Cold-Adapted Microorganisms | Book
Caister Academic Press
Isao Yumoto National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
x + 226 (plus colour plates)
September 2013Buy book
GB £159 or US $319
October 2013Buy ebook
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The earth is dominated by low-temperature environments including 90% of oceans and 26% of terrestrial soil ecosystems. Once thought too cold for life these environments have been shown to support diverse microbial communities. Psychrophiles use a wide variety of metabolic pathways, including photosynthesis, chemoautotrophy and heterotrophy and form robust, diverse communities. Cold-adapted microorganisms play a major role in nutrient turnover and primary biomass production in cold ecosystems and have important applications in biotechnology and in the study of food spoilage microorganisms.
In this up-to-date book, prominent authors present cutting-edge knowledge and current concepts on cold-adapted microorganisms. Divided into three main sections the book covers the major aspects of biodiversity in cold ecosystems, the physiology and molecular adaptation mechanisms, and the various biomolecules related to cold adaptation. Individual chapters cover the various habitats and the diverse strategies employed to cope with the cold. This major new work represents a valuable source of information to all those scientists interested in cold-adapted microorganisms, extremophiles, microbial ecology and environmental microbiology.
"carefully edited and with an extensive bibliography ... a wealth of interesting findings and a very good access to the primary literature " from Erhard Bremer (Marburg, Germany) writing in BIOspektrum (2014) 20: 256-357.
"a wealth of interesting findings" (Biospektrum)
Diversity of Bacteria in Permafrost
Shannon Hinsa-Leasure and Corien Bakermans
In the cold challenging environment of the permafrost, bacteria have found a way to survive and grow for thousands to millions of years. In this chapter, we explore bacterial diversity in permafrost from around the world, identified through culture-dependent and -independent techniques. Members of the phylum Actinobacteria, Firmicutes and Proteobacteria have been found in every environment studied thus far, indicating that these bacteria are well suited for life at low temperatures with low water activity. Also, unique species specific to individual environments have been discovered at each site. Researchers are faced with the challenge of determining which bacteria are active in the permafrost and which are in a dormant state. The ability of bacteria to reside in a dormant state further complicates culture-independent experimental results, as DNA from both dormant and active cells has been analyzed. We are only beginning to understand the metabolic capabilities of permafrost bacteria, many discoveries are still to come.
Ecology and Taxonomy of Psychrotolerant Bacteria in Artificial Cold Environments
Isao Yumoto and Koji Yamazaki
A variety of artificial cold environmental conditions exist around human activities. These environments involve several factors that define the kinds of bacteria existing in niches. These environmental factors change with time owing to changes in the environment caused by existing microorganisms and their metabolisms. Namely, the inevitable selection of bacteria occurs in each artificial cold environment and the successive changes in microbiota occur according to changes in environmental factors. Some of the microorganisms in these microbial communities are useful for the degradation of organic matter in cold environments and for food preservation. On the other hand, several microorganisms adapted to artificial cold environments cause food spoilage. The frequently isolated psychrotolerant bacterial genera in artificial cold environments are Pseudomonas, Psychrobacter, Staphylococcus and Photobacterium. Lactic acid bacteria are also frequently detected under anaerobic conditions. To date, it has been reported that these genera are widely distributed in natural as well as artificial cold environments. It is intriguing why these bacterial genera are widely distributed in cold environments and why certain species belonging to these genera are able to survive in artificial cold environments. The frequent detection of members of above-mentioned genera in artificial cold environments suggests that the important factors that define the existence of these genera in cold artificial environments are i) chances of invasion of such cold environments from ambient environments, ii) chances of invasion through their own basic components, iii) ability to rapidly propagate at low temperature and iv) presence or absence of oxygen. It is also considered that these genera are genetically widely diverse, and cold artificial environment adaptation mechanisms of certain species belonging to these genera make their distribution wider not only in natural cold environments but also in artificial cold environments.
Psychrophilic Microorganisms in Marine Environments
Psychrophilic microorganisms are extremophiles that are capable of growth and reproduction at low temperatures. They are present in marine environments, which occupy slightly more than 70% of Earth's surface, especially in the Arctic, Antarctica, and deep seas at temperatures lower than 15°C. Marine psychrophiles utilize a wide variety of metabolic pathways, including photosynthesis, chemoautotrophy, and heterotrophy. The deep-sea bacteria called psychropiezophiles "love" both high pressure and low temperature. Marine psychrophiles are characterized by lipid cell membranes chemically resistant to hardening in response to the cold. Most psychrophiles are Bacteria, and psychrophily is present in widely diverse microbial lineages within the broad groups of Alpha-, Beta-, Delta-, and Gammaproteobacteria and the Bacteroidetes phylum.
