Author Archives: nbudaeva

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International School of Bergen visit to the University Museum

In June 2024, two school classes (grades 2 & 3) visited the University Museum of Bergen during their educational module “Water and Soil”. The students had a guided tour around the museum exhibit and then participated in organized activities on different marine invertebrates including marine annelids.

One Ocean Week 2024

is a city festival for everyone interested in a sustainable ocean. It combines cultural and educational activities for different audiences from small children starting to learn about marine environment to professionals and policy makers in sustainable approach to the ocean. MAnDAriN contributed with our activity on annelid diversity and with a public lecture at the University Museum venue on the polychaetes with developed jaw apparatuses and their important role in understanding past diversity preserved in marine fossil deposits.

 

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Eva Samson (UiB) - ongoing

 

 

 

 

Supervisors: Nataliya Budaeva & Tom Alvestad

Bylgides scale worm. Photo by A. Semenov (Moscow State University)

Background:

The scale worm genus Bylgides is relatively small (combining 9 described species worldwide) but at the same time very conspicuous with all species being very large in size (up to 5-7 cm long). Our materials combine specimens collected from the Nordic waters as well as from the Siberian part of the Arctic. Comparative genetic data are available from the Canadian Arctic and from Alaska.

Preliminary data show the presence of at least 5 species of Bylgides in our samples including a potentially new species.  The objective of this project is to revise the Arctic Bylgides species matching genetic information with the known morphotypes.  One of the tasks will be building the annotated barcode library of the arctic Bylgides and to generate an identification key with illustrations.

The project is a great opportunity for a student to become familiar with all aspects of biosystematics and integrative taxonomy, acquire a wide range of skills in the morphology and molecular analysis, and participate in a scientific publication. The student will have an opportunity to participate in field work in Svalbard and/or Troms and Finnmark (depending on the time frame of the Master thesis).

The project will include:

  • Examination of specimens of several species of Bylgides from the University Museum of Bergen collection
  • Study of species morphology using light and scanning electron microscopy (SEM)
  • Preparation of scientific illustrations (Adobe illustrator and Photoshop)
  • DNA extraction, PCR, gel electrophoresis, and Sanger sequencing of selected molecular markers
  • Work with the Barcode of Life Database (BOLD), data upload, annotation, and analysis
  • Phylogenetic analyses of the obtained data (BLAST, alignment, Maximum Likelihood, Bayesian Analysis)
  • Species delimitation analysis
  • Presenting results on a conference
  • Contributing to a publication in a peer-reviewed journal

Contact: Nataliya Budaeva

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Jessica Sagerer (UiT/UNIS) - ongoing

Supervisors: Arunima Sen, University Centre in Svalbard (UNIS) 

Main objective: Investigate the species diversity of Arctic seep and fjord siboglinid polychaetes and community composition of their internal bacterial symbionts. Specifically, mtCOI and 18S will be targeted to reveal the identities of worms that are often morphologically cryptic, and metabarcoding of their symbiont bearing organ (trophosome) will be used to characterize their internal bacterial communities that provide them with food from seafloor chemicals.

Background: The Arctic is known for its vast oil and gas reserves, and these can create special ecosystems where chemosynthesis, the chemical equivalent of photosynthesis, is used to fix carbon from chemicals such as methane or sulfide, independently of sunlight. In the Arctic, the hypoxic basins of fjords add to where chemosynthesis can occur.

Most chemosynthesis based ecosystems around the world are dominated by siboglinid polychaetes. These worms have no mouth or digestive organs and instead host chemosynthetic bacteria within their cells, from whom they obtain their nutrition. This makes siboglinids perfectly adapted for chemosynthesis based ecosystems and uniquely within the Arctic, not linked to the phenology of light and photosynthetic primary production. However, the diversity of these highly specialized and unique animals is still poorly understood since chemosynthesis based ecosystems and processes have only recently started being investigated in the Arctic. What makes understanding the diversity of these animals more difficult is that the worms are often morphologically cryptic and individual host species can have different combinations of bacterial symbionts leading to different ‘holobionts’ that can be niche specific.

The objective of this project is therefore to use molecular techniques to identify both siboglinids and their bacterial partners from Arctic and Norwegian gas seep sites and fjords.

Tasks: Mitochondrial COI and ribosomal 18S sequence analysis, 16S rRNA amplicon sequencing, bioinformatics processing, use of sediment geochemical data. If desired (and encouraged), the results will be put together for a scientific article.

