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62 Cards in this Set
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What are the properties of microbes that make them ideal tools for various applications? |
-size -rate of reproduction -cost -vast biochemical abilities -ease of genetic manipulation |
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what were the earliest (ancient) uses of microbes? give examples.
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-primarily for food/beverages (cheese in eastern Europe, beer in Mesopotamia, sake in ancient China) |
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what were the four major discoveries that impacted applied microbiology?
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-microbes seen for the first time -germ theory developed -Industrial revolution -molecular biology developed |
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what was observed in early microscopy?
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Leeuwenhoek created better lenses and used them to visualize microorganisms that moved and looked like mini-animals (animalcules) tested rainwater, tooth scrapings, feces, blood |
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what were earlier theories of infectious disease transmission?
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people thought diseases were caused by imbalances in body fluids (humours), bad air (miasma), or evil spirits. |
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how did the work of early microbiologists impact germ theory?
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Koch - first to show a specific disease is caused by a specific organism using anthrax Listeur - drastically reduced infection by sterilizing surgical wounds/tools/hands Pasteur - discovered silkworms were dying from protozoa disease Semmelweis - proved childbirth fever caused by pathogen from cadavers |
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how did the industrial revolution impact microbiology? |
mechanization and large scale production and distribution of fermentation products occurred for the first time. |
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how has molecular biology impacted microbiology? |
-being able to manipulate DNA changed: *sequencing whole microbial genomes *determining how microbes cause disease *easily identifying new species *genetically engineering microbes |
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bacteria
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cell structure: prokaryotic, unicellular, small, fast replication may produce toxins some actively mobile with flagella/pili characterized by cell wall (gram + vs -) |
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archae |
cell structure: prokaryotic, similar to bacteria in every way but genetics ancient live in extreme environments none are pathogenic to humans |
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fungi |
cell structure: eukaryotic with nucleus and internal organelles, unicellular or multicellular
growth occurs as multi-branched tubes called hyphae/mycelium acquire nutrients from scavenging organic compounds |
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algae |
all are photosynthetic some are unicellular/microscopic (phytoplankton) and some are macroscopic (seaweed); eukaryotic not plants because they lack roots, stems, leaves |
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protozoa |
mostly aquatic and non-photosynthetic all are microscopic and unicellular; eukaryotic classified by mode of motility: amoeba, ciliates, flagellates |
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nonliving infectious agents |
not composed of cells therefore not alive much smaller than any other infectious agent can infect and kill every other living thing |
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viruses |
obligate intracellular parasites: MUST be intracellular (or use other cells for its own replication) to continue to exist composed of proteins and nucleic acid with either a RNA or DNA genome extremely small - smaller than bacteria |
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prions |
abnormally folded proteins that are infectious when consumed, moves to brain and causes normal versions of proteins to misfold; accumulation of misfolded proteins is toxic |
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viroids |
infectious RNA molecules that cause disease in plants work by binding to host mRNAs and initiating their destruction |
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helminths |
multicellular and usually macroscopic, but most have a microscopic stage in life cycle have members in different phyla including tapeworms, flukes, and roundworms difficult to treat because they are composed of the same parts as a human |
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why is soil microbiology important? |
soil is a microbiologically rich substance; important for agriculture, decomposition, antibiotic discovery, bioremediation, ground water composition, and some human diseases |
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why is aquatic microbiology important?
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microbes are the base of all aquatic food webs changes in composition can give rise to major disease epidemics in both humans and animals |
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how can microbes be used to clean the environment? |
microbes can detoxify the chemical wastes that humans release into the water supply with help from mechanical engineering so contaminated water can be cleaned and returned into the water cycle |
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how are microbes used in food and beverage industry? |
many foods/beverages are products of fermentation which aids in both taste and preservation some foods/drugs are spiked with good microbes - or probiotics - in order to alter normal flora and help health |
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what are some ways to use microbes in clinical medicine? |
the process of determining how microbes cause disease
helps to diagnose, prevent, and treat microbial diseases using different immune tests, antimicrobial drugs, vaccines, or disinfection |
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how have biotechnology and genetic engineering altered microbiology? |
by purposely manipulating the genome of microbes in order to enhance their biochemical abilities or give them new ones
creating novel subunit vaccines
or creating mutant viruses to be gene delivery agents, vaccines, or cancer therapy
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what is soil composed of?
