Since ancient times, humans have attempted to classify living organisms. Early efforts were often intuitive and based on practicality, focusing on the uses of organisms for food, shelter, and clothing, rather than scientific criteria.

Aristotle made one of the earliest attempts at a more scientific classification. He classified plants simply based on their morphology into trees, shrubs, and herbs. Animals were divided into two groups: those with red blood and those without.

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During the time of Linnaeus, a Two Kingdom Classification system was prominent, dividing all living organisms into Plantae and Animalia.

However, this system had significant limitations as it:

• Did not differentiate between prokaryotic and eukaryotic organisms.
• Grouped unicellular and multicellular organisms together.
• Included both photosynthetic organisms (like green algae) and non-photosynthetic organisms (like fungi) under 'Plants', despite vast differences in their cell wall composition (cellulose in plants, chitin in fungi) and mode of nutrition.

While simple and easy to understand initially, the two-kingdom system was found to be inadequate because many organisms did not fit neatly into either kingdom.

Recognizing these limitations, a need arose to incorporate additional characteristics into classification, such as cell structure, cell wall composition, mode of nutrition, habitat, methods of reproduction, and evolutionary relationships (phylogenetic relationships).

Consequently, classification systems have undergone numerous revisions over time.

Although the kingdoms Plantae and Animalia have remained relatively constant features in different systems, the understanding of which groups belong to these kingdoms has evolved, and the number and nature of other kingdoms have also been interpreted differently by scientists.

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In 1969, R.H. Whittaker proposed a comprehensive Five Kingdom Classification. The five kingdoms he defined are: Monera, Protista, Fungi, Plantae, and Animalia.

The main criteria used by Whittaker for this classification were:

• Cell structure (Prokaryotic vs. Eukaryotic)
• Body organisation (Unicellular vs. Multicellular, Tissue, Organ, Organ system)
• Mode of nutrition (Autotrophic - photosynthetic or chemosynthetic, Heterotrophic - saprophytic or parasitic)
• Reproduction (Asexual, Sexual, or both)
• Phylogenetic relationships (Evolutionary history and relatedness)

The classification systems continue to evolve as our understanding of biological characteristics and evolutionary links improves. The attempt is to create a system that reflects not just morphological, physiological, and reproductive similarities but also evolutionary history.

A three-domain system, which splits Kingdom Monera into two domains (Archaea and Bacteria) and places all eukaryotes in a third domain (Eukarya), resulting in a six-kingdom classification, has also been proposed but is studied in higher classes.

Below is a comparative summary of the characteristics of Whittaker's five kingdoms:

Characters	Monera	Protista	Fungi	Plantae	Animalia
Cell type	Prokaryotic	Eukaryotic	Eukaryotic	Eukaryotic	Eukaryotic
Cell wall	Noncellulosic (Polysaccharide + amino acid)	Present in some	Present (with chitin)	Present (cellulose)	Absent
Nuclear membrane	Absent	Present	Present	Present	Present
Body organisation	Cellular	Cellular	Multiceullar/ loose tissue	Tissue/ organ	Tissue/organ/ organ system
Mode of nutrition	Autotrophic (chemosynthetic and photosynthetic) and Heterotrophic (saprophytic/ parasitic)	Autotrophic (Photosynthetic) and Heterotrophic	Heterotrophic (Saprophytic/ Parasitic)	Autotrophic (Photosynthetic)	Heterotrophic (Holozoic/ Saprophytic etc.)

Kingdom Monera

Kingdom Monera is exclusively comprised of bacteria, which are the most abundant microorganisms on Earth.

Bacteria are nearly ubiquitous, found in almost every environment, including extreme habitats like hot springs, deserts, snow, and deep oceans, where other life forms struggle to survive.

Many bacteria also exist as parasites on or within other organisms.

