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Mbp 02 microbial taxonomy classification

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Subashkumar Rathinasamy

The document provides an overview of microbiological taxonomy, detailing the classification systems, levels of classification, definitions of species, and the historical evolution of taxonomy. It highlights the transition from traditional morphological classification to molecular systematics, emphasizing genetic methods for identifying and classifying bacteria and archaea. The text underscores the importance of databases and manuals, like Bergey's Manual, in aiding the systematic arrangement and identification of microorganisms.

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19MBT103 - MICROBIOLOGY MBP-02 Microbial Taxonomy & Classification systems SRI RAMAKRISHNA COLLEGE OF ARTS AND SCIENCE (AUTONOMOUS) COIMBATORE – 641 006.
Taxonomy is a subset of systemics. Systemics is the study of organisms in order to place organisms having similar characteristics into the same group. Taxonomy has three components: • Classification: The arrangement of organisms into groups based on similar characteristics, evolutionary similarity or common ancestry. These groups are also called taxa. • Nomenclature: The name given to each organism. Each name must be unique and should depict the dominant characteristic of the organism. • Identification: The process of observing and classifying organisms into a standard group that is recognized throughout the biological community. Taxonomy has two functions • First to identify and describe as completely as possible to the basic taxonomic unit or species and • second, to devise a method for arranging and cataloguing these species.
Benefits To distinguish one individual from another, we need to establish certain criteria and this art of biological classification is known as taxonomy or systematics. Taxonomy is therefore, the systematic arrangement of organisms in groups or categories called taxa (taxon-singular).
Microbial Taxonomy • Classification Systems • Levels of Classification • Definition of “Species” • Nomenclature • Useful Properties in Microbial Classification • Microbial Phylogeny
Levels of Classification • Taxon: – A group or “level” of classification – Hierarchical; broad divisions are divided up into smaller divisions: • Kingdom (Not used by most bacteriologists) • Phylum (Called “Division” by botanists) • Class • Order • Family • Genus (plural: Genera) • Species (Both singular & plural)
Definition of “Species” • The “basic unit” of taxonomy, representing a specific, recognized type of organism • For sexually reproducing organisms, a fundamental definition of “species” has been reproductive compatibility • This definition fails for many microbial species (including bacteria), because they do not reproduce sexually
• Definition of “species” in microbiology: – Classic definition: A collection of microbial strains that share many properties and differ significantly from other groups of strains – Species are identified by comparison with known “type strains”: well-characterized pure cultures; references for the identification of unknowns ATCC American Type Culture Collection Manassas, Virginia NCTC National Collection of Type Cultures Public Health England, UK BCCM Belgium Coordinated Collection of Microorganisms Ghent, Belgium CIP Collection d'Institut Pasteur Paris, France DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen Braunschweig, Germany JCM Japan Collection of Microorganisms Saitama, Japan NCCB Netherlands Culture Collection of Bacteria Utrecht, Netherlands NCIMB National Collection of industrial, Marine and food bacteria Aberdeen, Scotland ICMP International Collection of Microorganisms from Plants Auckland, New Zealand
Classification of bacteria is determined by publication in the International Journal of Systematic Bacteriology and Bergey's Manual of Systematic Bacteriology. The International Committee on Systematic Bacteriology (ICSB) maintains international rules for the naming of bacteria and taxonomic categories and for the ranking of them in the International Code of Nomenclature of Bacteria. The term "bacteria" was traditionally applied to all microscopic, single-celled prokaryotes. Molecular systematics showed prokaryotic life to consist of two separate domains, originally called Eubacteria and Archaebacteria, But now called Bacteria and Archaea that evolved independently from an ancient common ancestor. The archaea and eukaryotes are more closely related to each other than either is to the bacteria. These two domains, along with Eukarya, are the basis of the three-domain system, which is currently the most widely used classification system in microbiology
As with bacterial classification, identification of bacteria is increasingly using molecular methods. Diagnostics using such DNA-based tools, such as polymerase chain reaction, are increasingly popular due to their specificity and speed, compared to culture-based methods. These methods also allow the detection and identification of "viable but nonculturable” cells that are metabolically active but non- dividing. However, even using these improved methods, the total number of bacterial species is not known and cannot even be estimated with any certainty
mid-1700s, Swedish botanist Carl Linnaeus - a taxonomy for living organisms Linnaeus’ taxonomy grouped living things into two kingdoms: plants and animals Haeckel (1866) - Protista, - include microorganisms, is a heterogenous group consisting of protozoa, algae, fungi and bacteria. Although each one of these groups has distinct characteristics, within a group organisms show a great deal of similarity. 1969 Robert H. Whitteker - five kingdom classification Monera, protista, plantae (plants), fungi, and animalia (animals). Monera are organisms that lack a nucleus and membrane-bounded organelles, such as bacteria. Protista are organisms that have either a single cell or no distinct tissues and organs, such as protozoa. This group includes unicellular eukaryotes and algae. Fungi are organisms that use absorption to acquire food. These include multicellular fungi and single-cell yeast. Animalia and plantae include only multicellular organisms
Linnaeus 1735 2 kingdoms Haeckel 1866 3 kingdoms Chatton 1925 2 empires Copeland 1938 4 kingdoms Whittaker 1969 5 kingdoms Woese et al. 1977 6 kingdoms Woese et al. 1990 3 domains Cavalier-Smith 2004 6 kingdoms (not treated) Protista Prokaryota Monera Monera Eubacteria Bacteria Bacteria Archaebacteri a Archaea Eukaryota Protoctista Protista Protista Eukarya Protozoa Chromista Vegetabilia Plantae Fungi Fungi Fungi Plantae Plantae Plantae Plantae Animalia Animalia Animalia Animalia Animalia Animalia
Carl Woese and Ralph S. Wolfe (1977) proposed a new six-kingdom taxonomy. This came about with the discovery of archaea, which are prokaryotes that lives in oxygen- deprived environments Woese’s six-kingdom taxonomy consists of: • Eubacteria (has rigid cell wall) • Archaebacteria (anaerobes that live in swamps, marshes, and in the intestines of mammals) • Protista (unicellular eukaryotes and algae) • Fungi (multicellular forms and single-cell yeasts) • Plantae • Animalia Woese determined that archaebacteria and eubacteria are two groups by studying the rRNA sequences in prokaryotic cells. Woese used three major criteria to define his six kingdoms. These are: • Cell type. Eukaryotic cells (cells having a distinct nucleus) and prokaryotic cell (cells not having a distinct nucleus) • Level of organization. Organisms that live in a colony or alone and one-cell organisms and multicell organisms. • Nutrition. Ingestion (animal), absorption (fungi), or photosynthesis (plants).
