8 BACTERIAL BIOMINERALIZATION Kurt Konhauser1 and Robert Riding2 1Department of Earth & Atmospheric Sciences, University of Alberta, Edmonton, AB, T6G 2E3, Canada 2Department of Earth & Planetary Sciences, University of Tennessee, Knoxville, TN 37996, USA 8.1 Introduction 8.2 Mineral nucleation and growth A number of living organisms form mineral phases The thermodynamic principles underpinning biological through a process termed biomineralization. Two end mineral formation, irrespective of whether it is induced member mechanisms exist depending on the level of or controlled, are the same as those involved in inor- biological involvement. The first involves mineral ganic mineral formation. In all cases, before any solid formation without any apparent regulatory control. can precipitate, a certain amount of energy has to be Termed ‘biologically induced biomineralization’ by invested to form a new interface between the prospec- Lowenstam (1981), biominerals form as incidental by- tive mineral nucleus and both the aqueous solution and products of interactions between the organisms and the underlying substrate upon which it is formed. The their immediate environment. The minerals that form amount of energy required to do this can be viewed as through this passive process have crystal habits and an activation energy barrier. The standard free energy chemical compositions similar to those produced by (G0) of a solid is lower than that of its ionic constituents precipitation under inorganic conditions. By contrast, in solution, and if the activation energy barrier can be ‘biologically controlled biomineralization’, the subject overcome, the reaction proceeds towards mineral pre- of Chapter 10, is much more closely regulated, and cipitation. On the other hand, if the activation energy organisms precipitate minerals that serve physiologi- barrier is prohibitively high, metastable solutions per- cal and structural roles. This process can include the sist until either the barrier is reduced or the concentra- development of intracellular or epicellular organic tion of ions are diminished. matrices into which specific ions are actively intro- Mineral nucleation involves the spontaneous growth duced and their concentrations regulated such that of a number of nuclei that are large enough to resist appropriate mineral saturation states are achieved. rapid dissolution. Formation of these ‘critical nuclei’ Accordingly, minerals can be formed within the organ- requires a certain degree supersaturation wherein the ism even when conditions in the bulk solution are concentration of ions in solution exceeds the solubility thermodynamically unfavourable. In this chapter we product of the mineral phase (see Stumm and Morgan, focus on the role of bacteria. Specifically, we examine 1996, for details). Nucleation is termed homogeneous the formation of iron oxyhydroxides and calcium car- when critical nuclei form simply by random collisions of bonates throughout geological time, and explore how ions or atoms in a supersaturated solution. Such ‘pure’ our understanding of modern biomineralization pro- solutions, however, rarely exist; in nature, most solu- cesses is shedding new insights into the evolution of tions contain a wide variety of competing solid and dis- the Earth’s hydrosphere–atmosphere–biosphere over solved phases. In this regard, heterogeneous nucleation long time scales. occurs when critical nuclei form on those solid phases. Fundamentals of Geobiology, First Edition. Edited by Andrew H. Knoll, Donald E. Canfield and Kurt O. Konhauser. © 2012 Blackwell Publishing Ltd. Published 2012 by Blackwell Publishing Ltd. 105 KKnoll_c08.inddnoll_c08.indd 110505 22/16/2012/16/2012 11:22:59:22:59 AAMM 106 Fundamentals of Geobiology After critical nuclei are formed, continued addition of formation of magnetite on ferric hydroxide. At other ions is accompanied by a decrease in free energy, result- times, the reaction rates are immeasurably slow and the ing in mineral growth. This process goes on spontane- amorphous or metastable phases persist in sediments ously until the system reaches equilibrium. despite supersaturation with respect to more thermody- Mineral growth typically favours the initial formation namically stable minerals. Those phases can show little of amorphous solid phases that are characterized by discernible alteration for tens of millions of years until their high degree of hydration and solubility, and lack of pressure–temperature changes associated with burial intrinsic form (Nielson and Söhnel, 1971). Accordingly, cause the reaction sequence to advance to the next stage minerals such as amorphous silica (SiO2•nH2O), (Morse and Casey, 1988). For example, amorphous silica hydrated carbonate (CaCO3•H2O), or ferric hydroxide