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DIVERSITY OF THERMOPHILIC ARCHAEA AND THEIR BIOTECHNOLOGICAL USES

Year 2021, Volume: 14 Issue: 1, 155 - 166, 15.04.2021
https://doi.org/10.46309/biodicon.2021.781524

Abstract

Archaea, which constitute one of the three major domains of living things, in terms of both biochemical properties and structural features, are prokaryotic cell types that are separated from eukaryotes and bacteria. The vast majority of members of Archea survive in extreme ambient conditions thanks to their metabolic and molecular adaptations. Typical environments in which pure cultures of archaea species isolated; are hot springs, hydrothermal vents, solfataras, salt lakes, soda lakes. Microbial diversity analysis can be performed both with microbiology-based culture-dependent methods and culture-independent methods using molecular techniques. However, it is still difficult to create conditions in very hot and pressurized environments in laboratory environments and many different taxa can be overlooked. It is not possible to determine archaea types that have not yet been cultured in studies based on culture. Therefore, over the past two decades, the use of molecular techniques involving PCR-based amplification of 16S rRNA genes in environmental samples allows a culture-independent evaluation of microbial diversity. As a result of archaea's ability to function at nearly limit values in terms of temperature, salinity and pH, extremophilic enzymes (extremozymes) are now found in many applications. In this review, general properties of thermophilic archaea, archaeal diversity studies independent of culture, and usage areas of archaeal enzymes in biotechnology are discussed.

