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Thursday, 12 September 2024

Isolation of Antibiotic Resistance organisms using gradient plate method

 Isolation of Antibiotic Resistance organisms using gradient plate method

Aim

    To isolate antibiotic resistant mutant organisms using gradient plate method

Principle:

 Mutation is a heritable change in the nucleotide sequence of DNA. Mutations may be characterized according to either the kind of genotypic change that has occurred or their phenotypic consequences. Mutations can alter the phenotype of a microorganism in several different ways. Morphological mutations change the microorganism’s colonial or cellular morphology. Nutritional or biochemical variation may occur in a gene that encodes an enzyme involved in a metabolic pathway of amino acid synthesis. Changes in gene regulation occurs when mutation occur in a gene encoding a transcription factor. Lethal mutations prevent the reproducing capability of the organism, and when expressed, it results in the death of the microorganism.

Gradient Plate Technique:

An excellent way to determine the ability of organisms to produce mutants that are resistant to antibiotic is to grow them on a gradient plate of a particular antibiotic. The gradient plate consists of two wedges like layers of media: a bottom layer of plain nutrient agar and top layer of antibiotic with nutrient agar. The antibiotic in the top layer, diffuse into the bottom layer producing a gradient of antibiotic concentration from low to high. A gradient plate is made by using Streptomycin in the medium. E. coli, which is normally sensitive to Streptomycin, will be spread over the surface of the plate and incubated for 24 to 72 hours. After incubation colonies will appear on both the gradients. The colonies develop in the high concentration are resistant to the action of Streptomycin, and are considered as Streptomycin resistant mutants. For isolation of antibiotic resistant of gram negative enteric bacteria, the antibiotics commonly used are Rifampicin, Streptomycin, and Erythromycin etc.

Materials required:

  1. 24 hour old nutrient broth culture of Escherichia coli.

  2. Two nutrient agar deep tubes (10 ml per tube/culture).

  3. 1% Streptomycin sulphate solution (100 µg/ml).

  4. A beaker with 90% ethanol.

  5. Sterile Petri plates.

  6. Sterile 1 ml pipette.

  7. Glass rod spreader.

  8. Water bath.


Procedure:

I) Preparation of gradient plate:

  1. Melt two nutrient agar plates maintained at 96 degree C and cool to 55degree C

  2. Pour the contents of one agar tube into a sterile petriplate. Allow the medium to solidify in a slanting position by placing either a glass rod under one side.

  3. After the agar medium is solidified remove the glass rod and place the plate in the horizontal position.

  4. Pipette out 0.1mL of 1% Streptomycin solution into the second tube of the second nutrient agar medium.

  5. Rotate the tube between the palms and pour contents to cover the gradient layer agar and allow to the medium to solidify on a level table.

  6. Label the low and high antibiotic concentration area on the bottom of the plate.

 

Gradient plate

II) Inoculation of culture:

  1. Pipette out 200µl (0.2ml) of the overnight Escherichia coli culture onto the gradient plate after 24 hours of its preparation.

  2. Spread the inoculums evenly over the agar surface With a sterile bent glass rod by rotating the plate.

  3. Incubate the inoculated plate in an inverted position at 37o C for 48-72 hours.

  4. Observe the plate for appearance of E.coli colonies in the area of low streptomycin concentration (LSC) and high streptomycin concentration (HSC) and record the results.

Results:

Colonies which appear in the area of high concentration streptomycin region will be streptomycin resistant mutants.

 

III. Confirming presence of Streptomycin resistant colonies of E.coli.

  1. Select and mark an isolated colony of E.coli in the HSC region of the Nutrient agar plate.

  2. Pick the selected colony with a sterile inoculating loop and streak on to second gradient plate towards the HSC region.

  3. Repeat this step with one or two colonies of streptomycin resistant mutants from the HSC region.

  4. Incubate the inoculated plates in an inverted position at 37o C for 24-72 hours.

  5. Observe the growth of streaked colonies towards the HSC region.

Results:

Growth of E.coli colonies in HSC area indicates the successful isolation of streptomycin resistant mutants.

