Euendolithic Cyanobacteria

Insights into the world of euendolithic cyanobacteria.

There are several classes of endolithic organisms: euendoliths actively carve out or bore into mineral material, chasmoendoliths live in the crevices and cracks of mineral material, cryptoendoliths live within structural cavities of porous rock inluding previously excavated now vacant euendolithic dwellings.

Our research focuses on euendolithic organisms which bore into calcium carbonate containing minerals. Carbonate minerals like calcite or dolomite, and other carbonates like dead coral, carbonate sand, marble sculptures, fountains or even concrete represent some of the preferred substrates for euendolithic microbes. The reasoning behind the evolution of this particular lifestyle is poorly understood but we believe that by choosing this niche they improve their chances of survival, and consequently play both friend and foe in the environment taking an important role in the rock cycle (via bioerosive forces), and sometimes accelerating the deterioration time of monuments made of carbonates.

Autofluorescence test

Cyanobacteria are photoautotrophs which utilize the sun’s radiant energy to ultimately produce glucose which is then respired to produce ATP. The stars of our research are the true endoliths or “euendoliths” that actually dissolve the rock matrix, boring into the substrate and making a tunnel where the cells spend their life. This biogenic destruction of carbonates contributes to erosion and the transformation of the mineral matrix into microcrystalline carbonate or micrite. The process is not always negative; in some microbial communities like in the case of stromatolites the micritization actually contributes to the growth of these structures by cementing sediments together, providing support. This micrite layer often encases the organism which can lead to microfossil formation. The fascinating thing about these boring microbes is that we do not really know how they do it.

test BD-TH

Some researchers have suggested various mechanisms including mechanical destruction, symbiosis with heterotrophs, dissolution by acid secretion, and active transport of metal ions by ATP driven pumps, the later being our proposed mechanism of action.
Our current model organism, Mastigocoleus testarum strain BC008, is a marine cyanobacteria isolated from the coast of Cabo Rojo, a coastal town on the island of Puerto Rico. This particular microbe dissolves calcium carbonate by a mechanism that is not well understood and is the topic of our groups research. We hypothesize boring is mediated by a series of ATP-driven calcium pumps as well as calcium channels (García-Pichel, 2006). Our experimental approach includes using calcium-sensitive fluorescent dyes like Calcium Green 5N and confocal microscopy to try to image the dissolution of calcite (crystalline calcium carbonate) in situ. Other techniques include the use of calcium pump blockers to evaluate the effect on the boring activity, as well as measuring boring activity in minerals other than calcite. We are also interested in the genetics behind carbonate boring and will be utilizing high throughput RNA-seq in an attempt to identify transcripts putatively involved in carbonate boring.

Mechanisms of Carbonate Dissolution by Cyanobacteria.

Among the many interactions between biology and geology, the formation and subsequent destruction of carbonates stands as one of the most conspicuous and widespread. At the microscale one can go from calcification in biofilms to the accretion of coralline atolls. Historically biogenic carbonate precipitation has received the most attention, but its dissolution can also be mediated by organisms, and by microorganisms in particular. Fungi, microalgae and cyanobacteria that actively bore into calcareous substrates have been known for more than a century, and have been leaving fossils and trace fossils since the Precambrian. These organisms are fairly ubiquitious in both marine and fresh water ecosystems as well as in many terrestrial envronments. The mechanisms by which many of these euendolithic organisms bore into carbonate substrates has been studied predominately in fungi and microalgae. The boring mechanistics of euendolithic cyanobacteria are largely unknown but our lab has recently developed a model system to study cyanobacterial euendolithic carbonate boring in the laboratory.

Colonies of Hyella sp. growing on marine carbonates.

Colonies of Hyella sp. growing on marine carbonates.

Biogenic carbonate precipitation has received the most attention, but its dissolution can also be mediated by organisms, and by microorganisms in particular. Fungi, microalgae and cyanobacteria that actively bore into calcareous substrates have been known for more than a century, and have been leaving fossils and trace fossils since the Precambrian. These boring microorganisms are centrally implicated in a variety of geological phenomena, ranging from the erosive morphogenesis of coastal limestones, the destruction of coral reefs, the reworking of carbonaceous sands and the cementation of stromatolites. But for all their significance, the mechanism by which they can excavate carbonates in a controlled manner remains to be studied. The most common hypothesis as to their action mechanisms has been that they dissolve limestone by excretion of acids. However, we contend that, in the case of photosynthetic organisms like cyanobacteria, their activity constitutes an apparent paradox, since the dissolution of carbonates runs contrary to the well-known geomicrobial effects of oxygenic photosynthetic metabolism, which will tend to make the surrounding medium alkaline and therefore promote calcification, not carbonate dissolution. We will test three alternative models than can explain cyanobacterial boring and still be consistent with thermodynamic, physiological and mineralogical constraints. Two models are based on the separation of photosynthetic and respiratory activities (either temporally or spatially). The third model is based on localized and directed cellular calcium transport. We will undertake a three-tiered experimental approach using cultivated microorganisms and well characterized mineral substrates that should offer evidence regarding the validity of each of these models.

We are currently using: a) long-term monitoring of the rates of growth and boring with manipulations of various environmental parameters, b) short- term studies of microscale mass transfer in actively boring systems, including the effects of specific inhibitors, using microsensors, and c) advance microscopy studies of active mineral /microbe systems that offer both visual and micro-chemical information: laser scanning confocal microscopy using extracellular and intracellular calcium fluorophores, fluorescent localization, and secondary ion mass spectroscopy (SIMS).


García-Pichel, F. Ramirez-Reinat, E. Gao, Q., 2010. Microbial excavation of solid carbonates powered by P-type ATPase-mediated transcellular Ca2+ transport. Proc. Natl. Acad. Sci. U.S.A. 107:21749-21754.

García-Pichel, F., 2006. Plausible mechanisms for the boring on carbonates by microbial phototrophs. Sedimentary Geology 185 (2006) 205-213

See also an example of past microborers.