What is eating my rocks? A possible novel biological niche inside limestone

No comments

“It seems something biological has once lived inside rocks in Namibia.” With this rather cryptic statement, my husband, whose name is Cees Passchier, had my full attention. He is a geology professor at the University of Mainz, and one of his main research areas is Namibia, where he studies the remaining evidence of tectonic movements that once led to the formation of the supercontinent Gondwana. With decades of field experience, he has always kept an open mind to any features that he considers ‘unusual’. What he had stumbled upon in some marbles from Namibia was unusual, indeed.

He showed me some samples of rocks that contained multiple parallel hollow tubes, 2 to 3 cm long and with a width of about half a millimetre, that were aligned in what appeared on the rock surface as long bands. In reality, these tubes were arranged in a plane, which became apparent when rock samples were cut (Figure 1). No geological process is known that could be responsible for the formation of these tubes, which raised the hypothesis that something ‘biological’ had been active.

These initial observations led to a small research project that we pursued on and off for several years without funding, with some generous help from colleagues from the University of Mainz, Germany. The sampled rocks originated from a desert area in Namibia that in the past had experienced periods with a much more humid climate. The hollow tubes that were present in many marbles and limestone, and were later discovered in carbonate rocks in Oman and Saudi Arabia as well, were obviously ancient, possibly being formed millions of years ago, judging from the heavy erosion that had exposed them.

During the next few years, we collected some amazing data but were left with more questions than answers. One thing was clear, though: these tubes, which we called ‘micro-burrows’, had most likely been formed as a result of biological activity in a distant past. The nature of the organisms responsible remains unknown to date. Despite the lack of any definite answers, we decided to publish our findings, so that other scientists can eventually pursue new research objectives to discover what is behind this strange phenomenon.

Source: T Wassenaar. Reproduced from Subfossil Fracture-Related Euendolithic Micro-burrows in Marble and Limestone with permission from the author.

Micro-burrows in Namibia. (A): micro-burrows appear from under a broken slab of marble. Their presence has accelerated erosion, as is visible on the right-hand side of the photo. (B) close-up of the micro-burrows in panel A, viewed from the side. (C): three-dimensional scheme showing how micro-burrows form from a fracture inside a rock (D): the original sedimentary banding pattern of the rock is still visible in the walls separating micro-burrows. (E): two examples of freshly cut rocks show the white filling of micro-burrows, which in this case formed at an angle to the blue and white rock layering. The fracture above the micro-burrows, from which they originated, is also partially filled with white material.

Marbles are mainly made of calcium carbonate with some magnesium carbonate. They are formed from marine sediments when dissolved carbonate precipitates, by biological or non-biological processes, to form limestone. Under high temperature and pressure, limestone recrystallizes and this results in marble. Limestones and marbles often contain impurities in the form of other minerals or organic material, and only in the absence of such impurities is marble completely white. More often, it is grey, brown or blue shaded, commonly with banding patterns being visible (Fig. 1D, E). Any organic material present in the original marine sediments will have been heavily degraded by the heat and pressure that recrystallized the marble.

To live between a rock and a hard place

The surface of rocks is a common niche for microorganisms to grow on, and the weathering of limestones can be accelerated by biological surface pitting. However, such pits don’t penetrate deeper than a few millimetres and are caused by growth on the surface of rocks only. Some communities of microorganisms can assist in the formation of novel structures in rock fissures, collectively described as endostromatolites. In the research area in Namibia, there were plentiful fossilized remains of what communities of such ‘rock builders’ had deposited. Their structures were highly variable, and to describe all those morphologies would be a study in itself. But the discovered micro-burrows inside the rocks were not the result of ‘rock builders’, because here, rock material had been removed. These holes were the result of ‘rock boring’. One could tell, as the original banding that was present in the marbles remains visible in the walls dividing the holes. More importantly, they had not formed on the surface of a rock, but appeared inside the rock, only to come to the surface as a result of erosion.

Upon close inspection, it became clear that these micro-burrows were not hollow: they were filled with white material that turned out to be small crystals of pure calcium carbonate, which geologists call micrite. This white filling was only loosely attached to the inner walls of the micro-burrows and was frequently lost when rocks were eroded, cut, or polished. Another striking observation was that the bands of micro-burrows, which in situ grew downwards, started from what seemed to have been fractures in the rocks. This is a significant finding, as fractures can transport water and allow the entry of microorganisms into what would otherwise be an unattainable habitat. Frequently, such fractures were now also filled with micrite, apparently spilled over from the micro-burrows.

Source: N. Groschopf and C Passchier. Reproduced from Subfossil Fracture-Related Euendolithic Micro-burrows in Marble and Limestone with permission from the author.

Electron-microprobe analysis of three micro-burrows in cross-section. Enrichment for Mg, P, and S is visible at the border of the micro-burrow and the surrounding rock. The white filling inside the micro-burrow is not attached to the rock wall, as shown in the top two electron micrographs at the right. At the bottom left, an enlargement of the rim shown in the series above it illustrates the presence of growth rings of approximately 1 µm width. The bottom right shows the micro-burrows from the same rock sample under reflected light microscopy.

