Archaeoglobus Classification Essay

A Microbial Biorealm page on the genus Archaeoglobus

Classification

Higher order taxa:

Archaea; Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae

Species:

Archaeoglobus fulgidus, A. lithotrophicus, A. profundus, A. veneficus

Description and Significance

Archaeoglobus members are hyperthermophiles that can be found in hydrothermal vents, oil deposits, and hot springs. They can produce biofilm when subjected to environmental stresses such as extreme pH or temperature, high concentrations of metal, or the addition of antibiotics, xenobiotics, or oxygen. These archaeons are known to cause the corrosion of iron and steel in oil and gas processing systems by producing iron sulphide. Their bioflims, however, may have industrial or research applications in the form of detoxifying metal contaminated samples or to gather metals in an economically recoverable form.

Genome Structure

The Archaeoglobus fulgidus genome is a circular chromosome roughly half the size of E. coli at 2,178,000 base pairs. A quarter of the genome encodes preserved proteins whose functions are not yet determined, but are expressed in other archaeons such as Methanococcus jannaschii. Another quarter encodes proteins unique to the archaeal domain. One observation about the genome is that there are many gene duplications and the duplicated proteins are not identical. This suggests metabolic differentiation specifically with respect to the decomposing and recycling carbon pathways through scavenged fatty acids. The duplicated genes also gives the genome a larger genome size than it's fellow archaeon M. jannaschii. It is also noted that Archaeoglobus contained no inteins in coding regions where M. jannaschii had 18.

Cell Structure and Metabolism

Archaeoglobus species are a sulphur-metabolizing anaerobic organism whose cells are an irregular sphere with a glycoprotein envelope and monopolar flagella. The sulfur-oxide reduction pathway consists of sulphate being activated to adenylylsulphate, then reduced to sulfite and finally sulfide with adenylylsulphate reductase being the major enzyme.

Ecology

Archaeoglobus species utilize their environment by acting as scavengers with many potential carbon sources. They can obtain carbon from fatty acids, the degradation of amino acids, aldehydes, organic acids, and possibly CO as well. Higher temperatures (approx. 83oC) are ideal growth temperatures for Archaeoglobus, although a biofilm environment provides some environmental elasticity. Biofilm is composed of polysaccharides, proteins, and metals. The advantages to a biofilm environment is that extracellular enzymes will be more accessible, competition and predation can be controlled, and there is an increased resistance to antibiotics. LaPaglia and Hartzell (1997) found that one mechanism of biofilm protection was the sequestering of heavy metals. Cultures exposed to high concentrations of metals were able to integrate metals into an insoluble matrix.

Medicine

Cells protected by biofilm are difficult to destroy using conventional anti-microbial therapy, which gives them medicinal possibilities.

References

Klenk et al. 1997. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390:364-370.

LaPaglia, Christopher, Patricia L. Hartzell. 1997. Stress-Induced Production of Biofilm in the hyperthermophile Archaeoglobus fulgidus. Applied and Environmental Microbiology Vol. 63, No. 8: 3158-3163.

Cell surface of Archaeoglobus veneficus. Freeze-etched; copyright K.O. Stetter and R. Rachel, Univ. Regensburg, Germany.

An Archaeoglobus veneficus cell. Platinum-shadowed; copyright K.O. Stetter and R. Rachel, Univ. Regensburg, Germany.

Biofilm fibers courtesy of LaPaglia (1997)

The below mentioned article provides an overview on Bergey’s manual of systematic bacteriology.

Bergey’s manual, which first appeared in 1923 and, at present, is in its 9th edition under the title Bergey’s Manual of Systematic Bacteriology, is a major taxonomic treatment of bacteria (prokaryotes). This manual has served the community of microbiologists since more than 80 years and is a compendium of information on all recognized species of bacteria (prokaryotes).

Any discussion dealing with bacterial (prokaryotic) classification cannot go without a thorough acquaintance with this manual. Each chapter of this treatise, written by an expert, contains tables, figures, and other systematic information useful for identification of bacteria.

