MDM PhD project

Note: This project outline should be used as a starting point when writing the proposal on your dissertation project (max. 5 pages). Make sure to answer the questions in red font in your proposal.

“Exploring novel microbial lineages and their adaptations to survival in extreme environments”


The deep-subsurface is a vast environment harbouring an estimated 1029 microbial cells (Magnabosco et al. 2018), comprising up to 3.6% of Earth’s total living biomass (Kallmeyer et al. 2012). Conditions are challenging and characterized by carbon and energy constrains, extreme temperatures and high pressure. In response, deep subsurface microbes have evolved distinct traits to cope with these conditions. For example, adaptations to low energy availability include mutualistic relations ranging from metabolic cooperation (synthrophy) to symbiosis (Lau et al. 2016; Schwank et al. 2019). Syntrophy improves the utilization of complex carbohydrates, such as cellulose, starch, lipids, and hydrocarbons (Dombrowski et al. 2017), and facilitates the anaerobic oxidation of methane. Thereby, archaeal anaerobic methane oxidizers (ANME) form syntrophic partnerships with sulfate-reducing bacteria to perform the complete oxidation of methane to carbon dioxide. That way, over 90% of methane is oxidized before it reaches the sediment surface, and this microbial methane oxidation has been described as "one of the most important controls on greenhouse gas emissions and climate on Earth." (Orcutt et al. 2011)


In this project, we aim to explore microbial taxa recovered from deep-subsurface sediments in the Pacific Ocean. The specific aims, objectives and challenges are:

Aim 1: Discovering novel microbial lineages from deep subsurface sediments.

Background: The majority of bacterial and archaeal lineages remains uncultured and is often referred to as microbial dark matter (MDM). Deep-subsurface samples are a treasure trove for the discovery and description of novel MDM taxa. What methods have scientists used to recover uncultured lineages, and what have we learned from these discoveries? Also, are there any examples of uncultured deep-subsurface taxa? Which of these methods would you like to use in your PhD and why?

Objectives: Recover and classify high quality metagenome-assembled genomes (MAGs) from novel prokaryotic phyla. Propose wet-lab methods and bioinformatics workflows that you will use to accomplish this task.

Challenges: Which challenges could you encounter, and how would you overcome them?


Aim 2: Inferring microbial interactions through co-occurrence pattern analyses.

Background: Consistently co-occurring taxa may be associated with each other due to mutualistic relationships, or represent competition of taxa with similar ecological traits. However, the latter might be rare, since the resource-limiting conditions may not allow the survival of directly competing taxa (competitive exclusion). Synthesize the literature on microbial co-occurrence analysis and what we have learned from it. Also, are there any deep-subsurface examples? Do you want to expand on any of these findings in your PhD project?

Objective: Screen recovered metagenomes and publicly available datasets to establish co-occurrence patterns. Propose bioinformatics workflows that you will use to accomplish this task.

Challenges: Which challenges could you encounter, and how would you overcome them?


Aim 3: Exploring the metabolic potential of the recovered, co-occurring, novel microbial lineages

Background: Deep-biosphere microbes are capable of energy conservation by many pathways, including fermentation, acetogenesis, methanogenesis, anaerobic oxidation of methane, and reductive dehalogenation (the removal of halogen atoms from organic compounds). Synthesize the literature on the main metabolic pathways described for the dep-biosphere. Are there any examples of synthrophic relationships not covered in the introduction. Why could they be interesting for your project.

Objectives: Reconstruct the metabolic capabilities of selected microbial lineages. Propose bioinformatics workflows that you will use to accomplish this task.

Challenges: Which challenges could you encounter, and how would you overcome them?


Aim 4: Enrichment and culturing novel microbial lineages

Background: While the great majority of deep-subsurface bacteria remains uncultured, several successful attempts have been made to isolate archaea and bacteria from the deep biosphere. Given the rather involved experimental setup to culture microbes under pressure, it might be more feasible to focus on piezotolerant microbes that can grow at 1atm (Zhang, Wu, and Zhang 2018). Synthesize the literature on successful cultivation of deep-subsurface/ deep-biosphere microbes. Which of these results and insights can be applied to your PhD project? 

Objectives: Enrich and subsequently isolate several microbial strains from novel MDM lineages. Propose wet-lab methods that you will use to accomplish this task.

