Archaea

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  Eukaryote and Prokaryote Organisms

  • (Author)
  • 2014(Publication Date)
  • Academic Studio

    (Publisher)

  Woese argued that this group of prokaryotes is a fundamentally different sort of life. To emphasize this difference, these two domains were later renamed Archaea and Bacteria. The word Archaea comes from the Ancient Greek ἀ ρχα ῖ α, meaning ancient things. At first, only the methanogens were placed in this new domain, and the Archaea were seen as extremophiles that exist only in habitats such as hot springs and salt lakes. By the end of the 20th century, microbiologists realized that Archaea is a large and diverse group of organisms that are widely distributed in nature and are common in much less extreme habitats, such as soils and oceans. This new appreciation of the importance and ubiquity of Archaea came from using the polymerase chain reaction to detect prokaryotes in samples of water or soil from their nucleic acids alone. This allows the detection and identification of organisms that cannot be cultured in the laboratory, which generally remains difficult. Current classification The classification of Archaea, and of prokaryotes in general, is a rapidly moving and contentious field. Current classification systems aim to organize Archaea into groups of ________________________ WORLD TECHNOLOGIES ________________________ organisms that share structural features and common ancestors. These classifications rely heavily on the use of the sequence of ribosomal RNA genes to reveal relationships between organisms (molecular phylogenetics). Most of the culturable and well -investigated species of Archaea are members of two main phyla, the Euryarchaeota and Crenarchaeota. Other groups have been tentatively created. For example, the peculiar species Nanoarchaeum equitans , which was discovered in 2003, has been given its own phylum, the Nanoarchaeota. A new phylum Korarchaeota has also been proposed. It contains a small group of unusual thermophilic species that shares features of both of the main phyla, but is most closely related to the Crenarchaeota.

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  Types of Cells in Biology

  • (Author)
  • 2014(Publication Date)
  • Research World

    (Publisher)

  ________________________ WORLD TECHNOLOGIES ________________________ Chapter- 7 Archaea Archaea Temporal range: Paleoarchean – Recent Halobacteria sp. strain NRC-1, each cell about 5 μm long Scientific classification Domain: Archaea Woese, Kandler & Wheelis, 1990 Kingdoms and phyla Crenarchaeota Euryarchaeota Korarchaeota Nanoarchaeota Thaumarchaeota ________________________ WORLD TECHNOLOGIES ________________________ The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon (sometimes spelled archeon). They have no cell nucleus nor any other membrane-bound organelles wi thin their cells. In the past they were viewed as an unusual group of bacteria and named archaebacteria , but since the Archaea have an independent evolutionary history and show many differences in their biochemistry from other forms of life, they are now classified as a separate domain in the three-domain system. In this system the phylogenetically distinct branches of evolu -tionary descent are the Archaea, Bacteria and Eukaryota. Archaea are divided into four recognized phyla, but many more phyla may exist. Of these groups the Crenarchaeota and the Euryarchaeota are most intensively studied. Classification is still difficult, since the vast majority have never been studied in the laboratory and have only been detected by analysis of their nucleic acids in samples from the environment. Although Archaea have, in the past, been classed with bacteria as prokaryotes (or Kingdom Monera), this classification is regarded by some as outdated. Archaea and bacteria are quite similar in size and shape, although a few ar chaea have very unusual shapes, such as the flat and square -shaped cells of Haloquadratum walsbyi . Despite this visual similarity to bacteria, Archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes: notably the enzymes involved in transcription and translation.

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  Aspects and Types of Cells in Biology

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  • 2014(Publication Date)
  • College Publishing House

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  Woese argued that this group of prokaryotes is a fundamentally different sort of life. To emphasize this difference, these two domains were later renamed Archaea and Bacteria. The word Archaea comes from the Ancient Greek ἀ ρχα ῖ α, meaning ancient things. At first, only the methanogens were placed in this new domain, and the Archaea were seen as extremophiles that exist only in habitats such as hot springs and salt lakes. By the end of the 20th century, microbiologists realized that Archaea is a large and diverse group of organisms that are widely distributed in nature and are common in much less extreme habitats, such as soils and oceans. This new appreciation of the importance and ubiquity of Archaea came from using the polymerase chain reaction to detect prokaryotes in samples of water or soil from their nucleic acids alone. This allows the detection and identification of organisms that cannot be cultured in the laboratory, which generally remains difficult. Current classification The classification of Archaea and of prokaryotes in general, is a rapidly moving and contentious field. Current classification systems aim to organize Archaea into groups of organisms that share structural features and common ancestors. These classifications rely heavily on the use of the sequence of ribosomal RNA genes to reveal relationships between organisms (molecular phylogenetics). Most of the culturable and well-investigated species of Archaea are members of two main phyla, the Euryarchaeota and Crenarchaeota. Other groups have been tentatively created. For example, the peculiar species Nanoarchaeum equitans , which was discovered in 2003, has been given its own phylum, the Nanoarchaeota. A new phylum Korarchaeota has also been proposed. It contains a small group of unusual thermophilic species that shares features of both of the main phyla, but is most closely related to the Crenarchaeota.

