Untitled

Biological Classification

Introduction

• Living organism classification attempts have been made, driven by the practical need for food, shelter, and clothing, rather than scientific principles initially.
• These early classifications were instinctive instead of scientific, focusing on immediate human needs.
• Systems classifying organisms have changed.
• All systems keep the plant and animal kingdoms, but what organisms are placed inside changes.
• Likewise, the understanding of how many kingdoms there should be and what they are also evolves with scientific understanding

History of Taxonomy

• Aristotle is known to have initiated his classification, using a more scientific approach, mainly on readily visible traits.
• Plants were classified by Aristotle into trees, shrubs, and herbs based on morphology. Animals were divided into two groups by Aristotle by the presence or absence of red blood.

Theophrastus

• Theophrastus wrote "Historia Plantarum," which was the first book of botany
• Theophrastus is honored as the father of ancient plant taxonomy and botany. Plants were classified into four groups by Theophrastus based on their growth form: herbs, shrubs, undershrubs, and trees.

Carolus Linnaeus

• Carolus Linnaeus is known as the father of plant, animal and general taxonomy.
• Devised the two-kingdom system of classification which grouped organisms into Plantae and Animalia.
• Grouping was performed respectively on the primary basis of cell walls.
• Linnaeus wrote "Species Plantarum" and "Genera Plantarum", defining plant nomenclature and classification respectively.
• The classification scheme relied mainly on the male reproductive organs (stamens) and established 24 plant categories.

Demerits of Two Kingdom Classification

• Prokaryotes (bacteria, blue-green algae) and eukaryotes (fungi, mosses, ferns, gymnosperms, angiosperms) were placed under the same kingdom despite fundamental differences.
• Unicellular (Chlamydomonas, Chlorella) and multicellular organisms (Spirogyra) were grouped together in the plant kingdom due to the presence of a cell wall.
• Heterotrophic fungi and autotrophic green plants were not differentiated, even though fungi have chitin in their cell walls while plants have cell walls made of cellulose.
• Two-kingdom classification proved inadequate, necessitating considering cell structure, nutrition mode, habitat, reproduction, and evolutionary relationships.
• Haeckel proposed the three-kingdom , and Copeland created the four-kingdom classification.

George Bentham and Joseph Dalton Hooker

• Bentham and Hooker are linked to the Royal Botanic Gardens.
• They created the biggest and most natural classification system for spermatophyta (seed plants) in their book.
• Spermatophyta was divided into Dicotyledonae (165 families), Gymnospermae (3 families), and Monocotyledonae (34 families), consisting of 202 families overall.

R. H. Whittaker

• R.H. Whittaker proposed the five-kingdom classification system in 1969.
• The system included the kingdoms Monera, Protista, Fungi, Plantae, and Animalia.
• Complexity of cell structure, body and thallus organization, mode of nutrition, reproduction/lifestyle, and phylogenetic relationships were the most important factors.

Five Kingdoms

• Kingdom Monera includes all prokaryotes like Eubacteria, Rickettsia, Actinomycetes, BGA, Archaebacteria, and Mycoplasma.
• Kingdom Protista has all unicellular eukaryotes, including diatoms, dinoflagellates, slime molds, euglenoids, and protozoans.
• Fungi encompasses true fungi.
• Kingdom Plantae contains all multicellular plants like bryophytes, algae, pteridophyta, angiosperms and gymnosperms.
• Kingdom Animalia consists of all multicellular animals.
• Viruses, viroids, and lichens are not included in the five-kingdom classification.
• Chlamydomonas and Chlorella are categorized under kingdom Protista.

Categories

• Species are the basic unit of classification
• Taxonomic ranks represent units of classification that are distinct biological entities, not just morphological aggregates
• A genus can contain one ore more specific epithets of organisms with morphological similarities.
• A genus comprises related species sharing many common characteristics than unrelated genera.
• Insects collected for museums are preserved in insect boxes after being killed and pinned.
• Keys used to identify specimens are analytical in nature. Proposed classification by Hooker and Bentham is natural and non-phylogenetic. Whittaker's classification encompasses five kingdoms.

