Microbio Final Review Sheet PDF

Devora Weinstein Chapter 12: Protists Protists - Overview Eukaryotic organisms They have a nucleus and a nuclear envelope. They have membrane-enclosed organelles. They are very diverse organisms. Most protists are unicellular, although there are some that are multicellular. Pro...

Devora Weinstein Chapter 12: Protists Protists - Overview Eukaryotic organisms They have a nucleus and a nuclear envelope. They have membrane-enclosed organelles. They are very diverse organisms. Most protists are unicellular, although there are some that are multicellular. Protist Nutrition Some protists are photoautotrophs and contain chloroplasts. Other protists are chemoheterotrophs and feed on organic molecules by absorption or ingesting larger food particles. Other protists are called mixotrophs, as they use a mix of the two, and combine photosynthesis and heterotrophic nutrition. Endosymbiosis Endosymbiosis is a symbiotic relationship between two species that exists as one organism living within another organism. Some scientists believe that protists and other eukaryotes evolved from a host cell that engulfed a bacterium. What we do know is that many protists do exist by living within other organisms. In other words, their symbiotic relationship is parasitism. Symbiotic Relationships With Protists Q: How do protists relate to our environment and us as humans? Many protists are aquatic and are found wherever water is located. Some protists are mutualistic in the aquatic environment - for example, in the coral reefs. Some organisms depend on protists for food. There are photosynthetic protists and many are producers - organisms use energy from light to convert CO2 to organic compounds. Other organisms depend on them for food either by eating them or by eating an organism that ate a producer. There are parasitic protists such as those that inhabit intestines and malaria. Supergroups of Protists There are 4 supergroups of protists. Each have different features, and each have different clinical and/or environmental significance to us as humans: Excavata SAR Archaeplastida Unikonta Protists Excavata ○ Diplomonads ○ Parabasalids ○ Euglenozoans SAR ○ Stramenophiles Diatoms Golden Algae Brown Algae ○ Alveolates Dinoflagellates Apicomplexans Ciliates ○ Rhizarians Radiolarians Forams Archaeplastida ○ Red algae ○ Green algae Unikonta ○ Amoebazoans Slime mold ○ Ophisthokonts Excavata Possess an "excavated" feeding groove on one side of the cell body. Protists with modified mitochondria and unique flagella. Reduced mitochondria means less cellular respiration and more anaerobic respiration. These protists will live in and feed off of anaerobic environments. Unique flagella enhance mobility and enable predatory abilities. Include 3 categories: diplomonads, parabasalids, and euglenozoans. Diplomonads Have reduced mitochondria called mitosomes. These organelles lack functional electron transport chains. Therefore, they can not use oxygen to get energy from carbohydrates and other organic molecules. They get energy from anaerobic pathways. Additionally, diplomonads, from the root word diplo, have 2 equal nuclei and multiple flagella, which mean they can reproduce rapidly and move rapidly. Most diplomonads are parasitic. One example is Giardia intestinalis which can inhabit the intestines of mammals (including humans) and cause a severe intestinal infection. Parabasalids Like diplomonads, parabasalids have reduced mitochondria, however, these are called hydrogenosomes, and these organelles generate anaerobic energy and release hydrogen gas as a byproduct. Parabasalids are also parasitic. A classic example of parabasalids would be Trichomonas vaginalis, a sexually transmitted disease. Trichomonas vaginalis travels along the mucus lining of the reproductive and urinary tracts by moving its flagella and by changing part of its cell membrane. Euglenozoans Very diverse Have predatory heterotrophs, photosynthetic autotrophs, mixotrophs, and parasites Main feature is their rod with either a spiral or crystalline structure inside each of their flagella. An example of euglenozoans would be the kinetoplastid, Trypanosoma which is carried by a vector the tsetse fly and infects humans. It causes sleeping sickness. SAR Very diverse group of protists that have DNA similarities Include 3 categories: Stramenophiles, Alveolates, Rhizarians Stramenopiles Include many photosynthetic organisms Name comes from "stramen" - straw, and "pilos" - hair This is because their flagellum has hairlike projections. In most stramenopiles, their rough hairy flagellum is paired with a smooth non- hairy flagellum. There are three groups of stramenopiles: Diatoms Golden Algae Brown Algae Diatoms Unicellular A type of algae. Very diverse and photosynthetic. Live in ocean and lakes Have a unique glass-like wall made of silicon dioxide embedded in an organic matrix ○ The wall consists of 2 parts that overlap ○ The wall provides protection from predators and they can withstand pressure. Their photosynthetic activity affects CO2 levels. Usually diatoms are eaten by protists and invertebrates, but during a bloom when ample nutrition is available, they are not eaten. When these uneaten diatoms die, their bodies sink to the ocean floor and it may take years, decades, or centuries for them to decompose. Thus, the carbon in their bodies remains for some time and is transported to the ocean floor instead. Golden Algae Most are unicellular. Achieve their characteristic color through yellow and brown carotenoids. Cells of golden algae