Category Archives: DNA barcode

The 8th International Barcode of Life (IBOL) Conference

Logo by Åshild Stolsmo Viken, Norwegian Biodiversity Information Centre

For a week in June, a significant portion of the world’s barcoding community descended on the fair city of Trondheim. 460 participants from 61 countries met up to share their work, exchange ideas, and meet old and new fellow barcoders.

IBOL2019 delegates, photo by Åge Hojem CC-BY-SA-4.0

The University Museum of Bergen was well represented, with 10 scientific contributions being presented.

All the abstracts can be found in this special edition of the journal Genome.

Contributions people from UMB was involved with include:
DNA barcoding reveals cryptic diversity and genetic connectivity in the deep-sea annelids across the Greenland–Scotland Ridge (N. Budaeva et al.)

DNA barcoding assessment of species diversity in marine bristle worms (Annelida), integrating barcoding with traditional morphology-based taxonomy (T. Bakken et al.)

Five years as national research infrastructure: status of the Norwegian Barcode of Life Network (NorBOL) (T. Ekrem et al.)

Molecular study of Chaetozone Malmgren (Annelida, Polychaeta) reveals hidden diversity of a common benthic polychaete (M. Grosse et al.)

DNA barcodes of Nordic Echinodermata (K. Kongshavn et al.)

Ctenophores — native aliens in Norwegian waters (S. Majaneva et al.)

DNA barcoding of Norwegian forest Oribatida — preliminary results reveal several taxonomic problems (A. Seniczak and B. Jordal)

A barcode gap analysis for aquatic biomonitoring in Europe (H. Weigand et al.)

DNA barcoding marine fauna with NorBOL — current status (E. Willassen et al.)

It was a highly enjoyable conference to participate in, both as part of the support structure (“Team Orange”), and as presenter and/or audience.

A subset of “Team Orange”, who contributed to the smooth running of the event (photo: T. Ekrem)

The NorBOL barcode managers together with Paul Hebert, a Canada Research Chair and Director of the Centre for Biodiversity Genomics at the University of Guelph – and one of the masterminds behind IBOL.

The conference venue did a excellent job keeping us energized and happy with a steady supply of wonderful food and caffeinated beverages – and we were treated to a lovely organ concert in the Nidaros cathedral and a delicious dinner reception at  the Archbishop’s Palace.

Oh, my.

The introduction of BIOSCAN, “the newest phase of a 15-year research program that will transform our understanding of, and integration with global biodiversity” was greeted with enthusiasm – you can read more about this ambitious venture on the IBOL web pages.

It was a excellent conference, and we look  forward to continuing our work on building a validated barcode reference library for species found in Norway through the numerous Norwegian Taxonomy Initiative projects (Artsprosjekt) we have running here at UMB.

-Katrine

Some hydroids, four naturalists, and a small island in the North Sea

NorHydro partner (and hydrozoan expert) Joan J. Soto Àngel from the Sars International Centre for Marine Molecular Biology went in a sampling trip to Kinn to collect benthic hydroids. Here is an account of his experience in this trip:

Kinn is a small grassy island on the western Norwegian coast. Today it is a quiet, peaceful place with only a few inhabitants, but in the past it was an important fishing town and the center of the cultural and religious life of the area, as evidenced by its imposing medieval stone church (Kinnakyrkja). The island is also a place of historical relevance for biologists, since it is intimately tied to the life and discoveries of one of the most prominent naturalists of the XIX century, Michael Sars, who worked as a priest in Kinnakyrkja for many years.

Here I am, ready to sample! The island behind is Kinn, easy to recognize thanks to its characteristic cleft silhouette. Picture: Cessa Rauch

The islands in the area face the ocean and are rather exposed, so the vegetation is not particularly tall, but the waters are teeming with life. Picture: Joan J. Soto

The XIX century Norwegian naturalist Michael Sars. Picture from Wikicommons (public domain)

Sars described many species inhabiting the waters around Kinn and also made key observations about their distribution and life cycle. Indeed, he was the first to discover that jellyfish and polyps are in fact different stages of the same animals!

