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NEHRU ARTS AND SCIENCE COLLEGE
DEPARTMENTOF MICROBIOLOGY WITH NANOTECHNOLOGY
MICROBIAL DIVERSITY
I B.Sc.,
Unit I
Taxonomy – Principles – Modern approaches – Numerical – Genetic, Serotaxonomy
and Chemotaxonomy.
Taxonomy –science of grouping and naming organisms based on natural relationships
A. Classification is based mainly on physical traits
B. Behavioral and Chemical analysis is also used
Binomial Nomenclature – two work Latin description of an organism
A. ScientificName
B. Rules
1. Latin
2. 1st word capitalized and is called the genus
3. 2nd word lower case and is called the species
4. Both words are italicized or underlined
C. Examples
1. Acer rubrum
2. Homo sapiens
3. Canis familiaris
4. Equus asinus
III. Hierarchy of Names – method of classification where a series of names is used to
classify or organize a specimen. Each name gets more specific as you go down the
hierarchy.
A. Hierarchy
1. Kingdom
2. Phylum
3. Class
4. Order
5. Family
6. Genus
7. species
B. Example for Humans
1. Kingdom Animalia
2. Phylum
Chordata
3. Class
Mammalia
4. Order
Primate
5. Family
Homindae
6. Genus
Homo
7. Species
sapiens
Principles of Taxonomy
1.
2.
Why is a system of classification needed?
a.
Organize species into groups and discuss them.
b.
Identify new organisms.
c.
Show relationships between organisms.
Taxonomy
a.
Taxonomy is the science of classifying organisms.
b.
The Binomial system, also called binomial nomenclature, involves each
organism being given a two part name using Latin as a standard language.
i.
Developed by Carolus Linnaeus (1707-1778).
ii.
Provides a uniform means of communication for all people. This avoids
the confusion caused by organisms with different common names in
different areas.
iii.
The format is Genus species or G. species. e.g., Castor canadensis
(1)
The genus name is capitalized and may be abbreviated by the
first initial. The species name is not capitalized and cannot be
used alone. e.g., C. canadensis.
iv.
The 2 part name gives clues about relationships between organisms.
(1)
v.
Names were based largely on physical appearances but modern
taxonomists use genetic information, molecular biology, and
phylogeny (evolutionary relationships) as other criteria for
classifying.
(1)
c.
d.
For instance, Ursus americanus, U. horribilis, U. arctos, and U.
maritimus are all related.
The work of Charles Darwin introduced the idea of considering
evolutionary history.
The binomial classification system is hierarchical
i.
The levels of organization are kingdom, phylum, class, order, family,
genus, and species. In plants, fungi and algae phyla also called
divisions. Each of these levels is called a taxon (plural, taxa).
ii.
Note that the genus and species name are italicized because they are
Latin. When handwriting, underline the words. Other levels are
capitalized but no special print features are used.
What is a species?
i.
Capable of reproducing with one another. Individuals from different
species do not generally reproduce with one another.
ii.
Individuals of one species may appear quite dissimilar.
iii.
Offspring may appear different from one another.
iv.
Estimates on the number of species range from 2 and 100 million species
on the planet although about 1.4 million species are currently named
and described. Note that this is for eukaryotic species only. It is much
more difficult to estimate the number of prokaryotic species.
The six kingdoms (3 domains) system
a.
Originally there were only two kingdoms recognized by Linnaeus: animals and
plants.
b.
Later, these two were divided into five: animals, plants, fungi, protists, and
bacteria. Each kingdom evolved from different single-celled ancestors.
c.
Recent research has shown how long groups of organisms have been evolving
independently. This has ben used to place organisms into domains.
d.
Most people now recognize 6 kingdoms:
i.
ii.
Two prokaryotic (formally, Kingdom Monera) - reproduce asexually
(1)
Kingdom Archaebacteria (Domain Archaea) are very ancient
bacteria.
(2)
Kingdom Eubacteria (Domain Bacteria) are more modern
bacteria.
(a)
Inhabit nearly every known habitat
(b)
Consumers, producers, and decomposers
(c)
Some cause disease but most are harmless
Four eukaryotic
predominant
(1)
(Domain Eukarya) - sexual
reproduction
is
Kingdom Protista
(a)
Contains mostly unicellular organisms, including algae,
although there are some exceptions. Members have
been lumped together in this kingdom because they
don’t seem to fit anywhere else.
(b)
(2)
(3)
(4)
Some show characteristics of animals, some of fungi, and
some of plants
Kingdom Fungi
(a)
Contains multicellular species and single-celled yeasts.
(b)
Have some characteristics of plants but differ in that they
are not photosynthetic - they are decomposers.
Kingdom Plantae
(a)
Multicellular
(b)
Producers
Kingdom Animalia
(a)
Multicellular
(b)
Consumers
(c)
Motile
e.
There are greater differences between prokaryotes and eukaryotes than
between plants and animals. Also, there is greater diversity between the two
prokaryotic groups than among all eukaryotic groups.
f.
Evolution of kingdoms
ancestors
i.
Bacteria first appeared over 3 billion years ago and were the only
organisms on Earth for about 2 billion years.
ii.
Fungi, plants and animals are well-defined evolutionary groups, each
having arisen from different unicellular ancestors.
iii.
These groups are mostly multicellular, and derived from protist
RELATIONSHIPS BETWEEN THE SIX KINGDOMS
Numerical taxonomy
(a)
"Numerical taxonomy is based on the idea that increasing the number of
characteristics of organisms that we observe increases the accuracy with
which we can detect similarities among them. If the characteristics are
genetically determined, the more characteristics two organisms share, the
closer their evolutionary relationship."
(b)
So, basically, numerical taxonomy involves taking a good, long look at the
characteristics of two or more organisms, seeing how often these
characteristics correspond, and, typically, using a computer to keep track of
what you are doing
(c)
That is, this is a dichotomous-tree-like device that is less easy to walk
through manually so employs a computer to crunch the data
(d)
["Numerical taxonomy in the broad sense is the greatest advance in
systematics since Darwin or perhaps since Linnaeus. It has stimulated several
new areas of growth, including numerical phylogenetics, molecular
taxonomy, morphometrics, and numerical identification. It has wide
application outside systematic biology. Landmarks and trends are important
aspects of numerical taxonomy. In microbiology, the program of numerical
taxonomy has been successful, as indicated by the preponderance of papers
describing numerical relationships in the International Journal of Systematic
Bacteriology."
Taxonomy and Diversity


Purpose of taxonomy is to provide useful ways for identifying and comparing
organisms. Another goal is to assess the extent of diversity of different types
of organisms.
Two very different ways to construct a taxonomy:
1. Phenetic system: groups organisms based on mutual similarity of
phenotypic characteristics. May or may not correctly match evolutionary
grouping. Example: group (motile) organisms in one group, non-motile
organisms in another group. This is useful, but does it reflect underlying
evolutionary ancestry?
o
o
o
o
o
o
o
Numerical Taxonomy: a common approach to phenetic taxonomy
Use a variety of characteristics: e.g., Gram stain, cell shape, motility,
size, aerobic/anaerobic capacity, nutritional capabilities, cell wall
chemistry, immunological characteristics, etc.
Relies on similarity coefficients
If use 10 characteristics, then match organisms.
Ex. A and B share 8 characters out of 10: similarity coefficient Sab is
8/10 = 0.8
Can use many such values to establish similarity matrix
Dendrograms help display this information clearly.
Note: dendrogram is just a graphical display of similarity coefficients;
but one often assumes that these are representative of a deeper
evolutionary relationship. This may or may not be legitimate
conclusion, depending on the traits used.
2. Phylogenetic system: groups organisms based on shared evolutionary
heritage. Example: Mycoplasma (no wall) and Bacillus (walled Gram+ rods)
are not obviously similar, would not be grouped together phenetically. But
evolutionarily they are similar, more so than either to Gram- organisms.
o
The diagram below is a hypothetical evolutionary diagram,
superficially similar to a dendrogram but actually quite different,
since it seeks to portray an accurate picture of how and when
organisms diverged from common ancestors over time.
To get accurate phylogeny, must decide which characteristics give
best insight. DNA and RNA sequencing techniques are considered to
give the most meaningful phylogenies.
TAXONOMY AND CLASSIFICATION OF MICROBES
Three Kingdom System (1866)
Haeckel (1866), a Swiss naturalist, was the first to create a natural kingdom for the
microbes, which had been discovered nearly two centuries before by Antony van
Leeuwenhoek. Haeckel placed all unicellular (microscopic) organisms in a new kingdom,
"Protista", on the level with the existing kingdoms for plants (Plantae) and animals
(Animalia), which are multicellular (macroscopic) organisms.
Four Kingdom System (circa 1950)
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 compartment. 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.
Five Kingdom System (1967)
Whittaker, a botanist at the University of California, 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 nutrition.
Whittaker's phylogenetic Tree of 1967. The 5-Kingdom system is based on three
levels of organization- procaryotic (Kingdom Monera), eucaryotic unicellular
(Kingdom Protista), and eucaryotic multicellular (Kingdoms Plantae, Fungi and
Animalia). At he microbial levels there is divergence in relation to principal modes of
nutrition - photosynthetic, absorptive and ingestive. Ingestive nutrition is lacking in
Monera, but the three modes are continuous along numerous evolutionary lines in
the Protista giving rise to the three higher Kingdoms of Plantae, Fungi and Animalia.
Note that the tree is rooted in the Procaryotes (Monera) and that the more distant an
organism is removed from the root, the more highly (and recently) evolved is the
organism.
Carl Woese's Three Domain System (1988)
In the late 1970s, Carl Woese, at the University of Illinois, began phylogenetic analysis of all
forms of cellular life based on comparison of nucleotide sequences of the small subunit
ribosomal RNA (ssrRNA) that is contained in all organisms. Woese considered other
conserved molecules in cells including certain proteins, and conserved genes (DNA), but
settled for the ssrRNA for a number of reasons.
1. rRNA is found in all cells.
2. rRNA is present in thousands of copies and is easy to isolate from cells
3. rRNA can be analyzed to determine the exact sequence of nucleotide bases in its
makeup.
4. The sequence of bases in RNA is a complementary COPY of the sequence of bases
in the gene (DNA) that encodes for RNA.
5. Base sequences in different rRNA molecules can be compared by computer
analyses and statistical methods to reveal precise similarities and differences in
cellular genomes.