are usually biflagellated. ○ Both flagella are usually attached near one end of the cell. Many are components of freshwater and marine plankton. Golden algae are photosynthetic for the most part, although some are mixotrophic. Brown Algae All are multicellular Most are marine Especially common along temperate coasts with cold-water currents. Have brown or olive colors due to carotenoids. Many of the "seaweeds" are brown algae. Brown algae reproduce through "alternation of generations” Alveolates Alveolates - from the word "alveoli", meaning 'sac'. Alveolates have a membrane-enclosed sac just under the plasma membrane. Include a wide range of photosynthetic and heterotrophic protists. Include the dinoflagellates, apicomplexans, and ciliates Dinoflagellates Dinoflagellates - from the Greek dinos meaning to twirl. They have 2 flagella in grooves reinforced by cellulose plates. They can spin as they move through water Most of the dinoflagellates are purely heterotrophic, others are photosynthetic, and some are mixotrophic. The most common pigment in dinoflagellate plastids are carotenoids. At times, there can be explosive growths of dinoflagellates and this can make the waters appear red or pink from the carotenoids. Toxins produced by dinoflagellates have caused fish and invertebrates to die. Humans that eat molluscs accumulating these toxins have died as well. Apicomplexans Nearly all apicomplexans are parasites of animals Parasites spread as infectious cells called sporozoite cells. The apex contains a complex of organelles that are specialized for penetrating host cells and tissues. They are not photosynthetic, but they can retain a modified plastid called the apicoplast, likely of red algal origin. Most of them have a life cycle of both sexual and asexual stages which often require 2 or more host species to complete. An example would be Plasmodium, the parasite that causes malaria, and it lives in both humans and mosquitoes. Ciliates Large variety of protists Named for their use of cilia to move and feed Most are predators Prey on bacteria or other protists Have 2 types of nuclei: tiny micronuclei and large macronuclei. A cell has one or more nuclei of each type. Genetic variation is a result of conjugation - sexual process where two exchange haploid micronuclei but do not reproduce. Ciliates generally reproduce through binary fission. A classic example of a ciliate would be the Paramecium Rhizarians Many species of rhizarians are amoebas They move and feed through use of pseudopodia, which extend and bulge from their cell surface This includes radiolarians and forams Radiolarians Have delicate intricate symmetrical internal skeletons Skeletons are made of silica Pseudopodia radiate from central body Pseudopodia are reinforced by microtubules Forams Named for their porous shells, after Latin foramen Shells are called tests Foram tests consist of a single piece of organic material that is hardened with calcium carbonate. Pseudopodia extend through the pores and function in swimming, feeding, and test formation. Forams are in the ocean and fresh water. Most of the identified forams are known from fossils. Archaeplastida This includes red algae and green algae. Archaeplastida are the most similar to plants. Red Algae Also called rhodophytes, from the Greek rhodos, meaning red They are reddish, from their photosynthetic pigment phycoerythrin which masks the green of chlorophyll. Other species have less phycoerythrin if they adapted to shallow water. Red algae are abundant in warm coastal waters of tropical oceans. Most red algae are multicellular.  The largest red algae, although not as large as brown algae, are included in the "seaweeds". Porphyra, Japanese "nori" is used as sheets or wraps for sushi. Red algae do not have flagellated gametes, unlike other algae, so they rely on water currents to bring gametes together for fertilization. Green Algae Have a structure and pigment similar to chloroplasts in plants Green algae are divided into 2: charophytes and chlorophytes. ○ Charophytes are the most similar to plants. ○ Chlorophytes (from Green chloros meaning green) are diverse. Most live in freshwater, but there are also marine. Some are unicellular. Both charophytes and chlorophytes have complex life cycles with both sexual and asexual reproductive stages Unikonta Most closely related to fungi and animals Includes amoebazoans and ophisthokonts Amoebozoans Include many species of amoebas They are different than rhizarians. They have pseudopodia that have lobes or are tube-shaped, instead of the thread- like pseudopodia of the rhizarians. One category of amoebozoans is the slime molds Slime Molds Also called mycetozoans (from Latin, meaning fungus animals). Originally thought to be fungi since they also reproduce with fruiting bodies which aid in spore dispersal. However, unlike fungi, many are unicellular. Plasmodial slime molds have bright colors such as orange or yellow. They form a mass called a plasmodium as they grow. This is different from the Plasmodium that causes malaria. The plasmodium from the slime mold is large; it is a single mass of cytoplasm undivided by plasma membranes, and contains many nuclei. This is a "supercell". It is the product of mitotic cell division that did not follow with cytokinesis. The plasmodium extends pseudopodia through moist soil and engulfs food particles through phagocytosis. If the area dries up or the food supply is exhausted, the plasmodium stops growing, and will then differentiate into fruiting bodies that function in sexual reproduction.