"a beneficial purchase for any institution or systems biology consortium ... a valuable resource that will appeal to experimentalists and modellers alike." from Alison Graham (Newcastle University, UK) writing in Microbiology Today (2012) 39: 237 read more ...

Systems Microbiology: Current Topics and Applications Edited by: Brian D. Robertson and Brendan W. Wren ISBN: 978-1-908230-02-7 Publisher: Caister Academic Press Publication Date: June 2012 Cover: hardback "a valuable resource" (Micro. Today)

from Rico Barsacchi, Varadharajan Sundaramurthy, Kees Korbee, Jacques Neefjes, Tom Ottenhoff, Tiziana Scanu and Marino Zerial writing in Systems Microbiology: Current Topics and Applications:

Host-microbe interactions are complex phenomena spanning multiple levels of complexity, from environmental and ecological factors up to the cellular and genetic levels of host responses. At each of these levels a relationship is established between one or more microorganisms and the host, resulting in formation of various forms of associations ranging from symbiosis to parasitism. Pathogens have the potential to cause disease in their hosts through host-pathogen interactions in which host defences are challenged by the invasive capacities of the pathogen. The aim of this chapter is to give an outline of attempts made to unravel the components of host-pathogen interactions at the cellular and molecular levels and to discuss strategies to skew the balance in favour of the host, focusing our attention on crucial intracellular pathogens causing globally relevant diseases such as tuberculosis, gastroenteritis, influenza and malaria.

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from Chris P. Barnes, Maxime Huvet, Nathan Harmston and Michael P.H. Stumpf writing in Systems Microbiology: Current Topics and Applications:

Modelling methodologies in the life- and biomedical sciences are hampered by the complexity of the processes and systems at work. Modelling studies into prokaryotic systems require the elucidation of the mechanistic model. In this chapter we introduction modelling methodologies and discuss the problem of model (and parameter) inference. We comment on state-of-the-art research questions and provide a general discussion on how models can and should be used in order to better understand the structure, function and dynamics of biological systems. The aim is not to provide an introduction to modelling per se, but to provide readers with an overview on the available methodologies. The modelling approach chosen depends on the biological question at hand as well as a range of social factors.

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from Sylvain Tollis, Navin Gopaldass, Thierry Soldati and Robert G. Endres writing in Systems Microbiology: Current Topics and Applications:

Phagocytosis is the fundamental cellular process by which eukaryotic cells bind and engulf particles by deforming their plasma membrane. Particle engulfment involves particle recognition by cell-surface receptors, signalling, and remodelling of the actin cytoskeleton to guide the membrane around the particle in a zipper-like fashion. The signalling complexity is daunting, involving hundreds of different molecular species during the initial stages of engulfment. For instance, the well-characterised immune Fcγ and the integrin CR3 receptors signal to tyrosine kinases and Rho GTPases, ultimately regulating a wide variety of proteins, which direct actin polymerization and myosin-motor proteins for force generation and contraction. Despite the signalling complexity, phagocytosis also depends strongly on simple biophysical parameters, such as shape and cell stiffness, or membrane biophysical properties that are independent of the type of cell or particle. We argue that these emergent, universal features are particularly important to address in order to explain this evolutionary well-conserved and robust mechanism. In this chapter we review these universal features to describe the principles of phagocytosis. Specifically, we use a recently published model of phagocytic engulfment as a guide. Finally, we discuss state-of-the-art live-cell fluorescence microscopy, recently used to elucidate the dynamics of phospholipids, actin polymerization and myosins in the particle-shape recognition by the amoeba Dictyostelium.

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from Dany J.V. Beste and Johnjoe McFadden writing in Systems Microbiology: Current Topics and Applications:

Despite decades of research many aspects of the biology of Mycobacterium tuberculosis remain unclear and this is reflected in the antiquated tools available to treat and prevent tuberculosis. Consequently, this disease remains a serious public health problem responsible for 2 to 3 million deaths each year. Important discoveries linking M. tuberculosis metabolism and pathogenesis have renewed interest in the metabolic underpinning of the interaction between the pathogen and its host. Whereas, previous experimental studies tended to focus on the role of single genes, antigens or enzymes the central paradigm of systems biology is that the role of any gene cannot be determined in isolation from its context. Therefore systems approaches examine the role of genes and proteins embedded within a network of interactions. We here examine the application of this approach to studying metabolism of M. tuberculosis. Recent advances in high throughput experimental technologies, such as functional genomics and metabolomics, provide datasets that can be analysed with computational tools such as flux balance analysis. These new approaches allow metabolism to be studied on a genome scale and have already been applied to gain insights into the metabolic pathways utilized by M. tuberculosis in vitro and identify potential drug targets. The information from these studies will fundamentally change our approach to tuberculosis research and lead to new targets for therapeutic drugs and vaccines.