This finding led him to be recognized as an outstanding zoologist of his time. Even now, ca 200 years after, his extensive work is regularly consulted by researchers of many fields. Like me and the other participants of the Artsdatabanken project NorHydro, Sars was fascinated by the group we call Hydrozoa, which is why it was very interesting for our project to join a sampling trip of the University Museum of Bergen in the same waters where he sampled and described many hydroids, hydromedusae and siphonophores.

Because Sars was also interested in other critters of the sea besides hydrozoans, it was only natural to make this sampling trip a joint, collaborative effort. In our case, three marine scientists were involved, each representing a different project: I was in charge of the hydrozoans for NorHydro, while Anne Helene Solberg Tandberg focused on amphipods (NorAmph2) and Cessa Rauch concentrated on sea slugs (Sea Slugs of Southern Norway). But we did not limit ourselves to our favorite animal groups; we also sampled some poychaetes, bryozoans, ascidians and echinoderms for two other projects based at UMB, Hardbunnsfauna and AnDeepNor. In addition, while we sampled extensively the waters around Kinn, we also stopped in the way to the island and back and collected some animals in two other localities in the coast of Sogn og Fjordane. Our efforts paid off and, despite some windy weather, we came home with many specimens to analyze and samples to sort.

Three more contemporary naturalists working for different projects: Joan (left, NorHydro), Cessa (middle, Sea Slugs of Southern Norway), and Anne Helene (right, NorAmph2). Picture: Joan J. Soto

For the hydrozoans, the majority of samples consisted in colonies of hydroids belonging to the families Sertulariidae, Haleciidae and Campanulariidae. This was not surprising as Sertulariidae (sensu lato) is the largest and most diverse family in all Hydrozoa, and their conspicuous colonies are relatively easy to recognize and collect. The haleciids are represented in Norway mainly by species of Halecium, whose colonies are among the largest benthic hydrozoans of the country. As for the campanulariids, particularly those belonging to genera Obelia, Laomedea and Clytia, they are common inhabitants of rocky and mixed bottoms all around the world, and are especially conspicuous when growing on macroalgae such as kelp. To correctly identify some of these specimens, we will look closely at their morphological characteristics and will also employ molecular techniques of DNA analysis. Hopefully this approach will help us understand the diversity of benthic hydroids living around Kinn, and will allow us to determine whether the species that we encountered are the same that Sars studied.

Dynamena pumila was one of the most conspicuous species of hydroid that we collected in this trip. It belongs to the speciose family Sertulariidae.

We were very lucky to have the help of the crew of RV Hans Brattström. This is how the command center of the boat looks like!

You’ll find the results of these and other NorHydro’s analyses here in the blog as we progress, and more updates on the project can be found on the Hydrozoan Science facebook page and in Twitter with the hashtag #NorHydro.

– Joan


References and related literature about Michael Sars

Tandberg AHS, L Martell (2018) En uimodstaaelig lyst til naturens studium. Yearbook of the University Museum of Bergen: 17 – 26.

Sars M (1835) Beskrivelser og Iagttagelser over nogle mærkelige eller nye i Havet ved den Bergenske Kyst levende Dyr af polypernes, acalephernes, radiaternes, annelidernes, og molluskernes classer. Thorstein Hallagers forlag, Bergen.

Windsor MP (1976) Starfish, jellyfish and the order of life. Issues in Nineteenth-Century Science. Yale University Press, New Haven. 228 pp

Travelouge from the Hardbunnsfauna-project: On a quest for samples

Tide pools and kelp forests in Lofoten (Photo: K. Kongshavn)

In late April Endre, Jon, Katrine and Tom set out from Bergen for what would turn out  to be a rather epic road trip (we ended at 4380 km..!) aiming to collect material for our project on Invertebrate fauna of marine rocky shallow-water habitats: species mapping and DNA barcoding (Hardbunnfauna), the other ongoing Artsprojects, and for the museum collections in general. We had little to no shallow water material in the collections from the region we targeted:

Dark dots are where we have museum material from (though it may be treated in such a a way that it is (no longer) suited for genetic work), and the pink stars are where we collected now (map by K. Kongshavn)

Details of our sampling – we used a variety of gear to collect material, and set up lab where we were staying to process the samples. (Graphic: K. Kongshavn)

Sampling in various habitats using different kinds of gear

The samples were processed (sorted and photographed) at our homes away from home; we managed to rig up quite serviceable lab spaces for ourselves in each spot.