\ Opisthokonts Very diverse group of protists Most similar to fungi and some similar to animals as well Chapter 13: Fungi Fungi Overview Fungi are diverse and widespread eukaryotic organisms. They have a nucleus, nuclear envelope, and membrane-enclosed organelles. Some fungi are unicellular but most are multicellular. They are essential for the well-being of most ecosystems. There may be as many as 1.5 million species of fungi Fungal Nutrition Fungi are heterotrophs. This means they can not make their own food like plants can. However, unlike animals, they do not ingest their food. They feed in a different mechanism entirely. Fungi feed by absorption. They will absorb nutrients from the environment outside of its body. Many fungi do this by secreting hydrolytic enzymes into their surroundings.The enzymes will then break down complex molecules into smaller organic compounds which the fungi can absorb into their cells for their use. Many fungi grow by forming multicellular filaments, and this body structure plays an important role in how they obtain food. Fungi Morphology and Growth The most common fungal body structures are multicellular filaments and single cells which are yeasts. ○ Some species can grow as both filaments and yeasts. ○ Many grow only as filaments. ○ There are very few that grow only as single- celled yeasts. Yeasts usually inhabit moist environments, such as plant sap and animal tissues (including human), where there is a large supply of nutrients such as amino acids and sugars Fungi Structure Multicellular fungal bodies are made of filaments. These filaments form a network called hyphae. Hyphae consist of tubular cell walls which surround the plasma membrane and cytoplasm of the cells. The cell walls are strengthened by chitin, which is a strong flexible polysaccharide.The chitin-rich walls can enhance the feeding by absorption. When fungi absorb nutrients from the environment, the concentration of the nutrients in the cells increase which cause water to move into the cell through osmosis. Without the strength of the chitin in the cell wall, the cells would otherwise burst. Hyphae are divided into cells by cross-walls called septa (singular septum). Septa have pores which allow ribosomes, mitochondria, and even nuclei to flow from cell to cell. Some fungi do not have septa. These fungi are called coenocytic fungi. These fungi are a continuous mass of cytoplasm with multiple nuclei.This is as a result of reproduction without cytokinesis. The hyphae form a mass called the mycelium (plural mycelia) which will infiltrate the material on which the fungus feeds. ○ The structure of the mycelium maximizes surface-to- volume ratio and enhances feeding efficiency. ○ Fungal mycelia grow rapidly. ○ Fungi concentrate energy on adding hyphae length. ○ For the most part, they are non-motile. ○ However, as they grow, they can extend and move beyond their initial territory. Specialized Hyphae Some fungi have specialized hyphae and these allow them to feed on living animals. Others have modified hyphae called haustoria which will allow them to extract nutrients from plants. There are fungi that have specialized branching hyphae called arbuscules which allow them to exchange nutrients with their plant hosts, a mutualistic relationship. This is called mycorrhizae, meaning fungus roots. Mycorrhizal fungi are fungi that improve delivery of phosphate ions and other minerals to plants, since the mycelial network of the fungi are more efficient at acquiring minerals from the soil than the plant's roots. ○ Ectomycorrhizal fungi (from Greek ektos, meaning "out""), form sheaths of hyphae over the root surface and grow into the root's extracellular space. ○ Arbuscular mycorrhizal fungi will extend arbuscules through the root cell wall and into tubes formed by pushing the root cell membrane inward. Fungal Reproduction Fungi reproduce by producing large numbers of spores. They reproduce either sexually or asexually. Spores can be carried long distances by wind or water. If they land in a moist place where there is sufficient food, the spores germinate, and they will produce a new mycelium. Fungal Sexual Reproduction Nuclei of fungal hyphae and spores of most fungi are haploid although many have transient diploid stages during sexual life cycles. Sexual reproduction begins when hyphae from 2 mycelia release sexual signaling molecules called pheromones- this will signal to them that they are ready to mate. If the mycelia are of different mating types , the pheromones from each partner bind to receptors on the other and the hyphae extend towards the pheromone source. When the hyphae meet, they fuse. ○ Plasmogamy - union of two cytoplasms. Hours, days, or even centuries with some fungi can pass between plasmogamy and the next stage. ○ Karyogamy – union of two nuclei, which will then produce diploid cells. Zygotes form during karyogamy. ○ Then fungi go into meiosis to restore the haploid state. ○ This will lead to spore production, and after spore production, germination – production of a new organism from the spores produced. Fungal Asexual Reproduction Many fungi reproduce both sexually and asexually. However, there are about 20,000 species that reproduce with asexual reproduction alone. The process of asexual reproduction will vary among the different species. Many fungi will reproduce by growing as filaments that produce haploid spores by mitosis. These are called molds if they form visible mycelia. They have rapid growth. Others reproduce by growing as single-celled yeasts. This will occur as