MONERA. REFERRAL CLASSIFICATION 3 Phylum Actinobacteria 3.1 Class Actinobacteria (class) 3.1.

2 Subclass Actinobacteridae Order Actinomycetales Suborder Actinomycineae Family Actinomycetaceae Genera Actinomyces Species A. canis

6 Phylum Chlamydiae 6.1 Class Chlamydiae (class) Order: Chlamydiales Family Chlamydiaceae Genus Chlamydia Genus Chlamydophila

10 Phylum CyanobacteriaOrder Chroococcales Order Nostocales The families included are Family - Microchaetaceae Family - Nostocaceae The genera are as follows = Genera - Anabaena Genera - Anabaenopsis Genera - Nodularia Genera - Nostoc

15 Phylum Firmicutes 15.1 Class Bacilli 15.3 Class Mollicutes Order Mycoplasmatales Genera -Ureaplasma Genera -Mycoplasma Species M. gallisepticum M. genitalium M. hominis

21 Phylum Proteobacteria 21.1 Class Alphaproteobacteria Order Rhizobiales Order Rickettsiales Family Rickettsiaceae Genus Rickettsia Genus Orientia Genus Wolbachia

NEW CLASSIFICATION SYSTEM An example of a halophile is Halobacterium salinarum. It's classification is as follows: Domain - Archaea Kingdom - Euryarchaeota Phylum - Euryarchaeota Class - Halobacteria Order - Halobacteriales Family - Halobacteriaceae Genus - Halobacterium Species - salinarium And example of an extreme thermophile/thermoacidophile is Pyrococcus furiosus and it's classified as follows: Domain - Archaea (Eukaya/ Bacteria) Kingdom - Euryarchaeota (newest in 6 kingdom classification) Phylum - Euryarchaeota Class - Thermococci Order - Thermococcales Family - Thermococcaceae Genus - Pyrococcus Species - furiosus An example of a methanogen is Methanomicrococcus blatticola, and it's classification is as follows: Domain - Archaea Kingdom - Euryarchaeota Phylum - Euryarchaeota Class - Methanomicrobia Order - Methanosarcinales Family - Methanosarcinaceae Genus - Methanomicrococcus Species - blatticola OLD CLASSIFICATION SYSTEM Thermoacidophile Kingdom: Monera (bacteria) Phylum: Archaebacteria Class: Thermoprotei Order: Thermoproteales Family: Thermoproteaceae Genus: Pyrobaculum Species: Pyrobaculum aerophilum Methanogen Kingdom: Monera (Bacteria) Phylum: Archaebacteria Class: Methanomicrobia (methanogens) Order: Methanomicrobiales Family: Methanomicrobiaceae Genus: Methanogenium Species: Methanogenium frigidum

MONERA
Definition: Kingdom monera is a kingdom of all prokaryotes. A moneran is: 1. the smallest organism in the animal kingdom 2. the simplest organism in the animal kingdom 3. the most ancient and rose from progenote (i.e. earliest living stock) 4. the most plentiful/abundant in nature (in comparison to others.) 5. lack a true nucleus (nuclear material is not enclosed within a nuclear membrane) 6. basic proteins are absent in the nucleoplasm Kingdom Monera is divided into many phyla. The most studied upon although, are:1. Phylum Bacteria 2. Phylum Cyanobacteria (Prominent Genus- Nostoc. Genus- Anabena) 3. Phylum Archaebacteria (according to the old system of classification) 4. Phylum Actinobacteria (Prominent Genus- actinomyces) 5. Phylum Chlamydiae (Prominent Genus- chlamydia) 6. Phylum Firmicutes (Prominent Class mollicutes. Genus- Mycoplasma. Genus- Ureaplasma) 7. Phylum Proteobacteria (Prominent Genus Rickettsia) BACTERIA Definition: Bacteria are moneran prokaryotic microorganisms which area. Prokaryotic b. Basically unicellular c. devoid of chlorophyll a d. possess nucleoid attached to mesosome e. have food reserve in the form of glycogen History: 1. Were discovered by Anthony Van Leeuwenhoek (inventor of the first microscope). And called animacules 2. Linnaeus called them vermes 3. Ehrenberg named them bacteria in 1828 4. Louis Pasteur laid the foundation of Bacteriology (i.e. the branch of science that deals with the study of bacteria) by developing culturing and steralization methods) Occurrence: 1. Are ubiquitous. 2. Can be ffound in high temperatures due to their ability of being a. thermophilic (can withstand temperatures as high as 78*C) b. psychrophilic (can withstand temperatures as low as -190*C) 3. Can be found on the surface and inside all kinds of organisms. Size: Average bacteria (1 - 10 micron in length)

