Door #9: To catch an Amphipod

As many of you might have read earlier in this blog, the projects NorAmph and Hypno have been regularly sampling in Hjeltefjorden for the past year. As a part of my master thesis, I was lucky to be able to come with! My thesis will be about amphipods and their seasonal variety in Hjeltefjorden, which is super exiting!

The RP-sled used for the sampling.

For each time we go out, we sample with a RP-sled, a WP3 plankton net and we collect CTD data. The samples from the RP-sled will be used for my thesis and other projects if we find something interesting. During the last year we collected samples 9 times, which has given us some great days out at sea!

During these cruises we have had lots of fun! We have had cake, snacks and regularly done yoga on deck! We have been mostly lucky with the weather (except for our original cruise day in February, which had to be moved due to lots of wind, which you can read about here: Solskinnstokt)

 

A great view from our February cruise, with a clear blue sky and no wind! (Photo: K. Kongshavn)

We have been mostly lucky in getting great samples!

Lots of exciting material to get our hands on! (photo: AH Tandberg)

But sometimes not so lucky…

It is not easy to be a happy master student when the codend is almost empty… (Photo: AH Tandberg)

In October we had our last cruise, which was a great end to a year of sampling! We were not as lucky with the weather this time, but the samples look very nice. We also had cake to celebrate the last cruise day!

A great view in Hjeltefjorden (Photo: C. Østensvig)

Coffee breaks on deck are always important! (Photo: AH Tandberg)

It is somewhat sad to be done with the sampling, but with all the material collected, it is time to hit the lab! With all the samples, I sort out and identify all the amphipods I find. So far, I have found lots of cool amphipods, and I am starting to see some patterns in the material.

Here are some of the Amphipods I have found. All photos: K. Kongshavn

My work in the lab is far from done, and I am excited to look for new cool amphipods and hopefully find something interesting in their seasonal variation.

-Christine

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 # 6: The key to the question

We often say that without knowing the species you examine, you really can’t know a lot about whatever it is you are examining. But how do you get from knowing for example “this is an amphipod” to knowing “this is Amphilochoides serratipes”?

Three different Amphilochidae from Iceland

Most researchers would usually stop at the “this is an amphipod”-stage, and many specialists  would call it a day at “this amphipod belongs to the familily Amphilochidae”. but then there are the one or two researchers who have gone on to specialise in this family (I think there are three of us in the world at the moment).

But finally – those days are over!
As a special gift on this Nicholaus-day when all German colleagues get a special gift from St Nicholaus (who is Father Christmas) we present to all of you – regardless of nationality or faith:

The interactive and illustrated key to the NorthEast Atlantic species of Amphilochidae

The key is a product of a collaboration between the NorAmph-project and the German-lead IceAGE project that examines benthic animals around Iceland, and the technical production and web-hosting of the key is from the Norwegian Taxonomy Initiative (Artsprosjekt) (who – we have to say – also have financed the NorAmph-project!) Hurrah for a great collaboration!

Figure 14 from Tandberg et al

You might still wonder what an Amphilochid amphipod is?

The family Amphilochidae are amphipods that are quite small (1-6mm in length) and quite stout. They are not extremely good swimmers, though much of that can be from their small size – and from their short appendages. They can be found all over the world, and are common at many depths in our cold waters. Even though they are small and easily overlooked, they sometimes occur in relatively large numbers, and can contribute significantly to both the biomass and diversity of a sample. They have been found on hydrothermal vents at the southern part of the Mid-Atlantic ridge, and some have been found as loose associates of other invertebrates.

Also – they are quite cute, don’t you think?  Good luck with the identification!

-Anne Helene

Literature:

Brix S et. al. 2018. Amphipod family distributions around Iceland. ZooKeys 731: 1-53. doi: 10.3897/zookeys.731.19854

Tandberg AHS, Vader W 2018. On a new species of Amphilochus from deep and cold Atlantic waters, with a note on the genus Amphilochopsis (Amphipoda, Gammaridea; Amphilochidae). ZooKeys 731: 103-134. doi: 10.3897/zookeys.731.19899

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/

Door #3: Mollusc hunting around the world

The study of molluscs (malacology) has a long tradition in Norway. Despite the nearly 50,000 species dwelling in the world oceans and seas, a number only barely supersede by the arthropods, new species continue to be discovered and our understanding of the relationships and systematics of molluscs to change.

At the Natural History Museum of Bergen, the study of molluscs is focal, and research is carried out on various aspects of their diversity, morphology, ecology, systematics, evolution, and biogeography, using state of the art methods like DNA barcoding, molecular phylogenetics, and electron microscopy. Understanding the patterns and processes that drive present diversity in the oceans is one of our main goals and our research foci are framed within several “big questions”: How many and how can we differentiate between species? How do species originate in the oceans? Why some regions in the oceans are more diverse than others? Are mechanisms responsible for the patterns of diversity in the deep-sea the same as in shallow ecosystems?

