Carbon Cycling in the Deep Biosphere

A multidisciplinary team of researchers studied Fennoscandian Shield field sites in Finland, looking for signs of abiotic and biotic carbon cycling, as well as residence times, in deep fracture fluids.

Understanding the origins and cycling of methane on Earth is a key area of investigation. Since methane can serve as a source of energy for the deep biosphere, research in this area links DCO’s Deep Energy and Deep Life Communities. Precambrian crystalline shields are among the most intriguing environments for methane occurrences because they consist of rocks formed at high temperature and pressure, which are generally carbon poor. A multidisciplinary team of hydrogeochemists from the Geological Survey of Finland (GTK) and microbiologists from VTT Technical Research Center of Finland has studied Fennoscandian Shield field sites in Finland, looking for signs of abiotic and biotic carbon cycling, as well as residence times, in deep fracture fluids.

In a suite of publications, DCO scientists Riikka Kietäväinen, Lotta Purkamo, Malin Bomberg, and colleagues analyzed groundwater from the Outokumpu Deep Drill Hole, a 2.5km borehole that is the deepest in Finland. Based on isotopic analysis of the water and the noble gases trapped in it, the team found that the groundwater at this site is tens of millions of years old [1,2]. 

”Noble gas residence times of up to 58 Ma make this one of the oldest known ecosystems on Earth, as the microbial communities in these isolated environments are likely as old as the liquid in which they are living,” said GTK’s research scientist Riikka Kietäväinen.

To analyze the microbes living in this ancient water, the team used molecular biological analyses based on marker genes. They did not detect communities using autotrophic carbon fixation; however they observed heterotrophic carbon assimilation by clostridia at various depths. Additionally, they identified both methane-producing and methane-oxidizing microbial communities [3].

“We concluded that the carbon for heterotrophic microbial metabolism could originate either from serpentinization of surrounding ophiolitic rocks or recalcitrant ancient organic carbon molecules remaining in the black schist interlayers in the Outokumpu bedrock. This work links the goals of both the Deep Energy and Deep Life Communities within DCO,” said research scientist Lotta Purkamo from VTT.

“In another site in SW Finland, Olkiluoto, we showed by RNA-targeted HTP amplicon sequencing that the active microbial communities in different bedrock fracture zones differed in regards to groundwater layer, i.e. sulphate-rich, methane-rich or the mixing phase (sulphate-methane transition zone; SMTZ) in between. In sulphate-rich and SMTZ water epsilonproteobacteria were most common, whereas in methane-rich water Pseudomonas dominated. ANME-2D were the dominant archaea” VTT’s senior scientist Malin Bomberg added [4].

The study continued with thorough HTP sequencing using the HiSeq platform as a part of DCO’s Census of Deep Life (CoDL) sequencing effort. The team found that the bacterial and archaeal diversity in the fracture waters was higher than expected, with 651 bacterial and 81 archaeal genera identified throughout the depth profile of 296 m to 798 m below ground level. This work defined specific communities corresponding to different geochemical parameters and, for the first time, estimated the metabolic pathways in the deep subsurface microbial communities of Olkiluoto [5].

A global assessment of the origins, sources, and cycling of abiotic and biotic methane shows that despite similarities in geochemistry and microbial community composition between different continental sites, the variation in isotopic composition of methane is difficult to explain. However, methanogens in these environments appear similarly distributed based on their preferred carbon metabolism. For example, hydrogenotrophic methanogens thrive in deeper parts of the crust, while aceticlastic methanogens are more common at shallower depths. Furthermore, methanotrophic microbes typically occur above 1 km [6].

But the story doesn’t end here. The team continues both microbiological and geochemical research at several sites within the Fennoscandian Shield. An upcoming project “DeepHotMicrobe” will address the limits of life in ultra-deep bedrock in Finland. Purkamo and colleagues will study the microbial ecology of hot formation fluids from depths down to 7 km. They will use these samples to probe the adaptations in microbial communities in isolated fractures to understand the environmental factors affecting the habitability of deep crystalline bedrock. Follow the project on Twitter and Facebook.  


Article based on a press release from the Geological Survey of Finland (link).

DCO researchers in the news (Finnish).

Images: Upper left: Outokumpu deep drill site in winter. The drill hole hides inside the "doghouse" field laboratory at the back. Credit: Ilmo Kukkonen/GTK Lower right: Riikka Kietäväinen taking microbiological samples at the field laboratory in Outokumpu in a glove-box with nitrogen atmosphere. Credit: VTT/GTK

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