Microorganisms: Introduction to Bacteria PDF

COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Introduction to Bacteria: Bacteria are fascinating and diverse microorganisms that play a crucial role in the biosphere. They are single-celled prokaryotic organisms, which means they lack a true nucleus and o...

COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Introduction to Bacteria: Bacteria are fascinating and diverse microorganisms that play a crucial role in the biosphere. They are single-celled prokaryotic organisms, which means they lack a true nucleus and other membrane-bound organelles. Despite their simplicity, bacteria are incredibly resilient and adaptable, existing in almost every environment on Earth, from the deepest oceans to the highest mountains and even inside the human body. Key Characteristics:  Prokaryotic Cells: Bacteria are among the simplest forms of life and lack a membrane-bound nucleus. Instead, their genetic material, typically a circular DNA molecule, is found in the nucleoid region.  Cell Structure: Bacterial cells are surrounded by a rigid cell wall made up of peptidoglycan, a unique molecule not found in eukaryotic cells. Some bacteria also possess an outer capsule that provides protection and aids in adhesion.  Shape and Arrangement: Bacteria can have various shapes, such as cocci (spherical), bacilli (rod-shaped), and spirilli (spiral-shaped). They can occur as single cells, pairs (diplo), chains (strepto), or clusters (staphylo).  Reproduction: Bacteria reproduce asexually through binary fission, where a single cell divides into two identical daughter cells. This process is highly efficient and can lead to rapid population growth.  Metabolism: Bacteria exhibit diverse metabolic pathways. Some are autotrophs, capable of synthesizing their own food from inorganic substances, while others are heterotrophs, relying on organic compounds for sustenance. Some bacteria can also thrive in extreme conditions, known as extremophiles. Figure 11: Animated representation of structure of a typical bacterial cell Compiled by: Dr. Malay Shah, VESASC 14 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Figure 12: Metabolic diversities in bacteria Roles and Importance of Bacteria:  Decomposers: Bacteria play a vital role in the ecosystem by breaking down dead organic matter and recycling nutrients. They help convert complex organic compounds into simpler forms that can be absorbed by plants and other organisms.  Nitrogen Fixation: Certain bacteria are capable of converting atmospheric nitrogen into a form usable by plants (ammonia), thus contributing to the nitrogen cycle and providing essential nutrients for the growth of living organisms.  Symbiotic Relationships: Bacteria form symbiotic relationships with various organisms. For instance, some bacteria live in the guts of animals, aiding in digestion and providing mutual benefits.  Biotechnology and Industry: Bacteria are used in various biotechnological applications, such as producing enzymes, antibiotics, and other valuable compounds. They are also involved in food fermentation processes.  Disease and Pathogens: While most bacteria are harmless or even beneficial, some can cause diseases in humans, animals, and plants. These disease- causing bacteria are known as pathogens and can be responsible for various illnesses. In conclusion, bacteria are a diverse group of microorganisms that have a significant impact on our planet. Their ability to adapt, their ecological roles, and their importance in various fields of science make them a subject of great interest and importance in the study of biology and microbiology. Understanding bacteria is crucial for advancing our knowledge of life processes and for developing strategies to address both the beneficial and harmful aspects of bacterial interactions with the world around us. Compiled by: Dr. Malay Shah, VESASC 15 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Introduction to Archaea: The term ‘Archaea’ is derived from a Greek word, ‘archaios’ which means primitive or ancient, indicating the primitive structure of these organisms. Archaea, are a fascinating group of microorganisms that form one of the three domains of life, alongside Bacteria and Eukarya. Archaea were first discovered in the 1970s by American microbiologist Carl Woese, who recognized their uniqueness and distinct evolutionary history. Key Characteristics:  Ancient lineage: Archaea are some of the oldest known life forms on Earth, with their origins dating back over 3.5 billion years. They thrived in extreme environments long before more complex life forms appeared.  Cellular structure: Archaea are single-celled microorganisms. Their cellular structure is prokaryotic, meaning they lack a true nucleus and other membrane-bound organelles found in eukaryotic cells.  Genetic differences: Archaea have genetic differences from both Bacteria and Eukarya. They possess a unique RNA polymerase enzyme that distinguishes them from bacteria and shares some similarities with eukaryotes.  Extremophiles: Some of the most fascinating members of the Archaea domain are extremophiles. These microorganisms can survive and thrive in extreme environmental conditions that are hostile to most other life forms. Examples include thermophiles (heat-loving), halophiles (salt-loving), acidophiles (acid-loving), and methanogens (organisms that produce methane in anaerobic environments).  Importance in biogeochemical cycles: Archaea play critical roles in various biogeochemical cycles, such as the nitrogen cycle and carbon cycle. Methanogenic archaea, for instance, are involved in the production of methane, a potent greenhouse gas, and are significant contributors to global warming.  