Woese's analysis of RNA molecules from different types of cells revealed a new dichotomy,
this time among the procaryotes. There exist two types of procaryotes, as fundamentally
unrelated to one another as they are to eucaryotes. Thus, Woese defined three cellular
domains of life as they are displayed in Figure 5 (below): Eukaryotes, Eubacteria and
Archaebacteria. Whittaker's Plant, Animal and Fungi kingdoms (all of the multicellular
eucaryotes) are at branch tips of the Eukaryote Domain, while other eukaryote branches
lead
to
protists
(unicellular
algae
and
protozoa).
Carl Woese's "universal" phylogenetic tree of 1988 determined from ribosomal RNA
sequence comparisons. Note the three major domains of living organisms: The
Eubacteria (Bacteria), the Archaebacteria (Archaea) and the Eukaryotes (Eucarya).
The evolutionary distance between two groups of organisms is proportional to the
cumulative distance between the end of the branch and the node that joins the two
groups. Compare with the Pace Tree, Figure 5 below.
Although the definitive difference between Woese's Archaea and Bacteria is based on
fundamental differences in the nucleotide base sequence in the ssrRNA, there are many
biochemical and phenotypic differences between the two groups of procaryotes as shown
in Table 2 above. 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.
The Universal Tree of Life
On the basis of small subunit ribosomal RNA (ssrRNA) analysis, the Woesean tree of life
gives rise to three cellular domains of life: Archaea, Bacteria, and Eucarya.
Genetic homology
(a)
A homology is a similarity between two organisms that exists because the
two organisms are closely evolutionarily related (that is, the feature in
question existed in the common ancestor to the two organisms)
(b)
The similarity of the DNA (or RNA) of organisms may be determined by a
number of means including determinations of base composition, nucleotide
sequence, or DNA hybridization rates
(c)
Typically these means include very powerful ways by which organisms may
be classified, either in terms of distinctions between organisms (i.e., the
organisms may be classified as representing two or more species) or
similarities (i.e., it may be concluded from evidence of genotypic similarity
that the organisms are closely related, i.e., evolutionarily related); the latter
similarities we would classify as a genetic homology
(d)
The downside of genetic homology is that the acquisition of data often
requires a laboratory and at least a little effort
(e)
The upside is that genetic homology describes evolutionary relationships
with only minimal interference from phenotype (which notoriously may be
similar even without close evolutionary relationship)
Base composition
(f)
We know from Chargaff's rule that adenines (A's) and thymines (T's) are
always present in DNA in equal proportions, and that the same is true for
cytosines (C's) and guanines (G's)
(g)
However, this says nothing about the relative proportions of A-T's to G-C's
(h)
In fact, these vary from species to species, with more closely related species
displaying more-similar ratios of A-T to G-C
(i)
[base composition bias (Google Search)] [Chargaff's rule (MicroDude)]
DNA and RNA sequencing
(j)
Genotype information at highest precision may be determined as DNA (or
RNA) nucleotide-base sequences
(k)
Very precise determination of base sequences can do wonders for
establishing evolutionary relationships, but determining DNA or RNA
sequence information is time consuming and relatively expensive, though
becoming less so as time goes on
(l)
RNA's are often sequenced either by converting the RNAs into DNA or by
sequencing the DNA gene that gives rise to the RNA
(m)
[DNA sequencing (MicroDude)] [cDNA (MicroDude)] [genomics grapevine
(genomics is the study of organisms from genome sequence up, rather than
from phenotype down) (Pharmaceutical Research and Manufacturers of
America)]
DNA hybridization
(n)
DNA hybridization takes advantage of the fact that heat will cause a DNA
double helix to come apart into two strands of DNA (two individual
molecules, not hydrogen bonded together)
(o)
Allowing the DNA solution to cool will allow the DNA to reform (reanneal)
into double helices again
(p)
If the DNA from two different organisms is put together and treated thus, the
total amount of reannealling accomplished will be dependent on how similar
the organism's DNA sequences are (more similarity = more annealing), and in
turn that will be dependent on how closely related to the two organisms are
evolutionaril
Chemotaxonomy
Chemotaxonomy (from chemistry and taxonomy), also called chemosystematics, is the
attempt to classify and identify organisms (originally plants), according to demonstrable
differences and similarities in their biochemical compositions. The compounds studied in
most of the cases are mostly proteins, amino acids and peptides. Examples of
chemotaxonomic markers are phospholipid-derived fatty acids and enzymes.
E.G. Family Rutaceae can be distinguished by the presence of oil glands; Families
Aschepiadaceae and Apocyanaceae can be differentiated based on the presence of latex.
Chemosystematics can be viewed as a hybrid science that complements available
morphological data to improve plant systematics.
John Griffith Vaughan was one of the pioneers of chemotaxonomy.
Unit II
Eubacteria
Bacteria (formerly known as eubacteria) and Archaea (formerly called archaebacteria)
share the procaryotic type of cellular configuration, but otherwise, they are not related to
one another any more closely than they are to the eucaryotic domain, Eucarya. Between
the two procaryotes, Archaea are apparently more closely related to Eucarya than are the
Bacteria. Eucarya consists of all eucaryotic cell-types, including protista, fungi, plants and
animals.
The Universal Tree of Life as derived from sequencing of ssrRNA. N. Pace. Note the
three major domains of living organisms: Archaea, Bacteria and Eucarya. The
"evolutionary distance" between two organisms is proportional to the measurable
distance between the end of a branch to a node to the end of a comparative branch.
For example, in Eucarya, humans (Homo) are more closely related to corn (Zea) than
to slime molds (Dictyostelium); or in Bacteria, E. coli is more closely related to
Agrobacterium than to Thermus.
Taxonomy of Eubacteria
The Eubacteria is a prokaryotic domain of life with a set of characters that
unite its extraordinarily diverse taxa. Unlike the Archaea, the Eubacteria have been
known and studied for more than 150 years. This is because all known bacterial
pathogens DOMAIN EUBACTERIA are Eubacteria (I reserve the use of the term
bacteria as a descriptive term that is a synonym of prokaryote). Also, some of them
like Lactobacillus are otherwise economically important. Perhaps more importantly,
many of them inhabit environments that are easily studied and sampled. The
Eubacteria differ from the Archaea in the form and structure of their ribosomes, the
type and linkage of their lipids, the structure of their cell covering, and the type of
RNA polymerase (Margulis and Schwartz 1998). Traditionally, the Eubacteria have
been separated into the Gram positive and Gram negative groups, based upon a
standard stain technique. As it turns out, the way a cell stains is related to the type
and structure of the cell wall. Gram positive cells have a single membrane with a
murien or peptidoglycan wall to the outside of the single membrane. Gram negative
cells have an inner membrane and an outer membrane with a murein layer
sandwiched between them. The system of Margulis and Schwartz (1998) is based on
the fundamental separation of gram positive and gram negative cells (called
Firmicutes and Gracilicutes, respectively). Phylogenies based on small subunit r
RNA, however, show that the eubacteria are marked by 10 or 11 deep clades that I
interpret as kingdoms. This could just be the tip of the iceberg with respect to their
true diversity. Garrity et al. (2001) separate the Eubacteria (a group that they call
"Bacteria") into 23 groups. Also, the problems of lateral gene transfer further blur
the distinctions of the groups. I present a tentative system for the Eubacteria with 9
kingdoms This system is based largely on Margulis and Schwartz (1998), with
modifications from Garrity et al. (2001, 2003, and 2005), Tudge (2000), and Black
(2002
Phenotypic properties of Bacteria and Archaea compared with Eucarya.
Property
Biological Domain
Eucarya
eucaryotic
present
Cell configuration
Nuclear membrane
Number
of
>1
chromosomes
Chromosome topology linear
Bacteria
procaryotic
absent
Archaea
procaryotic
absent
1
1
circular
circular
Murein in cell wall
Cell membrane lipids
ester-linked
glycerides;
unbranched;
polyunsaturated
present
Cell membrane sterols
Organelles
(mitochondria
and present
chloroplasts)
Ribosome size
80S (cytoplasmic)
Cytoplasmic streaming +
Meiosis and mitosis
present
Transcription
and
translation coupled
Amino acid initiating
methionine
protein synthesis
Protein
synthesis
inhibited
by
streptomycin
and
chloramphenicol
Protein
synthesis
inhibited by diphtheria +
toxin
+
-
ester-linked glycerides; ether-linked
unbranched; saturated or branched;
monounsaturated
saturated
absent
absent
absent
absent
70S
absent
70S
absent
+
+
N-formyl methionine
methionine
+
-
-
+
Eukaryotic Microbial Diveristy
1. Pasteur's investigations of wine and Lister's experiments on milk helped them to
A.
invent wine and yogurt fermentations
B.
develop culture media for the growth of microbes.
C.
develop the germ theory of disease.
D.
discover treatments for the prevention of illness
2. Which of the following processes is performed primarily by microbes (as opposed to
other organisms or by chemical processes) on Earth
A.
Photosynthesis
B.
Production of oil
C.
Production of natural gas
D.
Nitrogen fixation
3. Which of the following claims are correct about the classification of bacteria in the early
20th century:
A.
You could not identify traits that allowed one to group bacteria.
B.
You could identify traits that allowed one to group bacteria, but the classification
changed when different traits were considered.
C.
The evolutionary history of different bacteria became clear from them physiology.
D.
he discovery of chemolithotrophy allowed a broader understanding of bacterial
classification.
5. A virulence factor for Blastomyces dermatitidis is
A.
melanin
B.
its slime layer
C.
basidiotoxin
D.
120 kDa protein
6. Men are infected far more often than women with B. dermatitidis because the have a
genetic predisposition for the disease.
True
False
7. Yeast and molds are two distinct types of growth and are species specific.
True
False
8. Infection by T. gondii is elminated from the body by the immune system
True
False
A simple taxonomy of the Domain Eubacteria.
A HIGHER-LEVEL CLASSIFICATION OF THE EUBACTERIA:
PROTEOBACTERIAE
SPIROCHAETAE
OXYPHOTOBACTERIAE
SAPROSPIRAE
CHLOROFLEXAE
CHLOROSULFATAE
PIRELLAE
FIRMICUTAE
THERMOTOGAE
PHYLA OF UNCERTAIN STATUS
Proteobacteriae (pro-te-o-bak-TE-re-e) is derived from two Greek roots meaning
"changeable" (proteakos -πρωτεϊκός) "little stick" (bakterion -βακτήριον). The
name is in reference to Proteus, the name of a Greek sea god who could change his
shape (Stackebrandt et al. 1988).
