BIOLOGICAL CLASSIFICATION – PART 2
Members of Protista are unicellular, Eukaryotes, Free-living; Exception with few organisms found in colonies. It is an intermediate between Monera, plants and animals.
General Characteristic of Kingdom Protista
Some Protists are colonial and lack higher cellular differentiation. Hence, there is no tissue organization in the members of this kingdom. Many protists are aquatic organisms in nature. The cell structure is eukaryotic in nature having membrane-bound organelles of all the types along with the 80S cytoplasmic ribosomes. Some organisms have a cellulosic cell wall. All the protists possess well-defined nucleus with varying number i.e. uninucleate, binucleate, multinucleate.
Flagella and cilia have microtubule organization consisting of tubulin protein arranged in (9 + 2) pattern. Movement of the organisms is by pseudopodia, flagella and cilia where the ciliary mode is the fastest among them giving a speed of 2mm/s. Mode of nutrition among all the Protists ranges from photosynthetic (holophytic), holozoic (ingestive), saprobic to parasitic (absorptive). Some have mixed type of nutrition (photosynthetic and saprobic) like the one in Euglena.
Reproduction takes place by both: asexual and sexual methods. The life cycle in Protists is of 2 types –major one showing zygotic meiosis and the minor one showing gametic meiosis. The Protists are decomposers, photosynthetic or parasitic in nature. Parasitic protists may cause diseases like dysentery, malaria, sleeping sickness etc. when encountered a host.
Diatoms are photosynthetic Protists that are also called as Chrysophytes (including both diatoms and desmids). They grow in both aquatic and terrestrial environments.
Their important characters are:
These are organisms that show diversity in colour having a size in micrometres hence called as microscopic Protists. They are generally unicellular, however, some diatoms may form pseudo filament and colonies. They lack flagella in their life except when in the reproductive stage and may be free floating in underwater (phytoplanktonic) or floating on the surface of the water when they have lightweight lipids.
The cells have the covering of cellulosic cell wall that is impregnated with silica to form a transparent siliceous shell, known as frustule. Depending upon the symmetry, diatoms may be pennate type, having bilateral symmetry (e.g., Navicula) and centric type, having radial symmetry (e.g., Melosira). The cell wall is characteristic, made up of two halves; one half covering the other (epitheca over hypotheca) resembling a soapbox. The cell wall encloses the peripheral layer of the cytoplasm (primordial utricle) surrounding a large central vacuole. Nucleus lies in the central vacuole, suspended with the help of cytoplasmic strands.
Mode of nutrition is holophytic (photoautotrophic), photosynthetic pigments are chlorophyll a, chlorophyll c, β carotene and special carotenoids containing fucoxanthin; xanthophylls like diatoxanthin, diadinoxanthin. The reserve food material is in the form of oil and a polysaccharide called leucosin (chrysolaminarin), even the cell shows the presence of volutin granules.
As the cells produce oils as food material they contribute almost 50% of the total organic matter and oils synthesized in the biosphere. Movement of diatoms is with the mucilage propulsion. The reproduction of diatoms is by asexual method, binary fission being most common mode. They reproduce sexually varying from isogamy to oogamy. Diatoms are diploid thus involving gametic meiosis (diplontic life cycle). During binary fission, the parent cell takes the first half of the cell wall and other is secreted afresh. Resting spores that have thick covering is formed within the diatoms are called statospores (centric diatoms).
Dinoflagellates are photosynthetic Protists having a golden brown colour that belongs to the class Dinophyceae (Pyrrophyta). They are mainly marine dwellers with few organisms growing in freshwater forms. They show red, yellow, green, brown or blue appearance that occurs due to the pigment present in the cell.
General characters of dinoflagellates are as follows
They are motile, biflagellate showing golden brown photosynthetic Protists (some are non-motile, amoeboid, palmelloid or filamentous). They are mostly marine, and some of them are found in fresh water. The body has the rigid coating called the theca or lorica that consists of 2 and above articulated or sculptured plates of cellulose and pectin, hence are also called armoured dinoflagellates. Theca shows two grooves, the longitudinal one called as sulcus and the other transverse called as cingulum or annulus or girdle.
