1. Prologue
The first member of the Archaea was described in 1880 [1–3]. Yet, the recognition and formal description of the domain Archaea, as separated from Bacteria and Eukarya, occurred in 1977 during early phylogenetic analyses based upon ribosomal DNA sequences [4–6]. Indeed, members of the archaeal domain are characterized by several distinguishing traits [3] as confirmed later based on the first complete archaeal genome sequence obtained by Bult
The archaeal domain is composed of the
The Archaea are ubiquitous in most terrestrial, aquatic and extreme environments (acidophilic, halophilic, mesophilic, methanogenic, psychrophilic and thermophilic) [20, 22]. Although very diversified with a great number of species, luckily, no member of the domain Archaea has been described as a pathogen for humans, animals or plants [23–25]. Thus, Archaea are a potentially valuable resource in the development of new biocatalysts, novel pharmaceuticals and various biotechnological applications. Applications of Archaea (for review, see [26–32] and references therein) may be subdivided into four main fields (Figure 1): (i)
The book ‘Archaea - New Biocatalysts, Novel Pharmaceuticals and Various Biotechnological Applications’ contains five chapters.
The
The
The
The
The book concludes with a
Finally, we would like to thank all authors for their contributions. We are also grateful to InTech Publishing Process Managers, particularly Ms. Mirena Čalmić, Ms. Romina Rovan and Ms. Ana Pantar, who assisted us with patience until the publication of this book.
References
- 1.
Farlow WG. Part IV. Report for the commissioner. In: United States Commission of Fish and Fisheries. Washington DC: Government Printing Office; 1878. pp. 969-973. 1880 - 2.
Kocur M, Hodgkiss W. Taxonomic status of the genus Halococcus Schoop. International Journal of Systematic and Evolutionary Microbiology. 1973;23 (2):151-156 - 3.
Cavicchioli R. Archaea—timeline of the third domain. Nature Reviews Microbiology. 2011; 9 (1):51-61 - 4.
Balch WE, Magrum LJ, Fox GE, Wolfe RS, Woese CR. An ancient divergence among the bacteria. Journal of Molecular Evolution. 1977; 9 (4):305-311 - 5.
Fox GE, Magrum LJ, Balch WE, Wolfe RS, Woese CR. Classification of methanogenic bacteria by 16S ribosomal RNA characterization. Proceedings of the National Academy of Sciences of the United States of America. 1977; 74 (10):4537-4541 - 6.
Woese CR, Fox GE. Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proceedings of the National Academy of Sciences of the United States of America. 1977; 74 (11):5088-5090 - 7.
Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD, et al. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii . Science. 1996;273 (5278):1058-1073 - 8.
Reddy TB, Thomas AD, Stamatis D, Bertsch J, Isbandi M, Jansson J, Mallajosyula J, Pagani I, Lobos EA, Kyrpides NC. The Genomes OnLine Database (GOLD) v.5: A metadata management system based on a four level (meta)genome project classification. Nucleic Acids Research. 2015; 43 (Database issue):D1099-D1106 - 9.
Tatusova T, Ciufo S, Fedorov B, O’Neill K, Tolstoy I. RefSeq microbial genomes database: New representation and annotation strategy. Nucleic Acids Research. 2014; 42 (Database issue):D553-D559 - 10.
Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, et al: Insights into the phylogeny and coding potential of microbial dark matter. Nature. 2013; 499 (7459):431-437 - 11.
Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, Frischkorn KR, Tringe SG, Singh A, Markillie LM, et al. Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Current Biology: CB. 2015; 25 (6):690-701 - 12.
Da Cunha V, Gaia M, Gadelle D, Nasir A, Forterre P. Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes. PLoS Genetics. 2017; 13 (6):e1006810 - 13.
Guy L, Ettema TJ. The archaeal ‘TACK’ superphylum and the origin of eukaryotes. Trends in Microbiology. 2011; 19 (12):580-587 - 14.
Nunoura T, Takaki Y, Kakuta J, Nishi S, Sugahara J, Kazama H, Chee GJ, Hattori M, Kanai A, Atomi H, et al. Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Research. 2011; 39 (8):3204-3223 - 15.
Meng J, Xu J, Qin D, He Y, Xiao X, Wang F. Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses. The ISME Journal. 2014; 8 (3):650-659 - 16.
Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences of the United States of America. 1990; 87 (12):4576-4579 - 17.
Barns SM, Delwiche CF, Palmer JD, Pace NR. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proceedings of the National Academy of Sciences of the United States of America. 1996; 93 (17):9188-9193 - 18.
Spang A, Saw JH, Jorgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJ. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature. 2015; 521 (7551):173-179 - 19.
Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P. Mesophilic Crenarchaeota: Proposal for a third archaeal phylum, the Thaumarchaeota. Nature Reviews Microbiology. 2008; 6 (3):245-252 - 20.
Amils R. Euryarchaeota. In: Gargaud M, Irvine WM, Amils R, Cleaves HJ, Pinti DL, Quintanilla JC, Rouan D, Spohn T, Tirard S, Viso M, editors. Encyclopedia of Astrobiology Berlin, Heidelberg: Springer Berlin Heidelberg; 2015. pp. 764-765 - 21.
Probst AJ, Moissl-Eichinger C. “ Altiarchaeales ”: Uncultivated archaea from the subsurface. Life. 2015;5 (2):1381-1395 - 22.
Ferrera I, Takacs-Vesbach CD, Reysenbach A-L. Archaeal ecology. In: Encyclopedia of Life Sciences (ELS). Chichester: John Wiley & Sons, Ltd; 2008. DOI: 10.1002/9780470015902.a9780470000338.pub9780470015902 - 23.
Cavicchioli R, Curmi PM, Saunders N, Thomas T. Pathogenic archaea: Do they exist? BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology. 2003; 25 (11):1119-1128 - 24.
Reeve JN. Archaebacteria Then … Archaes Now (Are There Really No Archaeal Pathogens?). Journal of Bacteriology. 1999; 181 (12):3613-3617 - 25.
Aminov RI. Role of archaea in human disease. Frontiers in Cellular and Infection Microbiology. 2013; 3 :42 - 26.
Schiraldi C, Giuliano M, De Rosa M. Perspectives on biotechnological applications of archaea. Archaea. 2002; 1 (2):75-86 - 27.
Eichler J. Biotechnological uses of archaeal extremozymes. Biotechnology Advances. 2001; 19 (4):261-278 - 28.
Reed CJ, Lewis H, Trejo E, Winston V, Evilia C. Protein adaptations in archaeal extremophiles. Archaea. 2013; 2013 :373275 - 29.
Litchfield CD. Potential for industrial products from the halophilic Archaea. Journal of Industrial Microbiology and Biotechnology. 2011; 38 (10):1635-1647 - 30.
Egorova K, Antranikian G. Industrial relevance of thermophilic Archaea. Current Opinion in Microbiology. 2005; 8 (6):649-655 - 31.
Dumorne K, Cordova DC, Astorga-Elo M, Renganathan P. Extremozymes: A potential source for industrial applications. Journal of Microbiology and Biotechnology. 2017; 27 (4):649-659 - 32.
Antunes A, Simões MF, Grötzinger SW, Eppinger J, Bragança J, Bajic VB. Bioprospecting Archaea: Focus on extreme halophiles. In: Paterson R, Lima N, editors. Bioprospecting: Success, Potential and Constraints. Cham: Springer International Publishing; 2017. pp. 81-112 - 33.
Letunic I, Bork P. Interactive tree of life (iTOL) v3: An online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Research. 2016; 44 (W1):W242-W245 - 34.
You X, Zhang Q, Zheng H, Jiang C. Adaptation of Acidianus hospitalis W1 to oligotrophic and acidic hot spring environments. Wei Sheng Wu Xue Bao = Acta Microbiologica Sinica. 2014;54 (10):1193-1203 - 35.
Krupovic M, Peixeiro N, Bettstetter M, Rachel R, Prangishvili D. Archaeal tetrathionate hydrolase goes viral: Secretion of a sulfur metabolism enzyme in the form of virus-like particles. Applied and Environmental Microbiology. 2012; 78 (15):5463-5465 - 36.
Gumerov VM, Rakitin AL, Mardanov AV, Ravin NV. A novel highly thermostable multifunctional beta-glycosidase from crenarchaeon Acidilobus saccharovorans . Archaea. 2015;2015:978632 - 37.