In the 1990s Woese studied rRNA sequences in prokaryotic cells (archaebacteria and eubacteria) proving that these organisms should be divided into two distinct groups. Today organisms are grouped into three categories called domains that are represented as bacteria, archaea, and eukaryotes. Archaea lack muramic acid in the cell walls. Bacteria have a cell wall composed of peptidoglycan and muramic acid. Bacteria also have membrane lipids with ester-linked, straight-chained fatty acids that resemble eukaryotic membrane lipids. Most prokaryotes are bacteria. Bacteria also have plasmids, which are small, double-stranded DNA molecules that are extrachromosomal. Eukarya are of the domain eukarya and have a defined nucleus and membrane bound organelles.
Mbp 02 microbial taxonomy classification
INTRODUCTION - BACTERIAL CLASSIFICATION Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Bacteria can be classified on the basis of cell structure, cellular metabolism or on differences in cell components such as DNA, fatty acids, pigments, antigens and quinones. While these schemes allowed the identification and classification of bacterial strains, it was unclear whether these differences represented variation between distinct species or between strains of the same species. This uncertainty was due to the lack of distinctive structures in most bacteria, as well as lateral gene transfer between unrelated species. Due to lateral gene transfer, some closely related bacteria can have very different morphologies and metabolisms. To overcome this uncertainty, modern bacterial classification emphasizes molecular systematics, using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridization, as well as sequencing genes that have not undergone extensive lateral gene transfer, such as the rRNA gene.
Classification of Bacteria and Archaea • Prokaryotes can be classified using artificial or natural (phylogenetic) systems. • Historically, prokaryotes were classified on the basis of their phenotype (morphology, staining reactions, biochemistry, substrates/products, antigens etc). In other words a phenotypic characterization is based on the information carried in the products of the genes. These classification systems were artificial. • Modern characterization is based on the information carried in the genes i.e. the genome. This is genetic information and can also tell us something about the evolution of the organism. In other words phylogenetics.
Bergey's Manual of Determinative Bacteriology  The bacteria are a group of great diversity with a procaryotic cellular organization.  Active interest in classifying bacteria led by Chester in 1899 and 1901 to publish the manual of determinative bacteriology.  This manual subsequently was modified by David Bergey into what is now known as Bergey's manual of Determinative Bacteriology  A major treatise on bacterial taxonomy since its first publication in 1923.  it is used to classify bacteria based on their structural and functional attributes by arranging them into specific familial orders. However, this process has become more empirical in recent years
• The change in volume set to "Systematic Bacteriology" came in a new contract in 1980 • The new style included "relationships between organisms" and "expanded scope". • This new style was picked up for a four-volume set that first began publishing in 1984. 1. Volume 1 included information on all types of Gram-negative bacteria that were considered to have "medical and industrial importance." 2. Volume 2 included information on all types of Gram-positive bacteria. 3. Volume 3 deals with all of the remaining, slightly different Gram-negative bacteria, along with the Archaea. 4. Volume 4 has information on filamentous actinomycetes and other, similar bacteria.[
The current grouping is: • Volume 1 (2001): The Archaea and the deeply branching and phototrophic Bacteria • Volume 2 (2005): The Proteobacteria—divided into three books: • 2A: Introductory essays • 2B: The Gammaproteobacteria • 2C: Other classes of Proteobacteria • Volume 3 (2009): The Firmicutes • Volume 4 (2011): The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes • Volume 5 (in two parts) (2012): The Actinobacteria The Annals of Internal Medicine described the volumes as "clearly written, precise, and easy to read" and "particularly designed for those interested in taxonomy
Bergey’s Manual of Determinative Bacteriology: Is standard reference for laboratory identification of bacteria. Morphology, differential staining, biochemical tests to test for presence of various enzymes. Bergey’s Manual of Systematic Bacteriology Provides phylogenetic information on bacteria and archaea Based on rRNA sequencing Bergey’s Manual: Classifying and Identifying Prokaryotes
Classification based mainly on Morphology – Cocci, rod, spiral and pleomorphic Stains – Gram staining, Acid fast Oxygen requirement – Aerobic and Anaerobic Spore forming Addition factors Culture properties Antigenic properties Biochemical reactions DNA based – % G+C content, ribosomal rRNA, Total genomic DNA
Identification Methods • Morphological characteristics: Useful for identifying eukaryotes  Differential staining: Gram staining, acid-fast staining  Biochemical tests: Determines presence of bacterial enzymes
species –a collection of bacterial cells which share an overall similar pattern of traits in contrast to other bacteria whose pattern differs significantly strain or variety – a culture derived from a single parent that differs in structure or metabolism from other cultures of that species (biovars, morphovars) type – a subspecies that can show differences in antigenic makeup (serotype or serovar), susceptibility to bacterial viruses (phage type) and in pathogenicity (pathotype).
Procaryotic groups are divided among the four volumes in the following manner: (1) Gram negative bacteria of general, medical, or industrial importance; (2) gram-positive bacteria other than actinomycetes; (3) Gram negative bacteria with distinctive properties, cyanobacteria, and archaea (4) actinomycetes (gram-positive filamentous bacteria).
Mbp 02 microbial taxonomy classification
Mbp 02 microbial taxonomy classification
Identification Methods cont.: Serology • Involves reactions of microorganisms with specific antibodies: Combine known anti-serum with unknown bacterium • Useful in determining the identity of strains and species, as well as relationships among organisms. Fig 10.10: Slide Agglutination  Examples:  Slide agglutination  ELISA (see lab)  Western blot (no details)
Identification Methods cont.: Phage TypingFigure 10.13 Identification of bacterial species and strains by determining their susceptibility to various phages. More details on bacteriophages in Ch 13
Numerical Taxonomy In the 19th century, microorganisms were grouped according to, their evolutionary affinities and the arrangement of organisms into groups was on the basis of inherited and stable structural and physiological characters. This arrangement is known as the Natural or the Phylogenetic classification. This approach, of classifying microorganisms is now almost abandoned in favour of a more empirical approach based on quantification of similarities and differences among organisms. Suggested by Micheal Adanson and is known as Adansonian or Numerical taxonomy
• Numerical taxonomy is a methods which is used to differentiate a large number of similar bacteria, i.e. species. • A large number of tests (~100) are carried out and the results are scored as positive or negative. Several control species are included in the analysis. • All characteristics are given equal weight and a computer based analysis is carried out to group the bacteria according to shared properties.
