A Survey of Microbial World PDF

A Survey of Microbial World Prepared by: Celle Altiz-Marcelo Classification of Microorganisms Bergey’s Classification Of Bacteria  Bergey’s Manual of Systematic Bacteriology is a manual referring to the taxonomy of prokaryotic...

A Survey of Microbial World Prepared by: Celle Altiz-Marcelo Classification of Microorganisms Bergey’s Classification Of Bacteria  Bergey’s Manual of Systematic Bacteriology is a manual referring to the taxonomy of prokaryotic bacteria. It was prepared by the American bacteriologist, David Hendricks Bergey in 1923. It is a manual that deals with the identification of bacteria. It has been published in 9 editions. The first eight editions were published under the name ‘Bergey’s Manual of Determinative Bacteriology’. In the 9th edition, it was renamed as ‘Bergey’s Manual of Systematic Bacteriology’ and was published in four volumes in 1984, 1986, 1989 and 1991.  The First Edition Volume I: It talks about all Gram-negative bacteria and considers them important for medicinal and industrial purposes. Volume II: It includes all the information about Gram-positive bacteria. Volume III: It includes information about the remaining Gram-negative bacteria and about Archaea as well. Volume IV: It talks about filamentous actinomycetes and similar types of bacteria.  The Second Edition Volume I: It was published in 2001 and talks about the archaea and the branching phototrophic bacteria. Volume II: It was published in 2005 and gives details about the proteobacteria. Volume III: It was published in 2009 and gives details about the firmicutes. Volume IV: It was published in 2011. It mentions the Spirochaetes, Bacteroidetes, Tenericutes (Mollicutes), Chlamydiae, Acidobacteria, Verrucomicrobia, Fusobacteria, Dictyoglomi, Fibrobacteres, Gemmatimonadetes, Lentisphaerae, and Planctomycetes. Volume V: It was published in 2012 and talks about the actinobacteria. Volume I. The Archaea and the Deeply Branching and Phototrophic Bacteria 1A. Domain Archaea Phylum Crenarchaeota Phylum Euryarchaeota Class I. Methanobacteria Class II. Methanococci Class III. Halobacteria Class IV. Thermoplasmata Class V. Thermococci Class VI. Archaeglobi Class VII. Methanopyri Volume I. The Archaea and the Deeply Branching and Phototrophic Bacteria 1B. Domain Bacteria Phylum Aquificae Phylum Thermotogae Phylum Thermodesulfobacteria Phylum “Deinococcus-Thermus” Phylum Chrysiogenetes Phylum Chloroflexi Phylum Thermomicrobia Phylum Nitrospira Phylum Deferribacteres Phylum Cynobacteria Phylum Chlorobi  Volume II. The Proteobacteria Domain Bacteria Phylum Proteobacteria Class I. Alphaproteobacteria Class II. Betaproteobacteria Class III. Gammaproteobacteria Class IV. Deltaproteobacteria Class V. Epsilonproteobacteria  Volume III. The Low G + C Gram-Positive Bacteria Phylum Firmicutes Class I. Clostridia Class II. Mollicutes Class III. Bacilli  Volume IV. The High G + C Gram-Positive Bacteria Phylum Class Actinobacteria actinobacteria  Volume V. The Gram-Negative Bacteria Phylum Planctomycetes Phylum Chlamydiae Phylum Spirochaetes Phylum Fibrobacteres Phylum Acidobacteria Phylum Bacteroidetes Phylum Fusobacteria Phylum Verrucomicrobia Phylum Dictyoglomus Survey of Procaryotic Groups with Unusual Characteristics  Free-Living Nonpathogenic Bacteria Photosynthetic Bacteria Cynobacteria: Blue-Green Bacteria Green and Purple Sulfur Bacteria Gliding, Fruiting Bacteria  Unusual Forms of Medically Significant Bacteria Rickettsias – Rickettsia rickettsia (transmitted by ticks) – Rickettsia typhi (transmitted by lice) Chlamydias – Chlamydia trachomatis (the cause of both a severe eye infection (trachoma) that can lead to blindness and one of the most sexually transmitted diseases – Chlamydiophila pneumoniae (an agent in lung infections) Archaea: The Other Prokaryotes Characteristics of Archaebacteria  Characteristics of Archaea Archaebacteria are obligate or facultative anaerobes, i.e., they flourish in the absence of oxygen and that is why only they can undergo methanogenesis. The cell membranes of the Archaebacteria are composed of lipids. The rigid cell wall provides shape and support to the Archaebacteria. It also protects the cell from bursting under hypotonic conditions.  Characteristics of Archaea The cell wall is composed of Pseudomurein, which prevents archaebacteria from the effects of Lysozyme. Lysozyme is an enzyme released by the immune system of the host, which dissolves the cell wall of pathogenic bacteria. These do not possess membrane-bound organelles such as nuclei, endoplasmic reticulum, mitochondria, lysosomes or chloroplast. Its thick cytoplasm contains all the compounds required for nutrition and metabolism. They can live in a variety of environments and are hence called extremophiles. They can survive in acidic and alkaline aquatic regions, and also in temperature above boiling point.  Characteristics of Archaea They can withstand a very high pressure of more than 200 atmospheres. Archaebacteria are indifferent towards major antibiotics because they contain plasmids which have antibiotic resistance enzymes. The mode of reproduction is asexual, known as binary fission. They perform unique gene transcription. The differences in their ribosomal RNA suggest that they diverged from both prokaryotes and eukaryotes.  