INTRODUCTION TO THE KINGDOM PROTEOBACTERIAE
Stackebrandt et al. (1988), using 16S rRNA sequences, defined a seemingly unrelated
group of eubacteria as Proteobacteria, the purple bacteria, which they defined as a
class that they called Proteobacteria. Within that group, they defined five separate
lines, each defined by a Greek letter: α, β, γ, δ, ε. The second edition of Bergey's
Manual of Systematic Bacteriology (Garrity et al. 2003) adopted Proteobacteria, but
raised it to phylum level with each of the five groups becoming classes. In order to
bring the prokaryotes into line with kingdom-level divisions in the eukaryotes, I felt
that it was necessary to raise the Proteobacteria to kingdom-level status with each of
the five groups also raised to the level of phylum.
The purple bacteria is the largest and most diverse of the microbial kingdoms. The
alpha, beta, and gamma groups have many taxa that are phototrophic, but most are
chemolithotrophs or chemoorganotrophs. The delta and epsilon groups have no
phototrophic taxa. The interpretation is that phototrophy is primitive in this line.
Also, oxidative metabolism seems to have evolved several times in this kingdom.
The structure of this kingdom is under intense scrutiny because there are so many
taxa that are of great economic importance, both as necessary symbionts and
important pathogens. Furthermore, the microbial endosymbiont that gave rise to
the ancestral mitochondrion likely came from among the rickettsia
(Alphaproteobacteria). Now, there is evidence emerging to suggest a sixth line that
Emerson et al. (2007) refer to as "Zetaproteobacteria".
PHYLUM ALPHAPROTEOBACTERIA
CLASS RICKETTSIAE
ORDER RICKETTSIALES
Rickettsia, Orientia, Anaplasma, Ehrlichia, Neorickettsia, Wolbachia, Aegyptianella
(incertae sedis)
Holospora
Incertae
Sedis:
Caedibacter,
Pseudodolyticum, Tectibacter
Lyticum,
Candidatus,
Pseudocaedibacter,
CLASS RHODOBACTERIAE
ORDER RHODOSPIRILLALES
Rhodospirillum, Azospirillum, Levispirillum, Magnetospirillum, Phaeospirillum,
Rhodocista, Rhodospira, Rhodovibrio, Roseospira, Roseospirillum, Skermanella,
Sporospirillum (incertae sedis)
Acetobacter, Acidiphilium, Acidisphaera, Acidocella, Acidomonas, Asaia, Craurococcus,
Gluconacetobacter, Gluconobacter, Paracraurococcus, Rhodopila, Roseococcus,
Roseomonas, Stella, Zavarzinia
ORDER RHODOBACTERALES
Rhodobacter, Ahrensia, Amaricoccus, Antarctobacter, Gemmobacter, Hirschia,
Hyphomonas, Ketogluconicigenium, Maricaulis, Methylarcula, Octadecabacter,
Paracoccus, Rhodobaca, Rhodovulvum, Roseibium, Roseinatronobacter, Roseivivax,
Roseobacter, Roseovarius, Rubrimonas, Rugegeria, Sagittula, Staleya, Stappia,
Sulfitobacter, Rhodothalassium (incertae sedis)
ORDER SPHINGOMONADALES
Sphingomonas, Blastomonas, Citromicrobium, Erythrobacter, Erythromicrobium,
Erythromonas, Porphyrobacter, Sandaracinobacter, Zymomonas
ORDER CAULOBACTERIALES
Caulobacter, Asticcacaulis, Brevundimonas, Phenylobacterium
ORDER RHIZOBIALES
Rhizobium, Agrobacterium, Allorhizobium, Carbophilus, Chelatobacter, Ensifer,
Sinorhizobium
Bartonella
Brucella, Mycoplana, Ochrobactrum
Phyllobacterium,
Aminobacter,
Aquamicrobium,
Mesorhizobium, Pseudaminobacter
Defluvibacter,
Candidatus,
Methylocystis, Albibacter, Methylosinus, Methylopila (incertae sedis)
Beijerinckia, Chelatococcus, Methylocella
Bradyrhizobium, Afipia, Agromonas, Blastobacter, Bosea, Nitrobacter, Oligotropha,
Rhodoblastus, Rhodopseudomonas
Hyphomicrobium, Ancalomicrobium, Ancylobacter, Angulomicrobium, Aquabacter,
Azorhizobium, Blastochloris, Devosia, Dichotomicrobium, Filomicrobium, Gemmiger,
Labrys, Methylorhabdus, Pedomicrobium, Prosthecomicrobium, Rhodomicrobium,
Rhodoplanes, Seliberia, Starkeya, Xanthobacter
Methylobacterium
Rhodobium
PHYLUM BETAPROTEOBACTERIA
CLASS BETAPROTEOBACTERIAE
ORDER BURKHOLDERIALES
Burkholderia, Cupriavidus, Lautropia, Pandoraea, Paucimonas, Polynucleobacter,
Ralstonia, Thermothrix
Oxalobacter, Duganella, Herbaspirillum, Janthinobacterium, Massilia, Telluria
Alcaligenes, Achromobacter, Bordetella, Derxia, Oligella, Pelistega, Pigmentiphaga,
Sutterella, Taylorella
Comamonas, Acidovorax, Brachymonas, Delftia, Hydrogenophaga, Lampropedia,
Macromonas, Polaromonas, Rhodoferax, Variovorax
Incertae Sedis: Aquabacterium, Idernella, Leptothrix,
Sphaerotilus, Tepidomonas, Thiomonas, Xylophilius
Roseateles,
Rubrivivax,
ORDER HYDROGENOPHILALES
Hydrogenophilus, Thiobacillus
ORDER METHYLOPHILALES
Methylophilus, Methylobacillus, Methylovorus
ORDER NEISSERIALES
Neisseria, Alysiella, Aquaspirillum, Chromobacterium, Eikenella, Formivibrio,
Iodobacter, Kingella, Microvirgula, Prolinoborus, Simonsiella, Vitreoscilla, Vogesella
ORDER NITROSOMONADALES
Nitrosomonas, Nitrosolobus, Nitrosospira, Nitrosovibrio
Spirillum
Gallionella
ORDER RHODOCYCLALES
Rhodocyclus, Azoarcus, Azonexus, Azospira, Azovibrio, Dechloromonas, Dechlorosoma,
Ferribacterium, Propionibacter, Propionivibrio, Thauera, Zoogloea
PHYLUM GAMMAPROTEOBACTERIA
CLASS CHROMATIAE
ORDER CHROMATIALES
Chromatium, Allochromatium, Halochromatium, Isochromatium, Lamprobacter,
Lamprocystis, Marichromatium, Nitrosococcus, Pfennigia, Rhabdochromatium,
Thermochromatium, Thioalkalicoccus, Thiocapsa, Thiococcus, Thiocystis, Thiodictyon,
Thioflavicoccus, Thiohalocapsa, Thiolamprovum, Thiopedia, Thiorhodococcus,
Thiorhodovibrio, Thiospirillum
Ectothiorhodospira, Arhodomonas, Halorhodospira, Nitrococcus, Thioalkalivibrio,
Thiorhodospira
Halothiobacillus
CLASS ENTEROBACTERIAE
ORDER ACIDITHIOBACILLALES
Acidithiobacillus
Thermithiobacillus
ORDER XANTHOMONADALES
Xanthomonas, Frateuria, Luteimonas, Lysobacter, Nevskia, Pseudoxanthomonas,
Rhodanobacter, Schineria, Stenotrophomonas, Thermomonas, Xylella
ORDER CARDIOBACTERIALES
Cardiobacterium, Dichelobacter, Suttonella
ORDER THIOTRICHALES
Thiothrix, Achromatium, Beggiatoa, Leucothrix, Thiobacterium, Thiomargarita,
Thioploca, Thiospira
Piscirickettsia, Cycloclasticus, Hydrogenovibrio, Methylophaga, Thioalkalimicrobium,
Thiomicrospira
Francisella
ORDER LEGIONELLALES
Legionella
Coxiella, Rickettsiella
ORDER METHYLOCOCCALES
Methylococcus, Methylobacter, Methylocaldum, Methylomicrobium, Methylomonas,
Methylosarcina, Methylosphaera
ORDER OCEANOSPIRILLALES
Oceanospirillum, Balneatrix, Marinomonas, Marinospirillum, Neptunomonas
Alcanivorax
Hahella
Halomonas, Carnimonas, Chromohalobacter, Zymobacter
ORDER PSEUDOMONADALES
Pseudomonas, Azomonas, Azotobacter, Cellvibrio, Mesophilobacter, Rhizobacter,
Rugamonas, Serpens
Moraxella, Acinetobacter, Psychrobacter
Incertae Sedis: Enhydrobacter
ORDER ALTEROMONADALES
Alteromonas, Alishewanella, Colwellia, Ferrimonas, Glaciecola, Idiomarina,
Marinobacter, Marinobacterium, Microbulbifer, Moritella, Pseudoalteromonas,
Psychromonas, Shewanella
ORDER VIBRIONALES
Vibrio, Photobacterium, Salinivibrio
ORDER AEROMONADALES
Aeromonas, Oceanimonas, Tolumonas (incertae sedis)
Succinivibrio, Anaerobiospirillum, Ruminobacter, Succinimonas
ORDER ENTEROBACTERIALES
Escherichia, Alterococcus, Arsenophonus, Brenneria, Buchneria, Budvicia, Buttiauxella,
Calymmatobacterium, Cedecea, Citrobacter, Edwardsiella, Enterobacter, Erwinia,
Ewingella, Hafnia, Klebsiella, Kluyvera, Leclercia, Leminorella, Moellerella,
Morganella,
Obesumbacterium,
Pantoea,
Pectobacterium,
"Candidatus",
Photorhabdus, Plesiomonas, Pragia, Proteus, Providencia, Rahnella, Saccharobacter,
Salmonella, Serratia, Shigella, Sodalis, Tatumella, Trabulsiella, Wigglesworthia,
Xenorhabdus, Yersinia, Yokenella
ORDER PASTEURELLALES
Pasteurella, Actinobacillus, Haemophilus, Lonepinella, Manheimia, Phocoenobacter
PHYLUM DELTAPROTEOBACTERIA
CLASS ANOXYDELTABACTERIA
ORDER DESULFURELLALES
Desulfurella, Hippea
ORDER DESULFOVIBRIONALES
Desulfovibrio, Bilophila, Lawsonia
Desulfomicrobium, Desulfonatronovibrio, Desulfothermus
Desulfonatronum
ORDER DESULFOBACTERALES
Desulfobacter, Desulfobacterium, Desulfobacula, Desulfobotulus, Desulfocella,
Desulfococcus, Desulfofaba, Desulfofrigus, Desulfonema, Desulfosarcina, Desulfospira,
Desulfotignum
Desulfobulbus, Desulfocapsa, Desulfofustis, Desulfotalea
Nitrospina
ORDER DESULFARCALES
Desulfarculus
ORDER DESULFUROMONALES
Desulfuromonas, Desulfuromusa, Malonomonas, Pelobacter
Geobacter, Trichlorobacter
ORDER SYNTROPHOBACTERALES
Syntrophobacter, Desulfacinum, Desulforhabdus, Desulfovirga, Thermodesulforhabdus
Syntrophus, Desulfobacca, Desulfomonile, Smithella
CLASS OXYDELTABACTERIA
ORDER BDELLOVIBRIONALES
Bdellovibrio, Bacteriovorax, Micavibrio, Vampirovibrio
ORDER MYXOCOCCALES
Myxococcus, Corallococcus, Pyxicoccus
Cystobacter, Archangium, Hyalangium, Melettangium, Stigmatella
Polyangium, Byssophaga, Chondromyces, Haploangium, Jahnia, Sorangium
Nannocystis
Kofleria
PHYLUM EPSILONPROTEOBACTERIA
CLASS CAMPYLOBACTERIAE
ORDER NAUTILIALES
Nautilia, Caminibacter, Lebetimonas
Incertae Sedis: Hydrogenimonas, Nitratiruptor, Thioreductor
ORDER CAMPYLOBACTERALES
Campylobacter,
Arcobacter,
Nitratifractor,
Sulfurovum, Sulfiricurvum, Thiomicrospira
Sulfurospirillum,
Sulfurimonas,
Helicobacter, Thiovulum, Wolinella
INTRODUCTION TO
CYANOBACTERIA
THE
OXYPHOTOBACTERIA
AND
ITS
SINGLE
PHYLUM
Oxyphotobacteria (ak-se-fo-to-bak-TE-re-a) is a combination of three Greek roots
that mean oxygen (oxygono -οξυγόνο), light (photos -φωτός), and little stick
(bakterion -βακτήριον). The reference is to a photosynthetic bacterium that yields
oxygen as a product.
