Which is the term for the scheme that represents the natural relatedness between groups of living beings?

Taxonomy is the science of naming, describing and classifying organisms and includes all plants, animals and microorganisms of the world. Using morphological, behavioural, genetic and biochemical observations, taxonomists identify, describe and arrange species into classifications, including those that are new to science. Taxonomy identifies and enumerates the components of biological diversity providing basic knowledge underpinning management and implementation of the Convention on Biological Diversity. Unfortunately, taxonomic knowledge is far from complete. In the past 250 years of research, taxonomists have named about 1.78 million species of animals, plants and micro-organisms, yet the total number of species is unknown and probably between 5 and 30 million.

Índice Show

What theory states that living things change gradually over time through?
Is the term applied to the method of assigning a scientific or specific name to an organism?
Which of the following is the orderly arrangement of organisms into groups that indicate evolutionary relationships and history?
What are the three primary concerns of taxonomy?

Click here for information on the biography and legacy of the "father of taxonomy", Carl Linnaeus.

What's in a Name?1

Different kinds of animals, fungi and plants and microorganisms are called different ‘species’. This reflects a real biological difference – a species is defined as a potentially interbreeding group of organisms that can produce viable offspring that themselves can interbreed. Thus animals of two different species, like a horse and a zebra, cannot interbreed, while animals of the same species can. Taxonomists provide unique names for species, labels that can help us find out more about them, and enable us to be sure that we are all talking about the same thing. Of course, there are names for organisms in many languages, but it is important, for example, when discussing the hedgehog to know whether one is talking about the small spiny insectivore Erinaceus europaeus, other members of the same family, cacti of the genus Echinocerus, or the orange fungus Hydnum repandum, all of which have the same ‘common’ name in English. For this reason the Latin ‘scientific’ name, is given as a unique universal identifier.

How to Name a Species: the Taxonomic Process1

Taxonomists begin by sorting specimens to separate sets they believe represent species. Once the specimens are sorted the next job is to see whether or not they already have names. This may involve working through identification guides, reading descriptions written perhaps 200 years ago, and borrowing named specimens from museums or herbaria to compare with the sample. Such comparison may involve external characters, need to dissect internal structures, or even molecular analysis of the DNA. If there is no match the specimens may represent a new species, not previously given a name. The taxonomist then has to write a description, including ways in which the new species can be distinguished from others, and make up a name for it, in a Latin format. The name and the description must then be properly published so that other taxonomists can see what has been done, and be able to identify the species themselves. From finding the specimens to the name appearing in print can take several years.

1. Text taken from: Secretariat of Convention on Biological Diversity. 2007. Guide to the Global Taxonomy Initatiative, CBD Technical Series # 27

CLASSIFICATION AND EVOLUTION OF MICROBES

Taxonomy is one aspect of classification. Organisms are ordered into groups (taxa) and ranked in a
hierarchy according to established procedures and guidelines. In this manner, organisms are placed
into taxa of different organizational levels and the inter-relationships and boundaries between groups are
established.

Nomenclature is another aspect of taxonomy. Names are assigned to organisms in a systematic
manner.

Identification of an organism is made possible by following the classification and nomenclature
guidelines and by various scientific approaches. This allows us to place an organism within its correct
position in the classification scheme.

I. Before scientists had a clear understanding of the nature of microbes the biological world was
    classfied into: plants and animals. Bacteria were placed with plants. Clearly, this scheme was
    inadequate. The electron microscope demonstrated obvious differences between bacteria and
    eukaryotes.

II. Based on nuclear and cellular properties a two kingdom was also produced: Prokaryotae and
Eukaryote. This was based primarily on presence of a true nucleus and having organelles sorrounded
or enclosed by a membrane.

III. In 1968 Whittaker proposed his famous 5 Kingdom system of living organisms. Bacteria were
classified under Kingdom Monera. Members of the Monera Kingdom were defined as "cells in
which nuclear material is not surrounded by a nuclear membrane."

