Microscopic observations of many fossil samples revealed several notions of the silicification process. Firstly, it indicated that silicification of microbes is a rapid process. [19] The speed of silicification also suggested that there are inorganic driving forces controlling the process. Further microscopic studies also suggested that microbes may have acted as nucleation sites for silica precipitation. [20] The initial step in such biomineralization process comprises of chemical interactions with mineralising ions in the bulk aqueous phase, [21] and that it is well known that bacterial surfaces possess many reactive binding sites. [22, 23]
However, beyond the bacterial surfaces, the controlling factors are still unknown and that there is no direct proof of the bacteria role in silica biomineralization. Studying the bacterial metabolism however, did create evident chemical / physical changes at the cell surface. Some of the changes include excretion of complexing ligand by-products, [24] ultra-structural growths of different mineral reactivity, [25] and changes in H- in the cell interfacial region. [26] Other changes can also be observed in the difference between active cell and inactive cells (dead or non-metabolically active). This is due to the difference in the localized microenvironment surrounding the two types of cells, with the former having the potential to create cell-associated biominerals with different features from the passive biomineralization as observed in the latter, or from inorganic driven mineral formation. Other investigations also pointed out that entombment of SiO2 biominerals do not interfere with bacterial metabolism nor it affect the viability of the cell. [27, 28] However, despite all the research, the impact of metabolic activity on silica biomineralization is still not well described.
There are, however, some interesting discoveries on silicification of microorganism, especially in cyanobacteria. Cyanobacteria reacted to silicification by initially producing more polymeric shealth material, and this directly allows more silica to aggregate freely on their surface. [29] Further studies concluded that this thicken exo-polymeric shealth has another function besides being a surface for silica growth and aggregation, the shealth also protect the internal cell structure from biomineralization damage. [30] The ability of cyanobacteria to produce such exo-polymeric shealth help “proved” the theory that some microorganisms thrive in aqueous environments with high dissolved silica levels. Unsurprisingly, many ancient microfossils verifiable appear to be cyanobacteria in origin.
There is also a distinct, unique biosilicification pattern the live metabolically active Synechococcus cyanobacterial cell surfaces was compared to dead Synechococcus cells under identical experimental conditions. The live cell treatments bound more tightly and twice the amount of colloidal SiO2 as compared to the dead one. The former also showed signs of cell division and fimbriae growth also indicated metabolic activity, the live treatment cells were also re-cultivable after the experiments. This confirmed the continued viability of the live treatment cells, [31] although there is no known metabolic advantages. [32]
There are also further differences between the two set of bacteria under silicification. Biosilicification of the dead cells occured across the entire cell surface with no observable localized pattern and was heterogeneous, whereas biosilicification of the live, actively bacteria was unipolar, with the core surface mostly unencrusted. Such directed biosilicification localization of live cell surfaces might also be another bacterial strategy to protect the cell functionality against any potentially inhibitory effects of mineral encrustation. Moreover, the unipolar biomineralization pattern is consistent with regulated cell polarity in bacteria, which favours silica biomineralization to the polar end of the cell. Colloidal SiO2 is net positively charged at the experimental pH 3, which is a similar environment to early earth. This indicated that cell polar end encrusted with CSiO2 would have a negative charge. By localizing biosilicification away from the cell core housing their photosynthetic machinery, these bacteria can minimize cell functional impairment and strategically increase their survival chances in silica-rich environments. [32] While bacterial encrustation with CSiO2 forming insoluble crust can be detrimental to the microbes functionality, [33] the cell-regulated directional localization of CSiO2 may be yet another strategy to indiscriminate mineral encrustation of the cell core thereby maintaining exposure of the cell's photosynthetic components such as thylakoid membranes and enabling photosynthetic light harvesting capabilities. [34]
In conclusion, silicification could be metabolically driven process and that some bacteria such as cyanobacteria do exert some degree of control to exert and mange their surface biomineralization burden in order to maintain the cell core functions, which are consistent with known bacterial strategies to avoid or delay cell entombment. [35] This, along with other strategies, enables bacteria to “outlive” all from the early earth to the modern times.
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