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Archaea: Evolution, Physiology, and Molecular Biology
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Archaea: Evolution, Physiology, and Molecular Biology

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: closed (30 November 2014) | Viewed by 176033

Special Issue Editors

Prof. Dr. Hans-Peter Klenk

grade E-Mail Website
Guest Editor
School of Biology, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
Interests: origins of life; archaea; actinomycetes; phages; life in extreme environments; microbial genomics; phylogenomics; taxonomy; microbial diversity; systems biology
Prof. Dr. Michael W. W. Adams

E-Mail Website
Guest Editor
Distinguished Research Professor, Department of Biochemistry and Molecular Biology, The University of Georgia Athens, GA 30602, USA
Interests: life at extreme temperatures; physiology, metabolism, genetics and enzymology of hyperthermophilic archaea; metabolic engineering and biofuel production; hydrogen metabolism; metal metabolism and metalloenzymes
Prof. Dr. Roger A. Garrett

E-Mail Website
Guest Editor
Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
Interests: comparative archaeal genomics; CRISPR adaptive immune systems; crenarchaeal viruses and plasmids; archaeal mobile elements and toxin-antitoxin systems; biochemistry; genetics and cell biology of extremophilic archaea
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The Archaea are a unique and interesting group of microorganisms that form the last discovered of the three domains of life. The study of these fascinating life forms is an exciting area of research with the potential to provide new insights into a wide range of basic and applied sciences. As one of the most ancient lineages of living organisms, the Archaea set a boundary for evolutionary diversity and have the potential to offer key insights into the early evolution of life, including the origin of the eukaryotes.
Archaea have furnished us with novel paradigms for understanding fundamentally conserved processes across all domains of life. In addition, they have provided numerous examples of novel biological mechanisms that give us a much broader view of the forms that life can take and the way in which microorganisms can interact with other species.
Many archaea are extremophiles flourishing in environments that are hostile to other living organisms and their biomolecules provide numerous opportunities for biotechnological development. However, representatives of the Archaea are not restricted to extreme environments; new studies are showing that they are also widespread in a broad range of ordinary habitats, including soils, oceans, marshlands, and the human colon and navel. Archaea are particularly numerous in the oceans and the archaea in plankton may be one of the most abundant groups of organisms on the planet. Consequently, some of these microorganisms might be essential components of the biogeochemical cycles. Furthermore, since methanogens are the primary source of atmospheric methane and are responsible for most of the world's methane emissions, these archaea might contribute to global greenhouse gas emissions and global warming. Finally, due to their ability to thrive in extreme environments on Earth, Archaea are quite relevant in the astrobiological context for studying the possible presence of life forms that resemble the Archaea in extraterrestrial environments.
For these reasons, studies on archaeal biology are growing quite fast and represent a promising field of research. In this Special Issue, some of the recent advances and discoveries involving the underlying biology of this fascinating domain of life are presented.

Prof. Dr. Hans-Peter Klenk
Prof. Dr. Michael W. W. Adams
Prof. Dr. Roger A. Garrett
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


Keywords

  • crenarchaeota
  • euryarchaeota
  • methanogens
  • biogeochemistry
  • biotechnology
  • archaeal viruses
  • extremophiles
  • non-extremophilic archaea
  • genetics, genomics and proteomics
  • ecology, diversity and evolution

Published Papers (20 papers)

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Research

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1819 KiB  
Article
The Effects of Temperature and Growth Phase on the Lipidomes of Sulfolobus islandicus and Sulfolobus tokodaii
by Sara Munk Jensen, Vinnie Lund Neesgaard, Sandra Landbo Nedergaard Skjoldbjerg, Martin Brandl, Christer S. Ejsing and Alexander H. Treusch
Life 2015, 5(3), 1539-1566; https://doi.org/10.3390/life5031539 - 25 Aug 2015
Cited by 30 | Viewed by 6475
Abstract
The functionality of the plasma membrane is essential for all organisms. Adaption to high growth temperatures imposes challenges and Bacteria, Eukarya, and Archaea have developed several mechanisms to cope with these. Hyperthermophilic archaea have earlier been shown to synthesize tetraether membrane [...] Read more.
