- Email: [email protected]
Editorial overview: Extremophiles: From extreme environments to highly stable biocatalysts
Available online at www.sciencedirect.com
ScienceDirect Editorial overview: Extremophiles: From extreme environments to highly stable biocatalysts Elizaveta Bonch-Osmolovskaya and Haruyuki Atomi Current Opinion in Microbiology 2015, 25:vii–viii For a complete overview see the Issue Available online 23rd June 2015 http://dx.doi.org/10.1016/j.mib.2015.06.005 1369-5274/# 2015 Elsevier Ltd. All rights reserved.
Elizaveta BonchOsmolovskaya1 1 Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospekt 60 Let Oktyabrya 7, Bldg 2, Moscow 117312, Russia e-mail: [email protected]
Elizaveta Bonch-Osmolovskaya is Professor and Head of the Laboratory in Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia. She and her group are studying phylogenetic and metabolic diversity of thermophilic prokaryotes. They have isolated many new thermophilic and hyperthermophilic archaea and bacteria, including those representing new taxa of high level (phyla, orders, families). The main interest of the group is in discovering new metabolic processes in the world of thermophiles, either by enrichment with unusual energy substrates or electron acceptors, or by exploring genomes of new isolates and metagenomes from thermal environments. Search of thermostable enzymes with a possible application in bioindustry makes another important side of their work.
Haruyuki Atomi1,2 1 Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan 2
JST, CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan e-mail: [email protected]
Haruyuki Atomi is a Professor and Head of the Biochemical Engineering Laboratory at the Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University. Research in the Atomi group is focused on understanding the metabolism in extremophiles, particularly members of the Archaea. The group utilizes genome sequence data to select microorganisms likely to harbor atypical metabolism, and using conventional biochemical and genetic tools, tries to identify the enzymes involved. There is also strong interest in how gene expression is regulated in these organisms. The group is also engaged in metabolic engineering studies with the aim to enhance applicable properties in hyperthermophilic archaea.
www.sciencedirect.com
With the dramatic increase in environmental sequences and metagenome analyses in recent years, we are finally starting to understand how diverse life is on our planet. The diversity is alarmingly wider than what we had expected just a few decades ago, and made us realize how little we actually understand of microbial life. There are a number of ways to classify life, or judge the relatedness of one organism to another. One can focus on the modes of energy/carbon metabolism, resulting in classes such as chemolithotrophs, chemoorganotrophs, and photoautotrophs. One can also look to the relatedness in sequence of a particular gene or protein, such as the 16S/18S ribosomal RNA sequence, and perform phylogenetic analysis. In this section, we focus on organisms that prefer extremes of a particular environmental parameter. Until the 1960s, life was thought sustainable only under ‘ambient’ conditions; normal climate temperatures, neutral pH, 1 atm pressure and salinity somewhere between fresh water and sea water. Now we know that microbial life is found in the most extreme conditions, relative to the ‘ambient’ conditions just mentioned. In terms of temperature, there are the thermophiles (high temperatures) and psychrophiles (low temperatures). Thermophiles are further divided by the temperature range they prefer most, the moderate thermophiles (optimal growth temperature of 40–60 8C), the extreme thermophiles (60–80 8C) and hyperthermophiles (above 80 8C). Organisms that prefer extremely high pressure are designated the piezophiles. In terms of pH, there are the acidophiles (low pH) and alkaliphiles (high pH). Concerning salinity, we have the halophiles, and these can be further divided into the moderate halophiles and extreme halophiles. Together, these organisms constitute the major groups of extremophiles recognized at present (Table 1). One point that should be emphasized is that these organisms are in no way enduring or tolerating these extreme conditions. The conditions are what they prefer (hence -phile for -loving in Greek), and are thus not extreme at all for them. The present issue aims to introduce the most recent developments in the research on life under extreme conditions. The physiology and/or ecology of extremophiles including thermophiles, alkaliphiles, acidophiles, halophiles and their viruses, will be presented. Topics will also include studies on uncultured microbes and metagenomes from the extreme environments. Proteins from extremophiles are known to be adapted to optimally function Current Opinion in Microbiology 2015, 25:vii–viii
viii Extremophiles
Table 1 A list of the major groups of extremophiles recognized at present Group of extremophiles
Environmental parameter
Thermophiles Psychrophiles Piezophiles Acidophiles Alkaliphiles Halophiles
Temperature (high) Temperature (low) Pressure (high) pH (low) pH (high) Salinity (high)