regular cell division or by bud cells pinching off of parent cells. Fungal Diversity There are 5 major groups of fungi and they are very diverse: ○ Chytrids ○ Zygomycetes ○ Glomeromycetes ○ Ascomycetes ○ Basidiomycetes Chytrids Phylum Chytridiomycota 1,000 species Some are multicellular with branched hyphae and others are single-celled. Chytrids have flagellated spores. Common in lakes and soil Some are decomposers Others are parasites of protists, plants, other fungi, and animals Some are important mutualists - anaerobic chytrids live in the digestive tract of sheep and cattle helping to break down plant matter and contributing to the animal's growth. Zygomycetes Phylum Zygomycota Approximately 1,000 known species Includes species of fast-growing molds that usually affect foods such as breads, strawberries, peaches. ○ Rhizopus stolonifer (black bread mold) is a classic example of zygomycetes. Other zygomycetes are parasitic, or commensal symbionts of animals. If the food is dead, zygomycetes are great decomposers Glomeromycetes Phylum Glomeromycota 160 known species although may in fact be much higher. Formerly thought to be zygomycetes, however, recent molecular studies including DNA analysis show them to be separate. Nearly all of them form arbuscular mycorrhizae. The tips of the hyphae push into plant root cells and branch into tiny treelike arbuscules. They supply minerals and other nutrients to the roots. More than 80% of all plant species will have mutualistic relationships with glomeromycetes. Ascomycetes Phylum Ascomycota 65,000 species Exists in a wide variety of marine and freshwater habitats. Ascomycetes produce spores called ascospores in saclike asci, so they are called sac fungi. During the sexual reproductive stage,most ascomycetes develop fruiting bodies called ascocarps which have a wide range of sizes from microscopic to macroscopic.The ascocarps contain the asci which form the spores. Ascomycetes vary in size - there can be unicellular yeasts to very large organisms. Some are plant pathogens. Others are decomposers, particularly of plant material.  More than 25% live with green algae or cyanobacteria in beneficial symbiotic relationships. Basidiomycetes Phylum Basidiomycota Name is derived from the basidium, (Latin for little pedestals), a cell where karyogamy occurs. 30,000 species Includes mushrooms, puffballs, shelf fungi Includes mutualists that form mycorrhizae Includes 2 groups of destructive plant parasites - rusts and smuts. Include decomposers of wood and other plant material. Also are the best at decomposing complex polymer lignin which is a large component of wood Fungi and Symbiotic Relationships Q: How do fungi affect the environment, other organisms and us as humans? Fungi are decomposers of organic material which includes cellulose and lignin of plant cell walls. Fungi can decompose almost any carbon-containing substrate, as can bacteria, which is why they are so vital for maintaining our ecosystems. Fungi are mutualists with plants, algae, certain bacteria, and animals.They absorb nutrients from their host but they benefit the host as well. Fungi can be parasitic by absorbing nutrients off hosts with no benefit in return. Practical Uses of Fungi Decomposers and recyclers of organic matter Fermentation for alcoholic beverages Fermentation for bread baking Cheese preparation Production of antibiotics such as penicillin Production of other medications such as cyclosporine to suppress the immune syste Research for studying molecular genetics of eukaryotic organisms Chapter 14: Viruses How Viruses Were Discovered Light microscopy made it possible to see bacteria, fungi, and protozoa, which was very useful for diagnosing many diseases. However, microscopy techniques were useless when it came to viruses. Scientists had no idea of the cause of multiple viral infections for years, including smallpox and polio, which caused rampant disease. It was clear the diseases were transmitted from person to person, however, no one really knew much more than that. Louis Pasteur: was the first to make headway, by theorizing that rabies is caused by a "living thing" smaller than bacteria. In 1884, Pasteur was able to develop the first vaccine for rabies. Dmitri Ivanovsky and Martinus Beijerinck: The 1890s = the first substantial revelations of the unique characteristics of viruses occurred - Ivanovsky/Beijerinck showed that a disease in tobacco was caused by a virus. Beijerinck was the one to coin the term virus as it literally means "poison". Friedrich Loeffler and Paul Frosch 1898 - Loeffler and Frosch were then able to isolate the virus which causes foot- and-mouth disease in cattle. They found that when infectious fluids from host organisms were passed through porcelain filters designed to trap bacteria, the filtrate remained infectious microbes even though they could not see the infectious agent with a microscope. With the next several decades, scientists began to get a picture of the physical, chemical, and biological nature of viruses. Experiments proved that viruses are noncellular particles with a definitive size, shape, and chemical composition. They used specialized techniques to culture them in the lab. Now, we have since made tremendous advances in the field of virology. How Did Viruses Originate? Viruses are very old. Studies at the molecular level show relationships with viruses affecting all three domains which suggest that viral proteins pre-date divergence of life. There are a few theories on how viruses originated: ○ Virus-first hypothesis: viruses