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  Microbiology

  • Dave Wessner, Christine Dupont, Trevor Charles, Josh Neufeld(Authors)
  • 2016(Publication Date)
  • Wiley

    (Publisher)

  Like the bacteria that we examined in Chapter 2, Archaea lack a true nucleus. These organisms, however, differ in fundamental ways from both bacteria and eukarya. Although we still know relatively little about Archaea, our studies of these microorganisms have shed light on important aspects of how proteins and cells function and future studies promise to provide insight into the evolution of all living organisms. The story of the domain Archaea is both exciting and exotic; it begins in some of the most inhospitable environments on Earth. Since the discovery of the first organisms that grow optimally in environments with extreme chemical and/or physical properties, microbiologists have searched for signs of life in almost every imaginable environment on Earth. Perhaps surprisingly, or perhaps not, we have found living organisms that thrive in every explored environment. From the boiling waters of hot springs to the frigid environments of Antarctica, and from the low-pH, sulfur-rich waters often associated with volcanoes to the high-pH waters of lakes containing sodium carbonate, life, it seems, exists everywhere. Underwater, hydrothermal vents are no exception. Often referred to as black smokers, these vents actually represent fissures in Earth’s crust through which geothermally super-heated water escapes. Often topping 400°C initially, this mineral-laden water cools quickly, causing the precipitation of its mineral contents and the gradual formation of the characteristic rock chimneys. Studies of black smokers in oceans throughout the world have demonstrated that a wonderful array of life calls these very hot environments home (Figure 4.1), including many Archaea. We should note, however, that Archaea are not relegated solely to these seemingly harsh environments. Current studies show that Archaea inhabit myriad environments that we may consider to be more hospitable, such as soils, freshwater, marine water, and even the human body

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  Microbiology

  • Dave Wessner, Christine Dupont, Trevor Charles, Josh Neufeld(Authors)
  • 2020(Publication Date)
  • Wiley

    (Publisher)

  In fact, the entire story of the domain Archaea is somewhat hard to imagine. For many years, cultured members of this domain were lumped together with bacteria into a single kingdom. Indeed, Archaea bear striking similarities to bacteria. Most notably, Archaea and bacteria are very similar in size and have chromosomes of similar size and organization. Members of both groups also lack a membrane‐bound nucleus. Despite these super- ficial similarities, genetic studies have revealed that bacteria and Archaea form two highly distinct evolutionarily groups. Additional studies have provided more evidence that Archaea differ substantially from both bacteria and eukarya. In Section 4.2, we will examine the structure of Archaeal cells, focusing on how common structures differ among Archaea, bacteria, and eukarya. In this section, we will focus on a more fundamental question. How do we know that Archaea is a distinct domain of life? Phylogeny The question posed above can best be answered by phyloge- netic studies, or studies of the evolutionary relatedness of organisms. The question, then, becomes: How can we deter- mine the evolutionary relatedness of all living organisms? In 1977, while Carl Woese and George Fox were research- ers at the University of Illinois at Urbana‐Champaign, they 112 CHAPTER 4 Archaea Yersinia Pseudomonas Rickettsia Clostridium Bacillus Staphylococcus Streptococcus Mycoplasma Borrelia Methanothermobacter Methanosarcina Methanococcus Methanocaldococcus Vibrio Haemophilus Bordetella Neisseria Mycobacterium Chlamydia Bacteroides Thermatoga FIGURE 4.2 Methanogens are genetically distinct from bacteria In 1977, Woese and Fox proposed that methanogens were distinct from all commonly known bacteria. Subsequent SSU rRNA gene sequence analysis has confirmed this hypothesis. As shown in this schematic, when the 16S rRNA sequences of various bacteria and the four methane-producing microorganisms are compared, the methanogenic species form a distinct cluster.

