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Nature Microbiology Jul 2020Compared to bacteria, our knowledge of archaeal biology is limited. Historically, microbiologists have mostly relied on culturing and single-gene diversity surveys to... (Review)
Review
Compared to bacteria, our knowledge of archaeal biology is limited. Historically, microbiologists have mostly relied on culturing and single-gene diversity surveys to understand Archaea in nature. However, only six of the 27 currently proposed archaeal phyla have cultured representatives. Advances in genomic sequencing and computational approaches are revolutionizing our understanding of Archaea. The recovery of genomes belonging to uncultured groups from the environment has resulted in the description of several new phyla, many of which are globally distributed and are among the predominant organisms on the planet. In this Review, we discuss how these genomes, together with long-term enrichment studies and elegant in situ measurements, are providing insights into the metabolic capabilities of the Archaea. We also debate how such studies reveal how important Archaea are in mediating an array of ecological processes, including global carbon and nutrient cycles, and how this increase in archaeal diversity has expanded our view of the tree of life and early archaeal evolution, and has provided new insights into the origin of eukaryotes.
Topics: Archaea; Biodiversity; Biological Evolution; Ecology; Energy Metabolism; Environmental Microbiology; Genetic Variation; Genome, Archaeal; Phylogeny
PubMed: 32367054
DOI: 10.1038/s41564-020-0715-z -
Research in Microbiology 2023Archaea are microorganisms with great ability to colonize some of the most inhospitable environments in nature, managing to survive in places with extreme... (Review)
Review
Archaea are microorganisms with great ability to colonize some of the most inhospitable environments in nature, managing to survive in places with extreme characteristics for most microorganisms. Its proteins and enzymes are stable and can act under extreme conditions in which other proteins and enzymes would degrade. These attributes make them ideal candidates for use in a wide range of biotechnological applications. This review describes the most important applications, both current and potential, that archaea present in Biotechnology, classifying them according to the sector to which the application is directed. It also analyzes the advantages and disadvantages of its use.
Topics: Archaea; Biotechnology
PubMed: 37196775
DOI: 10.1016/j.resmic.2023.104080 -
Journal of Microbiology (Seoul, Korea) Mar 2021The third domain Archaea was known to thrive in extreme or anoxic environments based on cultivation studies. Recent metagenomics-based approaches revealed a widespread... (Review)
Review
The third domain Archaea was known to thrive in extreme or anoxic environments based on cultivation studies. Recent metagenomics-based approaches revealed a widespread abundance of archaea, including ammonia-oxidizing archaea (AOA) of Thaumarchaeota in non-extreme and oxic environments. AOA alter nitrogen species availability by mediating the first step of chemolithoautotrophic nitrification, ammonia oxidation to nitrite, and are important primary producers in ecosystems, which affects the distribution and activity of other organisms in ecosystems. Thus, information on the interactions of AOA with other cohabiting organisms is a crucial element in understanding nitrogen and carbon cycles in ecosystems as well as the functioning of whole ecosystems. AOA are self-nourishing, and thus interactions of AOA with other organisms can often be indirect and broad. Besides, there are possibilities of specific and obligate interactions. Mechanisms of interaction are often not clearly identified but only inferred due to limited knowledge on the interaction factors analyzed by current technologies. Here, we overviewed different types of AOA interactions with other cohabiting organisms, which contribute to understanding AOA functions in ecosystems.
Topics: Ammonia; Archaea; Ecosystem; Nitrification; Oxidation-Reduction; Phylogeny
PubMed: 33624267
DOI: 10.1007/s12275-021-1005-z -
Trends in Microbiology Apr 2021Latin binomials, popularised in the 18th century by the Swedish naturalist Linnaeus, have stood the test of time in providing a stable, clear, and memorable system of... (Review)
Review
Latin binomials, popularised in the 18th century by the Swedish naturalist Linnaeus, have stood the test of time in providing a stable, clear, and memorable system of nomenclature across biology. However, relentless and ever-deeper exploration and analysis of the microbial world has created an urgent need for huge numbers of new names for Archaea and Bacteria. Manual creation of such names remains difficult and slow and typically relies on expert-driven nomenclatural quality control. Keen to ensure that the legacy of Linnaeus lives on in the age of microbial genomics and metagenomics, we propose an automated approach, employing combinatorial concatenation of roots from Latin and Greek to create linguistically correct names for genera and species that can be used off the shelf as needed. As proof of principle, we document over a million new names for Bacteria and Archaea. We are confident that our approach provides a road map for how to create new names for decades to come.
