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13: Bacteria

Introduction

Bacteria, single-celled organisms visible only through a microscope(microscopic).Bacteria lack a true nucleus, and internal structures and are therefore ranked among the unicellular life-forms called prokaryotes. Bacteria inhabit virtually all environments, including soil, water, organic matter, and the bodies of multicellular animals.

Systematic position of bacteria

All life forms are classified as either prokaryotes or eukaryotes. Prokaryotes are simple, single-celled organisms like bacteria. They lack a defined nucleus of the sort found in plant and animal cells. More complex organisms, including all plants and animals, whose cells have a nucleus, belong to the group called eukaryotes.

  • Haeckel (1866) was the first to create a natural Kingdom for the microorganisms, placed all unicellular (microscopic) organisms in a new kingdom, Protista, separated from plants (Plantae) and animals (Animalia), which were multicellular (macroscopic) organisms.
  • After the development of the electron microscope in the 1950s, there is addition of fourth kingdom, Monera (or Moneres), the prokaryotes (also called Prokaryotae). Protista remained as a kingdom of unicellular eukaryotic microorganisms.
  • 1967 Whittaker identified Fungi as a separate multicellular eukaryotic kingdom of organisms (distinguished by their absorptive mode of nutrition). All life on earth divided into 5 kingdoms -Monera, Protista, Fungi, Plantae, and Animalia.
  • Woese (1980s) began phylogenetic analysis of all forms of cellular life based on comparative sequencing of the small subunit ribosomal RNA that is contained in all organisms.Because rRNA shows relatively little variation from one generation to the next, it proved to be an excellent tool for determining evolutionary relationships.
  • Thus, Woese defined the three cellular domains of life on the basis of Molecular phylogeny : Eucarya, Bacteria and Archaea.

 

  • The phylogenetic tree indicates that Archaea are more closely related to Eukarya than are Bacteria.
  • Although the definitive difference between Woeses Archaea and Bacteria is based on fundamental differences in the nucleotide base sequence in the 16S ribosomal RNA, there are many biochemical and phenotypic differences between the two groups of prokaryotes.
  • Bacteria (formerly known as eubacteria) and Archaea (formerly called archaebacteria) share the prokaryotic type of cellular configuration, but otherwise are not related to one another any more closely than they are to the eukaryotic domain, Eukarya.

lassification of bacteria:-Sequence analysis of macromolecules such as the small subunit ribosomal RNA found in all cells has allowed bacteriologists to classify bacteria into a typical hierarchal scheme based on genetic relatedness. The current edition (2001) of Bergey's Manual of Systematic Bacteriology has established 24 phyla of bacteria, systematically ordered into class, order, family, genus and species.Bergey's Manual describes affiliated groups of Bacteria based on a few easily observed microscopic and physiologic characteristics. Further identification requires biochemical tests which will distinguish genera among families and species among genera. For example, E. coli is in the

 

Species:- A collection of bacterial cells which share an overall similar pattern of traits in contrast to other bacteria whose pattern differs significantly.

Binomial nomenclature :- Genus and species :-Escherichia coli (E.coli) - Genus name is always capitalized. Species name is never capitalized example coli Both names are always either italicised when printed or underlined when handwritten.

Recognized Phyla of the Domain Bacteria
Phyla Phyla Phyla Phyla Phyla Phyla
Acidobacteria Actinobacteria Aquificae Bacteroidetes Chlamydiae Chlorobi
Chloroflexi Chrysiogenetes Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi .
Fibrobacteres Firmicutes Fusobacteria Gemmatimonadetes Nitrospirae Planctomycetes
Proteobacteria Spirochaetes Thermodesulfobacteria Thermomicrobia Thermotogae Verrucomicrobia

Shape and Size of bacteria

Bacteria typically have one of three shapes: Cocci (spheres), Bacilli (rods) or Spirilla(spiral).

An average coccus is about 0.5-1.0 micrometer (m) in diameter. (A micrometer equals 1/1,000,000 of a meter.)