Upper/lower limits of growth 122 8C a 20 8C 120 MPa pH < 0 pH > 12 NaCl saturation concentrations
under atypical conditions. Application of the enzymes from halophiles and thermophiles towards biotechnology will also be discussed in detail. In four reviews the recent achievements in the field of diversity and physiology of extremophilic prokaryotes will be presented. Ishino and Narumi describe our recent understanding on how microorganisms protect their genetic material from damage whose frequency is high at elevated temperatures or when exposed to doses of irradiation. Our present knowledge on DNA repair mechanisms in both bacteria and archaea will be discussed. Diversity and physiology of alkaliphilic prokaryotes is reviewed in the paper by Sorokin et al., as well as in that of Banciu and Muntyan. When in the first review new cultivated alkaliphilic prokaryotes are presented that participate in carbon, nitrogen and sulfur cycles in soda lakes, the second paper deals with different adaptive strategies of haloalkaliphiles inhabiting saline (NaCl) alkaline and soda (NaHCO3/Na2CO3) containing environments. Atanasova et al. describe the viruses that are present in hypersaline environments. The viruses that infect archaea, bacteria and eukaryotes will be described, along with their structural characterization. Ecological investigations of extremophilic microbial communities started in last decade of XX century revealing the uncultured majority of prokaryotes inhabiting thermal springs of Yellowstone National Park in USA. Three reviews on the extreme environments ecology will illustrate how the development of sequencing technologies and bioinformatic approaches could help the researchers to decipher the functional structure of extremophilic communities. The review by Cowan presents the metagenomic analyses of microbial communities inhabiting different types of extreme environments — hot and cold, saline and acidic, as well as those of deep subsurface where microorganisms could be affected by several extremes (geostatic pressure, elevated temperature and salinity). Another review — by Ventosa — is focused on
Current Opinion in Microbiology 2015, 25:vii–viii
metagenomics of environments with high salinity, either hyper, or moderately saline; it will show how the representatives of new bacterial taxa could be isolated based on the metagenomic data. A third review on this subject written by Hedlund shows how the uncultured thermophilic prokaryotes representing deep phylogenetic lineages get their metabolic characterization by means of metagenomic and single cell genomic approaches. Highly stable enzymes of extremophiles find application in different fields of contemporary biotechnology. Elleuche et al. introduce the latest developments in the application of thermostable enzymes from (hyper)thermophiles. In particular, the utilization of polysaccharide-degrading enzymes, lipolytic enzymes and proteases in various fields of industries is discussed. DasSarma and DasSarma describe the structural and biochemical properties of enzymes from halophiles and their differences with those of enzymes from non-halophilic organisms. They further describe the potential processes in biotechnology in which halophilic enzymes would make a great contribution. So, the reviews of this issue show that the main trends of extremophiles research are the same as in other fields of contemporary microbiology. New molecular tools make it possible at least to look in a keyhole on ‘microbial dark matter’ of extreme environments. Not only do we learn more about the phylogeny of numerous uncultured microorganisms inhabiting these habitats as it has been in previous decades — we can predict metabolic capacities of these unknown creatures, and, thus, start deciphering their environmental functions. Metagenomes from extreme environments could be regarded as a vast source of novel genes encoding highly stable biocatalysts for different biotechnological applications. At the same time, we should not forget that long ago all microorganisms were ‘uncultured’. Later some of them moved to the ‘cultured’ camp, which became larger and larger until we realized its proper size (1–5% of the whole microbial diversity). Still, the achievements of molecular techniques do not indicate that microbe hunting is over, just the contrary — hunters have got new weapons, a kind of laser swords (in reality, optical tweezers, not speaking about molecular tools helping to monitor enrichments, etc.). Still, the skill and devotion determine the success — from the review of Dmitry Sorokin et al. we see how much could be done with classical cultivation approach when prejudices are overridden. New metabolically diverse extremophilic isolates become the subjects for thorough investigations of their metabolism, adaptation strategies, repair mechanisms and new enzymes for biotechnology.
www.sciencedirect.com
ScienceDirect Editorial overview: Extremophiles: From extreme environments to highly stable biocatalysts Elizaveta Bonch-Osmolovskaya and Haruyuki Atomi Current Opinion in Microbiology 2015, 25:vii–viii For a complete overview see the Issue Available online 23rd June 2015 http://dx.doi.org/10.1016/j.mib.2015.06.005 1369-5274/# 2015 Elsevier Ltd. All rights reserved.