Electron-microprobe analysis (illustrated by examples in Figure 2) revealed an enrichment of P and S and, in some case,s Mg, located at the inner walls of the micro-burrows, while the micrite only showed enrichment of Mg (Ca could not be analysed as it is the internal standard in this methodology). In some examples, the enriched P and S were visible as thin growth rings of approximately one micrometer thickness. Some layering of the micrite was also observed with Mg, more towards the rim of the filling than in the middle. In all, these observations suggested a kind of radial growth filling up the growing micro-burrow, while the actual growth took place at the interface of the micro-burrow inner rock wall and the micrite.

The inner micro-burrow walls were fluorescent, which indicates that biomolecules (or parts thereof) are still present. Raman analysis confirmed the presence of organic carbonaceous material here, whose nature could not be further determined. Stable isotope analysis revealed that the surrounding, unaffected marble rock had a different ratio of d¹³C and d¹⁸O compared to the white filling of the micro-burrows. All these observations, described in detail in the original publication, pointed towards a microbiological origin. But what had grown inside these rocks? And what did they feed on?

Current hypotheses and (rather wild) speculations

One possible explanation is that the micro-burrows were formed by hyphae of a fungal mycelium that penetrated the rocks through the fractures. However, that would not explain the deposition of the micrite in their middle. Moreover, hyphae typically have the thickness of one (eukaryotic) cell, which wouldn’t account for a diameter of approximately 0.5 mm. Neither individual hyphae nor bundles of them would form the radial growth patterns that we observed. For these reasons, it is unlikely that fungal hyphae had formed the micro-burrows, though that explanation is not yet ruled out.

The current hypothesis is that microorganisms entered the rock through fissure water and started to form colonies that, at first, fed on the nutrients in the fissure water. Nutrients also eluted out of the neighbouring rock. When this became limited, the colonies started to grow downwards into the rock, apparently at an even distance from each other, possibly as a result of competition for nutrients. This downward growth was enabled by dissolving the calcium carbonate and extracting the valuable nutrients. Any unused calcium carbonate would be secreted, which would explain the formation of the micrite filling they left behind. Growth could continue in a radial direction (depositing micrite in the middle of the formed hollow tube) until any nutrients in the neighbouring rock were depleted, after which the only direction of growth was downwards, deeper inside the rock.

This model depends on a certain level of cellular organisation, as the colony would have to grow radially and then downwards, depositing the calcium in the opposite direction of growth.

”The big question is, where these organisms got their energy from?”

Nutrients must provide all essential elements, but an energy source and a suitable electron donor (reducing power) are also required for life. Apart from Ca, C, H, O and Mg present in carbonate, life also depends on the presence of P, N, S, and, in lower amounts, Cl, K, Na, Se, Zn, Fe, Mn, Cu, Co, Ni, and Mo. During anabolism, microorganisms must reduce oxygenated carbon to a less oxygenated state to produce the C-C, C-N, C-P, and other bonds that are present in biomolecules. Cyanobacteria and other phototrophs do this by means of the electrons generated by the photosynthetic reaction, together with the energy they harvest from sunlight, but they can only grow in light-exposed niches, not inside a rock. Lithotrophic bacteria use reduced metal ions as an electron donor, for instance, ferric iron (Fe³⁺) present in minerals such as pyrite, biotite, or hornblende, but these are notoriously absent in the marbles of Namibia, excluding canonical lithotrophs as culprits for micro-burrow formation. At present, the model does not explain the energy source or the reducing power that microorganisms need to grow inside a rock.

The exact nature of these proposed microorganisms thus remains obscure. Whether nucleic acids remain present in rocks of this age needs to be investigated. Proteins can be more persistent, and if the dissolution and precipitation of calcium carbonate is essential in these life forms, calcium ion pumps must have been abundant, making it quite possible that their remains are still present. Whether analysis of nucleic acid or protein fragments will shed light on the nature of their possessors remains to be seen. Our team didn’t have access or funding for such analyses, but we would be happy to provide samples to researchers who would want to pursue this further.

What if these organisms were an entirely new life form, unlike the known biological Kingdoms? That is a wild speculation, although no organism that we know of can live inside limestone as the sole medium. If these organisms were an ‘unknown unknown’, being completely different from what we know of the biological world, their identification would be a real challenge, if a few short DNA or protein sequences were all we had to go on. Then their identification might be really complicated and challenging, but also extremely interesting.

Are these creatures still alive? Not in the deserts of Namibia, Oman, or Saudi Arabia, as far as we can tell. But who knows, inside limestones in wetter (tropical?) regions, something might currently slowly be eating away at those rocks, forming micro-burrows that are hidden from view. Now that we know this has likely happened in the past, we can start to look for living evidence of their presence. That discovery would be truly spectacular.

The data discussed in this feature was originally published by Passchier et al. Click here to read.