Homologous genes are used in the construction of phylogenetic trees • Homologous means that genes have a common anscestor • Orthologs are homologous genes that belong to different species but still retain their original function • Paralogs are homologous genes that have arrisen by gene duplication and are found in the same organism • Only orthologes can be used in the construction of phylogenetic trees. The classical example is the 16S ribosomal RNA gene.
16S RNA Secondary structure of the 16S rRNA molecule from the small ribosomal subunit of the bacterium Escherichia coli. The bases are numbered from 1 at the 5' end to 1,542 at the 3' end. Every tenth nucleotide is marked with a tick mark, and every fiftieth nucleotide is numbered. Tertiary interactions with strong comparative data are connected by solid lines. From the Comparative RNA Web Site, www.rna.icmb.utexas.edu; courtesy of Robin Gutell.
Conservation and variation in small subunit rRNA This diagram shows conserved and variable regions of the small subunit rRNA (16S in prokaryotes or 18S in eukaryotes). Each dot and triangle represents a position that holds a nucleotide in 95% of all organisms sequenced, though the actual nucleotide present (A, U, C, or G) varies among species. Figure by Jamie Cannone, courtesy of Robin Gutell; data from the Comparative RNA Web Site: www.rna.icmb.utexas.edu
Conservation and variation in small subunit rRNA The starred region from part A as it appears in a bacterium (Escherichia coli), an archaean (Methanococcus vannielii), and a eukaryote (Saccharomyces cerevisiae). This region includes important signature sequences for the Bacteria and Archaea. Figure by Jamie Cannone, courtesy of Robin Gutell; data from the Comparative RNA Web Site: www.rna.icmb.utexas.edu
Phylogenetic trees Two different formats of phylogenetic trees used to show relatedness among species.
Unrooted and rooted trees Representations of the possible relatedness between three species, A, B, and C. (A) A single unrooted tree (shown in both formats; see Figure 17.4). (B) Three possible rooted trees (in one format). UPGMA - Unweighted Pair Group Method with Arithmetic Mean
Universal phylogenetic tree as determined from comparative ribosomal RNA sequencing.
Detailed phylogenetic tree of the major lineages (phyla) of Bacteria based on 16S ribosomal RNA sequence comparisons
Novel phyla discovered by molecular analysis of natural habitats A phylogenetic tree of 16S rDNA sequences of Bacteria, based on pure cultures and clonal libraries from natural samples. Note the existence of many phyla (shown in outline rather than as solid black lines) that have not yet been cultivated. Courtesy of Phil Hugenholz and ASM Publications (Hugenholz, P., B. M. Goebel and N. R. Pace. 1998. J. Bacteriol. 180:4765-4774).
Horizontal gene transfer
Horizontal gene transfer
Species concept • The species concept applied to eukaryotes cannot be applied to bacteria and archaea. In fact it is quite difficult to define prokaryote species. • In order to be of the same species prokaryotes must share many more properties with each other than with other prokaryotes. • They must have similar mol % G+C. Note that two species having the same mol % G+C are not necessary of the same species. • The DNA from organisms of the same species must show a minimum of 70% reassociation.
DNA melting curve Melting curve for a double-stranded DNA molecule. As the temperature is raised during the experiment, the double-stranded DNA is converted to the single-stranded form and the UV absorbance of the solution increases. The midpoint temperature, Tm, can be calculated from the curve. This process is reversible if the temperature of the solution is slowly lowered to allow the single strands to reanneal.
Tm and DNA base composition Graph showing the direct relationship between mol % G + C and midpoint temperature (Tm) of purified DNA in thermal denaturation experiments.
DNA base composition range Range of mol % G + C content among various groups of organisms. Note the broad range of GC ratios for bacteria in comparison to plants and animals and other eukaryotes. The best method of distinguishing two organisms should therefore be on the basis of composition of their genetic material. In recent years, the genetic characterization of organisms has been substantially developed.
Nucleic Acid Hybridization Fig 10.15 Single strands of DNA or RNA, from related organisms will hydrogen-bond to form a double-stranded molecule; this bonding is called nucleic acid hybridization. Examples of Applications: • Southern blotting, • DNA chips, and • FISH Figs. 10.17 and 10.18
DNA/DNA reassociation In this example, which is a control experiment (the radiolabeled sample is reannealed with unlabeled DNA from the same strain), the degree of reassociation is highest and treated as 100%. If a different strain is reannealed with the radiolabeled DNA, it will show a lower degree of reannealing (compared with the 100% attributed to the control), indicative of the similarity between the two strains being tested. Strains with reannealing values of 70% or greater are considered to be the same species.
Mole percent guanine + cytosine (Mol% G+C)
• Since every microorganism has its specific FAME profile (microbial fingerprinting), • Used as a tool for microbial source tracking (MST). • The types and proportions of fatty acids present in cytoplasm membrane and outer membrane (Gram negative) lipids of cells are major phenotypic traits. • Clinical analysis can determine the lengths, bonds, rings and branches of the FAME. • Bacterial culture is taken, and the fatty acids extracted and used to form methyl esters. • The volatile derivatives are then introduced into a gas chromatagraph (GC), and the patterns of the peaks help identify the organism. This is widely used in characterizing new species of bacteria, and is useful for identifying pathogenic strains. FAME – Fatty acids Methyl Ester Analysis
Mbp 02 microbial taxonomy classification
Fatty acid analysis Fatty acid methyl ester (FAME) chromatogram of an unknown species, showing chromatographic column retention times and peak heights. Note: 10:0, 12:0, 16:0, and 19:0 indicate saturated fatty acids with 10, 12, 16, and 19 carbons; 16:1 and 18:1, monounsaturated 16-carbon and 18-carbon fatty acids; omega number, the position of the double bond relative to the omega end—that is the hydrocarbon end (not the carboxyl end)—of the fatty acid chain; cis and trans, the configuration of the double bond.