These organisms use water as the electron donor in photosynthesis thereby
releasing oxygen as a waste product. They all use chlorophyll A and some use
chlorophyll B in their photosynthetic machinery. Indeed, ultrastructural and
molecular evidence suggest that they gave rise to chloroplasts through
endosymbiosis. They can be complex in their growth form and many are very large.
These are aerobic photosynthetic bacteria that use water for their source of
electrons in reducing carbon dioxide. Many of them fix nitrogen and are indicators
of water quality in freshwater. They are abundant in salt marshes and significant
members of the marine picoplankton. They occur as single cells, colonies of cells,
filaments and colonies of filaments (Figures A-C). Some taxa typically have true
branching in which a cell within a filament divides in more than one plane and forms
a branch. Others like Tolypothrix grow within the same sheath and emerge in what
appears to be a branch, but actually the trichomes just grow past each other and
make a branch-like structure if one breaks through the common sheath (Figure D).
Fossil evidence suggests that the group is very old and likely responsible for the
early formation of an oxidizing atmosphere. Indeed, taxa on the order of billions of
years old have been found in fossilized structures called stromatolites. In addition,
all chloroplasts were derived from the cyanobacteria in one or a few endosymbiotic
events.
B. Nostoc, a colony
A. Gloeocapsa taken of filaments, each
with
a
DIC with akinetes and C.
microscope
heterocysts.
filaments.
D.
Tolypothrix
showing
Lyngbya characteristic false
branching.
A rRNA (16S) cladogram showing presumed phylogenetic realtionships between the three
superkingdoms: Bacteria (yellow), Archaea (archaeans, green) and Eucarya (eukaryotes,
blue)
Unit III
Archaebacterial Microbial Diveristy
1. Pasteur built on Jenner's work by
A.
proving that spontaneous generation was false
B.
developing the germ theory of disease.
C.
developing techniques to isolate small pox.
D.
through his work with chicken cholera.
2. How do you suppose microbiology differs from biology?
3. Why do you suppose that Needham's experiment "failed" (in that it gave growth)?
4. Think of an example of a seemingly trivial discovery that turned out to have a major
impact on human society. What does this tell you about basic research?
5. C albicans used to be responsible for the vast majority of candidiasis. This has changed
since 1980 because
A.
antifungals have eliminated this pathogen
B.
topical ointments have removed it from the body of susceptible patients
C.
The increase in immunocompromised due to HIV infection and medical treatments,
has allowed other Candida species to become more prevalent as pathogens.
D.
C albicans is still responsible for most candidiasis.
6. Hemagglutinin (HA) of influenza virus can be can be mutationally changed to avoid the
immune system without compromising it functional role in viral infection
True
False
7. The number of Rhinovirus genes is
A.
1
B.
3
C.
5
D.
10
8. A double infection with two influenza viruses in a pig is not a serious problem for
humans.
True
False
9. You have found a new organism that displayed a number of obvious features, but this set
does not match that of any described organism. You can conclude that this new organism
should be placed in a new group/genus.
True
False
10. For RNA to direct the synthesis of protein, there needs to be some sort of translation
apparatus, albeit a primitive one.
True
False
11. There are biological system today on which RNA molecules are completely selfreplicating.
True
False
12. Which of the following molecules would make good candidates for phylogenetic
analysis
A.
tRNA genes
B.
the gene for a subunit of DNA polymerase
C.
The gene for 23S rRNA
D.
The genes for synthesis of a particular antibiotic
E.
The genes for ribosomal proteins
F.
The gene for hemoglobin
G.
The gene for a critical step in the synthesis of an amino acid
KINGDOM PROTEOBACTERIAE
PHYLUM ALPHAPROTEOBACTERIA
CLASS RICKETTSIAE
ORDER RICKETTSIALES
Rickettsia, Orientia, Anaplasma, Ehrlichia,
Wolbachia, Aegyptianella (incertae sedis)
Holospora
Incertae
Sedis:
Caedibacter,
Lyticum,
Pseudocaedibacter, Pseudodolyticum, Tectibacter
Neorickettsia,
Candidatus,
CLASS RHODOBACTERIAE
ORDER RHODOSPIRILLALES
Rhodospirillum, Azospirillum, Levispirillum, Magnetospirillum,
Phaeospirillum, Rhodocista, Rhodospira, Rhodovibrio, Roseospira,
Roseospirillum, Skermanella, Sporospirillum (incertae sedis)
Acetobacter, Acidiphilium, Acidisphaera, Acidocella, Acidomonas,
Asaia,
Craurococcus,
Gluconacetobacter,
Gluconobacter,
Paracraurococcus, Rhodopila, Roseococcus, Roseomonas, Stella,
Zavarzinia
ORDER RHODOBACTERALES
Rhodobacter,
Ahrensia,
Amaricoccus,
Antarctobacter,
Gemmobacter, Hirschia, Hyphomonas, Ketogluconicigenium,
Maricaulis, Methylarcula, Octadecabacter, Paracoccus, Rhodobaca,
Rhodovulvum, Roseibium, Roseinatronobacter, Roseivivax,
Roseobacter, Roseovarius, Rubrimonas, Rugegeria, Sagittula,
Staleya, Stappia, Sulfitobacter, Rhodothalassium (incertae sedis)
ORDER SPHINGOMONADALES
Sphingomonas, Blastomonas, Citromicrobium, Erythrobacter,
Erythromicrobium,
Erythromonas,
Porphyrobacter,
Sandaracinobacter, Zymomonas
ORDER CAULOBACTERIALES
Caulobacter, Asticcacaulis, Brevundimonas, Phenylobacterium
ORDER RHIZOBIALES
Rhizobium,
Agrobacterium,
Allorhizobium,
Carbophilus,
Chelatobacter, Ensifer, Sinorhizobium
Bartonella
Brucella, Mycoplana, Ochrobactrum
Phyllobacterium, Aminobacter, Aquamicrobium, Defluvibacter,
Candidatus, Mesorhizobium, Pseudaminobacter
Methylocystis, Albibacter, Methylosinus, Methylopila (incertae
sedis)
Beijerinckia, Chelatococcus, Methylocella
Bradyrhizobium, Afipia, Agromonas, Blastobacter, Bosea,
Nitrobacter, Oligotropha, Rhodoblastus, Rhodopseudomonas
Hyphomicrobium,
Ancalomicrobium,
Ancylobacter,
Angulomicrobium, Aquabacter, Azorhizobium, Blastochloris,
Devosia, Dichotomicrobium, Filomicrobium, Gemmiger, Labrys,
Methylorhabdus,
Pedomicrobium,
Prosthecomicrobium,
Rhodomicrobium, Rhodoplanes, Seliberia, Starkeya, Xanthobacter
Methylobacterium
Rhodobium
PHYLUM BETAPROTEOBACTERIA
CLASS BETAPROTEOBACTERIAE
ORDER BURKHOLDERIALES
Burkholderia, Cupriavidus, Lautropia, Pandoraea, Paucimonas,
Polynucleobacter, Ralstonia, Thermothrix
Oxalobacter, Duganella, Herbaspirillum, Janthinobacterium,
Massilia, Telluria
Alcaligenes, Achromobacter, Bordetella, Derxia, Oligella, Pelistega,
Pigmentiphaga, Sutterella, Taylorella
Comamonas, Acidovorax, Brachymonas, Delftia, Hydrogenophaga,
Lampropedia, Macromonas, Polaromonas, Rhodoferax, Variovorax
Incertae Sedis: Aquabacterium, Idernella, Leptothrix, Roseateles,
Rubrivivax, Sphaerotilus, Tepidomonas, Thiomonas, Xylophilius
ORDER HYDROGENOPHILALES
Hydrogenophilus, Thiobacillus
ORDER METHYLOPHILALES
Methylophilus, Methylobacillus, Methylovorus
ORDER NEISSERIALES
Neisseria, Alysiella, Aquaspirillum, Chromobacterium, Eikenella,
Formivibrio, Iodobacter, Kingella, Microvirgula, Prolinoborus,
Simonsiella, Vitreoscilla, Vogesella
ORDER NITROSOMONADALES
Nitrosomonas, Nitrosolobus, Nitrosospira, Nitrosovibrio
Spirillum
Gallionella
ORDER RHODOCYCLALES
Rhodocyclus,