Types of Archaea Crenarchaeota The Crenarchaeota are Archaea, which exist in a broad range of habitats. They are tolerant to extreme heat or high temperatures. They have special proteins that help them to function at temperatures as high as 230 degrees Celsius. They can be found in deep-sea vents and hot springs, regions with superheated water. These include thermophiles, hyperthermophiles, and thermoacidophiles.  Types of Archaea Euryarchaeota These can survive under extremely alkaline conditions and have the ability to produce methane, unlike any other living being on earth. These include methanogens and halophiles. Korarchaeota They possess the genes common with Crenarchaeota and Euryarchaeot a. All three are believed to have descended from a common ancestor. These are supposed to be the oldest surviving organism on earth. These include hyperthermophiles.  Types of Archaea Thaumarchaeota These include archaea that oxidize ammonia. Nanoarchaeota This is an obligate symbiont of archaea belonging to the genus Ignicoccus. Survey of Eukaryotic Microorganisms The Kingdom Fungi  The Kingdom Fungi or Mycetae Large and filled with forms of great variety and complexity Macroscopic fungi (mushrooms, puffballs, gill fungi) Microscopic fungi (yeasts, molds) Either unicellular or colonial A few complex forms are considered multicellular  Cells of Microscopic Fungi Hyphae – long, threadlike cells that make up the bodies of filamentous fungi, or molds. Yeast cell – distinguished by its round to oval shape and by its mode of asexual reproduction. It grows swellings on its surface called buds which then become separate cells. Hyphae and Yeast Cell  Cells of Microscopic Fungi Pseudohypha – a chain of yeasts formed when buds remain attached in a row. Some fungal cells exist only in a yeast form and others occur primarily as hyphae, a few, called dimorphic, can take either form, depending upon growth conditions such as changing temperature.  Fungal Nutrition All fungi heterotrophic (substrates) Most fungi are saprobes Fungi can also be parasites on the bodies of living animals or plants. In general, the fungus penetrates the substrate and secretes enzymes that reduce it to small molecules that can be absorbed by the cells. Algae “Alga is a term that describes a large and incredibly diverse group of eukaryotic, photosynthetic lifeforms. These organisms do not share a common ancestor and hence, are not related to each other (polyphyletic).”  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 Algae 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. Types of Algae  Euglenophyta (Euglenoids) Euglena are fresh and salt water protists. Like plant cells, some euglenoids are autotrophic. They contain chloroplasts and are capable of photosynthesis. They lack a cell wall, but instead are covered by a protein-rich layer called the pellicle. Like animal cells, other euglenoids are heterotrophic and feed on carbon-rich material found in the water and other unicellular organisms. Some euglenoids can survive for some time in darkness with suitable organic material. Characteristics of photosynthetic euglenoids include an eyespot, flagella, and organelles (nucleus, chloroplasts, and vacuole).  Chrysophyta Golden-brown algae and diatoms are the most abundant types of unicellular algae, accounting for around 100,000 different species. Both are found in fresh and salt water environments. Diatoms are much more common than golden-brown algae and consist of many types of plankton found in the ocean. Instead of a cell wall, diatoms are encased by a silica shell, known as a frustule, that varies in shape and structure depending on the species. Golden-brown algae, though fewer in number, rival the productivity of diatoms in the ocean. They are usually known as nanoplankton, with cells only 50 micrometers in diameter.  Pyrrophyta Fire algae are unicellular algae commonly found in oceans and in some fresh water sources that use flagella for motion. They are separated into two classes: dinoflagellates and cryptomonads. Dinoflagellates can cause a phenomenon known as a red tide, in which the ocean appears red due to their large abundance. Like some fungi, some species of Pyrrophyta are bioluminescent. During the night, they cause the ocean to appear to be aflame. Dinoflagellates are also poisonous in that they produce a neurotoxin that can disrupt proper muscle function in humans and other organisms. Cryptomonads are similar to dinoflagellates and may also produce harmful algal blooms, which cause the water to have a red or dark brown appearance.  Chlorophyta Green Algae It is a large, informal grouping of algae having the primary photosynthetic pigments chlorophyll a and b, along with auxiliary pigments such as xanthophylls and beta carotene. Higher organisms use green algae to conduct photosynthesis for them. Other species of green algae have a symbiotic relationship with other organisms. Members are unicellular, multicellular, colonial and flagellates. Prominent examples of green algae include Spirogyra, Ulothrix, Volvox, etc.  