Reference 

  1. Brown E. Alfred, Benson’s Microbiological Applications, ninth edition, McGraw Hill Publication
  2. Prescott M. Lansing, Harley P. John, Klein A. Donald, Laboratory Exercises in Microbiology, fifth edition, McGraw-Hill college division.
  3. Aneja K R. Experiments in microbiology, plant pathology and biotechnology, fourth edition, New Age International (P) Limited .Publishers.
  4. Prescott M. Lansing, Harley P. John, Klein A. Donald, Microbiology, sixth edition, McGraw-Hill Higher Education
  5. Lederberg, J and Lederberg, EM (1952) Replica plating and indirect selection of bacterial mutants. J Bacteriol. 63: 399–406
  6. Madigan & Martinko, Brock Biology of Microorganisms, Eleventh Edition, Pearson Prentice Hall, Inc.

Monday, 17 July 2023

KINGDOM CLASSIFICATION

 KINGDOM CLASSIFICATION


FIVE KINGDOM CLASSIFICATION

R.H. Whittaker proposed the five-kingdom classification in 1969. This classification was based upon certain characters like mode of nutrition, thallus organization, cell structure, phylogenetic relationships and reproduction.  This form of kingdom classification includes five kingdoms Monera, Protista, Fungi, Plantae and Animalia.

Five Kingdom Classification

The five-kingdom classification that we see today was not the initial result of the classification of living organisms. Carolus Linnaeus first came up with a two-kingdom classification, which included only kingdom Plantae and kingdom Animalia.

The two-kingdom classification lasted for a very long time but did not last forever because it did not take into account many major parameters while classifying. There was no differentiation of the eukaryotes and prokaryotes; neither unicellular and multicellular; nor photosynthetic and the non-photosynthetic.

Putting all the organisms in either plant or animal kingdom was insufficient because there were a lot of organisms which could not be classified as either plants or animals.

All this confusion led to a new mode of classification which had to take into account cell structure, the presence of cell wall, mode of reproduction and mode of nutrition. As a result, R H Whittaker came up with the concept of the five-kingdom classification.

The five-kingdom classification of living organisms included the following kingdoms:

Kingdom Monera

Bacteria are categorized underneath the Kingdom Monera.

Features of Monerans

  • They possess the following important features:
  • Bacteria occur everywhere and they are microscopic in nature.
  • They possess a cell wall and are prokaryotic.
  • The cell wall is formed of amino acids and polysaccharides.
  • Bacteria can be heterotrophic and autotrophic.
  • The heterotrophic bacteria can be parasitic or saprophytic. The autotrophic bacteria can be chemosynthetic or photosynthetic.

Types of Monerans

Bacteria can be classified into four types based on their shape:

  • Coccus (pl.: cocci) – These bacteria are spherical in shape
  • Bacillus (pl.: bacilli) – These bacteria are rod-shaped
  • Vibrium (pl.: vibrio) – These bacteria are comma-shaped bacteria
  • Spirillum (pl.: spirilla) – These bacteria are spiral-shaped bacteria

Monera has since been divided into Archaebacteria and Eubacteria.

 

Kingdom Protista

Features of Protista

Protista has the following important features:

  • They are unicellular and eukaryotic organisms.
  • Some of them have cilia or flagella for mobility.
  • Sexual reproduction is by a process of cell fusion and zygote formation.

Sub-groups of Protista

Kingdom Protista is categorized into subsequent groups:

Chrysophytes: The golden algae (desmids) and diatoms fall under this group. They are found in marine and freshwater habitats.

Dinoflagellates: They are usually photosynthetic and marine. The colour they appear is dependent on the key pigments in their cells; they appear red, blue, brown, green or yellow.

Euglenoids: Most of them live in freshwater habitation in unmoving water. The cell wall is absent in them, instead, there is a protein-rich layer called a pellicle.

Slime Moulds: These are saprophytic. The body moves along putrefying leaves and twigs and nourishes itself on organic material. Under favourable surroundings, they form an accumulation and were called Plasmodial slime moulds.

Protozoans: They are heterotrophs and survive either as parasites or predators.

Kingdom Fungi

The kingdom fungi include moulds, mushroom, yeast etc. They show a variety of applications in domestic as well as commercial purposes.

Features of Kingdom Fungi

  • The fungi are filamentous, excluding yeast (single-celled).
  • Their figure comprises slender, long thread-like constructions called hyphae. The web of hyphae is called mycelium.
  • Some of the hyphae are unbroken tubes which are jam-packed with multinucleated cytoplasm. Such hyphae are labelled Coenocytic hyphae.
  • The other type of hyphae has cross-walls or septae.
  • The cell wall of fungi is composed of polysaccharides and chitin.
  • Most of the fungi are saprophytes and are heterotrophic.
  • Some of the fungi also survive as symbionts. Some are parasites. Some of the symbiont fungi live in association with algae, like lichens. Some symbiont fungi live in association with roots of higher plants, as mycorrhiza.

