Category Archives: Crustacea

Sled test for copepods

R.P. sled onboard R/V. H. Brattström

Happy new year to everyone! We managed to start 2021 with a day at sea, testing the R.P. sled for collecting benthic copepods from greater depths . January 27 we went out with research vessel Hans Brattström, crew and research scientist Anne Helene Tandberg who also turns out to be a true sled expert! She would join HYPCOP to teach how to process the samples from the R.P. sled on the boat.

 

 

 

 

Anne Helene Tandberg (left) joining HYPCOP (Cessa Rauch right) for teaching how to use the sled.

But first, what is an R.P. sled and why is it such an important key in the collection of copepods? The R.P. sled is an epibenthic sampler. That means that it samples the epibenthic animals – the animals that live just at the top of the (soft) seafloor – and a majority of these are often small crustaceans. The “R.P.” in the name stands for Rothlisherg and Pearcy who invented the sled. They needed to collect the juveniles of species of pandalid shrimp that live on the sea bottom floor. These animals are very small so a plankton net was necessary to collect them; a ‘normal’ dredge would not quite cut the job. They needed a plankton net that could be dragged over the bottom without damaging the net or the samples and also would not accidently sample the water column (pelagic); and so, the R.P. sled was born. This sled was able to go deeper than 150m, sample more than 500m3 at the time and open and close on command which was a novelty in comparison to the other sleds that where used in those days (1977). The sled consists of a steel sled like frame that contains a box that has attached to it a plankton net with an opening and closing device. The sled is heavy, ca. 150kg, and therefore limits the vessel sizes that can operate it; the trawl needs to be appropriately equipped including knowledgeable crew. It is pulled behind the vessel at slow speed to make sure the animals are not damaged and to make sure it does not become too full of sediment that is whirled up.

 

 

Sieved animals from the decanting process

So off we went with r/v Hans Brattström pulling the heavy gear at ca. 700m depth with 1 knot and a bottom time of 10 minutes sampling the Krossfjorden close to Bergen. It was a beautiful day for it with plenty of sun and calm seas. The crew handled most of the sled, leaving sorting the samples up to HYPCOP under the guidance of Anne Helene. Which is not as straight forward as it may sound! The process of filtering the samples after collecting them from the sled is done by decanting, which you can see in this movie from an this blog (in Norwegian) from earlier.

Decanting set-up for R.P. sled samples

Decanting means separating the mixture of the animal soup from the liquid by washing them in a big bucket, throw the liquid through a filter and collect the animals.

Sieved animals from the decanting process

This all needs to be done with care as the animals are often very small and fragile. After collecting, the most time-efficient and best preservation for the samples is to fixate them immediately with ethanol, so they don’t go bad while traveling back to the museum.

Fixating collected animals with technical ethanol

For collecting copepods we use a variety of methods; from snorkeling, to scoping up water and plankton nets, but for greater depths and great quality benthic samples the R.P. sled will be the most important method. We thank Anne Helene for her wisdom and enthusiasm that day for showing HYPCOP how to work with such interesting sampling method

 

We got some nice samples that will be sequenced very soon so we can label them appropriately. Although this first fieldwork trip off the year was mainly a teaching opportunity, we still managed to sample two stations with plenty of copepods and lots of other nice epibenthic crustacea, and Anne Helene is especially happy with all the amphipods she collected during the day. So for both of the scientists aboard this was a wonderful day – sunshine and lovely samples to bring back to the lab!

Some fresh copepods caught with the R.P. sled

– Cessa & Anne Helene


Follow HYPCOP @planetcopepod Instagram, for pretty copepod pictures https://www.instagram.com/planetcopepod/

Twitter, for copepod science news https://twitter.com/planetcopepod

Facebook, for copepod discussions https://www.facebook.com/groups/planetcopepod

See you there!

Brattström baby, HYPCOP goes offshore!

Last days of November HYPCOP spend two days (26th & 27th) offshore. We had the possibility to join some sampling efforts of NorHydro and others on the research vessel Hans Brattström.

Research Vessel Hans Brattström ready early in the morning, photo Cessa Rauch

This vessel is owned by the University of Bergen and operated by the institute of Marine Research (IMR, Havforskningsinstituttet).

H. Brattström is used 200 – 230 days a year along the West coast of Norway. It has the capability of operating different sampling gear, which makes it useful for multiple projects, studying a variety of marine organisms, from fish, to worms, jellyfish, and yes, also copepods!

