Introduction
.Bacteria are microscopic, relatively simple prokaryotic organism whose cells lacks a nucleus.They lack extensive complex internal membrane system.
.size range from 0.5 to 5 micrometer in length.
.large surface area to volume ratio so that the nutrients can easily and quickly reach all parts of the cell.It also allows rapid uptake and intracellular distribution of nutrients and excretion of wastes.
.The most important gene for prokaryote phylogeny is 16s ribosomal rRNA gene which is present in all cells. This gene is approximately 1500bp in length and possesses signature sequence.these sequences are conserved and found in the organism of one group but not in other groups. Based on these sequence Carl Woese split the kingdom monera in to eubacteria and archaea.
.Eubacteria are true bacteria possesses all characteristics of prokaryotes while archaea live in extreme environmental conditions and show some similarity with eukaryotes so can act as a connecting link between prokaryotes and eukaryotes.
#Bergey’s classification-
David Bergey, professor of bacteriology and his colleagues published a classification of bacteria that could be used for identification of bacterial species.
#Bergey’s manual of determinative bacteriology-provide identifying scheme for bacteria and archaea based on morphology ,differential staining and biochemical tests.
First edition of Bergey’s manual of systemic bacteriology mainly based on phenetic data published in four volumes-
Volume 1 issued in 1984, provides information about Gram-negative bacteria having medical and industrial importance.
Volume 2 issued in 1986 provides information about all Gram-positive bacteria other than actinomycetes.
Volume 3 issued in 1989 ,provide information about gram negative bacteria other than included under volume 1 and archaea.
Volume 4 issued in 1991 provide information about filamentous actinomycetes(gram positive bacteria).
All prokaryotes in this division in a single kingdom prokaryotiae divided in to 4 divisions –
1. Gracilicutes – thin skin, possess gram negative cell wall.
2. Firmicutes – thick and strong skin, possess gram positive cell wall.
3. Tenericutes – Soft or tender skin, lack cell wall represented by mycoplasmas.
4. Mendosicutes – Skin with faults, archaebacteria that lack conventional peptidoglycan.
#Bergey’s manual of systemic bacteriology-provides phylogenetic information on bacteria and archaea based on rRNA sequencing.
second edition consist of five volumes-
Volume1 issued in 2001
includes archaea, deeply branching and phototrophic bacteria.
Domain- Archaea
Phylum AI-Crenarchaeota
Thermophilic and hyper thermophilic sulphur metabolising prokaryotes.Single class thermoprotei ,3 orders and 5 families.Ex. Thermoproteus ,Sulfolobus.
Phylum A II:Euryarchaeota
methanogens and halophiles.Seven classes (Methanobacteria, Methanococci. Halobacteria, Thermoplasmata, Thermococci, Archeoglobi, and Methanopyri), 9orders, and 16families.
Ex. Methanobacterium, Methanococcus, Halobacterium, Thermococcus.
Domain- Bacteria
Phylum BI-Aquificae
The phylum contains autotrophic bacteria such as Aquifex and Hydrogenobacter that can use hydrogen for energy production. Aquifex (meaning “water maker”) actually produces water by using hydrogen to reduce oxygen.
Phylum BII-Thermotogae
This phylum is composed of one class and six genera. Thermotoga and other members of the class Thermotogae are anaerobic, thermophilic, fermentative, gram- negative bacteria that have unusual fatty acids and resemble Aquifex with respect to their ether linked lipids. Ex.Thermotoga, Geotoga, Fervidobacterium.
Phylum BIV-Dienococcus Thermus
The order Deinococcales contains bacteria that are extraordinarily radiation resistant. The genus Deinococcus stains gram positive. It has unique lipids and a high concentration of carotenoid pigments, which
may protect it from radiation.
Phylum BIll-Thermodesulfobacteria
one class (Thermodesulfobacteria) The bacteria are anaerobic, thermophilic, and sulfate-reducing.it includes only 2 genera Thermosulfobacterium and Thermodesulfatator.
Phylum BVI-Chloroflexi
The phylum Chloroflexi has one class and two orders. Many members of this gram-negative group are called green nonsulfur bacteria. Chloroflexus carries out anoxygenic photosynthesis and is a gliding bacterium; in contrast, Herpetosiphon is a nonphotosynthetic, respiratory gliding bacterium.Both genera have unusual peptidoglycans and lack lipopolysaccharides in their outer membranes.
