Category Archives: Student Projects

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

Course on “Preparation, curation, and databasing of marine biodiversity collections” at University Lurio, Pemba, Mozambique (27th August–7th September 2018)

Manuel shares his recent experience of teaching at University Lurio in Mozambique

My collaboration with the University Lurio (UniLurio) in northern Mozambique started back in 2015 when together we organized a fieldtrip to Vamizi island in the Quirimbas archipelago off the northern coast of Mozambique.

Since then, I had the opportunity to participate in several academic activities; I lectured, have reviewed and evaluated theses for the “licenciatura” degree, and most rewarding I have supervised two master students (2015/17) that are now professors at UniLurio. In 2017 I had the pleasure to integrate a mission organized by the Norwegian Embassy in Mozambique to establish a collaborative programme between UniLurio and Norway and later in the same year I was awarded a “Visiting Scholarship” by the International Council for Science, Scientific Committee on Oceanic Research (SCOR) to teach a course about biological collections at UniLurio.

The tropical location of Mozambique in the Indian Ocean results in an impressively rich biological diversity which is nevertheless extremely vulnerable to climate change and warming of ocean waters.

Aspect of part of the UniLurio wet spider collection and dry collection of corals

Therefore, better knowledge of biodiversity and long-term preservation of biological collections are important tools to better understand shifts in faunal and flora composition and the arrival of new species supporting the definition of mitigation and conservation strategies.

The University Lurio has a “Collections Room” with specimens representing the local fauna and flora with marine invertebrates, reptiles, fish, vascular plants, etc., and has a special focus on the study of biodiversity, but simultaneously acknowledges the need to reinforce its infrastructure and build up capacities to develop and manage its collections.

 

This was the framework that led us to decide to organize the course and apply together for funding with SCOR. Later in 2017 the good news arrived, the funding was approved, and so, suddenly I had an entire new course to put together!

All my entire career from the time I undertook my “licenciatura” thesis back in 1994 all the way up to my PhD, postdocs, until the moment I got my first permanent job (the one I still hold) has been always inside natural history museums (Europe, US, Australia, etc.) and consequently working with biological collections has become part of my daily routines for quite a while! And yes, during these more than 20 years I have seen quite a bit and learn a few things, but suddenly for the first time I had to put together this knowledge in a way that it could be presented and shared with others. It turned out to be quite a challenge…, but definitely a rewarding one!

Course structure

During a lecture on curatorial procedures

Photoshoot before setting off for sampling in a local Pemba tidal flat

At UniLurio the course was attended by 15 participants (8 students and 7 professors / technical staff). It was organized in four lectures (2h each), two sampling trips (ca. 4h each) to the tidal zone to collect marine invertebrates (molluscs, echinoderms, crustaceans, etc.), and three laboratory sessions (4h each) to identify the samples and go through all the necessary curatorial steps to ensure proper preservation for long-term storage of the collection (relaxation, fixation, preservation, DNA samples, registration, labeling).

Registering and labelling the lots

All sample lots generated by the students throughout the course were registered in the UniLurio databasing system following DarwinCore standards and at the end integrated in the biological collections.

Bringing the new curated samples to the UniLurio collection room

We finished the course with a very participated open session where it was discussed how could the new acquired competences benefit the development of the local infrastructure bearing in mind the local reality and constrains. A very interesting exercise confronting ideal scenarios with sometimes the harsh and challenging reality of a country with limited infrastructure capacities and in economical strain. At last we had a simple but cozy ceremony attended by the Director of the Faculty of Natural Sciences, UniLurio where certificates of attendance of the course were handed over to the students.

Certification ceremony with awarding of course diplomas.

The course was sponsored by the International Council for Science, Scientific Committee on Oceanic Research (SCOR), the University Lurio, Mozambique and the University of Bergen, Norway

-Manuel

Keeping an eye open for mud jellies

Working on a team makes for the best discoveries in science, and we at the HYPNO and NorAmph artsprojects know it well, especially after we stumbled upon a large number of the elusive mud jellyfish Tesserogastria musculosa in one of our joint sampling trips to Raunefjord (you can read Christine’s account of our sampling here, in Norwegian).