Largest bacteria Beggiatoa mirabilis (16-45 micron in diameter and many cm in length) Smallest bacteria Dialister pneumosintes (0.15 micron) Shape: In shape we study a. form b. flagellation Form: 1. Bacteria are generally amorphous. Very few maybe pleomorphic or morphous. E.g. - The bacterium Rhizobium has 3 forms: a. atrichous rods b. petritrichous oval swarmers c. atrichous irregular bacteriods 2. The 4 main forms are Bacillus, Coccus, Sprillum, Vibrium. 3. Others are secondary forms spirochete, mycelial, stalked, budding. Bacillus: Rod like bacteria. Like a cigar. Subtypes are a. Single bacillus b. Diplobacillus c. Palisade bacillus (in piles) d. Streptobacillus (in chains) Coccus: Spherical bacteria. Like a berry. Subtypes area. Monococcus b. Diplococcus c. Tetracoccus (4 together. Like a 4 on the dice, only closer) d. Sarcina (8 together. Like a cube) e. Streptococcus (in chains) f. Staphylococcus (in irregular bunches) Spirillum: Rigid, helical bacteria with 1-3 curves. Like a cut-up portion of a string. Vibrium (pl. Vibrio): Like a single turn of a spiral. Like a comma. ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Spirochete: A long lined filament. Like a snake with a line through the centre. Mycelial: A branched, aseptate, filamentous bacteria. Like a witches fingers. Stalked: A stalk is borne on one end of the bacteria. Like an alien head with an antenna Budding: A bacteria which may have off-spring buds attached to it. Like a hydra without tentacles. Diagram (Dinesh 2.11):

Flagellation: 1. Definition: Flagella are fine protoplasmic threads which occur in many organisms primarily for swimming in the aquatic habitat. Bacterial flagella have antigenic properties. 2. Flagella are of 2 kinds a. prokoaryotic flagella b. eukaryotic flagella (see differences: Dinesh- page 63 ) 2. Flagellation is determined by 2 factors a. number of flagella b. mode of attachment of flagella 3. There are 2 conventions followed a. the general convention b. the Thimann convention A. General convention:a. Atrichous: 0 flagella. b. Monotrichous: 1 flagella. At one polar end c. Lophotrichous: 1 tuft of flagella. At one polar end d. Amphitrichous: 2 flagella/ 2 tufts of flagella. One at each polar end e. Peritrichous: x flagella. All around the surface. B. Thimann convention:a. Amphitrichous: b. Cephalotrichous: c. Lophotrichous: Diagram: (Dinesh 2.13) 2 flagella. One at each polar end 1 tuft of flagella. At one polar end 2 tufts of flagella. One at each polar end

C. Present convention:a. Atrichous: b. Monotrichous: c. Cephalotrichous: d. Amphitrichous: e. Lophotrichous: e. Peritrichous: Diagram: (Pradeep 2.2)

0 flagella. 1 flagella. At one polar end 1 tuft of flagella. At one polar end 2 flagella. One at each polar end 2 tufts of flagella. Oneat each polar end x flagella. All around the surface.

