Halophiles: Genetics and Genomes
"up-to-date and highly readable" (Biospektrum)
Caister Academic Press
R. Thane Papke and Aharon Oren
Department of Molecular and Cell Biology, University of Connecticut, Storrs CT 06269-3125, USA; Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; respectively
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Extreme halophilic environments, including salt lakes and springs, seawater evaporation facilities for the production of sea salt, and subterranean salt deposits derived from ancient oceans are distributed patchily all over the earth. The life that dominates them is microbial e.g., prokaryotes and the viruses that infect them. The best studied in these environments are the haloarchaea (family Halobacteriaceae), a diverse group of salt-loving organisms in the archaeal phylum Euryarchaeota. These remarkable organisms have an obligate requirement for salt concentrations between 10% and 35% NaCl for survival (sea water has ~3.5% salt). Haloarchaea have evolved several biochemical and molecular strategies to counteract the deleterious effects of their salty environments including efficient ion pumps, UV absorbing pigments, proteins that can resistant the effects of osmotic stress and the denaturing effects of salts. The best studied extremely halophilic member of the Bacteria is Salinibacter, which is abundant in saltern crystallizer ponds worldwide. The application of modern genomic approaches to research on halophilic Archaea and Bacteria and their viruses in recent years has yielded fascinating insights into the adaptations and evolution of these unique organisms.
This book highlights current genetics and genomics research to provide a timely overview. Chapters are written by expert authors from around the world and include topics such as: ecology and evolution of Haloquadratum walsbyi; microdiversity of Salinibacter ruber; horizontal gene transfer in halobacteria; comparative genomics of haloarchaeal viruses; genomics of the halophilic bacteria Natranaerobius thermophilus and Halobacillus halophilus; the haloarchaeal cell wall; cell cycle and polyploidy in haloarchaea; cell regulation by proteolytic systems and protein conjugation.
This major new work represents a valuable source of information to all those scientists interested in halophilic microorganisms, extremophiles, microbial ecology and environmental microbiology.
"coherent, well written, and with many references to provide access to the original literature. The two editors and the authors have made great efforts to create an up-to-date and highly readable book" from Biospektrum (2014) 20: 827.
Table of contents
1. Ecology and Evolution of Haloquadratum walsbyi Through the Lens of Genomics and Metagenomics
Lejla Pašić and Francisco Rodríguez-Valera
In this chapter we summarize the current knowledge on the ecology of natural populations of Haloquadratum walsbyi obtained through genomics and metagenomics. The cells of this enigmatic microbe populate crystallizer brines and deal with a high viral predation pressure. The natural populations of Haloquadratum walsbyi differ in genomic regions known as metagenomic islands that impart environmental adaptation: they are enriched in genes that are involved in transport of nutrients, but also in genes that code for cells surface components that can serve as viral recognition sites. Likewise, similar genomic variability is observed in natural populations of viruses that prey on this species. Natural populations of Haloquadratum walsbyi are not dominated by a single ecologically most successful lineage. Instead, they are composed of numerous (up to 80) clonal lineages that are preserved in space and time. The observed phenomena favors the 'Constant diversity' model of population dynamics which assumes that the expansion of metabolically superior clonal lineages will be selected against by predating viruses in a density-dependent fashion. This way, the microbial population would avoid catastrophic losses due to viral lysis, preserve intragenomic diversity and efficiently exploit niche resources.
2. Salinibacter ruber: The Never Ending Microdiversity?
Arantxa Peña, María Gomariz, Marianna Lucio, Pedro González-Torres, Jaime Huertas-Cepa, Manuel Martínez-García, Fernando Santos, Phillippe Schmitt-Kopplin, Toni Gabaldón, Ramon Rosselló-Móra and Josefa Antón
Salinibacter ruber is an extremely halophilic bacterium of the Bacteroidetes phylum that thrives in hypersaline environments. This bacterium shares the environment, as well as many phenotypic traits, with extremely halphilic Archaea. The study of the wide collection of strains of S. ruber isolated from around the world has shown that the species is very homogeneous from a phylogenetic point of view although it shows a very wide genomic microdiversity. In this chapter, we provide stat-of-the art data on abundance, distribution, metabolomic and genomic microdiversity of S. ruber and discuss the contribution of recombination and lateral gene transfer to the shaping of this species.
3. Horizontal Gene Transfer in Halobacteria
Matthew S. Fullmer, J. Peter Gogarten and R. Thane Papke
The Halobacteria are a class of Archaea that have been fundamentally shaped by Horizontal Gene Transfer (HGT). The mechanisms for HGT are not well understood, or are unreported. A noteworthy exception exists for the genus Haloferax, where a novel mating system exists that includes the fusion of cytoplasm between two cells. Despite shallow insight into mechanisms evidence from phylogenetics and population genetics studies demonstrate that these organisms have been able to exchange genes since their distant origins and continue to actively do so today. Single gene studies have uncovered transfer of halobacterial rhodopsins into diverse lineages such as the fungi and multiple bacterial taxa, construction of novel biosynthetic pathways, homologous recombination of parts or whole ribosomal proteins and RNAs, as well as divergent tRNA synthetases being exchanged between distant lineages. Furthermore, the very origin of the Halobacteria appears to have resulted from an influx of genes from the bacterial domain, which reshaped the fundamental metabolism from an anaerobic chemoautolithotrophic methanogen into a facultative aerobic heterotroph. Population genetics analysis demonstrated that gene flow with phylogenetically defined populations is so frequent that allele distributions resemble that of sexually reproducing eukaryotes, and acts as both a homogenizing and diversifying evolutionary force. Given all of the evidence for abundant recombination into, out of and between these lineages, how then do new, distinct, lineages such as these stably emerge? The answer appears to lie in a balance between recombination as a cohesive force holding populations together as entities recognizable as taxonomic units, and barriers to that transfer for promoting diversification. A primary candidate appears to be geographic barriers that reduce gene transfer between populations sufficiently to allow regional signatures to emerge.