Our quest for answers necessitate the continuous collection of new specimens and the exploration of remote geographies. We conduct regular fieldwork around the world including Norway, through numerous projects and partnerships.

Here are some snapshots from recent fieldwork from Manuel & team:

Working during October 2017 together with Professor João Macuio from the University Lurio (Pemba, Mozambique) in Nangata Bay (Nuarro, Mozambique) on a survey of the sea slug diversity inhabiting this pristine coral reef area and on an assessment of the structure and conservation status of the population of the threatened giant clam species (Tridacna maxima). Left image: Manuel Malaquias and João Macuio photographing sea slugs at the Nuarro Research Center.

João Macuio measuring underwater the total length of a specimen of the giant clam Tridacna maxima

Working in remote places requires often some capacity to improvise and during a fieldtrip to Taiwan while in the Penghu islands we had to convince the manager of our hostel to let us set up a field-lab in the garage among his gear and pet-cage!

Manuel and Trond Oskars, PhD candidate at the Museum, searching for molluscs during May 2017 at mangrove systems near the city of Kaohsiung, Taiwan

In the Penghu islands we had the opportunity to work in the field together with students from the National Penghu University of Science and Technology, here depicted in the right image helping collecting sea slugs along a water stream lined by few mangrove bushes.

After a three weeks fieldtrip to Vamizi island in the Quirimbas archipelago, north of Mozambique during May 2015, we were finally brought to shore at Palma village near the border with Tanzania where we had to do some final sorting and organization of samples under the curious eyes of the local villagers (Manuel Malaquias and Yara Tibiriça from the Zavora Marine Lab in Mozambique).

Fieldwork during May 2018 in the Oslo fjord as part of the project “Sea slugs of southern Norway” funded by Artsdatabanken. Left image: part of the team working through the catch of the day at the Tolboden Course Center in Drøbak, University of Oslo (left to right: Cessa Rauch, Manuel Malaquias, Torkild Bakken, Anders Schouw)

You can read more about some of these expeditions by exploring the posts found here (workshops) and here (fieldwork).

–Manuel

Door #2: A glimpse of Hydrozoan anatomy

Hydroids and hydromedusae are abundant and widespread, but they can be difficult to identify, in part due to the overwhelming amount of terminology used to describe their polyps, colonies and medusae. The diversity of shapes and life cycle strategies in Hydrozoa is in fact so high that it is almost impossible to find a single set of descriptive terms for all species, and different glossaries have been developed for closely related families, sometimes genera, and also for the different stages in the life cycle of the same organism. To further complicate things, the terminology we use for the characterization of hydrozoan morphology has been adapted in many cases from other fields of science (like botany and geometry), and some of the words ended up with very different meanings depending of the organism we are looking at.

But if you are interested in these fascinating creatures, fear not! We at the invertebrate collections have thought about giving you a little visual aid in the form of four plates including some of the basic structures of hydroids and hydromedusa (courtesy of artsprosjekt HYPNO and upcoming artsprosjekt NORHYDRO).

Figure 1: Thecate polyps, like the ones of Aglaophenia harpago, are protected by rigid structures called “thecae” into which the polyp can retract. In many species they live all together forming colonies. Credit: Joan J. Soto Àngel and L. Martell.

Figure 2: Unlike their “protected” relatives, athecate polyps (e.g. those of Pennaria disticha) lack the skeletal protection of the theca, but can also form large colonies with many polyps. Credit: Joan J. Soto Àngel and L. Martell.

Figure 3: The hydromedusae produced by thecate polyps are called leptomedusae, and can be recognized by the development of gonads in the radial canals (among other characteristics). From left to right and top to bottom in the picture are three species present in Norwegian waters: Tiaropsis multicirrata, Modeeria rotunda, and Tima bairdii. Credit: L. Martell and A. Hosia, HYPNO project.

Figure 4: Anthomedusae (hydromedusae produced by athecate polyps) usually have the gonads developed in the manubrium. From left to right and top to bottom in the picture are Leuckartiara octona, Rathkea octopunctata, and Sarsia tubulosa. Credit: L. Martell and A. Hosia, HYPNO project.

Hopefully these images can be used as a starting point for the uninitiated, and why not? perhaps also as a source of inspiration for cool marine-related presents for the season!

-Luis Martell and Joan J. Soto Àngel

Door #1: Last Christmas…

The cushioned sea star, Porania pulvillus, has been recruited to help advertise our little advent enterprise. Click for bigger image!

Last Christmas* we did in fact not make an Invertebrate Advent Calendar, as half the people of the collections were off in South Africa attending the IBOL (International Barcode of Life) conference. You can read more about what we were up to there in this blog post (which is liberally peppered with photos of local vertebrates): The 7th International Barcode of Life (IBOL) conference

However, the year before, and the year before that again, we did hold our own countdown for the 24 first days of December – just like most kids do here in Norway.

We will try to do the same this year, so make sure to check back often for posts on the weird and wonderful critters that live in the sea!