skeletons (such as diatoms) deposited onto the seafloor [Fe(OH)3] will nucleate readily if the solution composi- slowly dissolve at shallow depths and re-precipitate as tion exceeds their solubility. In contrast, their respective cristobalite, which remains stable to depths of hundreds crystalline equivalents, quartz (SiO2), calcite (CaCO3), of meters until it too transforms into quartz. and hematite (Fe2O3), have higher interfacial free ener- gies. Therefore, they nucleate slowly at ambient temper- 8.3 How bacteria facilitate biomineralization atures, even in the presence of substrates favouring heterogeneous nucleation. Often the transition between Bacteria contribute significantly to the development of amorphous and crystalline phases involves the precipi- extremely fine-grained (often <1 µm in diameter) min- tation of metastable phases. eral precipitates. All major mineral groups, whether The nucleation rate also affects the size of the critical metal oxyhydroxides, silicates, carbonates, phosphates, nuclei formed. At high ion activities, above the critical sulfates, sulfides, and even native metals, have been supersaturation value, new surface area is created shown to precipitate as a consequence of bacterial activ- mainly by the nucleation of many small grains ity. Although not directly associated with biologically characterized by high surface area to mass ratios, a controlled biomineralization, bacteria may influence the regime referred to as nucleation-controlled. At lower initial stages of mineralization in two significant ways: activities, surface area generation is crystal-growth controlled, with surface area increasing by the accretion of additional ions or atoms to existing grains. In a nucle- 8.3.1 Development of an ionized cell surface ation-controlled regime, the generation of new surfaces Bacterial surfaces are highly variable, but commonly they by nucleation occurs rapidly and causes the solution have a cell wall that is overlain by additional organic supersaturation to drop below the critical value needed layers, such as extracellular polymeric substances (EPS), for nucleation. This means that in nature, supersatura- sheaths and S-layers, which differ in terms of their tion above the critical value does not typically occur for hydration, composition and structure. In all cases, lengthy periods of time. For silica precipitation as an bacterial surfaces act as highly reactive interfaces. Organic example, if a concentrated silica solution were emitted ligands within the bacterial surface (such as carboxyl, from a hot spring vent, it would thermodynamically be hydroxyl, phosphoryl, sulfur and amine functional groups) supersaturated with regard to all silica phases, but deprotonate with increasing pH and thus impart the cells because amorphous silica has the lower interfacial free with a net negative surface charge (see Konhauser, 2007 energy it nucleates first despite quartz being the more for details). In its most simplistic form, deprotonation can stable phase with lower solubility. Then as amorphous be expressed by the following equilibrium reaction: silica nucleates it drives the dissolved silica concentra- tion down to its critical value below which quartz nuclei B−↔− AH B A−1+1 + H (8.1) formation is prohibitively slow. Crystalline minerals that would otherwise be difficult where B denotes a bacterium to which a protonated or impossible to nucleate directly at low temperatures ligand type, A, is attached. The distribution of proto- can circumvent activation energy barriers by making nated and deprotonated sites can be quantified with the use of the more soluble precursors as templates for their corresponding mass action equation: own growth. Once they begin to grow, the crystals −11+ increase in surface area, and in doing so, they drive the BA− H K = (8.2) proximal free ion concentration below the solubility of a []BAH− the amorphous precursor, causing it to dissolve (Steefel −1 and Van Cappellen, 1990). However, despite thermody- where Ka is the dissociation constant; [B-A ] and [B-AH] namics predicting the transformation sequence based represent the respective concentrations of exposed on energetics, they say nothing about the kinetics. deprotonated and protonated ligands on the bacterium Sometimes the reactions are relatively quick, such as the (in mol l−1); and [H+1] represents the activity of protons KKnoll_c08.inddnoll_c08.indd 110606 22/16/2012/16/2012 11:22:59:22:59 AAMM Bacterial Biomineralization 107 OH Net (+) charge Net (–) charge COO– OH OH OH PO– Fe OH OH Si O Si OH OH OH OH Bacterium OH 2– OH SO 4 – H2PO4 COO– Fe OH Cell wall HS– – OH – PO HCO3 OH Sheath Figure 8.1 Schematic diagram of bacterial surface showing how the deprotonation of exposed functional groups leads to metal