Cell structure: 1. The bacterial cell is a prokaryotic cell. 2. It lacks membrane bound organelles and has a large numner of ribosomes or polyribosomes and therefore has a granular interior. 3. The mucilage/ glycocalyx, cell wall & plasma membrane are together called cell envelope. 4. It has 9 basic structures: i. Mucilage/ glycocalyx/ capsule/ slime layer ii. Cell wall iii. Plasma membrane/ Plasmalemma/ Cell membrane a. mesosome b. flagella c. pillus d. fimbriae (see difference b/w pilli & fimbriae: Dinesh page 63) iv. Cytoplasm a. Inclusion bodies i. Food reserve ii. Gas vacuoles iii. Inorganic granules/ inorganic inclusions/ Metachromatic granules b. Ribosomes c. Photosynthetic pigments v. Nucleoid/ Genophore/ Nuclear body/ Bacterial chromosome/ Prochromosome vi. Plasmids vii. Flagella Diagram Dinesh 2.2

Details of each structure: 1. Mucilage/ glycocalyx/ capsule/ slime layer:

i. ii.

iii. iv. v.

Definition: It Is the outermost covering of bacterial cells It is rich in polysaccharides A lose sheath of slime (i.e.) a gelatinous substance secreted by the protoplast, is called a slime layer A thick and tougher sheath is called capsule. Capsules are generally found in parasitic bacteria. Capsulated bacteria are generally atrichous. The layer has many functions 1. Protection from desiccation 2. Protection from viral attack 3. protection from phagocytosis and antibodies (mostly in capsules)

2. Cell wall: i.

Definition: It is the rigid and tough covering of the bacterial cell that lies inner to the glycocalyx. ii. It ranges from 50 100 armstrong in thickness iii. It is mainly composed of a polymer called peptidoglycan/ murein/ mucopeptide (i.e. acetyl glucosamine, acetyl muramic acid & a peptide chain of 4/5 aminio acids) iv. Otherwise it may contain teichoic acid, protein polysaccharides, lipoproteins and lipopolysaccharides. (Depending on gram +ve or Gram -ve) v. Lysozyme can dissolve a bacterial cell wall. As it hydrolyses peptidoglycan. (Lysozyme is present in our tears and saliva) vi. A periplasmic space b/w the cell wall and plasma membrane is observed. 3. Plasma membrane/ Plasmalemma/ Cell membrane: i. Each bacterial cell has a plasma membrane situated just internal to the cell wall. It covers the cytoplasm on the outside. ii. It is thin and elastic iii. It is composed mainly of phospholipids and proteins. It lacks sterols (like cholesterol found in eukaryotic membranes). Very few contain pentacyclic sterols called hopanoids. iv. It bears electron carriers, respiratory enzymes, and enzymes for lipid synthesis. v. It is selectively/ differentially permeable so as to allow the passage of dissolved substances into the cell. vi. It provides a site for metabolism 4. Mesosome: i. Definition: It is a multilaminated convulated membranous structure which is formed by invagination of plasma membrane. It is basically an infolding. ii. It is thin and elastic iii. A mesosome is composed of the same chemicals as a plasma membrane. iv. A mesosome is of 2 kindsa. Septal mesosome: it is in contact with the nucleoid. It helps in septa formation and replicates with the nucleoid during division. b. Peripheral mesosome/ Chondroid: It is not in contact with the nucleoid. It contains repiratory enzymes v.A mesosome may also be useful as such: a. Secreation of intracellular substances to the outside b. Sensory activity

c.Increasing the surface area of the plasma membrane.