Live specimens of mud jellyfish (Tesserogastria musculosa) collected in Raunefjord. Foto: L Martell

We were able to compare our specimens with the holotype (i.e. the original specimen upon which the description of the species was made, pictured above), thanks to a loan from the Natural History Museum of the University of Oslo. Collaboration between museums make science happen! Foto: L Martell

Mud jellyfish can be very abundant, but they are also easily overlooked, and only a gentle way of collecting animals will reveal its presence on a benthic sample. These hard-to-catch benthic jellyfish are so fragile that many previous surveys of the bottom of the fjords may have missed them because the jellies were simply too damaged to be identified at any level, but thanks to the careful processing of the samples and an expert eye we were able to obtain living specimens in good shape. This finding led to the evaluation of all the records of the species in the world, obtaining the first genetic data (including the DNA-barcode) for the species and genus, and finally to a redescription and a joint publication (available here: https://link.springer.com/article/10.1186/s10152-018-0515-5).

Getting the sample and carefully separating the animals. Fotos: AHS Tandberg (left), L Martell (right)

Searching for (and finding!) many jellyfish. Fotos: AHS Tandberg

Mud jellyfish are the only species in genus Tesserogastria, which takes its name from the square-shaped stomach of the animals (Tesserogastria comes from ancient Greek τέσσαρες “four, square” and Latin gaster “stomach”). The specific name musculosa (Latin for “muscular”) was given to them because they look quite sturdy, with extremely well developed muscles around the opening of the “bell”. They are not the typical free-swimming and pulsating jellyfish, as they prefer to live in muddy bottoms, where they use their tentacles to walk around (they really don’t like to swim) until finding a place to sit and wait for dinner (which is usually some small crustacean). We still don’t know many things about this species because mud jellyfish are tiny and live on the bottom of the sea far away from the surface, but now that a new population has been discovered in Western Norway we will have the opportunity to investigate more on its behavior and body structure, perhaps answering some questions such as why do these jellies need very strong bell muscles if they don’t swim very often, or how the species is related to the other crawling jellyfish species from the North Atlantic.

-Luis

PhD thesis defence

On June 7th Nina Therese Mikkelsen presented her thesis ” Phylogeny and systematics of Caudofoveata (Mollusca, Aplacophora)” for a public audience.  She was questioned by the opponents dr Mikael Thollesson, University of Uppsala, and dr Suzanne Williams, The Natural History Museum of London, and did an excellent performance explaining the results of her studies.

Guest researcher: Marla

Marla, who has been visiting several times to work on our amphipod collections, sent us this “travelogue” from her longest stay. In her own words:

I am a third year PhD student, and my project is shared between the University of Southampton at the National Oceanography centre and the Natural History Museum in London. I am supervised by Dr Tammy Horton (NOC), Dr Andrew Gates (NOC), Dr Phil Fenberg (UoS), Dr Miranda Lowe (NHM), and Dr Andrea Waschenbach (NHM).

I spent 8 glorious weeks in Bergen working with the invertebrate collections at the Department of Natural History of the University Museum of Bergen (UiB) together with the wonderful Anne Helene Tandberg and Endre Willassen. Also a massive thank you to Katrine Kongshavn, Morten Stokkan, Jon Kongsrud, Luis Felipe Martell Hernández, Aino Hosia, Tom Alvestad, Nataliya Budaeva, Manuel Malaquias, Louise Lindbloom, and Kenneth Meland for your help in the lab and support with my project and lunchtime conversations!

I arrived to Bergen mid- September just in time for the 2017 UCI Road World Championships! As a huge fan (and very amateur road cyclist) this was such a bonus to have the chance to see it. The race took over the town, and one late afternoon Anne Helene and I climbed half-way up Mount Fløyen to watch the men’s Time Trial. The sun was out, the streets were packed, atmosphere was electric and we had prime seats–I couldn’t wait to see Chris Frome (GB) and Tom Dumoulin (NL) cycling in action.  It was a fantastic afternoon!

Anne Helene and I enjoying the afternoon UCI race from our prime viewing spot

The classic road graffiti to show support to the cyclists. Here Tom Dumoulin is forever immortalized on Mount Fløyen.

Tom Dumoulin won first place in the men’s Time Trial, Chris Froome took third.

Back in the lab…

I was working with amphipods from the family Phoxocephalidae from the Western African Waters, focussing particularly on the amphipods from the sub-family Harpiniinae [crustacea; Amphipoda; Phoxocephalidae; Harpiniinae]. Phoxocephalid amphipods are highly speciose and abundant in deep sea sediments globally. Species identity is critical to understanding mechanisms driving observed biodiversity patterns and to asses community change. The aim of the project while in Bergen was to use both DNA barcoding and traditional morphological taxonomic approaches in order to create a robust library of Phoxocephalidae species from the poorly known West African waters. Large scale projects such as Marine Invertebrates of West Africa (MIWA) provide the perfect opportunity for collaborative work! More about the MIWA-project can be found here.

