1.

TAXANOMY OF PROKARYOTES:
In recent past all living organisms are grouped into five kingdoms and Prokaryotes were placed into
the kingdom Monera (Prokaryotae) but now the status of of classification has been changed in late 90's. The
pioneer work had been conducted by Carl Woese (1990) and his colleagues proposed domain system of
classification based upon the differences of subcellular structure ribosomes and cell menmbranes. He
described that life has evolved on earth along three lineages called domain which include Bacteria,
Archaebacteria (Archaea) and Eukaryotes (Eukarya). This division is widely accepted throughout the world.

In view of recent classification two out of three domains' Eubacteria and Archaebacteria are prokaryotes. The
domain Eubacteria comprises all bacterial organisms and recently given status as kingdom bacteria,
domain Archaea comprises the rest of the prokaryotes, and the domain Eukarya includes all eukaryotes,
including organisms in the kingdoms Protista, Fungi (Mycota), Plantae and Animalia

Table 6.1
Classification of organisms given by different scientist in different era.
Linnaeus 1758 Haekel 1866 Chatton 1925 Copeland Whittaker Woese et al.
1938 1969 1990
2 Kingdoms 3 Kingdoms 2 empires 4 Kingdoms 5 Kingdoms 3 domains
Protista Porkaryota Monera Monera Bacteria
Protoctista Protista Arhcea

Eukaryota Plantae Plantae

Eukarya
Plantae Plantae Funji

Animalia Animalia Animalia Animalia

Phylogeny of Prokaryotes:
Prokaryotes are the most primitive and first inhabitant on earth. Earth at that time highly exposed to
radiations and probably had a very less molecular oxygen therefore prokaryotes were adapted to those
conditions. The prokaryotes may have evolved from protobionts ancestors. Their early selective habitat
could be the microbial mats as evidenced by the fossil presence aged 3.5 billion years ago. These mats are
few centimeters thick, moist and sticky due to the secretion of extracellular matrix from
Prokaryotes and found near hydrothermal vents to obtain energy and food from these vents. These mats
when dried becomes stromatolite as a sedimentary structure represents the earliest fossilized record of life
on earth
 Prokaryotes present in every habitat and each comprised of several smaller
taxonomic groups. The domain Bacteria of the Prokaryote also include cyanobacteria or blue-green algae.
This primitive prokaryotic alga perform photosynthesis and are called photoautotrophs. Higher
phototrophic autotrophs are thought to have evolved from this group. They have well developed pigment
system and can reproduce by fragmentation. Bacteria also exist as decomposers or saprotroptus and
symbionts. Prokaryotes have tremendous ability to adapt according to the changing environment. Their
genome has much role in developing this ability extending up to genetic level for example bacterial
species Escherichia coli contains approximately 5,000 genes. On average, about one in every 200 bacteria
is likely to have a mutation in at least one of the genes.

DOMAIN ARCHEA:
Archaea is a very diverse group in a domain system of classification They were initially classified as
Archaebacteria but this classification is obsolete now they are a separate domain. They are present in
different shapes like spherical, rod, lobed, square etc. their diameter ranging 0.1 to over 15um. Archaea
are slightly different from bacteria. They don't have peptidoglycan in their cell wall as it is present in
bacteria and also some metabolic activities are different from bacteria. Archea reproduce asexually
by binary fission, fragmentation or budding

Curd may contain a wide variety of bacteria like Lactobacillus acidophilus, Lactococcus lactis, etc.,
whereas yogurt contains Streptococcus thermophilus and Lactobacillus bulgaricus. Anaerobic
bacteria in the oral cavity include:, Eubacterium, Lactobacillus, Selenomonas, Treponema, etc.

Archaea can live in different habitats of extreme condition and classified accordingly like those living in
hot springs called thermophiles, high acidic conditions dwellers called acidophiles and methanogens are
found in marshy areas and in gut produces biogas to obtain energy another group includes halophiles that
live in high salt concentration environment as they require high salt for their growth. Although they are
almost similar with bacteria in shape and size but genetically, they also have some affinity
with eukaryotes like they have genes that produce enzymes particularly polymerase used in metabolic
activities during translation and transcription as present in eukaryotic organisms. Archeal membrane
composition is bit different from bacterial membranes marking as unique character. They have
hydrocarbons attached to glycerol by ether linkage rather than ester linkages this combination is also
called archaeol specially in methanogens while in bacterial membrane glycerol ester lipids are presents.
Example Methanococcus, Halobacterium
 They do not live as pathogens or parasites instead they develop useful
associations with others as mutualists or commensals for example methanogen archea [Link] live in
human intestine and helps in digestions, marine archean Cenarcheaum symbiosum lives within sponge
Axinella mexicana as symbiont, some thermophile archea used in biotechnology due to their endurance of
high temperature.
Table: Comparision of domain system classification
DOMAINS
Characteristics Arches Bacteria Eukarya
Cell Membrane Ether linked lipids, Ester-linkled Ester-linkled lipids,
pseudopeptidoglycans peptidoglycan various structure
Gene Structure Circular chromosomes, Circular chromosomes, Multiple, linear
similar translation and unique translation and chromosomes, similar
transcription to Eukarya transcription translation and
transcription to Archea