Fungi in Cryosphere: Their Adaptation to Environments
Tamotsu Hoshino, Nan Xiao, Yuka Yajima and Oleg B. Tkachenko
Cold-adapted fungi are widely distributed in the cryopsphere where biosphere is constantly or seasonally covered with snow and/or ice. Fungi normally have different cells in their lifecycle; therefore, thermal dependence of fungal lifecycle stages is completely different from that of bacteria. We showed examples from fungi that the concept of "psychrophile" by Moria in 1975 was not applicable and propose a new term "cryophilic fungi" for those that spend a certain life stage or whole life cycle (sexual and/or asexual reproductions) in cryosphere. Several groups of fungi associated with snow and/or ice, i.e., cryophilc fungi, are illustrated in terms of their ecology, and their ecophysiological adaptation mechanisms to freezing stress are reviewed, here.
Energy Metabolism in Low-temperature and Frozen Conditions in Cold-adapted Microorganisms
Managing biochemical energy is a challenge that microorganisms have to face for maintaining activity at low temperatures, at which metabolic processes are altered by the decrease of reactions rates and by the rigidification of cellular structures, notably enzymes and membranes. Cold-adapted prokaryotes and eukaryotes, while exhibiting distinct trophic modes, share specificities for compensating these thermodynamic effects and keep the cellular machinery running: they elevate the concentration of adenylate compounds, the key molecules of the energy metabolism. This is achieved by tight adjustments acting at several levels of the metabolism in a global strategy of energy saving: strong orientation of the adenylate metabolism toward the production and regeneration of AMP and its phosphorylation, whereas its destruction is repressed; elevation of the respiration rate; intervention of specific enzymes allowing the rapid synthesis of ATP (polyphosphatases and interferases), shifts in the utilization of substrates; and rerouting of central metabolic pathways. These are presented here and illustrated by examples of metabolic regulations in cold-adapted microorganisms evidenced by recent transcriptomic and proteomic approaches.
Proteins Involved in Cold-adaptation
Kazuaki Yoshimune, Jun Kawamoto and Tatsuo Kurihara
This chapter primarily describes cold shock proteins (CSPs), which are induced in response to temperature downshift in both psychrophiles and mesophiles. These proteins are important for various cellular processes, including transcription, translation, protein synthesis and folding, and membrane functions, to maintain their viability under cold conditions. Here, the CSPs in psychrophilic and mesophilic microorganisms are represented on the basis of the results of proteome analyses. In particular, CSPs that were isolated from the Antarctic psychrophile Shewanella livingstonensis Ac10 are described in detail. A number of microorganisms induce molecular chaperones in response to the cold, although the majority of chaperones are induced as a result of heat shock. Chaperones with peptidyl prolyl cis-trans isomerase activity are often induced by cold to accelerate protein folding by interconverting the cis and trans isomers of proline imidic peptide bonds, and these cold shock chaperones are also discribed here. Cold adapted proteins often have higher flexibility as compared to mesophilic proteins. The features of cold adapted proteins are briefly described. Finally, the production of recombinant proteins in psychrophiles is shown to suggest a future application of psychrophiles.
Heat Shock Responce in Psychrophilic Microorganisms
Seiji Yamauchi, Shinsuke Fukuda and Hidenori Hayashi
Psychrophilic microorganisms can optimally grow at temperatures below 15°C. In these microorganisms, heat stress occurs at relatively low temperatures in comparison with that in mesophilic microorganisms. The majority of psychrophilic microorganisms possess genes encoding a complete set of heat shock proteins (Hsps). Therefore, psychrophilic microorganisms respond to heat stress by producing Hsps like other microorganisms; however, they need a specific system to enable the expression and function of Hsps at relatively low temperatures. In this chapter, we summarize the heat shock response of psychrophilic microorganisms, focusing on how this response starts working at relatively low temperatures and what the features of psychrophilic Hsps are.
Catalysis and Protein Folding in Psychrophiles
Enzymes have the property to catalyze most of the chemical reactions occuring in living organisms and their efficiency is exponentially depending on temperature through the Arrhenius law. On the other hand psychrophiles are organisms that live in permanently cold habitats so, in the absence of adaptation, the rate of the chemical reactions would be to slow to sustain life. In fact, these organisms display, at the low temperature of their environment, metabolic fluxes close to that of their mesophilic counterparts. That means that their enzymes have been modified in order to compensate for the cooling effect on reaction rates. The analysis of the structure, catalytic properties and thermal stability of an already large number of psychrophilic enzymes has demonstrated that discrete changes in the amino acid sequence of these enzymes can confer a high catalytic efficiency at low and moderate temperatures. This is accompanied by a significant decrease of the thermal stability itself inducing a large increase of the flexibility of the molecular structure that enables the accomodation of the substrate even at temperatures lower than the freezing point of water. The folding process,which, in theory, is also rendered uneasy due to the large increase in viscosity, the low residual energy in the system and the depressive effect of low temperatures, notably on hydrophobic interactions, is also rescued, mainly, through the overexpression of peptidyl prolyl cis/trans isomerases and of the trigger factor which is the first to take in charge the nascent polypeptide chain.