One of the things we were after was kelp stems – or rather, the animals living associated with them

A part of our catch!

A closer look at some of what we found: Hydrozoa and Bryozoa, various crustaceans (pictured are two Mysida, an Isopod and an Amphipod), Nudibranchs and other Gastropods, Polyplacophorana, Ascidians, a Platyheminth and various Cnidaria. 

It was a highly successful – and very lovely! – field trip, and the samples collected will benefit a multitude of ongoing and future research.

Follow us on social media for frequent updates, we are at Instagram and Twitter,  as @hardbunnsfauna

-Endre, Jon, Tom & Katrine

 

Workshop week at Espegrend field station

The final week of March was teeming with activity, as no less than three Norwegian Taxonomy Projects (Artsprosjekt) from the Invertebrate Collections arranged a workshop and fieldwork in the University of Bergen’s Marine biological field station in Espegrend.

The projects – Sea Slugs of Southern Norway(SSoSN), Norwegian Hydrozoa (NorHydro) and Invertebrate fauna of marine rocky shallow-water habitats: species mapping and DNA barcoding (Hardbunnfauna) fortunately overlap quite a bit in where and how we find our animals (as in, Cessa’s seaslugs are eating the organisms the rest of us are studying..!), and so it made sense that we collaborated closely during this event.

That meant more hands available to do the work, more knowledge to be shared – and definitely more fun! All projects had invited guests, mostly specialists in certain groups, but also citizen scientists, and our students participating. We stayed at the field station, which has excellent facilities for both lodging and lab work.

Participants on our Artsprojects workshop in March. Left from back: Peter Schuchert, Manuel Malaquias, Bjørn Gulliksen, Jon Kongsrud, Tom Alvestad, Gonzalo Giribet. Middle row from left: Heine Jensen, Luis Martell, Endre Willassen, Eivind Oug, Front row from left: Katrine Kongshavn, Cessa Rauch and Jenny Neuhaus (Photo: Heine Jensen)

The fieldwork was carried out in the Bergen region, and was done in various ways. We had the R/V “Hans Brattstrøm” available for two days, where we were able to use triangular dredges, plankton net, and grab to sample.

Other days we used a small boat from the station to go to the islands close to Espegrend to examine the tide pools and tidal belt. We also went to local marinas and scraped off what was living on the piers, and a brave soul donned her wet suit and went snorkeling, which enabled us to sample very specific points of interest (“take that green thing over there!”).

We are fortunate here in Bergen in that we have a very active local student dive club, SUB-BSI, whose divers kindly kept an eye out for – and even collected – some of our target animals, as well as sharing their photos of the animals in their natural habitat, all of which is amazing for our projects!
We gave short presentations of each of the projects at SUB in the beginning of the week, and invited the divers out to the lab to on the following Thursday to show some of the things we are working on. It was a very nice evening, with a lot of interested people coming out to look at our critters in the lab. We also decimated no less than 14 homemade pizzas during that evening – learning new stuff is hard work!

Guests in the lab (photos K. Kongshavn)

All together, this made it possible for us to get material from an impressive number of sites; 20 stations were sampled, and we are now working on processing the samples.

The locations where we samples during the week (map: K. Kongshavn)

We are  very grateful to all our participants and helpers for making this a productive and fun week, and we’ll make more blog posts detailing what each project found – keep an eye out for those!

You can also keep up with us on the following media:

 NorHydro: Hydrozoan Science on Facebook, and Twitter #NorHydro

@Hardbunnsfauna on Instagram and Twitter

SeaSlugs: on Instagram and in the Facebookgroup

 Cessa, Luis & Katrine

Project NorHydro: a quest for hydroids in Norwegian waters

One of this year’s new projects at the Invertebrate collections is NorHydro – Norwegian Marine Benthic Hydrozoa.

Both stages in the typical life cycle of a hydroid (polyp and jellyfish) are represented in the logo of the project

Funded by the Norwegian Biodiversity Information Centre (Artsdatabanken), NorHydro will be dedicated to the study of the ubiquitous (but commonly overlooked) marine hydrozoans of Norway.