5. Flagella:
i. ii. Definition: Flagella are fine protoplasmic threads which occur in many organisms primarily for swimming in the aquatic habitat. Flagella has 3 parts to it1. Basal body (blepharoplast): May have 1 pair of rings or 2 pairs of rings 2. Hook: Helps attach the flagellum to the cell membrane. 3. Filament: Is the long narrow, hollow tube It is 4-5 microns in length. It is composed of 3-8 identical subunits called flagellin arranged helically along the axis to give a hollow tube. Flagellin are basically special protein molecules. Bacterial flagella have antigenic properties. Flagellar movement: A 360* rotation of the flagellum lets the cell spin in a forward direction For difference b/w eukaryotic and prokaryotic flagella Dinesh page 63 Diagram Dinesh 2.14

iii. iv. v. vi. vii. viii.

6. Pillus:
i. ii. iii. Definition: Pilli are protoplasmic tubular outgrowths, minute, nonflagellar, appendages. They are straight and hair-like. It is 18-20 microns in length. A pillus is composed of protein sub units called pillin arranged helically around a central hollow axis. A sex pilli/ F-pilli form a bridge during conjugation. They are found only on the male/ donor cells. Definition: Fimbriae are small solid outgrowths from the bacterial cell. They are bristle like fibres which develop from the surface of bacterial cells. They are 0.1-0.15 microns in length A fimbriae is composed of _______________ They help in the attachment of the bacterial cell to a solid surface or to the host. (see difference b/w pilli & fimbriae: Dinesh page 63) Definition: Is a complex colloidal aqueous fluid/ semifluid ground substance or matrix. It is granular due to the amount of ribosomes or polyribosomes (groups of ribosomes) and fills up the entire cell. It is composed of mainly carbohydrates and soluble proteins.

iv. 7. Fimbriae:
i. ii. iii. iv. v. 8. Cytoplasm i. ii. iii.

iv. Cyclosis (streaming movement) is absent. v. Does not contain any eukaryotic organelles. vi. It is the site of most metabolic activity 9. Inclusion Bodies i. Definition: Inclusion Bodies are non-living non-structural materials of bacterial cells that may lie free in the cytoplasm (e.g. glycogen granules) or be covered by a single non-unit 2-4 nm thick membrane (e.g. vacuole) ii. There are three kinds of inclusion bodies a. food reserves b. inorganic granules/ inorganic inclusions c. gas vacuoles 10. Food reserve i. They are glycogen and protein granules. They are intermediates of fat synthesis. ii. Neutral fats are absent iii. Some bacteria may contain refractile granules of PHB. PHB is used to make biodegradable plastic 11. Gas vacuoles i. Gas vacuoles are storehouses for metabolic gases. ii. Each gas vacuole is made of a large number of extremely small cylindrical hexagonal units called gas vesicles. A gas vesicle is covered by a protein membrane iii. Gas vacuoles are permeable to gases but not to liquids iv. Vacuoles help in buoyancy regulation and against harmful radiations 12. Inorganic granules/ inorganic inclusions/ Metachromatic granules: i. Definition: They are inclusions made of inorganic substances such as sulphur or magnetite etc found either in the cytoplasm or in the periplasmic space. ii. All granules are covered by a non-unit or a single-layered membrane iii. E.g. Volutin granules contain reserve phosphate. Magnetite occurs in small vacuoles called magnetosomes in bacterium Aquaspirillum Magnetotacticum. Magnetosomes help the bacterium orientate along geometric lines. iv. Are called metachromatic granules as they pick up different colours with basic dyes. 13. Ribosomes: i. Definition: Is a minute cell organelle responsible for the production of soluble proteins. ii. Ribosomes are of 2 kinds 1. Plamsa membrane ribosomes: Produce proteins for transport to the outside. 2. Matrix ribosomes: Produce proteins for intracellular use. iii. A ribosome is 15 x 20 nm in volume. iv. Ribosomes often create polyribosomes/ polysomes (4-6 ribosomes together in a helical series) with the help of mRNA 14. Photosynthetic pigments: i. They are bacteriochlorophylls, bacteriophaeophytins and cartenoids ii. In purple bacteria, pigments are associated with thylakoid membranes that are formed by an invagination of plasmalemma; In green bacteria, pigments are not associated with membranes and occur inside small sacs called

iii. 15.

