Special Issue "Extremophiles and Extreme Environments"

Type of Paper: Article
Title: Surface Appendages of Archaea: Structure, Function, Genetics and Assembly
Author: Ken F. Jarrell
Affiliation: Queen’s University, Kingston, Canada; E-Mail: jarrellk@queensu.ca
Abstract: Organisms representing diverse subgroupings of the Domain Archaea are known to possess unusual surface structures. These can include ones unique to Archaea such as cannulae and hami as well as archaella (archaeal flagella) and various types of pili that superficially resemble their namesakes in Bacteria, although with significant differences. Major advances have occurred particularly in the study of archaeal flagella and pili using model organisms with recently developed advanced genetic tools. There is common use of a type IV pili-model of assembly for several archaeal surface structures including flagella and certain pili. In addition, there are widespread posttranslational modifications of flagellins and pilins with N-linked glycans, some containing novel sugars. Archaeal surface structures are involved in such diverse functions as swimming, attachment to surfaces, cell to cell contact resulting in genetic transfer and biofilm formation. Sometimes functions are co-dependent on two surface structures. These structures and the regulation of their assembly are important features that allow cells to survive and thrive in extreme environments commonly inhabited by archaea including thermoacidophilic, hyperthermophilic, halophilic and anaerobic ones.

Type of Paper: Review
Title: Halophilic Bacteria as a Source of Novel Hydrolytic Enzymes 
Authors: María de Lourdes Moreno, Dolores Pérez, María Teresa García and Encarnación Mellado 
Affiliation: Department of Microbiology and Parasitology. University of Seville. C/ Profesor García González, nº2. 41012 Sevilla, Spain; E-Mail: emellado@us.es
Abstract: Hydrolases constitute a class of enzymes widely distributed in nature from bacteria to higher eucaryotes. The halotolerance of many enzymes derived from halophilic bacteria can be exploited wherever enzymatic transformations are required to function under physical and chemical conditions such as in presence of organic solvents and extremes in temperature and salt content. In the last years different screening programs have been performed in saline habitats in order to isolate and characterize novel enzymatic activities with different properties to conventional enzymes. Several halophilic hydrolases have been described, including amylases, lipases and proteases, and used for biotechnological applications. Moreover, the discovery of biopolymer-degrading enzymes offers a new solution to the treatment of oilfield waste where high temperature and salinity are typically found, while providing valuable information about heterotrophic processes in saline environments. In this work, we describe the results obtained in different screening programs specially focused on the diversity of halophiles showing hydrolytic activities in saline and hypersaline habitats, including the description enzymes with special biochemical properties. The intracellular lipolytic enzyme LipBL, produced by the moderately halophilic bacterium, Marinobacter lipolyticus showed advantages over other lipases, in particular the finding that the enzyme was active over a wide range of pH values and temperatures. The immobilized LipBL derivatives obtained and tested in regio- and enantioselective reactions, showed an excellent behavior in the production of free polyunsaturated fatty acids (PUFAs). On the other hand, the extremely halophilic bacterium, Salicola marasensis sp. IC10 showing lipase and protease activities was studied for its ability to produce promising enzymes in terms of salinity and temperature.

Type of Paper: Article
Title: Microorganisms in Extreme Temperatures: Evolution, Distribution and Molecular Mechanisms of Adaptation
Authors: Laura García-Descalzo ¹, Eva García-López ¹, Marina Postigo ¹, Alberto Alcazar ² and Cristina Cid ¹
Affiliations: ¹ Microbial Evolution Laboratory, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Spain; E-Mail: cidsc@inta.es
² Department of Investigation, Hospital Ramon y Cajal, Madrid, Spain
Abstract: There is considerable interest in investigating the microbial forms that thrive in extreme environments, especially under those environmental conditions that can provide information about evolutionary studies, applications in biotechnology or research in astrobiology. Life exists almost everywhere on the Earth. The organisms that inhabit and have adapted to these diverse environments are often classified by the extreme condition they cope with, such as temperature (psychrophiles to hyperthermophiles), pH (acidophiles and alkaliphiles), high salinity (halophiles) or pressure (barophiles). Temperature is one of the most important environmental factors for life as it influences most biochemical reactions. A reduction in temperature slows down most biochemical physiological responses, and it has been demonstrated that a reduction in temperature slows protein-protein interactions, changes the regulation of ion channel permeability and modifies enzyme kinetics. However, a temperature rise generally cannot be avoided by compensatory mechanisms, and thus the cellular components themselves, specifically the proteins, have to achieve thermostability. Here we review the main aspects on the evolution, distribution and molecular mechanisms of adaptation to extremes temperatures in psychrophilic and thermophilic microorganisms as well as summarize our latest original research results on this topic in environmental samples.

