Microbiology exam 3 Flashcards
What do biogeochemical cycles do?
Biogeochemical cycles link metabolic processes of organisms for production and deflation of biomass.
What does it mean when all biomass consists of biogenic elements in roughly similar proportions?
Cycling of elements
What are the four types of reservoirs?
Terrestrial, aquatic, atmospheric, and living
What is the movement of elements between reservoirs (reaching equilibrium over the long term)?
Flux
What detects atmospheric gases?
When chemical cycling is monitored. Air will be collected in a sealed container is subjected to infrared radiation. If more is absorbed, more CO2 is present and will absorb the infrared radiation.
What method is used to monitor chemical changes over time (artificially enclosed ecosystems)?
Mesocosms
What method is used to monitor chemical changes over time that will label molecules with radioactive elements prior to release in a mesocosm?
radioisotope tracers
How do microbes influence the cycling of carbon? A balance is maintained between organic and inorganic carbon reservoirs.
global carbon cycle
What occurs when CO2 fixation exceeds respiration?
Organic matter will accumulate and create a positive net community productivity.
What is the production of methane as a byproduct of biodegradation of organic carbon in an anoxic environment?
Methanogenesis
What are syntrophic partnerships?
The relationship between the individuals of different species (especially of bacteria) in which one or both benefit nutritionally from the presence of the other.
What are archaea that produce methane as the end product, can only use specific substrates, and live in a community of microbes to utilize products from each other?
Methanogens
What does hydrogenotrophic methanogens produce CH4 from?
CO2 and H2
What does acetotrophic methanogens produce CH4 from?
acetate
What is the metabolism of CH4 into other forms which allows greater carbon cycling and occurs aerobically or anaerobically?
Methanotrophy
What are aerobic methods of methanotrophy dependent upon?
methane monooxygenase
What are anaerobic methods of methanotrophy dependent upon?
archaea (anaerobic methane oxidizers, ANMEs)
What are the three steps of the nitrogen cycle?
Notrogen fixation
nitrification
denitrification
What is the process that converts N2 into NH4+ by a nitrogenase complex and is carried out by aerobic/anaerobic bacteria and archaea?
nitrogen fixation
What is the process that converts NH4+ into nitrite (NO2-) or nitrate (NO3-)?
Nitrification
What enzymes produce nitrate?
ammonia monooxygenase and hydroxyl amine oxidoreductase
What enzyme produces nitrate with nitrifiers?
nitrite and nitrite oxidoreductase
What is the use of nitrate/nitrite as a terminal electron acceptor which eventually produces N2?
Dentridication
What process produces synthetic nitrogen fertilizer?
Haber-Bosch process
What are “dead zones”?
Overuse of fertilizers contribute to marine dead zones, imbalancing nitrogen reservoirs and ecosystems
What process actively cycles reservoirs of O2, CO2 and H2O, is cycled back and forth between photosynthesis and respiration reactions, and can be used marginally in anaerobic respiration using SO4(-2))?
Cycling of Oxygen
What process is usually found in rocks and dissolves in water, incorporation occurs through terrestrial and aquatic microorganism into higher-order organisms, and its decomposition reactions release the elements back into the terrestrial and aquatic systems?
Cycling of sulfur and phosphorus
What are abiotic and biotic interactions and exchanges of materials between organisms and their surrounding environment?
Ecosystems
What community of organisms capture energy through photosynthesis?
primary producers
What community of organisms ingest/utilize stored photosynthetic energy?
consumers
What community of organisms recycle components back into environments?
decoposers
What are function groups of members of communities and satisfies as a niche?
guild
What is the specific functional role of an organism within an ecosystem?
Niche
What are groups/layers of microbes on a surface that interact with an support each other?
Biofilms
any surface with water on it can form a biofilm for microbes
How does biofilm formation begin?
Appendaged bacteria form the primary layer on a surface and then secondary colonizers join the biofilm.
What do appendaged bacteria and secondary colonizers secrete?
Exopolysaccharide (EPS)
When microbes can be grown in the lab setting, they may grow slowly or may be rare in a mixed population. What method promotes the grown of desired microbes over undesired cells?