Mbp 02 microbial taxonomy classification
Ribosomal Database project • The database contains over 78,000 bacterial 16S rDNA sequences • Approximately 7000 Type strains (the bacteria are in pure culture) • Approximately 70000 Environmental samples (bacteria and archaea samples have been collected from the environment and characterized by molecular methods)
CLEAVED AMPLIFIED POLYMORPHIC SEQUENCE (CAPS) ANALYSIS CAPS analysis refers to the analysis of polymorphism of DNA fragments obtained from the restriction analysis of PCR amplified DNA. Cleaved Amplified Polymorphic Sequences polymorphisms are differences in restriction fragment lengths caused by mutations or SNPs that create or abolish restriction endonuclease recognition sites in PCR amplicons produced by locus-specific oligonucleotide primers. CAPS assay: How it works? The CAPS assay uses amplified DNA fragments that are digested with a restriction endonuclease to display RFLP. Example of CAPS assay: Amplification – Digestion - Separation Unique sequence primers are used to amplify a mapped DNA sequence from two different individuals (for example, from two different bacterial genera), A/A and B/B refer to two different bacteria. The amplified fragments from A/A and B/B contain two and three RE recognition sites, respectively. When fractionated by agarose or acrylamide gel electrophoresis, the PCR products digested by the RE will give readily distinguishable patterns. This CAPS pattern becomes the prototype CAPS map for identification of the given bacteria.
RESTRICTION FRAGMENT LENGTH POLYMORPHISM (RFLP) RFLP is a difference in homologous DNA sequences that can be detected by the presence of fragments of different lengths after digestion of the DNA samples in question with specific restriction endonucleases. RFLP, as a molecular marker, is specific to a single clone/restriction enzyme combination. In RFLP analysis the DNA sample is broken into pieces (digested) by restriction enzymes and the resulting restriction fragments are separated according to their lengths by gel electrophoresis.
Identification Methods cont.: Genetics • DNA fingerprinting: Number and sizes of DNA fragments (fingerprints) produced by RE digests are used to determine genetic similarities. • Ribotyping: rRNA sequencing • Polymerase chain reaction (PCR) can be used to amplify a small amount of microbial DNA in a sample. The presence or identification of an organism is indicated by Fig 10.14: Electrophoresis of RE digest of plasmid DNA
The classical Adansonian approach of classifying microbes is based on phenotypic characteristics. Such characteristics are expressions of a large number of genes that control cellular activities through enzymes. It is now generally agreed that the phenotype is the reflection of the DNA base sequence. One is the analysis of the base composition of DNA i.e. to determine the mole per cent of guanine and cytosine in DNA (% G+C). The second, is to determine the degree of similarity between two DNA samples by hybridization between DNA and DNA or DNA and RNA. (G+C / A+T+G+C ) x 100
Microcomputer application of Bayesean probability testing for the identification of bacteria A computer program (BACTID) is described which facilitates the identification of bacteria based on a priori data and Bayesean probability testing. The program is not limited to a specific format, has a short execution time, can be easily applied to a variety of situations, and can be run on almost any microcomputer system operating under either 8-bit CP/M or 16-bit MS-DOS/PC-DOS. Additionally, BACTID (1) is not limited to one type of computer (hardware independent), (2) is not limited by size of the computer's random access (RAM independent), (3) can recognize various data bases matrices (format independent), (4) is able to compensate for missing data and (5) allows for various methods of data entry.
Mbp 02 microbial taxonomy classification
• Study describes a computer-based technique for classifying and identifying bacterial samples sing Fourier-transform infrared spectroscopy (FT-IR) patterns. • Classification schemes were tested for selected series of bacterial strains and species from a variety of different genera. • Dissimilarities between bacterial IR spectra were calculated using modified correlation co-efficients. Dissimilarity matrices were used for cluster analysis, which yielded dendrograms broadly equated with conventional taxonomic classification schemes. • Analyses were performed with selected strains of taxa Staphylococcus, Streptococcus, Clostridium, Legionella and Escherichia coli in particular, and with a database containing 139 bacterial reference spectra. • The latter covered a wide range of Gram-negative and Gram-positive bacteria. Unknown specimens could be identified when included in an established cluster analysis. • Thirty-six clinical isolates of Staphylococcus aureus and 24 of Streptococcus faecalis were tested and all were assigned to the correct species cluster. It is concluded that: (1) FT-IR patterns can be used to type bacteria; (2) FT-IR provides data which can be treated such that classifications are similar and/or complementary to conventional classification schemes; and (3) FT-IR can be used as an easy and safe method for the rapid identification of clinical isolates.
Mbp 02 microbial taxonomy classification
Archaea bacteria A group of single-celled microorganisms. Single individual or species from this domain is called an archaeon (sometimes spelled "archeon"). They have no cell nucleus or any other membrane-bound organelles within their cells. Archaea have an independent evolutionary history and show many differences in their biochemistry from other forms of life, and so they are now classified as a separate domain in the three-domain system Archaea were first classified as a separate group of prokaryotes in 1977 by Carl Woese and George E. Fox in phylogenetic trees based on the sequences of ribosomal RNA (rRNA) genes. 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, because 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. Archaea and bacteria are quite similar in size and shape, although a few archaea have very unusual shapes, such as the flat and square-shaped cells of Haloquadratum walsbyi.
Mbp 02 microbial taxonomy classification
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. Archaean biochemistry are unique, such as their reliance on ether lipids in their cell membranes. Archaea use a much greater variety of sources of energy than eukaryotes: ranging from familiar organic compounds such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea (the Halobacteria) use sunlight as an energy source and other species of archaea fix carbon; however, unlike plants and cyanobacteria, no species of archaea is known to do both. Archaea reproduce asexually and divide by binary fission, fragmentation, or budding; unlike bacteria and eukaryotes, no known species form spores. Initially, archaea were see
HABITAT Initially, archaea were seen as extremophiles that lived in harsh environments, such as hot springs and salt lakes, but they have since been found in a broad range of habitats, including soils, oceans, marshlands and the human colon. 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. Archaea are now recognized as a major part of Earth's life and may play roles in both the carbon cycle and the nitrogen cycle. No clear examples of archaeal pathogens or parasites are known, but they are often mutualists or commensals. One example is the methanogens that inhabit the gut of humans and ruminants, where their vast numbers aiddigestion. Methanogens are used in biogas production and sewage treatment, and enzymes from extremophile archaea that can endure high temperatures and organic solvents are exploited in biotechnology.
Relation to eukaryotes The evolutionary relationship between archaea and eukaryotes remains unclear. Aside from the similarities in cell structure and function that are discussed below, many genetic trees group the two. Complicating factors include claims that the relationship between eukaryotes and the archaeal phylum Euryarchaeota is closer than the relationship between the Euryarchaeota and the phylum Crenarchaeota and the presence of archaean-like genes in certain bacteria, such as Thermotoga maritima, from horizontal gene transfer.The leading hypothesis is that the ancestor of the eukaryotes diverged early from the Archaea and that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and cytoplasm; this explains various genetic similarities but runs into difficulties explaining cell structure.

