A Sequence-Based Map of Biodiversity

Before the development of sequence-based methods, it was impossible to know the evolutionary relationships connecting all of life and thereby to draw a universal evolutionary tree.

Whittaker, in 1969, just as the molecular methods began to develop, summarized evolutionary thought in the context of the "Five Kingdoms" of life: animals, plants, fungi, protists ("protozoa"), and monera (bacteria). There also was recognized a higher, seemingly more fundamental taxonomic distinction between eukaryotes, organisms that contain nuclear membranes, and prokaryotes, predecessors of eukaryotes that lack nuclear membranes .

These two categories of organisms were considered independent and coherent relatedness groups. The main evolutionary diversity of life on Earth, four of the five traditional taxonomic kingdoms, was thought to lie among the eukaryotes, particularly the multicellular forms.

The breakthrough that called to question many previous beliefs and brought order to microbial, indeed biological, diversity emerged with the determination of molecular sequences and the concept that sequences could be used to relate organisms .

The incisive formulation was reached by Carl Woese who, by comparison of ribosomal RNA (rRNA) sequences, established a molecular sequence-based phylogenetic tree that could be used to relate all organisms and reconstruct the history of life .

Woese articulated the now-recognized three primary lines of evolutionary descent, termed "urkingdoms" or "domains": Eucarya (eukaryotes), Bacteria (initially called eubacteria), and Archaea (initially called archaebacteria)

Microbial Diversity

The History & Scope of Microbiology :

1) Members of the Microbial World :-

Study of the object less than one millimeter in diameter cannot be seen clearly and must be examined under microscope .

UNIVERSAL PHYLOGENETIC TREE

What comes in Microbiology : Topics

Microbial Diversity
Bacteriology & Virology
Mycology & Phycology
Microbial Technique
Microbial Genetics
Microbial Physiology
Immunology
Bioinformatics & Statics
Molecular Microbiology
Recombinant DNA Technology
Environmental Microbiology
Food Microbiology
Medical Microbiology
Agriculture Microbiology
Industrial Microbiology
Fermentation Technology
Pharmacology

Microorganism

ARCHEA

EUCARYOTES

EUBACTERIA

some more branches of microbiology

-	Environmental Microbiology
-	Food Microbiology
-	Industrial Microbiology
-	Medical Microbiology
-	Veterinary Microbiology General Microbiology

Fields in Microbiology

The field of microbiology can be generally divided into several subdisciplines:

• Microbial physiology: The study of how the microbial cell functions biochemically. Includes the study of microbial growth, microbial metabolism and microbial cell structure.
• Microbial genetics: The study of how genes are organized and regulated in microbes in relation to their cellular functions. Closely related to the field of molecular biology.
• Cellular microbiology: A discipline bridging microbiology and cell biology.
• Medical microbiology: The study of the pathogenic microbes and the role of microbes in human illness. Includes the study of microbial pathogenesis and epidemiology and is related to the study of disease pathology and immunology.
• Veterinary microbiology: The study of the role in microbes in veterinary medicine or animal taxonomy.
• Environmental microbiology: The study of the function and diversity of microbes in their natural environments. Includes the study of microbial ecology, microbially-mediated nutrient cycling, geomicrobiology, microbial diversity and bioremediation. Characterisation of key bacterial habitats such as the rhizosphere and phyllosphere, soil and groundwater ecosystems, open oceans or extreme environments (extremophiles).
• Evolutionary microbiology: The study of the evolution of microbes. Includes the study of bacterial systematics and taxonomy.
• Industrial microbiology: The exploitation of microbes for use in industrial processes. Examples include industrial fermentation and wastewater treatment. Closely linked to the biotechnology industry. This field also includes brewing, an important application of microbiology.
• Aeromicrobiology: The study of airborne microorganisms.
• Food microbiology: The study of microorganisms causing food spoilage and foodborne illness. Using microorganisms to produce foods, for example by fermentation.
• Pharmaceutical microbiology: the study of microorganisms causing pharmaceutical contamination and spoil

About Microbiology

Microbiology (from Greek μῑκρος, mīkros, "small"; βίος, bios, "life"; and -λογία, -logia) is the study of microorganisms, which are unicellular or cell-cluster microscopic organisms. This includes eukaryotes such as fungi and protists, and prokaryotes. Viruses, though not strictly classed as living organisms, are also studied. In short; microbiology refers to the study of life and organisms that are too small to be seen with the naked eye.

