Reflections from a DNA barcoding course in Norway – From sequences to species

Reflections from a DNA barcoding course in Norway – From sequences to species

REFLECTIONS FROM A DNA BARCODING COURSE IN NORWAY – FROM SEQUENCES TO SPECIES

The Norwegian Research School on Biosystematics (ForBio) and the Swedish Taxonomy Initiative (STI) organized a DNA barcoding course welcoming 16 university students from 10 nations to the scenic outer coastline of Central Norway.

Students and teachers attending the course DNA barcoding – from sequences to species.

PHOTO CREDIT: Thomas Stur Ekrem

What exactly is DNA barcoding? What are the major challenges with the identification of species using DNA sequences? How can we evaluate the quality of barcode reference libraries? How will international agreements like the Nagoya protocol influence the use of genetic data to assess and monitor biodiversity? These are a few of the questions that were explored during the recent DNA barcoding course at Sletvik Field Station near Trondheim, Norway.

The landscape around Sletvik Field Station
PHOTO CREDIT: Torbjørn Ekrem

The Norwegian Research School on Biosystematics (ForBio) and the Swedish Taxonomy Initiative (STI) organized the course welcoming 16 university students from 10 nations to the scenic outer coastline of Central Norway. The students came from universities in Norway and Sweden, and one even travelled all the way from Mozambique. The course was taught and organized by Rakel Blaalid, Norwegian Institute of Nature Research; Filipe O. Costa, CBMA, University of Minho; Torbjørn Ekrem, NTNU University Museum; Galina Gusarova, The Arctic University Museum of Norway; Malin Strand, Swedish University of Agricultural Sciences; and Elisabeth Stur, NTNU University Museum.

Primarily aimed at PhD students and early career researchers, while still open to nature managers and MSc students, the course focused on increasing the in-depth knowledge of molecular techniques for identification of species. The packed program included four days of lectures, practical exercises and seminars and concluded on day five with a three-hour exam, rewarding students with two European Credit Transfer and Accumulation System (ECTS) credits if they passed. In order to meet the requirements by some universities’ PhD program, an additional ECTS credit was offered to students that opted for a home assignment after the course.

Even the teabags took active participation in the course.
PHOTO CREDIT: Torbjørn Ekrem

The Sletvik Field Station run by the Norwegian University of Science and Technology was a marvellous and very practical setting for the course with lots of space, nice lecture rooms and a large kitchen where instructors and students prepared meals together and socialized.

The teachers were impressed by the students’ efforts and active participation. We hope everyone had a good experience and gathered useful knowledge for their current and future careers!

Daniel Abiriga, Katharina Bading and Misganaw Gessese preparing homemade pizza for 24 people.
PHOTO CREDIT: Anna Seniczak

Reflections from three participants:

The DNA barcoding course – from sequence to species was really useful for me because although I knew how to clean DNA sequences, I was missing how to do various analyzes in databases such as BOLD. The time spent on each topic was good, but due to poor internet connections, we could have had more time for the practicals. I think that the topics were well covered, and I gained a lot of knowledge on the theory of DNA barcoding and the challenges faced when using barcode sequences to describe new species. The knowledge acquired in this course will help me analyze sequence data for my PhD project on fishes.

A big challenge for African countries, specifically for Mozambique, is the lack of expert taxonomists working with DNA barcoding. Moreover, the whole process of sample processing is still expensive, and many African species do not have sequences in public reference libraries. My next challenge will be to start a small dataset for the species I’m working on. I already have sequences for some, and I only need to check if they fulfill all the requirements to be deposited on BOLD.

Thanks a lot for the opportunity to attend the course. Hope to attend more ForBio courses next year!

Erica Tovela

Museu de Historia Natural, Mozambique

I found the DNA barcoding course very interesting, particularly to a junior researcher like me. Before joining the course, I did not know about the different DNA markers that are widely being used in species delimitation. Through a broad spectrum of experts from different disciplines, e.g., entomology, plant, fungi, and marine invertebrates, we were taken through current applications of DNA barcoding in the various fields. This has greatly enhanced my understanding of DNA barcoding, including its strengths and limitations. Overall, the course was very enlightening, and I would recommend it to fellow junior researchers who employ DNA barcoding in their work.

Daniel Abiriga

PhD student, University of South-Eastern Norway

Tucked away in the fjords of Slettvik, we were a couple dozen scientists discussing the best way to designate barcodes to all of life. What is a species? How do we identify one from another? How different does their DNA need to be to assign this designation? From at least ten different countries and various continents, we (the students) were able to learn from our professors and from each other. Globally, as computing power increases and genetic data becomes easier to sample, DNA barcoding has become more popular. Having a place for systematists—those classifying organisms using a small piece of standardized genetic information—to converge is pretty unique.  At the barcoding course, ForBio brought together researchers from many different silos to explore the intricacies of genetic barcoding as a group.