The functionality of the plasma membrane is essential for all organisms. Adaption to high growth temperatures imposes challenges and Bacteria, Eukarya, and Archaea have developed several mechanisms to cope with these. Hyperthermophilic archaea have earlier been shown to synthesize tetraether membrane lipids with an increased number of cyclopentane moieties at higher growth temperatures. Here we used shotgun lipidomics to study this effect as well as the influence of growth phase on the lipidomes of Sulfolobus islandicus and Sulfolobus tokodaii for the first time. Both species were cultivated at three different temperatures, with samples withdrawn during lag, exponential, and stationary phases. Three abundant tetraether lipid classes and one diether lipid class were monitored. Beside the expected increase in the number of cyclopentane moieties with higher temperature in both archaea, we observed previously unreported changes in the average cyclization of the membrane lipids throughout growth. The average number of cyclopentane moieties showed a significant dip in exponential phase, an observation that might help to resolve the currently debated biosynthesis pathway of tetraether lipids. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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909 KiB  
Article
A Manual Curation Strategy to Improve Genome Annotation: Application to a Set of Haloarchael Genomes
by Friedhelm Pfeiffer and Dieter Oesterhelt
Life 2015, 5(2), 1427-1444; https://doi.org/10.3390/life5021427 - 02 Jun 2015
Cited by 31 | Viewed by 7970
Abstract
Genome annotation errors are a persistent problem that impede research in the biosciences. A manual curation effort is described that attempts to produce high-quality genome annotations for a set of haloarchaeal genomes (Halobacterium salinarum and Hbt. hubeiense, Haloferax volcanii and Hfx. [...] Read more.
Genome annotation errors are a persistent problem that impede research in the biosciences. A manual curation effort is described that attempts to produce high-quality genome annotations for a set of haloarchaeal genomes (Halobacterium salinarum and Hbt. hubeiense, Haloferax volcanii and Hfx. mediterranei, Natronomonas pharaonis and Nmn. moolapensis, Haloquadratum walsbyi strains HBSQ001 and C23, Natrialba magadii, Haloarcula marismortui and Har. hispanica, and Halohasta litchfieldiae). Genomes are checked for missing genes, start codon misassignments, and disrupted genes. Assignments of a specific function are preferably based on experimentally characterized homologs (Gold Standard Proteins). To avoid overannotation, which is a major source of database errors, we restrict annotation to only general function assignments when support for a specific substrate assignment is insufficient. This strategy results in annotations that are resistant to the plethora of errors that compromise public databases. Annotation consistency is rigorously validated for ortholog pairs from the genomes surveyed. The annotation is regularly crosschecked against the UniProt database to further improve annotations and increase the level of standardization. Enhanced genome annotations are submitted to public databases (EMBL/GenBank, UniProt), to the benefit of the scientific community. The enhanced annotations are also publically available via HaloLex. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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722 KiB  
Article
Freshwater Ammonia-Oxidizing Archaea Retain amoA mRNA and 16S rRNA during Ammonia Starvation
by Elizabeth French and Annette Bollmann
Life 2015, 5(2), 1396-1404; https://doi.org/10.3390/life5021396 - 19 May 2015
Cited by 14 | Viewed by 5986
Abstract
In their natural habitats, microorganisms are often exposed to periods of starvation if their substrates for energy generation or other nutrients are limiting. Many microorganisms have developed strategies to adapt to fluctuating nutrients and long-term starvation. In the environment, ammonia oxidizers have to [...] Read more.
In their natural habitats, microorganisms are often exposed to periods of starvation if their substrates for energy generation or other nutrients are limiting. Many microorganisms have developed strategies to adapt to fluctuating nutrients and long-term starvation. In the environment, ammonia oxidizers have to compete with many different organisms for ammonium and are often exposed to long periods of ammonium starvation. We investigated the effect of ammonium starvation on ammonia-oxidizing archaea (AOA) and bacteria (AOB) enriched from freshwater lake sediments. Both AOA and AOB were able to recover even after almost two months of starvation; however, the recovery time differed. AOA and AOB retained their 16S rRNA (ribosomes) throughout the complete starvation period. The AOA retained also a small portion of the mRNA of the ammonia monooxygenase subunit A (amoA) for the complete starvation period. However, after 10 days, no amoA mRNA was detected anymore in the AOB. These results indicate that AOA and AOB are able to survive longer periods of starvation, but might utilize different strategies. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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1140 KiB  
Article
The Heptameric SmAP1 and SmAP2 Proteins of the Crenarchaeon Sulfolobus Solfataricus Bind to Common and Distinct RNA Targets
by Birgit Märtens, Gustavo Arruda Bezerra, Mathias Josef Kreuter, Irina Grishkovskaya, Andrea Manica, Valentina Arkhipova, Kristina Djinovic-Carugo and Udo Bläsi
Life 2015, 5(2), 1264-1281; https://doi.org/10.3390/life5021264 - 21 Apr 2015
Cited by 18 | Viewed by 7070
Abstract
Sm and Sm-like proteins represent an evolutionarily conserved family with key roles in RNA metabolism. Sm-based regulation is diverse and can range in scope from eukaryotic mRNA splicing to bacterial quorum sensing, with at least one step in these processes being mediated by [...] Read more.