Kingdom – Monera

• Monera kingdom contains all bacteria. Microorganisms, particularly bacteria, thrive in diverse conditions.
• A handful of soil contain millions of bacteria
• Bacteria can live in hostile environments, such as hot springs, deserts, snow, and the deep ocean. Bacteria can be parasitic and live in the bodies of organisms.

Prokaryote Characteristics

• The cell wall of prokaryotes is composed of peptidoglycan/murein, a mucopeptide. Peptidoglycan comprises amino acids and polysaccharides..
• Similar to eukaryotes, prokaryotes have a lipoprotein cell membrane.
• The region between the cell wall and membrane is known as the periplasmic space.
• This space functions analogously to a lysosome.
• Cytoplasm in prokaryotes lacks cell organelles that are membrane bound.
• Prokaryotes have an indistinct nucleus, it often goes by fibrillar., nucleoid, or genophore nucleus.
• Nuclear membrane and nucleolus are not present.
• Prokaryotes possess a false chromosome consisting of ds circular naked DNA and non-histone proteins like polyamines.
• The false chromosome is coiled forming a chromosomal region called nucleoid
• Protein synthesis occurs at 70S ribosomes

Eubacteria

Shape

Bacteria can be grouped into four types based on shape:

• Spherical coccus (e.g., Streptococcus)
• Rod-shaped bacillus (e.g., Escherichia coli)
• Comma-shaped vibrium (e.g., Vibrio cholerae)
• Spiral spirillum (e.g., Spirillum)

Motility

• Bacteria can be motile or non-motile, moving using flagella.
• Flagellation indicates the number and arrangement of flagella.
• Peritrichous indicates that flagella cover the organism, (e.g., E. coli, Salmonella typhi).

Pili

• Hair-like structures called pili, cover the bacterial cell wall.
• Pili are different from flagella as they are smaller
• Two kinds exist, shorter and longer pili.
• Longer pili, known as "F" or "sex" pili, aid in conjugation and are absent in recipient or female bacteria.
• Shorter "infective" pili, or fimbriae, are present in pathogenic bacteria and aid in adhering to the host's tissues and to rocks.

Structure of Prokaryotic cell

• Bacterial architecture is deceptively complex, as inside the cell there is very limited physical structure.
• The bacterial cell wall is comprised of an envelope.
• The cell envelope consists of a bound tightly, three-layered structure.
• The layers being: a capsule (glycocalyx), cell membrane and cell wall.
• The layers in an envelope have distinct individual functions, but act collectively.
• Some bacteria are surrounded by a capsule and are called capsulated bacteria.
• Capsules are generated by cell membranes mostly.Capsules consist of polysaccharides and polypeptides. Glycocalyx protects against white blood cells and helps with colony formation
• Molecules of polysaccharides loosely formed as slime then creates a sticky layer, known as a slime layer.
• Most bacteria's rigid cell wall comprise peptidoglycan or murein (mucopeptide).
• The cell wall is the main differing factor in the gram test. Gram (+) bacteria have one thick peptidoglycan layer, with small quantities of lipids.
• Gram (-) bacteria have two layers - a thin peptidoglycan layer and a thick lipopolysaccharide outer layer along with lipoproteins and phospholipids.
• The cytoplasm of the bacterial cell does not stream, nor does it contain cyclosis, mitochondria, chloroplasts, or other structures that are membrane bound.
• The cytoplasm contains cytoplasmic structures. One such structure is mesosomes these are structures formed in the plasma.
• Mesosomes assist in cell wall secretion and cell respiration, these features create a larger surface area of enzymatic content and plasma membrane to cover.
• They help separate daughter cell DNA, along with DNA replication for distribution to daughter cells upon division.
• Some bacteria's cytoplasm contains storage for nutrients and inorganic phosphate granules.
• In bacteria, nuclear material (nucleoid) lacks a nuclear membrane and nucleolus.
• Bacteria have a double stranded circular DNA and Non-histone proteins instead of true DNA.
• Polyamines replace histone proteins with non-histone ones . Nucleoid attaches to mesosome.
• Another small, circular DNA that is genetically separate is extra chromosomal or extranuclear or extra genomic genetic material, also called plasmid.