Microbiology is a broad term which includes virology, mycology, parasitology, bacteriology and other branches. A microbiologist is a specialist in microbiology.

Microbiology is researched actively, and the field is advancing continually. We have probably only studied about one percent of all of the microbe species on Earth. Although microbes were directly observed over three hundred years ago, the field of microbiology can be said to be in its infancy relative to older biological disciplines such as zoology and botany.

TABLE OF CONTENT

• PLANT VIRUSES

• Plant viruses are also known as "PHYTOPHAGINAE". They are usually rod shaped. They contain nucleic acid in the form of RNA. They attack only plants. They are harmless to all other organisms. The plant viruses multiply within living cells but some may be able to reside within the bodies of aphides and nematodes. Some of the examples are:- TMV, CaMV etc.

  Plant viruses enters cells through wounds made mechanically or by vectors or by deposition on to an ovule by an infected pollen grain.

  ROUTE OF INFECTION

  1) VEGETATIVE PROPAGATION: Whenever plants are propagated vegetatively by budding or grafting, any virus present in the mother plant from which these organs are taken almost always will be transmitted to the progeny. such transmission is common in almost all fruit, many ornamental trees and shrubs, field crops like potatoes etc. 2) THROUGH SAP: It implies direct transfer of sap by contact of an wounded plant with a healthy one. Such process occurs during agricultural practices by tools, hands, or by animal feeding on the plant. generally TMV, potato viruses and cucumber mosaic viruses are transmitted via sap.

  3) TRANSMISSION THROUGH SEED: More than 110 viruses are transmitted via seeds. Infected seeds are produced by the fertilization of healthy ovule by infected pollen. The viruses then reside in the integument of seed

  and infects seedling as they germinate. viruses transmitted by pollen results in reduction of fruit yield.

  4) TRANSMISSION THROUGH INSECTS: The most common means of viral transmission is by insect vectors. These include the members of order-Homoptera (Aphides, leaf hoppers, white flies, plant hoppers, tree hoppers.), Order- Hemiptera( tree bugs) & Order- Coleoptera( bettles).

  
  ANIMAL VIRUSES

• The animal viruses are also called as Zoophaginae. They are generally poly hedral or spherical in shape. They contain nucleic acid in the form of either DNA or RNA.

  There are at present 20 recognized families of viruses that contain viruses of humans or animals.

  Pappiloma Virus

  Herpes Virus

  Historically, properties used most often in classification derive from electron microscopic examination e.g. virion morphology, structure and dimensions, and presence or absence of an envelope.

  Additional characterization is supplied by the type and nature of the genomic nucleic acid.

  Examples- rabbies, dog distemper virus, HIV etc
  

  GENERAL CHARACTERISTICS:

  • Attachment sites are plasma membrane proteins and glycoproteins.
  • Capsid enters by endocytosis or fusion.
  • Uncoating-Enzymatic removal of capsid proteins.
  • Biosynthesis (Eclipse)-In nucleus (DNA viruses) or cytoplasm (R.NA viruses).
  • Chronic infection-Latency; slow viral infections; cancer.
  • Release-Enveloped viruses bud out; non-enveloped viruses rupture plasma membrane.
  • 
    
  BACTERIOPHAGES

• Bacteriophages (phages) are viruses that infect bacteria. Typical phages have hollow heads (where the phage DNA or RNA is stored) and tunnel tails, the tips of which have the ability to bind to specific molecules on the surface of their target bacteria.

  Several bacteriophages are used as cloning vectors, the most commonly used E.coli phages being lambda & M13 phages. plasmid vectors have to be introduced into the bacterial cells, which are then cloned and selected for the recovery of recombinant DNA.In contrast, the phage vectors are directly tested on an appropriate bacterial lawn.( a continuous bacterial growth on an agar plate) where each phage particle forms a plaque.( a clear bacteria free zone in the bacterial lawn).

  The viral DNA is then injected through the tail into the host cell, where it directs the production of progeny phages often over a hundred in half an hour. These "young" phages burst from the host cell (killing it) and infect more bacteria.

• 
  
  VIROIDS
• Structure:
  Viroids are infectious agents composed exclusively of a single piece of circular single stranded RNA which has some double-stranded regions.
  Because of their simplified structures both prions and viroids are sometimes called subviral particles. Viroids mainly cause plant diseases but have recently been reported to cause a human disease.

  Catalytic RNAs are those that have the intrinsic ability to break and form covalent bonds; Viroids are catalytic RNA's (ribozymes) that cleave RNA to produce fragments containing a 5'-hydroxyl and a 2', 3'-cyclic phosphate.