Sm and Sm-like proteins represent an evolutionarily conserved family with key roles in RNA metabolism. Sm-based regulation is diverse and can range in scope from eukaryotic mRNA splicing to bacterial quorum sensing, with at least one step in these processes being mediated by an RNA-associated molecular assembly built on Sm proteins. Despite the availability of several 3D-structures of Sm-like archaeal proteins (SmAPs), their function has remained elusive. The aim of this study was to shed light on the function of SmAP1 and SmAP2 of the crenarchaeon Sulfolobus solfataricus (Sso). Using co-purification followed by RNASeq different classes of non-coding RNAs and mRNAs were identified that co-purified either with both paralogues or solely with Sso-SmAP1 or Sso-SmAP2. The large number of associated intron-containing tRNAs and tRNA/rRNA modifying RNAs may suggest a role of the two Sso-SmAPs in tRNA/rRNA processing. Moreover, the 3D structure of Sso-SmAP2 was elucidated. Like Sso-SmAP1, Sso-SmAP2 forms homoheptamers. The binding of both proteins to distinct RNA substrates is discussed in terms of surface conservation, structural differences in the RNA binding sites and differences in the electrostatic surface potential of the two Sso-SmAP proteins. Taken together, this study may hint to common and different functions of both Sso-SmAPs in Sso RNA metabolism. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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1019 KiB  
Article
Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis
by Guanghong Zuo, Zhao Xu and Bailin Hao
Life 2015, 5(1), 949-968; https://doi.org/10.3390/life5010949 - 17 Mar 2015
Cited by 22 | Viewed by 10518
Abstract
A tripartite comparison of Archaea phylogeny and taxonomy at and above the rank order is reported: (1) the whole-genome-based and alignment-free CVTree using 179 genomes; (2) the 16S rRNA analysis exemplified by the All-Species Living Tree with 366 archaeal sequences; and (3) the [...] Read more.
A tripartite comparison of Archaea phylogeny and taxonomy at and above the rank order is reported: (1) the whole-genome-based and alignment-free CVTree using 179 genomes; (2) the 16S rRNA analysis exemplified by the All-Species Living Tree with 366 archaeal sequences; and (3) the Second Edition of Bergey’s Manual of Systematic Bacteriology complemented by some current literature. A high degree of agreement is reached at these ranks. From the newly proposed archaeal phyla, Korarchaeota, Thaumarchaeota, Nanoarchaeota and Aigarchaeota, to the recent suggestion to divide the class Halobacteria into three orders, all gain substantial support from CVTree. In addition, the CVTree helped to determine the taxonomic position of some newly sequenced genomes without proper lineage information. A few discrepancies between the CVTree and the 16S rRNA approaches call for further investigation. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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515 KiB  
Communication
The Role of Active Site Residues in ATP Binding and Catalysis in the Methanosarcina thermophila Acetate Kinase
by Cheryl Ingram-Smith, Jeffrey Wharton, Christian Reinholz, Tara Doucet, Rachel Hesler and Kerry Smith
Life 2015, 5(1), 861-871; https://doi.org/10.3390/life5010861 - 12 Mar 2015
Cited by 3 | Viewed by 6133
Abstract
Acetate kinase (ACK), which catalyzes the reversible phosphorylation of acetate by ATP, is a member of the acetate and sugar kinase/heat shock cognate/actin (ASKHA) superfamily. ASKHA family members share a common core fold that includes an ATPase domain with five structural motifs. The [...] Read more.
Acetate kinase (ACK), which catalyzes the reversible phosphorylation of acetate by ATP, is a member of the acetate and sugar kinase/heat shock cognate/actin (ASKHA) superfamily. ASKHA family members share a common core fold that includes an ATPase domain with five structural motifs. The PHOSPHATE1 motif has previously been shown to be important for catalysis. We have investigated the role of two of these motifs in the Methanosarcina thermophila ACK (MtACK) and have shown that residues projecting into the ACK active site from the PHOSPHATE2 and ADENOSINE loops and a third highly conserved loop designated here as LOOP3 play key roles in nucleotide triphosphate (NTP) selection and utilization. Alteration of Asn211 of PHOSPHATE2, Gly239 of LOOP3, and Gly331 of ADENOSINE greatly reduced catalysis. In particular, Gly331, which is highly conserved throughout the ASKHA superfamily, has the greatest effect on substrate selection. Alteration at this site strongly skewed MtACK toward utilization of purines over pyrimidines, unlike the wild type enzyme that shows broad NTP utilization. Further investigation into differences between the ATPase domain in MtACK and other acetate kinases that show different substrate preferences will provide us with a better understanding of the diversity of phosphoryl donor selection in this enzyme family. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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1297 KiB  
Article
Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales
by Kira S. Makarova, Yuri I. Wolf and Eugene V. Koonin
Life 2015, 5(1), 818-840; https://doi.org/10.3390/life5010818 - 10 Mar 2015
Cited by 159 | Viewed by 12163
Abstract
With the continuously accelerating genome sequencing from diverse groups of archaea and bacteria, accurate identification of gene orthology and availability of readily expandable clusters of orthologous genes are essential for the functional annotation of new genomes. We report an update of the collection [...] Read more.