evolved from molecules of proteins and nucleic acids before cells appeared on earth and contributed to the rise of cellular life. This has been dismissed by some scientists since it does not agree with the definition of viruses which requires a host cell to replicate. ○ Reduction hypothesis: Viruses were once small cells which parasitized larger cells. The discovery of viruses with similar genetic material to parasitic bacteria supports this but does not explain why even the smallest cellular parasites do not resemble viruses at all. ○ Escape hypothesis: this idea is that some viruses evolved from DNA or RNA which escaped from genes of larger organisms. This does not explain the unique viral structure that is not seen anywhere else The General Structure of a Virus Viruses are the smallest infectious agents - in the realm of the ultramicroscopic. They are so minute at less than 2 micrometers that an electron microscope is necessary to detect them. Their host cells are way larger than they are – more than 2,000 bacterial viruses could fit into an average bacterium; more than 50 million polioviruses could fit into an average human cell. Animal viruses range from the really small such as parvovirus – around 20 nm in diameter to the really large megaviruses which are the size of small bacteria (up to 1,000 nm in width). Some cyclindrical viruses are relatively long but so narrow in diameter that they can not be seen without an electron microscope. Viruses have no resemblance to cells. Viruses contain only those parts needed to invade and control a host cell. They contain an external coating and a core which contains one or more nucleic strands of either DNA or RNA All viruses have a protein capsid, which is a shell surrounding the nucleic acid in the central core. ○ The capsid and the nucleic acid together form the nucleocapsid. ○ Viruses containing a nucleocapsid alone are considered naked. Viruses that have an additional covering are called enveloped. The Viral Capsid Capsid of a virus is made from several identical protein subunits called capsomeres. The capsomers self-assemble into the capsid. The shape and arrangement of the capsomers results in either a helical or icosahedral capsid. The Viral Envelope When enveloped viruses are released from the host cell, they take with them some of the host's membrane system in the form of an envelope. Some viruses bud off the cell membrane, others off the nuclear envelope or the endoplasmic reticulum. The envelope is derived from the host, but it is different, since some or all of the membrane proteins are replaced with viral proteins. Some proteins form a binding layer between the envelope and the capsid. Thus, glycoproteins will be exposed on the outside of the envelope. These molecules are called spikes or peplomers. They are essential for the attachment of the virus to the next host cell. Functions of the Viral Capsid and Envelope The outermost covering is absolutely necessary for viral function since it protects the nucleic acid from the effects of enzymes and chemicals when the virus is outside the host cell. An example of this is the capsids of intestinal viruses which are resistant to the acid and protein digesting enzymes of the digestive tract. Capsids and envelopes also introduce the viral DNA or RNA into the host cell. Parts of the viral capsids and envelopes stimulate the immune system to produce antibodies which neutralize the viruses. Complex Viruses: Atypical Viruses There are two groups of viruses called complex viruses which are more intricate in structure than helical and isacohedral; naked or enveloped viruses. ○ Poxviruses are very large DNA viruses and they lack a capsid and are covered by a dense layer of lipoproteins and coarse fibrils on their outer surface. ○ Bacteriophages have a polyhedral capsid head along with a helical tail and fibers for attachment to the host cell. Nucleic Acids in Viruses All the genetic information carried by an organism can be found on its genome. The genome of all organisms can be carried and expressed by nucleic acids - DNA/RNA. Unlike cells, which can contain both DNA and RNA, viruses contain either DNA or RNA but never both. The number of viral genes is usually very small and limited. There are about 9 genes in HIV to about 2,500 genes in pandoraviruses. E. coli by comparison has ~4,000 genes, and a human cell has around 21,000 genes. Other Substances in the Virus Particle Viruses may come with preformed enzymes which are required for replication. Examples include polymerases which synthesize DNA and RNA and replicate enzymes that copy RNA How Viruses are Classified and Named Viruses do not fall under domains and kingdoms, unlike bacteria, archaea, fungi, and protists. They have their own classification. Informally, they are classified as "naked" and "enveloped" viruses, "helical"/"icosahedral", "DNA"/"RNA" viruses. The International Committee on the Taxonomy of Viruses lists seven orders, 104 families, and 505 genera of viruses. Nomenclature of viruses follows these patterns: ○ Virus families are italicized and given the suffix – viridae and virus genera are italicized and end in – virus. ○ Standard species names are not so commonly used, so genus predominates. ○ Characteristics for naming in particular families goes by capsid, nucleic acid strand number, presence of envelope, viral size, and area of the host cell. Modes of Viral Replication Viruses penetrate the host's cell, take over the host's DNA and generate new viruses. The general phases in the life cycle of animal viruses are