Each of the grooves contains respective flagellum. There are two flagella in heterokont (different) position, one is longitudinal and the other is transverse outwards the cell. The flagella are across the pores in the lorica, lying in the grooves of the cell. The longitudinal flagellum is narrow, smooth directed posteriorly and the transverse flagellum is ribbon-like. Both are oriented at right angle to each other producing spinning movements for the cell. Thus, Protists are also called as ‘whirling whips’. Most of the species show brown, green or yellow colour as they have chromatophores with chlorophyll a, c, D -carotene, xanthophyll (e.g., Peridinin). Plastids have a 3-membrane envelope that contains 3-thylakoid lamellae. The species are photosynthetic (Ceratium) while few of them are saprobic or parasitic.
Reserve food is in the form of carbohydrate and oils. The nucleus is relatively larger in size with condensed chromosomes that lack histone. Nucleus envelops along with nucleus remain in the cell at all the stages of cell division. A non-contractile vacuole called as the pusule occur at the flagellar base. It may contain one or more vesicle and is involved in flotation and osmoregulation. Some dinoflagellates show the presence of trichocysts and cnidoblasts similar to the coelenterates.
Reproduction is asexual taking place through the usual cell division. Isogamous and anisogamous sexual reproduction are also observed in some dinoflagellates, e.g., Ceratium. The life cycle of dinoflagellates shows zygotic meiosis (Ceratium, Gymnodinium). Gametic meiosis takes place in Noctiluca.
The group of chlorophyllous and achlorophyllous flagellate Protists. Largest genera being Euglena amongst them.
General characteristics of Euglenoid
Flagellate Protists found in the aquatic region (freshwater organisms found in stagnant water) or damp soil. The body has spindle shape, blunt at the anterior part and pointed at the posterior end Cell wall is absent however the cell is covered by proteinaceous periplast or pellicle. Flagella causes locomotion.
The cell bears a pair of flagella arising at the anterior end. One of these is long tinsel type flagellum (stichonematic) and the other is reduced. The longer flagellum branches at the base in two that its own basal granule. The union of two flagella contains a photosensitive paraflagellar body. Euglenoids carry out creeping movement of contraction and expansion with the help of myonemes (strips in pellicle) which is called metaboly or Euglenoid movement. The apical end consists of an invagination having three distinct parts, i.e., mouth (cytostome), canal (gullet or cytopharynx) and reservoir. These help to take up the solid food particles. Stigma or an eyespot is present at the base of the paraflagellar body attached to the membrane. The eye is assumed to be perceptive for light stimulus. It has photosensitive red-orange pigment which is called as the astaxanthin.
A contractive vacuole occurs in the anterior end of the cell just below the reservoir, meant for osmoregulation and exception. A single large nucleus is approximately at the centre of the protoplast. Nutrition in Euglena viridis is photoautotrophic. However, when the light is insufficient, it takes nourishment from dead and decaying organic matter present in the substrate as it can secrete digestive enzymes (saprophytic nutrition). This nutrition dual mode is termed as mixotrophic. Holozoic nutrition is absent in Euglena, however, some forms are holozoic (Paranema) or saprobic (Rhabdomonas). Photosynthetic pigments in the cell are chlorophyll a, chlorophyll b, xanthophyll and β-carotene giving it the colour.
Reserve food material is called as paramylon. These paramylum granules are stored in the cytoplasm. They are chemically β -1, 3-glucans. Longitudinal binary fission is the reproduction mode under favourable conditions. During unfavourable conditions, palmella stage cysts are produced by the cells for perennation. e.g., Euglena and Paranema.
Slime Moulds or Consumer-Decomposer Protists
They were initially included in the class myxomycetes in the class fungi in the two-kingdom classification system of Plantae and Animalia. They were called as mycetozoa as they closely resemble animals, by DeBary. Slime moulds are included in Gymnomycota by Mycologists. As they are similar to fungi, they are called as Protistan fungi.