The important genera are Chloroflexus, Oscillochloris, Herpetosiphon and Anaerolinea.
Phylum BVII-Thermomicrobia
The phylum contains one class (Thermomicrobia) and is represented by a single genus, Thermomicrobium. Thermomicrobium is an aerobic thermophilic chemotroph possessing unusual lipids that contain 1, 2-dialcohols instead of glycerol, and have neither ester nor ether linkages.
This is in contrast to the lipids of Bacteria and Eukarya that contain fatty acids esterified to glucose. Also, the cells of Thermomicrobium differ from those of Bacteria in that they lack peptidoglycan in their cell walls.
Phylum B VIII-Nitrospirae
The phylum consists of one class (Nitrospira) and genera like Nitrospira and Leptospirillum.
Phylum BIX-Deferribacteres
The phylum Deferribacteres contains one class (Deferribacteres) and genera such as Deferribacter, Denitrovibrio, etc.
Phylum BX-Cyanobacteria
The phylum Cyanobacteria consists of a single class (Cyanobacteria) divided into five subsections. The taxonomic position of the cyanobacteria is left open in Bergey s Manual. The cyanobacteria are oxygenic phototrophs and show a distant relationship to gram-positive bacteria.
These organisms were the first oxygen-evolving phototrophs on Earth and were responsible for the conversion of the anoxic atmosphere of our planet to oxic. Genera belonging to this phylum are mentioned as “form genus” in the Manual because the latter refers to a group of cyanobaceria with very characteristic morphology found worldwide but not all isolates of such a type may actually fit into the same genus.
The important “form genera” are Microcytis, Cyanocytis, Lyngbya, Oscillatoria, Spirulina, Anabaena, Nostoc, Scytonema, Calothrix, Tolypothrix, etc.
Phylum B XI-Chlorobi
Only one class (Chlorobia) constitutes the phylum. The representative genera are Chlorobium, Pelodictyon, Chlorobaculum, etc. This phylum accommodates anoxygenic photosynthetic bacteria known as the green sulfur bacteria, which can assimilate CO2 through the reductive (reverse) tricarboxylic acid cycle rather than calvin cycle and oxidize sulfide to sulfur granules that accumulate outside the cell.
Volume 2 issued in 2005
Includes proteobacteria have three parts-
Part1-introductory essays.
Part2-gamma proteobacteria.
Part3-alpha proteobacteria, beta proteobacteria, delta proteobacteria and epsilon proteobacteria.
The phylum Proteobacteria consists of five classes (Alfaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria).
Alphaproteobacteria (∝-proteobacteria) consist of the most bacteria that are capable of growing at low nutrient levels (i.e., oligotrophic forms); the representative genera of this class are Rhodospirillum, Azospirillum, Rickettsia, Rhizobium, Agrobacterium, Nitrobacter, Hyphomicrobium, Methylobacterium, etc.
Betaproteobacteria (β-proteobacteria) utilize the substances that diffuse from organic decomposition in the anaerobic zone of their habitats. Some of its genera are pathogenic.
The important genera included in betaprotobacteria are Thermothrix, Bordetella, Leptothrix, Neissaria, Aquaspirillum, Nitrosomonas, Gallionella, Spirillum, etc.
Gammaproteobacteria (γ-proteobacteria) are chemoorganotrophic, facultative anaerobic, and the representative genera are Chromatium, Xanthomonas, Beggiatoa, Pseudomonas, Vibrio, Photobacterium, Escherichia, Klebsiella, Erwinia, etc.
Deltaproteobacteria (δ-proteobacteria) can mainly be categorized as of three groups.
Many of the deltaproteobacteia are anaerobic and cause desulfurication (generate sulfide from sulfate and sulfur); representative genera of such bacteria are Desulfovibrio, Deslfuromonas, Desulfobaca, etc. Some deltaproteobacteria (e.g., Bdellovibrio, Bacteriovorax) are predators on other bacteria.
Representatives such as Myxococcus, Polyangium and Chondromyces are the deltaproteobacteria that form fruiting bodies and also prey on other bacteria.