absorption, penetration, synthesis, assembly, and release from the host cell. Techniques in Cultivating and Identifying Animal Viruses Inoculation of virus into animals Inoculation of virus into embryonated eggs Tissue culture In vitro - Experiments performed in test tubes or artificial environments In vivo – Experiments performed in living organisms The purpose of viral cultivations are to isolate and identify viruses for clinical purposes and to prepare vaccines. Chapter 15: Food Microbiology Biotechnology There are multiple uses of microbes in the natural world. Human and microbial life are very clearly intertwined - this gave rise to many practical applications and the field of biotechnology. Applied Microbiology Microbes can be used for specific metabolic tasks to practically benefit humans. One area of interest is called applied microbiology. ○ This area takes advantage of the microbes living in natural habitats to treat wastewater and fix damaged environments.\ Industrial Microbiology Industrial microbiology – This area explores the use of microbes in making a wide variety of food, medical, manufacturing, and agricultural products. Artificial use of microbes, but applies the metabolic principles of microorganisms. Biotechnological Systems Most biotechnological systems involve the actions of bacteria, yeasts, and molds. They need to be able to synthesize a certain food, drug, organic acid, or vitamin. Many of the end products are obtained through fermentation Fermentation Fermentation - this is a general term used to refer to the mass, controlled culture of microbes to produce the desired organic compounds. Fermentation also includes use of microbes in sewage control, metal mining, and bioremediation. NOTE: Fermentation in biotechnology is not the same fermentation as metabolic fermentation, although some processes such as wine production will involve biochemical fermentation as well. Microorganisms in Water Management of Drinking Water Most drinking water comes from rivers and springs. It is used in its natural form only in remote areas. In cities, the water needs to be treated. Water supplies from deep wells which are relatively clean require less treatment than those from sources more contaminated. Steps of water purification: Management of Wastewater and Sewage In many parts of the world, the same water which serves as a source of drinking water is also used to dump solid and liquid wastes. Sewage - the used wastewater draining out of homes and industries which contains a variety of chemicals, debris, and microorganisms. There is a danger of typhoid, cholera, and dysentery linked to the unsanitary mixing of household water and sewage. Currently, some sewage is treated to reduce its microbial load before it is released, but a lot is released untreated into the aquatic environment.  Sewage contains large amounts of solid wastes, organic matter, and toxic chemicals. This poses a health hazard. To remove sewage and all health hazards properly, treatment requires 3 phases 1 Primary stage – floating bulkier materials (paper, bottles) are skimmed off. Remaining particles settle. Sedimentation usually takes 2-10 hours and the mixture is rich in organic matter. 2 Secondary stage - biodegradation. Bioremediators such as bacteria, algae, protozoa aerobically decompose remaining wood, paper, fabric, and organic molecules inside a large digester tank. This forms sludge. 3 Tertiary stage - further filtering and chlorinating prior to discharge. The treated sewage is released. Microbiology of Food All human food comes from some other organism. Rarely is it obtained in a sterile state. Microbes and humans are in direct competition for nutrients in food; microbes have very fast growth rates, so they generally have the winning edge over us. Somewhere along the lines with procuring food, with processing or preparation, food gets contaminated with microbes. The final effects depend on the amount of microbes present and whether the food is cooked or preserved. Beneficial Effects of Microbes in Food: Detrimental Effects of Microbes in Food: Food poisoning or food-borne illness Food spoilage – growth of microbes make food unfit for consumption, adds undesirable flavors, appearance and smell and destroys food value Neutral Effects of Microbes in Food: Presence/growth of microbes that do not cause disease or change the nature of the food Food Microbiology Many culinary procedures will deliberately add microbes in order to prepare foods. Food fermentation - common substances such as beer, wine, bread, cheese, yogurt, pickles are the products of food fermentation.  The microbes can occur naturally or they can be added. If added, they can be added as pure or mixed samples. Sometimes we use a starter culture - a sample of known bacteria or yeasts. Bread Making Microorganisms accomplish 3 functions: 1. Leavening the flour-based dough ○ Leavening - achieved through the release of gas to produce a porous and spongy product. ○ Without leavening, bread dough remains flat, dense, and hard. ○ The most common microbe and leavening agent present is a strain of baker's yeast Saccharomyces cerevisiae. Other gas-forming microbes such as Clostridium, heterofermentative lactic acid bacteria, and wild yeasts can be used depending on the bread desired. ○ Yeast metabolism requires a source of fermentable sugar such as glucose or maltose. Since the yeast undergoes aerobic respiration in bread dough, the products of maltose fermentation are co2 and water instead of alcohol. ○ Other contributions to bread texture come from kneading which brings air into the dough and from microbial enzymes which break down flour proteins (gluten) and give the dough some elasticity. 