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  Plant-Microbe Dynamics

  Recent Advances for Sustainable Agriculture

  • Tanveer Bilal Pirzadah, Bisma Malik, Khalid Rehman Hakeem, Tanveer Bilal Pirzadah, Bisma Malik, Khalid Rehman Hakeem(Authors)
  • 2021(Publication Date)
  • CRC Press

    (Publisher)

  10 Recent Biotechnological Applications of Archaeal Domain Ruth Gill, Rajinder Kaur, Nitu Rani, and Sukhminderjit Kaur Chandigarh University, Punjab, India Contents 10.1 Introduction 10.2 Cultivation Strategies of Archaea 10.3 Biotechnological Applications of Archaea 10.3.1 Archaea in Biomethane Production 10.3.2 Biosurfactant 10.3.3 Antibiotics 10.3.4 Extremozymes 10.3.5 Biomining 10.3.6 Bioremediation 10.3.7 Archeal Metabolites 10.3.8 Application in Biowaste 10.4 Conclusion References 10.1 Introduction The existing life forms on the earth are majorly divided into three domains: Archaea, Eubacteria, and Eukarya. The domain Archaea consists of single-celled prokaryotic organisms that lack nucleus and show combined characteristics of other two domains of Bacteria and Eukarya. The word “Archaea” comes from Greek word “archaios,” which means “primitive” or “ancient,” and in fact, some of the Archaea express characteristics that resemble that of the ancient times. The exceptional feature of Archaea is their survival potential in extreme conditions of scorching heat, high acidity, and saline environments (Leuko and Rettberg 2016). The Archaeal members such as Pyrolobus fumarii can grow in the hydrothermal vents where temperature reaches about 113°C (Blöchl et al. 1997). Picrophilus sp. can survive in acidic conditions where pH is low or even zero (Rampelotto 2013). The Dead Sea also harbors many Haloferax volcanii spp. which can grow in high salt concentration (Haque et al. 2020). In the year 1977, the whole scientific community was amazed when Carl-Woese et al. (1977) examined the prokaryotic DNA sequences and observed the variations within prokaryotes (Carl-Woese et al. 1977). They reported a group of bacteria was methane producing and able to proliferate at high temperature; therefore, they divided those bacteria in a separate group. The life was divided into three domains: Eubacteria, Archaebacteria, and Eukaryota

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  Biology 2e

  • Mary Ann Clark, Jung Choi, Matthew Douglas(Authors)
  • 2018(Publication Date)
  • Openstax

    (Publisher)

  22 | PROKARYOTES: BACTERIA AND Archaea Figure 22.1 Certain prokaryotes can live in extreme environments such as the Morning Glory pool, a hot spring in Yellowstone National Park. The spring’s vivid blue color is from the prokaryotes that thrive in its very hot waters. (credit: modification of work by Jon Sullivan) Chapter Outline 22.1: Prokaryotic Diversity 22.2: Structure of Prokaryotes: Bacteria and Archaea 22.3: Prokaryotic Metabolism 22.4: Bacterial Diseases in Humans 22.5: Beneficial Prokaryotes Introduction In the recent past, scientists grouped living things into five kingdoms—animals, plants, fungi, protists, and prokaryotes—based on several criteria, such as the absence or presence of a nucleus and other membrane- bound organelles, the absence or presence of cell walls, multicellularity, and so on. In the late 20 th century, the pioneering work of Carl Woese and others compared sequences of small-subunit ribosomal RNA (SSU rRNA), which resulted in a more fundamental way to group organisms on Earth. Based on differences in the structure of cell membranes and in rRNA, Woese and his colleagues proposed that all life on Earth evolved along three lineages, called domains. The domain Bacteria comprises all organisms in the kingdom Bacteria, the domain Archaea comprises the rest of the prokaryotes, and the domain Eukarya comprises all eukaryotes—including organisms in the kingdoms Animalia, Plantae, Fungi, and Protista. Two of the three domains—Bacteria and Archaea—are prokaryotic. Prokaryotes were the first inhabitants on Chapter 22 | Prokaryotes: Bacteria and Archaea 589 Earth, appearing 3.5 to 3.8 billion years ago. These organisms are abundant and ubiquitous; that is, they are present everywhere.

