Archaea Examples

6 Key excerpts on "Archaea Examples"

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  eBook - ePub

  Microbial Ecology

  • Larry L. Barton, Diana E. Northup(Authors)
  • 2011(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  Epulopiscium's extreme polyploidy may support the occurrence of the unstable long mononucleotide tract without harm to the cell. Polyploidy is not unknown in bacteria, but has never been observed before on this scale. Investigation of the evolutionary significance of this phenomenon promises new insights.

  2.5 Discovery of Archaea as a Separate Domain

  What are the roots of the discovery of the Archaea ? Woese and Fox (1977) stated:

  The biologist has customarily structured his world in terms of certain basic dichotomies. Classically, what was not plant was animal. The discovery that bacteria, which initially had been considered plants, resembled both plants and animals less than plants and animals resembled one another led to a reformulation of the issue in terms of a yet more basic dichotomy, that of eukaryote versus prokaryote.

  Thus began their paper that identified three major lines of descent that encompassed all living organisms, which included the separate division that they proposed to call the archaebacteria, which we now term the Archaea : “There exists a third kingdom which, to date, is represented solely by the methanogenic bacteria….These ‘bacteria’ appear to be no more related to typical bacteria than they are to eukaryotic cytoplasms.”

  It's fascinating to look back in time over the shoulders of the scientists who described the methanogens as a separate domain of life and forever changed our view of the living world. Woese and Fox (1977) went on to predict that additional domains would not be discovered. To date, their prediction has been borne out. Although known at the time, the halophiles were not included in the newly suggested archaebacterial domain.

  2.6 Archaeal Diversity

  During the 1970s, early phylogenetic trees of the Archaea showed two phyla: the Crenarchaeota and the Euryarchaeota. These trees were based on cultivated archaeal members and presented the Archaea as extremophiles that lived in high-temperature and high-salt environments or generated methane (i.e., methanogens). Beginning in the early to mid-1990s, environmental archaeal sequences in GenBank began to grow exponentially, and the archaeal tree of life changed from an extremophile tree to a much more diverse tree (Robertson et al. 2005). More than three-quarters of GenBank archaeal sequences are now uncultured, environmental isolates, from an amazing array of habitats, including the ocean, human mouths, the rhizosphere, caves, and lakes. The Crenarchaeota and the Euryarchaeota phyla differ dramatically in terms of the number of cultured members, as seen in Figure 2.8

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  eBook - ePub

  Microbiology For Dummies

  • Jennifer Stearns, Michael Surette(Authors)
  • 2019(Publication Date)
  • For Dummies

    (Publisher)

  Figure 12-7 . It’s likely that many more archaea will be discovered and that the current tree will change quite a bit.

  FIGURE 12-7: The phylogenetic tree of Archaea.

  Currently, there are two main phyla in the domain Archaea: the Euryarchaeota and the Crenarchaeota. However, within the Crenarchaeota, there may soon be a few new phyla, including the Thaumarchaeota, the Korarchaeota, and the Aigarchaeota.

  As new archaeal strains are discovered, the gaps in what we know about how all archaea are related get filled in.

  WHERE DO MY GENES COME FROM?

  The Archaea are interesting because they have many genes that resemble those in bacteria and others that resemble the genes in eukaryotes. This is part of the reason why they confounded microbiologists for years — they couldn’t squarely be placed within the domain of Bacteria or Eukarya.

  A great example of this is an archaeon (singular for archaea) called Methanocaldococcus jannaschii, which has core metabolic genes that bear some resemblance to those in bacteria, but most of the genes for molecular processes (things like RNA transcription and protein translation) have similarities to those in eukaryotes. More than a third of its genome (40 percent) contains genes that don’t resemble those in either bacteria or eukaryotes.

  Archaea likely evolved around the same time as the earliest bacteria. It’s even possible that eukaryotes came from an early archaeal ancestor. It’s mysteries like this that make the microbiology of the archaea so fascinating.

  As with the Bacteria, there are far too many archaeal species to describe them all here but you can go to www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2157 for a complete list. In this section, we discuss representatives of the different forms of archaeal life, filling you in on their ability to tolerate extremes of temperature, acidity, and salinity. It’s likely that the most extreme of the Archaea were some of the first life forms on earth, evolving during a time when the earth was hotter and harsher than it is now. How they’re able to thrive in extreme conditions is covered in Chapter 11

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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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  Extremophiles

  From Biology to Biotechnology

  • Ravi V. Durvasula, D. V. Subba Rao(Authors)
  • 2018(Publication Date)
  • CRC Press

    (Publisher)

  Biota that grow at low temperatures are known as mesophiles, compared with the cold-adapted psychrophilles or psychrotrophs that have slower metabolic rates. In their DNA replication, transcription, and translation, Archaea are similar to nucleated eukaryotes. Unique to Archaea are their membrane lipids, with branched fatty chains linked to head groups via ether linkages (Sarma et al. 2010), which facilitate biotechnological applications such as thermostable DNA polymerases.

  Thermophilic extremophiles are physiologically active at temperatures ranging from 0°C to 120°C and pH ranges from 0 to 12 (Antranikian and Egotova 2007). Molecular studies have demonstrated that eukaryotes are more adaptable than prokaryotes, which may explain the greater novel protist diversity in extreme environments (Roberts 1999).

