Final Exam 1 Flashcards
Dunfield Portion
1
Q
FIRST and MOST Numerous organisms on earth?
A
Bacteria
2
Q
Fermentation
Quick Definition
A
Supplying glucose to microorganisms and being able to utilize it in the absence of oxygen
3
Q
Louis Pasteur
A
- discovered alcoholic fermentation was a biologically mediated process
- disproved spontaneous generation theory
- developed vaccines for: Anthrax, cholera, rabies
- processes that were thought to be solely chemical are microbial
- Pasteurization technique
4
Q
Koch’s Postulates
A
- Suspected pathogen present in all cases and absent in healthy animals
- Obtained/grown pure culture of suspected pathogen
- Cells from pure culture put into healthy animal
- Suspected pathogen re-isolated and shown to be same as original
5
Q
Pasteurization Technique
A
- bend neck of bottle
- prevents from contamination of air particles
- sterilize by heating
- tilting: allows contact with dust
6
Q
What type of energy source is nitrogen fixation?
A
Lithotrophy
7
Q
Sergei Winogradsky
A
- father of environmental biology
- specific bacteria linked with certain biogeochemical transformations
- Winogradsky column
8
Q
What are the two carbon sources?
A
Heterotrophy: Organic C
Autotrophy: Inorganic C
9
Q
Explain Winogradsky Column
A
- more sulfide using bacteria at the bottom
- more aerobic/light using at the top
- 7 layers of bacteria (top -> down):
Cyanobacteria
Heterotrophic Bacteria
Iron Oxidizing Bacteria
Purple Non-Sulfer Bacteria
Purple Sulfer Bacteria
Green Sulfer Bacteria
Surface Reducing Bacteria
10
Q
4 Ways of Looking at Microbial Diversity
A
- Morphological Diversity
- cell shape + membrane structure - Metabolic Diversity
- physiological processes (how do they obtain carbon and energy) - Genomic Diversity
- Evolutionary Diversity
11
Q
4 Groups based on cell shapes
A
Sphaerobacteria - Spheres
Microbacteria - Rod
Desmobacteria - Filamentous
Spirobacteria - Spiral
12
Q
Who is the father of taxonomy
A
Ferdinand Cohn
13
Q
What is the GOLD STANDARD for species definition
A
DNA - DNA Hybridization
14
Q
What is DDH
A
- DNA-DNA Hybridization
- DDH value of 70% = arbitrary number
- DDH > 70% same species and will have 16s rRNA > 98%
15
Q
What would the DDH Value be if two species are evolutionary neighbors?
A
Less that 70%
16
Q
Explain how phylogenetic trees are constructed
A
- Sequence equivalent genes using PCR
- Align homologous sequences
- Distance method
- put into distance matrix
- compare mutations
- count mutations
* can only compare two at a time - Use matrix to create a tree that represents evolutionary history
- the lower the difference value = the more closely related
17
Q
What are the 3 distinct lineages (i.e. domains)?
A
Eukarya (eukaryotic)
Archaea (prokaryotic)
Bacteria (prokaryotic)
18
Q
What is Polyphasic Approach?
A
- A way to define species
- requires description of
1. Morphology
2. Metabolic
3. Genomic
4. Phylogenetic
19
Q
What is Endosymbiosis
A
- mitochondria & chloroplasts came about by being engulfed by eukaryotes
- mitochondria was thought to look like a microbe
- chloroplast was thought to look like cyanobacteria
- suggests eukaryotic cells are chimeric
20
Q
Through endosymbiosis, eukaryotes got what functions/components that were similar to what organism?
A
- lipids and energy metabolism similar to bacteria
- transcription and translation that is similar to archaea
21
Q
Why are rRNAs good candidates for phylogenetic analysis?
A
- Universal
- They are functionally constant
- They are highly conserved
- Adequate in length
22
Q
How are viruses different from Bacteria, Archaea, and Eukarya?
A
- They don’t have cytoplasm, cell, ribosomes
- they are obligate parasites
- can only replicate in the cytoplasm of a host cell
23
Q
What is catabolism?
A
“Catabolic Reactions”
- biogeochemical reactions leading to energy conservation (usually as ATP) by the cell
24
Q
What are the 4 phyla of Bacteria
A
- Proteobacteria
- Actinobacteria
- Firmicutes
- Bacteroidetes
25
Explain Proteobacteria
- 1 of 4 Phylas of bacteria
- 40% of all cultured species
- most abundant and diverse
- divided into six classes:
Alpha, Beta, Delta, Gamma Epsilon, Zelta
26
Cyanobacteria
- caused the great oxygenation event
- ancestor of chloroplast
- evident as stromatolites
27
Enrichment Culture Technique
Isolating organisms by using highly selective media and certain incubation techniques
28
What are the different energy sources?