Azoarcus,
Azonexus,
Azospira,
Azovibrio,
Dechloromonas, Dechlorosoma, Ferribacterium, Propionibacter,
Propionivibrio, Thauera, Zoogloea
PHYLUM GAMMAPROTEOBACTERIA
CLASS CHROMATIAE
ORDER CHROMATIALES
Chromatium, Allochromatium, Halochromatium, Isochromatium,
Lamprobacter, Lamprocystis, Marichromatium, Nitrosococcus,
Pfennigia,
Rhabdochromatium,
Thermochromatium,
Thioalkalicoccus, Thiocapsa, Thiococcus, Thiocystis, Thiodictyon,
Thioflavicoccus, Thiohalocapsa, Thiolamprovum, Thiopedia,
Thiorhodococcus, Thiorhodovibrio, Thiospirillum
Ectothiorhodospira, Arhodomonas, Halorhodospira, Nitrococcus,
Thioalkalivibrio, Thiorhodospira
Halothiobacillus
CLASS ENTEROBACTERIAE
ORDER ACIDITHIOBACILLALES
Acidithiobacillus
Thermithiobacillus
ORDER XANTHOMONADALES
Xanthomonas, Frateuria, Luteimonas, Lysobacter, Nevskia,
Pseudoxanthomonas,
Rhodanobacter,
Schineria,
Stenotrophomonas, Thermomonas, Xylella
ORDER CARDIOBACTERIALES
Cardiobacterium, Dichelobacter, Suttonella
ORDER THIOTRICHALES
Thiothrix, Achromatium, Beggiatoa, Leucothrix, Thiobacterium,
Thiomargarita, Thioploca, Thiospira
Piscirickettsia, Cycloclasticus, Hydrogenovibrio, Methylophaga,
Thioalkalimicrobium, Thiomicrospira
Francisella
ORDER LEGIONELLALES
Legionella
Coxiella, Rickettsiella
ORDER METHYLOCOCCALES
Methylococcus,
Methylomicrobium,
Methylosphaera
Methylobacter,
Methylomonas,
Methylocaldum,
Methylosarcina,
ORDER OCEANOSPIRILLALES
Oceanospirillum, Balneatrix, Marinomonas, Marinospirillum,
Neptunomonas
Alcanivorax
Hahella
Halomonas, Carnimonas, Chromohalobacter, Zymobacter
ORDER PSEUDOMONADALES
Pseudomonas,
Azomonas,
Azotobacter,
Mesophilobacter, Rhizobacter, Rugamonas, Serpens
Moraxella, Acinetobacter, Psychrobacter
Incertae Sedis: Enhydrobacter
Cellvibrio,
ORDER ALTEROMONADALES
Alteromonas, Alishewanella, Colwellia, Ferrimonas, Glaciecola,
Idiomarina, Marinobacter, Marinobacterium, Microbulbifer, Moritella,
Pseudoalteromonas, Psychromonas, Shewanella
ORDER VIBRIONALES
Vibrio, Photobacterium, Salinivibrio
ORDER AEROMONADALES
Aeromonas, Oceanimonas, Tolumonas (incertae sedis)
Succinivibrio, Anaerobiospirillum, Ruminobacter, Succinimonas
ORDER ENTEROBACTERIALES
Escherichia, Alterococcus, Arsenophonus, Brenneria, Buchneria,
Budvicia, Buttiauxella, Calymmatobacterium, Cedecea, Citrobacter,
Edwardsiella, Enterobacter, Erwinia, Ewingella, Hafnia, Klebsiella,
Kluyvera, Leclercia, Leminorella, Moellerella, Morganella,
Obesumbacterium, Pantoea, Pectobacterium, "Candidatus",
Photorhabdus, Plesiomonas, Pragia, Proteus, Providencia,
Rahnella, Saccharobacter, Salmonella, Serratia, Shigella, Sodalis,
Tatumella, Trabulsiella, Wigglesworthia, Xenorhabdus, Yersinia,
Yokenella
ORDER PASTEURELLALES
Pasteurella, Actinobacillus, Haemophilus, Lonepinella, Manheimia,
Phocoenobacter
PHYLUM DELTAPROTEOBACTERIA
CLASS ANOXYDELTABACTERIA
ORDER DESULFURELLALES
Desulfurella, Hippea
ORDER DESULFOVIBRIONALES
Desulfovibrio, Bilophila, Lawsonia
Desulfomicrobium, Desulfonatronovibrio, Desulfothermus
Desulfonatronum
ORDER DESULFOBACTERALES
Desulfobacter, Desulfobacterium, Desulfobacula, Desulfobotulus,
Desulfocella,
Desulfococcus,
Desulfofaba,
Desulfofrigus,
Desulfonema, Desulfosarcina, Desulfospira, Desulfotignum
Desulfobulbus, Desulfocapsa, Desulfofustis, Desulfotalea
Nitrospina
ORDER DESULFARCALES
Desulfarculus
ORDER DESULFUROMONALES
Desulfuromonas, Desulfuromusa, Malonomonas, Pelobacter
Geobacter, Trichlorobacter
ORDER SYNTROPHOBACTERALES
Syntrophobacter, Desulfacinum, Desulforhabdus, Desulfovirga,
Thermodesulforhabdus
Syntrophus, Desulfobacca, Desulfomonile, Smithella
CLASS OXYDELTABACTERIA
ORDER BDELLOVIBRIONALES
Bdellovibrio, Bacteriovorax, Micavibrio, Vampirovibrio
ORDER MYXOCOCCALES
Myxococcus, Corallococcus, Pyxicoccus
Cystobacter, Archangium, Hyalangium, Melettangium, Stigmatella
Polyangium, Byssophaga, Chondromyces, Haploangium, Jahnia,
Sorangium
Nannocystis
Kofleria
PHYLUM EPSILONPROTEOBACTERIA
CLASS CAMPYLOBACTERIAE
ORDER NAUTILIALES
Nautilia, Caminibacter, Lebetimonas
Incertae Sedis: Hydrogenimonas, Nitratiruptor, Thioreductor
ORDER CAMPYLOBACTERALES
Campylobacter, Arcobacter, Nitratifractor, Sulfurospirillum,
Sulfurimonas, Sulfurovum, Sulfiricurvum, Thiomicrospira
Helicobacter, Thiovulum, Wolinella
KINGDOM SPIROCHAETAE
PHYLUM SPIROCHAETOBACTERIA
CLASS SPIROCHAETAE
ORDER SPIROCHAETIALES
Spirochaeta, Borrelia, Brevinema,
Diplocalyx,
Hollandia,
Pillotina,
Brachyspira. Leptonema, Leptospira.
Clevelandina,
Treponema.
Cristispira,
Serpulina,
Unit V
Algae
Classification of Algae
The classification of algae into taxonomic groups is based upon the same rules that are
used for the classification of land plants, but the organization of groups of algae above the
order level has changed substantially since 1960. Research using electron microscopes
has demonstrated differences in features, such as the flagellar apparatus, cell division
process, and organelle structure and function, that are important in the classification of
algae. Similarities and differences among algal, fungal, and protozoan groups have led
scientists to propose major taxonomic changes, and these changes are continuing.
Division-level classification, as with kingdom-level classification, is tenuous for algae. For
example, some phycologists place the classes Bacillariophyceae, Phaeophyceae, and
Xanthophyceae in the division Chromophyta, whereas others place each class in separate
divisions: Bacillariophyta, Phaeophyta, and Xanthophyta. Yet, almost all phycologists
agree on the definition of the respective classes Bacillariophyceae, Phaeophyceae, and
Xanthophyceae.
The classes are distinguished by the structure of flagellate cells (e.g., scales, angle of
flagellar insertion, microtubular roots, and striated roots), the nuclear division process
(mitosis), the cytoplasmic division process (cytokinesis), and the cell covering. Many
scientists combine the Micromonadophyceae with the Pleurastrophyceae, naming the
combined group the Prasinophyceae. “Phylum” and “division” represent the same level of
organization; the former is the zoological term, the latter is the botanical term
Properties of Major Algal Taxonomic Groups
S.N Taxonomic Group Chlorophyl Carotenoids
o
l
1.
Bacillariophyta
a, c
β-carotene
±
-carotene
rarely
fucoxanthin,.
Bilo
protein
s
Storage
products
Flagellation
&Cell
structure
Chrysolaminari 1
apical
n
flagellum in
male
oils
gametes:
cell in two
halves with
elaborate
markings.
2.
Chloro
a, b
phycophyta
β-carotene,
± -carotene
(green algae)
rarely carotene
and lycopene,
lutein.
3.
Chrysophycophyt a, c ,
a
fucoxanthin
(golden algae)
4.
Cyanobacteria
(blue green algae)
β-carotene,
a,c
β-carotene,
phycobilins
Starch, oils
1,2,4
many,
to
equal, apical
or
subapical
flagella.
Chrysolaminari 1
or
2
n
unequal,
apical
oils
flagella,
in
some,
cell
surface
covered by
characteristi
c scales.
5.
Phaeco
a,c
phycophyta
Dinophyta
(dinpflagellates)
Laminarin,
soluble
fucoxanthin,
(brown algae)
6.
β-carotene, ±
a,c
violaxanthin
carbohydrates,
oils
β-carotene,
Starch, oils
peridinin,
neoperididnin
dinoxanthin,
2
lateral
flagella
2 lateral, 1
trailing,1
girdling
flagellum, in
most, there
is
a
longitudinal
neodinoxanthin
.
and
transverse
furrow and
angular
plates.
7.