4. Comparative Genomics of Haloarchaeal Viruses
Haloarchaeal viruses have been among the least studied group with prokaryotic (i.e. bacteria and archaea) hosts. However, recent efforts have brought the number of isolated haloarchaeal viruses from 20 to almost 70, environmental phage genomes from 1 to more than 40 and increased the amount of environmental sequences of halophilic viral fraction with several megabases. Also, new research has further reinforced the observation that haloarchaeal viruses are more reminiscent of bacteriophages (i.e. bacteria infecting viruses) than the morphologically varying crenarchaeal viruses. This review will update the latest advances in genomics of haloarchaeal viruses, its impact on taxonomy, and suggest some additional aspects of the bacteriophage genomics that may prove to be of significance also in haloarchaeal viral genomics.
5. Microbial Adaptation to Saline Environments: Lessons from the Genomes of Natranaerobius thermophilus and Halobacillus halophilus
Noha M. Mesbah, Inga Häänelt, Baisuo Zhao and Volker Müller
The ability of extremophiles to survive and multiply under extreme conditions is of great importance for microbial physiology, evolution and industry. Whole genome sequencing has provided significant insight into mechanisms used by extremophiles for adaptation to extreme environments. This chapter reviews the current knowledge on the adaptation of two halophiles, the anaerobic alkalithermophilic Natranaerobius thermophilus, and the aerobic Halobacillus halophilus, to their extreme environments, with emphasis on traits delineated from their genome sequences. N. thermophilus and H. halophilus have developed different mechanisms for adaptation to their extreme environments. N. thermophilus faces multiple extremes and consequently employs different and diverse adaptive mechanisms, including accumulation of compatible solutes to counteract high salinity, multiple cation/proton antiporters for intracellular pH and ion regulation and changing intracellular amino acid content in response to high temperature. H. halophilus faces predominantly salt stress and has developed a hybrid strategy for adaptation involving accumulation of a mixture of compatible solutes in addition to accumulation of molar concentrations of chloride and probably potassium inside its cells. Intracellular solute composition in H. halophilus is strictly regulated to adjust to changing extracellular osmolarity. Genomic diversity of N. thermophilus indicates the presence of complex regulatory mechanisms necessary for survival under multiple extreme conditions.
6. Staying in Shape: The Haloarchaeal Cell Wall
Jerry Eichler, Adi Arbiv, Chen Cohen-Rosenzweig, Lina Kaminski, Lina Kandiba, Zvia Konrad and Shai Naparstek
Haloarchaea are surrounded by different macromolecular structures comprising a cell wall. The composition of these cell walls is thought to contribute to the ability of these microorganisms to remain intact in the face of molar concentrations of salt. In many instances, the haloarchaeal cell is surrounded by a surface layer comprising a single protein component, the S-layer glycoprotein. Analysis of the S-layer glycoprotein has provided insight into the archaeal version of various post-translational modification, such as glycosylation and lipid modification. In other cases, haloarchaeal cells are surrounded by glycan-based structures. In this chapter, selected aspects of haloarchaeal cell wall biology are considered.
7. Cell Cycle and Polyploidy in Haloarchaea
Karolin Zerulla, Anke Baumann and Jörg Soppa
Halobacterium salinarum has a very strict cell cycle control and stops cell division when replication is inhibited. Synchronized cultures were used to quantify cell cycle-specific changes of the transcriptome and the proteome. The number of cycling transcripts and proteins is much smaller than in other species. An explanation might be the surprising finding that H. salinarum does not have an S-phase but replicates constitutively. It is the first species found to have replication uncoupled from other cell cycle processes like intracellular DNA transport and cell division. Hbt. salinarum, Haloferax volcanii and Haloferax mediterranei are all polyploid with 15 to 25 copies of their major chromosome. It is tempting to speculate that polyploidy might be typical for haloarchaea. The copy numbers of the minor chromosomes and plasmids differ from those of the major chromosome and from one another, thus the dosage of haloarchaeal genes depends on their localization on different replicons and can differ by as much as a factor of five. Nine different possible evolutionary advantages of polyploidy for haloarchaea are discussed, including a low mutation rate, high desiccation/X-ray irradiation resistance, survival over geological times or at extraterrestrial places, gene redundancy enabling the existence of heterozygous cells, relaxation of replication control, global gene dosage control, statistical instead of stochastical regulation of gene expression, and the usage of DNA as phosphate storage polymer. The majority of these evolutionary advantages require the presence of intermolecular gene conversion, which could indeed be shown to exist in haloarchaea.
8. Cell Regulation by Proteolytic Systems and Protein Conjugation
Proteases and protein conjugation systems are important in regulating cell function. Archaea synthesize (or are predicted to encode) numerous types of regulatory proteases including proteasomes, Lon protease, intramembrane cleaving proteases and others. Of these, proteasomes are demonstrated to be important in stress responses and essential to the growth of halophilic archaea. Halophilic archaea also synthesize a protein conjugation system termed sampylation in which different ubiquitin-like SAMPs are conjugated to protein targets through isopeptide bonds. While as yet unknown, sampylation is thought to regulate cellular functions by targeting proteins for proteasome-mediated degradation and for other non-proteolytic modifications. This chapter is focused on how archaea may regulate cell function through proteolysis and protein conjugation with emphasis on the halophilic archaea.
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(EAN: 9781908230423 9781908230652 Subjects: [microbiology] [bacteriology] [virology] [environmental microbiology] [extremophiles] )