Chemotrophs (chemoorganotrophs + chemolithotrophs)
| Phototrophy
29
What is the difference between species richness and species abundance
SPECIES RICHNESS
- total number of different species present
SPECIES ABUNDANCE
- Proportion of each species
30
How can a "bloom" occur?
With high species abundance and low species richness
31
What is a Microbial Habitat?
- almost everything
| - constrained with physical limits: pH, temp, water activity
32
Define GUILD
- metabolically similar organisms that exploit the same resources
- having multiple guilds forms a microbial community
33
Define NICHE
- habitats that are shared by guilds / supplies what is required for growth
34
What are the forms of energy that come into a system
- light
| - chemicals (inorganic + organic)
35
What is the difference between microbial population and microbial community
Microbial population - might have come from a single cell
| Microbial community - is a collection of different populations
36
What is a biogeochemical cycle?
- Transformation of an element that are catalyzed by either biological or chemical means
- most are oxidaiton-reduction reactions
37
Why are biogeochemical cycles also called nutrient cycles?
Microorganisms are sometimes the only biological agent that is capable of creating things that other organisms need
38
What is Biofilms
Adhesive matrix (mixture of polysaccharides) that traps nutrients and protects the cells from detachment in a flowing system
39
What is Quorum Sensing
- sensing + responding to population density
- important in biofilms
- more signalling molecules produce = more signalling - turning on homoserine molecules
40
Why are biofilms formed?
- Self-defense
- staying in favourable niche
- close association with one another
41
What are Microbial Mats
- Very thick biofilms
- can be phototrophic or chemolithotrophic bacteria
- usually in extreme environments
- usually in low predation/grazing
42
What is soil composed of?
Inorganic Mineral Matter (~40%)
Organic Matter (~5%)
Water and Air (~50%)
Living organisms
43
What the different layers in the soil?
O Horizon
- top layer
A Horizon
- high organic layer
- microbial life
B Horizon
- inorganic
- root penetrating
D Horizon
- soil base/sediment
44
What is the Rhizosphere
Around the plant roots where organic matter and microbial life is high
45
What is Phylotype
Species defined with 16S rRNA sequence. There is a <3% chance that it differs from all other sequences
3% underestimates species diversity
46
What is the 'Great Plate Count Anomaly'
- hard to cultivate all bacteria
- some have special metabolic requirements
- some grow more abundantly that overwhelm the system
- might be dormant
- might not be able to grown on agar
47
Most primary productivity in the oceans due to photosynthesis is:
Cyanobacteria
48
Prochlorococcus
- Accounts for 40% of all marine biomass
| - Accounts for ~50% of all marine net production
49
What is Oligo-
Organisms that grow in environments where nutrients are extremely rare
50
What is the most abundant marine heterotroph
Peligabacter
51
What is an extremophile?
Organisms that can survive in environments that are considered outside the "normal"
52
What is cardinal temperature?
the minimum, maximum, and optimum temperature in which an organism grows
53
What happens when an organism reaches its maximum temperature?
- the proteins start to denature
- collapse of the cytoplasmic membrane
- thermal lysis
54
What are the temperature classes of microorganisms?
Psychrophile - < 15
Mesophile - 15-60
Thermophile - 60-80
Hyperthermophile - > 80
55
What is the temperature limit for bacteria?
95 degrees
56
What is the temperature limit for organotrophs?
Less than 95 degrees
57
What is the temperature limit for phototrophs?
73 degrees
58
What is the organism that can survive at the highest temperature possibly known (temperature and organism)?
Methanopyrus Kandlerii
| 122 degrees
59
Eukarya cannot grow above what temperature?
62 degrees Celsius
60
Hyperthermophiles
Above 80
- almost all are hydrogen or sulfer metabolisers
- no hyperthermic bacteria
61
What temperature does photosynthesis stop at?
73 degrees celsius
62
What is the temperature limit for Archaea
122 degrees (possibly 150)
63
What are the primary energy sources at higher temperatures?
Hydrogen and Sulfide
64
What are hydrothermal vents
- spill out reduced sulfur and iron
- become the main energy source
- hyperthermophiles and thermophiles
- usually has chemolithotrophic prokaryotes
- it is a chemosynthetic system that does not rely on light
