Isolation and characterization of deep-sea sediment bacteria and viruses.

Project type: MSc in Biology, 44 ECTS
Student: Larissa Baan
Supervisor: Mathias Middelboe and Sachia Jo Traving
Start: 1. December 2022
End: 21. July 2023

The main objectives of my project are to (1) isolate and characterize the culturable prokaryotes and bacteriophages present in deep-sea sediment samples; and (2) compare the spatial distribution of the isolated microbial communities between four different depths ranging from the Tokyo Bay to the Japan Trench, using culture-based methods followed by 16s rRNA amplicon sequencing. Many bacterial species cannot grow under standard cultivation methods, also known as the great plate count anomaly. Therefore, we will use isolation chips, which consist of a plastic plate with multiple holes filled with agar plugs which are incubated at in situ substrate and temperature conditions. This technique allows for only single cells to be immobilized in each chamber, so fast-growing bacteria can no longer hinder the growth of slow-growing bacteria, hopefully increasing the number and diversity of environmental isolates found.

Investigating virus-bacteria interactions in deep-sea sediments.

Project type: MSc in Biology, 60 ECTS
Student: Thor Amdi Bastiansen
Supervisor: Mathias Middelboe
Start: 1. September 2022
End: 31 August 2023

The project will have its main focus on viral and bacterial production and distribution across a depth gradient from coastal to abyssal sediments throughout Tokyo Bay and to the Japan Trench. Bacteriophages, viruses infecting bacteria, can be integrated in the host genome and provide important genetic properties for the host cell. Additionally, upon infection, bacteriophages also contribute to the turnover of organic matter in marine sediments. Following sampling from a variety of depths we will quantify viral production and their effects ofn bacterial mortality. Further, we will isolate bacteria and viruses in order to sequence and characterize them, for further investigation of specific phage-encoded genes. We will try to isolate and characterize specific virus-bacterium interaction systems and quantify the impact of viruses on bacterial mortality and turnover of organic material throughout the depths.

Finished MSc projects:

The Importance of temperature on degradation of organic matter.

Project type: MSc in Biology, 60 ECTS
Student: Silje Waaler Pedersen
Supervisor: Ronnie N. Glud,John Paul Balmonte
Start: 1. February 2022
End: 31. January 2023

In my current research, I investigate the effects of temperature on microbial enzymatic degradation of organic matter in coastal sediments across different seasons. Temperature in coastal areas can fluctuate substantially on a day-to-day basis, but the extent to which these temperature changes affect the activities of different enzymes is little understood. I carry out enzyme assays and compare rates of activity by intact microbial communities versus those on size-separated, dissolved enzymes from the same microbial communities. With this approach, I can resolve the relative importance of temperature effects on enzyme production versus pure enzyme kinetics along a broad temperature gradient and across seasons.

The importance of sediment resuspension for benthic redox and O2 dynamics

Project type: MSc in Biology, 60 ECTS
Student: Lisbeth Fürst Sørensen 
Supervisor: Ronnie N. Glud, Karl Attard
Start: 1. September 2021
End: 1. Juni 2022

Most studies have investigated coastal biogeochemical cycling during calm weather, whereas more dynamic weather events such as storms have been largely ignored. Such events might have major effects on costal biogeochemical function due to sediment resuspension. In this study, controlled sediment resuspension will be performed in the laboratory by using an optimized EROMES-system, where the implications for key factors of coastal biogeochemical function will be explored. I will examine the impacts across season with a special focus on the fate of oxygen during and after resuspension and investigate the implications of resuspension for organic carbon mineralization and re-oxidization of reduced constituents in the sediment.

Organic petrology, geochemistry, and depositional environment of the recent sediments from deep hadal trenches in the Pacific Ocean

• Project type: MSc in Geology-Geoscience, 60 ECTS
  Student: Marco Benkhettab Sindlev
  Supervisor: Ronnie N. Glud, Hamed Sanei
  Start: 1. September 2020
  End: 1. January 2021

This project involves advanced petrographic and geochemical characterization of organic matter in recent sediments obtained from 12 sediment cores from two ultra-deep, oceanic trenches in the Pacific Ocean. The two trenches in question are Atacama Trench and Kermadec Trench. In this project, white light photometry and fluorescence spectrometry of organic matter preserved in the samples are used to determine depositional environment, diagenetic degradation and source of the organic matter. Furthermore, pyrolysis organic geochemistry is used to determine the molecular composition of organic matter in the context of bacterial degradation.