Journal Pre-proof Archaea biotechnology Kevin Pfeifer, İpek Ergal, Martin Koller, Mirko Basen, Bernhard Schuster, Simon K.-M.R. Rittmann PII: S0734-9750(20)30170-1 DOI: https://doi.org/10.1016/j.biotechadv.2020.107668 Reference: JBA 107668 To appear in: Biotechnology Advances Received date: 24 July 2020 Revised date: 19 November 2020 Accepted date: 20 November 2020 Please cite this article as: K. Pfeifer, İ. Ergal, M. Koller, et al., Archaea biotechnology, Biotechnology Advances (2019), https://doi.org/10.1016/j.biotechadv.2020.107668 This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. © 2019 Published by Elsevier. Journal Pre-proof Archaea Biotechnology Kevin Pfeifer1,2, İpek Ergal1, Martin Koller3, Mirko Basen4, Bernhard Schuster2, Simon K.-M. R. Rittmann1,* [email protected] 1Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Wien, Austria 2Institute of Synthetic Bioarchitectures, Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Wien, Austria 3Office of Research Management and Service, c/o Institute of Chemistry, University of Graz, Austria 4Microbial Physiology Group, Division of Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany *Corresponding author at: Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Althanstraße 14, 1090 Wien, Austria. Abstract Archaea are a domain of prokaryotic organisms with intriguing physiological characteristics and ecological importance. In Microbial Biotechnology, archaea are historically overshadowed by bacteria and eukaryotes in terms of public awareness, industrial application, and scientific studies, although their biochemical and physiological properties show a vast potential for a wide range of biotechnological applications. Today, the majority of microbial cell factories utilized for the production of value-added and high value compounds on an industrial scale are bacterial, fungal or algae based. Nevertheless, archaea are becoming ever more relevant for biotechnology as their cultivation and genetic systems improve. Some of the main advantages of archaeal cell factories are the ability to cultivate many of these often extremophilic strains under non-sterile conditions, and to utilize inexpensive feedstocks often toxic to other microorganisms, thus drastically reducing cultivation costs. Currently, the only commercially available products of archaeal cell factories are bacterioruberin, squalene, bacteriorhodopsin and diether-/tetraether-lipids, all of which are produced utilizing halophiles. Other archaeal products, such as carotenoids and biohydrogen, as well as polyhydroxyalkanoates and methane are in an early to advanced development stage, respectively. The aim of this review is to provide an overview of the current state of Archaea Biotechnology by describing the actual state of research and development as well as the industrial utilization of archaeal cell factories, their role and their potential in the future ofJournal sustainable bioprocessing Pre-proof, and to illustrate their physiological and biotechnological potential. Keywords Microbial cell factory, prokaryotes, bacteria, eukaryotes, bioprocess, biofuel, bioproduct, biorefinery, bioeconomy, bio-technology readiness level (B-TRL) 1. Introduction Production of high value bioproducts and commodity chemicals by microbial cell factories or isolated enzymes through biotransformation, biocatalysis or fermentation progressed tremendously in the last decades. As the market demand for biopharmaceuticals, fine and commodity chemicals as substitutes for various petrol-based synthetic products rises, Microbial Biotechnology is becoming ever more relevant. The earliest forms of biotechnology date back several thousand years, before the existence of microbes would be Journal Pre-proof discovered. Anaerobic beer and wine fermentation for example dates back to about 6000 BC, while the pickling of foods in acetic acid (vinegar) produced though microbial acidification of wine dates back to 5000 BC (Buchholz and Collins, 2013; Lück and Jager, 1997). It was only in 1860, that Pasteur’s ground-breaking discovery of the involvement of yeast, acetogenic and lactic acid bacteria in these processes caused a paradigm shift in the perception of microbes. Microbes were now widely accepted as living organisms that could be utilized as chemical reactors (Mir, 2004). Today, microbial cell factories are indispensable. They are involved, among others, in the production of bio-based