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Bacteria are classified into four major categories based on their shape:

• Coccus (plural: Cocci): Spherical shape
• Bacillus (plural: Bacilli): Rod shape
• Vibrium (plural: Vibrio): Comma shape
• Spirillum (plural: Spirilla): Spiral shape

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Despite their relatively simple structure compared to other organisms, bacteria exhibit remarkable complexity in their behaviour and the most extensive metabolic diversity within the biological world.

Their modes of nutrition include:

• Autotrophic: Synthesising their own food from inorganic substances. This can be Photosynthetic autotrophic (using light energy) or Chemosynthetic autotrophic (using chemical energy from oxidising inorganic compounds).
• Heterotrophic: Depending on other organisms or dead organic matter for nutrients. These can be Saprophytic (feeding on dead organic matter) or Parasitic (living on or inside living hosts).

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Archaebacteria

Archaebacteria are a special group of bacteria known for living in some of the most harsh and extreme environments.

These extreme habitats include:

• Extreme salty areas (Halophiles)
• Hot springs and acidic environments (Thermoacidophiles)
• Marshy areas (Methanogens)

The ability of Archaebacteria to survive in these harsh conditions is attributed to differences in their cell wall structure compared to other bacteria.

Methanogens are found in the gut of ruminant animals like cows and buffaloes. They play a crucial role in producing methane gas (biogas) from the dung of these animals.

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Eubacteria

Eubacteria, or "true bacteria," constitute a vast and diverse group.

They are characterised by the presence of a rigid cell wall.

If motile, they possess a flagellum.

Cyanobacteria (also known as blue-green algae) are photosynthetic eubacteria. They contain chlorophyll 'a', similar to green plants.

Cyanobacteria can be unicellular, colonial, or filamentous and are found in freshwater, marine, or terrestrial environments.

Their colonies are often surrounded by a gelatinous sheath.

They can form extensive "blooms" in polluted water bodies.

Some cyanobacteria, such as Nostoc and Anabaena, have specialized cells called heterocysts that can fix atmospheric nitrogen.

Chemosynthetic autotrophic bacteria obtain energy by oxidising various inorganic substances like nitrates, nitrites, and ammonia. They use this released energy to produce ATP.

These bacteria are vital in the recycling of nutrients such as nitrogen, phosphorus, iron, and sulphur.

Heterotrophic bacteria are the most abundant group in nature.

A large number of heterotrophic bacteria function as important decomposers.

Many heterotrophic bacteria have significant beneficial impacts on humans, for example:

• Making curd from milk
• Production of antibiotics (e.g., *Streptomyces*)
• Fixing nitrogen in the roots of leguminous plants (e.g., *Rhizobium*)

However, some heterotrophic bacteria are pathogens, causing diseases in humans, crops, and animals. Examples of bacterial diseases include cholera, typhoid, tetanus (in humans), and citrus canker (in plants).

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Bacteria primarily reproduce asexually through fission (binary fission), where a single cell divides into two (Figure 2.3).

Under unfavourable conditions, some bacteria can produce resistant spores to survive.

They also exhibit a form of genetic exchange, sometimes referred to as a primitive type of sexual reproduction, involving the transfer of DNA from one bacterium to another (e.g., conjugation).

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Mycoplasma are a unique group of organisms under Monera that completely lack a cell wall.

They are known as the smallest living cells.

Mycoplasma can survive even without oxygen (anaerobic).

Many species of Mycoplasma are pathogenic, causing diseases in both animals and plants.

Kingdom Protista

Kingdom Protista includes all single-celled eukaryotic organisms.

The boundaries of this kingdom are not rigidly defined, leading to some organisms potentially being classified differently by various biologists (e.g., a photosynthetic protistan could be considered a plant by some).

Protista is considered a connecting link kingdom because its members share characteristics with plants, animals, and fungi.

Members of Protista are predominantly aquatic.

As eukaryotes, protistan cells possess a well-defined nucleus and other membrane-bound organelles.

Some protists are mobile, having flagella or cilia.

Protists reproduce both asexually and sexually, with sexual reproduction involving processes like cell fusion and zygote formation.