The average bacterial cell has dimensions of nearly 0.5 to 1.0 m by 2.0 to 5.0 m.But Epulopiscium fishelsoni, a bacillus-shaped bacterium that is typically 80 micrometers (m) in diameter and 200-600 m long, and Thiomargarita namibiensis, a sperical bacterium between 100 and 750 m in diameter.

The Structure of the Bacterial Cell

Bacterial (Prokaryotic) cells consists of three regions -

  • Appendages (proteins attached to the cell surface) in the form of flagella and pili
  • A cell envelope consisting of a capsule, cell wall and plasma membrane
  • A cytoplasmic region that contains the cell genome (DNA) and ribosomes and various sorts of inclusions.

Bacterial cell structures may be divided into two groups-

  1. External Structures :-Those external to the cell proper.

Flagella or organs of locomotion :- Flagellae (singular -flagellum) are long filamentous protein structures located in or just inside the cell wall. Basically, the flagellar apparatus consists of a basal body, a hook-like structure and a flagellar filament. The flagellar filament is rotated by a motor apparatus in the plasma membrane allowing the cell to swim in fluid environments. Bacterial flagella are powered by proton motive force or chemiosmotic potential established on the bacterial membrane, rather than ATP hydrolysis, which powers eukaryotic flagella. About half of the rod-shaped (bacilli) and all of the spiral and curved bacteria are motile by means of flagella.Bacteria exhibit a variety of tactic behaviour (the ability to move or swim) in response to environmental stimuli. During chemotaxis, a bacterium can sense the quality and quantity of certain chemicals in its environment. They swim towards the chemicals, if they are useful nutrients or turn away from them, if they are harmful substances. Other types of tactic response in prokaryotes include phototaxis (movement in response to light), aerotaxis (movement in response to air-flow), and magnetotaxis (movement in response to magnetic field).

Fimbriae (singular fimbria) or pili (singular pilus) Fimbriae or pili are interchangeable terms used to designate short, hair-like protein structures on the surfaces of bacterial cells. They are shorter and stiffer than flagella. Fimbriae are very common in Gram-negative bacteria, but occur in some archaea and Gram-positive bacteria. Fimbriae are responsible in adherence of bacteria to surfaces, substrates and other cells or tissues in nature. A specialized type of pilus, the F or sex pilus, mediates the transfer of DNA between mating bacteria during the process of conjugation e.g. in E.coli.

Cell envelope :-The cell protoplasm (cytoplasm) is protected by the plasma membrane, a cell wall and a capsule.

 

Capsules:-Most bacteria contain some sort of a polysaccharide layer outside of the cell wall or outer membrane. In some bacteria, a loose structure or matrix is formed, which embed the cells and is a called a slime layer or a biofilm. The thin layer of tangled polysaccharide is also called as glycocalyx. Bacteria may also have an additional proteinaceous coat called an S-layer.The capsule exhibits several functions, including

  • protection of bacterial cells from engulfment by predatory protozoa or phagocytes
  • protection against the attack by antimicrobial agents of plant or animal origin,
  • protection of cells from perennial effects of drying or desiccation
  • acts as a reserve of carbohydrate for metabolism.

Cell wall :- The cell wall is an essential structure that protects the delicate cell protoplast from mechanical damage and osmotic rupture. The cell wall of bacteria consists of a polymer of disaccharides cross-linked by short chains of amino acids (peptides). This molecule is a type of peptidoglycan, which is called murein,which is unique in nature to bacterial cell walls.Based on the properties of their cell wall, the bacteria are categorized as :-

  • Gram-positive cells :- Consists of
    1. A thick, homogenous sheath of peptidoglycan 20 - 80 nm thick
    2. Tightly bound acidic polysaccharides, including teichoic acid and lipoteichoic acid
    3. Retains purple crystal violet dye when subjected to the Gram-staining procedure.

