Term
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Definition
| transfer of genetic material to other individuals other than offsprings (not directly related to them); independent of reproduction |
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Term
| Function of Genes Transferred |
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Definition
1. gene for infection host
2. gene for metabolizing compounds
3. genes for antibiotic resistance |
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Term
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Definition
| genetic elements that can be exchanged with others |
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Term
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Definition
| process by which a molecule of nucleic acid is broken and then joined to a different one |
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Term
| Elements of Horizontal Gene Transfer |
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Definition
| plasmids, prophages, islands, random DNA, transposons |
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Term
| Methods of Horizontal Gene Transfer |
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Definition
| transformation, transduction, genomic transfer agents, conjugation |
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Term
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Definition
| some piece of DNA that can behave as a unit |
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Term
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Definition
| DNA sequence that can change its relative position within the genome of a cell; it can do this in a copy and paste method or cut and paste method; these sequences code for transposase; coding region in a transposon is usually flanked by inverted repeats; often produce flanking direct repeats |
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Term
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Definition
| short DNA sequence and only code for proteins implicated in the transposition activity (transposase that catalyses the enzymatic reaction allowing the transposon to move) and one regulatory protein that either stimulates or inhibits transposition |
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Term
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Definition
| two insertion sequences that flank other DNA; typically an antibiotic resistance gene is included |
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Term
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Definition
| small, typically circular, independently replicating pieces of DNA with useful but not essential information that make up 1 to 10% of the total genome |
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Term
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Definition
| fertility, resistance, catabolic, bacteriocin, virulence, tumor-inducing, cryptic |
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Term
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Definition
| 1 to >1000 kbp single to high copy number plasmids |
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Term
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Definition
| F-plasmid contains genes to make a sex pilus; replicates, and a copy is passed on to another cell |
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Term
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Definition
| genes that make the cell resistant to antibiotics, heavy metals |
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Term
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Definition
| i.e. tol plasmid with genes for breaking down and using toluene |
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Term
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Definition
| codes for bateriocins, toxins produced bacteria to inhibit the growth of similar or closely related bacterial strains |
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Term
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Definition
| genes needed for the bacterium to infect the host |
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Term
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Definition
| The Ti plasmid found in Agrobacterium tumefaciens. Codes for plant growth hormones. When the bacterium infects the plant cell, the plasmid is passed to the plant cell and the genes are expressed, causing local overgrowth of plant tissue = gall. Very useful plasmid for cloning genes into plants |
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Term
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Definition
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Term
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Definition
| sections of DNA separate from the genome; evidence of horizontal origins meaning they are or once were mobile with flanking repeats; contain one or more genes that assist bacterium in pathogenicity, adaption, etc; i.e. P Fimbriae Island in E. coli and SCCmec in Staph aureus |
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Term
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Definition
| SCCmec, or staphylococcal cassette chromosome mec, is a mobile genetic element of Staphylococcus bacterial species. This genetic sequence includes the mecA gene coding for resistance to the antibiotic methicillin and is the only known way for Staphylococcus strains to spread the gene in the wild by horizontal gene transfer. Not all SCCmec elements are identical (in fact, SCC elements without the mecA gene do exist.) SCCmec elements have been classified into six types (I through VI) on the basis of two specific regions of their nucleotide sequences. One region is the mec complex including the mecA gene. The other is the ccr gene complex including genes coding for recombinases. The mec complex is divided further into five types (I through V) based on the arrangement of regulatory genetic features such as mecR1, an inducer. |
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Term
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Definition
1. nutrient
2. repair of genome damage
3. acquire new genetic information |
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Term
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Definition
| taking up of naked DNA from solution; occurs in both Gram + and Gram -; due to the negative charge of the cell membrane the negatively charged DNA is unable to enter the cell; cells in a state in which they can take up DNA are called competent; competence can be artificially induced by the introduction of calcium or natural |