On the first day HYPCOP joined NorHydro consisting of Luis Martell (UiB) and Joan Soto Angel (Sars):

NorHydro team and HYPCOP; from ltr Cessa Rauch, Luis Martell and Joan Soto Angel, photo Cessa Rauch

Plankton net being lowered in the ocean with some early morning sun, photo Cessa Rauch

 

 

The main sampling gear consisted of a large plankton net that was slowly dropped to 660m, 245m and 128m depth.  We sampled close to Bergen in Raunefjord, Krossfjord and Fanafjord.

Sampling for jellyfish needs to be done with caution, with the net going up to fast, the animals will just fall apart because of the pressure. So, a depth of 660m can take up to an hour and more before we could see the results.

 

 

Joan Angel Soto scanning the shore for birds, photo Cessa Rauch

During the waiting times we didn’t let our time go to waist, with binoculars we scanned the air and shore for birds.

After waiting for some time, the plankton net was brought back on board and contained, besides jellyfish and other pelagic planktonic dwellers, many million copepods. Mostly consisting of a few species. One of the species had a distinguishable blue egg sack, this is Paraeuchaeta norvegica (Boeck, 1872). This species is an active predator that feeds on other (smaller) copepods by rapidly jumping on them and catching their prey with their large maxillipeds (mouthparts).

 

 

The second day HYPCOP joined head engineer Bjørn Reidar Olsson (UiB) and PhD student Miguel Meca (UiB)

HYPCOP (Cessa Rauch left) joining Miguel Meca (middle) and Bjørn Olsson (right), photo Cessa Rauch

They were looking for shark teeth and polychaetes (marine worms) respectively and used the grab, which is perfect for benthic copepod sampling. The grab is basically a big metal clamshell that collects sediment from the seafloor. Working with grab samples gets dirty very quickly, you have to wash through the sediment to find your animals.

The grab with Cessa Rauch (HYPCOP left), Miguel Meca (middle) plus operator Bjørn Frode Grønevik (right), photo Bjørn R. Olsson

Most of the sediment was filtered out in order to find our copepod friends. Although less plentiful in comparison to the plankton net sampling the previous day, we still found some copepods hiding in the dirt. At moment of this writing, the the copepod species we collected have not be named yet, however, the last months we have been experimenting with barcoding the first batch of 60 different specimens. We had a 43% success rate. Usually, marine invertebrates have a success rate between 40 – 70%, so it was still within the margin, but not with a lot of enthusiasm. HYPCOP will spend the remainder of 2020 and the beginning of 2021 in the laboratory figuring out what the culprit of this low success rate could be.

For HYPCOP this will be the last blog before the Christmas holidays and the New Year. Therefore, we want to take the opportunity to wish you happy holidays and hope to see you around in 2021 with from us more copepod news to share!

-Cessa


Follow HYPCOP @planetcopepod

Instagram, for pretty copepod pictures https://www.instagram.com/planetcopepod/

Twitter, for copepod science news https://twitter.com/planetcopepod

Facebook, for copepod discussions https://www.facebook.com/groups/planetcopepod

See you there!

Scavengers in the ocean

Lysianassoid amphipods from a trap in Raudfjorden, Svalbard. Photo: AHS Tandberg

Most animals are sloppy eaters. They have their favourite piece of food that they go for, and then they leave the rest. This allows for others to pick up where others leave. One of the laws of ecology is that “there is no such thing as an empty ecological niche”. That can be translated to “where there is a food-source (or a place to live) someone or something will use that food-source (or place to live). And that gets us to the sloppy eaters out there, and not least the animals picking up after all the sloppy eaters.

From the pigeons crowding under your cafe-table for your panini-crumbs to the rats in our sewers, our “local scavengers” tend to be animals we feel slightly uncomfortable around. Is it different with the scavengers we dont see so often? It does not seem that way. Vultures  are not the most popular birds, even the word “vulture” has a negative connotation – and we mainly use it in its non-bird meaning.

How about the scavengers of the sea? As on land, we have many different animal-groups that can be classified as scavengers. Many of the marine scavengers are invertebrates (even if some fishes also scavenge). Let us look at the scavenging Lysianassoid amphipods. Are these as little loved in our world as the rats and vultures seem to be?