Ubiquitous distribution: Archaea are found in diverse habitats, including terrestrial and marine environments, hot springs, hydrothermal vents, salt flats, acidic lakes, and even the human gut.  Symbiotic relationships: Some archaea form symbiotic relationships with other organisms. For example, some methanogenic archaea live in the intestines of certain animals, aiding in the digestion process.  Taxonomy and classification: Archaea are classified into several phyla, but our understanding of their diversity is still evolving due to ongoing research and discoveries.  Archaea's unique properties and evolutionary significance have led scientists to study them extensively to gain insights into the origins of life and understand their biological adaptations to extreme environments. As research continues, archaea's importance in various ecological and biochemical processes becomes increasingly apparent, further expanding our understanding of life on Earth. Compiled by: Dr. Malay Shah, VESASC 16 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Introduction to Fungi: Fungi are a diverse group of eukaryotic organisms that play critical roles in ecosystems and have significant impacts on human life. They belong to their own kingdom, separate from plants, animals, and bacteria. Fungi exhibit a wide range of forms and functions, and they can be found in almost every environment on Earth. Key Characteristics:  Eukaryotic cells: Unlike bacteria and archaea, fungi are composed of eukaryotic cells. This means they have a true nucleus and other membrane- bound organelles within their cells.  Heterotrophs: Fungi are heterotrophic organisms, which means they cannot produce their own food through photosynthesis like plants. Instead, they acquire nutrients by absorbing organic matter from their environment. They are primarily decomposers, breaking down dead organic material and recycling nutrients back into the ecosystem.  Chitin cell walls: The cell walls of fungi are made of chitin, a tough, complex carbohydrate that provides structural support and protection for the fungal cells. This sets them apart from the cell walls of plants, which are composed of cellulose. Yeasts and molds are two distinct groups of fungi, each with unique characteristics and roles in various environments. While they are both types of fungi, they differ in their morphology, lifestyles, and applications. Yeasts: Yeasts are single-celled fungi that belong to the class Ascomycota. They are widely distributed in nature, and some species have been used by humans for thousands of years for various purposes. Key features of yeasts include:  Morphology: Yeasts are unicellular organisms that typically appear as small, rounded cells under a microscope.  Reproduction: Yeasts reproduce asexually through a process called budding. During budding, a small daughter cell forms as an outgrowth from the parent cell and eventually separates to become a new yeast cell.  Fermentation: One of the most well-known characteristics of yeasts is their ability to ferment sugars. This process converts sugars into alcohol and carbon dioxide, a property utilized in the production of bread, beer, wine, and other fermented foods.  Applications: Yeasts have significant applications in the food and beverage industry, biotechnology, and research. They are used to leaven bread, brew beer, ferment wine, and produce biofuels, enzymes, and pharmaceuticals. Compiled by: Dr. Malay Shah, VESASC 17 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Molds: Molds are filamentous fungi that belong to various groups, including Ascomycota and Zygomycota. Unlike yeasts, molds are composed of multiple cells and form a network of thread-like structures called hyphae. Key features of molds include:  Morphology: Molds have a filamentous and multicellular structure, consisting of a mass of hyphae called mycelium. The mycelium allows molds to spread and grow over large areas.  Reproduction: Molds can reproduce both sexually and asexually. They produce spores, which are tiny reproductive structures that can be dispersed through the air to start new colonies in suitable environments.  Colonization and Decomposition: Molds are known for their ability to colonize various organic materials. Some molds can cause decay and decomposition, while others are involved in breaking down dead plant and animal matter, playing a vital role in nutrient recycling in ecosystems.  Applications: While some molds can be harmful to human health and cause food spoilage, others are utilized in the production of various food items, such as cheese, soy sauce, and certain types of fermented foods. Both yeasts and molds are essential in various industries and ecological processes. Yeasts' ability to ferment sugars and produce alcohol has been exploited by humans for millennia in food and beverage production. On the other hand, molds play significant roles in decomposition and nutrient cycling in ecosystems, as well as in the creation of many culturally important food products. Their diversity and biological significance continue to be areas of active research and exploration. Protists Protists are a diverse group of eukaryotic microorganisms that do not fit into the classification of plants, animals, or fungi. They belong to the kingdom Protista and are typically unicellular, although some species can be multicellular. Protists are known for their remarkable diversity in terms of size, shape, and lifestyle. They can be found in various aquatic and