Category Archives: NorBOL

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

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 # 8: The DNA-barcode identification machine

In a previous blog post I explained briefly how DNA-sequences are produced for the DNA-barcode library. Now I will show how the BOLD database can be utilized to identify species from sequences.

Some of the equipment used to produce DNA-sequences in our lab.

Say you have access to a lab that can produce DNA-sequences and you have a sample of a crab you cannot identify because some of the key characters are on body parts that have been broken and lost. You produce a DNA-sequence from the “barcode-gene” and open the identification engine in BOLDSYSTEMS.org.

Internet start window for the BOLD identification engine where you paste your unknown DNA sequence into the bottom blank window. (Click on picture to expand)

Having submitted your query to BOLD, you wait for some seconds for results. In this example BOLD returned the following window.

Example of results from a query to the BOLD identification engine. (Click on picture to expand)

The results window lists the top matches in terms of sequence similarity, and in this case we have 100 % similarity match with the crab Atelecyclus rotundatus. There is also an option to display the results as a TREE BASED IDENTIFICATION. When clicking on the option tab, the closest hits are clustered in a so-called Neighbour Joining Tree. In the window below you see parts of the tree where our unknown DNA-sequence has been joined to a group of other sequences in BOLD that have been deposited as Atelecyclus rotundatus barcodes by other biodiversity labs.

Part of TREE BASED IDENTIFICATION of an unknown DNA sequence (in red). We see that the unknown clusters with with other sequence of Atelecyclus rotundatus. The nearest neighbour branch is Atelecyclus undecimdentatus. (Click on picture to enlarge.)

The species page for Atelecyclus rotundatus gives us more information about this crab and about its records in BOLD.

Species page for the individual we identified with the BOLD identification engine. (Click picture to enlarge.)

If in fact your sequence was produced from an unknown crab, this identification seems convincing. But sometimes you should think twice about search results, and this will be the topic of a future blog post.

-Endre

Door #7: New shipment of tissue samples for barcoding

In the upper right corner is a “plate”: the microplates with 96 wells where we deposit small tissue samples that are to be processed at the CCDB lab in Canada for NorBOL

On the third day of Christmas,
we sent eleven microplates away:
one plate cnidarians (A)
two with worms a-wriggle (B)
two plates of insects (C)
three plates crustaceans (D)
two (and a half) plates of mites (E)
and a half-plate assorted a-arthropods (F)!

Ahem. Yes.

As Endre explained in the fifth post of the calendar, collecting, identifying, documenting and keeping specimens used for DNA barcoding is an important part of what we do here at the invertebrate collections. 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 the BOLD database. These samples contribute to the building of a validated reference library of the genetic barcodes of the species found in Norway. You can search for different taxonomic groups here to see if they have been barcoded from Norwegian territory: Search NorBOL

The process is fairly straight forward (at least on paper!): Animals are collected and identified. Those species relevant for barcoding are selected, and a specimen (=1 animal) is chosen to be barcoded. We take a small tissue sample from the specimen, and keep the rest of the animal as the barcode voucher; if the need should arise to check if it really is what we initially thought, it is crucial to be able to go back and check the animal again. The tissue samples are collected in wells on a plate like the one pictured above, and the information about the animals – where they were collected, who collected them, what species they are, who identified them and so on is uploaded to BOLD together with images of the animals.

Representatives for the tissue sample plates that we just shipped off. Thank you Steffen, Anna and Per for contributing the terrestrial animals and images! Photos: L. Martell, A. Seniczak, S. Roth, K. Kongshavn. Illustration: K. Kongshavn

On Monday we shipped a new batch of plates – as (attempted) illustrated in song above.

Included is material from several of the Norwegian Taxonomy Initiative projects (artsprosjekt) that are happening at the University Museum of Bergen. We are coordinating the efforts on marine life, but are of course also facilitating the NorBOL barcoding of other organisms that take place at the UMB.  There are animals from NorAmph (Norwegian Amphipoda), Hydrozoan pelagic diversity in Norway (HYPNO), Orbatid mites, and the insects found associated with nutrient rich marshes in Hedmark in this shipment.