Many schemes for identification of bacteria have been devised prior to 1923 but all were usually fragmentary. There was need for a single scheme which could cover all the described bacteria. David Hendricks Bergey, a professor of bacteriology at the university of Pennsylvania (USA), proceeded in this direction and began preparing a complete review of the enormous literature of bacterial taxonomy.

To aid the publication of this work, the Society of American Bacteriologists (now called the American Society of Microbiologists) appointed an Editorial Board headed by Bergey. This resulted in the publication of the first edition of Bergey’s Manual of Determinative Bacteriology in 1923. The second edition of the manual was published in 1925 and the third edition in 1930.

In 1934, the Society of American Bacteriologists transferred to Dr. Bergey all its rights, title, and interests in the Manual in order to allow Bergey to create an independent, non-profit trust, namely, The Bergey’s Manual Trust. Throughout the years, this trust continues to prepare and publish successive editions of the manual and promotes research in the field of bacterial taxonomy.

The first eight editions of this manual appeared under the title ‘Bergey’s Manual of Determinative Bacteriology’. The 9th edition was retitled and was published as the 1st edition under the title. ‘Bergey’s Manual of Systematic Bacteriology’, which consisted of four volumes published in 1984, 1986, 1989, and 1991, respectively. This infect was the first edition of the Manual under the changed title.

The change of the title of the manual from determinative bacteriology to systematic bacteriology indicates that manual’s usefulness is no longer restricted to a determinative role, i.e., mere identification, but it is now aimed at a systematic classification of bacteria.

However, Bergey’s Manual of Systematic Bacteriology has appeared in the form of its 2nd edition consisting of five volumes; its first volume was published in 2001, second in 2005 and three additional volumes expected shortly.

Bergey’s Manual of Systematic Bacteriology (First Edition):

Phenetic Classification:

The first edition of Bergey’s Manual of Systematic Bacteriology is primarily phenetic, i.e., based on the natural similarity of phenotypic characteristics of microorganisms, and has appeared in four volumes consisting of sections.

The four volumes, their year of publication, and the sections and the groups of bacteria included in each of them are the following:

Vol. I: 1984 (sections 1-11): Gram-negative bacteria of general, medical, or industrial importance.

Vol. II: 1986 (sections 12-17): Gram-positive bacteria other than actinomycetes.

Vol. Ill: 1989 (sections 18-25): Gram-negative bacteria with distinctive properties, cyanobacteria, and archaea.

Vol. IV: 1991 (sections 26-23): Actinomycetes (Gram-positive filamentous bacteria).

All prokaryotes were retained in this edition in a single kingdom Prokaryotiae, divided into four divisions called Gracilicutcs, Firmicutes, Tenericutes, and Mendosicutes.

Despite many other differences in characteristics among the divisions, the Gracilicutes (thin skin) possess gram-negative cell wall; the Firmicutes (thick and strong skin) have gram-positive cell wall; the tenericutes (soft or tender skin) lack cell wall and represented by mycoplasmas; and the Mendosicutes (skin with faults) accommodating archaeobacteria that lack conventional peptidogycan.

Each of the 33 sections in the four volumes contain prokaryotes that share a few easily determined characteristics and bears a title that either describes these properties or provides the vernacular names of the prokaryotes included.

The characteristics used to define sections are normally features such as general shape and morphology, Gram-staining properties, oxygen relationships, motility, the presence of endospores the mode of energy production, and so forth.

Bergey’s Manual of Systematic Bacteriology (Second Edition):

Phylogenetic Classification:

Prokaryotic taxonomy enjoyed enormous progress after the publication of the first edition of Bergey’s Manual of Systematic Bacteriology. It became possible with the aid of newer molecular techniques such as the sequencing of ribosomal RNA (rRNA), DNA, and proteins. These techniques has made phylogenetic analysis of prokaryotes practicable.

In the light of the availability of considerable knowledge of phylogenetic relationships amongst prokaryotes, the second edition of Bergey’s Manual of Systematic Bacteriology is largely phylogenetic rather than phenetic.

