Category Archives: DNA barcode

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