terrestrial environments, including freshwater, marine, and soil habitats. Due to their vast diversity, protists can be broadly categorized into several groups: Protozoa: These are unicellular protists that primarily feed on organic matter, bacteria, and other small particles. They can move using structures like cilia, flagella, or pseudopodia (temporary extensions of the cell). Algae: Algae are photosynthetic protists that can be either unicellular or multicellular. They play a significant role in aquatic ecosystems by producing oxygen and serving as a primary food source for various aquatic organisms. Compiled by: Dr. Malay Shah, VESASC 18 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Slime Molds: Slime molds are unique protists that undergo fascinating transformations during their life cycle. They can be either plasmodial (forming a multinucleate mass) or cellular (consisting of individual cells). Water Molds: Water molds are filamentous protists that often live in water and can be parasitic or saprophytic, meaning they feed on decaying organic matter. Protists have historically been studied as a single group, but advancements in molecular biology have revealed their diverse evolutionary relationships. Consequently, the kingdom Protista is no longer considered a valid taxonomic group in modern classification systems like the five-kingdom system. Protists are now distributed across multiple kingdoms, depending on their phylogenetic relationships and characteristics. Compiled by: Dr. Malay Shah, VESASC 19 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Algae Algae are a diverse group of photosynthetic organisms that can range from single-celled microorganisms to large, multicellular seaweeds. They belong to the kingdom Protista in the old classification system, while in more modern classifications, they are distributed among several groups, including the Chromista, Archaeplastida, and others. Characteristics of Algae Specific general characteristics of algae are common to plants as well as animals. Algal cells are eukaryotic. For instance, algae can photosynthesize like plants, and they possess specialized structures and cell-organelles, like centrioles and flagella, found only in animals. The algal cell walls consist of mannans, cellulose and Galatians. Listed below are some of the general characteristics of algae.  Algae are photosynthetic organisms  Algae can be either unicellular or multicellular organisms  Algae lack a well-defined body, so, structures like roots, stems or leaves are absent  Algaes are found where there is adequate moisture.  Reproduction in algae occurs in both asexual and sexual forms. Asexual reproduction occurs by spore formation.  Algae are free-living, although some can form a symbiotic relationship with other organisms. Figure 13: Classification of Algae Compiled by: Dr. Malay Shah, VESASC 20 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Key characteristics of algae include: Photosynthesis: Like plants, algae use sunlight to synthesize their own food through photosynthesis. They contain chlorophyll and other pigments that absorb light energy for this process. Habitat: Algae can be found in various aquatic environments, such as freshwater, saltwater, and even damp terrestrial habitats like rocks and tree bark. Diversity: Algae come in a wide range of shapes, sizes, and colors. Some are unicellular, like Chlorella and diatoms, while others are multicellular, forming complex structures like kelp and seaweed. Importance: Algae play a crucial role in aquatic ecosystems and the planet's overall ecology. They are primary producers, meaning they form the foundation of the food chain by providing food and oxygen to other organisms. Additionally, they are vital in carbon dioxide sequestration, helping regulate the Earth's atmosphere. Human Uses: Algae have practical applications as well. For example, they are used in food products like sushi wraps (nori) and as dietary supplements. Some species of algae are also cultivated for biofuel production, as they can generate large amounts of biomass and oils. Harmful Algal Blooms (HABs): Under certain conditions, some types of algae can undergo rapid and excessive growth, leading to harmful algal blooms. These blooms can produce toxins that are harmful to aquatic life, humans, and animals. Overall, algae are essential components of various ecosystems and have significant ecological, economic, and industrial importance. They are a fascinating group of organisms with immense potential for various applications and research endeavors. Compiled by: Dr. Malay Shah, VESASC 21 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Protozoa Protozoa are a group of unicellular, eukaryotic microorganisms belonging to the kingdom Protista. As the name suggests, the term "protozoa" translates to "first animals" in Greek, as they were historically among the first unicellular organisms observed under a microscope. Protozoa are the simplest animals, usually measuring only a few microns in size. The most primitive group of animal organisms is the protozoa. They are unicellular cells with no cell wall, motile organisms and form a very large, highly diverse group originating from several phylogenetic lines. Currently, there are roughly more than 50,000 different protozoa species. Some protozoa live as unwanted guests or parasites inside the bodies of other animals, causing serious diseases in their hosts such as malaria, kala-azar, sleeping sickness, dysentery, and so on. Read more about the definition of protozoa, classification, reproduction, importance and diseases caused by