 Learning outcomes:

  • Sequencing and metabarcoding
  • Familiarity with bioinformatics processing and pipelines
  • Experience with sediment geochemistry
  • Scientific article writing

Collaborations: NGU (Norwegian Geological Survey), Stockholm University, IOPAN (Polish Academy of Sciences)

Publications for more background:

Bacterial symbiont diversity in Arctic seep Oligobrachia siboglinids.

https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-023-00251-x

The phylogeography and ecology of Oligobrachia frenulate species suggest a generalist chemosynthesis-based fauna in the arctic.

https://doi.org/10.1016/j.heliyon.2023.e14232

Cryptic frenulates are the dominant chemosymbiotrophic fauna at Arctic and high latitude Atlantic cold seeps.

https://doi.org/10.1371/journal.pone.0209273

 Frenulate siboglinids at high Arctic methane seeps and insight into high latitude frenulate distribution.

https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.5988

Contact: Arunima Sen

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Supervisors: Nataliya Budaeva, Dimitar Dimitrov

Background:

Nothria conchylega is a large and peculiar bristle worm with unique lifestyle. The worms live inside their tubes which they build of sediment particles or shell fragments and carry along almost like trichopteran larvae. The species is very abundant and has an extremely large geographical distribution in the Arctic, the North Atlantic and the North Pacific. Despite being a common species, little is known about the population structure of Nothria conchylega. The project aims to analyze the mitochondrial genomes and several nuclear markers obtained from the specimens sampled across the whole geographical range of the species and to study the mechanism supporting the gene flow within its large circumarctic geographical range.

The project supervisors already have data available for the analysis which makes the students work focused more of the data analysis. However additional data can be generated to learn the wet lab techniques. The project is a great opportunity for a student to become familiar with the bioinformatic tools, learn how to analyze large datasets and address complex questions in the Arctic species phytogeography. A motivated student will have an opportunity to join field work in Svalbard or Finnmark (depending on the time frame of the Master project and availability).

The project will include:

  • Examination of specimens of Nothria conchylega from the University Museum of Bergen collection
  • Sampling tissues for Illumina sequencing
  • DNA extraction and library preparation (optional)
  • Basic bioinformatic training and handling data in a terminal, learning bash commands
  • Basic training on how to work on a remote computer cluster
  • Mt-genome and nuclear RNA cluster assembly, BLAST
  • Annotation of assembled mitochondrial genomes
  • Phylogeographic analysis of the obtained data
  • Presenting results on a conference
  • Participating in a publication in a peer-reviewed journal

Contact: Nataliya Budaeva

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Nataliya Budaeva

University Museum of Bergen, University of Bergen, Norway

Nataliya.Budaeva@uib.no

Tom Alvestad

University Museum of Bergen, University of Bergen, Norway

Tom.Alvestad@uib.no

Jon Kongsrud

University Museum of Bergen, University of Bergen, Norway

Jon.Kongsrud@uib.no

Katrine Kongshavn

University Museum of Bergen, University of Bergen, Norway

Katrine.Kongshavn@uib.no

Nicolas Straube

nicolas.straube@uib.no

University Museum of Bergen, University of Bergen, Norway

 

Torkild Bakken

NTNU University Museum, Norway

torkild.bakken@ntnu.no

Arunima Sen

University Centre in Svalbard - UNIS, Norway

 arunimas@unis.no

Eivind Oug

Norwegian Institute for Water Research, Norway

eivind.oug@niva.no

Joachim Langeneck

University of Piza, Italy

langeneck@conisma.it

Maël Grosse

Natural History Museum, University of Oslo, Norway

maelgrosse@gmail.com

Martha Everett

PhD candidate

 

Eva Samson

MSc student (UiB)

 

 

Jessica Sagerer

MSc student (UiT/UNIS)

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Supervisors: Nataliya Budaeva & Miguel Meca

Background:

Phylo and Orbinia from Norwegian waters. Photo by: K. Kongshavn (UiB)

Orbiniidae is a diverse group of annelids, comprising more than 200 described species grouped into 20 genera. Orbiniids are common and abundant in shelf habitats, representing essential food resources for fish (including commercial), and are subjects of ecological monitoring investigations. Despite their common appearance in benthic studies, orbiniids are one of the annelid families with unresolved system and unclear diagnoses of most genera. Recent genomic studies showed strong evidence for combining the genera Phylo and Orbinia into one monophyletic group. Both genera comprise the largest is size orbiniid worms reaching several cm in length, they are very conspicuous and are easy to study. Nevertheless, the Nordic Orbinia and Phylo are poorly described and require formal revision, barcode library preparation, and clarification of taxonomic validity.