References

  • Referans [1] Lever, M. A., Teske, A. P. (2015). Diversity of methane-cycling archaea in hydrothermal sediment investigated by general and group-specific PCR primers. Applied and Environmental Microbiology, 81(4), 1426-1441.
  • Referans[2]Garrett, R.A., Klenk, H. P. (2007). Archaea: evolution, physiology, and molecular biology. Blackwell Publishing, Oxford, United Kingdom.
  • Referans[3]Spang,A., Caceres, E. F., Ettema, T. J. G. (2017). Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science, 357, (6351).
  • Referans[4]Aslan, Z. (2019). Termal kaynaklardan izole edilen bakterilerin enzimleri üzerine çalışmalar (Master's thesis).
  • Referans[5]Stetter, K. O. (2006). History of discovery of the first hyperthermophiles. Extremophiles, 10(5), 357–362.
  • Referans[6]Merkel, A. Y., Podosokorskaya, O. A., Chernyh, N. A., Bonch-Osmolovskaya, E. A. (2015). Occurrence, diversity, and abundance of methanogenic archaea in terrestrial hot springs of Kamchatka and Saõ Miguel Island. Microbiology, 84(4), 577-583.
  • Referans[7] Barahona, S., Cortés, J., Hengst, M., Dorador, C., Remonsellez, F. (2017). Diversity of Thermophilic Iron-Pyrite-Oxidizing Enrichments from Solfataric Hot Springs in the Chilean Altiplano. In Solid State Phenomena,262, 526-530.
  • Referans[8]Moore,T.A. (2012). Coalbed methane: A review. International Journal Of Coal Geology, 101, 36–81.
  • Referans[9]Lebeis,S. L. (2014). The potential for give and take in plant–microbiome relationships. Frontiers İn Plant Science, 5, 287.
  • Referans[10]Pace, N. R., Stahl, D. A., Lane, D. J., Olsen, G. J. (1986). The analysis of natural microbial populations by ribosomal RNA sequences. In Advances İn Microbial Ecology, 1-55.
  • Referans[11]Aouad, M., Taib, N., Oudart, A., Lecocq, M., Gouy, M., Brochier-Armanet, C. (2018). Extreme halophilic archaea derive from two distinct methanogen Class II lineages. Molecular Phylogenetics and Evolution,127, 46-54.
  • Referans[12]Guzzo, J. (2012). Biotechnical applications of small heat shock proteins from bacteria. International Journal Of Biochemistry Cell Biology, 44 (10),1698–1705.
  • Referans[13]Silva, S. B., Pinheiro, M. P., Fuzo, C. A., Silva, S. R., Ferreira, T. L., Lourenzoni, M. R., Ward, R. J. (2017). The role of local residue environmental changes in thermostable mutants of the GH11 xylanase from Bacillus subtilis. International journal of biological macromolecules, 97, 574-584.
  • Referans[14]Norris, P. R., Burton, N. P., Foulis, N. A. (2000). Acidophiles in bioreactor mineral processing. Extremophiles, 4(2), 71-76.
  • Referans[15]Wiseman, A., Dalton, H. (1987). Enzymes versus enzyme-mimetic systems for biotechnological applications. Trends İn Biotechnology, 5(9), 241-244.
  • Referans[16]Schocke, L., Bräsen, C., Siebers, B. (2019). Thermoacidophilic Sulfolobus species as source for extremozymes and as novel archaeal platform organisms. Current Opinion İn Biotechnology,59, 71-77.
  • Referans[17]Cabrera, M. Á., Blamey, J. M. (2018). Biotechnological applications of archaeal enzymes from extreme environments. Biological Research, 51.
  • Referans[18]Amoozegar, M. A., Siroosi, M., Atashgahi, S., Smidt, H., Ventosa, A. (2017). Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes. Microbiology, 163(5), 623-645.
  • Referans[19]Herrero-Fresno, A., Espinel, I. C., Spiegelhauer, M. R., Guerra, P. R., Andersen, K. W., Olsen, J. E. (2018). The homolog of the gene bstA of the BTP1 phage from Salmonella enterica serovar Typhimurium ST313 is an antivirulence gene in Salmonella enterica serovar Dublin. Infection and İmmunity, 86(1).
  • Referans[20]Chakdar, H., Kumar, M., Pandiyan, K., Singh, A., Nanjappan, K., Kashyap, P. L., Srivastava, A. K. (2016). Bacterial xylanases: biology to biotechnology. 3 Biotech, 6(2), 150.
  • Referans[21]Szilágyi, A., Závodszky, P. (2000). Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey. Structure, 8(5), 493-504.
  • Referans[22]Leigh, J. A., Albers, S. V., Atomi, H., Allers,T. (2011). Model organisms for genetics in the domain Archaea: Methanogens, halophiles, Thermococcales and Sulfolobales. FEMS Microbiology Reviews, 35(4) , 577–608.
  • Referans[23]Takagi, M. (1997). Characterization of DNA polymerase from Pyrococcus sp. strain KOD1 and its application to PCR. Applied and Environmental Microbiology, 63(11), 4504–4510.
  • Referans[24]Malkawi, H. I., Al-Omari, M. N. (2010). Culture-dependent and culture-independent approaches to study the bacterial and archaeal diversity from Jordanian hot springs. African Journal of Microbiology Research, 4(10), 923-932.
  • Referans[25]Budakoglu, M., Kurt, H., Karaman, M., Kumru, M., Kumral, M., Akarsubaşi, A. T. (2014). Archaeal microbial diversity of hypersaline Lake Acıgöl, Denizli, Turkey. Geomicrobiology Journal, 31(6), 454-460.
  • Referans[26]Çınar,S., Mutlu, M.B. (2016). Comparative analysis of prokaryotic diversity in solar salterns in eastern Anatolia (Turkey). Extremophiles, 20(5), 589–601.
  • Referans[27]Gulecal-Pektas, Y., Temel, M. (2017). A Window to the subsurface: Microbial diversity in hot springs of a sulfidic cave (Kaklik, Turkey). Geomicrobiology Journal, 34(4), 374-384.
  • Referans[28]Guven, K., Bekler, F. M., Guven, R. G. (2018). Thermophilic and Halophilic Microorganisms Isolated from Extreme Environments of Turkey with Potential Biotechnological Applications. In Extremophiles İn Eurasian Ecosystems: Ecology, Diversity, and Applications, 219-264.
  • Referans[29]Yücelşengün, İ.,Gargı, A. (2020). Comparative Study of Total Phenolic Contents, Antioxidant and Antimicrobial Activities of Different Extracts of Corchorus olitorius L. Growing in North Cyprus. Biological Diversity and Conservation, 13(3), 298-304.

Diversity of thermophilic archaea and their biotechnological uses

Year 2021, Volume: 14 Issue: 1, 155 - 166, 15.04.2021
https://doi.org/10.46309/biodicon.2021.781524

