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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?


-rate of reproduction


-vast biochemical abilities

-ease of genetic manipulation

what were the earliest (ancient) uses of microbes? give examples.

-primarily for food/beverages

(cheese in eastern Europe, beer in Mesopotamia, sake in ancient China)

what were the four major discoveries that impacted applied microbiology?

-microbes seen for the first time

-germ theory developed

-Industrial revolution

-molecular biology developed

what was observed in early microscopy?

Leeuwenhoek created better lenses and used them to visualize microorganisms that moved and looked like mini-animals (animalcules)

tested rainwater, tooth scrapings, feces, blood

what were earlier theories of infectious disease transmission?

people thought diseases were caused by imbalances in body fluids (humours), bad air (miasma), or evil spirits.

how did the work of early microbiologists impact germ theory?

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

how did the industrial revolution impact microbiology?

mechanization and large scale production and distribution of fermentation products occurred for the first time.

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


cell structure: prokaryotic, unicellular, small, fast replication

may produce toxins

some actively mobile with flagella/pili

characterized by cell wall (gram + vs -)


cell structure: prokaryotic, similar to bacteria in every way but genetics


live in extreme environments

none are pathogenic to humans


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


all are photosynthetic

some are unicellular/microscopic (phytoplankton) and some are macroscopic (seaweed); eukaryotic

not plants because they lack roots, stems, leaves


mostly aquatic and non-photosynthetic

all are microscopic and unicellular; eukaryotic

classified by mode of motility: amoeba, ciliates, flagellates

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


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


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


infectious RNA molecules that cause disease in plants

work by binding to host mRNAs and initiating their destruction


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

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

why is aquatic microbiology important?

microbes are the base of all aquatic food webs

changes in composition can give rise to major disease epidemics in both humans and animals

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

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

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

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

what is soil composed of?

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



*macroorganisms - athropods, mammals

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

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

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

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

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

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

what are the principle nutrients that are cycled between air and soil/water?

carbon, nitrogen, phosphorus, sulfur

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

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

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

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

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)

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

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

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

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

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

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

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

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)


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

metabolic stimulants

contain hormones, vitamins, and enzymes that stimulate microbial metabolism

thought to be a safer, alternative method to fertilizers

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

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

what are biofilms, what are they composed of, and why would they enhance survival in the soil?

-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

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

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

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

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

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)

symbiosis with plants:

four major ways that symbiotic microbes help plants

-enhance plant immunity

-osmoregulatuon and drought tolerance

-protection against pollution

-temperature regulation


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

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

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

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

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

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...