As a result, the second edition is quite different from the first edition in the characteristics chosen as basis for classification. However, the second edition consists of five volumes. Its first volume was published in 2001, second in 2005, and three additional volumes expected shortly.

The details of the five volumes are the following:

Vol. I: The Archaea, and the Deeply Branching and Phototropic Bacteria

Vol. II: The Proteobacteria

Vol. III: The Low G + C Gram-positive Bacteria

Vol. IV: The High G + C Gram-positive Bacteria

Vol. V: The Planctomycetes, Spirochaetes, Fibrobacteres, Bacteriodetes, and Fusobacteria (Vol. V also contains a section accommodating the update descriptions and phylogenetic arrangements that have been revised since publication of volume I)

A Concise Account of the Classification:

Volume I. The Archaea and the Deeply Branching and Phototrophic Bacteria:

Domain Archaea:

Phylum AI:

Crenarchaeota:

The phylum Crenarchaeota contains thermophilic and hyperthcrmophilic sulfur-metabolizing prokaryotes arranged in single class Thermoprotei divided into three orders and five families. The important genera are Thermoproteus, Desulgurococcus, Pyrodictium, and Sulfolobus.

Phylum A II:

Euryarchaeota:

The phylum Euryarchaeota contains primarily methanogens and halophiles; thermophilic, sulfur-reducers also are included in this phylum. This phylum is divided into seven classes (Methanobacteria, Methanococci. Halobacteria, Thermoplasmata, Thermococci, Archeoglobi, and Methanopyri), nine orders, and sixteen families.

The representative genera of each class are Methanobacterium, Methanococcus, Halobacterium, Thermophasma, Thermococcus, Archaeoglobus, and Methanopyrus, respectively.

Domain: Bacteria:

Phylum BI. Aquificae:

The phylum Aquificae has one class (Aquificae) that contains autotrophic bacteria possessing ability to use hydrogen for energy production. Aquifex and Hydrogenobacter are the representative genera. Aquifex means “water maker” as this genus reduces oxygen by using hydrogen and produces water.

Phylum BII:

Thermotogae:

The phylum thermotogae consists of one class (Thermotogae). It contains anaerobic, thermophilic, fermentative, gram-negative bacteria. The representative genera are Thermotoga, Geotoga, Fervidobacterium, etc.

Phylum Bill:

Thermodesulfobacteria:

This phylum contains one class (Thermodesulfobacteria) and only two genera, Thermodesulfobacterium and Thermodesulfatator. The bacteria are anaerobic, thermophilic, and sulfate-reducing.

Phylum BIV:

Dienococcus-Thermus:

The phylum contains one class (Dienococci). The representative genera are Dienococcus, Thermus, Marinithermus, etc. The bacteria are gram-positive and extraordinarily radiation resistant.

Phylum BVI:

Chloroflexi:

The phylum Chloroflexi consists of two classes (Chloroflexi and Anaerolieae). Many members of this phylum are gram-negative and are called green nonsulfur bacteria. The important genera are Chloroflexus, Oscillochloris, Herpetosiphon and Anaerolinea.

Phylum BVII:

Thermomicrobia:

The phylum contains one class (Thermomicrobia) and is represented by a single genus, Thermomicrobium. Thermomicrobium is an aerobic thermophilic chemotroph possessing unusual lipids that contain 1, 2-dialcohols instead of glycerol, and have neither ester nor ether linkages.

This is in contrast to the lipids of Bacteria and Eukarya that contain fatty acids esterified to glucose. Also, the cells of Thermomicrobium differ from those of Bacteria in that they lack peptidoglycan in their cell walls.

Phylum B VIII:

Nitrospirae:

The phylum consists of one class (Nitrospira) and genera like Nitrospira and Leptospirillum.

Phylum BIX:

Deferribacteres:

The phylum Deferribacteres contains one class (Deferribacteres) and genera such as Deferribacter, Denitrovibrio, etc.