protozoa. These microorganisms are typically found in various aquatic environments, such as freshwater, marine habitats, and moist soil. Some protozoa are free-living, meaning they can survive independently, while others may be parasitic, relying on a host organism for their nutrition and survival. What are Protozoa? Single-celled organisms are known as protozoa. They range in size and shape from an amoeba, which can change shape, to Paramecium, which has a fixed shape and sophisticated structure. They can be found in a range of damp conditions, such as freshwater, marine environments, and soil. The body of acellular protozoa is not separated into cells, and organelles are parts of protoplasm set aside for performing certain activities. Most protozoa are aerobic, mesophilic organisms that thrive at temperatures ranging from 16 to 25 degrees Celsius. Entamoeba, for example, is anaerobic. Figure 14: Euglena, Amoeba, Paramecium Compiled by: Dr. Malay Shah, VESASC 22 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Classification of Protozoa Figure 15: Classification of Protozoa Characteristics of Protozoa Habitat - Protozoans exhibit mainly two forms of life; free-living (aquatic, freshwater, seawater) and parasitic (ectoparasites or endoparasites). They are also commensal in habitat. Size and Shape – They’re microscopic and can only be seen under a microscope. They are the most basic and rudimentary of all organisms. The body is made up of only one cell (without tissue and organs). Spherical, oval, elongated, or flattened body form variables are present. Body symmetry is either none or bilateral or radial or spherical. The body form is usually constant, varied in some, while changing with environment or age in many. The body is usually naked or bounded by a pellicle, but it can be covered in shells and has an internal skeleton in other species. Cellular Structure –  Body organisation is simple, that is, with a protoplasmic grade of organisation. They have one or more nuclei that are monomorphic or dimorphic. They are solitary (existing alone/single) or colonial (individuals are alike and independent). Compiled by: Dr. Malay Shah, VESASC 23 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance  The protozoal cells are not enclosed by a cell wall; rather, their protoplasts are protected by a special thin and pliable layer which is commonly known as a pellicle or periplast.  The cytoplasm of many protozoal cells is separated into two layers: an outside layer called ectoplasm and an interior layer called endoplasm.  The consistency of the ectoplasm is often denser than that of the endoplasm. The protoplast consists of the ingredients typically present in eukaryotic cells, like the membrane-bound nucleus, Golgi bodies endoplasmic reticulum, ribosomes and mitochondria.  The single-cell body performs all the essential and vital activities, which characterise the animal body; hence only the subcellular physiological division of labour.  Another distinguishing trait of some protozoa, such as ciliates, is that they have two different types of nuclei: a polyploid macronucleus and a diploid micronucleus. Locomotory organs are fingers like pseudopodia, whip-like flagella, hair-like cilia or none. Membrane-bound proteins play a role in how the body reacts to various environmental stimuli. Nutrition may be holozoic (animal-like), holophytic (plant-like), saprozoic or parasitic. Euglena, for example, has chromatophores and does photosynthesis. These photosynthetic protozoa are commonly referred to as algae. The majority of protozoa are, however, heterotrophic or holozoic, i.e. they live by phagocytosis of other organisms. Digestion takes place inside the food vacuoles, which is an intracellular process. Solid food particles collected by the protozoa are stored and digested in the food vacuoles. Enzymes are found in secretory vacuoles. Respiration occurs by diffusion via the general body surface. Excretion occurs primarily through the surface, although it can also occur through a brief opening in the ectoplasm or a permanent pore termed the cytopyge. In freshwater species, contractile vacuoles regulate osmoregulation and assist in the removal of excretory products. Reproduction- Asexual and sexual reproduction are both possible for protozoa. However, sexual reproduction is less common and only happens in select taxa. A. Asexual (binary or multiple fission, budding, sporulation) B. Sexual (conjugation (hologamy), gamete formation (syngamy) a) Syngamy: A motile microgamete unites with a non-motile macrogamete (anisogamy) to generate a diploid zygote in Sporozoa (Apicomplexa) similar to Plasmodium (malarial parasite). Compiled by: Dr. Malay Shah, VESASC 24 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance b) Conjugation is another way of sexual reproduction found in ciliate protozoa such as Tetrahymena and Paramecium. c) Autogamy: The male and female gametes give rise to the same unicellular fusion to form a diploid zygote. Thus, in autogamy, both gametes are produced by the same parent. It occurs in some ciliated protozoa like Paramecium. The life cycle is often complicated with alternation of asexual and sexual phases (alternation of generation). Most protozoa have a life cycle that alternates between a latent cyst stage and a proliferating vegetative stage, such as trophozoites. Without water or nutrition, the cyst stage can survive in extreme environments. It can stay outside the host for prolonged periods of time before being transmitted. The trophozoite stage is contagious, and it is during this stage that they feed and multiply. Encystment commonly occurs to resist unfavourable conditions of food, temperature, and moisture and also helps in dispersal. Examples: Euglena, Amoeba, Plasmodium, Paramecium, Podophyra, etc. Importance of Protozoans 1. Protozoans have a critical function in soil fertility. They manage bacterial populations and keep them in a state of physiological youth, or active growth phase, by feeding on soil bacteria. This accelerates the decomposition of dead organic substances by microbes. 