IV. The 3 Kingdom of classification proposed by Woese in the 70's utilizes the sequence of the 16S
ribosomal RNA to classify organisms into: Eubacteria, Archaebacteria and Eukaryota.

The Linnean system of Binomial Nomenclature
Carolus Linneaus developed a scientific system of naming organisms. The names used by Linneaus in
the Species Plantarum (1753) and the Systema Naturae (1758) are the basis of the system for plants and animals, respectively. He assigned two latinized names to each organism:

A genus consists of a group of similar species. Similar genera are grouped into a family. The species
name or "specific epithet" is unique to the new species. The genus name is indicated by a capital letter
whereas the species name starts with a lower case letter. By convention both names are italicized (or
underlined).

Example: Streptococcus pyogenes ---- Once a scientific name has been used in entirety it can subsequently be abbreviated as follows: S. pyogenes

Scientific names should be unique, unchanging and descriptive. For example, the name may reflect
    - the name of the person describing the organism
    - the habitat of the organism
    - the appearance of the organism
    - some names may reflect a disease or infectious process caused by an organism (e.g., 'pyogenes'
      describes the ability to produce pus)

The genetic variability of microbes is further subdivided into subspecies or types:
a) A strain is equivalent to a clone and represents a population of genetically identical organisms that
    have arisen from a single cell. Some strains of a bacterial species may be virulent, whereas others are
    not.
b) Serovars are antigenically distinct organisms. For example, over 2,000 serovars of Salmonella
    have been identified which are typed according to their flagellar (H) and somatic (O) antigens.

Classification: The Three Domain System
The Three Domain System, proposed by Woese, is an evolutionary model of classification based on differences in the sequences of nucleotides in the cell's ribosomal and transfer RNAs, membrane lipid structure, and sensitivity to antibiotics. This system proposes that a common ancestor cell ("Cenancestor") gave rise to three different cell types, each representing a domain. The three domains are the Archaea (archaebacteria), the Bacteria (eubacteria), and the Eukarya (eukaryotes). The Eukarya are then divided into 4 kingdoms: Protists, Fungi, Anamalia, and Plantae. A description of the three domains follows:

1. The Archaea (archaebacteria)
· The Archae are prokaryotic cells. Unlike the Bacteria and the Eukarya, they have membranes
    composed of branched carbon chains attached to glycerol by ether linkages and have cell walls
    which contain no peptidoglycan. While they are not sensitive to some antibiotics which affect the
    Bacteria, they are sensitive to some antibiotics that affect the Eukarya. The Archae have rRNA and
    tRNA regions distinctly different from the Bacteria and Eukarya. They often live in extreme
    environments and include methanogens, extreme halophiles, and hyperthermophiles.

2. The Bacteria (eubacteria)
   · The Bacteria are prokaryotic cells. Like the Eukarya, they have membranes composed of straight
    carbon chains attached to glycerol by ester linkages. They have cell walls containing
    peptidoglycan, are sensitive to traditional antibacterial antibiotics, and have rRNA and tRNA
    regions distinctly different from the Archaea and Eukarya. They include: mycoplasmas,
    cyanobacteria, Gram-positive bacteria, and Gram-negative bacteria.

3. The Eukarya (eukaryotes)
· The Eukarya (also spelled Eucaryota\a) have eukaryotic cells. Like the Bacteria, they have
    membranes composed of straight carbon chains attached to glycerol by ester linkages. If they
    possess cell walls, those walls contain no peptidoglycan. They are not sensitive to traditional
    antibacterial antibiotics and have rRNA and tRNA regions distinctly different from the Bacteria and
    the Archaea. They include the following kingdoms:
          a. Protista Kingdom: Protista are simple, predominately unicellular eukaryotic organisms.
                Examples includes slime molds, euglenoids, algae, and protozoans.
          b. Fungi Kingdom: Fungi are unicellular or multicellular organisms with eukaryotic cell
                types. The cells have cell walls but are not organized into tissues. They do not carry out
                photosynthesis and obtain nutrients through absorption. Examples include sac fungi, club
                fungi, yeasts, and molds.
          c. Plantae Kingdom: Plants are multicellular organisms composed of eukaryotic cells.
                The cells are organized into tissues and have cell walls. They obtain nutrients by
                photosynthesis and absorption. Examples include mosses, ferns, conifers, and flowering
                plants.
          d. Animalia Kingdom: Animals are multicellular organisms composed of eukaryotic cells.
                The cells are organized into tissues and lack cell walls. They do not carry out photosynthesis
                and obtain nutrients primarily by ingestion. Examples include sponges, worms, insects, and
                vertebrates.