Phylum BX:

Cyanobacteria:

The phylum Cyanobacteria consists of a single class (Cyanobacteria) divided into five subsections. The taxonomic position of the cyanobacteria is left open in Bergey s Manual. The cyanobacteria are oxygenic phototrophs and show a distant relationship to gram-positive bacteria.

These organisms were the first oxygen-evolving phototrophs on Earth and were responsible for the conversion of the anoxic atmosphere of our planet to oxic. Genera belonging to this phylum are mentioned as “form genus” in the Manual because the latter refers to a group of cyanobaceria with very characteristic morphology found worldwide but not all isolates of such a type may actually fit into the same genus.

The important “form genera” are Microcytis, Cyanocytis, Lyngbya, Oscillatoria, Spirulina, Anabaena, Nostoc, Scytonema, Calothrix, Tolypothrix, etc.

Phylum B XI. Chlorobi:

Only one class (Chlorobia) constitutes the phylum. The representative genera are Chlorobium, Pelodictyon, Chlorobaculum, etc. This phylum accommodates anoxygenic photosynthetic bacteria known as the green sulfur bacteria, which can assimilate CO2 through the reductive (reverse) tricarboxylic acid cycle rather than calvin cycle and oxidize sulfide to sulfur granules that accumulate outside the cell.

Volume II:

The Proteobacteria:

Phylum B XII:

Proteobacteria:

The phylum Proteobacteria consists of five classes (Alfaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria).

Proteobacteria contains over 400 genera which are all gram-negative, show extreme metabolic diversity, and represent the majority of bacteria of pharmaceutical, industrial, agricultural, and biological research significance. It is believed by many that the proteobacteria evolved from a photosynthetic ancestor and, presumably, many strains lost photosynthetic activity during adaptation to new ecological niches.

Alphaproteobacteria (∝-proteobacteria) consist of the most bacteria that are capable of growing at low nutrient levels (i.e., oligotrophic forms); the representative genera of this class are Rhodospirillum, Azospirillum, Rickettsia, Rhizobium, Agrobacterium, Nitrobacter, Hyphomicrobium, Methylobacterium, etc.

Betaproteobacteria (β-proteobacteria) utilize the substances that diffuse from organic decomposition in the anaerobic zone of their habitats. Some of its genera are pathogenic.

The important genera included in betaprotobacteria are Thermothrix, Bordetella, Leptothrix, Neissaria, Aquaspirillum, Nitrosomonas, Gallionella, Spirillum, etc. Gammaproteobacteria (γ-proteobacteria) are chemoorganotrophic, facultative anaerobic, and the representative genera are Chromatium, Xanthomonas, Beggiatoa, Pseudomonas, Vibrio, Photobacterium, Escherichia, Klebsiella, Erwinia, etc. Deltaproteobacteria (δ-proteobacteria) can mainly be categorized as of three groups.

Many of the deltaproteobacteia are anaerobic and cause desulfurication (generate sulfide from sulfate and sulfur); representative genera of such bacteria are Desulfovibrio, Deslfuromonas, Desulfobaca, etc. Some deltaproteobacteria (e.g., Bdellovibrio, Bacteriovorax) are predators on other bacteria.

Representatives such as Myxococcus, Polyangium and Chondromyces are the deltaproteobacteria that form fruiting bodies and also prey on other bacteria. Epsilonproteobacteria (Ɛ- proteobacteria) is a small class and its members like Helicobacter and Campylobacter are important human pathogens causing intestinal infections.

Volume III:

The Low G + C Gram-Positive Bacteria:

Phylum B XIII:

Firmicutes:

Phylum Firmicutes consists of the gram-positive bacteria with low G + C content (mol% value below 50%) in their DNA. Most of the bacteria of this phylum are heterotroptic. Though mycoplasmas lack cell wall and stain gram-negative, they are classified under this phylum because of their close relationship to low G + C gram-positive bacteria. The phylum is classified into three classes, Clostridia, Mollicutes, and Bacilli.

Class Clostridia contains a very wide variety of gram-positive bacteria that vary in morphology and size but tend to be anaerobic. Some produce endospores but others do not. Important genera are Clostridium, Acetobacterium, Desulfotomaculum, Eubacterium, Heliobacterium, Syntrophomonas, etc.