Elizaveta BonchOsmolovskaya1 1 Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospekt 60 Let Oktyabrya 7, Bldg 2, Moscow 117312, Russia e-mail: [email protected]
Elizaveta Bonch-Osmolovskaya is Professor and Head of the Laboratory in Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia. She and her group are studying phylogenetic and metabolic diversity of thermophilic prokaryotes. They have isolated many new thermophilic and hyperthermophilic archaea and bacteria, including those representing new taxa of high level (phyla, orders, families). The main interest of the group is in discovering new metabolic processes in the world of thermophiles, either by enrichment with unusual energy substrates or electron acceptors, or by exploring genomes of new isolates and metagenomes from thermal environments. Search of thermostable enzymes with a possible application in bioindustry makes another important side of their work.
Haruyuki Atomi1,2 1 Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan 2
JST, CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan e-mail: [email protected]
Haruyuki Atomi is a Professor and Head of the Biochemical Engineering Laboratory at the Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University. Research in the Atomi group is focused on understanding the metabolism in extremophiles, particularly members of the Archaea. The group utilizes genome sequence data to select microorganisms likely to harbor atypical metabolism, and using conventional biochemical and genetic tools, tries to identify the enzymes involved. There is also strong interest in how gene expression is regulated in these organisms. The group is also engaged in metabolic engineering studies with the aim to enhance applicable properties in hyperthermophilic archaea.
www.sciencedirect.com
With the dramatic increase in environmental sequences and metagenome analyses in recent years, we are finally starting to understand how diverse life is on our planet. The diversity is alarmingly wider than what we had expected just a few decades ago, and made us realize how little we actually understand of microbial life. There are a number of ways to classify life, or judge the relatedness of one organism to another. One can focus on the modes of energy/carbon metabolism, resulting in classes such as chemolithotrophs, chemoorganotrophs, and photoautotrophs. One can also look to the relatedness in sequence of a particular gene or protein, such as the 16S/18S ribosomal RNA sequence, and perform phylogenetic analysis. In this section, we focus on organisms that prefer extremes of a particular environmental parameter. Until the 1960s, life was thought sustainable only under ‘ambient’ conditions; normal climate temperatures, neutral pH, 1 atm pressure and salinity somewhere between fresh water and sea water. Now we know that microbial life is found in the most extreme conditions, relative to the ‘ambient’ conditions just mentioned. In terms of temperature, there are the thermophiles (high temperatures) and psychrophiles (low temperatures). Thermophiles are further divided by the temperature range they prefer most, the moderate thermophiles (optimal growth temperature of 40–60 8C), the extreme thermophiles (60–80 8C) and hyperthermophiles (above 80 8C). Organisms that prefer extremely high pressure are designated the piezophiles. In terms of pH, there are the acidophiles (low pH) and alkaliphiles (high pH). Concerning salinity, we have the halophiles, and these can be further divided into the moderate halophiles and extreme halophiles. Together, these organisms constitute the major groups of extremophiles recognized at present (Table 1). One point that should be emphasized is that these organisms are in no way enduring or tolerating these extreme conditions. The conditions are what they prefer (hence -phile for -loving in Greek), and are thus not extreme at all for them. The present issue aims to introduce the most recent developments in the research on life under extreme conditions. The physiology and/or ecology of extremophiles including thermophiles, alkaliphiles, acidophiles, halophiles and their viruses, will be presented. Topics will also include studies on uncultured microbes and metagenomes from the extreme environments. Proteins from extremophiles are known to be adapted to optimally function Current Opinion in Microbiology 2015, 25:vii–viii
viii Extremophiles
Table 1 A list of the major groups of extremophiles recognized at present Group of extremophiles
Environmental parameter
Thermophiles Psychrophiles Piezophiles Acidophiles Alkaliphiles Halophiles
Temperature (high) Temperature (low) Pressure (high) pH (low) pH (high) Salinity (high)
Upper/lower limits of growth 122 8C a 20 8C 120 MPa pH < 0 pH > 12 NaCl saturation concentrations