Some of the most conspicuous Norwegian hydroids are large colonies somewhat resembling branching trees. Many other animals and algae may grow on these colonies making them their home

Hydrozoans are an ecologically and economically important group of animals. With approximately 3800 described species –and probably many more to be discovered– they are the most diverse group of medusozoan cnidarians in terms of number of species and life cycle strategies. Some hydrozoans live all their lives as jellyfish in the water column (thus they are holoplanktonic), but the vast majority of the species either take the form of polyps permanently connected to the sea-floor (benthic) or are meroplanktonic (i.e. possessing both a benthic polyp and pelagic jellyfish stage). Most of the time, the benthic marine hydrozoans (also called hydroids) go unnoticed by the public, but at times they can grow massively on submerged structures, causing problems for aquaculture, fisheries, and navigation, or producing huge numbers of jellyfish that in turn have a great impact on the local marine environment.

Hydroids come in different sizes and shapes. Colonies living on the same substrate (like these members of Cuspidella, Sertularella, and Grammaria) do not necessarily resemble each other.

To get a better overview of which hydroid species are present in Norwegian waters, NorHydro will sample, record, chart, and DNA-barcode specimens occurring all along the Norwegian coasts. The project will rely on specimens deposited in museum collections as well as on constantly obtaining new live animals that will be identified and documented with photos before they are fixed in ethanol for DNA barcoding of CO1 and 16S sequences. Producing information on the morphology (how does it look) and the DNA sequences (the information within) of Norwegian hydroids is very important, because together these data will allow NorHydro to generate useful tools for the future identification of hydroids from all around the world.

Dredges, grabs, sledges, diving and simply taking them by hand are all valid sampling methods when it comes to marine benthic hydroids. The specimens are then sorted, identified, documented with images, processed for DNA barcoding, and finally incorporated to the museum’s collection for future reference.

Understanding hydroid diversity in Norway is not an easy task, but fortunately NorHydro is not alone in this quest: several partners in Norway and abroad will team up with our project, including NorBOL (the Norwegian Barcode of Life), NTNU University Museum, Norwegian Institute of Marine Research, ForBio Research School in Biosystematics, Natural History Museum of Geneva, University of the Balearic Islands, and the Institute of Oceanology of the Polish Academy of Sciences. NorHydro will also benefit from collaborations with the other four currently ongoing NBIC projects at the Invertebrate Collections of the museum (see an overiview of each of these projects here, in Norwegian), which we are sure will result in a lot of exciting discoveries in the near future.

One important goal of NorHydro is to present marine hydroids to all those not familiar with these amazing creatures. In order to do that, we will regularly write entries here on the blog, as well as posting updates in Facebook and in Twitter with the hashtag #NorHydro. The official info webpage for the project is available here in English, and here in Norwegian, so don’t forget to check it out!

-Luis

New year, new field work!

2019 will bring a lot of field work for us at the invertebrate collections – not only do we have our usual activity, but we will also have *FIVE* Norwegian Taxonomy Initiative projects (Artsprosjekt) running!

On a rather windy Tuesday in January, four of us – representing four of these projects – set out with R/V “Hans Brattstrøm”.

Four projects on the hunt for samples! Photo: A.H.S. Tandberg

Our main target for the day was actually not connected to any of the NTI-projects – we were hunting for the helmet jellyfish, Periphylla periphylla. We need fresh specimens that can be preserved in a nice way, so that they can be included in the upcoming new exhibits we are making for our freshly renovated museum. We were also collecting other “charismatic megafauna” that would be suitable for the new exhibits.

We have been getting Periphylla in most of our plankton samples since last summer, so when we decided this was a species we would like to show in our exhibits about the Norwegian Seas, we did not think it would be a big problem to get more.

This is a species that eats other plankton, so normally when we get it, we try to get rid of it as fast as possible; we want to keep the rest of the sample! But we should have known. Don’t ever say out loud you want a specific species – even something very common. Last November, we planned to look specifically for Periphylla, and we brought several extra people along just because of that. But not a single specimen came up in the samples – even when we tried where we “always” get them…

Lurefjorden is famous for being a hotspot for Periphylla – so the odds were in our favor! Map: K. Kongshavn

Wise from Novembers overconfident cruise, this time we planned to call to the lab IF we got anything to preserve. The Plankton-sample did not look too good for Periphylla: we only got a juvenile and some very small babies. So we cast the bottom-trawl out (the smallest and cutest trawl any of us have ever used!), and this sample brought us the jackpot! Several adult Periphylla, and a set of medium-sized ones as well! Back in out preparation-lab an entire size-range of the jelly is getting ready for our museum – be sure to look for it when you come visit us!