Class Mollicutes consists of the members that are wall-less and are generally called mycoplasmas. These bacteria are pleomorphic in shape, normally nonmotile, stain gram-negative due to absence of cell wall, and require sterols for growth. The important genera include Mycoplasma, Phytoplasma, Spiroplasma. that contain several important animal and plant pathogens.

Class Bacilli comprises a variety of bacteria which are aerobic or facultatively anaerobic cocci and rods, and many of them are endospore-forming (e.g., Bacillus, Sporosarcina, Paenibacillus). Many genera of this phylum are pharmaceutical and industrially significant (e.g., Bacillus, Lactobacillus, Enterococcus, Leuconostoc, Streptococus, Lactococcus).

Volume IV:

The High G + C Gram-Positive Bacteria:

Phylum B XIV:

Actinobacteria:

The phylum Actinobacteria is classified into a single class Actinobacteria which contains high G + C gram-positive bacteria with mole% value above 50 to 55%. These bacteria show enormous morphological variations ranging from cocci to regular or irregular rods to extensively branching hyphae. Endospore formation lacks but many genera do form a variety of asexual spores.

The phylum consists of five subclasses, six orders, forteen suborders, forty four families, and many a number of genera.

The important genera of actinobacteria are Actinomyces, Arthrobacter, Brevibacterium, Cellulomonas, Clavibacter, Corynebacterium, Mycobacterium, Nocardia, Actinoplanes, Propionibacterium, Streptomyces, Frankia, etc. The largest and the most complex genes is Streptomyces containing over 500 species.

Volume V:

The Plantomycetes, Spirochaetes, Fibrobacters, Bacteroidetes, and Fusobacteria:

Phylum B XV:

Planctomycetes:

This phylum consists of a single class (Planctomycetacia) containing four genera named Planctomyces, Gemmata, Pirellula and Isosphaera. Members lack peptidoglycan and their cell walls are of an S-layer type consisting of protein. They divide by budding and may produce non- prosthecate appendages called stalks.

Phylum B XVI:

Chlamydias:

Phylum Chlamydiae contains a single class (Chlamydiae) and seven genera. The genus Chlamydia is by far the most important genus; its species cause many human diseases.

Phylum B XVII:

Spirochaetes:

Phylum Spirochaetes is classified into one class (Spirochaetes) containing thirteen genera, the important ones are Spirochaeta, Borellia, Treponema, Cristispira, Leptospira, etc. They are gram-negative, motile, helically-shaped bacteria characterized by a unique motility behaviour.

Phylum B XVIII:

Fibrobacteres:

This phylum is represented by a single class (Fibrobacteres) and a single genus (Fibrobacter). Fibrobacter is a cellulolytic gram-negative bacterium occurring in the rumen of ruminant animals where it breaks down cellulose.

Phylum B XIX:

Acidobacteria:

The phylum contains only one class (Acidobacteria) represented by three genera named Acidobacterium, Geothrix and Holophaga.

Phylum B XX:

Bacteroidetes:

The phylum is divided into three classes (Bacteroides, Flavobacteria, and Sphingobacteria) exemplified by genera like Bacteroides, Flavobacterium, Flexibacter, Cytophaga, Toxothrix, etc. Flexibacter and Cytophaga are gliding bacteria and are ecologically significant.

Phylum B XXI:

Fusobacteria:

The phylum contains one class (Fusobacteria) with genera like Fusobacterium, Leptotrichia, and Cetobacterium. Fusobacterium is filamentous and occurs in the oral cavity of humans.

Phylum B XXII:

Verrucomicrobia:

This phylum consists of a single class (Verrucomicrobiae) and genera such as Verrucomicrobium, Prosthecobacter, and Xiphinematobacter. Members form cytoplasmic appendages called prosthecae and divide symmetricaly.

Phylum B XXIII:

Dictyoglomus:

The phylum is represented by a single class (Dictyoglomi) consisting of a single genes named Dictyogomus.

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