Abstract

Arkeler canlıların üç büyük domaininden birini oluşturan, biyokimyasal özellikleri bakımından hem bakterilerden hem de ökaryotlardan farklı olan, prokaryotik hücre tipinde tek hücreli canlılardır. Arkeler pek çok canlının hayatta kalamayacağı aşırı sıcak, aşırı soğuk ve aşırı tuzlu ve benzeri ekstrem ortamlarda yaşayabilirler. Yakın zamana kadar arkelerin sadece ekstrem ortam koşullarında yaşayabildikleri zannedilirken, son dönemlerde yapılan çalışmalardaa arkelerin başka canlı gruplarının bulunduğu normal yaşam ortamlarında da geliştikleri tespit edilmiştir. Arke türlerinin saf kültürlerinin izole edildiği tipik ortamlar; kaplıcalar, hidrotermal bacalar, solfataralar, tuz gölleri, soda gölleridir. Mikrobiyal çeşitlilik analizleri hem mikrobiyoloji temelli kültür bağımlı yöntemlerle hem de moleküler teknikler kullanılarak kültürden bağımsız yöntemlerle yapılabilmektedir. Ancak yine de çok sıcak ve basınçlı çevrelerdeki koşulları laboratuvar ortamlarında oluşturmak zordur ve birçok farklı takson gözden kaçabilir. Kültüre bağlı olarak yapılan çalışmalarda henüz kültüre edilmemiş arke türlerinin belirlenmesi söz konusu değildir. Bu nedenle son yirmi yılda, çevresel örneklerdeki 16S rRNA genlerinin PCR-bazlı amplifikasyonunu içeren moleküler tekniklerin kullanılması, kültürden bağımsız bir mikrobiyal çeşitlilik değerlendirmesine izin vermektedir. Arkelerin sıcaklık, tuzluluk ve pH açısından neredeyse sınır değerlerde işlev gösterme kabiliyetlerinin bir sonucu olarak, ekstremofilik enzimleri (ekstremozimleri) günümüzde birçok uygulamada kullanım alanı bulmaktadır. Bu derlemede termofilik arkelerin genel özelliklerine, kültürden bağımsız arkeal çeşitlilik çalışmalarına ve arke enzimlerinin biyoteknolojide kullanım alanlarına değinilmiştir.