With the continuously accelerating genome sequencing from diverse groups of archaea and bacteria, accurate identification of gene orthology and availability of readily expandable clusters of orthologous genes are essential for the functional annotation of new genomes. We report an update of the collection of archaeal Clusters of Orthologous Genes (arCOGs) to cover, on average, 91% of the protein-coding genes in 168 archaeal genomes. The new arCOGs were constructed using refined algorithms for orthology identification combined with extensive manual curation, including incorporation of the results of several completed and ongoing research projects in archaeal genomics. A new level of classification is introduced, superclusters that untie two or more arCOGs and more completely reflect gene family evolution than individual, disconnected arCOGs. Assessment of the current archaeal genome annotation in public databases indicates that consistent use of arCOGs can significantly improve the annotation quality. In addition to their utility for genome annotation, arCOGs also are a platform for phylogenomic analysis. We explore this aspect of arCOGs by performing a phylogenomic study of the Thermococci that are traditionally viewed as the basal branch of the Euryarchaeota. The results of phylogenomic analysis that involved both comparison of multiple phylogenetic trees and a search for putative derived shared characters by using phyletic patterns extracted from the arCOGs reveal a likely evolutionary relationship between the Thermococci, Methanococci, and Methanobacteria. The arCOGs are expected to be instrumental for a comprehensive phylogenomic study of the archaea. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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668 KiB  
Communication
Haloferax volcanii, as a Novel Tool for Producing Mammalian Olfactory Receptors Embedded in Archaeal Lipid Bilayer
by Simona Lobasso, Rita Vitale, Patrizia Lopalco and Angela Corcelli
Life 2015, 5(1), 770-782; https://doi.org/10.3390/life5010770 - 09 Mar 2015
Cited by 5 | Viewed by 5529
Abstract
The aim of this study was to explore the possibility of using an archaeal microorganism as a host system for expressing mammalian olfactory receptors (ORs). We have selected the archaeon Haloferax volcanii as a cell host system and one of the most extensively [...] Read more.
The aim of this study was to explore the possibility of using an archaeal microorganism as a host system for expressing mammalian olfactory receptors (ORs). We have selected the archaeon Haloferax volcanii as a cell host system and one of the most extensively investigated OR, namely I7-OR, whose preferred ligands are short-chain aldehydes, such as octanal, heptanal, nonanal. A novel plasmid has been constructed to express the rat I7-OR, fused with a hexahistidine-tag for protein immunodetection. The presence of the recombinant receptor at a membrane level was demonstrated by immunoblot of the membranes isolated from the transgenic archaeal strain. In addition, the lipid composition of archaeonanosomes containing ORs has been characterized in detail by High-Performance Thin-Layer Chromatography (HPTLC) in combination with Matrix-Assisted Laser Desorption Ionization—Time-Of-Flight/Mass Spectrometry (MALDI-TOF/MS) analysis. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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658 KiB  
Article
pTC Plasmids from Sulfolobus Species in the Geothermal Area of Tengchong, China: Genomic Conservation and Naturally-Occurring Variations as a Result of Transposition by Mobile Genetic Elements
by Xiaoyu Xiang, Xiaoxing Huang, Haina Wang and Li Huang
Life 2015, 5(1), 506-520; https://doi.org/10.3390/life5010506 - 12 Feb 2015
Cited by 2 | Viewed by 5979
Abstract
Plasmids occur frequently in Archaea. A novel plasmid (denoted pTC1) containing typical conjugation functions has been isolated from Sulfolobus tengchongensis RT8-4, a strain obtained from a hot spring in Tengchong, China, and characterized. The plasmid is a circular double-stranded DNA molecule of 20,417 [...] Read more.
