Haeckel (1866) was the first to create a natural Kingdom for the
microorganisms,
which had been discovered nearly two centuries before by van
Leeuwenhoek.
He placed all unicellular (microscopic) organisms in a new kingdom, "Protista",
separated from plants (Plantae) and animals (Animalia),
which
were multicellular (macroscopic) organisms. The development of the
electron
microscope in the 1950's revealed a fundamental dichotomy among
Haeckel's
"Protista":
some cells contained a membrane-enclosed nucleus, and some cells lacked
this intracellular structure. The latter were temporarily shifted to a
fourth kingdom, Monera (or Moneres), the procaryotes
(also
called Procaryotae). Protista remained as a kingdom of
unicellular
eucaryotic microorganisms. Whittaker refined the system into five
kingdoms
in 1967, by identifying the Fungi as a separate multicellular
eucaryotic
kingdom of organisms, distinguished by their absorptive mode of
heterotrophic nutrition.
Figure 9 (above) The structure
of a typical procaryotic cell, in this case, a Gram-negative bacterium,
compared with (below) a typical eucaryotic cell (plant cell). The
procaryote
is about 1 micrometer in diameter and about the size of the eucaryotic
chloroplast or mitochondrion. Drawings by Vaike Haas, University of
Wisconsin-Madison.
In the 1980's, Woese began phylogenetic analysis of
all forms of
cellular
life based on comparative sequencing of the small subunit ribosomal RNA
(ssrRNA) that is contained in all organisms. A new dichotomy was
revealed,
this time among the procaryotes: there existed two types of
procaryotes,
as fundamentally unrelated to one another as they are to eucaryotes.
Thus,
Woese defined the three cellular Domains of life as they are
displayed
in Figure 3 (above): Eucarya, Bacteria and Archaea.
Whittaker's Plant, Animal and Fungal Kingdoms (all of the multicellular
eucaryotes) are at the end of a very small branch of the tree of life,
and all other branches lead to microorganisms, either procaryotes
(Bacteria
and Archaea), or protists (unicellular algae and protozoa), thus
establishing clearly that microbial life is the predominant form
of life on the planet.
Sequence analysis of macromolecules such as the small subunit
ribosomal RNA found in all cells has allowed bacteriologists to
classify bacteria into a typical hierarchal scheme based on genetic
relatedness. The current edition (2001) of Bergey's Manual of
Systematic Bacteriology
has established 24 phyla of bacteria, systematically ordered into
class, order, family, genus and species. For example, E. coli is in the Domain Bacteria, Phylum Proteobacteria, Class Gamma Proteobacteria, Order Enterobacteriales, Family Enterobacteriaceae, Genus Escherichia,
Species E. coli.
You can download Bergey's 400-page taxonomic outline of the procaryotes
at Bergey's Manual of Systematic Bacteriology 2nd ed (2001),
or you can back in to a taxonomic outline of bacteria in Wikipedia by
looking up the scientific name of any well-known bacterium and viewing
the right-hand frame, Scientific classification.
Although the definitive difference between Woese's Archaea
and
Bacteria
is based on fundamental differences in the nucleotide base sequence in
the 16S ribosomal RNA, there are many biochemical and phenotypic
differences
between the two groups of procaryotes. (Table 1). The phylogenetic tree
indicates that Archaea are more closely related to Eucarya
than are Bacteria. This relatedness seems most evident in the
similarities
between transcription and translation in the Archaea and the Eucarya.
However, it is also evident that the Bacteria have evolved into
chloroplasts and mitochondria, so that these eucaryotic organelles
derive
their lineage from this group of procaryotes. Perhaps the biological
success
of eucaryotic cells springs from the evolutionary merger of the two
procaryotic
life forms.
Table 1. Phenotypic properties
of Bacteria and Archaea compared with Eucarya.
ester-linked glycerides; unbranched;
saturated or monounsaturated
ether-linked branched; saturated
Cell membrane sterols
present
absent
absent
Organelles (mitochondria and chloroplasts)
present
absent
absent
Ribosome size
80S (cytoplasmic)
70S
70S
Cytoplasmic streaming
+
-
-
Meiosis and mitosis
present
absent
absent
Transcription and translation coupled
-
+
+
Amino acid initiating protein synthesis
methionine
N-formyl methionine
methionine
Protein synthesis inhibited by streptomycin
and chloramphenicol
-
+
-
Protein synthesis inhibited by diphtheria
toxin
+
-
+
IDENTIFICATION OF BACTERIA
Classic Methods
The criteria used for microscopic identification of procaryotes include
cell shape and grouping, Gram-stain reaction, and motility. Bacterial
cells
almost invariably take one of three forms: rod (bacillus),
sphere
(coccus), or spiral (spirilla and spirochetes).
