a different autecology. For each species, we included samples from approximately every 25 years from present to about 150 years back in time. We used a two-step PCR-based approach followed by sequencing on an Ion Torrent PGM to produce target sequences (mtSSU) of degraded DNA. We received satisfactory DNA sequence information for 54 of 56 specimens. We recovered full-length sequences for several more than 100-years-old specimens, including a 127-years-old specimen, and retrieved enough sequence information for species identification of a 150-years-old specimen. As expected, sequencing success was negatively correlated with age of the specimens. It also varied with taxonomic affinity. We found no significant correlation between sequencing success and habitat ecology of the investigated specimens. The herein tested Ion Torrent sequencing approach outperformed Sanger sequencing with regard to sequencing success and efficiency. We find the protocol used herein highly suitable for obtaining sequences from both young and old lichen specimens and discuss potential improvements to it.
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Bendiksby, Mika; Brysting, Anne Krag; Thorbek, Lisbeth; Gusarova, Galina & Ryding, Olof
(2011).
Molecular phylogeny and taxonomy of the genus Lamium L. (Lamiaceae): Disentangling origins of presumed allotetraploids.
Taxon.
ISSN 0040-0262.
60(4),
p. 986–1000.
doi:
10.1002/tax.604004.
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This is the first comprehensive molecular investigation of the genus Lamium L. We have addressed phylogenetic
relationships and presumed allopolyploid speciation by use of nuclear (NRPA2, 5S-NTS) and chloroplast (matK, psbA-trnH,
rps16, trnL, trnL-F, trnS-G) DNA sequence data. Nuclear and chloroplast data were incongruent, and nuclear data showed
better correlation with morphology. Bayesian and parsimony phylogenetic results show that (1) Lamium galeobdolon is sister
to all remaining Lamium species; (2) Wiedemannia is nested within Lamium; (3) L. amplexicaule is polyphyletic; (4) most
tetraploids are of hybrid origin; (5) L. amplexicaule var. orientale is allotetraploid; and (6) Mennema’s (1989) infrageneric
classification is not corroborated by molecular data. Based on the molecular results, and taking morphology into account, we
suggest resurrection of two species: L. aleppicum and L. paczoskianum.
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Bendiksby, Mika; Thorbek, Lisbeth; Scheen, Anne-Cathrine; Lindqvist, Charlotte & Ryding, Olof
(2011).
An updated phylogeny and classification of Lamiaceae subfamily Lamioideae.
Taxon.
ISSN 0040-0262.
60(2),
p. 471–484.
doi:
10.1002/tax.602015.
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Oppegård, Camilla; Emanuelsen, Linda; Thorbek, Lisbeth; Fimland, Gunnar & Nissen-Meyer, Jon
(2010).
The Lactococcin G Immunity Protein Recognizes Specific Regions in Both Peptides Constituting the Two-Peptide Bacteriocin Lactococcin G.
Applied and Environmental Microbiology.
ISSN 0099-2240.
76(4),
p. 1267–1273.
doi:
10.1128/AEM.02600-09.
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Pereira, Kerly; Rincon, Getúlio; Rodrigues, Alan Erik Souza; Rosa, Fabricio dos Anjos Santa; Reis, Orlando & Thorbek, Birgitte Lisbeth Graae
[Show all 11 contributors for this article]
(2024).
eDNA metabarcoding identifies the diet of the Freshwater Stingray (Potamotrygon motoro) (Myliobatiformes: Potamotrygonidae) in Maranhão, Brazil.
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Tabosa, Ana Elena Souza; Kimura, Naelma Gonçalves; Pinheiro, Yany Victória Rabêlo; Anjos, Marcia da Silva; Carvalho, Cintia Oliveira & Thorbek, Birgitte Lisbeth Graae
[Show all 9 contributors for this article]
(2024).
METABARCODING IDENTIFICATION OF ARTHROPODS IN BULK SAMPLES FROM CDC LIGHT TRAPS IN POST-BAUXITE MINING AREAS IN PARÁ.
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Bendiksby, Mika; Thorbek, Birgitte Lisbeth Graae; Bjorå, Charlotte Sletten & Halvorsen, Rune
(2022).
Simple procedures for obtaining DNA sequences from old herbarium specimens.
Full text in Research Archive
View all works in NVA
Published
Sep. 1, 2014 12:38 PM
- Last modified
Sep. 26, 2014 2:04 PM