References

  • Referans [1] Lever, M. A., Teske, A. P. (2015). Diversity of methane-cycling archaea in hydrothermal sediment investigated by general and group-specific PCR primers. Applied and Environmental Microbiology, 81(4), 1426-1441.
  • Referans[2]Garrett, R.A., Klenk, H. P. (2007). Archaea: evolution, physiology, and molecular biology. Blackwell Publishing, Oxford, United Kingdom.
  • Referans[3]Spang,A., Caceres, E. F., Ettema, T. J. G. (2017). Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science, 357, (6351).
  • Referans[4]Aslan, Z. (2019). Termal kaynaklardan izole edilen bakterilerin enzimleri üzerine çalışmalar (Master's thesis).
  • Referans[5]Stetter, K. O. (2006). History of discovery of the first hyperthermophiles. Extremophiles, 10(5), 357–362.
  • Referans[6]Merkel, A. Y., Podosokorskaya, O. A., Chernyh, N. A., Bonch-Osmolovskaya, E. A. (2015). Occurrence, diversity, and abundance of methanogenic archaea in terrestrial hot springs of Kamchatka and Saõ Miguel Island. Microbiology, 84(4), 577-583.
  • Referans[7] Barahona, S., Cortés, J., Hengst, M., Dorador, C., Remonsellez, F. (2017). Diversity of Thermophilic Iron-Pyrite-Oxidizing Enrichments from Solfataric Hot Springs in the Chilean Altiplano. In Solid State Phenomena,262, 526-530.
  • Referans[8]Moore,T.A. (2012). Coalbed methane: A review. International Journal Of Coal Geology, 101, 36–81.
  • Referans[9]Lebeis,S. L. (2014). The potential for give and take in plant–microbiome relationships. Frontiers İn Plant Science, 5, 287.
  • Referans[10]Pace, N. R., Stahl, D. A., Lane, D. J., Olsen, G. J. (1986). The analysis of natural microbial populations by ribosomal RNA sequences. In Advances İn Microbial Ecology, 1-55.
  • Referans[11]Aouad, M., Taib, N., Oudart, A., Lecocq, M., Gouy, M., Brochier-Armanet, C. (2018). Extreme halophilic archaea derive from two distinct methanogen Class II lineages. Molecular Phylogenetics and Evolution,127, 46-54.
  • Referans[12]Guzzo, J. (2012). Biotechnical applications of small heat shock proteins from bacteria. International Journal Of Biochemistry Cell Biology, 44 (10),1698–1705.
  • Referans[13]Silva, S. B., Pinheiro, M. P., Fuzo, C. A., Silva, S. R., Ferreira, T. L., Lourenzoni, M. R., Ward, R. J. (2017). The role of local residue environmental changes in thermostable mutants of the GH11 xylanase from Bacillus subtilis. International journal of biological macromolecules, 97, 574-584.
  • Referans[14]Norris, P. R., Burton, N. P., Foulis, N. A. (2000). Acidophiles in bioreactor mineral processing. Extremophiles, 4(2), 71-76.
  • Referans[15]Wiseman, A., Dalton, H. (1987). Enzymes versus enzyme-mimetic systems for biotechnological applications. Trends İn Biotechnology, 5(9), 241-244.
  • Referans[16]Schocke, L., Bräsen, C., Siebers, B. (2019). Thermoacidophilic Sulfolobus species as source for extremozymes and as novel archaeal platform organisms. Current Opinion İn Biotechnology,59, 71-77.
  • Referans[17]Cabrera, M. Á., Blamey, J. M. (2018). Biotechnological applications of archaeal enzymes from extreme environments. Biological Research, 51.
  • Referans[18]Amoozegar, M. A., Siroosi, M., Atashgahi, S., Smidt, H., Ventosa, A. (2017). Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes. Microbiology, 163(5), 623-645.
  • Referans[19]Herrero-Fresno, A., Espinel, I. C., Spiegelhauer, M. R., Guerra, P. R., Andersen, K. W., Olsen, J. E. (2018). The homolog of the gene bstA of the BTP1 phage from Salmonella enterica serovar Typhimurium ST313 is an antivirulence gene in Salmonella enterica serovar Dublin. Infection and İmmunity, 86(1).
  • Referans[20]Chakdar, H., Kumar, M., Pandiyan, K., Singh, A., Nanjappan, K., Kashyap, P. L., Srivastava, A. K. (2016). Bacterial xylanases: biology to biotechnology. 3 Biotech, 6(2), 150.
  • Referans[21]Szilágyi, A., Závodszky, P. (2000). Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey. Structure, 8(5), 493-504.
  • Referans[22]Leigh, J. A., Albers, S. V., Atomi, H., Allers,T. (2011). Model organisms for genetics in the domain Archaea: Methanogens, halophiles, Thermococcales and Sulfolobales. FEMS Microbiology Reviews, 35(4) , 577–608.
  • Referans[23]Takagi, M. (1997). Characterization of DNA polymerase from Pyrococcus sp. strain KOD1 and its application to PCR. Applied and Environmental Microbiology, 63(11), 4504–4510.
  • Referans[24]Malkawi, H. I., Al-Omari, M. N. (2010). Culture-dependent and culture-independent approaches to study the bacterial and archaeal diversity from Jordanian hot springs. African Journal of Microbiology Research, 4(10), 923-932.
  • Referans[25]Budakoglu, M., Kurt, H., Karaman, M., Kumru, M., Kumral, M., Akarsubaşi, A. T. (2014). Archaeal microbial diversity of hypersaline Lake Acıgöl, Denizli, Turkey. Geomicrobiology Journal, 31(6), 454-460.
  • Referans[26]Çınar,S., Mutlu, M.B. (2016). Comparative analysis of prokaryotic diversity in solar salterns in eastern Anatolia (Turkey). Extremophiles, 20(5), 589–601.
  • Referans[27]Gulecal-Pektas, Y., Temel, M. (2017). A Window to the subsurface: Microbial diversity in hot springs of a sulfidic cave (Kaklik, Turkey). Geomicrobiology Journal, 34(4), 374-384.
  • Referans[28]Guven, K., Bekler, F. M., Guven, R. G. (2018). Thermophilic and Halophilic Microorganisms Isolated from Extreme Environments of Turkey with Potential Biotechnological Applications. In Extremophiles İn Eurasian Ecosystems: Ecology, Diversity, and Applications, 219-264.
  • Referans[29]Yücelşengün, İ.,Gargı, A. (2020). Comparative Study of Total Phenolic Contents, Antioxidant and Antimicrobial Activities of Different Extracts of Corchorus olitorius L. Growing in North Cyprus. Biological Diversity and Conservation, 13(3), 298-304.
There are 29 citations in total.

Details

Primary Language Turkish
Subjects Biochemistry and Cell Biology (Other)
Journal Section Review
Authors

Gülsu Özkan 0000-0002-2379-0696

Gamze Başbülbül 0000-0001-8151-6321

Publication Date April 15, 2021
Submission Date August 17, 2020
Acceptance Date March 21, 2021
Published in Issue Year 2021 Volume: 14 Issue: 1

Cite

APA Özkan, G., & Başbülbül, G. (2021). Diversity of thermophilic archaea and their biotechnological uses. Biological Diversity and Conservation, 14(1), 155-166. https://doi.org/10.46309/biodicon.2021.781524

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