Biological Classification Systems

Biological Classification Overview

• Attempts to classify living organisms have been made since the dawn of civilization based on usage (food, shelter, clothing) rather than scientific criteria

Early Classification Attempts

• Aristotle used simple morphological characteristics to classify plants into trees, shrubs, and herbs
• Animals were divided into those with red blood and those without

Linnaeus's Two Kingdom System

• The two-kingdom system, with Plantae and Animalia, classified all organisms as either plants or animals
• This system failed to differentiate between eukaryotes and prokaryotes
• It also failed to distinguish between unicellular and multicellular organisms, or photosynthetic and non-photosynthetic organisms

Limitations of the Two Kingdom System

• Many organisms could not be definitively placed into either the plant or animal kingdom
• Gross morphology was deemed inadequate, necessitating consideration of cell structure, nature of the cell wall, mode of nutrition, habitat, methods of reproduction, and evolutionary relationships

Evolution of Classification Systems

• Classification systems have undergone multiple revisions over time
• While the plant and animal kingdoms have remained constant, the understanding of which organisms belong to them has evolved
• Different scientists have had different understandings of the number and nature of kingdoms

Whittaker's Five Kingdom Classification

• R.H. Whittaker proposed the Five Kingdom Classification in 1969
• Kingdoms include Monera, Protista, Fungi, Plantae, and Animalia
• Classification was based on cell structure, body organization, mode of nutrition, reproduction, and phylogenetic relationships

Characteristics of the Five Kingdoms

• Monera: Prokaryotic with noncellulosic cell wall, cellular organization and the mode of nutrition is autotrophic or heterotrophic
• Protista: Eukaryotic, cellular organization, and their mode of nutrition is autotrophic and heterotrophic
• Fungi: Eukaryotic, multicellular/loose tissue organization, cell wall is present with chitin and the mode of nutrition is heterotrophic (saprophytic/parasitic)
• Plantae: Eukaryotic, tissue/organ organization, cell wall is present made up of cellulose and the mode of nutrition is autotrophic
• Animalia: Eukaryotic, tissue/organ/organ system organization, cell wall is absent and the mode of nutrition is heterotrophic (holozoic/saprophytic etc.)

Three-Domain System

• The three-domain system divides Kingdom Monera into two domains
• It leaves the remaining eukaryotic kingdoms in the third domain, resulting in a six-kingdom classification.

Issues in Five Kingdom Classification

• Earlier systems placed bacteria, blue-green algae, fungi, mosses, ferns, gymnosperms, and angiosperms all under 'Plants' because of the unifying characteristic of cell walls
• Prokaryotic bacteria and blue-green algae (cyanobacteria) were grouped with eukaryotic organisms
• Unicellular (Chlamydomonas) and multicellular (Spirogyra) organisms were both placed under algae

Refinements in Classification

• Fungi were separated into Kingdom Fungi due to the presence of chitin in their cell walls, whereas green plants have cellulosic cell walls
• Prokaryotic organisms were grouped into Kingdom Monera
• Unicellular eukaryotic organisms were placed in Kingdom Protista
• Kingdom Protista brought together Chlamydomonas, Chlorella, Paramoecium and Amoeba

Modern Classification Goals

• Modern classification aims to reflect morphological, physiological, and reproductive similarities, and also be phylogenetic (based on evolutionary relationships).

Focus of the Chapter

• This chapter examines the characteristics of Kingdoms Monera, Protista, and Fungi under the Whittaker system.
• Kingdoms Plantae and Animalia are covered separately in later chapters

Kingdom Monera

• Bacteria are the sole members, and are the most abundant microorganisms, found almost everywhere
• Bacteria can survive in extreme habitats such as hot springs, deserts, snow, and deep oceans, and many live as parasites

Bacterial Shapes

• Bacteria are grouped into four categories based on shape
  • Spherical Coccus (pl.: cocci)
  • Rod-shaped Bacillus (pl.: bacilli)
  • Comma-shaped Vibrium (pl.: vibrio)
  • Spiral Spirillum (pl.: spirilla)