Two alternative approaches to microbial taxonomy:
I. Phenetic system: groups organisms based on similarity of shared phenotypic characteristics. For
example, we could place anaerobes in one group and aerobes in another. This may not always reflect
the correct evolutionary groupings of the organisms.

Bergey's manual is an example of a phenetic system. Microbes are organized into groups based on
both morphological (staining reactions, cell shape and arrangement, pigment production, appearance on
media) and physiological (growth requirements, biochemical tests, type of metabolism). This system can
be useful for identifying an unknown organism as you are doing in our laboratory.

This classical approach allows one to 'key'out an organism using a series of mutually exclusive
characteristics. For example: Is the organism gram positive or gram positive? Is the shape of the
organism a coccus, bacillus or some other morphology? The key eventually narrows down the organism until an identification is possible.

Numerical Taxonomy
    - Calculates the percentage of characteristics that two organisms or groups have in common
    - A large range of traits (morphology, motility, biochemistry) are considered (at least 50!)
    - The result of this classification is a similarity coefficient (the percentage of the total number of
        characters measured that are common to two organisms. Dendograms are produced to indicate
        relatedness....do not worry about this computers programs can do all this for you!

II. Phylogenetic system: groups organisms based on their shared evolutionary heritage and descent.
Unlike, a phenetic system, organisms do not have to be phenotypically similar in order to belong to the
same phylogenetic group. For example, based on genetic and molecular evidence, Pneumocystis
carinii is now considered to be more closely related to the fungi and is no longer believed to be a
protozoan (although it resembles a protozoan in many respects).

Molecular methods used to type and identify microbes
Two main approaches:

a) comparing DNA or RNA sequences in one or more ways comparing amino acid sequences of a
protein or proteins

Molecular taxonomy
Uses some key assumptions in order to establish a time-line of evolutionary relatedness

     - genetic mutations are random
     - once a mutation occurs, all descendants of that cell will carry the mutation
     - organisms that differ only slightly at the genetic level have diverged more recently over the course
        of evolution than organisms that differ significantly

a) DNA base composition
    - Indicates relatedness of organisms
    - Base composition is usually expressed as GC content
    - If the GC content differs by a small percentage the organisms are not closely related
    - The GC content itself does not always mean that organisms are related. For example,
         Mycoplasma and Bacillus have similar GC contents but are very different organisms

b) DNA fingerprinting
Comparison of the cleavage pattern (fingerprint) of the DNA from two organisms (one known, the
other unknown) can determine if they are related. Each organism has a unique restriction digest
profile

c) Hybridization of DNA probes
    - The most widely used molecular method used to determine relatedness or organisms
    - ssDNA is separated from ds DNA on a filter
    - The DNA of one organism is radiolabelled and mixed at low concentrations with the
        nonradioactive denatured DNA of the other organism
    - The more related the organisms, the higher the degree of complementary base pairing which can
        be detected by a higher reading of radioactivity.

d) Nucleic acid hybridization
    - Two organisms: grow one in [3H] thymine, the other one without it.
    - Harvest and isolate DNA
    - Denature DNA from one organism (heating) and bind it to a filter membrane
    - Add denatured DNA from the other organism
    - Wash and add S1 nuclease to remove any single stranded DNA
    - Expose to X-ray film.
    - If closely related they would anneal (bind) if conditions are right (60-70 C). You can get binding
        using lower temperatures (35-55 C) but this is just background!!