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from Dirk Bumann writing in Systems Microbiology: Current Topics and Applications:

Microbial infections still cause around one quarter of all deaths globally, despite the advances that have been made in the treatment of infectious disease. The increasing occurrence of drug resistant pathogens, both old and new, coupled with an increasingly mobile human population has creatd many novel opportunities for potential pathogens to meet new human hosts. All of this requires new prevention and control strategies but progress has been slow, despite recent technological advances and increased investment. The rapid increase in data proved difficult to translate into practical applications for human health care, and new approaches and analyses are needed to make the most of new opportunities. One of these is the use of the new tools of systems biology and this chapter will review the application of these to microbial pathogens.

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"This book collects the work of renowned researchers to provide chapters outlining the mechanisms Archaea, Bacteria and Eukarya use to survive extremes of temperature, pH, pressure and ionizing radiation. It focuses strongly on commercial applications ... recommended for senior undergraduates' independent reading or the reference of workers in the field alike" from Arwyn Edwards, Aberystwyth University, UK writing in Microbiology Today (2012) read more ...

Extremophiles: Microbiology and Biotechnology Edited by: Roberto Paul Anitori ISBN: 978-1-904455-98-1 Publisher: Caister Academic Press Publication Date: January 2012 Cover: hardback "recommended" Micro. Today

"a solid and critical review of the impact that extremophiles have in biotechnology. It discusses the adaptation of thermophilic, psychrophilic, acidophilic, and radiation-resistant microorganisms in their respective habitats ... the book offers newcomers to the biotechnology industry a good overview and a simple introduction to the subject, above all on future trends and web sources. " from Sonja Albers (Marburg) writing in BIOspektrum (2012) 18: 224. read more ...

Extremophiles: Microbiology and Biotechnology Edited by: Roberto Paul Anitori ISBN: 978-1-904455-98-1 Publisher: Caister Academic Press Publication Date: January 2012 Cover: hardback "a good overview" (Biospektrum)

from Mark Paul Taylor, Lonnie Van Zyl, Marla Tuffin and Don Cowan writing in Extremophiles: Microbiology and Biotechnology:

In principle, extremophiles have much to offer the biotechnology industry, from robust, process hardy enzymes to metabolically and physiologically diverse whole cell biocatalysts. However, the penetration of extremophilic organisms and their products into biotechnology markets has been modest at best, with preference given to engineered, cost effective enzyme variants and organisms for which established genetic tools are widely available. Interest in 'xtreme' products has often been dissuaded due to the unattractive need for the sometimes costly and complicated cultivation equipment and the complexities of culture maintenance. The lack of suitable genetic tools by which to improve, adapt or engineer a process involving an extremophilic host further complicates the issue. Legislative controls over national biological resources and allegations of biopiracy have also retarded commercialisation and industry-academia collaborations. However, commercial success stories have been described and form part of this review. Future prospects are optimistic, as several new biotechnology companies involved in the production of biomolecules from renewable resources have based their platform technology on extremophiles.