Bacterial Complexity and Diversity

• Despite their simple structure, bacteria exhibit complex behavior and the most extensive metabolic diversity
• Some bacteria are autotrophic, creating their own food from inorganic substances, either through photosynthesis or chemosynthesis
• Most bacteria are heterotrophic, depending on other organisms or dead organic matter for food

Archaebacteria

• Archaebacteria live in harsh habitats: extreme salty areas (halophiles), hot springs (thermoacidophiles), and marshy areas (methanogens)
• They differ from other bacteria due to their unique cell wall structure, enabling survival in extreme conditions
• Methanogens in the gut of ruminant animals produce methane (biogas) from dung

Eubacteria

• Eubacteria, or 'true bacteria,' have thousands of different types
• Characterized by a rigid cell wall and, if motile, a flagellum

Cyanobacteria

• Cyanobacteria (blue-green algae) contain chlorophyll a, similar to green plants, and are photosynthetic autotrophs
• They can be unicellular, colonial, or filamentous, and live in freshwater, marine or terrestrial environments
• Colonies are surrounded by a gelatinous sheath
• They can form blooms in polluted water
• Some fix atmospheric nitrogen in specialized cells called heterocysts (e.g., Nostoc and Anabaena)

Chemosynthetic Autotrophic Bacteria

• Chemosynthetic autotrophic bacteria oxidize inorganic substances like nitrates, nitrites, and ammonia
• They use the released energy for ATP production and recycle nutrients like nitrogen, phosphorous, iron, and sulphur

Heterotrophic Bacteria

• Heterotrophic bacteria are most abundant in nature and act as important decomposers
• Many have a significant impact on human affairs
• Help in making curd from milk, producing antibiotics, and fixing nitrogen in legume roots

Bacterial Reproduction

• Bacteria reproduce mainly by fission
• Under unfavorable conditions, they produce spores
• They reproduce sexually by adopting a primitive type of DNA transfer from one bacterium to another

Mycoplasma

• Mycoplasma lack a cell wall
• They are the smallest living cells and can survive without oxygen
• Many mycoplasma are pathogenic in animals and plants

Kingdom Protista

• Protista includes all single-celled eukaryotes with not well defined boundaries
• Includes Chrysophytes, Dinoflagellates, Euglenoids, Slime molds, and Protozoans
• Members are primarily aquatic
• Acts as a link between plants, animals, and fungi
• Protistan cell body contains a well-defined nucleus and other membrane-bound organelles
• Some have flagella or cilia
• Reproduce asexually and sexually through cell fusion and zygote formation

Chrysophytes

• Includes diatoms and golden algae (desmids)
• Found in freshwater and marine environments
• Microscopic and float passively in water (plankton)
• Mostly photosynthetic
• Diatom cell walls form two overlapping shells, like a soap box
• Walls are embedded with silica, making them indestructible
• Accumulation of cell wall deposits over billions of years forms ‘diatomaceous earth’
• Used in polishing and filtration of oils and syrups
• Diatoms are the chief 'producers' in the oceans

Dinoflagellates

• Mostly marine and photosynthetic
• Appear yellow, green, brown, blue, or red based on the main pigments in their cells
• Cell wall has stiff cellulose plates on the outer surface
• Usually have two flagella: one longitudinal, other transverse in a furrow
• Red dinoflagellates (Gonyaulax) can rapidly multiply, causing "red tides"
• Toxins released can kill other marine animals like fishes

Euglenoids

• Mostly freshwater organisms in stagnant water
• Have a protein-rich layer called pellicle instead of a cell wall, making their body flexible
• Possess two flagella (one short, one long)
• Photosynthetic in sunlight, but heterotrophic by predating on smaller organisms when deprived of sunlight
• Pigments identical to those in higher plants (e.g., Euglena)

Slime Moulds

• Saprophytic protists
• Body moves along decaying twigs and leaves, engulfing organic material
• Under suitable conditions, they form a plasmodium aggregation that can spread over feet
• During unfavorable conditions, plasmodium differentiates and forms fruiting bodies bearing spores at their tips
• Spores have true walls, are resistant, survive for years, and are dispersed by air currents

Protozoans

• All protozoans are heterotrophs, living as predators or parasites
• Believed to be primitive relatives of animals
• Four major groups: Amoeboid, Flagellated, Ciliated, and Sporozoans

