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New Species of Cyanobacteria Forms Intracellular Carbonates Print

A new species of cyanobacteria—photosynthetic bacteria that occupy a wide array of habitats—was discovered in the Mexican Lake of Alchichica where massive carbonate rocks form. Cyanobacteria have been impacting the global carbon cycle of the Earth for more than 2.3 billion years by assimilating CO2 into organic compounds and triggering calcium carbonate (CaCO3) precipitation. Despite the importance of this cyanobacteria-mediated CaCO3 biomineralization, the mechanistic details of this process are still poorly understood. Scientists agree that calcification in cyanobacteria is an extracellular process: Photosynthesizing cells commonly export the photosynthesis byproduct CO32- outside their cells where it bonds with an alkaline earth metal like Ca2+. The cyanobacteria recently found in Lake Alchichica, however, forms amorphous Ca-, Mg-, Sr- and Ba-rich carbonates intracellularly. This discovery significantly modifies the traditional view of how bacteria induce CaCO3 precipitation and may improve understanding of the fossil record by hinting at ancient traces of life in rocks, or designing new routes for sequestering CO2 or 90Sr in minerals.

Unraveling the
Precambrian Enigma

The exact timing of cyanobacteria appearance is still debated, but there is a consensus on an age older than 2.3 billion years, since that is approximately when O2 began to appear in the Earth’s atmosphere. Yet the oldest fossils yielding undisputed traces of extracellularly-calcified cyanobacteria are dated at only 750–700 million years. The huge difference in timing between the oldest cyanobacteria and the oldest microfossils of calcified cyanobacteria has been called the “Precambrian Enigma.”

Interestingly, Gm. lithophora was identified by molecular methods as a member of a deeply phylogenetically divergent order, whichdiverged from other cyanobacterial orders several billion years ago. Gm. lithophora suggests that ancestral cyanobacteria living from 2.3 billion to 750 million years ago may have formed carbonates intracellularly and not extracellularly as previously thought. If ancient cyanobacteria created internal carbonates rather than external precipitates, cells may not have been entombed within mineral shells, and so calcified cyanobacteria microfossils may not have formed, explaining the Precambrian Enigma! To challenge this hypothesis, there is now a crucial need to understand further how Gm. lithophora forms intracellular carbonates and what makes this species different from other, modern cyanobacteria.

The new species of cyanobacteria is named Candidatus Gloeomargarita lithophora (gloeo means glutinous, margarita means pearl, and lithophora means “bearing stones”). The team of scientists that discovered this species found that mineral inclusions can compose up to 6% of the total cell volume of Gm. lithophora, increasing cell density by approximately 12%. This extra weight may help to weigh down the microorganisms, which live on rock substrates.

Scanning electron microscopy image of two intracellularly calcifying cyanobacterial cells.  Ca-, Mg-, Sr- and Ba-carbonate inclusions appear as bright spheres. Cells are deposited on a filter with 200-nm wide pores. Scale bar is 1 micron.

Researchers performed a combination of microscopies, including soft x-ray scanning transmission x-ray microscopy (STXM), on ALS Beamlines 11.0.2 and 5.3.2. When coupled with x-ray absorption near edge spectra (XANES) over a relatively extended range of energies (100–2000 eV), the STXM provided key chemical speciation–sensitive images at a spatial resolution better than 25 nm. The soft x-ray STXM enabled characterization of the type (i.e., coordination and/or reduction-oxidation state) of carbon composing the cells, the carbonates’ inclusions could be identified based on XANES spectroscopy at the C K-edge, and the speciation of calcium was based on the Ca L2,3-edges.

Spectromicroscopy of carbon and calcium in Gm. lithophora cultures. Left: composite image showing the distribution of Ca-rich carbonate inclusions within the bacterial cells. The distribution of inclusions was assessed based on the spectral differences between the material composing the cells and the Ca-carbonate inclusions at the C K-edge and the Ca L2,3-edges. Right: XANES spectra at the C K-edge and the Ca L2,3 edges of the carbonate inclusions and the cells.

Surprisingly, intracellular inclusions formed by Gm. lithophora are amorphous by electron diffraction and have a very different stoichiometry from the minerals forming outside the cells: for example, (Sr1Ba2.7Mg1.4Ca0.9)Ca6Mg(CO3)13 for intracellular inclusions vs.  Mg5(CO3)4(OH)2•4(H2O) or CaCO3 for extracellular well-crystallized minerals. This intracellular chemistry represents a 90-fold and 1370-fold increase, respectively, in inclusion Sr/Ca and Ba/Ca ratios as compared to the extracellular solution, suggesting the existence of an unknown biological mechanism concentrating Sr and Ba.

These alkaline earth elements usually have similar chemical behavior, which can make them difficult to separate. This could be useful, for example, in isolating 90Sr contamination after a nuclear accident. It seems that Gm. lithophora have developed a mechanism that allows them to separate Sr from Ca. Studying it will be of interest for designing remediation strategies for such pollutants.

Phylogenetic analyses place this new species within the deeply divergent order Gleobacterales, a branch that diverged genetically from modern cyanobacteria a long, long time ago. If Gm. lithophora is a representative of these ancestral cyanobacteria, this process of intracellular carbonate formation could help explain the gap in their fossil record (read the sidebar for the full story).

Not only is Gm. lithophora the first observed cyanobacteria to form intracellular carbonates, it is also only the second group of bacteria found to control mineral formation. Commonly viewed as a eucaryotic ability, controlling the formation of mineral materials (such as bones, teeth, and shells) has only been observed in one other bacterial system: bacteria forming intracellular magnetites, which are nanomagnets. This research provides a new example.



Research conducted by: E. Couradeau, K. Benzerara, E. Gérard, D. Moreira and P. López-García (CNRS, France), S. Bernard, G.E. Brown Jr. (Stanford University and SLAC National Accelerator Laboratory).

Research funding: CNRS interdisciplinary program “Environnements planétaires et origines de la vie” and Institut National des Sciences de l’Univers (INSU) program “InteractionsTerre/Vie."Operation of the ALS is supported by the U.S. Department of Energy, Office of Basic Energy Sciences.

Publications about this research:

E. Couradeau, K. Benzerara, E. Gérard, D. Moreira, S. Bernard, G.E. Brown Jr., and P. López-García, “An Early-Branching Microbialite Cyanobacterium Forms Intracellular Carbonates,” Science 336, 459 (2012).

R. Riding, "A Hard Life for Cyanobacteria," Science 336, 427 (2012).

ALS Science Highlight #262


ALSNews Vol. 338