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from Hans Kristian Kotlar writing in Extremophiles: Microbiology and Biotechnology:

In the deep biosphere, extraordinary new types of microorganisms, sedimented or buried 200 - 500 million years ago, can be found. These organisms can be identified and characterized. The information obtained can be developed into novel tools for searching for new oil in sensitive regions like the Arctic, Antarctica and jungle areas. Relatively few enzymes are used in large-scale industrial applications. Enzymes isolated from these extremophile/ thermophile organisms might provide “game changing” new possibilities. They may furnish new incentives for the development of entirely new technical processes. These microbes provide opportunities for new technologies in second generation biofuel production. Several companies are working on alternative routes for the production of fuels using biomass as the raw source material. Traditional heavy oil extraction methods have major difficulties in justifying their high energy usage, CO₂ emissions and soil and environment pollution. The first company implementing a large-scale process based on biotechnology principles in enhanced oil recovery will gain huge strategic and economic benefits. The knowledge of this huge subsurface population of diverse microorganisms provides excellent opportunities for bioprospecting. There should be a multitude of spin-offs outside the oil industry. The world is desperately in need of new enzymes, new antibiotics, new immunosuppressant, new anticancer agents, etc. This chapter reviews just some of the areas we have been working on at Statoil. Hopefully some of these investigations could one day solve some of the problems we will face in the future. One day these extremophiles could be on the payroll of many different companies.

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from Helena Nevalainen, Ron Bradner, Sania Wadud, Suja Mohammed, Christopher McRae and Junior Te'o writing in Extremophiles: Microbiology and Biotechnology:

Fungi are eukaryotic organisms and considered to be less adaptable to extreme environments when compared to bacteria. While there are no thermophilic microfungi in a strict sense, some fungi have adapted to life in the cold. Cold-active microfungi have been isolated from the Antarctic and their enzyme activities explored with a view to finding new candidates for industrial use. On another front, environmental pollution by petroleum products in the Antarctic has led to a search for, and the subsequent discovery of, fungal isolates capable of degrading hydrocarbons. The work has paved the way to developing a bioremedial approach to containing this type of contamination in cold climates. Here we discuss our efforts to map the capability of Antarctic microfungi to degrade oil and also introduce a novel cold-active fungal lipase enzyme.

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from Eivind Almaas, Per Bruheim, Rahmi Lale and Svein Valla writing in Systems Microbiology: Current Topics and Applications:

The functional repertoire of an organism's metabolic network is closely linked to its phenotype and potential for utility in metabolic engineering applications. In this chapter, we discuss a systems biology view of Escherichia coli metabolism by integrating current genome-scale computational modelling approaches with available molecular genetics tools, as well as the experimental framework for metabolite and metabolic flux determination.

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from T.A. Vishnivetskaya, B. Raman, T.J. Phelps, M. Podar and J.G. Elkins writing in Extremophiles: Microbiology and Biotechnology:

Conversion of lignocellulosic biomass to liquid fuels using biological processes offers a potential solution to partially offset the world's dependence on fossil fuels for energy. In nature, decomposition of organic plant biomass is brought about by the combined action of several interacting microorganisms existing in complex communities. Bioprospecting in natural environments with high cellulolytic activity (for example, thermal springs) may yield novel cellulolytic microorganisms and enzymes with elevated rates of biomass hydrolysis for use in industrial biofuel production. In this chapter, various cellulose-degrading microorganisms (in particular, thermophilic anaerobic bacteria), their hydrolytic enzymes, and recent developments in the application of biomass fermentations for production of sustainable bioenergy are reviewed. In this context, results from ongoing research at the Oak Ridge National Laboratory in the isolation and subsequent phylogenetic and metabolic characterization of thermophilic, anaerobic, cellulolytic bacteria from the hot springs of Yellowstone National Park are presented.

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from Diana Clausznitzer, Judith P. Armitage and Robert G. Endres writing in Systems Microbiology: Current Topics and Applications:

Bacterial chemotaxis is a paradigm for biological sensing and information transmission. The chemotaxis signal-transduction pathway allows cells to sense chemicals in their surroundings in order to regulate flagellated rotary motors, thus allowing them to swim towards nutrients and away from toxins. Importantly, cells are able to sense with remarkably high sensitivity over a wide range of chemical background concentrations. To make this possible, chemoreceptors do not signal independently but form clusters for amplification and integration of signals, as well as for adaptation to persistent stimulation. While chemotaxis in Escherichia coli has been exceptionally well characterised, new experimental facts still require revisions of existing models and thus further increase our understanding of sensing and signalling in bacteria. Additionally, experiments on other bacterial species such as Bacillus subtilis and Rhodobacter sphaeroides indicate that bacteria other than E. coli can have substantially different and more complex chemotaxis pathways, which provides renewed challenges for experimentalists and modellers alike. Here we discuss our current understanding as well as the frontiers of bacterial chemotaxis research.