They are free-living, similar to creeping over debris on fallen leaves and rotting woody logs. They lack a cell wall and have a naked protoplast in the vegetative stage of the life cycle and lack chlorophyll, thus have saprobic or phagotrophic nutrition mode. Slime moulds are amoeboid and lack cellulosic wall during the life cycle, but spores show cellulosic wall. Their vegetative phase is similar with animals while the reproductive phase is similar with plants. They have protozoa like an amoeboid plasmodial stage and fungi like in spore formation. Spores are extremely strong and resistant to adverse conditions. They survive for many years and get dispersed by air currents. Reproduction is by both asexual and sexual methods.
This group is represented by two separate types of organisms i.e. acellular and cellular.
Kingdom Fungi (Mycota)
Members of Fungi are Multicellular(except Yeast and Synchytrium), Decomposers (absorptive), Spore forming and Eukaryotes. The study of fungi and its characteristics are called as mycology.
General Characters of Fungi
They are found in air, water, soil, on animals and plants. They are Omnipresent in various conditions and Mostly terrestrial and love to grow in warm and humid places. Also, they may grow on wood, burnt wood, tree bark, and keratinous material (e.g., hair, horns), are thus called as corticolous (bark), coprophilous (cow dung), epixylic (wood), xylophilous (burnt wood) and keratinophilous (keratin) respectively.
The body is haploid (n) and thalloid, lacking proper root, stem and leaves. The fungal body shows thread like elongated tubular structures which is called as hyphae. These hyphae are in cris-cross pattern forming a network called as a mycelium. The hyphae show aseptate and multinucleate pattern termed as the coenocytic. The mycelium is septate in maximum species. The septum shows the presence of a pore which is continuous to the cytoplasm of the adjacent cells. The septum either has a simple central pore as in ascomycetes ordolipore septum in higher fungi (class basidiomycetes). Also the presence of a single nucleus (monokaryotic-feature of primary mycelium) or an intermediate phase of two nuclei (dikaryotic-feature of secondary mycelium) in the cell.
The cell wall is made up of chitin or fungal cellulose (acetyl glucosamine) in the hyphae. Some fungi have the cellulosic cell wall (e.g., Phytophthora, Pythia and other oomycetes). Oil and glycogen is the reserve food material. Cells contain unicisternal Golgi bodies and not the usual one. Mitosis in somatic cells is Karyochorisis type (mitosis with intranuclear spindle formation). Heterotrophic and absorptive nutrition mode which involves saprophytes, parasites and symbionts pattern.
The fungi have two distinct phases in their life cycle: the vegetative or assimilative phase and the reductive phase. During the vegetative phase, the fungus acquires microscopic size attached to the substratum. The fungus in the vegetative phase attains maturity then enters the reproductive phase. In unicellular yeasts, the cell functions in both the assimilative and reproductive phases. The fungal bodies get transformed into reproductive cells, they are then known as holocarpic. Fungal body is known as eucarpic when a part of the mycelium is involved in the developing process of reproductive structures.
Reproduction in Fungi
Fungi can reproduce by vegetative, asexual and sexual methods.
O Fragmentation: The mycelium gets an injury or decay and the cell is broken into two or more fragments. Each fragment has the ability to develop into independent mycelium.
O Fission: Vegetative cells simply split by a simple constriction into two daughters.
O Budding: Yeast has small outgrowths emerging from their vegetative body, called as buds. These buds mature into new individuals after they are separated from the parent cell.
Spores bring about the reproduction. Spores have single cell that are specialized structures, get detached from the cell, disperse and germinate under favourable conditions to produce new mycelium. The spores are a result of the mitotic division, thus termed as mitospores. The various means of asexual reproduction are as follows:
(i) Zoospore: Aquatic fungi produce such spores. It can be uniflagellate, e.g., Synchytrium or biflagellate, e.g., Saprolegnia, Pythium Naked uninucleate structures are formed in zoosporangia. They germinate to give rise to new mycelium. Biflagellate zoospores are of two kinds (e.g., Saprolegnia) pear-shaped or pyriform with 2 flagella placed at the anterior end (primary zoospore) and kidney-shaped or bean-shaped, bearing two laterally inserted flagella (secondary zoospore). This phenomenon of having two types of zoospores is called diplanetism.