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50% is air and water 40-45% is made of inorganic materials 5% is organic matter *humus - decayed leaves, branches, and other formerly living organic matter *roots *microorganisms *macroorganisms - athropods, mammals |
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explain the different horizons of soil and what is in each. |
-organic (O) horizon *live organic & partly decayed matter & includes humus -aerated (A) horizon *dark topsoil contained actively decomposing humus and microbes and nutrients -B horizon *subsoil with less organic matter; rich in minerals and clay -C horizon *little microbial life (lithotrophs), anoxic, mostly rock fragments |
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what are the steps by which soil is formed from rock? |
-algae, lichens, and mosses can grow on bare rock when water is available and produce organic matter, which attracts other microbes -communities form and produce CO2 from aerobic resp. -- mixes with water and creates carbonic acid -when acids freeze/thaw with water, causes rock to break and crack until crude soil forms |
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how diverse are bacteria in soil and where are they mainly located? |
1-10 billion prokaryotic cells per gram of soil most found within the top 10 cm of the O and A horizons some can be found deeper - archae, anaerobes, chemolithotrophs |
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how do fungi grow in soil and what is their primary function? |
equally diverse as soil bacteria
hyphae produced to interact with plant roots and other species as symbiotes or parasites
the major decomposers of the soil |
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what are the roles of protozoa and nematodes in the soil? |
protozoa: regulate soil bacteria populations and mineralizing many different nutrients, also important to the food web
nematodes: disperse soil components as they move, important link between microbes and larger predators in terrestrial food web
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how do viruses affect other organisms in the soil? |
they are the most abundant in soil, but also the smallest
can infect everything by altering metabolism or causing disease |
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what are the principle nutrients that are cycled between air and soil/water? |
carbon, nitrogen, phosphorus, sulfur |
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broad steps of nutrient cycling |
-gaseous form of the nutrient is in air
-gas is directly used by plants and/or animals
-organisms then die, fall into soil or excrete a waste
-soil microbes decompose dead organic matter, oxidize the nutrient repeatedly, and the nutrient returns to atmosphere as gas |
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what is meant by decomposition? |
also called decaying or rotting bacteria and fungi digest tissue of dead organic matter by secreting exoenzymes to destroy macromolecules then absorb them and oxidize simple sugars, amino acids, nucleotides process is heavily dependent on temperature, oxygen, and water availability |
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the role of standard bacteria in decomposition |
bacteria WITHIN a recently deceased animal begins decomposition immediately - cause of internal bloating bacteria from soil begin further decomp of all easy, common macromolecules |
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how do fungi decompose organic compounds? |
hyphal filaments embed in substrates and absorb nutrients from digested matter while excreting exoenzymes
retain most of the freed carbon they create and will produce a lot of organic acids during decomp
decompose difficult macromolecules like cellulose and lignin |
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what are actinomycetes? how are they different than the other decomposers? what are some examples of them? |
filamentous bacteria that grow like fungi by producing hyphae, asexual spores, etc.
give soil its earthy smell from releasing geosmin gas
slowest grower and usually last to begin decomp
includes streptomycin (TB cure) and actinomycetes (antibiotics) |
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the carbon cycle |
-CO2 is fixed into organic compounds during photosynthesis -these organic compounds are consumed, are broken down, and made into new ones while CO2 is released
some dead organisms are anaerobically decomposed and later converted with heat/pressure/time into fossil fuels in soil
majority of dead organisms are oxidized into CO2 gas in the atmosphere/hydrosphere |
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the nitrogen cycle |
fixation: molecular nitrogen in the air is converted to ammonia three methods: *ammonia added directly to fertilizer *by free living soil bacteria that produce enzyme nitrogenase that does the conversion *by symbiotic soil bacteria |
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what are cyanobacteria and heterocysts? |
cyanobacteria are filamentous photosynthetic bacteria that live on both water and land contain special cells called heterocysts that specialize in nitrogen fixation more efficient at fixation since it doesn't rely on acquiring glucose from environment |
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what are rhizobia and how/why do they form nodules on roots? |
a type of symbiotic bacteria attaches to the root hairs and enter into the cells; infected cells enlarge into nodules bacteria fixes nitrogen for plant and the plant provides the bacteria with nutrients |
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how is nitrogen transformed during nitrification and which organisms do it? what is the purpose of making nitrites and nitrates? |
nitrification: other microbes begin to alter ammonia further chemically
ammonia is oxidized into nitrites by Nitrosomas and nitrates by Nitrobacter
most plants assimilates nitrates and use the nitrogen for amino acid synthesis |
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how is nitrogen transformed during denitrification and which organisms do it? |
some microbes use nitrate as an electron acceptor; will reduce it back to nitrite and nitrogen gas is released
Pseudomonas, Bacillus, and others |
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the sulfur cycle |
Lithotrophic bacteria like Thiobacillus can use H2S as an electron source; oxidize it into elemental sulfur and sulfate sulfate incorporated into cytesine and methionine amino acids in organisms decomp of plants/animals & excretion releases H2S and or elemental sulfur |
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the phosphorus cycle |
primarily exists as a phosphate; undergoes very little change in oxidation state
plants rely on symbiotic fungi called mycorrhizae that either penetrate the root cell walls (endomycorrhizas) or remain outside (ectomycorrhizas) |
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fertilizers |
any material applied to soil/plants that provide nutrients essential for growth and/or enhance water retention
contain a combination of ammonia, phosphate, and potassium
replace or enhance the work of soil microbes; excessive use dangerous by altering nutrient content or leaching into water |
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metabolic stimulants |
contain hormones, vitamins, and enzymes that stimulate microbial metabolism thought to be a safer, alternative method to fertilizers |
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why do soil microbes attack one another and other species in the soil? |
-killing their neighbors to win the competition for space and nutrients
-invading hosts and utilizing its nutrients to multiply and spread
-accidentally making it into a host through injury or ingestion |
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what are hyphae/mycelia and why would they enhance survival in soil? |
-made by molds and dimorphic fungi and actinomycete bacteria -cells divide and stay attached to one another as long filaments, interact in huge networks = mycelia -long thin cells have lots of surface area for absorbing nutrients from depleted soil |
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what are biofilms, what are they composed of, and why would they enhance survival in the soil?