We have also prepared several plates of Crustaceans collected and identified by the Norwegian marine mapping programme Mareano – one of the great contributors of material to the collections.

Now we wait for the lab to process them, and for the genetic sequences to be uploaded to BOLD – fingers crossed for many interesting results!

-Katrine

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

Door #4: PSA: abstract submission for iBOL Conference is open!

For door #4 we are helping spread word about the 8th International Barcode of Life Conference, which will take place in Trondheim, Norway on June 17-20th next year.

Abstract submissions are open until January 15th 2019, so now is the time to start thinking (if you haven’t already).

The previous IBOL conference – the one in Kruger National Park, South Africa – was not just in an amazing location (which it undoubtedly was!), but covered a wide array of interesting topics and wonderful talks, and IBOL2019 is set to follow suit!

Check out the planned session themes and outstanding plenary speakers here.

The Norwegian participants at IBOL2017 – enthusiastic about launching Trondheim as the host for IBOL2019! Photo: Knut A. Hjelt

The University Museum in Bergen is one of the four University Museums that are coordinating the Norwegian Barcode of Life (NorBOL) project, and we will be presenting some of our findings on marine invertebrates at the conference  – hope to see you there!

You can find all the relevant information on the conference web page: http://dnabarcodes2019.org/

NorBOL and BOLDsystems course Trondheim 17th-19th of October

Travelogue from Cessa Rauch

Today the weekly event of MolluscMonday and the annual SeaSlugDay (29th of October) coincide!Bunch of sea slugs to celebrate sea slug day, collected in Askøy

What better way to celebrate it with another blog! Much has happened again since the last blog in August, in which we went on fieldwork in Askøy by joining the ladies of the jentedykketreff to find sea slug species in the Bergen area. We officially started to barcode our first specimens, got two new master students that will also work on the project by looking into a variety of topics (diversity of sea slugs in Hordaland, population genetics of Polycera quadrilineata and taxonomy of the genus Eubranchus).

In this blog I will share with you how we are uploading our slugs to the World Wide Web with help of the Barcode of Life data system and how the Norwegian Barcode of Life is helping us getting this done by organizing an informative course in Trondheim.

First step in trying to decode our precious species
The sea slugs of Southern Norway project is a two-year project funded by Artsdatabanken (The Norwegian Taxonomy Initiative) with the aim of mapping the biodiversity of sea slugs along the Southern part of the Norwegian coast

Sea slugs of Southern Norway being eaten by Doris pseudoargus

The focal area stretches from Bergen, Hordaland, all the way down to the Swedish border. In May, July and August of this year the project successfully completed its first fieldwork trips with an additional of 500 new registered museum specimens that cover roughly 90 sea slug species. The species names are attributed based on morphological characteristics, but several species exhibit amazing colour polymorphism, possibly hiding cryptic diversity.

Moreover, we cannot discard the possible occurrence of alien species with similar morphotypes to the native fauna. Therefore, we will need to DNA barcode our specimens to either confirm or change the species names credited to our collected specimens. Besides it will give us an overview for the relatedness of the sea slugs to one another and unravel maybe new species!

In order to successfully sequence 500+ specimen the project collaborates with the Norwegian Barcode of Life project (NorBOL). NorBOL is a network of Norwegian biodiversity institutions and individual scientists that coordinates the establishment of a library of DNA sequences (barcodes) of the fauna and flora of Norway. These barcodes)will be submitted to the open access database BOLD (Barcode of Life Data System), as part of the global Barcode of Life initiative and the International Barcode of Life project (iBOL).

Barcode of Life Data System course
Barcode of Life Data System (BOLD) is a globally orientated online workbench and database that supports the assembly and use of DNA barcode data, and is open access to the scientific community and public. At the moment it holds a record of 6235000 barcodes; 194000 of those are animal species, 67000 plant species and 21000 fungi and other species. The BOLD system is an amazing tool to work with for those interested in biodiversity research. Initially it can be a little overwhelming to fill in all available data into Excel file after Excel file, as this is mandatory and needs to be uploaded first to the system before any sequencing can be done. Especially for those who have many specimens to work with. But afterwards the reward is very fulfilling as you, in an instant, can see distribution maps, trees and images of all the specimens uploaded.