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Mbp 02 microbial taxonomy classification

  • 1. 19MBT103 - MICROBIOLOGY MBP-02 Microbial Taxonomy & Classification systems SRI RAMAKRISHNA COLLEGE OF ARTS AND SCIENCE (AUTONOMOUS) COIMBATORE – 641 006.
  • 2. Taxonomy is a subset of systemics. Systemics is the study of organisms in order to place organisms having similar characteristics into the same group. Taxonomy has three components: • Classification: The arrangement of organisms into groups based on similar characteristics, evolutionary similarity or common ancestry. These groups are also called taxa. • Nomenclature: The name given to each organism. Each name must be unique and should depict the dominant characteristic of the organism. • Identification: The process of observing and classifying organisms into a standard group that is recognized throughout the biological community. Taxonomy has two functions • First to identify and describe as completely as possible to the basic taxonomic unit or species and • second, to devise a method for arranging and cataloguing these species.
  • 3. Benefits To distinguish one individual from another, we need to establish certain criteria and this art of biological classification is known as taxonomy or systematics. Taxonomy is therefore, the systematic arrangement of organisms in groups or categories called taxa (taxon-singular).
  • 4. Microbial Taxonomy • Classification Systems • Levels of Classification • Definition of “Species” • Nomenclature • Useful Properties in Microbial Classification • Microbial Phylogeny
  • 5. Levels of Classification • Taxon: – A group or “level” of classification – Hierarchical; broad divisions are divided up into smaller divisions: • Kingdom (Not used by most bacteriologists) • Phylum (Called “Division” by botanists) • Class • Order • Family • Genus (plural: Genera) • Species (Both singular & plural)
  • 6. Definition of “Species” • The “basic unit” of taxonomy, representing a specific, recognized type of organism • For sexually reproducing organisms, a fundamental definition of “species” has been reproductive compatibility • This definition fails for many microbial species (including bacteria), because they do not reproduce sexually
  • 7. • Definition of “species” in microbiology: – Classic definition: A collection of microbial strains that share many properties and differ significantly from other groups of strains – Species are identified by comparison with known “type strains”: well-characterized pure cultures; references for the identification of unknowns ATCC American Type Culture Collection Manassas, Virginia NCTC National Collection of Type Cultures Public Health England, UK BCCM Belgium Coordinated Collection of Microorganisms Ghent, Belgium CIP Collection d'Institut Pasteur Paris, France DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen Braunschweig, Germany JCM Japan Collection of Microorganisms Saitama, Japan NCCB Netherlands Culture Collection of Bacteria Utrecht, Netherlands NCIMB National Collection of industrial, Marine and food bacteria Aberdeen, Scotland ICMP International Collection of Microorganisms from Plants Auckland, New Zealand
  • 8. Classification of bacteria is determined by publication in the International Journal of Systematic Bacteriology and Bergey's Manual of Systematic Bacteriology. The International Committee on Systematic Bacteriology (ICSB) maintains international rules for the naming of bacteria and taxonomic categories and for the ranking of them in the International Code of Nomenclature of Bacteria. The term "bacteria" was traditionally applied to all microscopic, single-celled prokaryotes. Molecular systematics showed prokaryotic life to consist of two separate domains, originally called Eubacteria and Archaebacteria, But now called Bacteria and Archaea that evolved independently from an ancient common ancestor. The archaea and eukaryotes are more closely related to each other than either is to the bacteria. These two domains, along with Eukarya, are the basis of the three-domain system, which is currently the most widely used classification system in microbiology
  • 9. As with bacterial classification, identification of bacteria is increasingly using molecular methods. Diagnostics using such DNA-based tools, such as polymerase chain reaction, are increasingly popular due to their specificity and speed, compared to culture-based methods. These methods also allow the detection and identification of "viable but nonculturable” cells that are metabolically active but non- dividing. However, even using these improved methods, the total number of bacterial species is not known and cannot even be estimated with any certainty
  • 10. mid-1700s, Swedish botanist Carl Linnaeus - a taxonomy for living organisms Linnaeus’ taxonomy grouped living things into two kingdoms: plants and animals Haeckel (1866) - Protista, - include microorganisms, is a heterogenous group consisting of protozoa, algae, fungi and bacteria. Although each one of these groups has distinct characteristics, within a group organisms show a great deal of similarity. 1969 Robert H. Whitteker - five kingdom classification Monera, protista, plantae (plants), fungi, and animalia (animals). Monera are organisms that lack a nucleus and membrane-bounded organelles, such as bacteria. Protista are organisms that have either a single cell or no distinct tissues and organs, such as protozoa. This group includes unicellular eukaryotes and algae. Fungi are organisms that use absorption to acquire food. These include multicellular fungi and single-cell yeast. Animalia and plantae include only multicellular organisms
  • 11. Linnaeus 1735 2 kingdoms Haeckel 1866 3 kingdoms Chatton 1925 2 empires Copeland 1938 4 kingdoms Whittaker 1969 5 kingdoms Woese et al. 1977 6 kingdoms Woese et al. 1990 3 domains Cavalier-Smith 2004 6 kingdoms (not treated) Protista Prokaryota Monera Monera Eubacteria Bacteria Bacteria Archaebacteri a Archaea Eukaryota Protoctista Protista Protista Eukarya Protozoa Chromista Vegetabilia Plantae Fungi Fungi Fungi Plantae Plantae Plantae Plantae Animalia Animalia Animalia Animalia Animalia Animalia
  • 12. Carl Woese and Ralph S. Wolfe (1977) proposed a new six-kingdom taxonomy. This came about with the discovery of archaea, which are prokaryotes that lives in oxygen- deprived environments Woese’s six-kingdom taxonomy consists of: • Eubacteria (has rigid cell wall) • Archaebacteria (anaerobes that live in swamps, marshes, and in the intestines of mammals) • Protista (unicellular eukaryotes and algae) • Fungi (multicellular forms and single-cell yeasts) • Plantae • Animalia Woese determined that archaebacteria and eubacteria are two groups by studying the rRNA sequences in prokaryotic cells. Woese used three major criteria to define his six kingdoms. These are: • Cell type. Eukaryotic cells (cells having a distinct nucleus) and prokaryotic cell (cells not having a distinct nucleus) • Level of organization. Organisms that live in a colony or alone and one-cell organisms and multicell organisms. • Nutrition. Ingestion (animal), absorption (fungi), or photosynthesis (plants).