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-formed by many bacteria and some fungi -cells adhere to inanimate surfaces and form microbial communities, often containing different species that will work together metabolically -secrete a thick, protective polysaccharide covering called a matrix -very resistant to antibiotics, drying, physical stresses |
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what are endospores? when are they made? why would they enhance survivals in the soil? |
-dormant cells extremely resistant to heat, UV, drying, chemicals, and time -not reproductive; the escape pod of the cell when it's about to die -one germinating cell = one endospore -many produce potent toxins and cause serious disease |
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how are endospores made? |
spore formation involves complex series of events that can take 8 hours -DNA divides and two copies separate -Septum forms between asymmetrically -larger compartment engulfs smaller, creating a forespore within larger mother cell -peptidoglycan and spore coat are produced, as well as DPA and SASPs -mother cell bursts, releasing spore |
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what is meant by the statement that soil bacteria often have metabolic flexibility? |
the soil is a harsh, toxic, rapidly changing environment. microbes must be versatile and adapt metabolically. can use a variety of organics as carbon sources, can obtain electrons from different in/organic compounds, many phototrophs |
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know the general idea behind the strategies of invasion and mass colonization. |
invasion: all viruses and some bacteria can infect other microbes and enter their cytosol; utilize host nutrients in order to replicate and spread. host organism dies as a result.
mass colonization: microbes replicate in high numbers in a given location, making it difficult for other microbes to come in by limiting nutrients, space, attachment sites |
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why produce toxins in the soil? what type of soil microbes make antibiotics, and what do they target? |
toxins: many fungi and bacteria use to kill other microbes, to eliminate competition (ex: Pseudomonas) antibiotics: also a toxin - agaisnt bacteria; targets bacterial cell walls, membranes, ribosomes, and enzymes (ex: Streptomyces) |
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symbiosis with plants: four major ways that symbiotic microbes help plants |
-enhance plant immunity -osmoregulatuon and drought tolerance -protection against pollution -temperature regulation
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symbiosis with plants: enhance plant immunity |
microbes at plant roots can affect levels of hormones
aid plant innate immunity by closing stomata when leaves are exposed to pathogens, protection against insects, killing invasive microbes
act as normal flora that coat plant surfaces and block pathogens
some will directly kill said pathogens |
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symbiosis with plants: osmoregulation and drought tolerance |
mycorrhiza fungi can extend root system of plants during drought conditions
some bacteria can increase rates of photosynthesis and other metabolic processes some secrete osmoprotectants that bind to roots exposed to excessive salt some induce plant to produce ethylene, which will protect them during flooding |
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symbiosis with plants: temperature regulation |
some symbiotic fungi (and viruses they may harbor) can increase heat tolerance in plants by increasing production of heat-shock proteins (heat stimulated chaperones), melanin, and enzyme SD
some bacteria secrete anti-freeze proteins around plant roots that prevent ice crystal formation and cell damage |
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symbiosis with plants: protection against pollution |
microbes have the ability to modify chemicals that can be toxic to plants (heavy metals, organic solvents, nuclear waste, oil, industrial toxins)
can be used by humans as agents of bioremediation |
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the role of microbes in the terrestial food web |
small microbes serve as a food source for larger ones, which are eaten by nematodes, arthropods, and other larger animals.
exist as the first trophic level |
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how do soil microbes help maintain the physical structure of soil? (particles sticking together) |
some types of mycorrhizal fungi secrete a glycoprotein called glomalin that attaches to other soil proteins; functions as a type of glue to help soil stay clumped
glomalin's other functions: helps soil retain and regular water, decreases erosion, helps sequester carbon and nitrogen |
Mycorrhizal fungi secrete glycoprotein... |
