Master's thesis projects

The biological carbon pump (BCP) plays an important role in regulating the Earth’s carbon cycle by
transporting photosynthetically fixed CO2 from the ocean surface to the seafloor, enabling long-term
carbon sequestration. The BCP includes the gravitational pump, which involves the sinking of
particulate organic carbon (POC) from the ocean surface to the deep ocean in the form of particles of
planktonic origin (Le Moigne, 2019). These particles, collectively referred to as marine snow, consist
of dense aggregates of microalgal and prokaryotic cells or of zooplankton fecal pellets (Stief et al.,
2023). During their descent the particles are colonized and degraded by heterotrophic microbes and
grazing metazoans, which weakens the BCP (Stief et al., 2026). With increasing hydrostatic pressure as
the aggregate sinks, it may inhibit microbial respiration and metabolic activity (Stief et al., 2021).
There is a decrease in both phylogenetic diversity and species richness of particle-associated
prokaryotes (Tamburini et al., 2021).

The aim of this thesis is to investigate how increasing hydrostatic pressure affects bacterial production,
cell abundance, cell division activity, and the occurrence of bacterial supercells in diatom aggregates
colonized by surface and deep-sea bacterial communities.

Diatom aggregates will be colonized by surface seawater bacterial communities using a plankton
wheel. The diatom aggregates will be exposed to increasing hydrostatic pressure to simulate their
descent from surface waters (0.1 MPa) into the deep ocean (100 MPa). Samples will be collected at 20,
40, 60, 80 and 100 MPa. Microbial responses will be assessed by measuring bacterial production, cell
abundance, cell division activity and the occurrence of bacterial supercells.

A subsequent experiment will use diatom aggregates colonized by surface seawater bacterial
communities collected at Tonga Trench. The diatom aggregates will then be transferred to deep-sea
bacterial communities, also collected at Tonga Trench. This will simulate de novo colonization of
aggregates by pressure-adapted deep-sea bacteria. The remainder of the experiment will follow the
same protocol as the previous experiment.

This project will unravel the importance of microbial priming for refractory carbon turnover in deep-sea sediments. Microbial priming occurs when the addition of fresh, labile organic matter stimulates microorganisms to degrade pre-existing, more refractory organic matter that might otherwise remain preserved in the sediment record. Anthropogenic changes in surface production and material deposition may therefore influence the balance between carbon remineralisation and long-term carbon burial in the deep ocean floor.

Microbial priming will be investigated using sediment cores retrieved from a reference site (2400m) and the Molloy Deep (5500m) in Fram Strait. Sediment from different redox zones, corresponding to the oxic (0-3 cm) and denitrification (10-13 cm) zones at the reference site, and the oxic (0-3 cm) and sulfate reduction zones (6-10cm and 26-30 cm) at the Molloy Deep, will be enriched with different carbon amendments to determine whether priming is occurring. The samples will be used for a series of treatments, including unamended controls and 12C- and 13C-labelled labile and refractory carbon, will be used to track the source of carbon turnover.

The central hypothesis is that the addition of fresh labile organic carbon will stimulate the microbial degradation of refractory sediment organic matter, but that the strength of this priming effect will vary among sedimentary redox zones. The results will contribute to understanding how fresh organic matter inputs influence the fate of refractory carbon in deep-sea sediments and whether microbial priming enhances carbon remineralisation at depths where organic matter is generally considered to be relatively resistant to degradation.

Phages can maintain host metabolism through the use of auxiliary metabolic genes (AMGs), which can alleviate energetic and biosynthetic bottlenecks in phage proliferation and provide important metabolic properties for the host when the phage is integrated as a prophage. In the project, we will analyze a collection of bacterial isolates obtained from deep sea sediments with respect to prophage/AMG content and phylogeny by whole genome sequencing and by induction of prophages from the cells. Induced prophages will be isolated on susceptible hosts and purified, and will be characterized with respect to host range, genomic composition and AMG content.

The collections of deep sea bacterial and phage isolates will be expanded during an upcoming research cruise, providing more information on the genomic content and spatial distribution of phages and their potential AMG content. This work will also include establishment of anaerobic culture conditions for isolation of anaerobic phage-host systems.

The collection and characterization of phage-host systems will allow for experimental lab-based studies on the role of AMG's for host metabolic function and regulation, expanding our knowledge  how phages interact with host functional properties and influence benthic biogeochemical cycling.

Genome-centric metagenomics offers a powerful, cultivation-independent window into hadal microbial communities. By linking metabolic potential to specific microbial lineages, Metagenome-Assembled Genomes (MAGs) are crucial for understanding the diversity and ecological functions of uncultured microbes. One of the central computational challenges in this process is binning, where assembled DNA fragments (contigs) are grouped together into ecologically meaningful units.

Binning algorithms leverage a variety of intrinsic biological signals to achieve this separation. Classic approaches use sequence composition (tetranucleotide frequencies) and differential coverage (correlated abundance patterns across samples). However, modern methods incorporate more sophisticated features, such as assembly graph connectivity, which provides information on which contigs were physically adjacent in the original DNA (Mallawaarachchi et al., 2024). Furthermore, the field is increasingly dominated by algorithms that utilize machine learning and deep learning models to integrate these diverse signals into a single, powerful framework for genome separation (Mallawaarachchi et al., 2024).