Amoeboid Protozoans

• Live in fresh water, sea water, or moist soil
• Move and capture prey by putting out pseudopodia (false feet), as in Amoeba
• Marine forms have silica shells
• Some (e.g., Entamoeba) are parasites

Flagellated Protozoans

• Either free-living or parasitic (e.g., Trypanosoma, which causes sleeping sickness)
• Possess flagella

Ciliated Protozoans

• Aquatic, actively moving organisms due to thousands of cilia
• Have a cavity (gullet) that opens to the outside of the cell surface
• Rows of cilia coordinate to steer water laden with food into the gullet (e.g., Paramoecium)

Sporozoans

• Diverse organisms with an infectious spore-like stage in their life cycle
• Plasmodium (malarial parasite) causes malaria, a disease with a staggering effect on the human population

Kingdom Fungi

• The fungi constitute a unique kingdom of heterotrophic organisms
• Show great diversity in morphology and habitat

Examples of Fungi

• Mushrooms and toadstools are fungi
• White spots on mustard leaves are due to a parasitic fungus
• Some unicellular fungi (e.g., yeast) are used to make bread and beer
• Other fungi cause diseases in plants and animals
• The wheat rust-causing Puccinia is an important example
• Some are the source of antibiotics (e.g., Penicillium)

Characteristics of Fungi

• Cosmopolitan, found in air, water, soil, and on animals and plants
• Prefer to grow in warm, humid places
• Except for unicellular yeasts, fungi are filamentous
• Bodies consist of long, slender, thread-like structures called hyphae
• The network of hyphae is known as mycelium
• Some hyphae are continuous tubes filled with multinucleated cytoplasm called coenocytic hyphae
• Others have septae or cross walls in their hyphae
• Cell walls are composed of chitin and polysaccharides

Nutrition in Fungi

• Most fungi are heterotrophic, absorbing soluble organic matter from dead substrates (saprophytes)
• Those that depend on living plants and animals are parasites
• They can also live as symbionts – in association with algae as lichens and with roots of higher plants as mycorrhiza

Reproduction in Fungi

• Reproduction can occur through vegetative means: fragmentation, fission, and budding
• Asexual reproduction is by spores (conidia, sporangiospores, or zoospores)
• Sexual reproduction is by oospores, ascospores, and basidiospores
• Various spores are produced in distinct structures called fruiting bodies
• Sexual cycle includes three steps: plasmogamy, karyogamy, and meiosis in zygote

Sexual Reproduction in Fungi

• When a fungus reproduces sexually, two haploid hyphae of compatible mating types come together and fuse
• Sometimes, fusion results directly in diploid cells (2n)
• In other fungi (ascomycetes and basidiomycetes), an intervening dikaryotic stage (n + n, two nuclei per cell) occurs, resulting in dikaryon and dikaryophase of fungus
• Parental nuclei fuse later, becoming diploid
• Fungi form fruiting bodies in which reduction division occurs, leading to formation of haploid spores

Classification of Fungi

• Morphology of the mycelium, mode of spore formation, and fruiting bodies form the basis for division into classes

Phycomycetes

• Found in aquatic habitats, on decaying wood in moist and damp places, or as obligate parasites on plants
• Mycelium is aseptate and coenocytic
• Asexual reproduction by zoospores (motile) or aplanospores (non-motile), produced endogenously in sporangium
• Zygospore formed by fusion of two gametes that are either similar (isogamous) or dissimilar (anisogamous or oogamous) Examples: Mucor, Rhizopus, and Albugo

Ascomycetes

• Commonly known as sac-fungi, mostly multicellular (e.g., Penicillium), or rarely unicellular (e.g., yeast / Saccharomyces)
• Saprophytic, decomposers, parasitic or coprophilous (growing on dung)
• Mycelium is branched and septate
• Asexual spores (conidia) produced exogenously on conidiophores
• Conidia on germination produce mycelium
• Sexual spores (ascospores) produced endogenously in sac-like asci, which are arranged in fruiting bodies (ascocarps)
• Neurospora is used extensively in biochemical and genetic work, edible members include morels and truffles