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from Theresa Kouril, Alexey Kolodkin, Melanie Zaparty, Ralf Steuer, Peter Ruoff, Hans V. Westerhoff, Jacky Snoep, Bettina Siebers and the SulfoSYS consortium writing in Systems Microbiology: Current Topics and Applications:

Life at high temperature challenges the stability of macromolecules and cellular components, but also the stability of metabolites, which has received little attention. For the cell, the thermal instability of metabolites means it has to deal with the loss of free energy and carbon, or in more extremes, it might result in the accumulation of dead-end compounds. In order to elucidate the requirements and principles of metabolism at high temperature, we used a comparative blueprint modelling approach of the lower part of the glycolysis cycle. The conversion of glyceraldehyde 3-phosphate to pyruvate from the thermoacidophilic Crenarchaeon Sulfolobus solfataricus P2 (optimal growth-temperature 80ºC) was modelled based on the available blueprint model of the eukaryotic model organism Saccharomyces cerevisiae (optimal growth-temperature of 30ºC). In S. solfataricus only one reaction is different, namely glyceraldehyde-3-phosphate is directly converted into 3-phosphoglycerate by the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase, omitting the extremely heat-instable 1,3-bisphosphoglycerate. By taking the temperature dependent non-enzymatic (spontaneous) degradation of 1,3-bisphosphoglycerate in account, modelling reveals that a hot lifestyle requires a cool design.

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from Kazem Kashefi writing in Extremophiles: Microbiology and Biotechnology:

The isolation and characterization of novel hyperthermophilic, microorganisms from modern hot environments have greatly increased our understanding of how microbes can live and thrive in such inhospitable environments. The finding that microorganisms have the ability to grow at these high temperature has implications for delimiting when and where life might have evolved on a hot, early Earth; the depth to which life exists in the Earth's subsurface; and the potential for life in hot, extraterrestrial environments. The study of hyperthermophilic microorganisms provides valuable insights into microbial respiration in a diversity of modern and ancient hydrothermal systems. In addition, it provides information about the fate of metals such as iron, uranium, technetium, and even gold. Reduction of these metals by hyperthermophiles provides, for example, a likely explanation for a number of geologically, environmentally and economically important ore deposits. This allows us to identify geological signatures for biological processes, something that may prove instrumental in our search for life on other planets. Finally, enzymes capable of functioning at high temperatures have a number of important applications in biomass conversion, in biotechnology, and in the pharmaceutical, food and cosmetic industries.

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from Kelley R. Gwin and John R. Battista writing in Extremophiles: Microbiology and Biotechnology:

Of all the phenotypes associated with microorganisms, ionizing radiation resistance - the ability to survive exposure to high dose gamma radiation - is perhaps the most difficult to rationalize in terms of the natural world. There is no obvious selective advantage to being ionizing radiation resistant on Earth, as average yearly exposures to ionizing radiation from cosmic rays and radioactive decay are extremely low. Yet a significant number of genera exhibit this characteristic, displaying a remarkable capacity to tolerate levels of damage to cellular macromolecules that eradicates other forms of life. We argue that ionizing radiation resistance is an incidental characteristic, an inadvertent consequence of an evolutionary path that permitted these species to survive a selective pressure capable of damaging the cell in a manner similar to that of ionizing radiation. The phylogenetic distribution of ionizing radiation resistant species argues that these events occurred multiple times during the evolution of the Bacteria and Archaea, suggesting that different mechanisms may mediate ionizing radiation resistance.

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from Elizaveta Bonch-Osmolovskaya writing in Extremophiles: Microbiology and Biotechnology:

Thermophilic microorganisms, though known since the beginning of the 20th century, were intensively studied in its last three decades. Natural terrestrial and submarine thermal environments were found to be populated by moderate, extreme and hyperthermophilic microorganisms representing diverse metabolic groups. However, during the past few years this knowledge has been extended, and new metabolic groups of thermophilic prokaryotes described. Among these are ammonia-oxidizing archaea, thermoacidophilic methanotrophs of the phylum Verrucomicrobia, microorganisms gaining energy for growth from the disproportionation of sulfur species, and archaea and bacteria metabolizing one carbon (C1) compounds. Other novel metabolic groups, such as thermophilic anammox bacteria, nitrite-oxidizing thermophiles, and microorganisms performing anaerobic methane oxidation in thermal ecosystems, have been detected using molecular or geochemical approaches. These data will, certainly, stimulate further cultivation and isolation efforts.