Rodophyta Red Algae it is a distinctive species found in marine as well as freshwater ecosystems. The pigments phycocyanin and phycoerythrin are responsible for the characteristic red colouration of the algae. Other pigments that provide green colouration (such as chlorophyll a) are present. However, they lack chlorophyll b or beta-carotene.  Phaeophyta Brown algae are among the largest species of algae, consisting of varieties of seaweed and kelp found in marine environments. These species have differentiated tissues, including an anchoring organ, air pockets for buoyancy, a stalk, photosynthetic organs, and reproductive tissues that produce spores and gametes. The life cycle of these protists involves alternation of generations. Some examples of brown algae include sargassum weed, rockweed, and giant kelp, which can reach up to 100 meters in length.  Xanthophyta Yellow-green algae are the least prolific species of algae, with only 450 to 650 species. They are unicellular organisms with cell walls made of cellulose and silica, and they contain one or two flagella for motion. Their chloroplasts lacks a certain pigment, which causes them to appear lighter in color. They usually form in small colonies of only a few cells. Yellow-green algae typically live in freshwater, but can be found in salt water and wet  Blue-Green Algae Not an Algae: Blue-Green Algae In the past, blue-green algae were one of the most well-known types of algae. However, since blue-green algae are prokaryotes, they are not currently included under algae (because all algae are classified as eukaryotic organisms). Also called cyanobacteria, these organisms live in moist or aquatic environments just like other algae. These include dams, rivers, reservoirs, creeks, lakes and oceans. This class of bacteria obtains energy through the process of photosynthesis. Ecologically, some species of blue-green algae are significant to the environment as it fixes the nitrogen in the soil. Hence, these are also called nitrogen-fixing bacteria. E.g. Nostoc, Anabaena, etc.  Algal Biofuel Algal Biofuel Recent developments in science and technology have enabled algae to be used as a source of fuel. Global demand for petroleum products and declining environmental health have prompted the use of eco-friendly alternatives such as algal biofuel. Hence, algae fuel is an increasingly viable alternative to traditional fossil fuels. It is used to produce everything from “green” diesel to “green” jet fuel. It is similar to the other biofuels made from corn and sugar cane. Protozoa What’s an animal, but not an animal? An animal-like protist, or a protozoa. These protists have the ability to move, usually with some sort of cilia or flagella, and must obtain their energy from other sources. But obviously, they are much simpler than animals.  Animal-Like Protists: Protozoa Animal-like protists are commonly called protozoa (singular, protozoan). Most protozoa consist of a single cell. They are animal-like because they are heterotrophs, and are capable of moving. Although protozoa are not animals, they are thought to be the ancestors of animals.  Ecology of Protozoa Protozoa generally feed by engulfing and digesting other organisms. As consumers, they have various roles in food chains and webs. Some are predators. They prey upon other single-celled organisms, such as bacteria. In fact, protozoa predators keep many bacterial populations under control. Other protozoa are herbivores. They graze on algae. Still others are decomposers. They consume dead organic matter. There are also parasitic protozoa that live in or on living hosts. For example, the protozoan that causes malaria lives inside a human host. Protozoa are also important food sources for many larger organisms, including insectsand worms. Classification of Protozoa Helminths  What are Helminths? Helminths are parasitic worms that can infect humans and other animals. There are three types of helminths: flukes (trematodes), tapeworms (cestodes), and roundworms (nematodes). When these worms get into the human body, they can cause parasitic infection, which appears as intestinal worms. This infection is known as helminthiasis, although it's sometimes called helminthosis or simply a worm infection. Types of Helminths  Three types of helminths infect humans. A fourth type primarily infects animals but can infect humans in rare cases. They are: Roundworms (Nematodes): These helminths, which have the scientific name nematodes, have a cylindrical body similar to earthworms. They can lead to infection in the intestines or elsewhere in the body. Flukes: These helminths, or trematodes, have a flat body and leaf-shaped head with a sucker that helps them attach. They generally infect the bile ducts (thin tubes from the liver to the small intestine), liver, or blood. Tapeworms: Tapeworms, or cestodes, are long, segmented flatworms found in or around the intestines. Thorny-headed worms: These helminths, or acanthocephalans, have a round body and barbs around their head. They mainly infect animals, and human infection is very rare Diseases cause by Helminths  Ascariasis Ascariasis is the most