Mardanov AV, Svetlitchnyi VA, Beletsky AV, Prokofeva MI, Bonch-Osmolovskaya EA, Ravin NV, Skryabin KG. The genome sequence of the crenarchaeon Acidilobus saccharovorans supports a new order, Acidilobales, and suggests an important ecological role in terrestrial acidic hot springs. Applied and Environmental Microbiology. 2010;76 (16):5652-5657 - 38.
Nishimura H, Sako Y. Purification and characterization of the oxygen-thermostable hydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum camini . Journal of Bioscience and Bioengineering. 2009;108 (4):299-303 - 39.
Mino K, Ishikawa K. Characterization of a novel thermostable O-acetylserine sulfhydrylase from Aeropyrum pernix K1. Journal of Bacteriology. 2003;185 (7):2277-2284 - 40.
Beblo-Vranesevic KA-Ohoo, Galinski EA, Rachel R, Huber H, Rettberg P. Influence of osmotic stress on desiccation and irradiation tolerance of (hyper)-thermophilic microorganisms. Archives of Microbiology. 2017; 199 (1):17-28 - 41.
Toso DB, Javed MM, Czornyj E, Gunsalus RA-O, Zhou ZH. Discovery and characterization of iron sulfide and polyphosphate bodies coexisting in Archaeoglobus fulgidus cells. Archaea . 2016. DOI: 10.1155/2016/4706532 - 42.
Letsididi R, Hassanin HA, Koko MY, Ndayishimiye JB, Zhang T, Jiang B, Stressler T, Fischer L, Mu W. Characterization of a thermostable glycoside hydrolase (CMbg0408) from the hyperthermophilic archaeon Caldivirga maquilingensis IC-167. Journal of the Science of Food and Agriculture. 2017;97 (7):2132-2140 - 43.
Susanti D, Johnson EF, Rodriguez JR, Anderson I, Perevalova AA, Kyrpides N, Lucas S, Han J, Lapidus A, Cheng JF, et al. Complete genome sequence of Desulfurococcus fermentans , a hyperthermophilic cellulolytic crenarchaeon isolated from a freshwater hot spring in Kamchatka, Russia. Journal of Bacteriology. 2012;194 (20):5703-5704 - 44.
Susanti D, Johnson EF, Lapidus A, Han J, Reddy TB, Pilay M, Ivanova NN, Markowitz VM, Woyke T, Kyrpides NC, et al. Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland. Standards in Genomic Sciences. 2016;11 :3 - 45.
Aklujkar M, Risso C, Smith J, Beaulieu D, Dubay R, Giloteaux L, DiBurro K, Holmes D. Anaerobic degradation of aromatic amino acids by the hyperthermophilic archaeon Ferroglobus placidus . Microbiology. 2014;160 (Pt 12):2694-2709 - 46.
Lebedinsky AV, Mardanov AV, Kublanov IV, Gumerov VM, Beletsky AV, Perevalova AA, Bidzhieva S, Bonch-Osmolovskaya EA, Skryabin KG, Ravin NV: Analysis of the complete genome of Fervidococcus fontis confirms the distinct phylogenetic position of the orderFervidicoccales and suggests its environmental function. Extremophiles. 2014;18 (2):295-309 - 47.
Cherin E, Melis JM, Bourdeau RW, Yin M, Kochmann DM, Foster FS, Shapiro MG. Acoustic behavior of Halobacterium salinarum gas vesicles in the high-frequency range: Experiments and modeling. Ultrasound in Medicine & Biology. 2017;43 (5):1016-1030 - 48.
Balakrishnan A, DasSarma P, Bhattacharjee O, Kim JM, DasSarma S, Chakravortty D. Halobacterial nano vesicles displaying murine bactericidal permeability-increasing protein rescue mice from lethal endotoxic shock. Scientific Reports. 2016; 6 :33679 - 49.
Alsafadi D, Al-Mashaqbeh O. A one-stage cultivation process for the production of poly-3-(hydroxybutyrate-co-hydroxyvalerate) from olive mill wastewater by Haloferax mediterranei . New Biotechnology. 2017;34 :47-53 - 50.
Salgaonkar BB, Braganca JM. Biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) by Halogeometricum borinquense strain E3. International Journal of Biological Macromolecules. 2015;78 :339-346 - 51.