A typical lysianassoid amphipod. Photo: AHS Tandberg

Lysianassoid amphipods can mostly be distinguished from other amphipods by their “telescope-like” antennae: a very fat inner article with the two next looking like a collapsed old fashioned radio-antenna; two short rings. We know that the antennae of crustaceans are often used to “smell” things in the water – food or mates or possibly even enemies. It is not thought that the radio-antenna-shape of the Lysianassoid antenna specifically has to do with being a scavenger, as other amphipods and indeed several other crustaceans not having such an antenna are also scavengers. But most Lysianassoids have that antennae, and it makes for an easy first-sorting for the scientist. (Getting further – towards a genus, or even species name on the other hand, is not so easy).

Other general traits in most Lysianassoids, are the smooth exterior, and their high swimming abilities. Both are good if you need to get to some leftover food-source fast, and to “dive” into the food-source while not getting stuck through the entry.

Leftovers of bait (polarcod) after 24 hrs in the trap. Not much left for dinner… Photo: AHS Tandberg

And this is where many Lysianassoids loose out when it comes to human appreciation. They seem to love to scavenge on fish caught in fishnets and traps, and both professional and hobby fishers don’t like to share their catch. We dont think it is very appetising to find our fish-dinner “infested” by non-fish. I am quite sure the scavengers being pulled up with their lovely find of dead or dying fish also are not pleased with having to share their dinner with us.

Lysianassoid scavenging amphipods are the focus of our NBIC-financed project NorAmph2. Here, we will collect and register what different species are present in Norway, and we will try to barcode them. These are quite tricky animals to identify properly, but luckily we have teamed up with the best lysianassoid-expert we know – Tammy Horton from the National Oceanography Centre in Southampton, UK.

We use baited traps to collect: put some lovely, smelly fish out there and see who comes to dine. So far, we have collected from Svalbard in the north to Kong Haakon VIIs Hav in the south, and from the intertidal to the deep. They are often many, and the size-variation is great. We look forward to continuing finding out what species we have, and to see if what morphologically seems one species really is (only) one species genetically. (This previous blog-post (in Norwegian) tells the story about one scavenging amphipod that turned out to be 15 (or maybe even more!) separate species)

Anne Helene

HYPCOP kickoff!

Follow us at @planetcopepod!

Tuesday may 19 was the first fieldwork of the new project called Hyperbenthic Copepoda (HYPCOP). You can read more about the field work and see some photos and videos from the field in the previous blog post. 

Copepoda are small crustaceans that are found all over the world in both marine and freshwater habitats. Species can be planktonic (drifting in the sea water) or can be parasitic and a large diverse group of them live on algae in the hyperbenthic (living near the bottom) zone. Copepoda are very important food source for many organisms like small fish, they are on the bottom of the food pyramid, together with other zooplankton. Without copepods, a lot of bigger animals would no exists. Despite being so important, not much is known about the biodiversity and taxonomy of these animals, especially that of the species that live near the bottom.Some species like Calanus finmarchicus are the main nutritional basis for many fish species, and therefore of great importance for the Norwegian fish strains.  Therefore Artsdatabanken is funding the new project HYPCOP in order to unravel the biodiversity and taxonomy of hyperbenthos copepods. With special focus on the species in the group Harpacticoida that live in the water masses just above or near the bottom. Copepods from shallow water will be collected in coastal areas, in deep fjords and on the continental shelf.

The Institute of Marine Research (IMR), Natural history museum of Bergen (UiB), Norwegian Institute for water research (NIVA) and the Norwegian Barcode of Life (NorBoL) are working together to survey the diversity of marine copepods in Norwegian waters and expect to find and describe species that are new to science and new for Norway! Currently some of the taxonomic competence in Norway is lacking, but through collaboration with foreign experts this knowledge will increase among Norwegian researchers and students!

The projects duration will run from 2020 until 2023 and last week was the official kickoff with some fieldwork to get fresh material to work with! Together with the project Hardbunnsfauna we drove to a local favorite collection site of us; Biskopshavn; very close to Bergen city center. Around the hard substrate we found lots of freshly grown algae that contained many small animals for us to collect! In order to get good quality samples we needed to be in the water and snorkel. With plankton nets we collected algae and sieved the water column catching the smallest of the animals; copepods!