  • 13. In the 1990s Woese studied rRNA sequences in prokaryotic cells (archaebacteria and eubacteria) proving that these organisms should be divided into two distinct groups. Today organisms are grouped into three categories called domains that are represented as bacteria, archaea, and eukaryotes. Archaea lack muramic acid in the cell walls. Bacteria have a cell wall composed of peptidoglycan and muramic acid. Bacteria also have membrane lipids with ester-linked, straight-chained fatty acids that resemble eukaryotic membrane lipids. Most prokaryotes are bacteria. Bacteria also have plasmids, which are small, double-stranded DNA molecules that are extrachromosomal. Eukarya are of the domain eukarya and have a defined nucleus and membrane bound organelles.
  • 15. INTRODUCTION - BACTERIAL CLASSIFICATION Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Bacteria can be classified on the basis of cell structure, cellular metabolism or on differences in cell components such as DNA, fatty acids, pigments, antigens and quinones. While these schemes allowed the identification and classification of bacterial strains, it was unclear whether these differences represented variation between distinct species or between strains of the same species. This uncertainty was due to the lack of distinctive structures in most bacteria, as well as lateral gene transfer between unrelated species. Due to lateral gene transfer, some closely related bacteria can have very different morphologies and metabolisms. To overcome this uncertainty, modern bacterial classification emphasizes molecular systematics, using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridization, as well as sequencing genes that have not undergone extensive lateral gene transfer, such as the rRNA gene.
  • 16. Classification of Bacteria and Archaea • Prokaryotes can be classified using artificial or natural (phylogenetic) systems. • Historically, prokaryotes were classified on the basis of their phenotype (morphology, staining reactions, biochemistry, substrates/products, antigens etc). In other words a phenotypic characterization is based on the information carried in the products of the genes. These classification systems were artificial. • Modern characterization is based on the information carried in the genes i.e. the genome. This is genetic information and can also tell us something about the evolution of the organism. In other words phylogenetics.
  • 17. Bergey's Manual of Determinative Bacteriology  The bacteria are a group of great diversity with a procaryotic cellular organization.  Active interest in classifying bacteria led by Chester in 1899 and 1901 to publish the manual of determinative bacteriology.  This manual subsequently was modified by David Bergey into what is now known as Bergey's manual of Determinative Bacteriology  A major treatise on bacterial taxonomy since its first publication in 1923.  it is used to classify bacteria based on their structural and functional attributes by arranging them into specific familial orders. However, this process has become more empirical in recent years
  • 18. • The change in volume set to "Systematic Bacteriology" came in a new contract in 1980 • The new style included "relationships between organisms" and "expanded scope". • This new style was picked up for a four-volume set that first began publishing in 1984. 1. Volume 1 included information on all types of Gram-negative bacteria that were considered to have "medical and industrial importance." 2. Volume 2 included information on all types of Gram-positive bacteria. 3. Volume 3 deals with all of the remaining, slightly different Gram-negative bacteria, along with the Archaea. 4. Volume 4 has information on filamentous actinomycetes and other, similar bacteria.[
  • 19. The current grouping is: • Volume 1 (2001): The Archaea and the deeply branching and phototrophic Bacteria • Volume 2 (2005): The Proteobacteria—divided into three books: • 2A: Introductory essays • 2B: The Gammaproteobacteria • 2C: Other classes of Proteobacteria • Volume 3 (2009): The Firmicutes • Volume 4 (2011): The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes • Volume 5 (in two parts) (2012): The Actinobacteria The Annals of Internal Medicine described the volumes as "clearly written, precise, and easy to read" and "particularly designed for those interested in taxonomy
  • 20. Bergey’s Manual of Determinative Bacteriology: Is standard reference for laboratory identification of bacteria. Morphology, differential staining, biochemical tests to test for presence of various enzymes. Bergey’s Manual of Systematic Bacteriology Provides phylogenetic information on bacteria and archaea Based on rRNA sequencing Bergey’s Manual: Classifying and Identifying Prokaryotes
  • 21. Classification based mainly on Morphology – Cocci, rod, spiral and pleomorphic Stains – Gram staining, Acid fast Oxygen requirement – Aerobic and Anaerobic Spore forming Addition factors Culture properties Antigenic properties Biochemical reactions DNA based – % G+C content, ribosomal rRNA, Total genomic DNA
  • 22. Identification Methods • Morphological characteristics: Useful for identifying eukaryotes  Differential staining: Gram staining, acid-fast staining  Biochemical tests: Determines presence of bacterial enzymes
  • 23. species –a collection of bacterial cells which share an overall similar pattern of traits in contrast to other bacteria whose pattern differs significantly strain or variety – a culture derived from a single parent that differs in structure or metabolism from other cultures of that species (biovars, morphovars) type – a subspecies that can show differences in antigenic makeup (serotype or serovar), susceptibility to bacterial viruses (phage type) and in pathogenicity (pathotype).
  • 24. Procaryotic groups are divided among the four volumes in the following manner: (1) Gram negative bacteria of general, medical, or industrial importance; (2) gram-positive bacteria other than actinomycetes; (3) Gram negative bacteria with distinctive properties, cyanobacteria, and archaea (4) actinomycetes (gram-positive filamentous bacteria).
  • 27. Identification Methods cont.: Serology • Involves reactions of microorganisms with specific antibodies: Combine known anti-serum with unknown bacterium • Useful in determining the identity of strains and species, as well as relationships among organisms. Fig 10.10: Slide Agglutination  Examples:  Slide agglutination  ELISA (see lab)  Western blot (no details)
  • 28. Identification Methods cont.: Phage TypingFigure 10.13 Identification of bacterial species and strains by determining their susceptibility to various phages. More details on bacteriophages in Ch 13
  • 29. Numerical Taxonomy In the 19th century, microorganisms were grouped according to, their evolutionary affinities and the arrangement of organisms into groups was on the basis of inherited and stable structural and physiological characters. This arrangement is known as the Natural or the Phylogenetic classification. This approach, of classifying microorganisms is now almost abandoned in favour of a more empirical approach based on quantification of similarities and differences among organisms. Suggested by Micheal Adanson and is known as Adansonian or Numerical taxonomy
  • 30. • Numerical taxonomy is a methods which is used to differentiate a large number of similar bacteria, i.e. species. • A large number of tests (~100) are carried out and the results are scored as positive or negative. Several control species are included in the analysis. • All characteristics are given equal weight and a computer based analysis is carried out to group the bacteria according to shared properties.