The 2015 edition can be found here, and cover the following topics:

Door #1: A day at sea
Door #2: The Leaf Sheep Sea Slug
Door #3: Prepare to be HYPNOtized
Door #4: A cushioned star
Door #5: A (so far) undescribed species of bristle worm
Door #6: Associated Amphipods
Door #7: Shrimp and salad
Door #8: One jar –> many, many vials
Door #9: Delving into the DNA
Door #10: Old Stoneface
Door #11: Just a white blob?
Door #12: Plankton sampling with a vertebrate view!
Door #13: Time for rejuvenation
Door #14: A world of colour and slime
Door #15: Guest researchers: Ivan
Door #16: First molecular-based phylogeny of onuphid bristle worms
Door #17: A marriage of art and science
Door #18: A photosynthetic animal
Door #19: The amphipods with the pointed hoods
Door #20: How many undescribed bristle worms live in Australian waters?
Door #21: A Norwegian oddity
Door #22: The Heart of the Museum
Door #23: Of MAREANO and the Museum
Door #24: Happy Holidays!

For 2016, this is what we came up with:

Door #1 Gammarus wilkitzkii – closer than Santa to the North Pole?
Door #2: The head of the Medusa
Door #3: a week in the field
Door #4: A spindly Sunday
Door #5: A visit from Mario
Door # 6: Stuffed Syllid
Door # 7: Always on my mind…?
Door #8: the ups and downs of a marine werewolf?
Door #9: Research stay of Juan Moles
Door #10: Siphonophores
Door #11 Invertebrately inspired art?
Door #12: All aboard the jelly cruise!
Door #13: Lucia – with a ray of enlightenment?
Door #14: Where the sun doesn’t shine. Lucifer, luciferin and luciferase
Door #15 Twinkle, twinkle, little animal?
Door #16: Chaetoderma nitidulum- a spiny, shiny mollusc
Door #17: New master student
Door # 18: MSc completed
Door #19: Going back to the roots
Door #20: Pretty Phyllodocidae
Door # 21: A tale of three fading buck-goats
Door #22 A jolly, happy family?
Door #23: How far away can a quill worm get?
Door #24: Happy Holidays!

We hope you will enjoy our little tidbits of invertebrate collections related information!

-Katrine

*you are so very welcome to the ear worm – maybe now I can get rid of it!

JESS! It’s World Jellyfish Day!

November 3 is World Jellyfish Day, and it is the perfect opportunity to celebrate the gelatinous creatures of the world by sharing experiences and plans with friends and colleagues. We at the Invertebrate Collections take every chance to share our love for jellies, which is why Aino and I were particularly happy to participate in the Jellyfish Research in Svalbard (JESS)-Workshop held last week in Tromsø (22-23 October).

Some examples of Arctic jellies. From left to right, in the top row: Catablema multicirratum, Beroe abyssicola, Botrynema ellinorae, Euphysa flammea; bottom row: Dimophyes arctica, Sminthea arctica, Bathykorus bouilloni, Aglantha digitale. Photos: HYPNO

Loved or hated, jellyfish are the kind of animals that either mesmerize beachgoers or make them go straight out of the water. Fortunately, all participants at the JESS Workshop belonged to the first category of people, and we had a very nice and productive meeting discussing methods, state-of-the-art, challenges, and opportunities of working with jellyfish in Arctic waters.

Happy jellyfish hunters in Tromsø

The workshop covered sessions on sampling, data management, ecology, and diversity, including an interesting discussion on how to obtain more (and better quality) jellyfish data from current plankton monitoring protocols. It was an international meeting (20 participants from more than 10 different countries) neatly organized by the University of Tromsø, but it still felt a lot like a bunch of friends getting together to talk about one fascinating subject, which is something I really enjoyed.

Sampling protocols and data curation were some of the most discussed topics during the JESS Workshop. Photos: Joan J. Soto Àngel

All that talking about feeding and predation made us hungry!

While the JESS Workshop was not exactly held on November 3rd, the spirit of commemoration of our gelatinous neighbors was present during the entire event. Celebrating World Jellyfish Day may be a rather recent activity (I could not find any reference of the first time this date was observed, but most likely it only started a couple of years ago), but being fascinated by the movement, color and shapes of jellyfish is certainly not a new thing. There has always been a lot of mystery surrounding the gelatinous inhabitants of the sea, so in a way it was only natural for the origin of the date dedicated to jellyfish to be as much of an enigma as the animals themselves. Mysterious or not, don’t miss the chance to celebrate your local jellies today!

Acknowledgements
Aino Hosia and Sanna Majaneva did a superb job organizing the JESS Workshop and making us feel at home in Tromsø: thank you so much for that! Many thanks as well to all the participants and speakers for the motivating talks and discussions.

Further reading
What could be better than adding some jelly-related reading to the celebration of World Jellyfish Day? I personally love the classics, so I would always recommend Sir Arthur Conan Doyle’s “The Adventure of the Lion’s Mane” for a case of a peculiar encounter with the beautiful Cyanea capillata. Enjoy!

– Luis