And even though this was just a first test of equipment and collection methods, it was not without success. Back in the lab the microscope revealed the beautiful and diverse world one drop of seawater contains. A lot off small crustaceans and of course the copepods were omnipresent.

Our findings had to be shared and especially for #InternationalDayForBiologicalDiversity the copepods cannot be left out as they from such an important group! See for yourself the beauty of our copepod planet!

-Cessa

Why study boring amphipoda and other strange taxa?

Bircenna thieli seen from the front and the side. SEM photo, Fig 6 in Hughes and Lörz, 2019.

This question (or a version of it) is something a lot of us taxonomists are faced with quite often when we try to explain what we do for a living. And I do understand the need to ask – couldn´t our talents be used better doing something it might be easier to understand the use of? We think the study of taxonomy is higly important, and does bring about useful knowledge for the world. Therefore, we have several taxonomic projects in our group, and we write about them here in the blog. (If you read norwegian, you can read about our projects here)

 

March 19th was the world Taxonomist Appreciation Day – a day we have “celebrated” since 2013. Why do we need this day? Taxonomy is the science of naming, defining, describing, cataloguing, identifying and classifying groups of biological organisms. We do this in labs and on fieldwork, and the natural history museums (these days represented from our home offices) have a special responsibility for this work, since one part of the formal description of a taxon is to designate a type and store that in a museum collection. We will come back to the importance of types in a later blog here.

Terry McGlynn, the professor and blogger who initiated the Taxonomist Appreciation Day wrote: ” I want to declare a new holiday! If you’re a biologist, no matter what kind of work you do, there are people in your lives that have made your work possible. Even if you’re working on a single-species system, or are a theoretician, the discoveries and methods of systematists are the basis of your work. Long before mass sequencing or the emergence of proteomics, and other stuff like that, the foundations of bioinformatics were laid by systematists. We need active work on taxonomy and systematics if our work is going to progress, and if we are to apply our findings. Without taxonomists, entire fields wouldn’t exist. We’d be working in darkness.”

Every year a large number of new taxa are described – last year almost 2000 of the new species described were marine. March 19th every year, the World Register of Marine Species (WoRMS) and LifeWatch publish their favourite 10 marine species described in the previous year, and this year – corona-shutdown and all – was no exception.

All ten new species are fun, beautiful and remarkable – but Polyplacotoma mediterranea Osigus & Schierwater, 2019 deserves special mentioning. P. mediterranea is the third species described ever in the phylum Placozoa – who are viewed as one of the key-taxa to understand early animal evolution. They were first described in 1883 (by Schulze), and the name Placozoa indicated what they looked like: small (around 1 mm for the largest of the specimens) platelike animals. 2018 saw the second species of placozoans described – genetically, as it was impossible to separate morphologically – but then our new placozoan came – and it is 10mm large, is branched, and has its natural habitat in the mediterranean intertidal! Phylum Placozoa will never be the same again, and our understanding of the early evolution of animals has become even more interesting.

 

What then about the boring amphipods? Or course they are not boring as in saying they are dull! The “boring amphipod” Bircenna thieli Hughes & Lörz, 2019 bores in the sense that they excavate tunnels into the stem of the common bull kelp Durvillaea potatorum (Labillardière) Areschoug, 1854 in the intertidal and shallow waters by Tasmania.

Bircenna thieli has a head almost like an ant, and a quite unusual shape of its back-body. Fig 8 from Hughes and Lörz, 2019

Their head has an ant-like ball-shape unlike many other amphipods where the head is more ornate or has a visible rostrum, but the exciting morphology comes at the other end of the animal – where the telson and last segment have structures never seen before in amphipods, and structures that only other vegetation-boring amphipods show.

So why do we think describing tiny animals, plants, fungi, bacteria and other organisms is so important? Let us ask you back: how can you appreciate what you have and care about what might be lost if you dont know who they are?

Anne Helene

(this post was written March 19th, but posted later..)


Literature:
Eitel M, Osigus H-J, DeSalle R, Schierwater B (2013) Global Diversity of the Placozoa. PLoS ONE 8(4): e57131. doi:10.1371/journal.pone.0057131

Hughes, L.E.; Lörz, A.-N. (2019). Boring Amphipods from Tasmania, Australia (Eophliantidae: Amphipoda: Crustacea). Evolutionary Systematics 3(1): 41-52. https://doi.org/10.3897/evolsyst.3.35340

Osigus, H.-J.; Rolfes, S.; Herzog, R.; Kamm, K.; Schierwater, B. (2019). Polyplacotoma mediterranea is a new ramified placozoan species. Current Biology 29(5): R148-R149. https://doi.org/10.1016/j.cub.2019.01.068


Do you want to find out more about Taxonomist Appreciation Day or about all the 10 exciting species?