We of course wanted to maximize the output of our boat time– so in addition to Periphylla-hunting, we sampled for plankton (also to be used for the upcoming ForBio-course in zooplankton), tested the traps that NorAmph2 will be using to collect amphipods from the superfamily Lysianassoidea, checked the trawl catch carefully for nudibranchs (Sea Slugs of Southern Norway, SSSN) and benthic Hydrozoa (NorHydro), and used a triangular dredge to collect samples from shallow hard-bottom substrate that can be part of either SSSN or the upcoming projects NorHydro (“Norwegian marine benthic Hydrozoa”) or “Invertebrate fauna of marine rocky shallow-water habitats; species mapping and DNA barcoding” (Hardbunnsfauna).

The Hardbunnsfauna project was especially looking for Tunicates that we didn’t already have preserved in ethanol, as we want to start barcoding these once the project begins in earnest (last week of March). We also collected bryozoans, some small calcareous sponges, and (surprise, surprise!) polychaetes.

When it comes to hydrozoans, we were lucky to find several colonies of thecate hydroids from families Campanulariidae and Bougainvilliidae that represent some of the first records for NorHydro. Hydroid colonies growing on red and brown algae were particularly common and will provide a nice baseline against which diversity in other localities will be contrasted.

Different hydroid colonies growing on algae and rocks at the bottom of Lurefjorden. Photo: L. Martell

There were not a lot of sea slugs to be found on this day, but we did get a nice little Cuthona and a Onchidoris.

But what about the Amphipod-traps? Scavengers like Lysianassoidea need some time to realize that there is food around, and then they need to get to it. Our traps have one small opening in one end, but the nice smell of decomposing fish also comes out in the other end of the trap. We therefore normally leave traps out at least 24 hours (or even 48), and at this trip we only had the time to leave them for 7 hours. The collected result was therefore minimal – we even got most of the bait back up. However, knowing that we have a design we can deploy and retrieve from the vessel is very good, and we got to test how the technical details work. It was quite dark when we came to retrieve the traps, so we were very happy to see them! All in all not so bad!

We had a good day at sea, and it will be exciting to see some of our animals displayed in the new exhibits!


If you want to know more about our projects, we are all planning on blogging here as we progress. Additionally you can find more on the

-Anne Helene, Cessa, Luis & Katrine 

Door #15: The eye of the beholder

It’s funny to see the different reactions to fresh material that comes in to the museum;  the exhibition team had  received some kelp that will be pressed and dried for the new exhibitions (opening fall 2019), and I ducked in to secure some of the fauna sitting on the kelp before it was scraped off and discarded. For the botanists, the animals were merely a distraction that needed to be removed so that they could deal with the kelp, whilst I was trying to avoid too much algae in the sample as it messes up the fixation of the animals.

I chose the right shirt for the day- it’s full of nudibranchs! (photo: L. Martell)

 

I then spirited my loot into the lab, and set up camp.

Count me in amongst the people who stare at lumps of seaweed.

 

Who’s there? The whole lump is ~12 cm.

How many animals do you see here? Which ones appeal to you?

I have made a quick annotation of some of the biota here:

Note that these are just some of the critters present…! (photo: K. Kongshavn)

Let’s go closer on a small piece of algae:

Now, what do you see? (photo: K. Kongshavn)

For Luis, the first thing to catch the eye was (of course) the Hydrozoa

Hydrozoans (the christmas light looking strings), encrusting bryozoans (the flat, encrusting growth on on the algae – you might also know them as moss animals), and some white, spiralling polychaete tubes  (photo: K. Kongshavn)

Did you spot the sea hare (Aplysia punctata?) Look a bit above the middle of the photo of the tiny aquarium with the black background. Do you see a red-pink blob?

