Refuting Creationism - Living Bacteria Sealed Inside 2 Billion-Year-Old Rock

Microbial cells stained green

© Y. Suzuki, S. J. Webb, M. Kouduka et al. 2024/ Microbial Ecology

2-billion-year-old rock home to living microbes | The University of Tokyo

The Bushveld Igneous Complex (BIC), South Africa.
This picture shows a very famous outcrop where nearly horizontal black and white layers are observed. The BIC made of layers of igneous rock in a basin shape, formed over a period of about 1 million years, after which it seems to have barely changed.

© Y. Suzuki.

In today's incidental rebuttal of creationist dogma, archaeologists have discovered living colonies of microbes sealed within cracks in 2-billion-year-old rocks from South Africa.

The microbes became sealed in the cracks by tightly-packed layers of clay so effectively creating sealed chambers from which nothing could escape and, more importantly, nothing could enter. They have survived over geological time by firstly having an extremely low metabolic rate, with a generation time measured in thousands, even millions of years, compared to surface-dwelling microbes with generation times in hours or minutes, and by utilising sulphates as their energy source.

What they demonstrate, apart from the fallacy of Earth only being made by magic 10,000 years ago, is that in a highly stable environment, a plentiful source of energy and the ability to recycle their dead with almost no loss of energy, there is no environmental pressure to evolve, so the microbes have remained virtually unchanged for hundreds of millions, even billions of years.

Tell me about bacteria that can live on sulphates and exists sealed inside ancient rocks, please. Microbes that live on sulphates and exist sealed inside ancient rocks are examples of extremophiles, specifically sulfate-reducing microorganisms. These microbes thrive in environments with limited oxygen and utilize sulfate (SO₄^2-) as their terminal electron acceptor in anaerobic respiration. This process is critical for their survival in nutrient-scarce and isolated environments, such as deep subsurface rocks and sediments.

Key Characteristics:

1. Sulfate Reduction Process:
   • Sulfate-reducing microbes metabolize organic matter or hydrogen by reducing sulfate to hydrogen sulfide (H₂S). This process releases energy that sustains the microbes in the absence of oxygen.
   • In anaerobic environments, they help in the recycling of nutrients and contribute to the biogeochemical sulfur cycle.
   
   
2. Habitat:
   • Subsurface and Ancient Rocks: These microorganisms are found in extreme environments such as deep-sea hydrothermal vents, deep underground aquifers, and inside ancient rocks that are isolated from external environments.
   • Deep Biosphere: Some sulfate-reducing bacteria have been discovered in ancient rocks over 2 billion years old, buried kilometers beneath the Earth's surface. These environments are thought to have been sealed for millions of years, and the microbes survive on minimal energy resources.
   • Mars Analogues: The presence of such microbes in extreme environments on Earth leads scientists to hypothesize that similar life forms could potentially exist on Mars or other celestial bodies.
   
   
3. Notable Examples:
   • Desulfovibrio: A genus of bacteria that is often found in environments where oxygen is absent, thriving on the reduction of sulfate.
   • Archaeal Extremophiles: Certain archaea can survive in subsurface environments, and some are known to use sulfate reduction as their energy mechanism.
   
   
4. Survival in Sealed Environments:
   • These microbes can survive for extremely long periods by entering a state of metabolic dormancy, relying on slow metabolic processes.
   • Their energy sources may come from trapped organic compounds in rocks or the breakdown of minerals, providing just enough fuel for survival.
   
   
5. Relevance to Geobiology:
   • The discovery of these sulfate-reducing microbes in ancient rocks has profound implications for understanding the limits of life on Earth, particularly in extreme, isolated environments.
   • They also play a role in the study of biogeochemistry, especially the sulfur cycle, and their ability to survive in the deep biosphere is a key area of research in astrobiology.

These ancient, rock-dwelling microbes highlight the remarkable adaptability of life and its capacity to endure even in the most inhospitable conditions.

I assume the age of the bacterial colonies is determined by the age of the sealant, not the rock?

Yes, you're correct! The age of bacterial colonies in these environments is generally determined by the age of the sealant or the point at which the microbes became trapped and isolated, not necessarily by the age of the rock itself.

Here's how this works:

1. Rock Formation vs. Isolation Event:
   • Rock Formation: The rocks may be ancient, sometimes billions of years old, but the microbes didn’t necessarily get trapped during the initial formation of the rock.
   • Sealant Formation: The critical event for the microbes is when the rock becomes sealed off from the surrounding environment, such as when fractures or porous spaces within the rock are filled with impermeable materials like clay, minerals, or other sediments. This sealing process traps the microbes in an isolated environment.
   