Preliminary obtained data show the presence of at least one potentially new species of Phylo in Norwegian waters confirmed with molecular data. A formal description of this species with subsequent publication in a per-reviewed journal will be one of the main tasks of the master project. The publication may be finalized beyond the master thesis time frame.

The project is a great opportunity for a student to become familiar with all aspects of biosystematics and taxonomy, acquire a wide range of skills and publish a scientific paper. A motivated student will have an opportunity to join field work in Svalbard or Finnmark (depending on the time frame of the Master thesis and availability).

The project will include:

  • Examination of specimens of several species of Orbinia and Phylo from the University Museum of Bergen collection
  • Examination of species morphology using light and scanning electron microscopy (SEM)
  • Preparation of scientific illustrations (Adobe illustrator and Photoshop)
  • DNA extraction, PCR, gel electrophoresis, and Sanger sequencing of selected molecular markers
  • Work with the Barcode of Life Database (BOLD), data upload, annotation, and analysis
  • Phylogenetic analyses of the obtained data (BLAST, alignment, Maximum Likelihood, Bayesian Analysis)
  • Formal description of the new species of Phylo from the Norwegian waters
  • Presenting results on a conference
  • Writing a publication for a peer-reviewed journal (with help of supervisors)

Contact: Nataliya Budaeva

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Annelida is often the dominant taxon in marine benthic communities, and can exceed other macrofaunal groups in density, biomass, and species diversity. Nevertheless, many species of marine annelids remain undescribed, for others, the distribution patterns and habitat preferences are poorly understood.

Arctic marine ecosystems are among the ones that suffer most from the current climate change. An enhanced heat transport from the Atlantic Ocean over the last two decades has led to ocean warming and reduced ice coverage in the Arctic. Comprehensive baseline data on Arctic biodiversity and habitats are required to monitor and successfully conserve the natural environment in times of fast and dramatic climate changes.

The primary aim of the proposed project is to describe and document the fauna of the Arctic marine annelids (formerly known as polychaetes, sipunculans and echiurans) inhabiting areas around Svalbard, Jan Mayen, Bjørnøya, the coastal areas of Troms and Finnmark, and the western part of the Barents Sea, and to make this information freely available to the research community and general public.

Project period: 09.2023 - 08.2026

The project is financially supported by the Norwegian Biodiversity Information Centre.

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Supervisors: Nataliya Budaeva, Jon A. Kongsrud & Tom Alvestad

Background:

Photo by: K. Kongshavn (UiB)

Arctic marine ecosystems are among the ones that suffer most from the current climate change. An enhanced heat transport from the Atlantic Ocean over the last two decades has led to ocean warming and reduced ice coverage in the Arctic. Comprehensive baseline data on Arctic biodiversity and habitats are required to monitor and successfully conserve the natural environment in times of fast and dramatic climate changes. Annelida is often the dominant taxon in marine benthic communities, and can exceed other macrofaunal groups in density, biomass, and species diversity.

In the project, we will cover both shallow and deep waters surroundings of Svalbard, Jan Mayen, Bjørnøya, coastal waters of Troms and Finnmark, and the western part of the Barents Sea. This region is characterized by significant seasonal and annual climate changes and moderately high productivity. It is a transition zone for warm and saline water flowing from the Atlantic to the Arctic Ocean, and for cold and less saline water moving from the Arctic to the Atlantic.

The student will assess general polychaete diversity but will also focus on one of the poorly studied families with in-depth species inventory using morphological and molecular data.

The proposed master project is a great opportunity for a student to become familiar with diversity of polychaetes in Norwegian waters - a skill highly desirable by potential employers in public and private marine monitoring agencies.

The project will include:

  • Yearly sampling trips in the Arctic coastal ecosystems (Svalbard, Finnmark) using a range of gear and small research vessels
  • Sorting of marine benthic samples
  • Identification of all polychaete families, the student will become familiar with polychaete diversity in Norwegian waters
  • Examination of species morphology using light and scanning electron microscopy (SEM)
  • DNA extraction, PCR, gel electrophoresis, and Sanger sequencing of selected molecular markers
  • Work with the Barcode of Life Database (BOLD), data upload, annotation, and analysis
  • Phylogenetic analyses of the obtained data (BLAST, alignment, Maximum Likelihood, Bayesian Analysis)
  • Presenting results on a conference
  • Contributing to a publication in a peer-reviewed journal

Contact: Nataliya Budaeva