2. Imparting flavor and odor 3. Conditioning the dough to make it workable Production of beer and alcohol Production of beer/ other alcoholic beverages takes advantage of alcohol fermentation. By fermenting carbohydrates in fruits or grains anaerobically, ethyl alcohol will be produced. Brewing Malting - releasing amylases that convert starch to dextrins and maltose, and proteases that digest proteins Mash – mix of the malt grain and warm water Wort- clear fluid that comes off during the brewing ▪ Lagered – freshly fermented beer is held for several weeks to months in vats near 0 degrees celsius as a maturation period. Preparation of Wine Wine - any alcoholic beverage which comes from the fermentation of grape juice However, any fruit can be rendered into wine. The starting point is the preparation of must - the juice given off by crushed fruit which is used as a substrate for fermentation. Grape wines are usually white or red. Color comes from the skin of the grapes.  ○ White wine can come from white skinned grapes or red skinned grapes with the skin removed. ○ Red wine comes from the red or purple skinned grapes. Steps: Must preparation Fermentation Pasteurization Storage Aging Microbes in Milk and Dairy Products Milk is very nutritious. It starts its journey in the cow's udder which is sterile, but as it passes out, it is inoculated with the cow's microbiota. Other microbes can be introduced with the milking utensils. Milk can be highly susceptible to microbial growth. This is one reason why milk should undergo pasteurization. Cheese Production Large scale cheese production is usually controlled and uses only freeze-dried samples of pure cultures. These are first inoculated into a small quantity of pasteurized milk to form an active starter culture. The amplified starter culture is inoculated into a large vat of milk where curd development takes place. Rennin is usually added to increase the rate of curd formation. After its separation from whey, the curd will be rendered to produce one of several types of cheeses – soft, semisoft, hard. The amount of fat, acid, or salt content can be adjusted in order to vary the composition. Food Poisoning Foodborne illnesses are often called food poisoning. Not all food poisoning though is caused by microbes or their products. Several illnesses are caused by poisonous plants and animal tissues or by ingesting food contaminated by pesticides or other poisonous substances Can be divided into 2 categories: ○ Food intoxication - results from the ingestion of exotoxin secreted by bacterial cells growing in food. The absorbed toxin disrupts a particular target such as the intestine or the nervous system. ○ Food infection - associated with ingestion of live intact microbial cells which target the intestine. Some cases target the surface of the intestine while others invade the intestine and other body structures. Most food infections cause abdominal distress and diarrhea Food Spoilage Major causes of food spoilage  Physical ○ Temperature ○ R.H. ○ Light ○ Mechanical damage Chemical ○ Enzymatic reactions ○ Nonenzymatic reactions ○ Rancidity ○ Chemical interactions Microorganisms ○ Bacteria ○ Yeasts ○ Molds Other ○ Insects ○ Rodents ○ Animals ○ Birds Chapter 16: Bioterrorism Bioterrorism - a form of terrorism where there is the intentional release of biological agents such as bacteria, viruses, or other microorganisms. This can also be referred to as germ warfare. Biological agents are organisms or toxins that can kill, harm, or disable people, animals, and plants. Biological agents can be spread by ○ spraying them into the air ○ through person-to-person contact ○ infecting animals which carry the disease to humans ○ contaminating food and water. Biological warfare is the deliberate release of germs or other biological substances that can deliberately cause illness. There are three basic groups of biological agents that could likely be used as weapons: ○ Bacteria ○ viruses ○ Toxins History of Bioterrorism and Biological Warfare: Overview Infectious diseases were recognized for their effect on people and armies as early as 600 BCE.  The use of filth and cadavers, animal carcasses, and contagion had devastating effects and weakened the enemy Polluting wells and other sources of water of the opposing army was a common strategy that continued to be used through the many European wars, during the American Civil War, and even into the 20th century. The Black Death During the siege of Caffa, a well-fortified Genoese- controlled seaport (now Feodosia, Ukraine), in 1346, the attacking Tartar force experienced an epidemic of plague. The Tartars, however, used this opportunity to throw the cadavers of their deceased into the city, thus initiating a plague epidemic in the city. The outbreak of plague followed, forcing a retreat of the Genoese forces. The plague pandemic, also known as the Black Death, swept through Europe, the Near East, and North Africa in the 14th century and was likely the most devastating public health disaster in recorded history. The ultimate origin of the plague remains uncertain: several countries in the Far East, China, Mongolia, India, and central Asia have been suggested. Cadavers/Dead Bodies Many other incidents indicate the various uses of disease and poisons during war. For example, bodies of dead soldiers were catapulted into the ranks of the enemy in Karolstein in 1422. A similar strategy using