   
2. Dating the Isolation:
   • The age of the microbial colony is typically estimated by dating the material that created the seal or by dating the event that isolated the habitat from the external environment. For instance, if minerals like clay or crystalline deposits seal off the cracks in the rock, the formation of those minerals can be dated using radiometric dating techniques.
   • In some cases, isotopic analysis of the trapped fluids or gases (e.g., noble gas dating) can also provide clues about when the environment became sealed and how long the microbes have been isolated.
   
   
3. Microbial Dormancy:
   • Once sealed, the microbes can enter a state of dormancy or survive on minimal energy, relying on the extremely slow turnover of available nutrients. The fact that they may remain viable for such long periods is a testament to their resilience, not necessarily that they were present since the rock’s formation.
   
   
4. Relevant Example:
   • Some microbes discovered in ancient subsurface environments have been dated to millions of years based on the age of the sealant that isolated them. For example, in deep-sea hydrothermal systems, the microbes may have been trapped during the formation of mineral deposits around the vents, and their age is linked to the event that sealed them inside the rock, not the rock's initial creation.

In summary, the age of the microbial colonies is typically linked to the timing of when they became trapped in the sealed environment, not the much older age of the rock itself.

This particular discovery was made by scientists from Japan, Germany and South Africa led by Associate Professor Yohey Suzuki, of the Department of Earth and Planetary Science, The University of Tokyo, Tokyo, Japan.

They have just published their findings, open access in the journalMicrobial Archaeology

2-billion-year-old rock home to living microbes

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New research could help us understand very early life on Earth and the hunt for evidence of life on Mars

Pockets of microbes have been found living within a sealed fracture in 2-billion-year-old rock. The rock was excavated from the Bushveld Igneous Complex in South Africa, an area known for its rich ore deposits. This is the oldest example of living microbes being found within ancient rock so far discovered. The team involved in the study built on its previous work to perfect a technique involving three types of imaging – infrared spectroscopy, electron microscopy and fluorescent microscopy – to confirm that the microbes were indigenous to the ancient core sample and not caused by contamination during the retrieval and study process. Research on these microbes could help us better understand the very early evolution of life, as well as the search for extraterrestrial life in similarly aged rock samples brought back from Mars.

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Deep in the earth lies something ancient and alive. Colonies of microbes live in rocks far beneath the surface, somehow managing to survive for thousands, even millions of years. These tiny, resilient organisms appear to live life at a slower pace, scarcely evolving over geological time spans and so offering us a chance to peek back in time. Now, researchers have found living microbes in a rock sample dated to be 2 billion years old.

Drill core sample with opened fractures.
This picture was taken on site when the drill core sample was washed, flamed and then cracked. The 30-centimeter-long, 85-millimeter-diameter core was taken back to Japan for further study.

© Y. Suzuki.

We didn’t know if 2-billion-year-old rocks were habitable. Until now, the oldest geological layer in which living microorganisms had been found was a 100-million-year-old deposit beneath the ocean floor, so this is a very exciting discovery. By studying the DNA and genomes of microbes like these, we may be able to understand the evolution of very early life on Earth.

Associate Professor Yohey Suzuki, lead author
Graduate School of Science
University of Tokyo, Tokyo, Japan.

The rock sample was taken from the Bushveld Igneous Complex (BIC), a rocky intrusion in northeastern South Africa which formed when magma slowly cooled below the Earth’s surface. The BIC covers an area of approximately 66,000 square kilometers (roughly the size of Ireland), varies in thickness by up to 9 km, and contains some of the richest ore deposits on Earth including about 70% of the world’s mined platinum.

Due to the way it was formed and minimal deformation or change occurring to it since then, the BIC is believed to have provided a stable habitat for ancient microbial life to continue until today.

With the aid of the International Continental Scientific Drilling Program, a nonprofit organization that funds exploration at geological sites, the team obtained a 30-centimeter-long rock core sample from about 15 meters belowground. The rock was cut into thin slices and analyzed, which is when the team discovered living microbial cells densely packed into cracks in the rock. Any gaps near these cracks were clogged with clay, making it impossible for the organisms to leave or for other things to enter.

The team built on a technique they had previously developed to confirm that the microbes were native to the rock sample, and not due to contamination during the drilling or examination process. By staining the DNA of the microbial cells and using infrared spectroscopy to look at the proteins in the microbes and surrounding clay, the researchers could confirm that the microorganisms were both alive and not contaminated.

I am very interested in the existence of subsurface microbes not only on Earth, but also the potential to find them on other planets. NASA’s Mars rover Perseverance is currently due to bring back rocks that are a similar age to those we used in this study. Finding microbial life in samples from Earth from 2 billion years ago and being able to accurately confirm their authenticity makes me excited for what we might be able to now find in samples from Mars.

Associate Professor Yohey Suzuki.