  Extremophiles live under harsh environmental conditions and carry out biochemical processes, where survival strategies hinge on the production of extremozymes. The study of these extremozymes is fascinating because they provide data on not only protein folding, stability, structure, and function, but also applications to biotechnology.

  The prokaryotes have flourished on earth for more than 3.5 giga-annum (Ga). The unicellular mitotic eukaryotes are autotrophic, appeared around 2.5 Ga (Horneck 2000), and are represented by microalgae, the first organisms to exhibit photosynthesis. Of the 4–6 × 1030 prokaryotes that include bacteria (eubacteria), archaea, and cyanobacteria that inhabit the earth (Whitman et al. 1998), about 1 million live in the oceans (Table 1.2

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  The New Microbiology

  From Microbiomes to CRISPR

  • Pascale Cossart(Author)
  • 2018(Publication Date)
  • ASM Press

    (Publisher)

  PART I New Concepts in Microbiology Passage contains an image

  CHAPTER 1 Bacteria: Many Friends, Few Enemies

  Bacteria are unicellular living organisms that make up one of the three domains of life: Bacteria, Archaea, and Eukaryota (Fig. 1 ). This model of three branches stemming from a common ancestor was first proposed by Carl Wo-ese in 1977. The absence of a nucleus is one major difference between prokaryotes and eukaryotes. Eukaryota or eukaryotes include animals, plants, fungi, and protozoa, which all have nuclei; bacteria and archaea are prokaryotes and do not have a nucleus. The DNA of prokaryotes is non-membrane bound, unlike in eukaryotes. But do not assume that bacteria are merely small sacks full of disorderly contents. Their “interior” is in fact very well organized.

  Archaea, like bacteria, are unicellular organisms but differ from bacteria in that they have lipids that are not found in bacteria and an ensemble of compounds that are similar to those of eukaryotes, in particular the machinery that regulates gene expression. When they were discovered, archaea were thought to exist only in extreme environments, such as very hot water springs, but we now know that they are present everywhere, including in our gut.

  Figure 1.

  The three large domains of life. Bacteria, Archaea, and Eukaryota have a common ancestor.

  Bacteria are extremely varied and make up the most diverse domain of life. They have been on Earth for billions of years and have evolved to survive in a great variety of conditions. There are more than 11,500 known species of bacteria in more than 2,000 genera (groupings of species). These numbers have so far been based only on gene comparisons, particularly the 16S RNA genes, and they keep rising. Classification methods are changing too. Now that we can compare entire genome sequences, the definition of “species” itself is evolving.

  Bacteria may have different shapes (Fig. 2 ). There are four main categories: cocci, or spheres; bacilli, or rods; spirals; and comma-shaped, or curved bacteria. All bacteria divide, regardless of their shape. One bacterium splits into two, via an asexual reproduction. Nevertheless, genetic material can be exchanged between two bacteria by means of mechanisms described as horizontal gene transfer

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  Extremophiles

  Sustainable Resources and Biotechnological Implications

  • Om V. Singh(Author)
  • 2012(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  5 FEATURES AND APPLICATIONS OF HALOPHILIC ARCHAEA Abrevaya Ximena C. Instituto de Astronomía y Física del Espacio, Universidad de Buenos Aires and CONICET, Ciudad Universitaria 5.1 INTRODUCTION

  Halophilic organisms are organisms that are able to live in saline environments, being the presence of salt (generally, NaCl) a specific requisite for their growth. It is possible to find these types of organisms in all three domains of life: Bacteria, Eukarya, and Archaea (Litchfield, 1998). In particular, some of the most extreme halophilic microorganisms to date have been found inside the Archaea domain, requiring concentrations of NaCl next to saturation (between 3 and 5 M NaCl) for optimal growth. These haloarchaea live in hypersaline environments in which the concentration of salt exceeds that of seawater. Examples of these hypersaline ecosystems are salterns, hypersaline lakes, and evaporitic water bodies such as the crystallizer ponds of solar salterns (Oren, 1999a, 2002). These microorganisms have also been found in evaporitic deposits millions of years old (Fendrihan et al., 2006).

  In addition to the natural environment, halophiles have also been isolated in molar concentrations from highly salty foods such as preserves, fermented products, and other foods preserved by salt treatment (Harrison and Kennedy, 1922; Thongthai et al., 1992; Namwong et al., 2011; Tapingkae et al., 2008). Most of the haloarchaea are orange, red, or purple, due to the presence of pigments in their cellular membranes, which are isoprenoid derivatives (Oren and Rodríguez-Valera, 2001).

  Additionally, several physiological characteristics make haloarchaea especially well adapted to live in such hypersaline conditions (Litchfield, 1998). Perhaps the most relevant are the particular osmotic mechanisms that these microorganisms possess, which allow them to keep high intracellular ionic concentrations, and as a consequence of this fact, their special physiological features, including enzymatic machinery, are able to function under these conditions (Oren, 1999a,b). The haloarchaea are much better adapted to live in these hypersaline environments, as these high salt concentrations are generally an indispensable requisite for their cell integrity and viability (Soppa, 2006).

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