Topics: Archaea; Bacteria; Metagenomics; Phylogeny
PubMed: 33288384
DOI: 10.1016/j.tim.2020.10.009 -
Nature Reviews. Microbiology Jan 2011The Archaea evolved as one of the three primary lineages several billion years ago, but the first archaea to be discovered were described in the scientific literature... (Review)
Review
The Archaea evolved as one of the three primary lineages several billion years ago, but the first archaea to be discovered were described in the scientific literature about 130 years ago. Moreover, the Archaea were formally proposed as the third domain of life only 20 years ago. Over this very short period of investigative history, the scientific community has learned many remarkable things about the Archaea--their unique cellular components and pathways, their abundance and critical function in diverse natural environments, and their quintessential role in shaping the evolutionary path of life on Earth. This Review charts the 'archaea movement', from its genesis through to key findings that, when viewed together, illustrate just how strongly the field has built on new knowledge to advance our understanding not only of the Archaea, but of biology as a whole.
Topics: Amino Acyl-tRNA Synthetases; Archaea; Evolution, Molecular; Gene Expression Regulation, Archaeal; Gene Expression Regulation, Enzymologic; Phylogeny
PubMed: 21132019
DOI: 10.1038/nrmicro2482 -
Current Biology : CB Oct 2015A headline on the front page of the New York Times for November 3, 1977, read "Scientists Discover a Way of Life That Predates Higher Organisms". The accompanying...
A headline on the front page of the New York Times for November 3, 1977, read "Scientists Discover a Way of Life That Predates Higher Organisms". The accompanying article described a spectacular claim by Carl Woese and George Fox to have discovered a third form of life, a new 'domain' that we now call Archaea. It's not that these microbes were unknown before, nor was it the case that their peculiarities had gone completely unnoticed. Indeed, Ralph Wolfe, in the same department at the University of Illinois as Woese, had already discovered how it was that methanogens (uniquely on the planet) make methane, and the bizarre adaptations that allow extremely halophilic archaea (then called halobacteria) and thermoacidophiles to live in the extreme environments where they do were already under investigation in many labs. But what Woese and Fox had found was that these organisms were related to each other not just in their 'extremophily' but also phylogenetically. And, most surprisingly, they were only remotely related to the rest of the prokaryotes, which we now call the domain Bacteria (Figure 1).
Topics: Adaptation, Biological; Archaea; Bacteria; Bacterial Physiological Phenomena; Biological Evolution; Eukaryota; History, 20th Century; History, 21st Century; Microbiology; Phylogeny
PubMed: 26439345
DOI: 10.1016/j.cub.2015.05.025 -
Archaea (Vancouver, B.C.) 2018Bioremediation is the use of microorganisms for the degradation or removal of contaminants. Most bioremediation research has focused on processes performed by the domain... (Review)
Review
Bioremediation is the use of microorganisms for the degradation or removal of contaminants. Most bioremediation research has focused on processes performed by the domain ; however, are known to play important roles in many situations. In extreme conditions, such as halophilic or acidophilic environments, are well suited for bioremediation. In other conditions, collaboratively work alongside during biodegradation. In this review, the various roles that have in bioremediation is covered, including halophilic hydrocarbon degradation, acidophilic hydrocarbon degradation, hydrocarbon degradation in nonextreme environments such as soils and oceans, metal remediation, acid mine drainage, and dehalogenation. Research needs are addressed in these areas. Beyond bioremediation, these processes are important for wastewater treatment (particularly industrial wastewater treatment) and help in the understanding of the natural microbial ecology of several genera.