(ii) Sporangiospores: Sporangiospores are thin-walled non-motile. Endogenous spores formed in a sporangium during unfavourable conditions liberate and give rise to a new mycelium, e.g., Rhizopus, Mucor.
(iii) Conidia: Non-motile, thin-walled exogenous spores. It is produced in the erect hyphae tips called conidiophore. Spores have a chain arrangement upon the conidiophore, e.g., Aspergillus and Penicillium.
(iv) Chlamydospore: Thick walled resistant spores getting separated from each other. Terminal or intercalary spores in a cell. They have viability for several years. In favourable conditions, new individuals germinate out. Thus, chlamydospores are structures for perennation also, e.g., Rhizopus.
(v) Oidia: Non-motile, thin-walled spores. Develop when in excessive sugar in the medium. Their budding conditions is termed as the torula stage.
Sexual reproduction takes place with the help of two fusing gametes. It includes 3 stages:
(i) Plasmogamy: Union of the two haploid protoplasts. The fusing nuclei of different parents thus come close. In some fungi, karyogamy occurs just after plasmogamy. However, Ascomycetes and Basidiomycetes have an intermediate step where dikaryotic (n + n) condition takes place, the phase is called as dikaryophase.
(ii) Karyogamy: Two haploid nuclei fuse to form diploid zygote after their fusion.
Meiosis: Zygote involves reduction division to divide the number of chromosomes to half. Plasmogamy occurs by the following methods:
Planogametic copulation/Gametic fusion: The simplest form in sexual reproduction. Fusion of two opposite sex or strains gamete occurs. Fusing gamete or both of them are motile. Production of a diploid zygote, e.g., Allomyces. This process is usually of three types: Isogamy, Anisogamy, and Oogamy.
Gametangial contact: Two gametangia come close in contact. The migration of complete male gametangium into the female gametangium is facilitated on the development of a fertilisation tube. Both the gametangia remain intact with their identity, e.g., Pythium, Albugo (Oomycetes).
Gametangial copulation: The direct fusion of the two gametangia completely occurs. It is due to the dissolution of their common walls forming a single cell. The protoplasts of two gametangia fuse in the cell, e.g., Mucor, Rhizopus (Zygomycetes).
Spermatisation: Minute, spore-like, single-celled structures are formed by few fungi called as the spermatia (non-motile male gametes) on spermatophores (hyphae). These spores are transferred through vectors to special female receptive hyphae (Basidiomycetes). The contents enter into the receptive structure causing a dikaryotic condition, e.g., Puccinia.
(iii) Somatogamy: Most of the higher true fungi have this step. The formation of gametes does not occur. In such fungi, direct fusion of somatic hyphal cells occurs to establish dikaryophase, e.g., Agaricus.
Classification of Fungi
There are various classifying systems for fungi. The major reasons for separation in this kingdom are Morphology of mycelium, mode of spore formation and fruiting bodies. The detailed description of the classes is as follows:
Mostly saprotrophic and rarely parasitic. Motile cells (zoospores or planogametes) are absent.
Mitospores are also non-motile. The spores are formed inside the sporangia present at the tips of special hyphae called sporangiophores. Spores are called sporangiospores. Zygospore, a diploid spore is formed in the sexual reproduction. Thus the class is called as zygomycetes. Zygospore is the meiosis site and does not give rise to new mycelium directly. Instead, it produces a new sporangium called germ sporangium. Germ sporangium forms meiospores called germ spores.
Ascomycetes: The Sac Fungi
The nutrition mode is saprophytic, decomposing, parasitic or coprophilous (growing on dung). The septa have central pores to communicate and transport nutrients among nearby cells called the septal pores. Motile structures are not present in the life cycle.