  • Gram-negative cells :-Consists of
  1. In the Gram-negative bacteria the cell wall is relatively thin(10 nanometers) .
  2. An outer membrane containing a unique component lipopolysaccharide (LPS or endotoxin), which is toxic to animals..
  3. Loses crystal violet-iodine complex when cells are exposed alcohol (decolorization step) and stains red with safranin counterstain. The assembly of peptidoglycan on the outside of the plasma membrane is mediated by a group of periplasmic enzymes, which are transglycosylases, transpeptidases and carboxypeptidases.The major shape determining protein is MreB which forms an actin-like cytoskeleton in bacteria and archea.
  4. Bacteria without cell walls :-A group of bacteria called Mycoplasma exist without a cell wall.
  5. Bacteria with chemically unique cell walls :- Acid Fasts bacteria- Mycobacterium species cell walls made of unique waxy layer called mycolic acid contain 60% lipids and Gram positive.

Plasma membrane or Cytoplasmic membrane:-The plasma membrane of the bacterial cell lies on the inner surface of the cell wall, separating it from the cell cytoplasm (or protoplasm). Plasma membrane consist of 40 percent phospholipids and 60 percent proteins. The phospholipids are amphoteric molecules, meaning they have a water-soluble hydrophilic region (the glycerol "head") attached to two insoluble hydrophobic fatty acid "tails" via an ester bond. The arrangement of proteins and lipids to form a bilayer in aqueous environments is represented in the fluid mosaic model. In bacteria, the plasma membrane invaginates into the cytoplasm and forms stack or vesicles attached to the inner membrane surface. These structures are called as mesosomes.The membranes of bacteria are structurally similar to the cell membranes of eucaryotes, except that bacterial membranes consist of saturated or monounsaturated fatty acids (rarely polyunsaturated fatty acids) and do not normally contain sterols.Functions of the bacterial plasma membrane

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  • Osmotic or permeability barrier.
  • Location of transport systems for specific solutes (nutrients and ions).
  • Energy generating functions, involving respiratory and photosynthetic electron transport systems, establishment of proton motive force, and ATP-synthesizing ATPase.
  • Synthesis of membrane lipids (including lipopolysaccharide in Gram-negative cells) Coordination of DNA replication and segregation with septum formation and cell division. >
  • Location of specialized enzyme systems, such as for CO2 fixation, nitrogen fixation.
  1. Internal structures :-Those which occur within the cell.  

Cytoplasm :- Contrary to eukaryotes, the cytoplasm of bacteria does not exhibit streaming.The cytoplasm of procaryotes is more gel-like than that of eucaryotes.The cytoplasmic constituents of bacterial cells invariably include the procaryotic chromosome (nucleoid), ribosomes, and several hundred proteins and enzymes.

  • Ribosomes:-The distinct granular appearance of prokaryotic cytoplasm is due to the presence and distribution of ribosomes. The ribosomes of prokaryotes are smaller than cytoplasmic ribosomes of eukaryotes. Procaryotic ribosomes are 70S in size, being composed of 30S and 50S subunits. Ribosomes are involved in the process of translation (protein synthesis), similar to that of eukaryotic ribosomes but they significantly differ in structure. Ribosomes are also important in the identification of bacteria, as the nucleic acid sequences that code for the ribosomal RNAs are often unique to the bacterial cell type and used for phylogenetic analysis.
  • Nucleoid :-The chromosome is typically one large circular molecule of DNA, more or less free in the cytoplasm. Procaryotes sometimes possess smaller extrachromosomal pieces of DNA called plasmids. The total DNA content of a procaryote is referred to as the cell genome. The cell chromosome is the genetic control center of the cell which determines all the properties and functions of the bacterium. During cell growth and division, the prokaryotic chromosome is replicated in to make an exact copy of the molecule for distribution to progeny cells.