  • 31. Homologous genes are used in the construction of phylogenetic trees • Homologous means that genes have a common anscestor • Orthologs are homologous genes that belong to different species but still retain their original function • Paralogs are homologous genes that have arrisen by gene duplication and are found in the same organism • Only orthologes can be used in the construction of phylogenetic trees. The classical example is the 16S ribosomal RNA gene.
  • 32. 16S RNA Secondary structure of the 16S rRNA molecule from the small ribosomal subunit of the bacterium Escherichia coli. The bases are numbered from 1 at the 5' end to 1,542 at the 3' end. Every tenth nucleotide is marked with a tick mark, and every fiftieth nucleotide is numbered. Tertiary interactions with strong comparative data are connected by solid lines. From the Comparative RNA Web Site, www.rna.icmb.utexas.edu; courtesy of Robin Gutell.
  • 33. Conservation and variation in small subunit rRNA This diagram shows conserved and variable regions of the small subunit rRNA (16S in prokaryotes or 18S in eukaryotes). Each dot and triangle represents a position that holds a nucleotide in 95% of all organisms sequenced, though the actual nucleotide present (A, U, C, or G) varies among species. Figure by Jamie Cannone, courtesy of Robin Gutell; data from the Comparative RNA Web Site: www.rna.icmb.utexas.edu
  • 34. Conservation and variation in small subunit rRNA The starred region from part A as it appears in a bacterium (Escherichia coli), an archaean (Methanococcus vannielii), and a eukaryote (Saccharomyces cerevisiae). This region includes important signature sequences for the Bacteria and Archaea. Figure by Jamie Cannone, courtesy of Robin Gutell; data from the Comparative RNA Web Site: www.rna.icmb.utexas.edu
  • 35. Phylogenetic trees Two different formats of phylogenetic trees used to show relatedness among species.
  • 36. Unrooted and rooted trees Representations of the possible relatedness between three species, A, B, and C. (A) A single unrooted tree (shown in both formats; see Figure 17.4). (B) Three possible rooted trees (in one format). UPGMA - Unweighted Pair Group Method with Arithmetic Mean
  • 37. Universal phylogenetic tree as determined from comparative ribosomal RNA sequencing.
  • 38. Detailed phylogenetic tree of the major lineages (phyla) of Bacteria based on 16S ribosomal RNA sequence comparisons
  • 39. Novel phyla discovered by molecular analysis of natural habitats A phylogenetic tree of 16S rDNA sequences of Bacteria, based on pure cultures and clonal libraries from natural samples. Note the existence of many phyla (shown in outline rather than as solid black lines) that have not yet been cultivated. Courtesy of Phil Hugenholz and ASM Publications (Hugenholz, P., B. M. Goebel and N. R. Pace. 1998. J. Bacteriol. 180:4765-4774).
  • 42. Species concept • The species concept applied to eukaryotes cannot be applied to bacteria and archaea. In fact it is quite difficult to define prokaryote species. • In order to be of the same species prokaryotes must share many more properties with each other than with other prokaryotes. • They must have similar mol % G+C. Note that two species having the same mol % G+C are not necessary of the same species. • The DNA from organisms of the same species must show a minimum of 70% reassociation.
  • 43. DNA melting curve Melting curve for a double-stranded DNA molecule. As the temperature is raised during the experiment, the double-stranded DNA is converted to the single-stranded form and the UV absorbance of the solution increases. The midpoint temperature, Tm, can be calculated from the curve. This process is reversible if the temperature of the solution is slowly lowered to allow the single strands to reanneal.
  • 44. Tm and DNA base composition Graph showing the direct relationship between mol % G + C and midpoint temperature (Tm) of purified DNA in thermal denaturation experiments.
  • 45. DNA base composition range Range of mol % G + C content among various groups of organisms. Note the broad range of GC ratios for bacteria in comparison to plants and animals and other eukaryotes. The best method of distinguishing two organisms should therefore be on the basis of composition of their genetic material. In recent years, the genetic characterization of organisms has been substantially developed.
  • 46. Nucleic Acid Hybridization Fig 10.15 Single strands of DNA or RNA, from related organisms will hydrogen-bond to form a double-stranded molecule; this bonding is called nucleic acid hybridization. Examples of Applications: • Southern blotting, • DNA chips, and • FISH Figs. 10.17 and 10.18
  • 47. DNA/DNA reassociation In this example, which is a control experiment (the radiolabeled sample is reannealed with unlabeled DNA from the same strain), the degree of reassociation is highest and treated as 100%. If a different strain is reannealed with the radiolabeled DNA, it will show a lower degree of reannealing (compared with the 100% attributed to the control), indicative of the similarity between the two strains being tested. Strains with reannealing values of 70% or greater are considered to be the same species.
  • 48. Mole percent guanine + cytosine (Mol% G+C)
  • 49. • Since every microorganism has its specific FAME profile (microbial fingerprinting), • Used as a tool for microbial source tracking (MST). • The types and proportions of fatty acids present in cytoplasm membrane and outer membrane (Gram negative) lipids of cells are major phenotypic traits. • Clinical analysis can determine the lengths, bonds, rings and branches of the FAME. • Bacterial culture is taken, and the fatty acids extracted and used to form methyl esters. • The volatile derivatives are then introduced into a gas chromatagraph (GC), and the patterns of the peaks help identify the organism. This is widely used in characterizing new species of bacteria, and is useful for identifying pathogenic strains. FAME – Fatty acids Methyl Ester Analysis
  • 51. Fatty acid analysis Fatty acid methyl ester (FAME) chromatogram of an unknown species, showing chromatographic column retention times and peak heights. Note: 10:0, 12:0, 16:0, and 19:0 indicate saturated fatty acids with 10, 12, 16, and 19 carbons; 16:1 and 18:1, monounsaturated 16-carbon and 18-carbon fatty acids; omega number, the position of the double bond relative to the omega end—that is the hydrocarbon end (not the carboxyl end)—of the fatty acid chain; cis and trans, the configuration of the double bond.