Other methods for identifying bacteria
Serological tests
    - Identify microbes by reactivity with specific antibodies
    - Serotyping developed by Rebecca Lancefield. Designed A through O system to identify variants
         (serovars or serotypes) of Streptococci
    - Enzyme-linked immunosorbent assay (ELISA)
    - Immunofluorescent antibody testing (IFAT)
    - Western blot

Evolutionary chronometers
Choosing the right chronometer:
   · the molecule should be universally distributed across the group chosen for study
   · it must be functionally homologous in each organism (phylogenetic comparisons must start with
        molecules of identical function)
   · the sequence should change at a rate commensurate with the evolutionary distance to be
        measured; the broader the phylogenetic distance to be measured, the slower must be the rate at
        which the sequence changes

Ribosomal RNAs as evolutionary chronometers:
    - It is likely that the protein-synthesizing process is very old, and so rRNA molecules are very good
        for discerning evolutionary relationships among living organisms
   - This rRNA is also found the ribosomes of chloroplasts and mitochondria and is therefore present
        in animals and plants.
    - As the ribosome plays a critical role in protein synthesis most mutations in rRNA are harmful and
        tend to occur very infrequently.
    - Therefore,16S rRNA is a very useful molecule for comparing relatedness of organisms over the
        course of evolution.
    - rRNAs are ancient molecules, functionally constant, universally distributed, and moderately
        well conserved across broad phylogenetic distances
    -the number of different possible sequences is large, so similarity in two sequences always indicates
        some phylogenetic relationship; the degree of similarity in rRNA sequences between two
        organisms indicates relative evolutionary relatedness

Ribosomal RNA molecules:
    -in prokaryotes they are 5S, 16S, and 23S
    -16S and 23S each contain several regions of highly conserved sequence that allows for proper
        sequence alignment, but contain sufficient sequence variability in other regions to serve as
        phylogenetic chronometers
    -5S has also been used but it is too small which limits its information usefulness
    -16S is more experimentally manageable than 23S RNA and has been used extensively for
        developing databases
    -in eukaryotes, the 18S rRNA counterpart is the 16S rRNA

Signature sequences: short oligonucleotide sequences unique to a certain group or groups of
organisms.
    -signatures defining each of the three primary domains have been identified
    -other signatures defining the major taxa within each domain have also been detected
    -signatures are generally found in defined regions of the 16S rRNA molecule, but are only readily
        apparent when the computer scans sequence alignments
    -they allow for placing unknown organisms in the correct major phylogenetic group, and can be
        useful for constructing genus and species-specific nucleic acid probes which are used exclusively
        for identification purposes in microbial ecology and diagnostics
    - As the 16SrRNA is so highly conserved organisms are classified as separate species if their
        sequences show less than 98% homology and are classified as different genera if their sequences
        show less than 93% identity. Specific base sequences in the rRNA known as signature
        sequences were commonly found in particular groups of organisms

What theory states that living things change gradually over time through?

The theory of evolution is based on the idea that all species^? are related and gradually change over time. Evolution relies on there being genetic variation^? in a population which affects the physical characteristics (phenotype) of an organism.

Is the term applied to the method of assigning a scientific or specific name to an organism?

Taxonomy is the science of naming, describing and classifying organisms and includes all plants, animals and microorganisms of the world.

Which of the following is the orderly arrangement of organisms into groups that indicate evolutionary relationships and history?

Taxonomy – the classification of organisms into a system that indicates natural relationships (evolutionary relationships); the theory and practice of describing, naming, and classifying organisms. Systematics – the systematic classification of organisms and the evolutionary relationships among them; taxonomy.

What are the three primary concerns of taxonomy?

Taxonomy consists of three components: classification, nomenclature and identification. Classification allows the orderly grouping of micro-organisms, whereas nomenclature concerns the naming of these organisms and requires agreement so that the same name is used unambiguously by everyone.

Which is the term for the scheme that represents the natural relatedness between groups of living beings?