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Term
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Definition
| transfer of DNA from one cell to another by a virus; generalized or specialized |
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Term
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Definition
| direct cell-cell transfer of DNA |
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Term
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Definition
| typically carries only bacterial DNA; bacterial chromosome DNA is inserted into the viral capsid; occurs in the lytic cycle |
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Term
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Definition
| non-viral DNA is carried as an insertion/substitution and into the viral capsid |
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Term
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Definition
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Term
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Definition
| genes necessary for non-sexual transfer of genetic material in both gram-positive and gram-negative bacteria. The tra locus includes the pilin gene and regulatory genes, which together form pili on the cell surface, polymeric proteins that can attach themselves to the surface of F- bacteria and initiate the conjugation |
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Term
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Definition
| viral genome inserted and integrated into the circular bacterial DNA chromosome |
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Term
| Methods of Bacterial Response to the Environment |
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Definition
| alarmones, cAMP and CRP, alternate sigma factors |
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Term
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Definition
| Bacteria produce a constant amount of signal; the more concentrated the bacteria, the more concentrated the signal. |
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Term
| Targets of Traditional Antibiotics |
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Definition
| peptidoglycan synthesis, protein synthesis, DNA replication |
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Term
| Response to Low Nutrient Levels |
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Definition
| induction of low Km uptake system |
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Term
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Definition
| acts to sequester and solubilize the iron |
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Term
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Definition
| cause lysis of red blood cells |
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Term
| Bacterial Response to Rapid Drop in Nutrients |
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Definition
Empty tRNA binds to ribosome
RelA component generates alarmones- (ppGpp which is a global controller)
Protein synthesis stops
Cell division stops
New DNA synthesis stops
Lipid synthesis stops
Resources diverted to amino acid synthesis |
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Term
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Definition
| protein needed only for initiation of RNA synthesis; a bacterial transcription initiation factor that enables specific binding of RNA polymerase to gene promoters; cascade effect |
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Term
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Definition
Positive chemotaxis: attraction towards nutrients
Negative: away from harmful chemicals
Aerotaxis: motility in response to oxygen
Phototaxis: motility to certain wavelengths of light
Magnetotaxis: response to magnetic fields |
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Term
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Definition
Five kingdoms: Animalia, Plantae, Fungi, Protista, and Monera
(prokaryotes) |
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Term
| Difficulty in Bacterial Classification |
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Definition
| unrelated bacteria develop similar physical and biochemical traits |
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Term
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Definition
| ribosomal RNA genes, membrane lipid chemistry, cell wall chemistry, environment prefrences |
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Term
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Definition
| a group of strains that are more closely related to each other than to another group. Members of a species have DNA that can hybridize. Because of gene exchange, mutation, phase variation, there are no sharp boundaries between species. |
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Term
| Bacterial Specie Identification Method |
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Definition
| DNA hybridization, ribotyping, DNA sequencing, serotyping (antibodies) |
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Term
| Hyperthermophilic Gram Negatives |
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Definition
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Term
| Green Sulfur and Green Non-Sulfur Bacteria |
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Definition
| photosynthetic, anoxygenic, sulfur bacteria uses H2S as electron donor |
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Term
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Definition
| highly radiation resistant; great DNA repair |
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Term
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Definition
| blue-green algae; oxygenic photosynthesis |
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Term
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Definition
| largest group of Gram - bacteria, enteric bacteria, vibria, pseudomonas (strictly respiratory), groups affecting N and sulfur cycles, purple sulfur and purple non-sulfur anoxygenic phototrophs, rickettsia (obligate intracellular parasite) |
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Term
| Bacteroides and Cytophaga |
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Definition
bacteroides strict anaerobes
cytophaga aerobic and gliding |
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Term
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Definition
Endospore formers (Bacillus, Clostridium)
Cocci (Staph, Strep, Micrococcus)
Other rods (Mycobacteria, Listeria, etc.)
