By Melina Krohn

When we go down below the surface of the Earth we go farther and farther away from everything we know and is familiar to us. This makes it hard to imagine how anything could survive there. And yet, microorganisms make this harsh, hostile environment their home. Supported by the circulating seawater and the surrounding rocks these organisms not only survive there but at some places they even thrive.

Figure 1 – A fictional representation of the deep biosphere inside the oceanic crust.

Figure 2 – A solid-rock drilling core from the oceanic crust. In there microbes are supposed to live? How? Follow me and find out!

The deep biosphere is one of Earth’s few underexplored frontiers. Studying the life in the subsurface is challenging and has been made possible by drilling programs like the International Ocean Discovery Program (IODP). There, specialized drilling ships like the JOIDES Resolution are used to retrieve samples from beneath the seafloor. What we find there challenges our definitions of life and offers profound insights into how organisms adapt to extreme environments. As technology advances, we will continue to uncover the secrets of this hidden world, shedding light on the origins of life on Earth and the possibility of life beyond our planet. As a doctoral candidate investigating this fascinating habitat, I invite you to follow me down into a world not comparable to our own.

What is the Deep Biosphere?

First, we sink deeper and deeper into the water, the sunlight slowly fading away until we are surrounded by complete darkness. Eventually, after drifting for ages through this everlasting night we reach the seafloor. But this is not the destination of our journey: We sink even lower, into the realm below the surface of the ocean floor. Here we find what we are looking for: The deep biosphere.

The ‘deep biosphere’, the ‘subsurface biosphere’ or ‘intraterrestrial life’ all describe the same thing: Organisms living hidden beneath the Earth’s surface, either within rocks or buried in layers of sand and mud. This can be as far down as 2.5 km below the surface on top of already being below several km of water [1].

Figure 3 – Deep biosphere habitats. The important structures highlighted within the habitats are examples of environments in which deep roaming organisms can be found.

These organisms are microscopic small, hence the name microbes. They can be different kinds of life-forms including bacteria, fungi or even tiny worm-like creatures.

But how do these organisms survive there? What do they eat? Where do they take the energy from? Simple: From what is there plenty of: Rocks! Now you might ask: Rock-eating organisms? That only exists in fantasy books! Well, with this you are only partly correct. Of course, the organisms that live so far below the surface don’t have teeth with which they chomp out pieces of the rocks. And they don’t have a digestive tract either. However, they use chemical reactions to create biomass and energy.

And how does that work?

Figure 4 – Depending on where in the crust the microbes live, they are called differently: Chasmoendoliths roam in existing cracks, euendoliths create cavities and cryptoendoliths reside in existing cavities within the rock.

How do rocks become food?

There are several ways how the bacteria make use of the rocks surrounding them. But before we can understand how that works, we need to know what a rock actually is: A rock is a solid mass made up of different minerals. Minerals are naturally occurring, crystalline substances with a defined chemistry. For example, a quartz is a mineral, salt is a mineral and, strictly speaking, ice of water is a mineral too. There are different types of minerals, depending on the chemistry and the temperature of the magma from which they were crystallized as well as the temperatures and pressures they were exposed to after.

And believe it or not: most rocks are interwoven with pores that are connected to each other by microscopic cracks. And as we drift in our journey through this interconnected pore network, we realize that these pores and cracks are not empty and they are not filled with air: water passes through the rocks of the oceanic crust. This water reacts with the rocks by exchanging elements and dissolving minerals. This way components are released like hydrogen or reduced metals like iron that can be used to generate energy. Additionally, carbon in the form of CO 2 or methane is produced [3][4]. Some microbes have the ability to accelerate these so-called fluid-rock reactions by releasing acids or oxidizing or reducing minerals [5][6].

So, with the dissolved components in the water, the microbes can generate biomass. This biomass can then be eaten up and consumed by other organisms. An underground circle of life!

Why does it matter to us?