2. Protozoans also excrete nitrogen and phosphorus as products of their metabolism, in the form of ammonium and orthophosphate, and studies have shown that the presence of protozoans in soils promotes plant growth. 3. In both activated sludge or slow percolating filter plants, protozoans play a significant role in wastewater treatment. 4. Protozoans provide shelter, carbon, and vital phytonutrients in exchange. 5. Protozoan grazing can have a significant impact on phytoplankton. These planktonic protozoans, like soil protozoans, expel a lot of nitrogen and phosphate. 6. Protozoans play a critical role in the phytoplankton’s recycling of key nutrients (nitrogen and phosphorus). Compiled by: Dr. Malay Shah, VESASC 25 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Protozoan Disease Diseases Etiological Agents Malaria Plasmodium falciparum, P. vivax African Trypanosomiasis Trypanosoma brucei Chagas Disease Trypanosoma cruzi Leishmaniasis Leishmania donovani, L. major Summary Single-celled organisms are known as protozoa. They range in size and shape from an amoeba, which can change shape, to Paramecium, which has a fixed shape and sophisticated structure. They can be found in a range of damp conditions, such as freshwater, marine environments, and soil. Protozoa are known for their ability to move on their own, which is a trait shared by the majority of species. They cannot frequently photosynthesise, even though the Euglena genus is known for both motility and photosynthesis (and is therefore considered both an alga and a protozoan). Compiled by: Dr. Malay Shah, VESASC 26 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Slime Moulds Slime moulds (or slime molds) are earlier grouped under fungi, however, later they are kept in the kingdom Protista with other unicellular and small multicellular eukaryotic organisms. They are saprophytic and feed on dead and decaying organic matter. The name ‘slime’ comes from the gelatinous appearance of macroscopic slime moulds. Under unfavourable conditions, they form aggregates, this is common in plasmodial or acellular slime moulds. Their size varies from a few centimetres to several square metres. They can live as a single-celled organism when there is abundant food, mainly cellular slime moulds. There are approximately 900 species of slime moulds present worldwide. General Characteristics of Slime Moulds  Slime moulds are found creeping on debris, decaying leaves or twigs, in soil, on the forest floor, on tree canopies and moist, dark and cool conditions  The protoplast is not surrounded by a cell wall in the vegetative phase  They are saprophytic and lack chlorophyll. They feed on microorganisms such as bacteria, fungi and yeasts and decompose dead organic matter  Some of the slime moulds are parasitic and found in the roots of cabbage and other plants of Brassicaceae family  The plasmodial stage resembles protozoa and fruiting bodies form spores resembling fungi  Spores have a cell wall made up of cellulose and are resistant to adverse conditions. They can survive for many years Slime Moulds Classification Slime moulds are classified under kingdom Protista. They resemble fungi as well as protozoa. In modern taxonomy, the true slime moulds come under Mycetozoa. They are further classified in different classes. The main classes of slime moulds are the following: Compiled by: Dr. Malay Shah, VESASC 27 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Myxomycetes- True slime moulds or acellular slime moulds. They are characterised by syncytial (multinucleated), plasmodial stage Myxomycetes (plasmodial stage) Figure 20: Myxomycetes Dictyostelia- Cellular slime moulds. They do not form huge coenocytes Figure 21: Dictyostelium discoideum Protostelia- Simple, minute, amoeboid slime moulds Figure 22: Life cycle of Plasmodial Slime moulds Compiled by: Dr. Malay Shah, VESASC 28 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Acrasia- Cellular slime moulds similar to dictyostelids but have eruptive pseudopodia Figure 23: Acrasia (sorocarpic amoebae). Light micrographs. Acrasiaceae. 1–3. Acrasis spp. 1. Sorocarp. Scale bar = 100 μm. 2. Spore; note the prominent hila on the spore. 3. Limax-type amoebae. Scale bar = 10 μm. Copromyxaceae. 4–6. Copromyxa protea. 4. Sorocarp. Scale bar = 100 μm. 5. Sorocyst (spore). 6. Limax-type monopodial amoeba. Fonticulaceae. 7–9. Fonticula alba. 7. Sorocarp. Scale bar = 100 μm. 8, 9. Amoebae of F. alba with filose pseudopodia near a fungal hypha. Guttulinopsidaceae. 10–12. Guttulinopsis vulgaris. 10. Two sorocarps fruiting near one another. Scale bar = 100 μm. 11. Spore. 