Preservation of protein globules and peptidoglycan in the mineralized cell wall of nitrate-reducing, iron(II)-oxidizing bacteria: a cryo-electron microscopy study

Abstract

Iron-oxidizing bacteria are important actors of the geochemical cycle of iron in modern environments and may have played a key role all over Earth's history. However, in order to better assess that role on the modern and the past Earth, there is a need for better understanding the mechanisms of bacterial iron oxidation and for defining potential biosignatures to be looked for in the geologic record. In this study, we investigated experimentally and at the nanometre scale the mineralization of iron-oxidizing bacteria with a combination of synchrotron-based scanning transmission X-ray microscopy (STXM), scanning transmission electron microscopy (STEM) and cryo-transmission electron microscopy (cryo-TEM). We show that the use of cryo-TEM instead of conventional microscopy provides detailed information of the successive iron biomineralization stages in anaerobic nitrate-reducing iron-oxidizing bacteria. These results suggest the existence of preferential Fe-binding and Fe-oxidizing sites on the outer face of the plasma membrane leading to the nucleation and growth of Fe minerals within the periplasm of these cells that eventually become completely encrusted. In contrast, the septa of dividing cells remain nonmineralized. In addition, the use of cryo-TEM offers a detailed view of the exceptional preservation of protein globules and the peptidoglycan within the Fe-mineralized cell walls of these bacteria. These organic molecules and ultrastructural details might be protected from further degradation by entrapment in the mineral matrix down to the nanometre scale. This is discussed in the light of previous studies on the properties of Fe-organic interactions and more generally on the fossilization of mineral-organic assemblies.

Fe(II) Oxidation Is an Innate Capability of Nitrate-Reducing Bacteria That Involves Abiotic and Biotic Reactions

“…If the rate of Fe(II) oxidation and Fe(III) mineral precipitation is faster than the rate of efflux, precipitation of Fe(II) minerals on periplasmic proteins will lead to their inhibition and NO 2 Ϫ , NO, and N 2 O accumulation (see Fig. S2d to f in the supplemental material) (13,14,62). In our study, NO 2 Ϫ , NO, and N 2 O did not accumulate to their maximum steady-state level and acetate was not completely consumed in NDFO cultures or cell suspensions until after the more rapid phase of Fe(II) oxidation ( Fig.…”

Experimental diagenesis of organo-mineral structures formed by microaerophilic Fe(II)-oxidizing bacteria

“…Also the formation of Fe minerals in the cell wall of the nitrate-dependent Fe(II)-oxidizing bacterium Acidovorax sp. BoFeN1 leads to the preservation of protein globules and peptidoglycan 10 . Microorganisms involved in biomineralization processes thus represent potential candidates to be preserved in the rock record 11,12 .…”

Calcification and Diagenesis of Bacterial Colonies

“…In addition, the location of mineral precipitation with respect to the bacterial ultrastructures has also been shown to influence the extent of biosignature preservation. For instance, periplasm encrustation has been described as favoring bacterial morphology preservation [26,61,86]. Specific crystallographic orientation (perpendicular to cell walls) of crystalline phases precipitated within bacterial periplasm [61,86,87], at the cell surface or in association with cyanobacterial sheaths [32] may also promote the preservation of specific biosignatures upon fossilization and diagenetic processes.…”

“…Biomineralized micro-organisms appear more resistant to diagenesis than non-biomineralized ones [26][27][28][29]. For instance, biologically mediated calcification of bacteria, which is involved in the formation of stromatolites or microbialites [30][31][32], has been described as a key process contributing to their fossilization [27,29,30,33].…”