Publication:

Yohey Suzuki, Susan J. Webb, Mariko Kouduka, Hanae Kobayashi, Julio Castillo, Jens Kallmeyer, Kgabo Moganedi, Amy J. Allwright, Reiner Klemd, Frederick Roelofse, Mabatho Mapiloko, Stuart J. Hill, Lewis D. Ashwal, Robert B. Trumbull,
Subsurface Microbial Colonization at Mineral‐Filled Veins in 2‐Billion‐Year‐Old Mafic Rock from the Bushveld Igneous Complex, South Africa. Microbial Ecology: October 2, 2024, doi:10.1007/s00248-024-02434-8.

Abstract
Recent advances in subsurface microbiology have demonstrated the habitability of multi-million-year-old igneous rocks, despite the scarce energy supply from rock-water interactions. Given the minimal evolution coupled with exceedingly slow metabolic rates in subsurface ecosystems, spatiotemporally stable igneous rocks can sustain microbes over geological time scales. This study investigated a 2-billion-year-old mafic rock in the Bushveld Igneous Complex, South Africa, where ultradeep drilling is being executed by the International Continental Scientific Drilling Program (ICDP). New procedures were successfully developed to simultaneously detect indigenous and contaminant microbial cells in a drill core sample. Precision rock sectioning coupled with infrared, fluorescence, and electron microscopy imaging of the rock section with submicron resolution revealed microbial colonization in veins filled with clay minerals. The entry and exit of microbial cells in the veins are severely limited by tight packing with clay minerals, the formation of which supplies energy sources for long-term habitability. Further microbiological characterization of drilled rock cores from the Bushveld Igneous Complex will expand the understanding of microbial evolution in deep igneous rocks over 2 billion years.

Introduction
The terrestrial subsurface is defined by depths greater than 8 m from the ground surface, excluding soil [1], where a significant portion of the Earth’s prokaryotic biomass resides [2,3,4]. The metabolic activities of subsurface microbiomes are exceedingly slow under survival mode [5, 6], leading to an estimated turnover time ranging from several thousand to million years. Consistent with the long turnover time [7], sulfate-reducing bacteria Candidatus Desulforudis audaxviator endemic to the deep subsurface have undergone minimal evolution since 55–165 million years ago [8]. Similarly, minimal evolution over geological time scales has been demonstrated for deep subsurface archaeal lineages called Candidatus Altiarchaeota [9]. Based on the ecological and evolutionary features of subsurface microbiomes, it is hypothesized that microbes can be sustained with minimal evolution for billions of years in a geologically and tectonically stable subsurface environment [10].

The basement of the oceanic and continental crust is dominated by igneous rocks. Microbiological studies of the igneous basement have been intensively studied by sampling fluids from drilled boreholes [11]. In cases where collecting pristine fluid samples was technically difficult or impossible, drilled rock cores were used for microbiological characterization.

For example, in the Oman ophiolite complex, ~ 100-million-year-old (Ma) mantle peridotite was drilled by the International Continental Scientific Drilling Program (ICDP). To examine contamination, fluorescent microspheres were added to the drilling fluid and counted in the crushed and homogenized drill core samples [12]. Cells were separated from rock particles, and then DNA-stained cells with SYBR Green I were counted by flow cytometry [13]. The cell density was up to six orders of magnitude higher at fractures and veins (~ 10⁷ cells/g) than in the rock matrix (~ 10^1–2 cells/g) [12]. In another example, 100-million-year-old basaltic oceanic crust was drilled by the Integrated Ocean Drilling Program (IODP) in the South Pacific Gyre, using fluorescent microspheres in the drilling fluid for contamination control [14, 15]. In addition to contamination control using fluorescent microspheres and microbial cells extracted from the bulk rocks with ultra-low cell abundances, new visualization approaches were successfully developed to enumerate microbial cell densities at fractures and veins that exceeded 10¹⁰ cells/cm³ [14, 15].

This contribution extends the formation age of igneous rocks for microbiological investigations by targeting mafic and ultramafic rocks formed 2.05 billion years ago in the Bushveld Igneous Complex of northeastern South Africa, which is the largest mafic–ultramafic layered intrusion on Earth [16, 17]. The Bushveld Drilling Project of the ICDP is undertaking a 2.5-km-deep drill hole in the lower zone and base of the intrusion, where ultramafic rocks are expected to possess the chemical signature of the mantle endmember of mantle-crust mixing during magma emplacement [18, 19]. Following comparatively rapid cooling of the magma chamber [20], the layered rocks have experienced minimal deformation and metamorphic alteration, based on general geological features such as the very minor occurrence of metamorphic rocks and the nearly horizontal dip [21]. Thus, the Bushveld Igneous Complex is considered to provide a stable habitat for microbial life for > 2 billion years. Additionally, the Bushveld Igneous Complex is hosted in the Kaapvaal Craton where the devoid of significant modern tectonic activity might help the long-term preservation of fluids and habitable environments [22, 23, and references therein].