The MIWA project submitted over 2700 tissue samples from over 600 morphospecies for DNA barcode sequencing, including Crustaceans, Echinoderms, Molluscs and Polychaetes. Out of these, 45 samples were from the family Phoxocephalidae, the target taxa. Working with Dr Anne Helene Tandberg and Prof Endre Willassen, the sequenced MIWA Phoxcephalid voucher specimens were dissected and mounted as permanent microscope slides to morphologically score them. Later, the phylogenetic analysis based on all molecular and morphological characters will be compared. Each appendage was photographed on the modular (Leica CTR6000) microscope and the images were stacked, resulting in incredible photos!

Harpinia abyssi P7. Photo: M. Spencer

As a result of some of this work, we think that we have identified 4 new species to the genus of Basuto. The genus was previously monotypic, with the type-locality in South Africa. Now we are awaiting the holotypes and paratypes to arrive so that we can compare. Together with Anne Helene, Endre Willassen and Tammy Horton, I am currently writing my first publication, formally describing these specimens as new species. Stay tuned for further updates!

Basuto specimen pereopod 5. Photo: M. Spencer

Basuto specimen Mandible, Photo: M. Spencer

At work in the DNA lab

Working with Anne Helene within the molecular biology labs at the University of Bergen, I had the chance to develop taxon specific primers and PCR conditions for the Harpiniinae MIWA specimens which were not successfully sequenced with the Universal primers. As a starting point, an additional 13 MIWA specimens had tissue extracted for DNA, and then dissected and permanent slides were made in order to morphologically score them. Each appendage was photographed and the images stacked. The primers and PCR conditions are a work in progress; however, this was a very successful trip resulting in a lot of data to analyse!

I also had the chance to explore the fantastic city of Bergen! I absolutely loved my time spent here- I generated a lot of data and learned so many new skills and new insight into my PhD project. Win-win! I look forward to returning again one day.

-Marla

Getting back in business

The blog has been quiet over summer – but we’ve been busy!

The #AnnelidaCourse2017 came to an end, and happy participants went back to their home institutions with a lot of new knowledge, a increased contact network, and many new friends.

a)Students working in the lab; b) Picking interesting animals from the samples onboard R/V Hans Brattström; c) Animals to be studied; d) Group photo of most of the participants; e) Detailed study and drawing of a specimen; f) Field work onboard R/V Aurelia Fotos: K.Kongshavn (a,b,e), G. Kolbasova (c), G.Jolly (d), S. Rosli (f)

a) Students working in the lab; b) Picking interesting animals from the samples onboard R/V Hans Brattström;
c) Animals to be studied; d) Group photo of most of the participants; e) Detailed study and drawing of a specimen; f) Field work onboard R/V Aurelia Fotos: K.Kongshavn (a,b,e), G. Kolbasova (c), G.Jolly (d), S. Rosli (f)

Heaps (HEAPS!) of samples have been cataloged and labeled, DNA-sequencing has completed on the shipment we sent in June and we’re working on analyzing the results, and samples from the cruises we particpated on have and are being sorted.

The next shipment of animals to be barcoded through NorBOL is being assembled – of marine invertebrates from our collections, one plate of polychaetes and one plate of isopods have been prepared, and we plan on completing a few more plates before shipping in October.

Isopods for barcoding - these have all been collected and identified by the MAREANO project. Photo: K.Kongshavn

Isopods for barcoding – these have all been collected and identified by the MAREANO project. Photo: K.Kongshavn

We will also get contributions from several of the Norwegian Taxonomy Initiative projects (Artsprosjekt) that are running, and a plate with insect samples made by the students of BIO233 (I was down there today giving them an introduction to barcoding, NorBOL and the BOLD database) – hopefully we’ll get good results on all of it.

-Katrine

Fieldtrip to Taiwan: sampling on the periphery of the coral triangle

As part of our research programme to study “opisthobranch” molluscs in the Indo-West Pacific and understand the drivers of present diversity and biogeography on this region, we carried out a 3-week fieldtrip to Taiwan during May 2017. Taiwan is located in the China Sea north of the Philippines on the periphery of the “coral triangle”, the richest marine hotspot in the world contained within Indonesia, Papua New Guinea, and the Philippines.