Enrichment cultures
What type of enrichment culture illustrates enrichment in action and displays how different microbes flourish in different areas of the column that correspond to different nutritional microenvironments?
Windogradsky column
What type of cultivation-independent technique is the extraction of DNA from an environmental sample and followed by PCR?
Direct sequencing
What type of cultivation-independent technique takes DNA from an environmental sample to construct a genomic library?
Metagenomics
What does “overfeeding” marine microbes leads to?
Anoxic water states (“dead zone” formation)
What are areas without enough oxygen to support much eukaryal life?
Dead zones
How are carbon and energy distributed through levels of marine ecosystems?
Zooplankton feeding on phytoplankton and through viral-mediated lysis
How does primary production occur in marine ecosystems?
phytoplankton
What marine ecosystem is when phytoplankton production drifts downward to feed zooplankton in the lower levels?
Dark mid-water zone
What marine ecosystem has an average seafloor depth of 3500 meters with the deepest spot being 11000 meters?
Deep-sea zone
What are microbes that can withstand intense pressures to grow?
Piezophiles
What kind of viruses are present in the ocean and liberate nutrients from cyanobacteria?
cyanobacteria viruses
What are categories of ecosystems based on vegetation characteristics?
Biomes
What are the dominant primary produces on land?
Plants
What is formed through microbial decomposition of plant and animal matter, combines with abiotic minerals and excreted nutrients from plant roots, and forms horizons based on physical type and characteristics?
Soils
What is the area of soil immediately surrounding plant roots that possess large amounts of organic carbon?
Rhizophere
What is the soil outside the rhizosphere that is not penetrated by plant roots
bulk soil
What are benefits that plants obtain from microbes
production of hormones
production of antibiotics
fixation of atmospheric nitrogen
solubilization of phosphate
What is the use of microbes to consume and remove human-made materials from soil?
Bioremediation
What are chemicals that are not normally found in nature?
Xenobiotics
What involves the addition of a nutrient that stimulates a broad substrate-range degradation pathway?
Cometabolism
What involves specific addition of a known degrading microbe to a contaminated environment?
Bioaugmentation
What type of symbiont occurs when one species does obvious harm to the other (pathogens)?
Parasitism
What type of symbiont occurs when one species benefits, but nothing happens to the other species (microbes on skin)?
Commensalism
What type of symbiont occurs when both species are getting some benefit from the arrangement?
Mutualism
What type of symbiont lives directly on the surface of their host?
Ectosymbionts
What type of symbiont lives within tissues or cells of the host?
Endosymbionts
What type of symbiotic relationship occurs when a specific fungal species will couple with 1-2 photosynthetic species?
Lichens
What are plant endosymbionts called?
Endophytes
What are endophytes that can infect plant root cells, fixing nitrogen and forming root nodules?
Rhizobia
What benefit does the plant provide to bacteria?
leghemoglobin
What benefit does bacteria provide to plants?
Nitrogen in a form that plants can easily use (ammonium)
What is the process of root nodule formation?
Bacterial nod genes are expressed in presence of plants.
An infection thread is formed to invade the root.
The nodule forms, providing a low-O2 environment.
The root cells form leghemoglobin to assist.
The plant provides carbon compounds to the bacteria while the bacteria provide ammonium in return.
What are common areas of humans that have symbionts?
Skin, vagina, oral cavity, digestive track
On the skin, what forms microbe habitat areas?
Oil glands and hair follicles
What are some common symbionts located in the vagina?
Staphylococcus epidermidis
E. coli and Enterococcus faecalis
Candida spp. (a yeast organism)
What are some common symbionts located in the oral cavity?
Gram-positive streptococci (e.g., Streptococcus mutans)
Anaerobic Fusobacterium spp. below the gumline
Anaerobic Porphyromonas gingivalis deep in plaque deposits
What is a major cause of cavities and periodontal disease?
Plaque biofilm
What human symbiont is the most diverse bio of microbes, includes a variety of bacteriophages, and might include between 880-2500 bacteria types?
digestive track
Where are the most microbes present in the human body?
colon (anaerobes or facultative anaerobes)
What are the benefits of symbiont relationships for humans?