Internal cell structure No membrane bound No membrane bound Membrane bound

organelles or nucleus organelles or nucleus organelles or nucleus
Metabolism Various Various including, Photosynthesis and
Methanogenesis unique photosynthesis, aerobic cellular respiration
to archea and anaerobic
respiration,
fermentation, and
autotrophy

Reproduction Asexual reproduction, Asexual reproduction, Sexual and asexual

horizontal gene transfer horizontal gene transfer reproduction

BACTERIA ECOLOGY AND DIVERSITY:

Earth is formed around 4.5 billion years ago. The evolution of this planet and its atmosphere gave rise to
life, which shaped earth's subsequent development. When earth was evolved the allover environmental
conditions are not so good for any living organism. Initial temperature is very high the volcanic activities
releasing gasses probably created the atmosphere and the oxygen almost unavailable. The earliest
undisputed evidence of life on earth dates at least from 3.5 billion years ago. Since then, life has evolved
into a wide variety of forms. As evolution proceeds fossil records indicate bacterial colonization
developed and acquired different areas of earth. Later on, some started making their own food using
carbon dioxide from the atmosphere and energy they harvested from the sun. These initial photosynthetic
organisms helped establish a stable atmosphere and produced oxygen in such quantities that eventually
life forms could evolve that needed oxygen. Soon afterward, new oxygen-breathing life forms came onto
the existence.
With a population of increasingly diverse bacterial life, the stage was set for more life
to form. There is compelling evidence that mitochondria and chloroplasts were once primitive bacterial
cells. The Russian botanist Konstantin Mereschkowski first outlined the theory of symbiogenesis
(Endosymbiotic) which states that some of the organelles in today's eukaryotic cells were once
prokaryotic microbes. Over millions of years of evolution, mitochondria and chloroplasts have become
more specialized and today they cannot live outside the cell. Mitochondria and chloroplasts have
striking similarities to bacteria cells. They have their own DNA, which is separate from the DNA found in
the nucleus of the cell and both organelles use their DNA to produce many proteins and enzymes required
for their function. A double membrane bounding both mitochondria and chloroplasts
is further evidence that each was ingested by a primitive host. The two organelles also reproduce like
bacteria, replicating their own DNA and directing their own division.

Mitochondrial DNA (mtDNA) has a unique pattern of inheritance. It is passed down directly from mother
to child, and it accumulates changes much more slowly than other types of DNA. Because of its unique
characteristics, mtDNA has provided important clues about evolutionary history. For example, differences
in mtDNA are examined to estimate how closely related one species is to another.

Bacterial habitat:
Bacteria can be found in almost all the habitat on earth. They are present in soil, water, plants, animals,
radioactive waste, deep in the earth's crust, arctic ice and glaciers and in hot springs. Their range
extending up to 30 miles up in the atmosphere and 10,000 meters deep in water. A gram of soil typically
contains about 40 million bacterial cells. A milliliter of fresh water usually holds about one million
bacterial cells. The earth is estimated to hold at least 5 nonillion bacteria, and much of the earth's biomass
is thought to be made up of bacteria. This distribution also ensures the evidence that bacterial colonization
and endurance develops due to the extreme environment when the earth is formed. Deep in the ocean
environment is total dark and both temperature and pressure are very high, bacteria living in these areas
survive by oxidizing sulfur that comes from deep inside the earth.

Table
Types of bacteria on the basis of mode of respiration
Aerobic bacteria Anaerobic bacteria
Live in places where oxygen is available Live in places where oxygen is not available
They produce CO2 and H2O They produce CO2, ethanol and lactic acid
Live in soil, water and open surfaces Lives in areas where oxygen is depleted like
intestine, marches

Produce more energy Produce less energy

Example Lactobacillus, Myobacterium Example Clostridium and E. coli

Likes arches different bacteria also live in different extreme environment

Major groups of bacteria:

Carl Woese studied the differences in rRNA sequences in different organisms and established the
evolutionary relationships among species. On that basis domain bacteria classified into five major
phylums namely Proteobacteria, Chlamydias (Gram-negative), Spirochetes, Cyanobacteria, and gram-
positive bacteria.

Table: Different groups of Bacteria

Phylum Character Example
Protobacteria Free living symboints Helicobactor pylori
some are pathogenic causes stomach ulcer
Salmonella causes food
poisoning
Chlamydias (Gram- Ovbbligate intracellular Chlamydia trachomatis
negative bacteria) parasite cell wall with causes sexually
low peptidoglycan transmitted disease
Spiurochetes Spiral shaped, free Treponema pallidum
living anaerobes causes Syphills
: DOMAINS Pathogenic flagella
BACTERIA present
Cyanobacteria Known as blue green Prochlorococcus most
algae chlorophyll abundant photosynthetic
present, Present in organism on earth
aquatic environment
Gram-positive Pathogenic and Clostridium botulinum
bacteria decomposers Thick cell causes botulism Bacillus
wall and without outer anthrax causes anthrax
membrane