The aim of this project is therefore to establish an optimized and benchmarked bioinformatics workflow for the recovery of microbial genomes from hadal sediments. By systematically evaluating state-of-the-art binning strategies, we intend to enhance our ability to characterize the "microbial dark matter" in the deep sea and provide a more accurate picture of the microbial diversity and functional capacity in these important ecosystems.

The formation of aggregates in the euphotic zone of the ocean and their subsequent sinking as “marine snow” is a crucial process in the biological carbon pump. This process enables the long-term sequestration of carbon while simultaneously delivering nutrients and energy to the deep ocean. Marine bacteria colonize those marine snow particles at the ocean surface and degrade them during descent encountering great increases in hydrostatic pressure. In this thesis we investigated the effect of increasing hydrostatic pressure from atmospheric to 100 MPa on bacterial surface communities through a simulation experiment. Incubations kept at atmospheric pressure (0.1 MPa) served as a control. With increasing pressure cell concentrations decreased significantly and were accompanied by reduced total nutrient uptake. Total community oxygen uptake was reduced in the pressure treated samples, whereas the maximum consumption per cell was similar in both treatments. Hydrostatic pressure induced shifts in bacterial community composition with specific taxa like Clade I and Clade II (SAR11) being relatively more abundant under pressure based on 16S rRNA gene analyses. Morphological changes of bacteria were investigated and cells emerged with strongly increased cell size (up to 32 μm) and multiple spatial separated DAPI stained centers. We introduced the term “Supercell” for this morphology and showed that they can make up to 13 % of total bacteria in a community and up to 78% of the total biomass. Through FISH staining we demonstrated that all of the observed Supercells belonged to Gammaproteobacteria. Antibody staining further supports that the emergence of Supercells may result from an inability of cells to divide, likely caused by altered FtsZ function under high hydrostatic pressure.

The DPANN superphylum (historically Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaea) is the most abundant archaeal lineage in the anoxic layers of hadal sediments. It encompasses some of the smallest and least understood archaea, presenting a unique opportunity to unravel their ecological roles and evolutionary history in extreme environments. (Zhang, et al., 2024; Rinke, et al., 2013; Lannes, Cavaud, Lopez, & Bapteste, 2020). This archaeal lineage is hypothesized to be living either in symbiosis or in consortia (Dombrowski, Lee, Williams, Offre, & Spang, 2019; Vigneron, Cruaud, Lovejoy, & Vincent, 2022).

In this project, I will take advantage of a large repository of metagenomes and associated metagenome-assembled genomes (MAGs), spanning four trench system in the Pacific Ocean and the Molloy Deep (Artic Ocean), to (i) describe the taxonomic diversity of DPANN archaea in deep sea benthic sediments, (ii) characterize the global and local distribution patterns and reveal the environmental factors driving them, (iii) identify potential ecological roles by characterizing the functional diversity and metabolism, and (iv) elaborate on the study of their evolutionary history through a comparison with representatives from other biomes (Liu, et al., 2018; Liu, Wang, & Gu, 2021).

This project will provide new insight into the diversity, biogeography and ecology of these archaea in deep-sea environment, and their potential implication in the global biogeochemical cycles.

This project will focus on the prokaryotic and viral distribution and activity across the depth gradient from surface water to the bathypelagic layer in the North-west Atlantic Ocean. A key focus will be on taxon-specific lysis, a novel perspective that uses the ratio between exocellular 16S rRNA and cellular 16S rRNA to quantify viral lysis on specific prokaryotic taxa. Additionally, given the profound effects of hydrostatic pressure on microbial distribution and activity, the project will specifically explore how pressure affects viral production and the regulatory role of viruses in regulating prokaryotic communities.

The key objectives will include 1) quantifying the prokaryotic and viral abundance across a depth gradient; 2) calculating the viral production at different depths and studying the effects of pressure; 3) extracting the cellular 16s rRNA and the exocellular 16s rRNA to explore the taxon-specific viral lysis across the depth gradient and under the different pressure conditions to study the viral regulation on prokaryotic communities.

This project aims at quantifying trace metal mobilization – with special focus on mercury - during resuspension experiments in coastal sediments. I am a student from the Technische Universität Braunschweig where the Department of Environmental Geochemistry (Prof. Harald Biester) is focused on the biogeochemical cycles of trace metals. An optimized experimental setup for simulating natural resuspension events (EROMES system) combined with appropriate measurements of biogeochemical parameters will be realized in a number of targeted sediment types.

Possible sites include the proximal Odense Fjord and the Limfjord. The latter being a shallow and eutrophic sound in the Jutland, would offer the possibility to compare sites rich in organic matter from mussel farming and references sites with lower organic matter content. Resuspension events are an inherent forcing in many marine settings, but the importance for the overall biogeochemical function of marine settings is underexplored. This topic is relevant and timely as coastal sediments are increasingly being affected by resuspension due to climate induced changes in weather patterns.

The aim of this work will be to investigate specific marine phage-host systems. Through isolation and subsequent sequencing, Lara will isolate and cultivate novel virus-host systems from environmental samples collected from different cruises in the North Atlantic and Japan. In addition, she will be extracting environmental DNA to characterize the natural communities from which these virus-host systems originate.

The project will have a special focus on the discovery and characterization of potential auxiliary metabolic genes (AMGs) in the isolated viruses and what impact they have on their host.

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.

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.

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.

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.

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.