Personally, I am particularly interested in understanding species composition in soil samples—metabarcoding. I came to this Forbio course with the expectation of understanding a bit better the best practices of barcoding in the field. We discussed phylogeography, practiced tree making with different parameters, went through workflows in different barcoding databases, and learned about cleaning up datasets. More importantly, however, I now have an understanding of how my work will fit a much larger context: of the past, present, future of molecular sequencing. I understand the implications DNA barcoding work on a global scale; I came away with an understanding of why we have the Nagoya Protocol and how it aims to secure access and benefit sharing of genetic resources. Through structured discussions with my classmates and our teachers we explored the consequences of moving taxonomy toward a more molecular basis and what this means in a global context. Thanks, ForBio for a great course! It is not very often you can get groups of scientists like this outside of their office and into such meaningful discussions.

Louisa Durkin

Nordic Academy for Biodiversity Systematics, University of Gothenburg, Gothenburg Global Biodiversity Center, Sweden

Written by

 Elisabeth Stur

Elisabeth Stur

NTNU University Museum

Torbjørn Ekrem

Torbjørn Ekrem

NTNU University Museum

November 11, 2019

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The celebrities of the microcosmos aren’t always easy to find: detecting tardigrades in environmental DNA

The celebrities of the microcosmos aren’t always easy to find: detecting tardigrades in environmental DNA

The celebrities of the microcosmos aren’t always easy to find: detecting tardigrades in environmental DNA

The hidden diversity of tardigrades is being uncovered in Norwegian forests using DNA barcoding and metabarcoding

Scanning electron microscopy image of Diploechiniscus oihonnae

PHOTO CREDIT: Lasse Topstad

Found across every continent on Earth, to now potentially living on our moon, tardigrades are some of the most resilient microorganisms we know of. But despite our fascination with these microscopic water bears, there is still much to discover. Our study is exploring the applicability of using environmental DNA to facilitate the examination of tardigrade diversity.

The popular narrative that tardigrades can withstand anything – from -272 degrees Celsius to as high as 150 degrees Celsius, 6,000 times the atmospheric pressure, extreme radiation, and vacuum – has earned them celebrity status of the microcosmos. However, tardigrades are more than just superstars. They constitute their own phylum of life, ranked at the same taxonomic level as arthropods (insects and spiders), and currently hold around 1,270 described species. Many of these species fulfill ecologically important roles related to the breakdown of organic material in the soil. Other species are found in freshwater streams, sediments, mosses, lichens, and leaf-litter, occurring in most ecosystems throughout the world. As with other tiny taxa, telling tardigrade species apart can be challenging. Confident identifications of many species depend on the presence of both adult specimens and eggs. Additionally, tardigrade taxonomy is traditionally based on a limited set of morphological traits. This has resulted in several complex species groups, comprising morphologically inseparable, but genetically distinct species.

The claws of one of the species in the Macrobiotus hufelandi group. These species are often inseparable based on morphology, but clearly distinct species based on the COI gene.

PHOTO CREDIT: Lasse Topstad

DNA barcodes offer a solution to these impediments by generating unique genetic characteristics for each of these species. In recent years, there has been an increase in the use of molecular tools on tardigrades, but currently, only a small portion of the known species have barcodes deposited in public databases. Such reference sequences are essential if tardigrades are to be included in large-scale biomonitoring methods such as metabarcoding of environmental DNA (eDNA). Our study is the first to compare the applicability of eDNA-based metabarcoding of tardigrade diversity with morphologically identified communities.

Collection of lichen samples during fieldwork in Southern Norway

PHOTO CREDIT: Torbjørn Ekrem

We extracted tardigrades and eggs from samples of moss, lichens, and leaf-litter and identified them using morphology. The 3,788 recorded tardigrade specimens and eggs were identified as 40 morphologically distinct species, of which 24 were successfully sequenced for the gene cytochrome c oxidase I (COI). These were represented by 151 successfully sequenced individuals. Interestingly, the barcodes revealed 32 genetically distinct linages among the 24 morpho-species, showing high levels of hidden diversity.

Figure 1. Overlap in species recovery by the different methods.

Next, we extracted eDNA from the same environmental samples and sequenced two fragments of the COI marker and one fragment of the 18S marker using the Illumina MiSeq next-generation sequencing platform. This method recovered 57 species of tardigrades compared to the 40 species detected by conventional methods. Mostly, the two methods identified the same species (Figure 1), yet, metabarcoding detected cryptic species elusive to morphological identification. This indicates that metabarcoding of eDNA successfully captures tardigrade diversity.