Epsilonproteobacteria (Ɛ- proteobacteria) is a small class and its members like Helicobacter and Campylobacter are important human pathogens causing intestinal infections.
Volume3- the low G+C gram positive bacteria
Phylum B XIII-Firmicutes
Most of the bacteria of this phylum are heterotroptic. Though mycoplasmas lack cell wall and stain gram-negative, they are classified under this phylum because of their close relationship to low G + C gram-positive bacteria.Three classes, Clostridia, Mollicutes, and Bacilli.
Class -Clostridia
This class contains three orders and 11 families. Although they vary in morphology and size, the members tend to be anaerobic. Genera such as Clostridium, Desulfotomaculum, and Sporohalobacter form true bacterial endospores; many others do not. Clostridium is one of the largest bacterial genera.
Class-mollicutes
It contains five orders and six families. Members of the class often are called mycoplasmas. These bacteria lack cell walls and cannot make peptidoglycan or its precursors. They are normally nonmotile and stain gram negative because of the absence of a cell wall. In contrast with almost all other bacteria, most species require sterols for growth.Ex. Mycoplasma and Spiroplasma
Class- Bacilli
This large class comprises a wide variety of gram-positive, aerobic or facultatively anaerobic, rods and cocci. The class Bacilli has two orders, Bacillales and Lactobacillales, and 17 families. As with the members of the class Clostridia, some genera (e.g., Bacillus, Sporosarcina, Paenibacillus, and Sporolactobacillus) form true endospores. The class contains many medically and industrially important genera: Bacillus, Lactobacillus, Streptococcus, Lactococcus, Enterococcus, Listeria, and Staphylococcus.
Volume4- the high G+C gram positive bacteria
Phylum B XIV-Actinobacteria
There is enormous morphological variety among these procaryotes. Some are cocci, others are regular or irregular rods. High G+C gram positives called actinomycetes often form complex branching filaments called hyphae. Although none of these bacteria produce true endospores, many genera form asexual spores and some have complex life cycles. Mycobacteria produce large mycolic acids that distinguish their cell walls from those of other bacteria.
single class Actinobacteria ,five subclasses, six orders, forteen suborders, forty four families, and many a number of genera.
Ex. Actinomyces, Corynebacterium, Mycobacterium, Nocardia, Actinoplanes, Propionibacterium, Streptomyces, Frankia.
Volume5-The Planctomycetes, Spirochaetes, Fibrobacteres, Bacteroidetes, Fusobacteria, Chlamydiae, Acidobacteria, Verrumicrobia, and Dictyoglomus
Phylum B XV-Planctomycetes
The planctomycetes are related to the chlamydias according to their rRNA sequences. The phylum contains only one order, one family, and four genera. Planctomycetes lack peptidoglycan. They divide by budding and may produce nonprosthecate appendages called stalks. Planctomycetes grow in aquatic habitats, and move by flagella or gliding motility.
Phylum B XVI-Chlamydiae
This small phylum contains one class, one order, and four families. Chlamydia are obligate intracellular parasites with a unique life cycle involving two distinctive stages: elementary bodies and reticulate bodies. Chlamydias are important pathogens and cause many human diseases
Phylum B XVII-Spirochaetes
This phylum contains helically shaped, motile, gram-negative bacteria. These chemoheterotrophs can be free living, symbiotic, or parasitic.Ex. Treponema and Borrelia contain several important human pathogens. The phylum has one class, Spirochaetes, three families, and 13 genera.
Phylum B XVIII-Bacteroidetes
This phylum has three classes (Bacteroides, Flavobacteria, and Sphingobacteria), three orders, and 12 families. Ex.Bacteroides, Flavobacterium, Flexibacter, and Cytophaga.
Bacterial classification is based on different criteria-
A.Cell morphology
Bacterial species are differentiated based on their shapes. They have different cell structure-
a) Bacillus (stick or filament or rod like shape)- Among them if a bacterium is
Single cell then it is bacillus, if more it is bacilli like
Two celled: Diplobacilli, four celled – tetrad etc.