products such as bioplastics, cosmetics, food additives, high-value chemicals, biopharmaceuticals, and biogenic energy conversion as well as energy storage solutions. As the world progresses towards a sustainable economy, industrial microbiology and biotechnology are appropriate tools to replace petrochemistry-based technologies by biological alternatives (Harwood et al., 2018). Biotechnology can be defined as: any technological application using biosystems, organisms, or derivatives thereof, to manufacture or modify bioproducts or to develop and engineer processes for specific application. It can be subdivided into the following categories: white (industrial), blue (marine and fresh-water), green (plant/agricultural), red (biomedical/pharmaceutical), grey (environment/bioremediation), brown (arid land/dessert), yellow (insect biotechnology) and dark (biological weapons/biowarfare). Because of its diverse of applications, the biotechnology industry is likely to become one of the most important high-tech industry branches within the next few decades, with revenues expected to exceed USD 720 billion by 2025, of which fermentative production is expected to make up USD 86 billion (ResearchAndMarkets.com, 2019). To date, the vast majority of industrialized microbial cell factories are fungal or bacterial based, with Escherichia coli and Saccharomyces cerevisiae as the predominant systems. However, the recent advances in bioprocessing technologies, bioinformatics, and synthetic biology have shown the potential of archaeal cell factories (Bill, 2014; Pecorari et al., 2015; Singh and Singh, 2017; Straub et al., 2018). In Microbial Biotechnology, Archaea are historically overshadowed by Bacteria and Eukarya in terms of public awareness, industrial application, and scientific studies, although their biochemical and physiological properties show a vast potential for a wide range of biotechnological applications. Archaea inhabit almost every environment on Earth and some archaea have adapted to survive under extreme environmental conditions (Rampelotto, 2013). Not only have archaea thrived in these extremes, but it has been shown that, methanogenic archaea (methanogens) and Thaumarchaeota are key organisms in the anaerobic and marine food webs, respectively (PesterJournal et al., 2011) Pre-proof. Methanogens are a physiologically and phylogenetically diverse group of anaerobic microorganisms, which produce methane (CH4) as an end product of their carbon and energy metabolism (Thauer et al., 2008). Thaumarchaeota are a metabolically diverse group of microbes found in almost every environment ranging from marine waters and arctic soils to the human skin biome; and representatives have shown to perform ammonium oxidation (Stieglmeier et al., 2014). Other ecologically and biotechnologically important archaea are found among the Sulfolobales (Huber and Prangishvili, 2006), first cultivated from volcanic hot springs at pH values of 2 to 3 and 80°C; the halophilic archaea (―haloarchaea‖), which grow in salt solutions up to saturation (Stan-Lotter and Fendrihan, 2015) and the anaerobic, hyperthermophilic Thermococcales cultivated at over 90°C (Bertoldo and Antranikian, 2006). Archaea have been utilized in undefined consortia with Bacteria for biomining, bioleaching, anaerobic digestion, and soil/waste water remediation, and are well known for their extremely stable enzymes, but there are very few industrialized applications of pure cultures (Straub et al., 2018a). Recently an extensive review summarized the bioremediation potential of archaea in the degradation of hydrocarbons, metal remediation, acid mine drainage, and Journal Pre-proof dehalogenation (Krzmarzick et al., 2018). Therefore, these applications will not be covered in this review. Here, we will focus on the utilization of archaea as microbial cell factories in bioproduction. Archaea have been shown to naturally produce or can be engineered to produce a range of products such as biofuels (e.g., biomethane, biohydrogen, bioethanol, or biobutanol), bioplastics (PHA), compatible solutes, nanobiotechnology components (surface- layer proteins, lipids) and precursor chemicals (e.g., acetate; 2,3-butanediol) needed for the industrial synthesis of high value chemicals. A major progress in facilitating Archaea Biotechnology is the relatively recent development of genetic techniques, methods which are essential for the development