F-plasmid (fertility factor)

• On the basis of presence or absence of plasmid, there exist two types of bacteria:
• The '"F+"' cell has plasmid F and is hence a donor or '"male"'. The '"F-"' cells lack plasmid F, these are '"female"'. When plasmid 'F' is linked to primary DNA that is cell line HFR is constructed (Highly frequent recombinant cell).

Resistance

• Bacteria may have plasmids, conferring resistance to some antibiotics (R factor).

Gram Staining

• H.C. Gram classified bacteria on staining basis.
• Crystal or gentian violet is applied followed by a Kl solution in the first step.
• Use acetone and ethyl alcohol, wash the bacteria after applying dye.
• Gram positive bacteria are those that retain the dye (purple or violet). Wash decolourised, are known as Gram-negative.. These bacteria use dye called saffronin, it stains with a contrasting color

Bacterial Nutrition

• Bacteria exhibits significant metabolic diversity.
• Most are autotrophic or heterotrophic, some being both.They can be categorised into three categories based on nutrition in three categories: symbiotic, autotrophic, and heterotrophic.
• Energy sources vary among autotrophs.
• Photosynthetic autotrophs use light to make food with light energy.
• Water is not the donor of photosynthesis, so that release of oxygen is not possible. This form constitutes none-oxygenic photosynthesis.
• Pigments are scattered
• Heterotrophic bacteria obtain energy by consuming organic matter or other organisms, also called saprophytes.
• Purple bacteria use bacteriochlorophylls ‘a’ & ‘b’
• Green species use chlorobium and bacterioviridin.
• Similarly, they are chemosynthetic in others who use energy of chemical origin.
• Use inorganic compounds. Energy makes food.
• Nitrifying oxidise compounds as well as nitrogen.
• Nitrite type uses nitrite for ammonia (Nitrosomonas & Nitrococcus)
• Nitrate use nitrite (Nitrobacter). Chemo synthesis is great for creating key nitrogen, phosphorus, iron sulfur nutrients in the cycle

Heterotrophs

• Most are unable to produce food.
• They secure nourishment from remains of decomposed organs or other organisms.
• Saprotrophic bacteria feed on death and decay through organic material like Bacillus vulgaris, Clostridium botulinum and P seudomonas
• On the other hand, parasite nutrition is gained of bacteria from a host or another organism, examples are tuberculosis, lepra, micobacterium among other such strains.

Symbiosis

• Some bacteria enter symbiosis. An example is transforming nitrogen in the air to amino acid, nitrite etc, by the genus Rhizobium.

Respiration

Based on bacteria respiration, there exist two variants

• Aerobic: Azobacter, and others, utilize air
• Anaerobic: C lostridium and related do not use air.

Reproduction

• Bacteria population multiplies through reproduction in large numbers
• Bacteria generally produce only by asexual production, nevertheless, some can perform gene transfers, referred to as genetic recombination.

Asexual Production

• Many bacteria reproduce asexually.
• Binary Fission is most widely utilized. As a first step bacteria perform the DNA replication in this phase in advance.
• When bacteria locate favourable conditions, they split into two through septum formation.
• Next, the two parts rise in magnitude creating a brand new bacteria.
• Bacterial cell division is carried out through amitosis, which is quicker than meiosis and mitosis

Endospore formation

• Endospore formation happens in unfavorable conditions.
• One cell carries only one kind of spore.
• It forms a very resistance structure, able to withstand heat and radiations.
• Contains large quantities of Ca-dipicolinate.

Genetic Recombination

• Bacteria transfer genes between cells during contact.
• Conjugation between F+ and F-happens with a transfer of genetic material
• Donor adheres to recipient by pili , they aid as sex transfer tube.
• One of F factors duplicates into a replica that migrates to a recipient. The tube then transfers.
• Eventually, they part in this process leading to a change in F cell, and then changes into + F
• During transformation or transfer, genetic composition alterations takes affect via the bacterial surroundings.

