In a quest for engineering acidophiles for biomining applications: challenges and opportunities

Abstract

Biomining with acidophilic microorganisms has been used at commercial scale for the extraction of metals from various sulfide ores. With metal demand and energy prices on the rise and the concurrent decline in quality and availability of mineral resources, there is an increasing interest in applying biomining technology, in particular for leaching metals from low grade minerals and wastes. However, bioprocessing is often hampered by the presence of inhibitory compounds that originate from complex ores. Synthetic biology could provide tools to improve the tolerance of biomining microbes to various stress factors that are present in biomining environments, which would ultimately increase bioleaching efficiency. This paper reviews the state-of-the-art tools to genetically modify acidophilic biomining microorganisms and the limitations of these tools. The first part of this review discusses resilience pathways that can be engineered in acidophiles to enhance their robustness and tolerance in harsh environments that prevail in bioleaching. The second part of the paper reviews the efforts that have been carried out towards engineering robust microorganisms and developing metabolic modelling tools. Novel synthetic biology tools have the potential to transform the biomining industry and facilitate the extraction of value from ores and wastes that cannot be processed with existing biomining microorganisms.

Keywords: acidophile, bioleaching, biohydrometallurgy, biomining, halophile, metal, microorganism, resistance, tolerance, synthetic biology.

Figure 1

Potential targets for engineering biomining microorganisms: (A) Acid tolerance. Multiple mechanisms for acid stress tolerance in acidophiles as suggested by Baker-Austin and Dopson [66]: i) Increased influx of potassium into the cell in order to maintain a reversed transmembrane potential, ii) Highly impermeable cell membranes to reduce the influx of protons, iii) Over-production of enzymes/chemicals to bind and sequester protons to maintain pH homeostasis, iv) Increase in active export of protons through transporters, v) Increased synthesis of organic acids to act as uncouplers, vi) Larger proportion of repair systems for DNA and protein repair. (B) Metal tolerance. Multiple transporters for the efflux of metal cations and toxic compounds to assist in the detoxification of the cell [67]. Additionally, the exopolyphosphatase (ppx) enzyme can convert polyphosphates (PolyP) into inorganic phosphate (P_i) that will bind to free metal cations and then be transported out of the cell through the transporters. (C) Osmotolerance. The ability to tolerate high levels of osmotic stress can be achieved through the accumulation of various osmoprotectants, such as ectoine, glycine betaine, trehalose, proline, glutamate, and perisplasmic glucans [73,74,75,76,77,78,79,80,81]. These compounds can either be synthesised in abundance or transported into the cell through transporters when the cell is challenged with osmotic stress. Alternatively, chloride ion channels and pores can be closed to reduce the entry of the ion into the cell [73,74,75,76,77,78,79,80,81]. (D) Thermotolerance. Incorporation of thermostable enzymes and proteins, increase in DNA repair systems, and expression of heat shock proteins as well as the incorporation of modified membrane composition (fatty acids and tetraether lipids) can help to increase the thermostability of cells [82,83].