Basidiomycetes

• Commonly known as mushrooms, bracket fungi, or puffballs
• Grow in the soil, on logs and tree stumps, and in living plant bodies as parasites (e.g., rusts and smuts)
• Mycelium is branched and septate
• Asexual spores are generally not found; vegetative reproduction by fragmentation is common
• Sex organs are absent, but plasmogamy occurs by fusion of two vegetative or somatic cells of different strains or genotypes
• Results in a dikaryotic structure that gives rise to basidium
• Karyogamy and meiosis occur in the basidium, producing four basidiospores
• Basidiospores are exogenously produced on the basidium, arranged in fruiting bodies called basidiocarps
• Common members: Agaricus (mushroom), Ustilago (smut), and Puccinia (rust fungus)

Deuteromycetes

• Commonly known as imperfect fungi because only the asexual or vegetative phases are known
• When sexual forms are discovered, they are moved into other classes
• Deuteromycetes reproduce only by asexual spores called conidia
• Mycelium is septate and branched
• Some are saprophytes or parasites, and many are decomposers of litter, aiding in mineral cycling
• Examples: Alternaria, Colletotrichum, and Trichoderma

Kingdom Plantae Characteristics

• Includes all eukaryotic chlorophyll-containing organisms
• A few members are partially heterotrophic like insectivorous plants or parasites (Bladderwort, Venus fly trap, and Cuscuta)
• The plant cells have an eukaryotic structure with prominent chloroplasts, and a cell wall made of cellulose
• Includes algae, bryophytes, pteridophytes, gymnosperms and angiosperms

Plant Life Cycle

• Life cycle of plants has two distinct phases –diploid sporophytic and haploid gametophytic
• These 2 phases alternate with each other
• Lengths of the haploid and diploid phases, and whether these phases are free-living or dependent on each other, can vary among different groups
• Phenomenon called alternation of generation

Kingdom Animalia Characteristics

• Characterized by heterotrophic eukaryotic organisms, which are multicellular and lack cell walls
• Directly or indirectly depend on plants for food
• Digest food in an internal cavity, storing food reserves as glycogen or fat
• Holozoic nutrition (ingestion of food)
• Animals follow a definite growth pattern, growing into adults with a definite shape and size
• Higher forms show elaborate sensory and neuromotor mechanisms
• Capable of locomotion
• Sexual reproduction by copulation, followed by embryological development

Viruses, Viroids, Prions and Lichens

• These acellular organisms are not included in Whittaker’s five kingdom classification
• Viruses are non-cellular, characterized by having an inert crystalline structure outside a living cell despite causing illness

Viruses

• Dmitri Ivanowsky (1892) recognized certain microbes which causes mosaic disease of tobacco
• M.W. Beijerinek (1898) named the new pathogen “virus” calling the fluid, Contagium vivum fluidum
• W.M. Stanley (1935) showed viruses could be crystallized consisting of proteins, remaining inert outside their specific host cell, acting as obligate parasites
• Viruses consist of proteins, and genetic material (either RNA or DNA but never both)
• Nucleoprotein genetic material can infect a host
• Plant viruses genetic material is single stranded RNA while animal infecting viruses genetic material is double stranded RNA or DNA
• Capsid (the protein coat) comprises small subunits called capsomeres protecting the nucleic acid
• They are arranged in helical or polyhedral geometric forms
• Viruses cause Mumps, small pox, herpes influenza, AIDS
• Plant virus symptoms include mosaic formation, leaf rolling and curling, yellowing and vein clearing, dwarfing and stunted growth.

Viroids :

• In 1971, T.O. Diener discovered a new infectious agent that was smaller than viruses and caused potato spindle tuber disease
• Free RNA lacked the protein coat
• Its RNA was of low molecular weight.

Prions

• Prions infectious neurological diseases due to abnormally folded protein, found to be similar in size to viruses
• Notable diseases include bovine spongiform encephalopathy (BSE) commonly called mad cow disease in cattle and its analogous variant Cr–Jacob disease (CJD) in humans.

Lichens

• Lichens are symbiotic associations between algae (phycobiont - autotrophic) and fungi (mycobiont - heterotrophic)
• Algae prepare food for fungi, and fungi provide shelter and absorb mineral nutrients and water for its partner
• Lichens are good pollution indicators, they do not grow in polluted areas.