Ten remarkable new marine species from 2019

Today is Taxonomist Appreciation Day!

A compendium of taxonomists on ORCID

and not least –  you can still follow the #TaxonomistAppreciationDay on Twitter (and be prepared for 2021!)

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 #20 The Hitchhikers Guide to the Ocean

The sea is for most of its inhabitants a vast place where danger can get to you anywhere. This might be especially true when you are one of those small and mostly harmless species spending your life slowly swimming around, minding your own business (eating and reproducing), somewhere in the upper 200m or so of water. Because there are many big-mouthed and possibly big eyed animals out there that think you might be one of the best things there is to eat.

Hyperiella antarctica with Spongiobranchaea australis. Photo: C Havermans, AWI.

For the small pelagic (living in the open ocean and not close to the sea floor) amphipods in the suborder Hyperiidea this is one of the dangers of everyday life. The genus Hyperiella can be found in the Southern Ocean, and one of their main predators are the icefishes (Nototheniidae). So what do you do when you are a small and quite tasty animal that is not a very fast swimmer and there are a lot of fishes out there to eat you?

Don´t panic!

Hyperiella antarctica with Spongiobranchaea australis (a and b) and Hyperiella dilatata with Clione limacina antarctica (c). Figure 2 Havermans et al 2018.

Two of the three Hyperiella-species have found a quite ingenious solution. They hitchhike with a group of other small slow-swimming pelagic animals – pteropods. Pteropods (from the greek “wing-foot”) are sea snails (gastropods). Hyperiella australis pics up a life with Spongiobranchaea australis, and Hyperiella dilatata hangs out with Clione limacina antarctica. Both pteropods are from the group we call Sea Angels (Gymnosomata), and in a way they are saving angels for the amphipods: the ice fish don´t eat these strange couples. Why?

It seems the pteropods have developed a chemical protection against predation. They obviously taste extremely bad, for observations of icefish trying to eat the hitchhiking amphipods together with the pteropods result in them both being spit out again. Most times, the fish would see what it thought was good food, and then swim away when they discovered what they were almost eating. Not so very strange, then, that Hyperiella are holding on to their colleagues for their life!

 

 

Clione limacina antarctica. Photo C Havermans, AWI.

It might not be hitchhiking after all, but rather kidnapping – or brute force. The amphipods hold on to the pteropods with their to-three hindmost pairs of legs, and keep the sea angel on their back – much like a backpack. Observations are that they are repositioning them there all the time – almost like kids running with bumpy backpacks on the way to school. They don´t even let go when the researchers preserve them!

Hyperiella antarctica with Spongiobranchaea australis backpack. Photo: C Havermans, AWI

What this treatment do to the pteropods we still don´t know. But it does not seem they are able to eat very much when being held hostage as chemical defence-backpacks. That may not be the biggest problem in a short time-scale – their Arctic relatives have been shown to survive almost a year without food. What happens when they really get hungry we do not know. The amphipods are still able to feed, even though the pteropods can be up to 50% of the amphipod size. Maybe the pteropods do some of the swimming for the amphipods?

This behaviour is much more common close to the coast than in the open sea: close to the McMurdo area, 75% of the Hyperiella were seen hitching with a pteropod. Now we know that this pairing can be found in the open sea, and maybe is it more common that we think. It is not the first thing we have looked for so far when examining samples. When the University Museum of Bergen joins the Norwegian Polar Institute and the Institute of Marine Research to the Southern Ocean in the austral autumn this coming March, we will make a special effort to search for such collaborators.

Anne Helene


Literature

Havermans C, Hagen W, Zeidler W, Held C, Auel H 2018. A survival pack for escaping predation in the open ocean: amphipod-pteropod associations in the Southern Ocean. Marine Biodiversity https://doi.org/10.1007/s12526-018-0916-3

McClintock JB, Janssen J 1990. Pteropod abduction as a chemical defence in a pelagic Antarctic amphipod. Nature 346:424-426.

 

 

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