Distribution map from Google earth with collected sea slugs from the Oslo area

Image library of all the collected sea slugs

It is the perfect tool for digitizing, analysing, storing and accessing your genetic and image library data from everywhere anytime. BOLD system standards for uploading actual specimen data are pretty high, the quality of what you can find on the platform is good, but in order to keep these standards great, NorBOL organizes special multi day courses for users in order to guide them through all the steps and features of the BOLD system. This year the course was organized by the NorBOL National coordinator NTNU in Trondheim.

It would take three full days of getting together with fellow participants and going through all the steps necessary in order to start a successful project in the BOLD platform. This year it took place from 17th till 19th of October and as such, me, Anna and Per travelled that Wednesday the 17th very early in the morning to Trondheim. The course was well attended with participants traveling from all over Norway and even from its neighbouring country Sweden. The first day consisted mainly of introduction talks and familiarizing ourselves with the many new abbreviations; NorBOL, BOLD, iBOL (et cetera).

It was a nice experience to meet and talk to other biologists working on such interesting topics, varying from flies, mites, sponges, jellyfish, worms, variety of plants, etc. Everything was taken care off, we could check in to our hotels and in the evening, we had a dinner together with the organizers and participants. The next two course days we were asked to work with our own brought specimens. The days consisted of registering the specimens, filling in as much data per specimens as possible. After finishing and uploading the first datasets, it was time to make pictures of every species, before sampling them for DNA barcoding tissue. Almost all participants brought a 96 wells plate worth of specimens so you can imagine the work that was put into getting everything finished in such a short amount of time.

Sea slug tissue in a 96 well plate ready to be shipped for barcoding

The course was an excellent way to get used to the different steps necessary in order to make the submission process a success. And it was very helpful that at any given moment we could ask the course organizers for advice during the preparations of the datasets and the submission.

All the participants were very excited about the course and happy they attended, it was nice meeting new people and as for someone that moved to Norway, a good opportunity to finally also see Trondheim, with its amazing large Cathedral, a real eyecatcher

 

 

Sea slug goals
The goal for the sea slugs of Southern Norway project is to barcode all, or at least as much as possible, collected specimen, in order to attribute species names to them, expose cryptic species, maybe find new species and look out for invasive and or alien species. Thanks to this course the first 95 species will be barcoded soon and be added to the image library that we already managed to set up (Image 8. Screenshot of the project page of sea slugs of Southern Norway in the BOLD system workbench).

Screenshot of the project page of sea slugs of Southern Norway in the BOLD system workbench

We are very much looking forward for the first results to be accessible and to analyse the data; keep an eye on the invertebrate blogs because for sure the follow up of this story is going to be pretty exciting.

Acknowledgements
I would like to thank Aina Mærk Aspaas for the coordination of the course, Katrine Kongshavn to help out with my first introduction to NorBOL and the BOLD system workbench and Anna Beata Seniczak and Per Djursvoll for being great colleagues during the course and lovely companions in discovering Trondheim together as real Bergen tourists!

 

Furthermore
Sea slugs of Southern Norway recently got its own Instagram account! Perfect for on the go if you would like to quickly check some species or just want to look at pretty pictures; click here, and don’t forget to follow us.

Curious about what we have been doing so far,  read about it in our blogs on the invertebrate website;
First fieldwork blog Drøbak may 2018;
Second fieldwork blog Haugesund July 2018;
Third fieldwork trip august 2018

Become a member of the sea slugs of southern Norway facebook group, stay updated and join the discussion; https://www.facebook.com/groups/seaslugsofsouthernnorway/

Why is it SeaSlugDay today? Read more about that here!  (link goes to Echinoblog)

Explore the world, read the invertebrate blogs!

-Cessa