Key groups included under Protista are Chrysophytes, Dinoflagellates, Euglenoids, Slime moulds, and Protozoans.

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Chrysophytes

This group consists of diatoms and golden algae (desmids).

Habitat: Found in both freshwater and marine environments.

Size and Movement: They are microscopic and float passively in water currents, making them part of the plankton.

Nutrition: Most chrysophytes are photosynthetic.

Cell Wall: In diatoms, the cell walls are unique, forming two thin, overlapping shells that fit together like the lid of a soap box. These walls are embedded with silica, making them virtually indestructible.

Diatomaceous Earth: Over billions of years, diatoms accumulate vast deposits of their cell wall remains in their habitat. This accumulation forms 'diatomaceous earth', which is gritty and used commercially for polishing and filtration of oils and syrups.

Ecological Role: Diatoms are considered the chief 'producers' in the oceans, forming the base of many aquatic food chains.

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Dinoflagellates

Habitat: Mostly marine.

Nutrition: They are photosynthetic.

Appearance: Their colour can be yellow, green, brown, blue, or red, depending on the primary pigments present in their cells.

Cell Wall: The outer surface of their cell wall has stiff cellulose plates.

Flagella: Most dinoflagellates have two flagella: one located longitudinally and the other lying transversely in a groove between the cell wall plates.

Red Tides: Certain red dinoflagellates, like *Gonyaulax*, can multiply very rapidly, causing the sea surface to appear red. This phenomenon is called a 'red tide'. These organisms often release potent toxins that can kill marine animals, particularly fishes.

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Euglenoids

Habitat: Majority are freshwater organisms, typically found in stagnant water.

Cell Covering: Instead of a rigid cell wall, they have a flexible, protein-rich layer called a pellicle, which allows their body to be quite flexible.

Flagella: They possess two flagella, one short and one long.

Nutrition: Euglenoids are mixotrophic. They are photosynthetic when sunlight is available. However, when deprived of light, they switch to a heterotrophic mode, feeding on smaller organisms.

Pigments: Interestingly, their photosynthetic pigments are identical to those found in higher plants.

Example: *Euglena*.

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Slime Moulds

Nutrition: Slime moulds are saprophytic protists, meaning they feed on dead and decaying organic matter.

Body Movement: Their body creeps along decaying twigs and leaves, engulfing organic material.

Life Cycle Stages:

• Under favourable conditions, they aggregate to form a structure called a plasmodium, which can grow and spread over large areas.
• During unfavourable conditions, the plasmodium differentiates and forms fruiting bodies at its tips.

Spores: The fruiting bodies bear spores. These spores possess true walls, making them extremely resistant and capable of surviving for many years even under harsh conditions. Spores are dispersed by air currents.

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Protozoans

Nutrition: All protozoans are heterotrophs, obtaining food either as predators (hunting and consuming other organisms) or as parasites (living on or inside a host).

Evolutionary Link: They are considered primitive relatives of animals.

Protozoans are divided into four main groups:

1. Amoeboid protozoans:
   • Habitat: Fresh water, seawater, or moist soil.
   • Movement and Feeding: They move and capture prey by extending temporary cytoplasmic projections called pseudopodia (false feet), as seen in *Amoeba*.
   • Cell Covering: Marine forms often have silica shells on their surface.
   • Examples: *Amoeba*, parasitic forms like *Entamoeba*.
2. Flagellated protozoans:
   • Life Style: Can be either free-living or parasitic.
   • Movement: Possess flagella for locomotion.
   • Diseases: Parasitic forms can cause serious diseases in humans, such as sleeping sickness, caused by *Trypanosoma*.
3. Ciliated protozoans:
   • Habitat: Mostly aquatic.
   • Movement: Characterized by the presence of thousands of tiny cilia covering their body surface, which beat coordinately for active movement.
   • Feeding Structure: They have a cavity called a gullet that opens to the outside. The coordinated movement of cilia directs water containing food particles into the gullet.
   • Example: *Paramoecium*.
4. Sporozoans:
   • Life Cycle: This diverse group is characterised by having an infectious spore-like stage in their life cycle.
   • Example: The most well-known sporozoan is *Plasmodium*, the malarial parasite, which causes malaria, a disease with a significant global impact on human populations.