cadavers of plague victims was utilized in 1710 during the battle between Russian troops and Swedish forces in Reval. On numerous occasions during the past 2000 years, the use of biological agents in the form of disease, filth, and cadavers have been mentioned in historical recordings. Smallpox Another disease which has been used as an effective biological weapon in the New World was smallpox. Pizarro was said to have presented South American natives with variola- contaminated clothing in the 15th century. In addition, during the French-Indian War (1754–1767), Sir Jeffrey Amherst, the commander of the British forces in North America, suggested the deliberate use of smallpox to diminish the native Indian population hostile to the British. An outbreak of smallpox in Fort Pitt led to an outbreak of fomites and provided Amherst with the means to execute his plan. On June 24, 1763, Captain Ecuyer, one of Amherst's subordinate officers, provided the Native Americans with smallpox-laden blankets from the smallpox hospital. He recorded in his journal: “I hope it will have the desired effect”. As a result, a large outbreak of smallpox occurred among the Indian tribes in the Ohio River Valley. Again, it has to be recognized that several other contacts between European colonists and Native Americans contributed to such epidemics, which had been occurring for over 200 years. In addition, the transmission of smallpox by fomites was inefficient compared with respiratory droplet transmission. Bioterrorism and WWI During World War I, reports of attempts by Germans to ship horses and cattle with disease-producing bacteria, such as Bacillus anthracis (anthrax) and Pseudomonas pseudomallei (glanders), to the USA and other countries. The same agents were used to infect Romanian sheep designated for Russia. Allegations of attempts by Germany to spread cholera in Italy and plague in St. Petersburg in Russia followed. ○ Germany denied all these allegations, including the accusation that biological bombs were dropped over British positions. In 1924, a subcommittee of the Temporary Mixed Commission of the League of Nations, in support of Germany, found no hard evidence that the bacteriological arm of warfare had been employed in war. However, the document indicated evidence of use of the chemical arm of warfare. In response to the horror of chemical warfare during World War I, international diplomatic efforts were directed toward limiting the proliferation and use of weapons of mass destruction, i.e., biological and chemical weapons. On June 17, 1925, the “Protocol for the Prohibition of the Use in War of Asphyxiating, Poisonous or Other Gases and of Bacteriological Methods of Warfare,” commonly called the Geneva Protocol of 1925, was signed. Because viruses were not differentiated from bacteria at that time, they were not specifically mentioned in the protocol. However, it did not address verification or compliance, making it a document which was less meaningful. Several countries that were parties to the Geneva Protocol of 1925 began to develop biological weapons soon after its ratification. These countries included Belgium, Canada, France, Great Britain, Italy, the Netherlands, Poland, Japan, and the Soviet Union. The USA did not ratify the Geneva Protocol until 1975 Bioterrorism and WWII During World War II, some countries began a rather ambitious biological warfare research program, especially Japan. Japan conducted biological weapons research from approximately 1932 until the end of World War II under the direction of Shiro Ishii and Kitano Misaji. The center of the Japanese biowarfare program was known as “Unit 731”. Besides the experiments performed in Unit 731, the Japanese military developed plague as a biological weapon by allowing laboratory fleas to feed on plague infected rats. On several occasions, the fleas were released from aircraft over Chinese cities to initiate plague epidemics. However, the Japanese had not adequately prepared, trained, or equipped their own military personnel for the hazards of biological weapons. An attack on the city of Changteh in 1941 reportedly led to approximately 10,000 casualties due to biological weapons. During this incident 1700 deaths were reported among Japanese troops. Thus, “field trials” were terminated in 1942. In December 1949, a Soviet military tribunal in Khabarovsk tried 12 Japanese prisoners of war for preparing and using biological weapons. The Japanese government, in turn, accused the Soviet Union of experimentation with biological weapons, referring to examples of B. anthracis, Shigella, and V. cholerae organisms recovered from Russian spies. Biological Warfare Post WWII During the years immediately after World War II, newspapers were filled with articles about disease outbreaks caused by foreign agents armed with biological weapons During the Korean War, the Soviet Union, China, and North Korea accused the USA of using agents of biological warfare against North Korea. Later on, the USA admitted that it had the capability of producing such weapons, although it denied having used them. However, the credibility of the USA was undermined by its failure to ratify the Geneva Protocol of 1925, by public acknowledgment of its own offensive biological warfare program, and by suspicions of collaboration with former Unit 731 scientists. By the late 1960s, the US military had developed a biological arsenal that included numerous biological pathogens, toxins, and fungal plant pathogens that could be directed against crops to induce crop failure and famine.