Some microbes produce vitamins
Some microbes assist I digestion of materials in food
Provides proper immune function
What are live microbes that when ingested, provide a beneficial effect to the human body?
Probiotics
What is cecal fermentation?
Host digestive enzymes used to break down food prior to absorption
What is rumen fermentation?
Microbes in the host break down food first, then the hosts absorb fermentation products and microbes
What is the use of biological processes or organisms for the production of goods or services?
Biotechnology
What are the three types of biotech applications?
Red, White, and Green
What are preserved specimens that other scientists can obtain at minimal cost and helps promote confirmation of findings through repeatable independent research?
Culture collections
What happens when scientists search for useful new microbes to cultivate and add to collections?
Bioprospecting
What is a controlled and regulated aerobic/anaerobic culture of microbes to produce desired substances?
Fermentation
What are the two types of bioreactors?
fed-batch reactors, and chemostats
What does a fed-back bioreactor do?
The bioreactor is filled with a base amount of media to support initial cell growth. Feed media is added when needed to replace nutrients depleted by the increasing cell population.
What does a chemostat bioreactor do?
Chemostats are continuously operated bioreactors wherein growing cells reach a steady-state condition at which specific growth rate as well as biomass, substrate, and the product concentrations remain constant.
What is a product of metabolic processes required for growth of the microbe and is produced in the exponential phase?
primary metabolite
What is not required for microbial growth, but is often produced during the stationary phase?
secondary metabolite
What type of mutagenesis occurs at specific mutations at different sites?
Site-directed
What does the CRISPR-Cas genome editing stand for?
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and a CRISPR- associated (Cas) enzyme
How does the CRISPR-Cas genome editing occur?
Provides resistance to bacteriophage in Streptococcus thermophilus, which conveys immunity. Does not rely on DNA-binding protein motifs
What is used to mass-produce recombinant proteins?
Expression vectors
What must occur for recombinant proteins to be produced?
Eukaryal genes must be reformatted to remove introns.
A Shine-Dalgarno sequence must be added to the sequence to promote eventual translation.
Appropriate stop codons must be added.
What type of biotechnology is red biotechnology?
medical applications (pharmaceutical)
What two major uses of microbes are in the pharmaceutical industry?
Secondary metabolites and recombinant human proteins
What are the two types of secondary metabolites?
Antibiotics (penicillin, streptomycin/actinomycin) and statins
What are two types of human proteins as therapeutics?
Type 1 interferons and human insulin
What type of biotech application is white biotechnology?
industrial applications
What is the biorefinery concept?
Renewable biomass feedstock put in.
Microbial activities act on feedstock.
Useful materials can be harvested out.
How is the biofuel ethanol produced?
Microbes (yeast) ferment sugars to produce 2-carbon ethanol.
Ethanol can be used in internal combustion engines with little modification.
What is also used in internal combustion engines, is made up of 4 carbons, and has more properties similar to gasoline than ethanol?
Butanol
What type of biotech application is green biotechnology?
Agriculture biotechnology
What is considered “nature’s genetic engineer”?
Agrobacterium
How does A. tumefaciens cause crown gall tumors on plants?
By carrying a tumor- producing plasmid.
* Part of this plasmid is transferred into plant cells.
* This makes it a good delivery system for gene insertion into plants (transgenic plant production).
* This represents a cross-kingdom transfer of DNA
What is an application of transgenic plants that have plasmid containing a gene for a resistant form of the enzyme EPSP was introduced into plants using biolistics by Monsanto scientists?
herbicide resistance
What is an application of transgenic plants that is produced by the bacterium Bacillus thuringiensis, is highly specific and lethal to certain insect larvae that might feed on crops, but it isn’t naturally in plants?
Bt toxin
What incident can reduce the amount of food available for consuming?
Food spoilage
What method can make food last longer without spoiling?
Food preservation methods
What are foods that can easily support microbe growth?
Perishable foods
What are foods that do not spoil very easily?
Semi-perishable foods
What are foods that remain edible for long periods of time?