Kingdom Fungi

Fungi form a distinct kingdom of heterotrophic organisms, displaying significant diversity in their form and habitats.

They are commonly observed on moist bread, rotten fruits, as mushrooms, and toadstools.

Some fungi are parasitic, causing diseases, such as the white spots on mustard leaves caused by *Albugo*, or wheat rust caused by *Puccinia*.

Certain fungi are beneficial, like unicellular yeast (*Saccharomyces*) used in baking bread and brewing beer, or *Penicillium*, a source of antibiotics.

Fungi are cosmopolitan, found in air, water, soil, and on/in plants and animals.

They thrive particularly well in warm and humid conditions, which is why refrigerating food helps prevent fungal (and bacterial) spoilage.

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With the exception of yeast (which is unicellular), most fungi are filamentous.

Their body consists of long, slender, thread-like structures called hyphae.

The interconnected network of hyphae is known as the mycelium.

Hyphae can be of two types:

• Coenocytic hyphae: Continuous tubes filled with multinucleated cytoplasm, lacking internal cross walls (septae).
• Others have cross walls or septae dividing the hyphae into cells.

The cell walls of fungi are composed of chitin and polysaccharides.

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Most fungi are heterotrophic, obtaining nutrients in various ways:

• Saprophytes: Absorb soluble organic matter from dead substrates.
• Parasites: Depend on living plants and animals for food.
• Symbionts: Live in mutually beneficial associations, such as:
  • Lichens: Association with algae.
  • Mycorrhiza: Association with the roots of higher plants.

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Reproduction in fungi occurs through different means:

• Vegetative reproduction: By fragmentation, fission, or budding.
• Asexual reproduction: By spores like conidia, sporangiospores, or zoospores. These spores are produced in specialized structures called fruiting bodies.
• Sexual reproduction: By spores like oospores, ascospores, or basidiospores, also produced in distinct fruiting bodies.

The sexual cycle in fungi involves the following three sequential steps:

1. Plasmogamy: Fusion of the protoplasms of two compatible motile or non-motile gametes or hyphae.
2. Karyogamy: Fusion of the two resulting nuclei.
3. Meiosis: Occurs in the zygote (or diploid structure), leading to the formation of haploid spores.

When sexual reproduction occurs, two haploid hyphae of compatible mating types fuse (plasmogamy).

In some fungi, karyogamy immediately follows plasmogamy, resulting directly in diploid (2n) cells.

However, in other fungi (like Ascomycetes and Basidiomycetes), there is an intermediate stage where the two haploid nuclei do not fuse immediately. This stage contains two nuclei per cell (n + n) and is called a dikaryotic stage, or the phase is known as the dikaryophase.

Later, these parental nuclei fuse (karyogamy), resulting in a diploid cell, which then undergoes meiosis to form haploid spores.

The classification of the Kingdom Fungi into various classes is based on the morphology of the mycelium, the method of spore formation, and the types of fruiting bodies produced.

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Phycomycetes

Habitat: Found in aquatic environments, on decaying wood in moist places, and as obligate parasites on plants.

Mycelium: Aseptate (lacking cross walls) and coenocytic (multinucleated).

Asexual Reproduction: Occurs via spores produced endogenously (inside) within a sporangium. These spores can be zoospores (motile) or aplanospores (non-motile).

Sexual Reproduction: A zygospore is formed by the fusion of two gametes. The gametes can be morphologically similar (isogamous) or dissimilar (anisogamous or oogamous).

Examples: *Mucor*, *Rhizopus* (common bread mould), and *Albugo* (parasitic fungus on mustard).

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Ascomycetes

Common Name: Often called sac-fungi because their sexual spores are contained within a sac-like structure.