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  Archaea

  Evolution, Physiology, and Molecular Biology

  • Roger A. Garrett, Hans-Peter Klenk, Roger A. Garrett, Hans-Peter Klenk(Authors)
  • 2008(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  al., 2005 homologues. By obtaining organisms (or at least their genes) with growth requirements that are not extreme with respect to temperature, salt, or oxygen, but instead compatible with those of eukaryotic model organisms, it will become possible to study Archaeal proteins in a eukaryotic cell context, by complementing mutants or using eukaryotic in vitro systems. Such studies will allow us to address questions about the conservation and evolution of information-processing systems in the Archaeal/ eukaryotic lineages from a novel perspective. 50 CHAPTER 4 Acknowledgments Thanks are due to G. Jurgens and M. Jonuscheit for help with Plate 4.1, to Graeme Nicol and Laila Reigstad for critical reading of the manuscript, and to G. Nicol, K. Knittel, G. Jurgens, K. Seifert, and R. Huber for kindly providing figures for this chapter. Only a subset of studies on Archaeal diversity has been cited due to space limitation. Introduction Until recently all cultivated Archaea belonged either to the Crenarchaeota or to the Euryarchaeota (Woese et al., 1990). A third Archaeal phylum (kingdom), the “Korarchaeota,” has been identified by amplification of 16S rDNAs from environmental samples (Barns et al., 1996), but the corresponding organisms still wait for detailed characterization. Archaea show a great variety in terms of morphology and cell size, physiology, adaptations to extreme environments, and genome size. Although they were for a long time regarded as thriv-ing only in extreme environments, it has become more and more evident that Archaea inhabit nearly all natural environments and even anthropogenic biotopes, such as burning heaps or heaters within power plants. Archaea have also been found as partners in a number of symbioses, e.g.

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  Microbes

  Concepts and Applications

  • Prakash S. Bisen, Mousumi Debnath, G. B. Prasad(Authors)
  • 2012(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  halobacteria), a group of Archaea, require at least a 2 M salt concentration and are usually found in saturated solutions (about 36% w/v salts). These are the primary inhabitants of salt lakes, inland seas, and evaporating ponds of seawater, such as the Dead Sea and solar salterns, where they tint the water column and sediments bright colors. In other words, they will most likely perish if they are exposed to anything other than a very high concentration salt conditioned environment. These prokaryotes require salt for growth. The high concentration of NaCl in their environment limits the availability of oxygen for respiration. Their cellular machinery is adapted to high salt concentrations by having charged amino acids on their surfaces, allowing the retention of water molecules around these components. They are heterotrophs that normally respire by aerobic means. Most halophiles are unable to survive outside their high salt native environment. Indeed, many cells are so fragile that when placed in distilled water, they immediately lyse from the change in osmotic conditions.

  HaloArchaea, and particularly, the family Halobacteriaceae are members of the domain Archaea and comprise the majority of the prokaryotic population. There are currently 15 recognized genera in the family. The domain Bacteria (mainly Salinibacter ruber) can comprise up to 25% of the prokaryotic community but comprises more commonly a much lower percentage of the overall population.

  A comparatively wide range of taxa have been isolated from saltern crystallizer ponds, including members of the following genera: Haloferax, Halogeometricum, Halococcus, Haloterrigena, Halorubrum, Haloarcula, and Halobacterium (Oren, 2002). However, the viable counts in these cultivation studies have been small when compared to total counts, and the numerical significance of these isolates has been unclear. Only recently it has become possible to determine the identities and relative abundances of organisms in natural populations, typically using polymerase chain reaction (PCR)-based strategies that target 16S small subunit ribosomal ribonucleic acid (16S rRNA) genes. While comparatively few studies of this type have been performed, results from these suggest that some of the most readily isolated and studied genera may not in fact be significant in the in situ community. This is seen in cases such as the genus Haloarcula, which is estimated to make up less than 0.1% of the in situ community but commonly appears in isolation studies.

  5.6.2. Extreme Thermophiles

  A thermophile is a type of extremophilic organism that thrives at relatively high temperatures, between 45 and 80 °C (113 and 176 °F, respectively). Many thermophiles are Archaea. Extreme thermophiles are critters that live in some of the most unwelcoming environments on the planet. Archaea such as Sulfolobus acidocaldarius live in hot springs and geysers where the water temperature can be up to 100 °C and the water is filled with sulfuric acid (Fig. 5.24 ). Chlororflexus aurantiacus can carry out photosynthesis at over 60 °C. Pyrococcus furiosus

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