12. Flabellate-type amoebae. – Scales for Figs. 2, 5, 6, 8, 9, 11, 12 as for Fig. 3. Images M. Brown. Plasmodiophomycetes- Parasitic slime moulds. They are found as an internal parasite in cabbage roots. They cause various diseases in plants such as clubroot disease of cabbage Club root disease Figure 24: Plasmodiophomycetes: Parasitic slime moulds Compiled by: Dr. Malay Shah, VESASC 29 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Labyrinthulae- Net slime moulds. Form a network of tubes in which amoeba without pseudopodia can swim freely Figure 25: Labyrinthula sp. Fonticula- Form volcano-shaped fruiting bodies Figure 26: Fonticula on agar medium Slime moulds are mainly of two types: Acellular and Cellular slime moulds. Acellular slime moulds are also known as Plasmodial slime moulds Acellular Slime Moulds (Plasmodial)  The feeding stage is a multinucleate mass of protoplasm, i.e. plasmodium  They can grow up to 1 ft in diameter  They are found creeping as a slimy mass over leaf litter, moist and decaying logs. It feeds on dead and decaying organic matter and microorganisms  When the food is scarce and moisture is less, they reproduce asexually  Examples: Physarum, Cribaria, Lycogala, Fuligo, Tubifera Compiled by: Dr. Malay Shah, VESASC 30 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Cellular Slime Moulds  The feeding stage is a single-celled amoeboid, which lives as a solitary organism  They have a close resemblance to amoebas  Individual cells feed on microorganisms and other food matter while creeping on decaying log or freely swimming in freshwater  Just like an amoeba, each cell has a haploid nucleus and divides mitotically  When the food is less they form aggregate but retain their individuality due to the presence of a thin plasma membrane and reproduce asexually by spore formation  When the food or moisture is depleted, they send out a cAMP-mediated chemical signal  The chemical diffuses out and binds to the receptors present on the surface of nearby cells resulting in the movement of cells towards cAMP (cyclic adenosine monophosphate)  Examples: Dictyostelium, Acytostelium, Polysphondylium Compiled by: Dr. Malay Shah, VESASC 31 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Water molds Water molds, also known as oomycetes, occupy a distinct position in the living world. They are classified as protists, which is a diverse group of eukaryotic microorganisms that do not fit neatly into other major categories such as animals, plants, or fungi. Here are some characteristics of water molds and their position in the living world:  Kingdom Classification: Water molds belong to the kingdom Stramenopila (chromista). This kingdom includes a variety of organisms, some of which have both photosynthetic and non-photosynthetic members. Diatoms and brown algae are also part of the Stramenopila group.  Eukaryotic: Water molds, like all protists, are eukaryotic. This means their cells have a defined nucleus and other membrane-bound organelles.  Habitats: Water molds are predominantly aquatic microorganisms and are commonly found in freshwater and marine environments. They thrive in moist conditions and are often associated with decaying organic matter. Figure 27: Water mould on organic matter and on dead gold fish  Filamentous Growth: Water molds exhibit a filamentous growth pattern, much like fungi. They consist of branching structures called hyphae, which collectively make up a mycelium.  Cell Wall Composition: The cell walls of water molds are composed of cellulose, a carbohydrate polymer. This sets them apart from true fungi, whose cell walls are made of chitin.  Heterotrophic Nutrition: Water molds are heterotrophic, meaning they obtain their nutrition by absorbing organic matter from their environment. They secrete enzymes into their surroundings to break down organic materials, which are then absorbed as nutrients. Compiled by: Dr. Malay Shah, VESASC 32 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance  Reproduction: Water molds have both sexual and asexual modes of reproduction. Sexual reproduction involves the production of specialized structures like oospores, which are formed when two different mating types come together. Asexual reproduction involves the production of zoospores, which are motile spores with flagella that enable them to move through water.  Pathogenicity: Some water molds are notorious plant pathogens, causing diseases in crops and other plants. Phytophthora infestans, responsible for the Irish Potato Famine, is a well-known example. Water molds can also be parasitic to aquatic animals, leading to diseases in fish and other aquatic organisms.  Ecological Role: Water molds play a role in decomposing organic matter in aquatic ecosystems. They help recycle nutrients and contribute to the breakdown of dead plant and animal material. In summary, water molds are a diverse group of protists with filamentous growth patterns, cellulose cell walls, and a mix of saprophytic and parasitic lifestyles. They are ecologically important for nutrient cycling but can also have negative impacts as pathogens. Water molds occupy a unique position in the living world due to their characteristics and ecological roles. Compiled by: Dr. Malay Shah, VESASC 33 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Viruses Viruses are small infectious agents that are not considered living organisms in the traditional sense. They are composed of genetic material (either DNA or RNA) surrounded by a protein coat called a capsid. Some viruses also have an outer lipid envelope derived from the host cell membrane. Viruses are unique in that they cannot carry out essential life processes on their own, such as metabolism or reproduction. Instead, they rely on infecting and hijacking the cellular machinery of living organisms to replicate and produce new viral particles. This process often involves the virus attaching to a host cell, injecting its genetic material into the cell, and then using the host cell's resources to replicate itself. Once new viral particles are produced within the host cell, they are released either by causing the host cell to burst (lytic cycle) or by budding off from the cell membrane (lysogenic cycle). This process can damage or destroy the host cell, leading to the symptoms of infection that are often observed in the host organism. Viruses can infect a wide variety of hosts, including animals, plants, bacteria (bacteriophages), and even other viruses (virophages). Here are some examples of different types of viruses and their respective hosts:  Animal Viruses: These viruses infect animals, including humans. Examples include: Influenza virus: Infects birds and mammals, including humans. Human immunodeficiency virus (HIV): Infects humans and attacks the immune system, causing AIDS. Herpes simplex virus: Causes oral and genital herpes in humans. Rabies virus: Infects mammals, including humans, and affects the nervous system.  