The long-term habitability of subsurface microbes has been studied in Precambrian cratons in Canada and South Africa where fluids and habitable environments have been preserved on a range of timescales from thousands to millions, to even billions of years [22, 23, and references therein]. In the previous studies, fracture waters were obtained from deep underground tunnels constructed at mines. In this study, the habitability of 2.05-billion-year-old igneous rocks was investigated through drilling from the ground surface rather than underground sampling of fracture waters. Alternatively, rock sampling is feasible at surface outcrops. However, the freshness of rocks is concerned, given that the rocks have experienced weathering.

This paper reports on the first subsurface rock sample obtained from the ICDP drilling used to test new approaches for the simultaneous visualization of microbial cells and fluorescent microspheres at fractures and veins. A new spectroscopic method was also applied to obtain diagnostic spectra from single microbial cells [24]. As a result, indigenous microbial cells locally distributed along clay-filled veins were detected.

Fig. 2

Microscopic inspection of the drill fluid sample. A 1000-fold magnification images of fluorescent microspheres and (B) microbial cells stained by SYBR Green I

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Fig. 3

Appearance of the studied drill core sample and visual inspection of drilling fluid contamination. Photos of the cleaned whole-round core sample before (A) and after opening fractures (B). Photos of a rock fragment collected for further analysis without (C) and with (D) UV light illumination. Photos of a fracture surface without (E) and with (F) UV light illumination. Yellow arrows in B and C point to the fracture, and yellow rectangle in E indicates the area shown in F

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Fig. 4

Characterization of a section from the fracture surface to the rock interior. A Photo of the section with a yellow arrow pointing to the fracture surface. B Microscopic image of a region of the section highlighted in a yellow rectangle in A. C Fluorescence microscopy image of the region highlighted by orange rectangle in B. Intensity maps of the section at 1000 cm⁻¹ (D), 1530 cm⁻¹ (E), and 1640 cm⁻¹ (F) obtained by optical photothermal infrared (O-PTIR) spectroscopy. The intensity maps were obtained from the area highlighted with a yellow square in B. G RGB color synthesis of the three intensity maps. A yellow rectangle in G indicates an area where the intensity maps for RGB color synthesis are obtained in Fig. 5A

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Fig. 5

Characterization of a vein-like region in a section. RGB color synthesis of the three intensity maps at 1000, 1530, and 1640 cm⁻¹ from areas highlighted by a yellow rectangle in Fig. 4G (A) and highlighted by an orange square in Fig. 5A (B). O-PTIR spectra from points 1 to 2 in A and from points 3 to 6 in B, cultured cells of Nanobdella aerobiophila strain MJ1^T (= JCM33616^T) and Metallosphaera sedula strain MJ1HA for an archaeal reference and Shewanella oneidensis strain MR-1.^T for a bacterial reference and smectite references of saponite, nontronite, and montmorillonite (C)

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Fig. 6

Visualization of microbial cells after SYBR Green I staining. A Fluorescence microscopic images of the large area from the section highlighted by an orange rectangle in Fig. 4B, and B the small area highlighted by a yellow rectangle in Fig. 5A. The yellow rectangle in A is the same as shown in Fig. 5A, and the orange square in B is the same as in Fig. 5B. Pink arrows in A point to the veins shown in Fig. 4

Suzuki, Y., Webb, S.J., Kouduka, M. et al. Subsurface Microbial Colonization at Mineral-Filled Veins in 2-Billion-Year-Old Mafic Rock from the Bushveld Igneous Complex, South Africa. Microb Ecol 87, 116 (2024). https://doi.org/10.1007/s00248-024-02434-8

Copyright: © 2024 The authors.
Published by [publisher]. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

The authors admit that more work is needed to determine the age of the veins in the rock and their sealing by clay - which will determine for how long the microbes have been isolated - but due to the nature of the rock and the extreme geological stability of the formation, this is likely to have been soon after the formation of the rock from volcanic lava 2 billion years ago. And being volcanic, it can be dated accurately using the highly accurate Uranium-Lead (U-Pb) geochronology that normally strikes terror in the mind of creationists.

And, as though it wasn't bad enough for creationism that microorganisms got locked inside these cracks in solidified volcanic lava, it all happened like almost everything else on Earth, in that long pre-Creation-Week period when 99,9975% of Earth history happened.

It seems almost superfluous therefore that the fact that isolated microbes in a highly stable environment remained almost unchanged for about 2 billion years, providing more evidence, if any were needed, that it is environmental change that drives evolution, just as the Theory of Evolution says. But no doubt there will be creationists who imagine they have another 'coelacanth' that by remaining 'unchanged' for tens of millions of years proves Earth is just 10,000 years old.

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