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from Chiaki Kato writing in Extremophiles: Microbiology and Biotechnology:

Piezophilic microorganisms, which are defined as "pressure-loving" microorganisms, are isolated and characterized from high pressure environments. They grow better at high-hydrostatic pressures than at atmospheric pressures, and only exist at deeper water column environments, particularly in the deep-sea bottoms. Therefore, piezophilic microorganisms are typical deep-sea microorganisms that are well adapted to deep-sea pressure and temperature conditions. These microorganisms have special strategies for surviving in such extreme environments, where gene expression and enzyme activities could be controlled by pressure. Studies on adaptations to high pressure environments have recently been studied in detail, and the mechanisms involved are being elucidated. In this chapter, the distribution, taxonomy, cultivation and molecular characters of piezophiles are described.

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from Mark Dopson writing in Extremophiles: Microbiology and Biotechnology:

Acidophilic microorganisms are capable of growth at low pH and are defined as having an optimum below pH 5, with some extreme acidophiles capable of growth at pH 0. Acidophiles have an important role in ecology by catalyzing the generation of acidic, metal-containing solutions that can inhibit plant and animal growth, and in biotechnology via their propensity to solubilize metals from sulfide minerals. This review summarizes the most important aspects of acidophile physiology, including growth substrates (e.g. inorganic and organic carbon) and energy sources; temperature optima (from cold environments to high temperature thermal pools); and adaptations to metals in solution and low growth pH. The exploitation of acidophiles in biotechnology (e.g. in biomining) and potential future trends in research are also discussed. Due to a lack of general genetic systems in acidophiles, much of the latest research has been generated by systems biology approaches and these data have been focused upon.

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from Corien Bakermans writing in Extremophiles: Microbiology and Biotechnology:

Psychrophilic, or cold-loving, organisms actively live at low temperatures. Psychrophily is not an uncommon trait; cold-adapted organisms are found throughout the three domains of life and successfully inhabit a wide variety of low temperature environments. The ongoing investigation of these environments continues to broaden our view of what is possible for life on Earth. Cold-adapted microorganisms have evolved mechanisms to deal with the thermodynamic constraints of low temperatures. To combat the stability and decreased flexibility of macromolecules, psychrophiles generally increase the disorder within macromolecules to maintain fluidity or flexibility and hence function at low temperatures. To contend with reduced water activity and the presence of ice crystals, cryoprotectants are produced. To counteract decreased reaction and diffusion rates, psychrophiles practice efficient growth. Currently, the functional low-temperature limits of psychrophiles are minus 12 degrees celsius for reproduction and minus 20 degrees celsius for metabolism. The availability of liquid water appears to be the major growth-limiting factor at subzero temperatures. Examination of molecular and physiological adaptations to low temperatures is increasing our comprehension and appreciation of the capabilities of psychrophiles and their contribution to nutrient cycling in low temperature environments.

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from Christine Moissl-Eichinger, Ruth Henneberger and Robert Huber writing in Extremophiles: Microbiology and Biotechnology:

The SM1 euryarchaeon represents an extraordinary microorganism: in the surface waters of cold, sulfidic springs, it lives together with filamentous bacteria, forming the so called string-of-pearls community. In the subsurface however, it can grow partner-independently as a "monospecies" biofilm. Even though the SM1 euryarchaeon is still uncultivated in the laboratory, it is accessible via an in situ cultivation technique using its own biotope as a natural chemostat. This approach allowed the study of its biology, and enabled the discovery of unique cell surface appendices with unexpected and unusually high complexity. Each of the archaeal cells is surrounded by approximately 100 protein filaments that are up to 3 micrometres long and show a high resemblance to barbwire with a tripartite grappling hook at their tip. Based on this structure the appendices were called "hami" (lat. hamus = (grappling) hook). These hami represent perfectly evolved, natural mechanical nano-tools that could find applications in the growing field of nanobiotechnology.

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