Actinomycetes (filamentous, antibiotic producers)
Mycoplasma (DNA says G+, but no cell wall) |
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Term
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Definition
| tight spirals, internal flagell, G- |
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Term
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Definition
| obligate intracellular parasite |
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Term
| Methanogens and Halophiles |
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Definition
Methanogens strict anaerobes, make methane; Exist as symbiotes with mammals, e.g. cows
Halophiles need at least 1.5 M salt |
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Term
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Definition
| Growth from 80 upwards to 120 degrees C |
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Term
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Definition
| based on rRNA; 3 kingdoms |
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Term
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Definition
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Term
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Definition
| decay non-living organic matte; i.e. fungi |
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Term
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Definition
| use pre-formed organic matter; not autotrophs and not photosynthetic |
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Term
| Fungi Absorption of Nutrients |
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Definition
| release extracellular enzymes, break down polymers into LMW compounds for transport |
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Term
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Definition
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Term
| Deuteromycota/ Fungi Imperfecti |
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Definition
| fungi that can not be coaxed into having sex and cannot be properly classified |
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Term
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Definition
| thread; may be partially separated into cells or not at all (ceonocytic); tubular; composed of chitin; multinucleate; grow at tips |
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Term
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Definition
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Term
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Definition
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Term
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Definition
| able to grow as mold or yeast |
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Term
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Definition
| can be sexual or asexual; formed directly on hyphae, inside sporangia, or fruiting bodies |
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Term
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Definition
| disease by fungus; infection; most are saprotrophs |
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Term
| Antibiotic Production by Fungus |
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Definition
| penicillium, cephalosporium |
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Term
| Function of Fungi in Food Industry |
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Definition
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Term
| Function of Fungi in Decomposition |
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Definition
Cellulose and other plant polymers, wood
stone, paintings, paint, plastic |
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Term
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Definition
“Fungus roots”
Mutualism between:
Fungus (nutrient & water uptake for plant)
Plant (carbohydrate for fungus)
Several kinds
Zygomycota – hyphae invade root cells
Ascomycota & Basidiomycota – hyphae invade root but don’t penetrate cells |
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Term
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Definition
| Aerobic bacteria use up O2, anaerobes begin to grow; Degradation in compost raises temperature; thermophiles take over; Fermentation lowers pH and produces acids which are good nutrient sources for aerobes |
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Term
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Definition
Photoautotrophic bacteria fix CO2, heterotrophs release it
Large geological reservoirs; carbons moves quickly through living things; in anoxic region polysaccharides are broken down to sugar then organic acids, the organic acids are dehydrolyzed in the oxic region and converted into carbon dioxide |
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Term
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Definition
Multiple redox states of N, moves through soil, water, air; Degradation of organic N from biomass releases ammonia;
Ammonia oxidized to nitrite for energy (e.g. Nitrosomonas)
Nitrite oxidized to nitrate for energy (e.g. Nitrobacter)
Nitrate N can be used by plants. |
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Term
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Definition
| Mostly as phosphate; removed from rocks and cycled |
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Term
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Definition
Sulfate reduced to sulfide for amino acids
Ammonium released from organics for amino acids
Reactions occur to the extent needed for biomass |
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Term
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Definition
Sulfate serves as electron sink, converted to sulfide
Ammonium serves as energy source, is oxidized
Amino acids broken down for carbon, excess N excreted
Dissimilation: much larger quantities of chemicals converted into different forms. |
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Term
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Definition
Surface may be a nutrient source
Organic molecules absorb to surfaces, also
Multiple species with different niches represented
Cells use fimbriae and slime to adhere
Channels allow diffusion of nutrients (in) and waste (out)
Quorum sensing helps direct remodeling of structure
Changes in gene regulation; e.g. loss of flagella
Cells move within biofilm; cells and pieces of biofilm can leave and colonize new areas
Part of food web; provide nutrients for protozoa |
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Term
| Industrial use of Biofilms |
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Definition
Plug pipes, stimulate corrosion, impair heat exchangers
Biocides less effective; only surface layers killed |
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Term
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Definition
Infections can lead to colonization of artificial structures
Heart valves; seed infections elsewhere in the body
Difficult for antibiotics to completely rid infection |
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Term
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Definition
Increasing the size of a specific population by specifying what nutrients it can use
To find a bacterium in a mixed population that can:
Use phenol: supply phenol as sole carbon source
Use N2 as N source: provide no other N |
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Term
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Definition
| anaerobic bacteria break down cellulose into glucose subunits and partially break it down by fermentation producing ethanol and other organic acids as by-products; H2S used by green sulfur bacteria (tolerates higher S concentration than purple) and purple sulfur bacteria and use CO2 as the carbon source and H2S as an electron donor; aerobic bacteria= cyanobacteria and algae |
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