Kingdom Plantae

Features of Kingdom Plantae

  • The kingdom Plantae is filled with all eukaryotes which have chloroplast.
  • Most of them are autotrophic in nature, but some are heterotrophic as well.
  • The Cell wall mainly comprises cellulose.
  • Plants have two distinct phases in their lifecycle. These phases alternate with each other. The diploid saprophytic and the haploid gametophytic phase. The lengths of the diploid and haploid phases vary among dissimilar groups of plants. Alternation of Generation is what this phenomenon is called.

Kingdom Animalia

Features of Kingdom Animalia

  • All multicellular eukaryotes which are heterotrophs and lack cell wall are set aside under this kingdom.
  • The animals are directly or indirectly dependent on plants for food. Their mode of nutrition is holozoic. Holozoic nutrition encompasses ingestion of food and then the use of an internal cavity for digestion of food.
  • Many of the animals are adept for locomotion.
  • They reproduce by sexual mode of reproduction.

 

Ø  The five-kingdom classification of living organisms took a lot into consideration and is till now the most efficient system.

Ø  The older system of classification was based only on one single characteristic according to which two highly varied organisms were grouped together. For example, the fungi and plants were placed in the same group based on the presence of the cell wall. In the same way, unicellular and multicellular organisms were also grouped together.

Ø  Therefore, all the organisms were classified again into the five kingdoms known as the five-kingdom classification, starting with Monera, where all the prokaryotic unicellular organisms were placed together.

Ø  Following that, all the eukaryotic unicellular organisms were placed under the kingdom Protista.

Ø  The organisms were then classified based on the presence and absence of a cell wall.  The ones without the cell wall were classified under kingdom Animalia and the ones with cell wall were classified under kingdom Plantae.

Ø  The organisms under kingdom Plantae were further classified into photosynthetic and non-photosynthetic, which included Plantae and fungi respectively.

Ø  This system of classification of living organisms is better than following the older classification of plants and animals because it eradicated the confusion of putting one species in two different kingdoms.



Six Kingdom classification

 


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Archaebacteria

Archaebacteria are single-celled prokaryotes originally thought to be bacteria. They are in the Archaea domain and have a unique ribosomal RNA type.

The cell wall composition of these extreme organisms allows them to live in some very inhospitable places, such as hot springs and hydrothermal vents. Archaea of the methanogen species can also be found in the guts of animals and humans.

  • Domain: Archaea
  • Organisms: Methanogens, halophiles, thermophiles, and psychrophiles
  • Cell Type: Prokaryotic
  • Metabolism: Depending on species, oxygen, hydrogen, carbon dioxide, sulfur, or sulfide may be needed for metabolism
  • Nutrition Acquisition: Depending on species, nutrition intake may occur through absorption, non-photosynthetic photophosphorylation, or chemosynthesis
  • Reproduction: Asexual reproduction by binary fission, budding, or fragmentation


EIGHT KINGDOM


The 8 kingdom classification, by Cavalier-Smith includes the following kingdoms:

Eubacteria

Eubacteria are prokaryotic microorganisms that have a single cell that lacks a nucleus and one circular chromosome that contains DNA.

Archaebacteria

  1. The oldest known living things on earth are archaebacteria.
  2. They are categorised as bacteria because, when viewed under a microscope, they resemble bacteria and are members of the Monera kingdom.

Archezoa

One of the kingdom-level taxa postulated by Cavallier-Smith, which is thought to be an intermediate form between prokaryotes and eukaryotes because it contains the oldest unicellular eukaryotes with a nucleus and rod-shaped chromosomes but no mitochondria or plastid.

Protozoa

  1. A category of single-celled eukaryotes that feed on organic substances, such as other microbes or organic tissues and waste, are known collectively as protozoa.
  2. They can be parasitic or free-living.

Chromista

Chromista is a kingdom of eukaryotic organisms that includes single-celled and multicellular species that have comparable characteristics in their photosynthetic organelles (plastids).

Plantae

  1. All plants are included in Kingdom Plantae.
  2. These organisms are eukaryotic, multicellular, and autotrophic.
  3. A stiff cell wall can be found in plant cells.
  4. The pigment chlorophyll and chloroplast found in plants are necessary for photosynthesis.