Isn’t it amazing how these tiny organisms have such an influence on their environment? But now that we resurface, we might wonder: Why does it matter to us? As you can see, there are a lot of chemical reactions going on. And the water that is passing through the oceanic crust is in permanent exchange with the water of the oceans. This means that the organisms in the crust that are influencing the chemistry of the water underground also have an influence on the chemistry of the entire ocean! With that these organisms have an influence on different elemental cycles like nitrogen or carbon. But how important can that be? These tiny things, in a habitat so hostile, there can’t be many, am I right? No! Estimates say that about 15% of all biomass on Earth is in the deep subsurface [7]. There are more cells in the oceanic sediment alone than stars in the universe [8][9]! The amount of deep life is therefore quite considerate and we need to understand them better.

Figure 5 – A sedimentary core – one of many that are lying in the 4°C cold core storage at MARUM

That is why we, at the MARUM – Center for marine environmental sciences, made it our task to not only investigate the ocean but also look below the seafloor.

And what helps us with this is one of the largest drill core repositories, located right here in Bremen – The Bremen Core Repository. There are about 192 km of drill cores stored, most of them from the Atlantic Ocean. The oldest one dating back to the very beginning of scientific oceanic drilling in the 1960s! You don’t believe me? Then come and see for yourself and discover the hidden world underneath the ocean floor: https://www.marum.de/en/Fuehrungen.html.

List of figures:

Figure 1: Created with AI image generator https://deepai.org/machine-learning-model/text2img , January 29, 2025

Figure 2: © MARUM − Center for Marine Environmental Sciences, University of Bremen; V. Diekamp

Figure 3: Krohn, JMS (2024). Investigation of fungal growth and its influence on the permeability of the oceanic crust-Method Development using Penicillium Rubens (Master’s thesis, The University of Bergen).

Figure 4: Krohn, JMS (2024). Investigation of fungal growth and its influence on the permeability of the oceanic crust-Method Development using Penicillium Rubens (Master’s thesis, The University of Bergen).

Figure 5: © MARUM − Center for Marine Environmental Sciences, University of Bremen; V. Diekamp

 References:

[1] Inagaki, F., Hinrichs, KU, Kubo, Y., Bowles, MW, Heuer, VB, Hong, WL, … & Yamada, Y. (2015). Exploring deep microbial life in coal-bearing sediment down to ~ 2.5 km below the ocean floor. Science, 349(6246), 420‑424.

[2] Orcutt, BN, Sylvan, JB, Knab, NJ, & Edwards, KJ (2011). Microbial ecology of the dark ocean above, at, and below the seafloor.  Microbiology and molecular biology reviews ,  75 (2), 361-422.

[3] Smith, AR, Kieft, B., Mueller, R., Fisk, MR, Mason, OU, Popa, R., & Colwell, FS (2019). Carbon fixation and energy metabolisms of a subseafloor olivine biofilm.  The ISME Journal ,  13 (7), 1737‑1749.

[4] Li, L., Wing, BA, Bui, TH, McDermott, JM, Slater, GF, Wei, S., … & Lollar, BS (2016). Sulfur mass-independent fractionation in subsurface fracture waters indicates a long-standing sulfur cycle in Precambrian rocks. Nature Communications ,  7 (1), 13252.

[5] Dong, H. (2012). Clay–microbe interactions and implications for environmental mitigation.  Elements ,  8 (2), 113-118.

[6] Dasgupta, S., Peng, X., & Ta, K. (2021). Interaction between microbes, minerals, and fluids in deep-sea hydrothermal systems.  Minerals ,  11 (12), 1324.

[7] Bar-On, YM, Phillips, R., & Milo, R. (2018). The biomass distribution on Earth.  Proceedings of the National Academy of Sciences ,  115 (25), 6506-6511.

[8] Kallmeyer, J., Pockalny, R., Adhikari, RR, Smith, DC, & D’Hondt, S. (2012). Global distribution of microbial abundance and biomass in subseafloor sediment.  Proceedings of the National Academy of Sciences ,  109 (40), 16213-16216.

[9] Manojlović, LM (2015). Photometry-based estimation of the total number of stars in the Universe.  Applied Optics ,  54 (21), 6589‑6591.