Palisade: Here two cells of bacillus are arranged side by side like sticks in match box
Streptobacilli: Bacilli bacteria arranged like a chain.
b) Coccus (These are spherical or oval shaped)- Of them
# Single-celled is called Monococcus,
#Two celled: Diplococci,
# Chain like arrangement: Streptococci.
# Bunch of grapes like: Staphylococci.
c) Comma shaped bacteria, Ex: Vibrio cholera bacteria causing cholera.
d) Spiral bacteria: They are also called as spirochetes. These are spiral or hair like in shape and hence called as spiral shaped bacteria. Ex: Campylobacter jejuni
Most bacteria maintain a single shape called monomorphic.while some bacteria like corynebacterium have many shapes and lack a single characteristic shape.these bacteria are called pleomorphic.
B.Presence of flagella
Based on the number and location of flagella bacterial classification is done as below-
#Atrichous bacteria: With no flagella on the bacterial cell wall. These are non-motile bacteria.
#Monotrichous bacteria: With one single flagella.
#Amphitrichous bacteria: Two flagella on both sides of cell.
#Polytrichous bacteria: Many flagella at different points.
#Lophotrichous bacteria: Flagella at one pole or point of the cell.
#Peritrichous bacteria.: The flagella are present all over the cell wall.
C.Nutritional requirements
Bacteria classified based on their mode of nutrition-
#Photoautotrophs: These are bacteria which prepare their own food. Due to presence of chlorophyll like pigment they perform photosynthesis. They do this by using sun-light as source of energy. Besides they take up CO2 and water from nature.Ex: Chlorella.
#Chemoautotrophs: These are bacteria synthesize their own food by use of energy obtained from chemical sources. They differ from photoautotrophs in that they do not need sunlight.
#Heterotrophs: These are bacteria which do not synthesize their own food but obtain it from others They can feed on food materials like animals do.
#Symbiotic bacteria: These are bacteria which obtain food by living together with other organisms. They reside in mutual beneficial support with others.
Ex: Rhizobium bacteria in leguminous plants.
#Saprophytic bacteria: These are bacteria survive by eating rotten material. They get their nutrition by consuming dead and decaying material. Thus there by help in cleaning the environment from accumulation of waste.
#Pathogenic bacteria: (patho+genisis =disease + causing) These are bacteria responsible for diseases in humans and plants. They grow only in the body of other animals or plants. They get their nutrition from the host. In doing so, they consume the vital living elements in them and induce diseases.
D.temperature dependence
Bacteria can at cold temperature and even hot temperatures besides normal room temperatures. So, they are classified based on the temperature they can survive at.
#Thermophilic (thermo+phyllic=temperature loving); Thermophylic bacteria are those which can survive at high temperature of 45 to 60 degree temperature.
# Mesothermic (medium+thermic= medium temperature) can survive at 25 to 45 degrees
#Hypoctermic (hypo = low ) These bacteria survive at low temperatures like 8 degree or even less.
In common most bacteria survive in between 25 to 45 degree i.e. they are mesotherms.
E.oxygen requirement
Aerobic: Which require oxygen to survive.
Anaerobic bacteria: These bacteria do not require oxygen for survival. They are further as two types
Obligate anaerobes: They survive in absence of oxygen. But when exposed to oxygen they die.
Facultative anaerobes: These also survive in environments without oxygen but when exposed to oxygen they can survive.
F.Staining
1.gram staining; The Gram stain procedure distinguishes between Gram positive and Gram negative groups by coloring these cells red or violet. Gram positive bacteria stain violet due to the presence of a thick layer of peptidoglycan in their cell walls, which retains the crystal violet these cells are stained with. Alternatively, Gram negative bacteria stain red, which is attributed to a thinner peptidoglycan wall, which does not retain the crystal violet during the decoloring process.
Acid fast staining; it is a differential stain identify acid fast organism such as members of genus mycobacterium involves heating of bacteria with a mixture of basic fuschin and phenol.Carbol Fuchsin stains every cell. When they are destained with acid-alcohol, only non-acid-fast bacteria get destained since they do not have a thick, waxy lipid layer like acid-fast bacteria. When counter stain is applied, non-acid-fast bacteria pick it up and become blue (methylene blue) or green (malachite green) when viewed under the microscope. Acid-fast bacteria retain Carbol Fuchsin so they appear red.