Rhodo
phycophyta
(red algae )
a, rarely d β-carotene,
zeaxanthin
± β carotene
Phyco
Floridean starch Flagella
absent
erythri oils
n
phyco
cyanin
Fung
Basic Characteristics of fungi












Have cell walls of glucans, mannans, and chitin (polysaccharides)
In the cell membrane sterol is present (ergosterol)
Eukaryotic
All are chemoheterotrophs: parasitic or saprophytic
Single or multicellular
All are nonmotile
All are gram positive
Most are aerobic or facultative anaerobe
o Very few fungi are anaerobic
Fungi produce spores
o Sexual spores
o Asexual spores
Usually have a filamentous (threadlike) structure
o Threads are called hyphae (singular: hypha)
 Two kinds of hyphae: septate and aseptate
Whole fungus is called a mycelium (a mass of hyphae)
Dimorphism: some fungi are dimorphic (have two forms: yeast cells and hyphae)
Taxonomic groups
Unikonta
Amoebozoa
Opisthokonta
Animalia
Choanozoa
Nucleariids
Fungi[40]
Rozellida
Microsporidia
Chytridiomycota
Neocallimastigomycota
Blastocladiomycota
Zoopagomycotina
Kickxellomycotina
Entomophthoromycotina
Mucoromycotina
Glomeromycota
Dikarya
Ascomycota
Basidiomycota
The major phyla (sometimes called divisions) of fungi have been classified mainly on the
basis of characteristics of their sexual reproductive structures. Currently, seven phyla are
proposed: Microsporidia, Chytridiomycota, Blastocladiomycota, Neocallimastigomycota,
Glomeromycota, Ascomycota, and Basidiomycota.[40]
Phylogenetic analysis has demonstrated that the Microsporidia, unicellular parasites of
animals and protists, are fairly recent and highly derived endobiotic fungi (living within the
tissue of another species).[94][117] One 2006 study concludes that the Microsporidia are a
sister group to the true fungi, that is, they are each other's closest evolutionary relative. [118]
Hibbett and colleagues suggest that this analysis does not clash with their classification of
the Fungi, and although the Microsporidia are elevated to phylum status, it is
acknowledged that further analysis is required to clarify evolutionary relationships within
this group.[40]
The Chytridiomycota are commonly known as chytrids. These fungi are distributed
worldwide. Chytrids produce zoospores that are capable of active movement through
aqueous phases with a single flagellum, leading early taxonomists to classify them as
protists. Molecular phylogenies, inferred from rRNA sequences in ribosomes, suggest that
the Chytrids are a basal group divergent from the other fungal phyla, consisting of four
major clades with suggestive evidence for paraphyly or possibly polyphyly.[119]
The Blastocladiomycota were previously considered a taxonomic clade within the
Chytridiomycota. Recent molecular data and ultrastructural characteristics, however, place
the Blastocladiomycota as a sister clade to the Zygomycota, Glomeromycota, and Dikarya
(Ascomycota and Basidiomycota). The blastocladiomycetes are saprotrophs, feeding on
decomposing organic matter, and they are parasites of all eukaryotic groups. Unlike their
close relatives, the chytrids, which mostly exhibit zygotic meiosis, the blastocladiomycetes
undergo sporic meiosis.[94]
The Neocallimastigomycota were earlier placed in the phylum Chytridomycota. Members
of this small phylum are anaerobic organisms, living in the digestive system of larger
herbivorous mammals and possibly in other terrestrial and aquatic environments. They
lack mitochondria but contain hydrogenosomes of mitochondrial origin. As the related
chrytrids, neocallimastigomycetes form zoospores that are posteriorly uniflagellate or
polyflagellate.[40]
Members of the Glomeromycota form arbuscular mycorrhizae, a form of symbiosis where
fungal hyphae invade plant root cells and both species benefit from the resulting increased
supply of nutrients. All known Glomeromycota species reproduce asexually.[71] The
symbiotic association between the Glomeromycota and plants is ancient, with evidence
dating to 400 million years ago.[120] Formerly part of the Zygomycota (commonly known as
'sugar' and 'pin' molds), the Glomeromycota were elevated to phylum status in 2001 and
now replace the older phylum Zygomycota.[121] Fungi that were placed in the Zygomycota
are now being reassigned to the Glomeromycota, or the subphyla incertae sedis
Mucoromycotina,
Kickxellomycotina,
the
Zoopagomycotina
and
the
[40]
Entomophthoromycotina.
Some well-known examples of fungi formerly in the
Zygomycota include black bread mold (Rhizopus stolonifer), and Pilobolus species, capable
of ejecting spores several meters through the air.[122] Medically relevant genera include
Mucor, Rhizomucor, and Rhizopus.
Diagram of an apothecium (the typical cup-like reproductive structure of Ascomycetes)
showing sterile tissues as well as developing and mature asci.
The Ascomycota, commonly known as sac fungi or ascomycetes, constitute the largest
taxonomic group within the Eumycota.[39] These fungi form meiotic spores called
ascospores, which are enclosed in a special sac-like structure called an ascus. This phylum
includes morels, a few mushrooms and truffles, single-celled yeasts (e.g., of the genera
Saccharomyces, Kluyveromyces, Pichia, and Candida), and many filamentous fungi living as
saprotrophs, parasites, and mutualistic symbionts. Prominent and important genera of
filamentous ascomycetes include Aspergillus, Penicillium, Fusarium, and Claviceps. Many
ascomycete species have only been observed undergoing asexual reproduction (called
anamorphic species), but analysis of molecular data has often been able to identify their
closest teleomorphs in the Ascomycota.[123] Because the products of meiosis are retained
within the sac-like ascus, ascomycetes have been used for elucidating principles of genetics
and heredity (e.g. Neurospora crassa).[124]
Members of the Basidiomycota, commonly known as the club fungi or basidiomycetes,
produce meiospores called basidiospores on club-like stalks called basidia. Most common
mushrooms belong to this group, as well as rust and smut fungi, which are major pathogens
of grains. Other important basidiomycetes include the maize pathogen Ustilago maydis,[125]
human commensal species of the genus Malassezia,[126] and the opportunistic human
pathogen, Cryptococcus neoformans.[127]
Fungus-like organisms
Because of similarities in morphology and lifestyle, the slime molds (myxomycetes) and
water molds (oomycetes) were formerly classified in the kingdom Fungi. Unlike true fungi
the cell walls of these organisms contain cellulose and lack chitin. Myxomycetes are
unikonts like fungi, but are grouped in the Amoebozoa. Oomycetes are diploid bikonts,
grouped in the Chromalveolate kingdom. Neither water molds nor slime molds are closely
related to the true fungi, and, therefore, taxonomists no longer group them in the kingdom
Fungi. Nonetheless, studies of the oomycetes and myxomycetes are still often included in
mycology textbooks and primary research literature.[128]
The Rozellida clade, including the "chytrid" Rozella, is a genetically disparate group known
mostly from environmental DNA sequences which is a sister group to fungi. Members of the
group which have been isolated lack the chitinous cell wall which is characteristic of fungi.
The nucleariids, currently grouped in the Choanozoa, may be the next sister group to the
eumycete clade, and as such could be included in an expanded fungal kingdom.[129]
Ecology
Although often inconspicuous, fungi occur in every environment on Earth and play very
important roles in most ecosystems. Along with bacteria, fungi are the major decomposers
in most terrestrial (and some aquatic) ecosystems, and therefore play a critical role in
biogeochemical cycles[130] and in many food webs. As decomposers, they play an essential
role in nutrient cycling, especially as saprotrophs and symbionts, degrading organic matter
to inorganic molecules, which can then re-enter anabolic metabolic pathways in plants or
other organisms.[131][132]
Symbiosis
Many fungi have important symbiotic relationships with organisms from most if not all
Kingdoms.[133][134][135] These interactions can be mutualistic or antagonistic in nature, or in
the case of commensal fungi are of no apparent benefit or detriment to the host.[
The life cycle of fungi
The life cycle of fungi can follow many different patterns. For most of the molds indoors,
fungi are considered to go through a four-stage life cycle: spore, germ, hypha, mature
mycelium. Brundrett (1990) showed the same cycle pattern using an alternative diagram of
the developmental stages of a mould. The majority of mold fungi do not have sexual stages
and following this simple life cycle pattern.
Other life cycle patterns differ from this four-stage cycle in that different reproduction
mechanisms and physiology characteristics are present, esp. for non-moldy fungi (such as
wood rots, etc.)
Fungi reproduce by releasing airborne spores, which have different shapes and
dimensions. Through spore liberation (the process of detachment of spore from the sporebearing structure) and spore dispersal (the subsequent movement of the spore before
settling on a material surface), spores travel through air, water and event on other insects
from fungal infesting areas into homes and rest on surfaces and in building envelope.
Concentrations of spores in outdoor and indoor air have been the target for much research
(Ingold, 1971 and Darrell, 1974).
Spore diameters (Unit: micron):







Alternaria, 8-75,
Aspergillus 2-10,
Cladosporium4-20,
Epicoccum 20,
Penicillium 3-5,
Periconia 16-18,
Stemphylium 23-75,
Spores present in the air settle on surfaces. When conditions are favorable, spores start the
growth process. Spores go through four stage of development: maturation, dormancy,
activation, and germination (Burnett, 1976). The combined process is usually referred to as
germination, and will be discussed in more detail in the next section.
Once activated and germinated, the resulting germ tube is ready to grow into hyphae, then
a cluster mycelium when conditions are favorable. In this (vegetative) growth stage, fungi
produce microscopic, cylindrical filaments, the thread-like cellular strands called hyphae,
into the food sources (material). These hyphae produce and excrete digestive enzymes in
the food and take up nutrients in watery form (Figure 4), and transport them to the
growing hyphal tips. The hyphae grow by extending itself on the tip or by branching out
new threads at the tip and in the older parts. The total quantities of hyphae produced by a
fungus are collectively termed as a mycelium. Figure 5 shows images of some mycelia.
The mycelium grows into the material (substrate), consumes its organic components in the
process, wakens the structure of the material, and eventually destroys the structure and
renders the material incapable to fulfil its function.
Fungal Reproduction
Fungi exhibit three major modes of reproduction - vegetative, asexual and sexual.
Vegetative Reproduction
It is the type of reproduction which involves the somatic portion of the fungal thallus. It
occurs by the following methods.
Fragmentation
In this process, the mycelium breaks into two or more similar fragments either accidentally
or due to some external force. Each fragment grows into a new mycelium.
Budding
The parent cell produces one or more projections called buds, which later develop
necessary structures and detach to grow into new individuals. Budding is common in
unicellular forms like yeast.
Fission
In this process, the parent cell splits into two equal halves, each of which develop into a
new individual. Fission is also common in yeast.