However, the credibility of such records needs to be evaluated thoroughly. While the COI marker distinguishes well between tardigrade species, the 18S marker might not be as useful as there is not sufficient sequence variation between species (a so-called barcode gap). Furthermore, the 18S marker detected Acutuncus antarcticus in two of the samples, a species endemic to Antarctica. This species is likely not found in Norway and highlights the danger of blindly trusting marker-based identifications without carefully evaluating taxonomic assignments and possibilities of contamination.

Our findings were dependent on our barcode reference library of locally sampled species and the use of multiple markers. As only a small portion of tardigrade species are deposited with reference sequences in public databases, both the COI and 18S markers are limited in their ability to detect species of tardigrades as most sequences will go unmatched. We demonstrate that metabarcoding is applicable for large-scale biomonitoring of tardigrades, but highlight the need for better reference libraries for tardigrade species.

Aknowledgements:

This research is part of a Master thesis at the NTNU University Museum and the project ‘Tardigrades in Norwegian Forests’ funded by the Norwegian Taxonomy Initiative and NorBOL. Special thanks to Roberto Guidetti at University of Modena and Reggio Emilia for his supervision during my stay in Italy.

Written by

Lasse Topstad

Lasse Topstad

Norwegian University of Science and Technology University Museum, Department of Natural History

September 18, 2019
https://doi.org/10.21083/ibol.v9i1.5722

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Update from the Norwegian Barcode of Life Network (NorBOL)

Update from the Norwegian Barcode of Life Network (NorBOL)

Update from the Norwegian Barcode of Life Network (NorBOL)

Norway is supporting projects to assess and monitor biodiversity in time and space, authenticate various products, and develop new methodologies with DNA barcode data.
Nereis pelagica barcoded by NorBOL.

PHOTO CREDIT: Katrine Kongshavn

Written by

Torbjørn Ekrem

Torbjørn Ekrem

NTNU University Museum, Coordinator of NorBOL, Trondheim, Norway

April 7, 2019

Five years have passed since the Norwegian Barcode of Life (NorBOL) obtained funding from the Norwegian Research Council to develop a national research infrastructure for DNA barcoding in Norway. This funding was the major boost needed to build a barcode reference library for Norwegian and polar biota, but it was also an important driver to ensure knowledge transfer and capacity building for DNA barcoding in Norway.

A central collaborator and funder over the years has been the Norwegian Taxonomy Initiative run by the Norwegian Biodiversity Information Centre; they are an important reason why we now have almost 19,000 species barcoded from Norway. The positive synergies between DNA barcoding and inventory projects targeting groups of little-known organisms were highlighted at the 7th iBOL Conference in Kruger.

NorBOL is a geographically distributed infrastructure with four hubs located at the university museums in Bergen, Oslo, Tromsø, and Trondheim. This has made it possible for us to take advantage of existing expertise and be particularly active in some areas. For instance, the University Museum of Bergen is currently the largest contributor to marine bristle worm data in the Barcode of Life Database (BOLD), while the Tromsø Museum is a key player in developing genome skimming of herbarium material to retrieve barcode regions from the chloroplast genome.

As an established national research infrastructure and member of iBOL, NorBOL continues the collaboration with the Norwegian Taxonomy Initiative and seeks additional funding to fill the gaps in the barcode library of Norwegian species. We will also continue supporting applied projects that use the generated data and knowledge to assess and monitor biodiversity in time and space, authenticate various products, and develop methodology.

 

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8th International Barcode of Life Conference in Trondheim

8th International Barcode of Life Conference in Trondheim

8th International Barcode of Life Conference in Trondheim

The 8th iBOL Conference (#iBOL2019) will be held in Trondheim, Central Norway between June 17-20, 2019.

Trondheim and the Trondheim Fjord.
PHOTO CREDIT: Åge Hojem

The 8th iBOL Conference (#iBOL2019) will be held in Trondheim, Central Norway between June 17-20, 2019. Judging by the 422 submitted abstracts and the 500-600 expected participants, the conference will be of comparable size with previous meetings. There will be two pre-conference workshops on June 16; one on the curation of the barcode library of marine invertebrates and the other on the use of mBRAVE to analyze invertebrate metabarcode data from eDNA in urban aquatic environments. Five different post-conference tours are offered and can be booked upon registration.

Late registration closes May 15th. Please visit the conference webpage for more information and follow @norwbol on Twitter for updates.

Welcome to Trondheim, we hope to see all of you there!

Torbjørn Ekrem,
On behalf of the organizing committee

Conference Venue – Clarion Hotel & Congress

 

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