In a majority of the ascomycetes, conidia is the common mode of asexual reproduction. Conidia are produced and stored on branched or unbranched hyphae called conidiophores, e.g., Penicillium, Aspergillus. Female sex organ is present which is called as ascogonium. Plasmogamy occurs by means of- Gametangial contact (e.g., Pyronema), Conjugation (e.g., Yeast), Spermatisation (e.g., Ascobolus), Somatogamy (e.g., Peziza) and Autogamy (e.g., Morchella). Karyogamy and plasmogamy have an intermediate phase of dikaryophase. The cells of dikaryophase are called dikaryotic cells that have two different nuclei. This is a shorter phase of the life cycle as compared to others.
A dikaryotic cell transfers the nucleus to other cells with the crozier method (method of dikaryotisation) in order to make them dikaryotic. Some dikaryotic cells function as ascus mother cells to convert them into asci (singular – ascus). Ascus is a sporangial sac which is specific to Ascomycetes. Ascus is where karyogamy and meiosis occurs. 4 to 8 haploid ascospores are endogenously produced in the ascus. The ascospores produced belong to both the mating type equally: 50% to one mating type (+) and 50% to the second mating type (-). Ascospores may have a linear or improper arrangement. The asci may occur freely or get aggregated into specific fructifications called ascocarps. Ascocarps are: cup-like (apothecium, e.g, Peziza), flask-shaped (perithecium, e.g., Neurospora, Claviceps), elongated with a slit (hysterothecium), closed (cleistothecium, e.g., Penicillium) cushion, like chambered (ascostroma, e.g., Pleospora). The fructification of some ascomycetes is used as food, e.g., morels, truffles.
Basidiomycetes have the best decomposing ability and enzymes for wood (cellulose and lignin). Lignin is a sugar that is undigested by many fungi and even bacteria. Ganoderma species decay wood when it is on standing trees. Motile structures or cells are lacking. Mycelia are primary and secondary. Primary mycelium is made of monokaryotic cells which have a short life. Secondary mycelium is the dominant phase with long life, called as dikaryophase. It contains branched septate hyphae.
Monokaryotic phase divide oidia, conidia-like spores and pycniospores. Septa possess dolipores or central pores that has outgrowths in barrel-shape (except rusts and smuts). Secondary mycelium is sclerotia or rhizomorph that has penetrating ability in the soil or wood. Dikaryophase or secondary mycelium form different types of spores for their division– Chlamydospore, aeciospores, uredospores, teleutospores etc.
There are two mating types (+) and (-) in thallus. Sexual reproduction is without sex organs. Fusion occurs either between basidiospores and other monokaryotic spores, between a spore or spermatium and a hypha or between two hyphal cells of primary mycelia. Karyogamy and meiosis take place in a club-shaped structure called as basidia (singular – basidium) which gives the class its name. A basidium contains four exogenous meiospores or basidiospores located at the tips of fine outgrowths called sterigmata or directly on the surface of basidium. The fungi may contain fructifications called basidiocarps which may vary from microscopic size to large macroscopic structures. Some fungi may have 50 cm diameter of the fruit body.
Deuteromycetes lacks actual forms of fungus and is an artificial class (form class) of fungi. This is to accumulate all the fungi where sexual stage (or perfect stage) is not known yet (absent or not reported). As the members included in this class are in research, as and when the perfect (sexual) stages of members of Deuteromycetes are known they are moved to Ascomycetes and basidiomycetes. They are decomposers of litter and thus help in recycling mineral while some members are saprophytes or parasites.
Pasteur coined the virus term. Viruses are obligate intracellular parasites. The main reason of their kingdom or class not decided is that the viruses are both living and non-living entities.
Viruses Show Non-Living Nature
They lack protoplast and functional autonomy and cannot live independently outside. They have the capability to crystallize, e.g., TMV poliomyelitis virus. High specific gravity common in non-living objects. The absence of respiration. Energy storing system is not there at all. Growth and division are not observed.