under atypical conditions. Application of the enzymes from halophiles and thermophiles towards biotechnology will also be discussed in detail. In four reviews the recent achievements in the field of diversity and physiology of extremophilic prokaryotes will be presented. Ishino and Narumi describe our recent understanding on how microorganisms protect their genetic material from damage whose frequency is high at elevated temperatures or when exposed to doses of irradiation. Our present knowledge on DNA repair mechanisms in both bacteria and archaea will be discussed. Diversity and physiology of alkaliphilic prokaryotes is reviewed in the paper by Sorokin et al., as well as in that of Banciu and Muntyan. When in the first review new cultivated alkaliphilic prokaryotes are presented that participate in carbon, nitrogen and sulfur cycles in soda lakes, the second paper deals with different adaptive strategies of haloalkaliphiles inhabiting saline (NaCl) alkaline and soda (NaHCO3/Na2CO3) containing environments. Atanasova et al. describe the viruses that are present in hypersaline environments. The viruses that infect archaea, bacteria and eukaryotes will be described, along with their structural characterization. Ecological investigations of extremophilic microbial communities started in last decade of XX century revealing the uncultured majority of prokaryotes inhabiting thermal springs of Yellowstone National Park in USA. Three reviews on the extreme environments ecology will illustrate how the development of sequencing technologies and bioinformatic approaches could help the researchers to decipher the functional structure of extremophilic communities. The review by Cowan presents the metagenomic analyses of microbial communities inhabiting different types of extreme environments — hot and cold, saline and acidic, as well as those of deep subsurface where microorganisms could be affected by several extremes (geostatic pressure, elevated temperature and salinity). Another review — by Ventosa — is focused on
Current Opinion in Microbiology 2015, 25:vii–viii
metagenomics of environments with high salinity, either hyper, or moderately saline; it will show how the representatives of new bacterial taxa could be isolated based on the metagenomic data. A third review on this subject written by Hedlund shows how the uncultured thermophilic prokaryotes representing deep phylogenetic lineages get their metabolic characterization by means of metagenomic and single cell genomic approaches. Highly stable enzymes of extremophiles find application in different fields of contemporary biotechnology. Elleuche et al. introduce the latest developments in the application of thermostable enzymes from (hyper)thermophiles. In particular, the utilization of polysaccharide-degrading enzymes, lipolytic enzymes and proteases in various fields of industries is discussed. DasSarma and DasSarma describe the structural and biochemical properties of enzymes from halophiles and their differences with those of enzymes from non-halophilic organisms. They further describe the potential processes in biotechnology in which halophilic enzymes would make a great contribution. So, the reviews of this issue show that the main trends of extremophiles research are the same as in other fields of contemporary microbiology. New molecular tools make it possible at least to look in a keyhole on ‘microbial dark matter’ of extreme environments. Not only do we learn more about the phylogeny of numerous uncultured microorganisms inhabiting these habitats as it has been in previous decades — we can predict metabolic capacities of these unknown creatures, and, thus, start deciphering their environmental functions. Metagenomes from extreme environments could be regarded as a vast source of novel genes encoding highly stable biocatalysts for different biotechnological applications. At the same time, we should not forget that long ago all microorganisms were ‘uncultured’. Later some of them moved to the ‘cultured’ camp, which became larger and larger until we realized its proper size (1–5% of the whole microbial diversity). Still, the achievements of molecular techniques do not indicate that microbe hunting is over, just the contrary — hunters have got new weapons, a kind of laser swords (in reality, optical tweezers, not speaking about molecular tools helping to monitor enrichments, etc.). Still, the skill and devotion determine the success — from the review of Dmitry Sorokin et al. we see how much could be done with classical cultivation approach when prejudices are overridden. New metabolically diverse extremophilic isolates become the subjects for thorough investigations of their metabolism, adaptation strategies, repair mechanisms and new enzymes for biotechnology.
www.sciencedirect.com