Type of Paper: Review
Title: Microbial Communication in Extreme Environments
Authors: Kate Montgomery, James Charlesworth, Rebecca LeBard and Brendan P. Burns
Affiliation: School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia; E-Mail: brendan.burns@unsw.edu.au
Abstract: Microbial communication, particularly that of quorum sensing plays critical roles in regulating gene expression in a range of bacteria. Although this phenomenon has been well studied in relation to, for example, virulence gene regulation, the focus of this article is to review our understanding of the role of microbial communication in extreme environments. Cell signaling regulates many important microbial processes and may play a pivotal role in driving microbial functional diversity and ultimately ecosystem function in extreme environments. Several recent studies have characterised cell signaling in modern analogs to early Earth communities (microbial mats), and characterization of cell signaling systems in in these communities is a key step in understanding the microbial interactions involved in function and survival in extreme environments. Cell signaling is a fundamental process that may have co-evolved with communities on the early Earth. Without cell signaling, evolutionary pressures may have even resulted in the extinction rather than evolution of certain microbial groups. One of the biggest challenges in extremophile biology is understanding how and why some microbial functional groups are located where logically they would not be expected to survive, and tightly regulated communication may be key. Finally, quorum sensing has been recently identified for the first time in archaea, and thus communication at multiple levels (potentially even inter-domain) may be fundamental in extreme environments.

Type of Paper: Review
Title: ABC Transport Proteins: The Case of the Arginine-binding Protein from Thermotoga Maritima
Authors: Alessio Ausili ¹, Maria Staiano ¹, Jonathan D. Dattelbaum ², Antonio Varriale ¹, Alessandro Capo ¹ and Sabato D’Auria ¹,*
Affiliation: ¹ Laboratory for Molecular Sensing, IBP-CNR, Napoli, Italy; E-Mail: s.dauria@ibp.cnr.it
² University of Richmond, Richmond, VA 23173, USA
Abstract: Arginine-binding protein from the extremophiles Thermotoga maritima is a 27.7 kDa protein possessing the typical two-domains structure of the periplasmic binding proteins family. The protein is characterized by very high specificity and affinity to bind to L-arginine also at high temperatures. These properties make the protein suitable as a sensitive probe for the design of a biosensor for L-arginine. It is an important requirement to investigate the stability of proteins when they are used for biotechnological applications. In this article we review the structural and functional features of an arginine-binding protein from the extremophile Thermotoga maritina as investigated by circular dichroism, fluorescence and infrared spectroscopy.

Type of Paper: Article
Title: A laboratory of the Extremophiles: Iceland CAREX Field Campaign
Authors: Viggó Marteinsson ¹, Parag Vaishampayan ² Angeles Aguilera ³, Jana Kviderova ⁴, Mauro Medori ⁵, Carlo Calfapietra ⁵, Domenica Hamisch ⁶, Francesca Mapelli ⁷, Eyjólfur Reynisson ¹,Sveinn Magnússon 1, Sara Borin ⁷, Daniele Daffonchio ⁷, Calzada-Diaz⁸, Virginia Souza-Egipsy ³, Elena González-Toril ³ and Ricardo Amils ³
Affiliations: ¹ Matis ohf. Food Safety, Environment and Genetics, Vinlandsleid 12, 113 Reykjavik, Iceland
² Planetary Protection, All the Planets – All the Time. Jet Propulsion Laboratory, NASA, California Institute of Technology Biotechnology and Planetary Protection Group
³ Centro de Astrobiología. INTA-CSIC. Spain
⁴ Institute of Botany AS CR Třeboň, Czech Republic
⁵ Consiglio Nazionale delle Ricerche Istituto di Biologia Agroambientale e Forestale via Marconi 2-05010 Porano (TR) ITALY
⁶ Department of Plant Biology Technical University of Braunschweig
⁷ DiSTAM, University of Milan, PhD School of “Earth, Environment and Biodiversity
⁸ Geology Department, University of Oviedo, Spain
Abstract: Existence of live in extreme environments has been known for a long time and such environments and their habitants have been investigated by different scientific disciplines for decades. However, reports of multidisciplinary research are uncommon. In this paper we report an interdisciplinary three day field campaign conducted in the frame work of CAREX FP7 EC program with participation of experts in different fields both in life and earth science. In situ experiments and sampling was performed in a vegetated hot springs system, about 20 m long with three interconnected main pools and a mud hot spring at the beginning of the system. The temperature was 20 °C to 100 °C and the pH 2.7 to 3.8. In situ ATP measurements revealed live in all samples and PCR and PhyloChip assay showed presence of high density of both bacterial and archeal microbes. A micro coloniser with different surfaces was successfully deployed for two days and the ARISA profiles of extracted DNA showed only a few peaks compared to the pool water, indicating low bacterial diversity on the surfaces. The CO2 was significantly highest in the top pool and decreased in the second and third pool respectively. The H2S concentration was 35 fold higher in mud opening than in other pools but the SO2 remained the same. Four biofilms were observed, mainly composed by four different algae and phototrophic protist: Zygnema sp., Klebsormidium sp., Cyanidium sp. and Euglena sp, at different sites in the stream and showed differences in photosynthetic performance. Variable chlorophyll fluorescence was measured in microbial mats and Juncus plants growing in the stream at different range of temperature. Juncus plants were collected in the temperature gradient from 30 ° C to 60 °C. The fluorescence measurements indicate that the plants are not seriously damaged by the environmental conditions and are able to maintain an optimal physiological status both in terms of stomatal conductance and assimilation in spite of elevated temperatures. Plants of Juncus sp. living in the higher water temperature showed higher CO2 assimilation than that measured in Juncus sp. living at lower temperature. The three days campaign rendered interesting results due to the collaboration of experts in different fields of science and such multidisciplinary approach are recommended for holistic studies of extreme ecosystems.