Plant Viruses: These viruses infect various types of plants and can lead to crop damage. Examples include: Tobacco mosaic virus: Infects tobacco plants and many other plant species. Potato virus Y: Infects potato and other Solanaceae family plants. Citrus tristeza virus: Affects citrus trees.  Bacteriophages (Phages): These viruses infect and replicate within bacterial cells. They are important for bacterial control and play a role in the regulation of bacterial populations. Examples include: T4 bacteriophage: Infects Escherichia coli bacteria. Lambda phage: Can establish both lytic and lysogenic cycles in E. coli.  Archaeal Viruses: These viruses infect archaea, which are single-celled microorganisms distinct from bacteria and eukaryotes. Examples include: Sulfolobus turreted icosahedral virus (STIV): Infects certain species of archaea from the genus Sulfolobus. Compiled by: Dr. Malay Shah, VESASC 34 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance  Virophages: These viruses are parasites of other viruses and can infect the hosts of those viruses. Examples include: Sputnik virophage: Infects mimivirus, a giant virus that infects amoebae. Figure 28: Different types of Viruses Because of their unique characteristics and their ability to cause disease, viruses are the focus of extensive scientific research in fields such as virology, immunology, and public health, with the aim of understanding their behavior, preventing their spread, and developing treatments and vaccines to combat viral infections. It's important to note that viruses are highly specific in terms of their hosts. Each virus tends to infect a particular species or a narrow range of species. This specificity is determined by the interactions between viral surface proteins and host cell receptors. Understanding these interactions is crucial for developing strategies to prevent and treat viral infections. Compiled by: Dr. Malay Shah, VESASC 35 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Viroids Viroids are small, infectious, circular RNA molecules that can cause disease in plants. They are unique in that they lack a protein coat, which is a characteristic feature of viruses. Despite their simplicity, viroids are able to replicate and spread within plant cells, leading to various symptoms of disease. Structure of Viroids Viroids differ from virus in structure and form. These consists of solely short strands of circular, and single-stranded RNA without the protein coats. The plants that are infected by viroids are responsible for the crop failures and also cause the loss of millions of dollars in agricultural revenue every year. Some of the plants that are affected by these pathogens are potatoes, tomatoes, cucumbers, chrysanthemums, coconut palms, avocados, etc. Viroids were first discovered by T.O. Diener in the year 1971. It was first examined in the potato spindle tuber viroid caused a huge loss to the potato industry. Viroids are the plant parasites like transcriptional machinery of the cell organelles such as the nucleus or the chloroplast since they are known to be non- coding. These replicate by the process of RNA–RNA transcription. They mainly infect the epidermis of the hosts after causing mechanical damage to the cell wall of the plant. Characteristic Features of Viroids  Viroids contain only RNA.  These are known to be smaller in size and infect only the plants.  These are among the smallest known agents causing infectious disease.  Viroids are species of nucleic acid with relatively low molecular weight and a unique structure.  They reproduce within the host cell which they affect and cause variations in them causing death.  Viroids are mainly classified into two families namely Pospiviroidae- nuclear viroids and Avsunviroidae- chloroplastic viroids.  Viroids are said to move in an intracellular manner, cell to cell through the plasmodesmata, and long distance through the phloem. Compiled by: Dr. Malay Shah, VESASC 36 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Viroid Diseases Some of the diseases that are caused by the infection of viroids in plants are citrus exocortis, cucumber pale fruit, and chrysanthemum stunt. These infectious diseases are spread by the propagation of seeds in plants by cutting, tubers, etc and also by mishandling the contaminated implements. Hepatitis- D is caused in humans by viroid-like particles. The symptoms that are caused by the infection of viroid in plants include stunting of growth, stem necrosis, deformation of the leaves and fruits, and at last causing the death of the plant. Most of the viroids are said to infect the plants, including coconut and apple trees. The (PSTV) potato spindle tuber viroid causes significant crop damage to the potato yields causing the tubers to elongate and then crack. The other