  • 53. Ribosomal Database project • The database contains over 78,000 bacterial 16S rDNA sequences • Approximately 7000 Type strains (the bacteria are in pure culture) • Approximately 70000 Environmental samples (bacteria and archaea samples have been collected from the environment and characterized by molecular methods)
  • 54. CLEAVED AMPLIFIED POLYMORPHIC SEQUENCE (CAPS) ANALYSIS CAPS analysis refers to the analysis of polymorphism of DNA fragments obtained from the restriction analysis of PCR amplified DNA. Cleaved Amplified Polymorphic Sequences polymorphisms are differences in restriction fragment lengths caused by mutations or SNPs that create or abolish restriction endonuclease recognition sites in PCR amplicons produced by locus-specific oligonucleotide primers. CAPS assay: How it works? The CAPS assay uses amplified DNA fragments that are digested with a restriction endonuclease to display RFLP. Example of CAPS assay: Amplification – Digestion - Separation Unique sequence primers are used to amplify a mapped DNA sequence from two different individuals (for example, from two different bacterial genera), A/A and B/B refer to two different bacteria. The amplified fragments from A/A and B/B contain two and three RE recognition sites, respectively. When fractionated by agarose or acrylamide gel electrophoresis, the PCR products digested by the RE will give readily distinguishable patterns. This CAPS pattern becomes the prototype CAPS map for identification of the given bacteria.
  • 55. RESTRICTION FRAGMENT LENGTH POLYMORPHISM (RFLP) RFLP is a difference in homologous DNA sequences that can be detected by the presence of fragments of different lengths after digestion of the DNA samples in question with specific restriction endonucleases. RFLP, as a molecular marker, is specific to a single clone/restriction enzyme combination. In RFLP analysis the DNA sample is broken into pieces (digested) by restriction enzymes and the resulting restriction fragments are separated according to their lengths by gel electrophoresis.
  • 56. Identification Methods cont.: Genetics • DNA fingerprinting: Number and sizes of DNA fragments (fingerprints) produced by RE digests are used to determine genetic similarities. • Ribotyping: rRNA sequencing • Polymerase chain reaction (PCR) can be used to amplify a small amount of microbial DNA in a sample. The presence or identification of an organism is indicated by Fig 10.14: Electrophoresis of RE digest of plasmid DNA
  • 57. The classical Adansonian approach of classifying microbes is based on phenotypic characteristics. Such characteristics are expressions of a large number of genes that control cellular activities through enzymes. It is now generally agreed that the phenotype is the reflection of the DNA base sequence. One is the analysis of the base composition of DNA i.e. to determine the mole per cent of guanine and cytosine in DNA (% G+C). The second, is to determine the degree of similarity between two DNA samples by hybridization between DNA and DNA or DNA and RNA. (G+C / A+T+G+C ) x 100
  • 58. Microcomputer application of Bayesean probability testing for the identification of bacteria A computer program (BACTID) is described which facilitates the identification of bacteria based on a priori data and Bayesean probability testing. The program is not limited to a specific format, has a short execution time, can be easily applied to a variety of situations, and can be run on almost any microcomputer system operating under either 8-bit CP/M or 16-bit MS-DOS/PC-DOS. Additionally, BACTID (1) is not limited to one type of computer (hardware independent), (2) is not limited by size of the computer's random access (RAM independent), (3) can recognize various data bases matrices (format independent), (4) is able to compensate for missing data and (5) allows for various methods of data entry.
  • 60. • Study describes a computer-based technique for classifying and identifying bacterial samples sing Fourier-transform infrared spectroscopy (FT-IR) patterns. • Classification schemes were tested for selected series of bacterial strains and species from a variety of different genera. • Dissimilarities between bacterial IR spectra were calculated using modified correlation co-efficients. Dissimilarity matrices were used for cluster analysis, which yielded dendrograms broadly equated with conventional taxonomic classification schemes. • Analyses were performed with selected strains of taxa Staphylococcus, Streptococcus, Clostridium, Legionella and Escherichia coli in particular, and with a database containing 139 bacterial reference spectra. • The latter covered a wide range of Gram-negative and Gram-positive bacteria. Unknown specimens could be identified when included in an established cluster analysis. • Thirty-six clinical isolates of Staphylococcus aureus and 24 of Streptococcus faecalis were tested and all were assigned to the correct species cluster. It is concluded that: (1) FT-IR patterns can be used to type bacteria; (2) FT-IR provides data which can be treated such that classifications are similar and/or complementary to conventional classification schemes; and (3) FT-IR can be used as an easy and safe method for the rapid identification of clinical isolates.
  • 62. Archaea bacteria A group of single-celled microorganisms. Single individual or species from this domain is called an archaeon (sometimes spelled "archeon"). They have no cell nucleus or any other membrane-bound organelles within their cells. Archaea have an independent evolutionary history and show many differences in their biochemistry from other forms of life, and so they are now classified as a separate domain in the three-domain system Archaea were first classified as a separate group of prokaryotes in 1977 by Carl Woese and George E. Fox in phylogenetic trees based on the sequences of ribosomal RNA (rRNA) genes. 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, because 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. Archaea and bacteria are quite similar in size and shape, although a few archaea have very unusual shapes, such as the flat and square-shaped cells of Haloquadratum walsbyi.
  • 64. 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. Archaean biochemistry are unique, such as their reliance on ether lipids in their cell membranes. Archaea use a much greater variety of sources of energy than eukaryotes: ranging from familiar organic compounds such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea (the Halobacteria) use sunlight as an energy source and other species of archaea fix carbon; however, unlike plants and cyanobacteria, no species of archaea is known to do both. Archaea reproduce asexually and divide by binary fission, fragmentation, or budding; unlike bacteria and eukaryotes, no known species form spores. Initially, archaea were see
  • 65. HABITAT Initially, archaea were seen as extremophiles that lived in harsh environments, such as hot springs and salt lakes, but they have since been found in a broad range of habitats, including soils, oceans, marshlands and the human colon. 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. Archaea are now recognized as a major part of Earth's life and may play roles in both the carbon cycle and the nitrogen cycle. No clear examples of archaeal pathogens or parasites are known, but they are often mutualists or commensals. One example is the methanogens that inhabit the gut of humans and ruminants, where their vast numbers aiddigestion. Methanogens are used in biogas production and sewage treatment, and enzymes from extremophile archaea that can endure high temperatures and organic solvents are exploited in biotechnology.
  • 66. Relation to eukaryotes The evolutionary relationship between archaea and eukaryotes remains unclear. Aside from the similarities in cell structure and function that are discussed below, many genetic trees group the two. Complicating factors include claims that the relationship between eukaryotes and the archaeal phylum Euryarchaeota is closer than the relationship between the Euryarchaeota and the phylum Crenarchaeota and the presence of archaean-like genes in certain bacteria, such as Thermotoga maritima, from horizontal gene transfer.The leading hypothesis is that the ancestor of the eukaryotes diverged early from the Archaea and that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and cytoplasm; this explains various genetic similarities but runs into difficulties explaining cell structure.