Sclerotia
In some cases, as in Claviceps, the hyphae become interwoven to form a compact mass and
get surrounded by a hard covering or rind. Such structures are called SCLEROTIA. They
remain dormant under unfavourable conditions and germinate into new mycelia on the
return of favourable conditions.
Rhizomorphs
In some higher fungi, several hyphae may become interwoven to form rope-like structures
called rhizomorphs. Under favourable conditions, they resume growth to give rise to new
mycelia.
Modes of Vegetative Reproduction
Asexual Reproduction
It is the type of reproduction in which special reproductive structures called spores or
propagates are formed. The fungal spores always result from mitosis and hence are
described as mitospores. Following are the types of spores produced in different groups of
fungi:
Zoospores
They are flagellated, motile spores produced inside structures called zoosporangia. These
spores do not have a cell wall. Such spores are produced in lower fungi such as Achyla and
Saprolegnia.
Sporagiospores
These are non-motile spores produced inside structures called sporangia in fungi such as
Rhizopus and Mucor. These spores are dispersed by wind.
Modes of Asexual Reproduction
Chlamydospores
These are thick walled resting spores which arise directly from hyphal cells. They store
reserve food.
Oidia
These are spore like structures formed by the breaking up of hypha cells. They do not store
reserve food and hence cannot survive under unfavourable conditions. Such spores are
produced in Rhizopus.
Conidia
These are non-motile spores produced singly or in chains at the tip of the hypha branches
that are called conidiophores. Such spores are produced in fungi like Aspergillus and
Penicillium.
Sexual Reproduction
Sexual reproduction is known to occur in all groups of fungi except the Fungi imperfecti or
Dueteromycetes. It may involve fusion of gametes, gametangia or hyphae. The process may
involve only fusion of cytoplasm (plasmogamy) or fusion of nuclei (karyogamy) or
production of meiotic spores (meiospores)
In most of the lower fungi plasmogamy is immediately followed by karyogamy and meiosis.
In higher fungi karyogamy is often delayed so that the hyphae remain dikaryotic. This
phase of fungal life cycle is called dikaryophase. Such fungi complete their life cycle in
three phases a haplophase, a dikaryophase and a diplophase.
Sexual fusion in fungi is of different types, as follows :
Planogametic Copulation
Here motile gametes called planogametes undergo fusion. When both the gametes are
motile and morphologically similar, the fusion process is called isogamy.
Eg.: Synchytrium When both the gametes are motile but differ in their size, the fusion
process is called anisogamy.
Eg.: Allomyces. When one gamete (male) is smaller and motile and the other (female)
gamete is larger and non motile, the fusion process is called heterogamy.
Gametangial Contact
Here, gamete bearing structures called gametangia come closer to each other and develop a
fertilisation tube through which the male gamete migrates into the female gametangium.
Eg. : Phytophthora, Albugo.
Gametangial Copulation
Here, the gametangia fuse with each other, lose their identity and develop into a zygospore
Eg.: Mucor, Rhizopus
Spermatisation
In some fungi like Puccinia, tiny unicellular spore like structures called spermatia are
formed. They get transferred to female gametangia through various agencies.
Types of Sexual Reproduction in Fungi
Somatogamy
In examples like Agaricus, fusion occurs between two somatic cells and involves only
plasmogamy. This results in the formation of dikaryotic hyphae. Hence, the process is
called dikaryotization.
Homothallism And Heterothallism
Based on the compatibility in sexual reproduction the fungal hyphae can be distinguished
into two types homothallic and heterothallic. In homothallic forms, fusion occurs
between the genetically similar strains or mating types. In such forms, meiosis results in
the formation of genetically identical spores. In the heterothallic forms, fusion occurs
between the genetically different mating types or strains. The strains are genetically
compatible and are designated as + strain and strain. In such forms meiosis results in the
formation of both the strains, in equal numbers. Heterothallism is a device to prevent
inbreeding and promote out breeding.
KINGDOM OXYPHOTOBACTERIA
PHYLUM CYANOBACTERIA
CLASS SYNECHOCOCCOPHYCEAE
ORDER SYNECHOCOCCALES
Acaryochloridae: Acaryochloris
Chamaesiphonaceae: Chamaesiphon, Clastidium, Cyanophanon,
Geitleribactron
Merismopediaceae: Merismopedia, Aphanocapsa, Coccopedia,
Coelomoron, Coelosphaeropsis, Coelosphaerium, Cyanotetras,
Eucapsis, Lithococcus, Lithomyxa, Mantellum, Paracapsa,
Siphonosphaera, Synechocystis
Synechococcaceae: Synechococcus, Alternaria, Alternantia,
Bacularia,
Chamaesiphon,
Cyanobium,
Cyanocatena,
Cyanocatenula, Cyanodictyon, Cyanonephron Cyanogranis,
Cyanothamnos, Epigloeosphaera, Lemmermanniella, Pannus,
Planktocyanocapsa,
Prochlorococcus,
Rhabdoderma,
Rhabdogloea, Rhodostichus, Thermosynechococcous, Tubiella,
Wolskyella
ORDER PSEUDANABAENALES
Pseudanabaenaceae: Pseudanabaena, Arthronema, Geitlerinema,
Halomicronema, Heteroleibleinia, Jaaginema, Leptolyngbya,
Limnothrix, Planktolyngbya, Prochlorothrix, Romeria, Sokolovia,
Tapinothrix
Schizothrichaceae: Schizothrix, Trichololeus
CLASS GLOEOBACTEROPHYCEAE
ORDER GLOEOBACTERALES
Gloeobacteraceae: Gloeobacter
CLASS OSCILLATORIOPHYCEAE
ORDER CHROOCOCCALES
Chroococcaceae:
Chroococcus,
Asterocapsa,
Chlorogloea,
Chroocogloeocystis, Cyanokybus, Cyanosarcina, Gloeocapsopsis,
Nephrococcus, Pseudocapsa,
Cyanobacteriaceae: Cyanobacterium, Aphanothece, Crocosphaera,
Cyanocomperia, Cyanothece, Gloeothece, Hormothece, Microcrocis,
Myxobaktron, Palikiella, Pseudoconbyrsa
Dermocarpellaceae: Cyanocystis, Dermocarpella, Stanieria
Entophysalidaceae: Entophysalis, Cyanoarbor, Cyanodermatium,
Cyanostylon,
Dzensia,
Hormathonema,
Johannesbaptistia,
Placoma, Siphonema, Tryponema
Gomphosphaeriaceae: Gomphosphaeria, Snowella, Woronichinia
Hydrococcaceae: Hydrococcus, Chroococcidium, Cyanoderma,
Cyanosaccus, Dalmatella, Ercegovicia, Hyella, Myxohyella,
Onkonema, Pascherinema, Pleurocapsa, Podocapsa, Radaisia,
Solentia
Microcystaceae:
Microcystis,
Chondrocystis,
Gloeocapsa,
Radiocystis, Sphaerocavum
Prochloraceae: Prochloron
Spirulinaceae: Spirulina, Glaucospira
Stichosiphonaceae: Stichosiphon, Chamaecalyx
Xenococcaceae: Xenococcus, Chroococcidopsis, Chroococcopsis,
Epilithia, Myxosarcina, Xenotholos
ORDER OSCILLATORIALES
Ammtoideaceae: Ammatoidea, Homeothrix, Phormidiochaete,
Pseudoscytonema
Borziaceae: Borzia, Komvophoron, Sinaiella, Yonedaella
Gomontiellaceae: Gomontiella, Crinalium, Starria
Oscillatoriaceae: Oscillatoria, Blenothrix, Hormoscilla, Lyngbya,
Plectonema, Polychlamydum
Phormidiaceae:
Phormidium,
Arthrospira,
Hydrocoleum,
Katagnymene,
Leibleinia,
Lyngbyopsis,
Microcoleus,
Planktothricoides, Planktothrix, Porphyrosiphon, Proterendothrix,
Pseudophormidium, Sirocoleum, Symploca, Symplocastrum,
Trichodesmium, Tychonema
CLASS NOSTOCOPHYCEAE
ORDER NOSTOCALES
Borzinemataceae: Borzinema, Handeliella, Schmidleinema,
Segurnzaea, Spelaeopogon
Chlorogloeopsidaceae: Chlorogloeopsis, Heterocyanococcus,
Hapalosiphonaceae: Albrightia, Brachytrichopsis, Chondrogloea,
Fischerella,
Fischerellopsis,
Hapalosiphon,
Leptopogon,
Loefgrenia, Mastidocladus, Mastigocoleopsis, Mastigocoleus,
Matteia, Nostochopsis, Parthasarathiella, Thalophilia, Westiella,
Westiellopsis
Loriellaceae: Loriella, Colteronema, Geitleria, Hyphomorpha,
Microchaetaceae:
Microchaete,
Camptylonemopsis,
Coleodesmiopsis, Coleodesmium, Fortiea, Hassallia, Petalonema,
Rexia, Spirirestris, Tolypothrix
Nostocaceae: Nostoc, Anabaena, Anabaenopsis, Aphanizomenon,
Aulosira,
Cuspidothrix,
Cyanospira,
Cylindrospermopsis,
Cylindrospermum, Hormothamnion, Hydrocoryne, Isocystis,
Nodularia, Raphidiopsis, Richelia, Thiochaete, Trichormus, Wollea
Rivulariaceae: Rivularia, Calothrix, Dichthrix, Gardnerula,
Gloeotrichia, Isactis, Sacconema,
Scytonemataceae:
Scytonema,
Brasilonema,
Kyrtuthrix,
Scytonematopsis
Stigonemataceae:
Stigonema,
Caposira,
Cyanobotrys,
Desmosiphon,
Doliocatella,
Homoeoptyche,
Letestuinema,
Nematoplaca, Pulvinularia, Stauromatonema
Symphyonemataceae: Symphonema, Adrianema, Brachytrichia,
Herpyzonema, Iyengariella, Mastigocladopsis, Parenchymorpha,
Symphonemopsis, Umezakia, Voukiella
KINGDOM SAPROSPIRAE
PHYLUM SAPROSPOBACTERIA
CLASS CYTOPHAGATIAE
ORDER CYTOPHAGIALES
Cytophaga, Sporocytophaga, Saprospira, Microscilla, Flexibacter.
ORDER BEGGIATOIALES
Beggiatoa,
Thiofilum,
Vitreoscilla.