Living Nature of Viruses
Organic macromolecules make the structure. Presence of genetic material. Genes that give the ability to multiply. They have mutating properties. They include certain enzymes like neuraminidase (first discovered), transcriptase and lysozyme in the body of viruses. Infectivity and host specificity. Viruses can be ‘’killed’’ by autoclaving and ultraviolet rays. The multiplication is through the biosynthetic machinery of the host cell that produces chemicals required for viruses. Viruses cause a number of infectious diseases like common cold, epidemic influenza, chicken pox, mumps, poliomyelitis, rabies, herpes, AIDS, SARS etc.
Structural Components of Viruses
Viruses are ultramicroscopic structures having a size in nanometres smaller than smallest bacteria. The outer covering of virus is a thin layer of protein (virus), lipids and carbohydrates (both from the host) called as an envelope. It includes smaller subunits that are called as peplomers, e.g., Herpes virus, HIV, vaccine virus etc. When the envelope is not present the virus is said to be naked.
Capsid: The outer protein coat is made up of subunits that are called as capsomeres, and their number is virus specific. These protein possess antigenic properties for the virus.
Nucleoid: Viruses contain either DNA or RNA. There is yet no virus with both DNA and RNA as genetic material. Viruses that have DNA as their genetic materials are called the deoxyviruses. These are of two types: Double-stranded DNA (dsDNA) virus, e.g., Pox virus, Cauliflower mosaic virus and Single-stranded DNA (ssDNA) virus, e.g., Coliphage φ x 174, M 13 phage.
RNA is the genetic material then viruses are known as riboviruses. They are of two types:
1. Double-stranded RNA (ds RNA) virus, e.g., Reovirus, Would Tumour virus.
2. Single-stranded RNA (ssRNA) virus, e.g., TMV, influenza virus, Foot and Mouth disease virus, Retroviruses (HIV).
Viroids (L. virus – poison, eidos – diminutive). Diener (1971) was working on viruses when he found some organisms smaller than them which could pass the filter for the virus. They are the smallest self-replicating particles which were discovered by Diener. Viroids are infectious RNA particles which are devoid of protein coat. They are obligate parasites. The molecular weight of a viroid is low. The RNA is tightly folded to form circular or linear structures. Viroids are known to cause diseases (some 20) in plants only, e.g., Potato spindle tuber disease (PSTD), Chrysanthemum stunt and Citrus exocortis.
Prions (Discovered by Alper et al.). Proteinaceous infectious particles, causing certain diseases like Kuru disease (laughing death disease in humans), Bovine spongiform encephalopathy (BSE or Mad cow disease), Scrapie disease in sheep, Creutz Feldt Jakob disease
Lichens are a permanent association of a fungal partner or mycobiont and an algal partner or phycobiont. Mycobiont is dominant partner belonging to ascomycetes (Ascolichens -, e.g., Graphis, Cladonia, Parmelia, Usnea, etc.) or basidiomycetes (Basidolichens – e.g., Corella, Cora etc.). Phycobiont is mostly a member of Chlorophyceae (e.g., Chlorella, Trebouxia, Protococcus, Palmella, etc.) or can be a BGA (e.g., Nostoc, Chlorococcus, Scytonema, etc.)
Lichens are found in uninhabited or inhospitable places like barren rocks (sexicolous), soil (terricolous), tundra ice or alpines, sand dunes, roots, walls, wood (lignicolous), tree bark (corticolous) leaves, etc. Humid and exposed conditions are common however the lichens can tolerate extreme desiccation. Lichens do not grow in air pollution, and in high sulphur dioxide content (so are considered indicators of SO2 pollution).
Lichens are greyish, yellowish-greenish, orange, and dark brown or blackish in colour growing throughout the year. The fungal partner called mycobiont makes the bulk of lichen body. It includes the surface, medulla (or interior) and rhizines (attaching devices) in lichens. The algal partner or phycobiont contributes only 5% of the lichens body and is restricted only to a narrow zone (algal zone) that is below the surface.