Inclusions :- Bacteria have the ability to store the food reserves intracellularly as inclusions or granules. In cytoplasm of bacterial cells different types of inclusion granules are present, which occupy a substantial part of the cytoplasm. For example, carbon and energy reserves may be stored as glycogen (a polymer of glucose) or as polybetahydroxybutyric acid (a type of fat) granules. Polyphosphate inclusions are reserves of PO4 and possibly energy; elemental sulfur (sulfur globules) are stored by some phototrophic and some lithotrophic procaryotes as reserves of energy or electrons. Some inclusion bodies are actually membranous vesicles or intrusions into the cytoplasm which contain photosynthetic pigments or enzymes.

Bacterial nutrition:-There are two sources a cell can use for carbon: inorganic compounds and organic compounds. On the basis of carbon utilization a cell, bacteria are grouped into two categories :-

  1. Autotrophic bacteria :-These bacteria are able to synthesis their own food from inorganic substances, as green plants do(photosynthesis). Autotrophs use C02 as a sole source of carbon for growth and obtain their energy from light or from the oxidation of inorganic compounds. Depending upon the source of energy these are further divided into two categories :-
    • Photoautotrophs:- These are photosynthetic and obtain energy from sunlight. The bacterial photosynthesis is different from that of green plants since here water is not used as a hydrogen donor. Hence oxygen is not released as a byproduct. Examples members of the family Chlorobacteriaceae (green sulphur bacteria) and family Thiorhodaceae (purple sulphur bacteria)
    • lithoautotrophs or Chemoautotrophs:- Lithoautotrophs or chemoautotrophs use inorganic compounds as sources of energy, i.e., they oxidize compounds such as H2 or H2S or NH3 to obtain electrons to feed in to an electron transport system and to produce ATP. Following are the common types of chemoautotrophic bacteria :-
      • Nitrifying bacteria which derive energy by oxidizing ammonia into nitrates. e.g. Nitrosomonas, Nitrobacter.
      • Sulphur bacteria which derive energy by oxidising hydrogen sulphide to sulphur. e.g. Thiobacillus, Beggiatoa.
      • Iron Bacteria which derive energy by oxidising ferrous ions into ferric form. e.g. Ferrobacillus, Gallionella.
  2. Heterotrophic Bacteria :-These are bacteria which are unable to manufacture their own organic food and hence are dependent on external source. These are either
    • Photoheterotrophy :- These bacteria use light energy for synthesising their food.The green and purple sulphur bacteria, metabolise in a photoheterotrophic mode.
    • Chemoheterotrophy :- These bacteria use energy through the oxidation of organic compounds via respiration.Most of the bacteria are chemoheterotrophic.The chemoheterotrophs are of three types :-
      • Parasitic Bacteria:- These are bacteria which occur in the body of animals and plants, obtaining their organic food from there. Most of these bacteria are pathogenic, causing serious diseases in the host organisms either by exploiting them or by releasing poisonous secretions called toxins. e.g. Agrobacterium , Pseudomonas etc.
      • Saprophytic Bacteria :-These bacteria grow on dead and decaying organic remains and obtain their nutritional requirements from dead organic matter.
      • Symbiotic Bacteria :- These are bacteria which live in a mutually beneficial association with other organisms. Such bacteria derive the essential nutrients from their host organisms and in that process help the host through some of their biological activities.The most familiar example of symbiotic bacteria are the nitrogen fixing bacteria Rhizobium and Pseudomonas found in the root nodules of leguminous plants.

Growth and reproduction :-Bacterial growth is defined as the increase in numbers of a microbial population. Bacteria reproduce only asexually (one parent), not sexually. Asexual reproduction of a bacterial cell can occur either by binary fission, budding or filamentous growth :-

  • Binary fission: Each cell increases in size and divides in half to yield two identical daughter cells. First the bacterial cells elongate. Then the bacterium replicates its chromosomal DNA. Each circular strand of DNA then attaches to the plasma membrane. The cell elongates, causing the two chromosomes to separate. The plasma membrane then invaginates (grows inwards) as a results a cross wall is formed. The cell splits into two daughter cells through a process called cytokinesis.The order and timing of these processes (DNA replication, DNA segregation, division site selection, invagination of the cell envelope and synthesis of new cell wall) are tightly controlled. The time interval required for a bacterial cell to divide or for a population of cells to double is called the generation time. Generation times for bacterial species growing in nature may be as short as 15 minutes or as long as several days.