Body Form: Primarily multicellular (e.g., *Penicillium*), but some are unicellular (e.g., yeast, *Saccharomyces*).

Nutrition: They are saprophytic, decomposers, parasitic, or coprophilous (growing on dung).

Mycelium: Branched and septate (with cross walls).

Asexual Reproduction: By spores called conidia, which are produced exogenously (outside) on specialized hyphae called conidiophores. Conidia germinate to form new mycelium.

Sexual Reproduction: By spores called ascospores, produced endogenously (inside) in sac-like structures called asci (singular: ascus). The asci are arranged in specific fruiting bodies called ascocarps.

Examples: *Aspergillus*, *Claviceps*, *Neurospora*. *Neurospora* is widely used in genetic and biochemical research. Edible delicacies like morels and truffles are also ascomycetes.

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Basidiomycetes

Common Names: Includes familiar forms like mushrooms, bracket fungi, and puffballs.

Habitat: Found in soil, on decaying logs and tree stumps, and as parasites on living plants (e.g., rusts and smuts).

Mycelium: Branched and septate.

Asexual Reproduction: Asexual spores are generally absent. Vegetative reproduction primarily occurs through fragmentation.

Sexual Reproduction: Sex organs are absent. Plasmogamy is achieved by the fusion of two vegetative or somatic cells of compatible strains, forming a dikaryotic structure.

The dikaryotic structure eventually gives rise to the basidium. Within the basidium, karyogamy and meiosis occur, producing four basidiospores.

Basidiospores are produced exogenously (outside) on the basidium (plural: basidia).

The basidia are organized within fruiting bodies called basidiocarps.

Examples: *Agaricus* (mushroom), *Ustilago* (smut), and *Puccinia* (rust fungus).

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Deuteromycetes

Common Name: Referred to as imperfect fungi.

Reason for Name: Only their asexual or vegetative phases (reproduction by conidia) are currently known.

Classification History: When the sexual forms of a deuteromycete are discovered, the fungus is typically reclassified and moved into the appropriate class (Ascomycetes or Basidiomycetes).

Mycelium: Septate and branched.

Asexual Reproduction: Reproduce exclusively by asexual spores called conidia.

Nutrition: Some are saprophytes or parasites. A large number of deuteromycetes are important decomposers of litter, playing a vital role in mineral cycling in ecosystems.

Examples: *Alternaria*, *Colletotrichum*, and *Trichoderma*.

Kingdom Plantae

Kingdom Plantae encompasses all eukaryotic organisms that contain chlorophyll, commonly known as plants.

Cell Structure: Plant cells are eukaryotic, characterized by prominent chloroplasts (where photosynthesis occurs) and a rigid cell wall primarily composed of cellulose.

Nutrition: The vast majority of plants are autotrophic, synthesizing their own food through photosynthesis.

Exceptions: A few members are partially heterotrophic, such as insectivorous plants (e.g., Bladderwort, Venus fly trap) that supplement their nutrition by trapping insects, or parasites (e.g., Cuscuta) that absorb nutrients from a host plant.

Groups Included: Kingdom Plantae includes diverse groups such as algae, bryophytes, pteridophytes, gymnosperms, and angiosperms.

Life Cycle: A defining characteristic of plants is their life cycle, which exhibits alternation of generation. This involves two distinct phases: a diploid sporophytic phase and a haploid gametophytic phase that alternate with each other. The duration and independence of these phases vary among different plant groups.

Detailed characteristics of this kingdom are typically studied in a dedicated chapter.

Kingdom Animalia

Kingdom Animalia is characterized by eukaryotic, heterotrophic, and multicellular organisms.

Cell Structure: Animal cells lack cell walls.

Nutrition: Animals depend directly or indirectly on plants for their food. They obtain nutrients through a holozoic mode of nutrition, which involves the ingestion of food.

Digestion and Storage: Digestion occurs in an internal cavity. Food reserves are stored primarily as glycogen or fat.

Growth and Body Plan: Animals follow a definite growth pattern, developing into adults with a predictable and defined shape and size.

