Extremophiles, a Nifty Tool to Face Environmental Pollution: From Exploitation of Metabolism to Genome Engineering

Abstract

Extremophiles are microorganisms that populate habitats considered inhospitable from an anthropocentric point of view and are able to tolerate harsh conditions such as high temperatures, extreme pHs, high concentrations of salts, toxic organic substances, and/or heavy metals. These microorganisms have been broadly studied in the last 30 years and represent precious sources of biomolecules and bioprocesses for many biotechnological applications; in this context, scientific efforts have been focused on the employment of extremophilic microbes and their metabolic pathways to develop biomonitoring and bioremediation strategies to face environmental pollution, as well as to improve biorefineries for the conversion of biomasses into various chemical compounds. This review gives an overview on the peculiar metabolic features of certain extremophilic microorganisms, with a main focus on thermophiles, which make them attractive for biotechnological applications in the field of environmental remediation; moreover, it sheds light on updated genetic systems (also those based on the CRISPR-Cas tool), which expand the potentialities of these microorganisms to be genetically manipulated for various biotechnological purposes.

Keywords: CRISPR-Cas; aromatic-compounds; bioremediation; biosensors; environmental pollution; extremophiles; genome-engineering; heavy-metal resistance.

Figure 1

Periodic table of elements. Metals/metalloids are highlighted on the basis of the main characteristic that define them as “heavy”: density > 5 g/cm³ (blue); toxic (red); rare (green); synthetic (yellow).

Figure 2

Schematic representation of metal bioprocesses in biometallurgy. Metals (blue circles) can be extracted from ores through biomining/bioleaching (green arrow) and they can be recovered into the cell by passive import (biosorption—blue arrow) or energy driven transport (bioaccumulation—red arrow).

Figure 3

Schematic representation of organic compounds in crude oil. Atoms are reported in grey (C), white (H), yellow (S), blue (N) and red (O).

Figure 4

Industrial applications of lignocellulolytic enzymes. In food processes cellulases and xylanases are employed to improve the shelf life of dairy products and to hydrolyze monosaccharides in milk processing; they are also used in winery industries and to decrease viscosity of fruit juice. Also, laccases are used to increase quality of beverages and food, for example eliminating toxic substances. In pulp/paper industry laccases and xylanases enhance pulp bleaching for paper manufacturing, and cellulases improve flexibility and softness of fibers. Lignocellulolytic enzymes can be employed for improving nutrient digestibility of animal feeds, for enhancing color and surface brightness of fabric in textile industry, for textile dye bleaching, for synthesis of complex polymers. In agriculture, they are involved in fruit ripening and defense mechanisms against insects. Laccases are employed in wastewater treatment of colored waters. Lignocellulolytic enzymes are used in biorefinery systems to produce biofuels [103,127,128] (Created with BioRender.com (accessed on 20 January 2021)).

Figure 5

Schematic representation of the genome editing tools for thermophilic microorganisms. The Zinc finger nuclease is the first genome editing tool setup for thermophilic microorganisms. The most common is the spontaneous homologous recombination. In the last decades, the Cre/lox and CRISPR-Cas based tools were adapted for thermophiles (Created with BioRender.com (accessed on 20 January 2021)).