Plasmids occur frequently in Archaea. A novel plasmid (denoted pTC1) containing typical conjugation functions has been isolated from Sulfolobus tengchongensis RT8-4, a strain obtained from a hot spring in Tengchong, China, and characterized. The plasmid is a circular double-stranded DNA molecule of 20,417 bp. Among a total of 26 predicted pTC1 ORFs, 23 have homologues in other known Sulfolobus conjugative plasmids (CPs). pTC1 resembles other Sulfolobus CPs in genome architecture, and is most highly conserved in the genomic region encoding conjugation functions. However, attempts to demonstrate experimentally the capacity of the plasmid for conjugational transfer were unsuccessful. A survey revealed that pTC1 and its closely related plasmid variants were widespread in the geothermal area of Tengchong. Variations of the plasmids at the target sites for transposition by an insertion sequence (IS) and a miniature inverted-repeat transposable element (MITE) were readily detected. The IS was efficiently inserted into the pTC1 genome, and the inserted sequence was inactivated and degraded more frequently in an imprecise manner than in a precise manner. These results suggest that the host organism has evolved a strategy to maintain a balance between the insertion and elimination of mobile genetic elements to permit genomic plasticity while inhibiting their fast spreading. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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705 KiB  
Article
Pilin Processing Follows a Different Temporal Route than That of Archaellins in Methanococcus maripaludis
by Divya B. Nair and Ken F. Jarrell
Life 2015, 5(1), 85-101; https://doi.org/10.3390/life5010085 - 05 Jan 2015
Cited by 6 | Viewed by 8434
Abstract
Methanococcus maripaludis has two different surface appendages: type IV-like pili and archaella. Both structures are believed to be assembled using a bacterial type IV pilus mechanism. Each structure is composed of multiple subunits, either pilins or archaellins. Both pilins and archaellins are made [...] Read more.
Methanococcus maripaludis has two different surface appendages: type IV-like pili and archaella. Both structures are believed to be assembled using a bacterial type IV pilus mechanism. Each structure is composed of multiple subunits, either pilins or archaellins. Both pilins and archaellins are made initially as preproteins with type IV pilin-like signal peptides, which must be removed by a prepilin peptidase-like enzyme. This enzyme is FlaK for archaellins and EppA for pilins. In addition, both pilins and archaellins are modified with N-linked glycans. The archaellins possess an N-linked tetrasaccharide while the pilins have a pentasaccharide which consists of the archaellin tetrasaccharide but with an additional sugar, an unidentified hexose, attached to the linking sugar. In this report, we show that archaellins can be processed by FlaK in the absence of N-glycosylation and N-glycosylation can occur on archaellins that still retain their signal peptides. In contrast, pilins are not glycosylated unless they have been acted on by EppA to have the signal peptide removed. However, EppA can still remove signal peptides from non-glycosylated pilins. These findings indicate that there is a difference in the order of the posttranslational modifications of pilins and archaellins even though both are type IV pilin-like proteins. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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Review

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7549 KiB  
Review
Assessing the Ecophysiology of Methanogens in the Context of Recent Astrobiological and Planetological Studies
by Ruth-Sophie Taubner, Christa Schleper, Maria G. Firneis and Simon K.-M. R. Rittmann
Life 2015, 5(4), 1652-1686; https://doi.org/10.3390/life5041652 - 03 Dec 2015
Cited by 49 | Viewed by 9262
Abstract
Among all known microbes capable of thriving under extreme and, therefore, potentially extraterrestrial environmental conditions, methanogens from the domain Archaea are intriguing organisms. This is due to their broad metabolic versatility, enormous diversity, and ability to grow under extreme environmental conditions. Several studies [...] Read more.
Among all known microbes capable of thriving under extreme and, therefore, potentially extraterrestrial environmental conditions, methanogens from the domain Archaea are intriguing organisms. This is due to their broad metabolic versatility, enormous diversity, and ability to grow under extreme environmental conditions. Several studies revealed that growth conditions of methanogens are compatible with environmental conditions on extraterrestrial bodies throughout the Solar System. Hence, life in the Solar System might not be limited to the classical habitable zone. In this contribution we assess the main ecophysiological characteristics of methanogens and compare these to the environmental conditions of putative habitats in the Solar System, in particular Mars and icy moons. Eventually, we give an outlook on the feasibility and the necessity of future astrobiological studies concerning methanogens. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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1040 KiB  
Review
Acetate Metabolism in Anaerobes from the Domain Archaea
by James G. Ferry
Life 2015, 5(2), 1454-1471; https://doi.org/10.3390/life5021454 - 09 Jun 2015
Cited by 26 | Viewed by 9847
Abstract
Acetate and acetyl-CoA play fundamental roles in all of biology, including anaerobic prokaryotes from the domains Bacteria and Archaea, which compose an estimated quarter of all living protoplasm in Earth’s biosphere. Anaerobes from the domain Archaea contribute to the global carbon cycle [...] Read more.
Acetate and acetyl-CoA play fundamental roles in all of biology, including anaerobic prokaryotes from the domains Bacteria and Archaea, which compose an estimated quarter of all living protoplasm in Earth’s biosphere. Anaerobes from the domain Archaea contribute to the global carbon cycle by metabolizing acetate as a growth substrate or product. They are components of anaerobic microbial food chains converting complex organic matter to methane, and many fix CO2 into cell material via synthesis of acetyl-CoA. They are found in a diversity of ecological habitats ranging from the digestive tracts of insects to deep-sea hydrothermal vents, and synthesize a plethora of novel enzymes with biotechnological potential. Ecological investigations suggest that still more acetate-metabolizing species with novel properties await discovery. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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465 KiB  
Review
Horizontal Gene Transfer, Dispersal and Haloarchaeal Speciation
by R. Thane Papke, Paulina Corral, Nikhil Ram-Mohan, Rafael R. de la Haba, Cristina Sánchez-Porro, Andrea Makkay and Antonio Ventosa
Life 2015, 5(2), 1405-1426; https://doi.org/10.3390/life5021405 - 19 May 2015
Cited by 25 | Viewed by 9926
Abstract
The Halobacteria are a well-studied archaeal class and numerous investigations are showing how their diversity is distributed amongst genomes and geographic locations. Evidence indicates that recombination between species continuously facilitates the arrival of new genes, and within species, it is frequent enough to [...] Read more.