Transduction

• Transduction - gene transfer between two distinct viruses (bacteriophages).

Economic Effects of some common Bacteria

• The diseases that infect human through bacteriological infection of animals are vast

Human Diseases

• Tuberculosis: caused by bacteria Mycobacterium
• Leprosy: Disease developed by bacterial agents of Mycobacterium leprae that is also a germ for tuberculosis
• Tetanus: bacterial cause by Clostridium tetani
• Typhoid: Salmonela Typhi infection.
• Cholera : bacterial pathogen called Vibrio cholerae is what generates this life-threatening disease.
• Anthrax impacts animals Citrus canker developed through Xanthomonas citi as well as crowd Gall from Agrobacterium Tumefaciens. Botulism, a form is initiated by the bacteria Clostridium botulinum, and leads to a severe food intoxication event. It inhibits sympathetic nervous system, it harms soft tissue. Pollution tests shows that they infect large bodies of water. E. coli. serves to measure bacteria that has pollutants. E coli number represents quality of water.

Useful Bacteria

• Bacteria are the cornerstones of multiple Antibiotic and Dairy products
• Antibodies are harvested by bacterias like as are Streptomycin and Streptomyces Griseus
• Streptomycin is attained of bacteria like as are Streptomyces Griseus LAB can check the microbes causing the disease throughout tummy by giving increased amount of B12 for curd development.
• Bacteria are a key factor for inherited science. Agrobacterium/E. coli, in general, are g(+) bacteria that can be integrated during cloning In conclusion, archaebacteria were first discovered as oldest life forms, mostly anaerobic organisms as cell walls were built with complex polysaccharide and polypeptide and highly complex cell membrane due to branched lipid chain. All live on severe environments like methanogens, thermophiles. Methanogens transform gases to manufacture methane/biogas.. Methanogen bacteria species, including as Methan coccus, Metanobacterium and Methno microbium are located is rumin of cattle for development gases.

Bacteria Nutrition and Characteristics

• Halophiles remain living throughout severe brackish surrounding

Cyano Bacteria [Blue Green Algae]

• Monera possess Cyanobacteria, prokaryotic algae and B.G.A are prokaryotic, and have prokaryotic traits
• Cynobacteria generate Ox. as one of first organisms
• Photosynthesis is achieved via thylakoids or symbiotic alga
• Chromatic extensions for cyano bacteria contain pigments for photosynthesis for their bodies Forms of cyanobacteria
• Cyano can be Unicellular or multicellular.
• The filament of B.G.A. know as trichrome. (examples: Oscillatoria, Nostoc)
• B.G.A is similar Gram-negative bacterium (Gram +-) and possesses same bilayer for such. the Gram outer covers of it has lipo polysaccharides whilst inside covers built of peptidoglycan.
• Some species from species Oscilla toria can release substances, that obstruct mosquitoes out from waters, so as they can protect it.
• Cyanophycean makes reserves if meals/ starch are absent by generating certain granules also cyano granules can lead to glycogen.
• Vacuoles for nitrogen fixation by bacteria, and anabena are produced by nitrogen fixation with species like in Azolla for cycads so with that they can fertilize.
• However others might fix in paddy fields as Anabena, Oscillario while the B.G.A can fix 50% in nitrogen.

Mycoplasmas

• As per Nocard as well as some scientist for cattle lung tissue research, mycoplasmas was PPLO
• Nowak put it all to their category or mycoplasma so that those can transform.
• These have cell that transform is between 0.1-0. Micrometers. Cell are lipoproteins including as RNA.
• Mycloplasmas do however, show polymorphism are cell is absence of joker or animal microbiology.

Kingdom - Prostista

• All are eukaryotic protists
• Many members of the Kingdom are mainly amphibious, plus they have protistan cells including nucleus and cell membrane for cytoplasm or flagella.
• Cell of Protisitians is cell wall comprised of cellulose or just proteins like algae