Challenges: Which challenges could you encounter, and how would you overcome them?


Aim 5: Assess the viral community and their potential hosts in the deep biosphere.

Background: Virus-like particles are abundant in the deep-subsurface, and prophages and viral populations have been identified, however only a small fraction (up to 11%) could be linked to potential hosts (Cheng et al. 2022). Why is it important to study viruses in deep subsurface sediments, and what roles do viruses play in microbial communities. Are there any exciting, recent studies on deep-sea sediment viruses? Are there any viruses you are excited about and want to focus on in your PhD project?

Objectives: Recover viral genomes (VMAGs) and their microbial hosts, by utilizing GTDB reference genomes and all MAGs recovered in this study. Propose bioinformatics workflows that you will use to accomplish this task.

Challenge: Which challenges could you encounter and how would you overcome them?



What potential applications in biotechnology could result from this project?



Becraft, Eric D., Maggie C. Y. Lau Vetter, Oliver K. I. Bezuidt, Julia M. Brown, Jessica M. Labonté, Kotryna Kauneckaite-Griguole, Ruta Salkauskaite, et al. 2021. ‘Evolutionary Stasis of a Deep Subsurface Microbial Lineage’. The ISME Journal 15 (10): 2830–42.

Cheng, Ruolin, Xiaofeng Li, Lijing Jiang, Linfeng Gong, Claire Geslin, and Zongze Shao. 2022. ‘Virus Diversity and Interactions with Hosts in Deep-Sea Hydrothermal Vents’. Microbiome 10 (1): 235.

Dombrowski, Nina, Kiley W. Seitz, Andreas P. Teske, and Brett J. Baker. 2017. ‘Genomic Insights into Potential Interdependencies in Microbial Hydrocarbon and Nutrient Cycling in Hydrothermal Sediments’. Microbiome 5 (August): 106.

Kallmeyer, Jens, Robert Pockalny, Rishi Ram Adhikari, David C. Smith, and Steven D’Hondt. 2012. ‘Global Distribution of Microbial Abundance and Biomass in Subseafloor Sediment’. Proceedings of the National Academy of Sciences of the United States of America 109 (40): 16213–16.

Lagier, Jean-Christophe, Grégory Dubourg, Matthieu Million, Frédéric Cadoret, Melhem Bilen, Florence Fenollar, Anthony Levasseur, Jean-Marc Rolain, Pierre-Edouard Fournier, and Didier Raoult. 2018. ‘Culturing the Human Microbiota and Culturomics’. Nature Reviews Microbiology 16 (9): 540–50.

Lau, Maggie C. Y., Thomas L. Kieft, Olukayode Kuloyo, Borja Linage-Alvarez, Esta van Heerden, Melody R. Lindsay, Cara Magnabosco, et al. 2016. ‘An Oligotrophic Deep-Subsurface Community Dependent on Syntrophy Is Dominated by Sulfur-Driven Autotrophic Denitrifiers’. Proceedings of the National Academy of Sciences 113 (49): E7927–36.

Magnabosco, C., L.-H. Lin, H. Dong, M. Bomberg, W. Ghiorse, H. Stan-Lotter, K. Pedersen, T. L. Kieft, E. van Heerden, and T. C. Onstott. 2018. ‘The Biomass and Biodiversity of the Continental Subsurface’. Nature Geoscience 11 (10): 707–17.

Orcutt, Beth N., Jason B. Sylvan, Nina J. Knab, and Katrina J. Edwards. 2011. ‘Microbial Ecology of the Dark Ocean above, at, and below the Seafloor’. Microbiology and Molecular Biology Reviews 75 (2): 361–422.

Schwank, Katrin, Till L. V. Bornemann, Nina Dombrowski, Anja Spang, Jillian F. Banfield, and Alexander J. Probst. 2019. ‘An Archaeal Symbiont-Host Association from the Deep Terrestrial Subsurface’. The ISME Journal 13 (8): 2135–39.

Zhang, Zenghu, Yanhong Wu, and Xiao-Hua Zhang. 2018. ‘Cultivation of Microbes from the Deep-Sea Environments’. Deep Sea Research Part II: Topical Studies in Oceanography, Exploring the Hadal Zone: Recent Advances in Hadal Science and Technology, 155 (September): 34–43.