  This is a nonhydrolytic reaction in which the same number of phosphodiester bonds are maintained and the transesterification reaction is theoretically reversible. This reaction is considered to play an essential role in the replication of these RNAs in vivo. Such reactions are all intramolecular and hence quasi-catalytic with single turnover. These RNAs can be manipulated, however, to provide true catalytic cleavage in trans-reactions.
  
  
  Replication:

  Circular, pathogenic RNAs are replicated by a rolling circle mechanism in vivo. There are two variations of this rolling circle mechanism:

  In the first variation (A), the circular plus strand is copied by viroid RNA-dependent RNA polymerase to form a concatameric minus strand (step 2). Site-specific cleavage (arrows) of this strand produces a monomer that is circularized by a host RNA ligase (step 3) and then copied by the RNA polymerase to produce a concatameric plus strand. Cleavage of this strand (step 5) produces monomers which, on circularization, produces the progeny circular, plus RNA, the dominant form in vivo.

  In the other variation (B), the concatameric minus strand of step 1 is not cleaved but is copied directly to give a concatameric plus strand (step 3), which is cleared specifically to monomers for ligation to the circular progeny. Those RNAs that self-cleave only in the plus strand in vitro are considered to follow this route.

  The hepatitis D viroid genome is a minus strand that gives rise to two RNA species. One of these is a mRNA for the delta antigen and the other is a complete complimentary copy (plus strand or anti-genome). The anti-genome acts as a template to make more minus strands. The minus strand self-cleaves and self-ligates. HDV replication takes place in the nucleus but delta antigen is made in the cytoplasm. The delta antigen is the only protein made by the HDV mRNA. It has a +12 charge at physiologic pH, accumulates in the nucleus and binds to minus strand RNA as a dimer. The delta antigen is necessary for viroid assembly but its exact mode of action is unknown.

  Human pathologies induced by viroids:

  The only human disease known to be caused by a viroid is hepatitis D. This disease was previously ascribed to a defective virus called the delta agent. However, it now is known that the delta agent is a viroid enclosed in a hepatitis B virus capsid. For hepatitis D to occur there must be simultaneous infection of a cell with both the hepatitis B virus and the hepatitis D viroid. There is extensive sequence complementarity between the hepatitis D viroid RNA and human liver cell 7S RNA, a small cytoplasmic RNA that is a component of the signal recognition particle, the structure involved in the translocation of secretory and membrane-associated particles. The hepatitis D viroid causes liver cell death via sequestering this 7S RNA and/or cleaving it.

  Transmission:
  The hepatitis D viroid can only enter a human liver cell if it is enclosed in a capsid that contains a binding protein. It obtains this from the hepatitis B virus. The delta agent then enters the blood stream and can be transmitted via blood or serum transfusions.

  
  PRIONS

• A prion — short for proteinaceous infectious particle that lacks nucleic acid (by analogy to virion) — is a type of infectious agent made only of protein. Prions are believed to infect and propagate by refolding abnormally into a structure which is able to convert normal molecules of the protein into the abnormally structured form. However, the term in itself does not preclude other mechanisms of transmission.

  Prions are generally quite resistant to denaturation by protease, heat, radiation, and formalin treatments,although potency or infectivity can be reduced. Ozone sterilization is currently being studied as a potential method for prion deactivation.
  Although genetic research may shed light on prions, and there is a genetic component to many prion diseases, prion diseases are not exclusively genetic diseases and are grouped as transmissible spongiform encephalopathies.

  Diseases as varied as fatal familial insomnia and kuru (translated as "to tremble with fear") are believed to be associated with prions. Other prion diseases include scrapie (a disease of sheep), chronic wasting disease, (in deer and elk), variant Creutzfeldt-Jakob disease (vCJD), and bovine spongiform encephalopathy (BSE or mad cow disease), all caused by similar proteins in different species It should be noted that the same gene is responsible for spongiform encephalopathies which are not known to be transmissible, as well as some non-neurological diseases.
  

  Some require a mutation for transmission to occur, and there are respective mutations which can prevent transmission for most of the TSEs. Whether or not the prion gene has a non-disease function is an area of considerable active research. All of these diseases affect the structure of the brain or other neural tissue, and all are untreatable and fatal. However, a vaccine has been developed in mice that may provide insight into providing a vaccine in humans to resist prion infections.
  Proteins showing prion behaviour are also found in some fungi. Some fungal prions may not be associated with any disease; it is unknown whether these prions represent an evolutionary advantage for their hosts. All known prions are believed to infect and propagate by formation of an amyloid fold, in which the protein polymerizes into a fiber with a core consisting of tightly packed beta sheets. Other mechanisms may exist in yet undiscovered infectious protein particles.