Goniobranchus kuniei. Longdong, NE Taiwan

Goniobranchus kuniei. Longdong, NE Taiwan

Although situated outside this hotspot, Taiwan is influenced by the warm water Kuroshio Current flowing from the Philippines along the Luzon Strait and striking the southern part of Taiwan where it splits in two branches which drift northwards along both the eastern and western coastlines of the country. This confers to Taiwan tropical characteristics on its southern regions with occurrence of vast and diverse coral reef systems, while the northern coasts are of sub-tropical affinity with waters up to five degrees cooler. This combination of different oceanographic and climatic features, result on the occurrence of an extremely diverse marine fauna with different ecological requirements.

To cover different oceanographic regimes in the best possible way within our limited timeframe, we visited three regions for about one week each.

We first sampled along the southern tip of Taiwan at the Kenting National Park together with Professor Chung-Chi Hwang from the National University of Kaohsiung.

The sampling team-at-Kenting-left-to-right-Trond-Oskars-Wei-Ban-Jie-Chung-Chi-Hwang-Manuel-Malaquias

The sampling team at Kenting. left to right: Trond Oskars, Wei Ban Jie, Chung Chi Hwang, Manuel Malaquias

Here are some of the animals we encountered at Kenting:

Who are you?

Who are you?

The second week was dedicated to the off shore island of Penghu in the Strait of Taiwan where we have worked together with Professor Yen-Wei Chang and his students from the National Penghu University of Science and Technology.

A happy party of sea slug hunters in Penghu, Taiwan

A happy party of sea slug hunters in Penghu, Taiwan

The garage of our hostel in Penghu, transformed into a wet lab for a week

The garage of our hostel in Penghu, transformed into a wet lab for a week

Goniobranchus cf. sinensis

Goniobranchus cf. sinensis

Hypselodoris maritima

Hypselodoris maritima

A beautiful flatworm

A beautiful flatworm

Finally, we sampled on the NE coast along the Longdong area in collaboration with Dr Vincent Chen and Dr Wei-Ban Jie, the first an authority on Taiwanese coastal ecology and the latter the author of the book “Taiwan Nudibranchs”.

A glimpse of the beautiful waterscapes at Longdong, Taiwan

A glimpse of the beautiful waterscapes at Longdong, Taiwan

Phyllidia ocellata Longdong, NE Taiwan

Phyllidia ocellata Longdong, NE Taiwan

Thuridilla sp. Longdong, NE Taiwan

Thuridilla sp. Longdong, NE Taiwan

Halgerda carlsoni Longdong, NE Taiwan

Halgerda carlsoni Longdong, NE Taiwan

Shallow habitats between the tidal zone down to 30 m deep were surveyed for “opisthobranchs”, and at the end we estimate to have collected a staggering 140 species.

The samples are now under curation and will soon be integrated in the systematic collections of the Natural History Museum of Bergen, becoming available for scientific study.

-Manuel Malaquias, Natural History Museum of Bergen, UiB

Update from the Annelida-course

20170609_100827

As told last week, we are currently hosting the international course on Annelid Systematics, Morphology and Evolution at the University of Bergen’s field station. Here’s a little update of what we have been up to since the previous post:

The days are pretty packed, with lectures, sampling, and lab work – thankfully both students and teachers are enjoying the work, and the mood in the lab is sunny (even if the Bergen “summer” is somewhat…fickle these days). We have covered a multitude of research topics, methods,  habitats, and annelid groups so far, with still more to come.

Happy, hard working  students in the lab

Happy, hard working students in the lab

"summer" sampling - we did get very nice samples!

“summer” sampling – we did get very nice samples!

Back in the lab, Torsten explaining todays exercises

Back in the lab, Torsten explaining todays exercises

Mixing the solution to get the tiny annelids out

Mixing the solution to get the tiny annelids out

The jaws of a small Ophryotrocha

Pointing out the jaws of a small Ophryotrocha

We’ll keep blogging from the from the course, so check back!

You can also get some glimpses of the exciting world of Worm researchers (!) by checking the tag #annelidacourse2017 on Twitter (you don’t need an account to do that, just click the link).

Congratulations to our latest PhD!

Freshly minted PhD!  (photo: Kenneth F. Bosch)

Freshly minted PhD!
(photo: Kenneth F. Bosch)

Andrea successfully defended her Ph.D. thesis “Dietary specialization and molecular phylogeny of the family Aglajidae (Cephalaspidea: Gastropoda) with species delimitation analysis and biogeography of two genera from the clade Chelidonura sensu lato” earlier today. She was supervised by Manuel A.E. Malaquias from the Department of Natural History, UM, and Henrik Glenner from the Department of Biology.

You can read more about her work here (in Norwegian)

Congratulations and all the best wishes from us!

Below are photos of some of the species, if you are wondering how they look (pics by Manuel)