Rods
that are curved are called vibrios. Fixed bacterial cells stain
either Gram-positive (purple) or Gram-negative (pink); motility is
easily
determined by observing living specimens. Bacilli may occur singly or
form
chains of cells; cocci may form chains (streptococci) or
grape-like
clusters (staphylococci); spiral shape cells are almost always
motile;
cocci are almost never motile. This nomenclature ignores the actinomycetes,
a prominent group of branched bacteria which occur in the soil. But
they
are easily recognized by their colonies and their microscopic
appearance.
Figure 10. Gram stain of Bacillus
anthracis, the cause of anthrax. K. Todar.
Such easily-made microscopic observations, combined with knowing the
natural environment of the organism, are important aids to identify the
group, if not the exact genus, of a bacterium - providing, of course,
that
one has an effective key. Such a key is Bergey's Manual of Determinative Bacteriology 9th ed,
the "field guide" to identification of the
bacteria.
Bergey's Manual describes affiliated groups of Bacteria and Archaea
based on a few easily observed microscopic and physiologic
characteristics.
Further identification requires biochemical tests which will
distinguish
genera among families and species among genera. Strains within a single
species are usually distinguished by genetic or immunological criteria.
A modification of the Bergey's criteria for bacterial
identification,
without a key, is used to organize the groups of procaryotes for
discussion
in a companion chapter Important
Groups of Procaryotes
Figure 11. Size and
fundamental
shapes of procaryotes revealed by three genera of Bacteria (l to r): Staphylococcus
(spheres),
Lactobacillus (rods),
and Aquaspirillum (spirals).
The sciences of genomics and bioinformatics have led to a radical
reclassification of procaryotes based on comparative analysis of
organismal DNA. Genomics
involves the study of all of the nucleotide sequences, including
structural genes, regulatory sequences, and noncoding DNA segments, in
the chromosomes of an organism. To date over 200 bacterial genomes have
been sequenced. We have seen how highly conserved genetic sequences,
such as those that encode for the small subunit ribosomal RNAs (16S
rRNA) of an
organism, can be analyzed to specifically relate two organisms. So can
the identification of certain genes provide information about
specific properties of an organism, and analysis of specific nucleotide
sequences may be used to indicate identity and degrees of genetic
relatedness among organisms.
The newest editions of Bergey's Manual are adapted to the new
phylogenetic classification. This has resulted in the formation of
several new taxa of bacteria and archaea at every hierarchical level.
Occasionally,
organisms thought to be more or less distantly related become unified;
but more likely, organisms thought to be closely-related due to similar
phenotypic properties
are found to be genetically distinct and warrant separation into a new
taxa.
Metagenomics. Sequencing of
16S rRNA genes obtained from environmental samples
produces a broad profile of microbial diversity and reveals that the
vast
majority of microbes present have been missed by reliance on
cultivation-based methods. This observation has given rise to the field
of metagenomics. Metagenomics
(also called environmental genomics) is the application of modern
genomics techniques to the
study of communities of microorganisms directly in their natural
environments, bypassing the need for isolation and lab cultivation of
individual species. Metagenomics provides a means to identify and
quantify microbes from environmental samples based on the presence of
distinctive genes. This enables studies of organisms that are not
easily cultured in the laboratory, as well as studies of organisms in
their natural environment.
"Shotgun" metagenomics is capable of sequencing nearly complete
microbial genomes directly from the environment. Because the collection
of DNA from an environment is largely uncontrolled, the most abundant
organisms in a sample are most highly represented in the resulting
sequence data. To achieve the high coverage needed to fully resolve the
genomes of underrepresented community members, large samples, often
prohibitively so, may be needed. However, the random nature of shotgun
sequencing ensures that many of these organisms will be represented by
at least some small sequence segments. Due to the limitations of
microbial isolation methods, the majority of these organisms would go
unnoticed using traditional culturing techniques.
Shotgun sequencing and screens of clone libraries reveal genes
present
in environmental samples. This provides information both on which
organisms are present and what metabolic processes are possible in the
community. This can be helpful in understanding the ecology of a
community, particularly if multiple samples are compared to one other.