  Prions in human disease:
  There are four principal disease syndromes associated with prions in humans:

  Creutzfeldt-Jakob Disease (CJD),

  Creutzfeldt-Jakob Disease (vCJD),

  Kuru and

  Fatal Familial Insomnia.

  Genetic engineering research:

  On 31 December 2006, Hematech, a biotechnology company based in Sioux Falls, South Dakota, announced that it had genetically engineered cattle lacking a necessary gene for prion production - thus theoretically making them immune to BSE.Research with mice had previously indicated that animals lacking endogenous prion protein are resistant to infection by scrapie prion protein.
  

GENERAL
CHARACTERISTICS

• They
  are ultramicroscopic in size
• they
  do not have a cell wall
• they
  do not have cellular organization
• they
  cannot survive or reproduce outside the host cell
• they
  are obligatory intracellular parasites
• they
  contain either DNA or RNA but never both
• there
  is no protein synthesis machinery

• they do not grow
  but replicate
• they can pass
  through bacterial filters
• they can be
  crystallized

LIVING CHARACTERS

• They contain either DNA or RNA as genetic material.
• They undergo mutations
• they are capable of multiplication.
• they are parasites and show very high host specificity
• they can be transmitted from one host to another.
• they react to heat, radiation and chemicals.
• they are ultramicroscopic disease producing entities.

NON LIVING CHARACTERS

• They can be crystallized
• They are inert outside the host.
• They do not posses cell wall
• They do not posses cellular machinery
• They are unaffected by antimicrobial antibiotics.
• They do not have energy producing enzyme systems

Virus

The term virus has been derived from latin word
"virion" means "poisonious fluid".

A Russian botanist
D.J.Ivanovasky in the year 1892 discovered these unidentified
organisms. In the year 1898 a Dutch microbiologist M.W.Beijerink
called them as contagium vivum fluidum i.e. living infectious fluid.
For the first time the term virus was used by Louis Pasteur.
These are submicroscopic entities ranging in size from about 20
microns to 50 microns. they are about 50 times smaller than
bacteria.

Microbiology

Microbiology is the study of micro organisms, which are unicellular or cell-cluster microscopic organisms. This includes eukaryotes such as fungi and protists, and prokaryotes such as bacteria and certain algaes. Viruses, though not strictly classed as living organisms, are also studied. People that study the field of microbiology are known as microbiologists.Although much is now known in the field of microbiology, advances are being made regularly. The most common estimates suggest that we have studied only about 1% of all of the microbes in any given environment. Thus, despite the fact that over three hundred years have passed since the discovery of microbes, the field of microbiology is clearly in its infancy relative to other biological disciplines such as zoology, botany and entomology. The major factor limiting widespread use of transgenic animals in agricultural production systems is the relatively inefficient rate (success rate less than 10 percent) of production of transgenic animals.

Definition of Koch's postulates

Koch's postulates: In 1890 the German physician and bacteriologist Robert Koch set out his celebrated criteria for judging whether a given bacteria is the cause of a given disease. Koch's criteria brought some much-needed scientific clarity to what was then a very confused field.
Koch's postulates are as follows:

• The bacteria must be present in every case of the disease.
• The bacteria must be isolated from the host with the disease and grown in pure culture.
• The specific disease must be reproduced when a pure culture of the bacteria is inoculated into a healthy susceptible host.
• The bacteria must be recoverable from the experimentally infected host.
However, Koch's postulates have their limitations and so may not always be the last word. They may not hold if:
• The particular bacteria (such as the one that causes leprosy) cannot be "grown in pure culture" in the laboratory.
• There is no animal model of infection with that particular bacteria.
A harmless bacteria may cause disease if:
• It has acquired extra virulence factors making it pathogenic.
• It gains access to deep tissues via trauma, surgery, an IV line, etc.
• It infects an immunocompromised patient.
• Not all people infected by a bacteria may develop disease-subclinical infection is usually more common than clinically obvious infection.
Despite such limitations, Koch's postulates are still a useful benchmark in judging whether there is a cause-and-effect relationship between a bacteria (or any other type of microorganism) and a clinical disease.