Hello, Aplysia punctata! (photo: K. Kongshavn)

There were also several other sea slugs that I have handed over to Cessa for inclusion in the sea slugs of Southern Norway project, here are a few:

Then there were the shelled gastropods:

The brittle star from the earlier image – this is a Ophiopholis aculeata, the crevice sea star (photo: K. Kongshavn)

In fact, they both are Ophiopholis aculeata (in Norwegian we call them “chameleon brittle stars” – they live up to the name!), one of the very common species around here. (photo: K. Kongshavn)

One of the colonial ascidian tunicates (and some of the ever present bryozoa just below it) (photo: K. Kongshavn)

Most of these animals will be barcoded, and will help build our reference library for species that occur in Norway. I also hope that they may have helped open your eyes to some of the more inconspicuous creatures that live just beneath the surface?

2019 will see the start of a new species taxonomy project where we will explore the invertebrate fauna of shallow-water rocky shores, so there will be many more posts like this to come!

-Katrine

Door #14: Annelids from the deep Norwegian waters

We have recently started a new mapping project funded by the Norwegian Taxonomy Initiative (Artsdatabanken) on the deep-sea annelids. The annelid fauna in the deep areas of the Norwegian Sea, deeper than 2000 m, has recently been shown to be significantly different from the upper slope and shelf fauna. Morphology-based studies indicate that as much as 40% of the deep-sea annelid species are new to science, and initial results from DNA-barcoding provided even higher numbers. This project aims to characterize, describe and map these unknown species of annelids and will provide much needed baseline knowledge for monitoring of environmental effects from future deep-sea mining and other human activities.

Figures: Tom selecting 96 specimens of annelids from HAUSGARTEN for DNA barcoding.

We have started the project by processing a number of samples from a German expedition on RV Polarstern to the long-term research observatory HAUSGARTEN located at the Fram Strait. The samples have been collected between 1000 and 5000 m depth and harbor more than 30 putative morphospecies. We are going to barcode 96 individuals from this material to supplement the barcode library of the Norwegian annelids and to help resolve taxonomical problems within several taxa.

-Nataliya

 

Door #5: DNA-barcoding with BOLD

Much of the activities in our invertebrate collections are dedicated to so-called DNA-barcoding. Our mission in the NORBOL consortium is to produce DNA-barcodes, particularly for marine fauna in Norwegian waters and to make these barcodes available with open access to records and metadata in Boldsystems.com. In the same manner we have also worked to produce DNA-barcodes for marine invertebrates on the West-African continental shelf in a project called we call MIWA.

These QR-codes will take you to maps with plots of specimens that have been barcoded in our projects (or simply click on them. The red dots on the maps are interactive):

QR-code to view our barcoding efforts in NORBOL

QR-code to view our barcoding in the MIWA project

The basic idea motivating these activities is very simple in principle. You collect specimens and identify them, preferably to species, take digital photographs, and upload information about collection site and other relevant data to a database (BOLDsystems.org).

The specimen page has a picture and other data about the organism that the DNA sequence (presumably) was produced from (click picture to enlarge).

You take a tissue sample to extract DNA from the specimen and use DNA-sequencing technology to target a special fragment of DNA to read the sequence of nucleotides. The expectation is that this sequence may be unique for the particular species you identified.  If indeed the expectation is fulfilled, you can use that sequence as an unambiguous identifier (“bar-code”) of that species.  You have produced a DNA-barcode!

A sequence page in BOLD contains the DNA-sequence (the barcode), the aminoacid translation of the sequence, and the trace-files from the DNA-sequencing machine.(Click picture to enlarge)

Your barcode should enter a DNA-barcode library so that, with an appropriate web-interface to a powerful computer with a search algorithm that compares similarities, you should be able to search with a second sequence from another individual of the same species and find that it is identical, or at least very similar to the one you produced for the DNA-barcode library.  The benefits are potentially many. One advantage is that you may be able to identify a species although all the morphological characteristics have been lost. For the biologist DNA-barcodes may help to identify juvenile stages of a species or even the stomach contents of a predator or scavenger. For conservation, customs, trade, and food authorities DNA barcodes are a powerful means to monitor resource exploitation and attempts to swindle with species identities or area of origin of  biological products.

A taxon window in BOLD fro the crab Atelecyclus undecimdentatus. (Click picture to enlarge)

DNA-barcoding certainly also contributes to the mapping of species distributions and to survey genetic characteristics of taxa. Perhaps initially somewhat unexpected, it also reveals many problems in taxonomy that call for resolution through closer studies. More about this will follow in other blog posts.

-Endre