The Halobacteria are a well-studied archaeal class and numerous investigations are showing how their diversity is distributed amongst genomes and geographic locations. Evidence indicates that recombination between species continuously facilitates the arrival of new genes, and within species, it is frequent enough to spread acquired genes amongst all individuals in the population. To create permanent independent diversity and generate new species, barriers to recombination are probably required. The data support an interpretation that rates of evolution (e.g., horizontal gene transfer and mutation) are faster at creating geographically localized variation than dispersal and invasion are at homogenizing genetic differences between locations. Therefore, we suggest that recurrent episodes of dispersal followed by variable periods of endemism break the homogenizing forces of intrapopulation recombination and that this process might be the principal stimulus leading to divergence and speciation in Halobacteria. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
4058 KiB  
Review
“Altiarchaeales”: Uncultivated Archaea from the Subsurface
by Alexander J. Probst and Christine Moissl-Eichinger
Life 2015, 5(2), 1381-1395; https://doi.org/10.3390/life5021381 - 12 May 2015
Cited by 22 | Viewed by 8615
Abstract
Due to the limited cultivability of the vast majority of microorganisms, researchers have applied environmental genomics and other state-of-the-art technologies to gain insights into the biology of uncultivated Archaea and bacteria in their natural biotope. In this review, we summarize the scientific findings [...] Read more.
Due to the limited cultivability of the vast majority of microorganisms, researchers have applied environmental genomics and other state-of-the-art technologies to gain insights into the biology of uncultivated Archaea and bacteria in their natural biotope. In this review, we summarize the scientific findings on a recently proposed order-level lineage of uncultivated Archaea called Altiarchaeales, which includes “Candidatus Altiarchaeum hamiconexum” as the most well-described representative. Ca. A. hamiconexum possesses a complex biology: thriving strictly anaerobically, this microorganism is capable of forming highly-pure biofilms, connecting the cells by extraordinary cell surface appendages (the “hami”) and has other highly unusual traits, such as a double-membrane-based cell wall. Indicated by genomic information from different biotopes, the Altiarchaeales seem to proliferate in deep, anoxic groundwater of Earth’s crust bearing a potentially very important function: carbon fixation. Although their net carbon fixation rate has not yet been determined, they appear as highly abundant organisms in their biotopes and may thus represent an important primary producer in the subsurface. In sum, the research over more than a decade on Ca. A. hamiconexum has revealed many interesting features of its lifestyle, its genomic information, metabolism and ultrastructure, making this archaeon one of the best-studied uncultivated Archaea in the literature. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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680 KiB  
Review
Archaeal Lineages within the Human Microbiome: Absent, Rare or Elusive?
by Hans-Peter Horz
Life 2015, 5(2), 1333-1345; https://doi.org/10.3390/life5021333 - 05 May 2015
Cited by 44 | Viewed by 8381
Abstract
Archaea are well-recognized components of the human microbiome. However, they appear to be drastically underrepresented compared to the high diversity of bacterial taxa which can be found on various human anatomic sites, such as the gastrointestinal environment, the oral cavity and the skin. [...] Read more.