Sensory and Neuromotor Systems: Higher forms of animals possess sophisticated sensory and neuromotor mechanisms, allowing for complex responses to the environment.

Locomotion: Most animals are capable of locomotion (movement from one place to another).

Reproduction: Sexual reproduction is the primary mode, typically involving the copulation of male and female individuals, followed by embryological development.

Detailed features and diversity within the various phyla of this kingdom are studied in a dedicated chapter.

Viruses, Viroids, Prions And Lichens

R.H. Whittaker's Five Kingdom classification system did not include certain acellular organisms like viruses, viroids, and prions, nor did it explicitly classify lichens.

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Viruses

Viruses are non-cellular organisms. They are not considered truly "living" outside a host cell because they have an inert crystalline structure in that state.

Obligate Parasites: Viruses are obligate intracellular parasites. They lack their own machinery for replication. Once they infect a living cell, they take over the host cell's metabolic machinery to reproduce themselves, often leading to the death of the host cell.

The term "virus" originally meant venom or poisonous fluid.

Historical Discoveries:

• Dmitri Ivanowsky (1892) identified certain microbes that caused the mosaic disease of tobacco. He found they were smaller than bacteria because they could pass through bacteria-proof filters.
• M.W. Beijerinek (1898) demonstrated that the extract from infected tobacco plants could cause infection in healthy plants. He named the infectious agent "virus" and referred to the fluid as Contagium vivum fluidum (infectious living fluid).
• W.M. Stanley (1935) showed that viruses could be crystallized. These crystals are largely composed of proteins. This crystallization suggested their non-living nature outside a host.

Structure: Viruses are essentially nucleoproteins, meaning they consist of a nucleic acid core enclosed within a protein coat.

• Genetic Material: Can be either RNA or DNA, but never both in a single virus. The nucleic acid is the infectious part.
  • Plant viruses generally have single-stranded RNA (ssRNA).
  • Animal viruses can have single or double-stranded RNA (ssRNA or dsRNA) or double-stranded DNA (dsDNA).
  • Bacteriophages (viruses that infect bacteria) typically have double-stranded DNA (dsDNA).
• Protein Coat: Called the capsid. It is made up of small protein subunits called capsomeres. The capsid protects the nucleic acid and gives the virus its shape, which can be helical or polyhedral (geometric).

Viral Diseases:

• In humans: Mumps, smallpox, herpes, influenza, AIDS.
• In plants: Mosaic formation, leaf rolling and curling, yellowing, vein clearing, dwarfing, stunted growth.

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Viroids

Discovery: Viroids were discovered by T.O. Diener in 1971 as a new infectious agent causing potato spindle tuber disease.

Characteristics: Viroids are smaller than viruses. They consist of free RNA (meaning the RNA is not enclosed in a protein coat). Their RNA is of low molecular weight.

Key Difference from Viruses: Viroids lack the protein coat (capsid) found in viruses.

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Prions

Prions are infectious agents identified in modern medicine as the cause of certain neurological diseases.

Composition: Prions are made up of abnormally folded proteins.

Size: They are similar in size to viruses.

Diseases caused by Prions: They cause neurodegenerative diseases, notably Bovine Spongiform Encephalopathy (BSE), commonly known as "mad cow disease," in cattle, and its human equivalent, Creutzfeldt-Jakob disease (CJD).

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Lichens

Lichens represent a classic example of a symbiotic association – a mutually beneficial relationship – between two different organisms: algae and fungi.

• Algal component (Phycobiont): This part is autotrophic. The alga performs photosynthesis and provides food (carbohydrates) for the fungus.
• Fungal component (Mycobiont): This part is heterotrophic. The fungus provides shelter, absorbs mineral nutrients and water from the substrate, and makes them available to the alga.

The association between the alga and fungus is so intimate that lichens appear as a single organism in nature.

Environmental Indicators: Lichens are well-known as excellent pollution indicators because they are highly sensitive to air pollution and generally do not grow in polluted areas.

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