Anderson I, Tindall BJ, Pomrenke H, Goker M, Lapidus A, Nolan M, Copeland A, Glavina Del Rio T, Chen F, Tice H, et al. Complete genome sequence of Halorhabdus utahensis type strain (AX-2). Standards in Genomic Sciences. 2009;1 (3):218-225 - 52.
Kanekar PP, Kulkarni SO, Kanekar SP, Shouche Y, Jani K, Sharma A. Exploration of a haloarchaeon, Halostagnicola larsenii , isolated from rock pit sea water, West Coast of Maharashtra, India, for the production of bacteriorhodopsin. Journal of Applied Microbiology. 2016;120 (4):1136 - 53.
Squillaci G, Finamore R, Diana P, Restaino OF, Schiraldi C, Arbucci S, Ionata E, La Cara F, Morana A. Production and properties of an exopolysaccharide synthesized by the extreme halophilic archaeon Haloterrigena turkmenica . Applied Microbiology and Biotechnology. 2016;100 (2):613-623 - 54.
Liu LJ, You XY, Zheng H, Wang S, Jiang CY, Liu SJ. Complete genome sequence of Metallosphaera cuprina , a metal sulfide-oxidizing archaeon from a hot spring. Journal of Bacteriology. 2011;193 (13):3387-3388 - 55.
Artz JH, White SN, Zadvornyy OA, Fugate CJ, Hicks D, Gauss GH, Posewitz MC, Boyd ES, Peters JW. Biochemical and structural properties of a thermostable mercuric ion reductase from Metallosphaera sedula . Frontiers in Bioengineering and Biotechnology. 2015;3 :97 - 56.
Kim JW, Flowers LO, Whiteley M, Peeples TL. Biochemical confirmation and characterization of the family-57-like alpha-amylase of Methanococcus jannaschii . Folia Microbiologica. 2001;46 (6):467-473 - 57.
Hei DJ, Clark DS. Pressure stabilization of proteins from extreme thermophiles. Applied and Environmental Microbiology. 1994; 60 (3):932-939 - 58.
Polosina YY, Zamyatkin DF, Kostyukova AS, Filimonov VV, Fedorov OV. Stability of Natrialba magadii NDP kinase: Comparisons with other halophilic proteins. Extremophiles. 2002;6 (2):135-142 - 59.
Waters E, Hohn MJ, Ahel I, Graham DE, Adams MD, Barnstead M, Beeson KY, Bibbs L, Bolanos R, Keller M, et al. The genome of Nanoarchaeum equitans : Insights into early archaeal evolution and derived parasitism. Proceedings of the National Academy of Sciences of the United States of America. 2003;100 (22):12984-12988 - 60.
Olszewski M, Balsewicz J, Nowak M, Maciejewska N, Cyranka-Czaja A, Zalewska-Piątek B, Piątek R, Kur J. Characterization of a single-stranded DNA-binding-like protein from Nanoarchaeum equitans —A nucleic acid binding protein with broad substrate specificity. PLOS ONE. 2015;10 (5):e0126563 - 61.
Kaper T, Talik B, Ettema TJ, Bos H, van der Maarel MJ, Dijkhuizen L. Amylomaltase of Pyrobaculum aerophilum IM2 produces thermoreversible starch gels. Applied and Environmental Microbiology. 2005;71 (9):5098-5106 - 62.
de Vries S, Momcilovic M, Strampraad MJ, Whitelegge JP, Baghai A, Schroder I. Adaptation to a high-tungsten environment: Pyrobaculum aerophilum contains an active tungsten nitrate reductase. Biochemistry. 2010;49 (45):9911-9921 - 63.
Satomura T, Zhang XD, Hara Y, Doi K, Sakuraba H, Ohshima T: Characterization of a novel dye-linked L-proline dehydrogenase from an aerobic hyperthermophilic archaeon, Pyrobaculum calidifontis . Applied Microbiology and Biotechnology. 2011;89 (4):1075-1082 - 64.
Shao H, Xu L, Yan Y. Biochemical characterization of a carboxylesterase from the archaeon Pyrobaculum sp. 1860 and a rational explanation of its substrate specificity and thermostability. International Journal of Molecular Sciences. 2014;15 (9):16885-16910 - 65.