common type of viroid infection symptoms includes stunting and leaf epinasty. It's important to note that viroids only infect plants and do not pose a direct threat to animals or humans. Compiled by: Dr. Malay Shah, VESASC 37 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Satellites Satellites are similar to viroids in that they also consist only of a nucleic acid (either DNA or RNA). Satellites are infectious agents that depend on the presence of a helper virus for their replication and transmission. They are much smaller than viruses and lack the ability to replicate on their own. Instead, they require the machinery and resources of a host cell that has been infected by a helper virus. They differ from viroids in that they may encode one or more gene products and need ahelper virus to replicate and infect host cells. There is no homology between the genome of the satellite and its helper virus. Satellites are further divided into three types: Satellite viruses, Satellite RNAs, and Satellite DNAs. Satellite viruses encode their own capsid proteins, whereas satellite RNAs and DNAs do not. Most satellites use plant viruses as their helper viruses. There are three main types of satellite nucleic acids: Satellite Viruses: These are small infectious agents that have their own nucleic acid genome but are only able to replicate and propagate within cells that are co- infected with a compatible helper virus. Satellite viruses are often dependent on the helper virus for essential functions such as replication, encapsidation, and movement within the host plant or animal. Satellite RNAs: Similar to satellite viruses, satellite RNAs are small RNA molecules that also require a helper virus for replication and transmission. They rely on the helper virus to provide the necessary proteins and enzymes for their replication. Satellite RNAs can either enhance or interfere with the replication and symptoms caused by the helper virus, depending on the specific interactions between the satellite RNA, helper virus, and host. Satellites can have various effects on their host organisms. Some satellite infections can lead to more severe symptoms in the host, while others might attenuate the symptoms caused by the helper virus. The relationship between satellites and their helper viruses can be quite complex and can vary depending on the specific interactions between the two. Satellites have been primarily studied in the context of plant viruses, where they can impact agricultural productivity by affecting the severity of viral diseases. Understanding the interactions between satellites, helper viruses, and host organisms can provide insights into the mechanisms of viral replication and pathogenesis and can also have implications for disease management strategies. Compiled by: Dr. Malay Shah, VESASC 38 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Prions Prions are unique and fascinating infectious agents that are composed of misfolded proteins. They are associated with a group of neurodegenerative diseases known as transmissible spongiform encephalopathies (TSEs), which affect the nervous system of humans and animals. The term "prion" itself stands for "proteinaceous infectious particle." Prions are proteins encoded by the PRNP gene that are composed of 253 amino acids. These proteins are found in two forms including the benign cellular form (PrPC) and the abnormal misfolded form (PrPSc). Prions were first discovered in the 1980s during laboratory research on neurodegenerative diseases. Scientists noticed how prion proteins were highly expressed in nerve cells and that the abnormal PrPSc form acted as an infectious pathogen with the capacity to degenerate the central nervous system. What makes prions remarkable is that they lack a traditional genetic material like DNA or RNA, which is typically responsible for encoding and transmitting information for biological processes. Instead, prions are misfolded versions of a normal cellular protein, usually a protein called PrP (prion protein). When a prion comes into contact with its properly folded counterpart, it can cause the normal protein to undergo a conformational change and adopt the misfolded, infectious form. This misfolding and accumulation of prions in the brain leads to the destruction of nerve cells and the formation of microscopic holes, giving the affected brain tissue a spongy appearance, hence the name "spongiform encephalopathies." Some well-known prion diseases in animals include: Bovine Spongiform Encephalopathy (BSE) or "mad cow disease" in cattle. Scrapie in sheep and goats. Chronic Wasting Disease (CWD) in deer, elk, and moose. In humans, prion diseases include:  Creutzfeldt-Jakob Disease (CJD), which has several variants including sporadic, familial, and acquired forms.  Variant Creutzfeldt-Jakob Disease (vCJD), linked to consumption of meat from cattle affected by BSE. Compiled by: Dr. Malay Shah, VESASC 39 COURSE TITLE: FUNDAMENTALS OF MICROBIOLOGY Unit 1: Microorganisms and their significance Prion diseases are often fatal and are challenging to treat or manage due to their unusual mode of transmission and lack of genetic material. The infectious nature of prions, their resistance to standard sterilization procedures, and the fact that they can arise spontaneously through protein misfolding make them a subject of significant scientific interest and concern. Furthermore, scientists are working to discover therapeutic strategies to treat prion diseases. The majority of which aim to reduce the level of abnormal PrPSc present to limit nerve damage. Compiled by: Dr. Malay Shah, VESASC 40