Archaea are well-recognized components of the human microbiome. However, they appear to be drastically underrepresented compared to the high diversity of bacterial taxa which can be found on various human anatomic sites, such as the gastrointestinal environment, the oral cavity and the skin. As our “microbial” view of the human body, including the methodological concepts used to describe them, has been traditionally biased on bacteria, the question arises whether our current knowledge reflects the actual ratio of archaea versus bacteria or whether we have failed so far to unravel the full diversity of human-associated archaea. This review article hypothesizes that distinct archaeal lineages within humans exist, which still await our detection. First, previously unrecognized taxa might be quite common but they have eluded conventional detection methods. Two recent prime examples are described that demonstrate that this might be the case for specific archaeal lineages. Second, some archaeal taxa might be overlooked because they are rare and/or in low abundance. Evidence for this exists for a broad range of phylogenetic lineages, however we currently do not know whether these sporadically appearing organisms are mere transients or important members of the so called “rare biosphere” with probably basic ecosystem functions. Lastly, evidence exists that different human populations harbor different archaeal taxa and/or the abundance and activity of shared archaeal taxa may differ and thus their impact on the overall microbiome. This research line is rather unexplored and warrants further investigation. While not recapitulating exhaustively all studies on archaeal diversity in humans, this review highlights pertinent recent findings that show that the choice of appropriate methodological approaches and the consideration of different human populations may lead to the detection of archaeal lineages previously not associated with humans. This in turn will help understand variations found in the overall microbiomes from different individuals and ultimately may lead to the emergence of novel concepts/mechanisms impacting human health. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
1491 KiB  
Review
CRISPR-Cas Adaptive Immune Systems of the Sulfolobales: Unravelling Their Complexity and Diversity
by Roger A. Garrett, Shiraz A. Shah, Susanne Erdmann, Guannan Liu, Marzieh Mousaei, Carlos León-Sobrino, Wenfang Peng, Soley Gudbergsdottir, Ling Deng, Gisle Vestergaard, Xu Peng and Qunxin She
Life 2015, 5(1), 783-817; https://doi.org/10.3390/life5010783 - 10 Mar 2015
Cited by 41 | Viewed by 8181
Abstract
The Sulfolobales have provided good model organisms for studying CRISPR-Cas systems of the crenarchaeal kingdom of the archaea. These organisms are infected by a wide range of exceptional archaea-specific viruses and conjugative plasmids, and their CRISPR-Cas systems generally exhibit extensive structural and functional [...] Read more.
The Sulfolobales have provided good model organisms for studying CRISPR-Cas systems of the crenarchaeal kingdom of the archaea. These organisms are infected by a wide range of exceptional archaea-specific viruses and conjugative plasmids, and their CRISPR-Cas systems generally exhibit extensive structural and functional diversity. They carry large and multiple CRISPR loci and often multiple copies of diverse Type I and Type III interference modules as well as more homogeneous adaptation modules. These acidothermophilic organisms have recently provided seminal insights into both the adaptation process, the diverse modes of interference, and their modes of regulation. The functions of the adaptation and interference modules tend to be loosely coupled and the stringency of the crRNA-DNA sequence matching during DNA interference is relatively low, in contrast to some more streamlined CRISPR-Cas systems of bacteria. Despite this, there is evidence for a complex and differential regulation of expression of the diverse functional modules in response to viral infection. Recent work also supports critical roles for non-core Cas proteins, especially during Type III-directed interference, and this is consistent with these proteins tending to coevolve with core Cas proteins. Various novel aspects of CRISPR-Cas systems of the Sulfolobales are considered including an alternative spacer acquisition mechanism, reversible spacer acquisition, the formation and significance of antisense CRISPR RNAs, and a novel mechanism for avoidance of CRISPR-Cas defense. Finally, questions regarding the basis for the complexity, diversity, and apparent redundancy, of the intracellular CRISPR-Cas systems are discussed. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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961 KiB  
Review
A Prokaryotic Twist on Argonaute Function
by Sarah Willkomm, Adrian Zander, Alexander Gust and Dina Grohmann
Life 2015, 5(1), 538-553; https://doi.org/10.3390/life5010538 - 16 Feb 2015
Cited by 26 | Viewed by 10461
Abstract
Argonaute proteins can be found in all three domains of life. In eukaryotic organisms, Argonaute is, as the functional core of the RNA-silencing machinery, critically involved in the regulation of gene expression. Despite the mechanistic and structural similarities between archaeal, bacterial and eukaryotic [...] Read more.
Argonaute proteins can be found in all three domains of life. In eukaryotic organisms, Argonaute is, as the functional core of the RNA-silencing machinery, critically involved in the regulation of gene expression. Despite the mechanistic and structural similarities between archaeal, bacterial and eukaryotic Argonaute proteins, the biological function of bacterial and archaeal Argonautes has remained elusive. This review discusses new findings in the field that shed light on the structure and function of Argonaute. We especially focus on archaeal Argonautes when discussing the details of the structural and dynamic features in Argonaute that promote substrate recognition and cleavage, thereby revealing differences and similarities in Argonaute biology. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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829 KiB  
Review
The Adaptive Immune System of Haloferax volcanii
by Lisa-Katharina Maier, Mike Dyall-Smith and Anita Marchfelder
Life 2015, 5(1), 521-537; https://doi.org/10.3390/life5010521 - 16 Feb 2015
Cited by 21 | Viewed by 8402
Abstract
To fight off invading genetic elements, prokaryotes have developed an elaborate defence system that is both adaptable and heritable—the CRISPR-Cas system (CRISPR is short for: clustered regularly interspaced short palindromic repeats and Cas: CRISPR associated). Comprised of proteins and multiple small RNAs, this [...] Read more.