Leucothrix,
Simonsiella,
KINGDOM CHLOROFLEXAE
PHYLUM CHLOROFLEXOBACTERIA
CLASS CHLOROFLEXI
ORDER CHLOROFLEXIALES
Chloroflexus, Chloronema, Heliothrix, Oscillochloris.
ORDER HERPITOSIPHONALES
Herpetosiphon.
Alysiella,
KINGDOM CHLOROSULFATAE
PHYLUM CHLOROBACTERIA
CLASS CHLOROBI
ORDER CHLOROBIALES
Chlorobium,
Prosthecochloris,
Clathrochloris, Chloroherpiton.
Ancalochloris,
Pelodictyon,
KINGDOM PIRELLAE
PHYLUM PIRELLOBACTERIA
CLASS PLANCTOMYCETAE
ORDER PLANCTOMYCIALES
Gemmatia, Isosphaera, Pirellula, Planctomyces.
CLASS CHLAMYDATIA
ORDER CHLAMYDIALES
Chlamydia, Chlamydophila, Parachlamydia, Simkania, Waddlia.
KINGDOM FIRMICUTAE
PHYLUM APHRAGMABACTERIA
CLASS MOLLICUTI
ORDER MYCOPLASMALES
Mycoplasma, Eperythrozoon, Haemobartonella, Ureaplasma.
ORDER ENTOMOPLASMALES
Entomoplasma, Mesoplasma, Spiroplasma.
ORDER ACHOLEPLASMALES
Acholeplasma.
ORDER ANAEROPLASMALES
Anaeroplasma, Asterolplasma.
ORDER INCERTAE SEDIS
Erysilelothrix, Bulleidia, Holdemania, Solobacterium.
PHYLUM ANOXYBACTERIA
CLASS CLOSTRIDIAE
ORDER CLOSTRIDIALES
Clostridium,
Acetivibrio,
Acidaminobacter,
Anaerobacter,
Arthromitus,
Caloramator,
Coprobacillus,
Natronincola,
Oxobacter,
Sarcina,
Sporobacter,
Thermobachium,
Thermohalobacter, Tindallia.
ORDER LACHNOSPIRALES
Lachnospira,
Acetitomaculum,
Anaerofilum,
Butyrivibrio,
Catenibacterium,
Catonella,
Coprococcus,
Johnsonella,
Pseudobutyrvibrio, Roseburia, Ruminococcus, Sporobacterium.
ORDER PEPTOSTREPTOCOCCALES
Peptostreptococcus, Filifactor, Finegoldia, Fusibacter, Helcococcus,
Micromonas, Tissierella.
ORDER EUBACTERIALES
Eubacterium, Acetobacterium,
Pseudoramibacter.
Anaerovorax,
Mogibacterium,
ORDER PEPTOCOCCALES
Peptococcus,
Anaeroarcus,
Anaerosinus,
Anaerovibrio,
Carboxydothermus, Centipeda, Dehalobacter, Dendrosporobacter,
Desulfitobacterium,
Desulfonispora,
Desulfosporosinus,
Desulfotomaculum, Mitsuokella, Propioispira, Succinispira,
Syntrophobotulus, Thermoterrabacterium.
ORDER HELIOBACTERIALES
Heliobacterium, Heliobacillus, Heliophilum, Heliorestis.
ORDER ACIDAMINOCOCCALES
Acidaminococcus,
Acetonema,
Anaeromusa,
Dialister,
Megasphaera, Papillibacter, Pectinatus, Phascolarctobacterium,
Quinella, Schwartzia, Selenomonas, Sporomusa, Succiniclasticum,
Veillonella, Zymophilus.
ORDER SYNTROPHOMONADALES
Syntrophomonas, Acetogenium, Aminobacterium, Aminomonas,
Anaerobaculum,
Anaerobrancha,
Caldicellulostruptor,
Dethiosulfovibrio, Pelospora, Syntrophospora, Syntrophothermus,
Thermaerobacter,
Thermanaerobacter,
Thermanaerovibrio,
Thermohydrogenium, Thermosyntropha.
CLASS THERMOANDEROBACTERIAE
ORDER THERMOANDEROBACTERIALES
Thermoanderobacterium,
Ammonifex,
Carboxydobrachium,
Coprothermobacter,
Moorella,
Sporomaculum,
Thermacetogenium, Thermoanaerobacter, Theremoanaerobium.
CLASS HALOANDEROBIAE
ORDER HALOANDEROBIALES
Haloanderobium, Halocella, Halothermothrix, Natroniella.
ORDER HALOBACTERALES
Halobacteroides, Acetohalobium,
Sporohalobacter.
Haloanaerobacter,
Orenia,
PHYLUM ENDOSPOROBACTERIA
CLASS BACCILLI
ORDER BACILLIALES
Bacillus,
Amphibacillus,
Anoxybacillus,
Exiguobacterium,
Gracilibacillus,
Halobacillus,
Saccharococcus,
Salibacillus,
Virigibacillus.
ORDER PLANNOCOCCALES
Planococcus, Filibacter, Kurthia, Sporosarcina.
ORDER CARYOPHANALES
Caryophanon.
ORDER LISTERIALES
Listeria, Brochothrix.
ORDER STAPHYLOCOCCALES
Staphylococcus, Gemella, Macrococcus, Salicoccus.
ORDER SPOROLACTOBACILLIALES
Sporolactobacillus, Marinococcus.
ORDER PAENIBACILLIALES
Paenibacillus, Ammoniphilus, Aneurinibacillus,
Oxalophagus, Thermicanus, Thermobacillus.
Brevibacillus,
ORDER ALICYCLOBACILLALES
Alicyclobacillus, Pasteuria, Sulfobacillus.
ORDER THERMOACTINOMYCETALES
Thermoactinomyces.
CLASS LACTOBACILLI
ORDER LACTOBACILLIALES
Lactobacillus, Paralactobacillus, Pediococcus.
ORDER AEROCOCCALES
Aerococcus, Abiotrophia, Dolosicoccus, Eremococcus, Facklamia,
Globicatella, Ignavigranum.
ORDER CARNOBACTERIALES
Carnobacterium,
Agitococcus,
Alloiococcus,
Desemzia,
Dolosigranulum, Granulicatella, Lactosphaera, Trichococcus.
ORDER ENTEROCOCCALES
Enterococcus, Atopobacter,
Vagococcus.
Melissococcus,
Tetragenococcus,
ORDER LEUCONOSTOCALES
Leuconostoc, Oenococcus, Weisella.
ORDER STREPTOCOCCALES
Streptococcus, Lactococcus.
INCERTAE SEDIS
Acetoanaerobium, Oscillospira, Syntrophococcus.
PHYLUM ACTINOBACTERIA
CLASS ACIDIMICROBIAE
ORDER ACIDIMICROBIALES
Acidimicrobium.
CLASS RUBROMICROBIAE
ORDER RUBROBACTERIALES
Rubrobacter.
CLASS CORIOBACTAERIAE
ORDER CORIOBACTERIALES
Coriobacterium,
Atopobium,
Collinsella,
Denitrobacterium, Eggerthella, Slackia.
Cryptobacterium,
CLASS SPAHEROBACTAERIAE
ORDER SPHAEROBACTERIALES
Sphaerobacter.
CLASS ACTINOBACTERIAE
ORDER ACTNOMYCETALES
Actinomyces, Actinobaculum, Arcanobacterium, Mobiluncus.
Micrococcus,
Arthrobacter,
Kocuria,
Nesterenkonia,
Renibacterium, Rothia, Stomatococcus, Bogoriella, Rarobacter,
Sanguibacter,
Brevibacterium,
Cellulomonas,
Oerskovia,
Dermabacter, Brachybacterium, Dermatophilus, Dermacoccus,
Demetria, Kytococcus, Intrasporangium, Janibacter, Ornithicoccus,
Ornithinimicrobium,
Nostocoidia,
Terrabacter,
Jonesia,
Microbacterium, Agrococcus, Agromyces, Aureobacterium,
Clavibacter, Cryobacterium, Curtobacterium, Frigoribacterium,
Leifsonia, Leucobacter, Rathaybacter, Subtercola.
Corynebacterium, Dietzia, Gordonia, Skermania, Mycobacterium,
Nocardia, Rhodococcus, Tsukamurella, Williamsia.
Micromoronspora, Actinplanes, Catellatospora, Catenuloplanes,
Couchioplanes, Dactylosporangium, Pilimela, Spirilliplanes,
Verrucosispora.
Propionibacterium, Luteococcus, Microlunatus, Propioniferax,
Tessaracoccus, Nocardoides, Aeromicrobium, Friedmanniella,
Hongia, Kribbella, Micropruina, Marmoricola.
Pseudonocardia,
Actinoalloteichus,
Actinopolyspora,
Amycolatopsis, Kibdelosporangium, Kuntzeria, Prauserella,
Saccharomonospora,
Saccharopolyspora,
Streptoalloteichus,
Thermobispora,
Thermocrispum,
Actinosynnema,
Actinkineospora, Lentzea, Saccharothrix.
Streptomyces, Kitasatospora, Streptoverticillium.
Streptosporangium, Acrocarpospora, Herbidospora, Microbispora,
Microtetraspora, Nonomurea, Planobispora, Planomonospora,
Planopolyspora, Planotetraspora, Nocardiopsis, Thermobifida,
Thermomonospora, Actinmadura, Spirillospora.
Frankia,
Geodermatophilus,
Blastococcus,
Modestobacter,
Microsphaera,
Sporichthya,
Acidothermus,
Kineosporia,
Cryptosporangium, Kineococcus, Glycomyces.
ORDER BIFIDOBACTERIALES
Bifidobacterium, Falcivibrio, Gardnerella.
Actinobispora, Actinocorallia, Excellospora, Pelczaria, Turicella.
PHYLUM DEINOCOCCOBACTERIA
CLASS DEINOCOCCI
ORDER DEINOCOCCALES
Deinococcus.
ORDER THERMALES
Thermus.
KINGDOM THERMOTOGAE
PHYLUM THERMOBACTERIA
CLASS AQUIFEXI
ORDER AQUAFICALES
Aquifex, Caulderobacterium,
Desulfurobacterium(?).
Hydrogenobacter,
Thermocrinis,
CLASS THERMOTOGIAE
ORDER THERMOTOGALES
Thermotoga, Fervidobacterium, Geotoga, Petrotoga, Thermosipho