chlorosomes. (Chlorosomes are joined to the plasmalemma through base plates) Both bacterial thyllakoids and chlorosomes are collectively called chromatophores

Nucleoid/ Genophore/ Nuclear body/ Bacterial chromosome/ Prochromosome: i. The genetic material is a single molecule of double stranded DNA. The DNA is circular and both its ends are covalently joined. There are no free ends ii. It is 1000 microns in length iii. It lacks basic proteins (i.e. histones) iv. The DNA is extensively looped to form a dumb-bell shaped structure. v. Nucleoid is attached to the plasma membrane directly or through a mesosome vi. During replication, mitotic apparatus is not seen vii. Bacterial nucleoid formed of a single molecule of DNA is equivalent to what is contained in a single chromosome of eukaryotes but without any organisation of the later. Thus it is called a prochromosome. 16. Plasmids i. Definitoin: They are small self-replicating extrachromosomal or extra-nuclear circular segments of DNA present in the cytoplasm of bacterial cells. ii. They give the cell some extra properties which are not very necessary for survival. iii. There are 2 main kids of plasmids 1. Transferable plasmids: plasmids that can be transferred from one bacterial cell to another. Eg. F-plasmid. R-plasmid (having resistance to antibiotics like streptomycin). Col-plasmid (producing colicins or bacteriocins that kill related bacteria) 2. Episomes: plasmids which get temporarily integrated with the nuclear body. Formation of an episome depends upon the chromosome memory. iv. Other plasmids may be antibiotic producing plasmids, pigment synthesising plasmids, nodule forming plasmids, etc

Types a. There are 2 kinds of bacteria on their ability to retain stain b. Christian Gram developed a technique of staining bacteria called gram staining. This was possible due to the concept that all bacteria pick up colouration. c. Process of gram staining a. Bacterial smear is heat fixed on a slide b. The slide is dipped into a solution of crystal violet or gentian violet for 1 minute c. The stain is fixed by dipping the slide in 0.5% iodine for I minute d. The slide in then kept in a polar organic solvent like alcohol or acetone for 10-30 seconds e. Bacteria which retain the blue or purple stain are called gram +ve. Those which lose the stain are called gram ve f. If counter stained with safranin for 20-30 seconds, gram +ve pick up pink stain alongwith its blue/purple stain. Gram ve bacteria only pick up pink stain. d. The major difference in Gram +ve and Gram ve bacteria which controls its ability to retain stain, is the lipid content of the cell walls.

e. Gram +ve bacteria: Streptococcus, Staphylococcus, Bacillus f. Gram ve bacteria: Pseudomonas, Escherichia, Vibrio, Rhizobium g. For differences b/w Gram +ve and Gram ve bacteria see Dinesh page 59. Teichoic Acid: is composed of glucose phosphate and alcohol. It is mixed with chemicals for protection against drastic changes in temperature and pH. Found in the cell wall. Mycolic acid: Hydroxy fatty acids produced by some actinomycetes. Pathogenic forms convert them into Wax-D or mycosides. Found in the cell wall. Porins: Protein-lined channels for passage of low molecular weight hydrophilic substances. Found in the cell wall Life processes -Respiration -Nutrition -Reproduction -Movement Respiration a. The bacteria may be Obligate aerobes or obligate anaerobes Facultative aerobes or facultative anaerobes Aerotolerant anaerobes or anaerotolerant aerobes. Will continue to respire in the later condition even in the presence of the opposite. Nutrition (Branched Diagram)

Nutrition in Bacteria may be of the following kinds a. Autotrophic a. Photoautotrophic/ Photosynthetic/ Photolithotrophic i. Anoxygenic Photosynthesis/ Non bacterial photosynthesis 1. Purple bacteria (association with thylakoids)

b. photoheterotroph) 2.