Type of Paper: Review
Title: The Function of Gas Vesicles in Halophilic Archaea and Bacteria: Theories and Experimental Evidence
Author: Aharon Oren
Affiliation: Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904 Jerusalem Israel; E-mail: aharon.oren@mail.huji.ac.il
Abstract: A few species of extremely halophilic Archaea (Halobacterium salinarum, Haloquadratum walsbyi, Haloferax mediterranei, Halorubrum vacuolatum, Halogeometricum borinquense, Haloplanus spp.) possess gas vesicles: hollow cylindrical or spindle-shaped structures built of protein subunits, that bestow buoyancy on the cells. Gas vesicles are also produced by the anaerobic endospore-forming halophilic Bacteria Sporohalobacter lortetii and Orenia sivashensis. We have extensive information on the properties of the gas vesicles in Hbt. salinarum and Hfx. mediterranei, and the regulation of their formation was investigated in-depth. Many different functions have been suggested for gas vesicle synthesis: buoying the cells towards more oxygen-rich surface layers in hypersaline water bodies to prevent oxygen limitation, reaching higher light intensities for the light-driven proton pump bacteriorhodopsin, positioning the cells in an optimal orientation for light absorption, light shielding, reducing the cytoplasmic volume leading to a higher surface-area-to-volume ratio (all for the Archaea) and dispersal of endospores (for the anaerobic spore-forming Bacteria). Except for Hqr. walsbyi which is abundantly found in saltern crystallizer brines worldwide, gas-vacuolate halophiles are not among the dominant and most successful forms of life in hypersaline environments. There only has been little research on gas vesicles in natural communities of halophilic microorganisms, and the few existing studies have failed to provide clear evidence for their possible function. This paper presents a summary of the current status of the different theories why gas vesicles may provide a selective advantage to some halophilic microorganisms.

Type of Paper: Article
Title: Changes in Salinity Drive Shifts in Microbial Communities in Hypersaline Pools in the Salton Sea Geothermal System
Authors: Steven Bolivar , Lizette Rojas and Jesse Dillon *
Affiliation: Department of Biological Sciences, California State University Long Beach, 1250 Bellflower Blvd., Long Beach, CA, USA; jesse.dillon@csulb.edu
Abstract: The Salton Sea Geothermal System (SSGS) is a geothermally active area containing mud volcanoes and hypersaline springs near the southern end of the Salton Sea, CA. Water samples were collected from springs in 2008, 2011 and 2012 to examine their microbial diversity using culture dependent and independent techniques. We hypothesized that due to their chemical and geothermal nature the hypersaline pools would contain unique microbial communities. In 2008 serial dilutions and streak plate isolations were performed to obtain pure cultures that were identified using 16S rRNA gene sequencing. Results showed the cultivation of only three haloarchaeal genera: Halorubrum, Halorhabdus and a third, previously uncultured clade. Direct environmental sequencing of 16S rRNA was employed on water samples collected in the 2011 and 2012, a period where salinity increased from 21 to 27%. This increase in salinity was accompanied by a shift away from a Haloferax-dominated community to a more diverse assemblage of members of Halobacteriaceae as well as other uncultured Euryarchaea and a single uncultured Crenarchaeal phylotype. Bacterial sequencing revealed diverse phylotypes including members of Proteobacteria, Bacteroidetes, and Firmicutes in both years, but again, little overlap in specific OTUs. These findings reveal a dynamic, remarkably diverse, prokaryotic community in the SSGS hypersaline springs.