Non-perishable foods
What are intrinsic factors that lead to the likelihood of spoilage?
Water availability
osmolarity
nutrient content
pH and buffering capacity
antimicrobial constituents
biological structures
What are extrinsic factors that lead to the likelihood of spoilage?
Temperature
humidity
presence and concentration of gases
What food preservation method is achieved by drying out food or adding solutes to food?
Reduction of water activity
What food preservation method is achieved when temperature is controlled and is cheap and highly effective?
Pasteurization
What food preservation method is achieved when pressure eliminates endospores?
canning
What pasteurization process for milk is the original method for milk preservation and requires 63C for 30 min?
Low-temperature hold
What pasteurization process for milk requires 72C for 15 sec?
High-temperature, short-time
What parturition process for milk is requires 138C for 2 sec?
Ultra-high temperature
What are the different types of natural antimicrobial preservatives?
Bacteriocins
Lactic acid
Acetic acid
What are the different types of artificial preservatives?
Sodium benzoate
propionate
sorbates
sulfur dioxide
nitrites
What type of radiation is surface level and not strong?
Non-ionizing radiation (UV)
What type of radiation is strong and more penetrating?
Ionizing radiation (gamma/X-rays)
What food preservation method uses modified-atmosphere packaging and takes oxygen out of the packaging?
Vacuum packing
What type of environment is red meat packed into to reduce growth of harmful anaerobic microbes and keep the meat a desirable red color?
high oxygen
What food preservation method uses multiple levels of antimicrobial control in food?
hurdle technology
What food preservation method can be used to produce a number of different types of foods, uses starter cultures of microbes to begin the process, and the process is monitored and controlled for a desirable outcome of flavors and textures?
fermentation
What fermenting microorganism changes meat into summer sausage?
Pediococcus spp. and other lactic acid bacteria
What does lactic acid bacteria produce?
cheese and yogurt
What occurs when lactic acid is used instead of ethanol, CO2 gas is made instead of lactic acid, and vinegar is made due to acetic acid bacteria?
Wine was originally supposed to fermate but vinegar was produced instead
Infection of what viruses can stop a desired fermentation from occurring?
lytic bacteriophages
What illness occurs when food contaminated with microbial toxins causes illness in humans and animals?
foodborne intoxication?
What illness occurs when food contaminated with microbes causes illness in humans and animals?
food borne infection
What are some goals for treating wastewater?
reducing total organic carbon
removal or inactivation of harmful microbes in wastewater
reduction of inorganic compounds
reduce persistent organic pollutant
What type of wastewater treatment is the physical removal of large objects?
Pre-treatment
What type of wastewater treatment is the physical removal of sediments and grease that form primary sludge?
primary treatment
What type of wastewater treatment is the use of trickling filter/activated sludge unit to form complex biofilms that break down organic compounds over time?
secondary treatment
What type of wastewater treatment is not always used and is a filtration method?
Tertiary treatment
What type of wastewater treatment uses chlorination, UV light exposure or ozonation?
Disinfection
What type of filter is simple, passive, inexpensive, and uses crushed material as a base support for a growing biofilm of microbes?
trickling filter
What type of filter depends on the formation of flocs, uses an aeration tank, and has a settling tank?
activated sludge
What is the last step in secondary treatment, digests remaining organic wastes in anaerobic processes, and takes 2-4 weeks to break down the sludge?
Anaerobic sludge digester
What material is dehydrated/incinerated or used as a fertilizer?
Biosolid material
What type of drinking-water purification method removes many microbes from the water?
filtration
What type of drinking-water purification method destroys remaining microbes?
Disinfection
What would a researcher use FISH to investigate?
number of cells with a conserved sequence
Why do microbiologists use the operational taxonomic unit to determine phylogenies?
Because traditional species concepts are difficult to apply
Which of the following methods is useful for identifying metabolic capabilities of unculturable microbes?
stable-isotope probing
How do giant tube worms survive in hydrothermal vents?
they have a bacterial symbiont that can use H2S as an electron donor
What is different about the microbes in terrestrial hot springs compared to microbes in hydrothermal vents?
The microbes in hot springs can perform photosynthesis