a. purple sulphur bacteria purple non-sulphur bacteria (may be a photo-organotroph/ Green bacteria (no association with thylakoids) a. green sulphur bacteria b. green non-sulphur bacteria ii. Oxygenic Photosynthesis/ Bacterial photosynthesis 1. cyanobacteria 2. eukaryotic photoautotrophs iii. For differences b/w oxygenic and anoxygenic photosynthesis, see Dinesh page 65

b. Chemoautotrophic/ Chemolithotrophic
i. Nitrifying bacteria 1. Nitrate bacteria 2. Nitrite bacteria ii. Sulphur Bacteria iii. Iron Bacteria iv. Hydrogen Bacteria v. Carboxydobacteria vi. Methane bacteria c. For differences b/w Photosynthesis & Chemosynthesis, see Dinesh page 67 b. Heterotrophic a. Saprotrophic b. Symbiotic c. Parasitic ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| a. Autotrophic: Is the mode of nutrition in which organisms prepare their own organic nutrients from raw materials a. Photoautotrophic/ Photosynthetic/ Photolithotrophic I. Is the mode of nutrition in which organisms prepare their own organic nutrients from inorganic raw materials (CO2 and H2 honor) and radiation energy. II. Photosynthetic pigments are bacteriochlorophylls, bacteriophaeophytins and cartenoids. i. Anoxygenic Photosynthesis/ Non bacterial photosynthesis I. Anoxygenic photosynthesis is photosynthesis which does not liberate oxygen. II. Reducing power is obtained from free hydrogen or hydrogen containing organic compounds. E.g. H2S, Na2S2O3 III. Reducing power is not water. IV. Equation:-

1. Purple bacteria (Photosynthetic pigments are found inside thylakoids/ chromatophores i.e. vesicular thylakoids.) a. purple sulphur bacteria b. purple non-sulphur bacteria (may be a photo-organotroph/ photoheterotroph. i.e. CO2 is not obtained. Source of carbon is taken from elsewhere)

2.

Green bacteria (no association with thylakoids. Photosynthetic pigment is inside chlorosomes bound to plasma membrane) a. green sulphur bacteria b. green non-sulphur bacteria (may be a photo-organotroph/ photoheterotroph. i.e. CO2 is not obtained. Source of carbon is taken from elsewhere) ii. Oxygenic Photosynthesis/ Bacterial photosynthesis: I. Oxygenic photosynthesis is photosynthesis which liberates oxygen II. Reducing power is water III. Equation

1. cyanobacteria E.g. 1 2. eukaryotic photoautotrophs E.g. 2

iii. For differences b/w oxygenic and anoxygenic photosynthesis, see Dinesh page 65 b. Chemoautotrophic/ Chemolithotrophic I. An inorganic substance is oxidised. An oxide and energy is produced (in the form of ATP). Instead of radiation energy, this energy is used in conversion. II. The 2 reactants are CO2 and a Hydrogen donor (which may have to be obtained from hydrogen containing compunds). III. The 2 products are Glucose and water IV. Equation:

iv. Nitrifying bacteria: Bacteria which oxidise ammonia and its

forms for energy 1. Nitrite bacteria: Bacteria that oxidise ammonia. 2. Nitrate bacteria: Bacteria which oxidise the resultant/ a nitrite to a nitrate for energy.

v. Sulphur Bacteria: Bacteria which oxidises hydrogen sulphur to

sulphur or sulphur to sulphate for energy.

vi. Iron Bacteria: Bacteria which oxidise ferrous salts to ferric I

vii. Hydrogen Bacteria: Bacteria which oxidise hydrogen or its forms for energy.

viii. Carboxydobacteria: Bacteria which oxidise CO to CO2 for

energy.

ix. Methane bacteria: Bacteria which oxidise methane (CH4) for energy and the carbon component of their chemosynthetic reaction. c. For differences b/w Photosynthesis & Chemosynthesis, see Dinesh page 67 b. Heterotrophic: I. a. Saprotrophic b. Symbiotic c. Parasitic