Cold-adapted H2O2 Tolerant Bacteria and their Catalases
Isao Yumoto and Isao Hara
Three novel species of psychrotolerant H2O2-resistant bacteria have been isolated from drain pools of a fish egg processing plant that uses H2O2 as a bleaching agent. Among them Vibrio rumoiensis was isolated from downstream of the drain pool, whereas Exiguobacterium oxidotolerans and Psychrobacter piscatorii were isolated from upstream. The catalase activity in the cell extract of the former was lower than that in the latter, which reflected the H2O2 concentration in their niches. The VktA (catalase from V. rumoiensis) and PktA (catalase from P. piscatorii) belonged to clade III, and EktA (catalase from E. oxidotolerans) belonged to clade I. From the temperature profile of their activities, these catalases exhibited heat sensitivity at higher than 60°C. The cell extract of V. rumoiensis exhibited lower catalase content (1.8%) than that of P. piscatorii (10%), whereas the former produces VktA, which exhibited a higher catalytic efficiency than the PktA. EktA content in the cell extract of E. oxidotolerans was 6.5% and EktA exhibited the highest catalase activity in both cell extract and the purified form among the three catalases. EktA possesses a wider bottleneck structure in the main channel for accepting substrates, enable it to react efficient with organic peroxides larger than H2O2 as substrates. Considering the environmental adaptation and distribution of microorganisms in this unique niche with high concentrations of H2O2 and low temperatures, certain variations of unknown bacterial species exist with certain variations of environmental adaptation mechanisms (e.g., cellular localization, production rate, and catalytic efficiency of catalase) depending on the environmental H2O2 concentration and fragility of cells. Furthermore, the characteristics of these catalase molecules reflect the environmental conditions (low temperatures and high concentrations of H2O2) under which these bacteria survive.
Microorganisms in Permafrost Ice Wedge and their Resuscitation Promoting Factor
Katayama Taiki and Michiko Tanaka
Bacteria and fungi preserved for long periods at sub-zero temperatures in Alaskan and Siberian permafrost ice wedge were reactivated on agar by aerobic cultivation at 15°C. Culturable bacteria differed among ice samples, but several phylogenetic groups were closely related to those in other frozen environments. Incubation under controlled temperatures and the Arrhenius profiles of bacterial isolates from the Alaskan ice wedge indicated that they could grow at temperatures below 0°C without remarkable alterations in their cellular process. The novel ice wedge isolates, Glaciibacter superstes AHU1791T and Tomitella biformata AHU1821T, increased membrane fluidity at lower to subzero temperatures by modulating the fatty acid composition of the cytoplasmic membrane. Reactivating the non-culturable state of ice wedge isolates using resuscitation promoting factor (Rpf) and culturing melted ice wedge with Rpf provided indirect evidence that non-culturable bacteria exist within the ice wedge in situ. Bacteria in ice wedges can change their membrane fatty acid composition and/or structure to survive, but may then lose the ability to grow under laboratory conditions, as a final adaptation to long periods in a frozen natural environment.
Lipids in Cold-adapted Microorganisms
Ahmad Iskandar Bin Haji Mohd Taha, Rifat Zubair Ahmed, Taro Motoigi, Kentaro Watanabe, Norio Kurosawa and Hidetoshi Okuyama
Ever since Escherichia coli, which is a mesophilic bacterium, was found to adjust its membrane fluidity in a liquid crystalline state by modulating fatty acid composition and the designation of this process as homeoviscous or homeophasic adaptation, numerous analogous phenomena have been reported in cold-adapted bacteria [psychrophilic or psychrotrophic (psychrotolerant) bacteria]. Unsaturation, which includes the biosynthesis of monounsaturated or long-chain polyunsaturated fatty acids and branched fatty acids, and branched-chain formation are the most important types of fatty acid modulation in psychrophilic and psychrotrophic (psychrotolerant) bacteria. The distribution of these fatty acids is not restricted to cold-adapted microorganisms: rather, it appears to depend on bacterial diversity (Gram- positive or negative) and/or habitat (terrestrial or marine environment) than on temperature. Eicosapentaenoic acid, which has been detected only in marine Gram-negative bacteria, had been regarded to confer significant membrane fluidity in bacteria, but it is now considered that it may also have a function in antioxidation or membrane modulation by constraining membrane fluidity. The mode of fatty acid modulation is unlikely to differ between psychrophilic and psychrotrophic bacteria, which had narrower and wider growth temperature ranges, respectively. The sole difference seems to be higher capacity to modulate fatty acid composition in psychrotrophic bacteria than in psychrophilic bacteria.
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(EAN: 9781908230263 Subjects: [microbiology] [bacteriology] [environmental microbiology] [extremophiles] )