Mardanov AV, Gumerov VM, Slobodkina GB, Beletsky AV, Bonch-Osmolovskaya EA, Ravin NV, Skryabin KG. Complete genome sequence of strain 1860, a crenarchaeon of the genus Pyrobaculum able to grow with various electron acceptors. Journal of Bacteriology. 2012;194 (3):727-728 - 66.
Ishikawa K, Ishida H, Matsui I, Kawarabayasi Y, Kikuchi H. Novel bifunctional hyperthermostable carboxypeptidase/aminoacylase from Pyrococcus horikoshii OT3. Applied and Environmental Microbiology. 2001;67 (2):673-679 - 67.
Jung JH, Seo DH, Holden JF, Park CS. Maltose-forming alpha-amylase from the hyperthermophilic archaeon Pyrococcus sp. ST04. Applied Microbiology and Biotechnology. 2014;98 (5):2121-2131 - 68.
Fu L, Li X, Xiao X, Xu J. Purification and characterization of a thermostable aliphatic amidase from the hyperthermophilic archaeon Pyrococcus yayanosii CH1. Extremophiles. 2014;18 (2):429-440 - 69.
Pennacchio A, Sannino V, Sorrentino G, Rossi M, Raia CA, Esposito L. Biochemical and structural characterization of recombinant short-chain NAD(H)-dependent dehydrogenase/reductase from Sulfolobus acidocaldarius highly enantioselective on diaryl diketone benzil. Applied Microbiology and Biotechnology. 2013;97 (9):3949-3964 - 70.
Zhu S, Huang R, Gao S, Li X, Zheng G. Discovery and characterization of a second extremely thermostable (+)-gamma-lactamase from Sulfolobus solfataricus P2. Journal of Bioscience and Bioengineering. 2016;121 (5):484-490 - 71.
Jolivet E, L’Haridon S, Corre E, Forterre P, Prieur D. Thermococcus gammatolerans sp. nov., a hyperthermophilic archaeon from a deep-sea hydrothermal vent that resists ionizing radiation. International Journal of Systematic and Evolutionary Microbiology. 2003;53 (Pt 3):847-851 - 72.
Washio T, Kato S, Oikawa T. Molecular cloning and enzymological characterization of pyridoxal 5’-phosphate independent aspartate racemase from hyperthermophilic archaeon Thermococcus litoralis DSM 5473. Extremophiles. 2016;20 (5):711-721 - 73.
Kim YJ, Lee HS, Kwon ST, Lee JH, Kang SG. Enhancing the processivity of a family B-type DNA polymerase of Thermococcus onnurineus and application to long PCR. Biotechnology Letters. 2014;36 (5):985-992 - 74.
Jeon EJ, Jung JH, Seo DH, Jung DH, Holden JF, Park CS. Bioinformatic and biochemical analysis of a novel maltose-forming alpha-amylase of the GH57 family in the hyperthermophilic archaeon Thermococcus sp. CL1. Enzyme and Microbial Technology. 2014;60 :9-15 - 75.
Kim JH, Sung MW, Lee EH, Nam KH, Hwang KY. Crystallization and preliminary X-ray diffraction analysis of 5,10-methylenetetrahydrofolate dehydrogenase/cyclohydrolase from Thermoplasma acidophilum DSM 1728. Journal of Microbiology and Biotechnology. 2008;18 (2):283-286 - 76.
Kim YK, Mizutani K, Rhee KH, Nam KH, Lee WH, Lee EH, Kim EE, Park SY, Hwang KY. Structural and mutational analysis of tRNA intron-splicing endonuclease from Thermoplasma acidophilum DSM 1728: Catalytic mechanism of tRNA intron-splicing endonucleases. Journal of Bacteriology. 2007;189 (22):8339-8346 - 77.
Kocabiyik S, Demirok B. Cloning and overexpression of a thermostable signal peptide peptidase (SppA) from Thermoplasma volcanium GSS1 in E. coli. Biotechnology Journal. 2009;4 (7):1055-1065 - 78.
Gumerov VM, Mardanov AV, Beletsky AV, Prokofeva MI, Bonch-Osmolovskaya EA, Ravin NV, Skryabin KG. Complete genome sequence of “ Vulcanisaeta moutnovskia ” strain 768-28, a novel member of the hyperthermophilic crenarchaeal genusVulcanisaeta . Journal of Bacteriology. 2011;193 (9):2355-2356