To fight off invading genetic elements, prokaryotes have developed an elaborate defence system that is both adaptable and heritable—the CRISPR-Cas system (CRISPR is short for: clustered regularly interspaced short palindromic repeats and Cas: CRISPR associated). Comprised of proteins and multiple small RNAs, this prokaryotic defence system is present in 90% of archaeal and 40% of bacterial species, and enables foreign intruders to be eliminated in a sequence-specific manner. There are three major types (I–III) and at least 14 subtypes of this system, with only some of the subtypes having been analysed in detail, and many aspects of the defence reaction remaining to be elucidated. Few archaeal examples have so far been analysed. Here we summarize the characteristics of the CRISPR-Cas system of Haloferax volcanii, an extremely halophilic archaeon originally isolated from the Dead Sea. It carries a single CRISPR-Cas system of type I-B, with a Cascade like complex composed of Cas proteins Cas5, Cas6b and Cas7. Cas6b is essential for CRISPR RNA (crRNA) maturation but is otherwise not required for the defence reaction. A systematic search revealed that six protospacer adjacent motif (PAM) sequences are recognised by the Haloferax defence system. For successful invader recognition, a non-contiguous seed sequence of 10 base-pairs between the crRNA and the invader is required. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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1649 KiB  
Review
Haloarchaea and the Formation of Gas Vesicles
by Felicitas Pfeifer
Life 2015, 5(1), 385-402; https://doi.org/10.3390/life5010385 - 02 Feb 2015
Cited by 44 | Viewed by 11060
Abstract
Halophilic Archaea (Haloarchaea) thrive in salterns containing sodium chloride concentrations up to saturation. Many Haloarchaea possess genes encoding gas vesicles, but only a few species, such as Halobacterium salinarum and Haloferax mediterranei, produce these gas-filled, proteinaceous nanocompartments. Gas vesicles increase the buoyancy [...] Read more.
Halophilic Archaea (Haloarchaea) thrive in salterns containing sodium chloride concentrations up to saturation. Many Haloarchaea possess genes encoding gas vesicles, but only a few species, such as Halobacterium salinarum and Haloferax mediterranei, produce these gas-filled, proteinaceous nanocompartments. Gas vesicles increase the buoyancy of cells and enable them to migrate vertically in the water body to regions with optimal conditions. Their synthesis depends on environmental factors, such as light, oxygen supply, temperature and salt concentration. Fourteen gas vesicle protein (gvp) genes are involved in their formation, and regulation of gvp gene expression occurs at the level of transcription, including the two regulatory proteins, GvpD and GvpE, but also at the level of translation. The gas vesicle wall is solely formed of proteins with the two major components, GvpA and GvpC, and seven additional accessory proteins are also involved. Except for GvpI and GvpH, all of these are required to form the gas permeable wall. The applications of gas vesicles include their use as an antigen presenter for viral or pathogen proteins, but also as a stable ultrasonic reporter for biomedical purposes. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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1298 KiB  
Review
Viruses of Haloarchaea
by Alison W. S. Luk, Timothy J. Williams, Susanne Erdmann, R. Thane Papke and Ricardo Cavicchioli
Life 2014, 4(4), 681-715; https://doi.org/10.3390/life4040681 - 13 Nov 2014
Cited by 43 | Viewed by 13262
Abstract
In hypersaline environments, haloarchaea (halophilic members of the Archaea) are the dominant organisms, and the viruses that infect them, haloarchaeoviruses are at least ten times more abundant. Since their discovery in 1974, described haloarchaeoviruses include head-tailed, pleomorphic, spherical and spindle-shaped morphologies, representing [...] Read more.
In hypersaline environments, haloarchaea (halophilic members of the Archaea) are the dominant organisms, and the viruses that infect them, haloarchaeoviruses are at least ten times more abundant. Since their discovery in 1974, described haloarchaeoviruses include head-tailed, pleomorphic, spherical and spindle-shaped morphologies, representing Myoviridae, Siphoviridae, Podoviridae, Pleolipoviridae, Sphaerolipoviridae and Fuselloviridae families. This review overviews current knowledge of haloarchaeoviruses, providing information about classification, morphotypes, macromolecules, life cycles, genetic manipulation and gene regulation, and host-virus responses. In so doing, the review incorporates knowledge from laboratory studies of isolated viruses, field-based studies of environmental samples, and both genomic and metagenomic analyses of haloarchaeoviruses. What emerges is that some haloarchaeoviruses possess unique morphological and life cycle properties, while others share features with other viruses (e.g., bacteriophages). Their interactions with hosts influence community structure and evolution of populations that exist in hypersaline environments as diverse as seawater evaporation ponds, to hot desert or Antarctic lakes. The discoveries of their wide-ranging and important roles in the ecology and evolution of hypersaline communities serves as a strong motivator for future investigations of both laboratory-model and environmental systems. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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