Topics: Archaea; Biodegradation, Environmental; Environmental Pollutants; Hydrocarbons
PubMed: 30254509
DOI: 10.1155/2018/3194108 -
FEMS Microbiology Reviews Sep 2015Over 40 years ago, Carl Woese and his colleagues discovered the existence of two distinctly different groups of prokaryotes-Bacteria and Archaea. In the meantime,... (Review)
Review
Over 40 years ago, Carl Woese and his colleagues discovered the existence of two distinctly different groups of prokaryotes-Bacteria and Archaea. In the meantime, extensive research revealed that several hundred of bacterial species are intensely associated with humans' health and disease. Archaea, originally identified and described to occur mainly in extreme environments, have been shown to be ubiquitous and to appear frequently and in high numbers as part of human microbiota in recent years. Despite the improvement in methodologies leading to increased detection, archaea are often still not considered in many studies focusing on the interdependency between members of the microbiota and components of the human immune system. As a consequence, the knowledge on functional role(s) of archaeal species within the human body is mainly limited to their contribution to nutrient degradation in the intestine, and evidence for immunogenic properties of archaea as part of the human microbiota is generally rare. In this review, the current knowledge of human mucosa-associated archaeal species, their interaction with the human immune system and their potential contribution to humans' health and disease will be discussed.
Topics: Archaea; Humans; Immune System; Intestines; Microbiota
PubMed: 25907112
DOI: 10.1093/femsre/fuv010 -
Molecular Microbiology Jan 2005Standard decoding of the genetic information into polypeptides is performed by one of the most sophisticated cell machineries, the translating ribosome, which, by... (Review)
Review
Standard decoding of the genetic information into polypeptides is performed by one of the most sophisticated cell machineries, the translating ribosome, which, by following the genetic code, ensures the correspondence between the mature mRNA and the protein sequence. However, the expression of a minority of genes requires programmed deviations from the standard decoding rules, globally named recoding. This includes ribosome programmed -/+1 frameshifting, ribosome hopping, and stop codon readthrough. Recoding in Archaea was unequivocally demonstrated only for the translation of the UGA stop codon into the amino acid selenocysteine. However, a new recoding event leading to the 22nd amino acid pyrrolysine and the preliminary reports on a gene regulated by programmed -1 frameshifting have been recently described in Archaea. Therefore, it appears that the study of this phenomenon in Archaea is still at its dawn and that most of the genes whose expression is regulated by recoding are still uncharacterized.
Topics: Archaea; Codon, Terminator; Frameshifting, Ribosomal; Lysine; Protein Biosynthesis; Selenocysteine
PubMed: 15659155
DOI: 10.1111/j.1365-2958.2004.04400.x -
The Journal of Biological Chemistry Nov 2018Most of the phylogenetic diversity of life is found in bacteria and archaea, and is reflected in the diverse metabolism and functions of bacterial and archaeal... (Review)
Review
Most of the phylogenetic diversity of life is found in bacteria and archaea, and is reflected in the diverse metabolism and functions of bacterial and archaeal polyamines. The polyamine spermidine was probably present in the last universal common ancestor, and polyamines are known to be necessary for critical physiological functions in bacteria, such as growth, biofilm formation, and other surface behaviors, and production of natural products, such as siderophores. There is also phylogenetic diversity of function, indicated by the role of polyamines in planktonic growth of different species, ranging from absolutely essential to entirely dispensable. However, the cellular molecular mechanisms responsible for polyamine function in bacterial growth are almost entirely unknown. In contrast, the molecular mechanisms of essential polyamine functions in archaea are better understood: covalent modification by polyamines of translation factor aIF5A and the agmatine modification of tRNA As with bacterial hyperthermophiles, archaeal thermophiles require long-chain and branched polyamines for growth at high temperatures. For bacterial species in which polyamines are essential for growth, it is still unknown whether the molecular mechanisms underpinning polyamine function involve covalent or noncovalent interactions. Understanding the cellular molecular mechanisms of polyamine function in bacterial growth and physiology remains one of the great challenges for future polyamine research.
Topics: Archaea; Archaeal Proteins; Bacteria; Bacterial Proteins; Polyamines
PubMed: 30254075
DOI: 10.1074/jbc.TM118.005670