  • Budding:- It is an alternative method of cell division in which a small protrusion expands outward from a mother cell, forming a daughter cell which contains a copy of the chromosome from the mother cell . The daughter cell increases in size until it breaks off from the mother cell. Eventually the daughter cell will reach a threshold size, and start producing buds of its own.Example:- stalked bacteria such as Caulobacter.
  • Filamentous growth: Some spore-forming bacteria like actinomycetes also exhibit filamentous growth and have an appearance similar to fungi. These microbes lengthen into a tubular shape as a long filament.

Sporulation -Endospore Formation:- In certain bacteria like Clostridium and Bacillus, the cells tide over unfavourable conditions by forming endospores. During this process, a portion of the cytoplasm and a copy of the bacterial chromosome undergo dehydration and get surrounded by a three-layered covering. The remaining part of cytoplasm and cell wall degenerate.

The resulting structure, called endospore can tolerate extreme environmental conditions and can remain viable for several years. When the environmental conditions are suitable, the endospore absorbs water, swells and the wall splits, releasing the cell inside. It develops a new cell wall and starts functioning as a typical bacterial cell. Endospore formation is not a method of reproduction. It is only a method meant for tiding over unfavourable conditions and allowing dispersal of the bacterial cells into new habitats.

Genetic variation :- Bacteria, as asexual organisms, inherit an identical copy of their parent's genes (i.e. All bacteria, however, have the ability to evolve through selection on changes to their genetic material (DNA) which arise either through mutation or genetic recombination:-

  • Mutation :-A mutation is a permanent alteration in the sequence of nitrogenous bases of a DNA molecule. The result of a mutation is generally a change in the end-product specified by that gene.Bacteria have only a single chromosome, which makes them haploid, there is a random genetic change within a cell's own genetic code . Consequently, mutations are not hidden by a dominant allele, and will be expressed and evaluated by natural selection more rapidly than in diploid eukaryotes.
  • Bacteria are known to exchange genes in nature by three fundamental processes:
    1. Conjugation :- Bacterial conjugation was first postulated in the 1940s by Joshua Lederberg and Edward Tatum. The essential feature of the process is that two bacterial cells come together and mate such that a gene transfer occurs between them. One cell, the donor cell (F+), gives up DNA; and another cell, the recipient cell (F−), receives the DNA. The transfer is nonreciprocal, and a special pilus called the sex pilus joins the donor and recipient during the transfer. The DNA most often transferred is a copy of the F factor plasmid. >

      The factor moves to the recipient, and when it enters the recipient, it is copied to produce a double-stranded DNA for integration. The channel for transfer is usually a special conjugation tube formed during contact between the two cells. Conjugation occurs only between bacteria in same or closely related species.
    2. Transformation :- Bacterial transformation was discovered by Frederick Griffith in 1928 in bacterium Diplococcus (=Pneumococcus) that cause bacterial pneumonia. 

      In transformation DNA is released by donor. It is actively taken up by the Competent cells of recipient bacteria. A competent cell takes up DNA and destroys one strand of the double helix. A single-stranded fragment then replaces a similar but not identical fragment in the recipient organism, and the transformation is complete.
    3. Transduction:- Example- Bacterium - Salmonella typhimurium by Zinder and Lederberg in 1952.In transduction, bacterial viruses (also known as bacteriophages) transfer DNA fragments from one bacterium (the donor) to another bacterium (the recipient). The viruses involved contain a strand of DNA enclosed in an outer coat of protein. Genetic recombination can follow the transfer of DNA from one cell to another leading to the emergence of a new genotype (recombinant). It is common for DNA to be transferred as plasmids between mating bacteria. Since bacteria usually develop their genes for drug resistance on plasmids (called resistance transfer factors, or RTFs), they are able to spread drug resistance to other strains and species during genetic exchange processes.