common type of helminthiasis in humans. It’s caused by the roundworm Ascaris lubricoides. Ascaris larvae and adult worms live in the intestines. Many people with ascariasis don’t have symptoms, but a severe infection can lead to abdominal symptoms. Ascariasis can also migrate outside the intestines, leading to cough and other symptoms as the worms spread  Whipworm Whipworm is an infection caused by a type of roundworm. Whipworms live in the large intestine and generally cause a more severe infection than ascariasis. The symptoms of whipworm include painful bowel movements, diarrhea that contains blood or mucus, and frequent defecation. As whipworm progresses, a person can experience anal prolapse, anemia (reduced ability of the blood to carry oxygen due to low red blood cells or low hemoglobin), and stunted growth.  Hookworm Hookworm infections are caused by the helminths Ancylostoma duodenale and Necator americanus. These worms infect the small intestine. Unlike other helminth infections that are passed by ingesting eggs, hookworm is most often contracted by walking barefoot on contaminated soil. Hookworm larvae in the soil can enter the body through the feet and travel to the intestine. After the hookworm enters the foot, a person might experience itchiness or a rash. With mild infections, there may be no symptoms after that. More severe infections will lead to diarrhea, abdominal pain, loss of appetite, weight loss, and anemia. Virus, Viroids, Prions  Virus Viruses are acellular parasitic entities that are not classified within any domain or kingdom. Viruses are diverse entities. They vary in their structure, their replication methods, and in their target hosts. Nearly all forms of life—from bacteria and archaea to eukaryotes such as plants, animals, and fungi—have viruses that infect them. While most biological diversity can be understood through evolutionary history such as how species have adapted to conditions and environments, much about virus origins and evolution remains unknown. Baltimore’s Classification of Virus  Virus Replication A temperate bacteriophage has both lytic and lysogenic cycles. In the lytic cycle, the phage replicates and lyses the host cell. In the lysogenic cycle, phage DNA is incorporated into the host genome, where it is passed on to subsequent generations. Environmental stressors such as starvation or exposure to toxic chemicals may cause the prophage to excise and enter the lytic cycle.  Viroids In 1971, Theodor Diener, a pathologist working at the Agriculture Research Service, discovered an acellular particle that he named a viroid, meaning “virus-like.” Viroids consist only of a short strand of circular RNA capable of self-replication. The first viroid discovered was found to cause potato tuber spindle disease, which causes slower sprouting and various deformities in potato plants (see Figure 6.4.16.4.1). Like viruses, potato spindle tuber viroids (PSTVs) take control of the host machinery to replicate their RNA genome. Unlike viruses, viroids do not have a protein coat to protect their genetic information. These potatoes have been infected by the potato spindle tuber viroid (PSTV), which is typically spread when infected knives are used to cut healthy potatoes, which are then planted. (credit: Pamela Roberts, University of Florida Institute of Food and Agricultural Sciences, USDA ARS)  Prions At one time, scientists believed that any infectious particle must contain DNA or RNA. Then, in 1982, Stanley Prusiner, a medical doctor studying scrapie (a fatal, degenerative disease in sheep) discovered that the disease was caused by proteinaceous infectious particles, or prions. Because proteins are acellular and do not contain DNA or RNA, Prusiner’s findings were originally met with resistance and skepticism; however, his research was eventually validated, and he received the Nobel Prize in Physiology or Medicine in 1997.  Prions A prion is a misfolded rogue form of a normal protein (PrPc) found in the cell. This rogue prion protein (PrPsc), which may be caused by a genetic mutation or occur spontaneously, can be infectious, stimulating other endogenous normal proteins to become misfolded, forming plaques Today, prions are known to cause various forms of transmissible spongiform encephalopathy (TSE) in human and animals. TSE is a rare degenerative disorder that affects the brain and nervous system. The accumulation of rogue proteins causes the brain tissue to become sponge-like, killing brain cells and forming holes in the tissue, leading to brain damage, loss of motor coordination, and dementia Infected individuals are mentally impaired and become unable to move or speak. There is no cure, and the disease progresses rapidly, eventually leading to death within a few months or years. Endogenous normal prion protein (PrPc) is converted into the disease-causing form (PrPsc) when it encounters this variant form of the protein. PrPsc may arise spontaneously in brain tissue, especially if a mutant form of the protein is present, or it may originate from misfolded prions consumed in food that eventually find their way into brain tissue. (credit b: modification of work by USDA)