 

Fungi

Fungi are eukaryotic organisms that include microorganisms such as yeasts, moulds and mushrooms.

Animalia

  1. Kingdom Animalia constitutes all animals. Amongst the five kingdoms, the largest kingdom is the animal kingdom.
  2. Animals are multicellular eukaryotes.
  3. However, like plants, they do not possess chlorophyll or a cell wall.
  4. Therefore, members of the animal kingdom exhibit a heterotrophic mode of nutrition.

 

 

Reference

 Kingdom Classification According to Whittaker - Biology LibreTexts

An Overview On The Five Kingdom Classification (byjus.com)

4.3.1: Kingdom Classification According to Whittaker - Biology LibreTexts

What are the 8 kingdoms? (byjus.com)

Biological Classification - Important Notes for NEET Biology (byjus.com)



BERGEY’S MANUAL OF SYSTEMATIC BACTERIOLOGY

 


Bacterial systematics has undergone several changes and is continuously in a state of flux as our knowledge of microorganisms is far from complete and new information is being added every day.

In 1923 David Hendricks Bergey, professor of bacteriology at the University of Pennsylvania, and four colleagues published a classification of bacteria that could be used for the identification of bacterial species.

The first eight editions were published under the name ‘Bergey’s Manual of Determinative Bacteriology’. In the 9th edition, it was renamed as ‘Bergey’s Manual of Systematic Bacteriology’ and was published in four volumes in 1984, 1986, 1989 and 1991.

It is highly regarded by bacteriologists as this manual is continuously updated with successive editions and helps in bacterial taxonomy and research.

The manual classifies bacteria on the basis of their functional and structural attributes and arranges the organisms into familial orders. In recent years, empirical evidence has also been considered in this classification.

Note: Since 2015, the manual has been replaced with Bergey’s Manual of Systematic of Archaea and Bacteria and is available online.

Organization

The 1980 edition of the manual took into consideration the relationship between organisms along with an expanded scope in bacterial taxonomy. The set of four volumes contains:

Volume I: It talks about all Gram-negative bacteria and considers them important for medicinal and industrial purposes.

Volume II: It includes all the information about Gram-positive bacteria.

Volume III: It includes information about the remaining Gram-negative bacteria and about Archaea as well.

Volume IV: It talks about filamentous actinomycetes and similar types of bacteria.


The second edition has been published in five volumes, the details of which are given below:

Volume I: It was published in 2001 and talks about the archaea and the branching phototrophic bacteria.

Volume II: It was published in 2005 and gives details about the proteobacteria.

Volume III: It was published in 2009 and gives details about the firmicutes.

Volume IV: It was published in 2011. It mentions the Spirochaetes, Bacteroidetes, Tenericutes (Mollicutes), Chlamydiae, Acidobacteria, Verrucomicrobia, Fusobacteria, Dictyoglomi, Fibrobacteres, Gemmatimonadetes, Lentisphaerae, and Planctomycetes.

Volume V: It was published in 2012 and talks about the actinobacteria.


The First Edition

In the first edition, Bergey classified the kingdom Prokaryotae in four divisions:

Gracilicutes: they have a gram-negative cell wall.

Firmicutes: they have a gram-positive cell wall.

Tenericutes: they do not have a cell wall.

Mendosicutes: they lack peptidoglycan in their cell wall and are similar to Archaea.

This classification was entirely based upon gram staining, presence of endospore, general shape, motility, morphology and mode of energy production. While the first edition of Bergey’s manual is entirely phenetic, the second edition was based on phylogenetic characters such as its DNA, RNA and protein.

In the current 9th edition, the manual is designed for identification of bacteria that is very different from the previous editions. In this edition, the bacteria are divided into 35 groups in the four major divisions.

The first division includes groups 1 to 16 (example: spirochete, sulphur-reducing bacteria, chlamydia and rickettsia), the second division includes groups 17 to 29 (example: gram-positive cocci, endospore forming, gram-positive cocci and rods, gram-positive, non-sporing rods), the third division includes group 30 such as Mycoplasma and the the last division includes groups 31 to 35 (example: methanogens, halophiles and archaebacteria).


Reference

Bergey's Classification of Bacteria (byjus.com)

Bergey's Manual of Systematic Bacteriology and Determinative Bacteriology (microbenotes.com)

Bergey's Manual of Systematics of Archaea and Bacteria | Major Reference Works (wiley.com)