MICR Midterm Flashcards
(221 cards)
1
Q
What did Robert Hooke Do?
A
Built first compound microscope; coined the term cell
2
Q
What did Antoine Van Leeuwenhoek do?
A
Made even stronger magnifying glasses; observed single celled organisms
3
Q
What did Edward Jenner do?
A
Introduced early form of vaccination
Used cow pox scabs and ground them up to use against small pox, was successful
4
Q
What did Lazzaro Spallanzani do?
A
Disproved spontaneous generation slightly by boiling broth which failed to grow microbes
5
Q
What did Louis Pasteur do?***
A
Discovered fermentative metabolism (beer)
Used swan neck flasks to fully disprove spontaneous generation, stuck in bed of flask and liquid was sterile
6
Q
What is the Germ theory of disease?
A
Florence Nightingale and medical epidemiology, infection killed more people than wounds so army should take on hygienic practices
7
Q
What did Robert Koch do?
A
Created Koch’s postulates and proved that a specific microbe caused a specific disease
8
Q
What are Koch’s Postulates?
A
- Microbe is found in all cases of disease but absent from healthy individuals
- Microbe is isolated from diseased host and grown in pure culture
- When the microbe is introduced in a healthy, susceptible, host the same disease occurs
- The same strain is taken from the newly diseased host
9
Q
What are some exceptions to Koch’s Postulates?
A
If it cannot be cultured outside of the human body…can it be classified as a pathogen/the disease giving microbe?
10
Q
What did Angela and Walter Hesse do?
A
Created a solid medium to culture microbes; agarose gel
11
Q
What did Ignaz Semmelwiez do?
A
Handwashing for doctors
12
Q
What did Joseph Lister do?
A
Clean (microbe free) operating area for patients
13
Q
What did Alexander Fleming do?
A
Discovery of penicilin as antibiotic
14
Q
What did Dmitry Ivanovsky do>
A
causative agent of disease was much smaller than bacteria (virus)
15
Q
What did Martinus Beijerinck do?
A
Agent of disease cannot be bacteria (virus)
16
Q
What did Wendell Stanley do?
A
Purified virus by crystallization (Virology)
17
Q
What is Microbial ecology?
A
Studying microbes in their natural habitat
18
Q
What is one important thing microbes do with respect to microbial ecology?
A
Biogeochemical cycling of Earth’s elements
19
Q
What did Sergei Winogradsky do?
A
First one to study bacteria in their natural habitats
20
Q
What are Lithotrophs?
A
Rock/inorganic compound eaters
21
Q
What is a Winogradsky Column?
A
A wetland ecosystem model where the microbes split themselves up by layers. (sulfate reducing, green sulfur, purple sulfur, cyanobacteria)
22
Q
What is the nitrogen cycle?
A
One of the most important geochemical cycles. Microbes fix nitrogen from the air and convert it to ammonia in soil so that plants can use it, no other way for plants to receive nitrogen from the atmosphere
23
Q
What is microbial endosymbiosis?
A
When organisms live symbiotically inside other organisms as endosymbionts
24
Q
What did Lynn Margulis prove?
A
Eukaryotic organelles evolved from endosymbiosis from prokaryotic cells engulfed by ancestors of eukaryotic cells
Cyanobacteria- phototrophic, chloroplasts
Proteobacteria- respiring/producing oxygen; mitochondria
25
What did Carl Woese discover\/
That there was a third domain of life separate from bacteria and eukarya, the prokaryotic archaea
26
What technique did Carl Woese perfect?
Analysis and sequencing of the 16s rRNA gene of several types of microbes and comparing to other types of microbes
27
What is the different between a prokaryote and a protozoa
Prokaryote is a cell who lacks a nucleus than is enveloped
| Protozoa is a eukaryotic protist who is a heterotroph
28
What are some common traits of all prokaryotes?
Thick, complex, outer envelope
Compact genome
coordinated cell functions are tight
29
What is a mollicutes?
Contains: DNA, ribosomes, cytoplasm, plasma membrane,
The simplest type of bacterial cell
Mycobacteria are an example
30
What are the pros of a mollicutes
Cheap, not a lot of energy required
| Small and can squeeze through small spaces
31
What are the cons of a mollicutes
Difficult to maintain and usually need a host cell
Complicated diet
unattractive blob
32
What is synthia 3.0?
An organism that was engineered to have the least amount of genes required to be able to carry out life functions (531 kBp)
33
What are cell walls of bacteria made of?
Peptidoglycan- polymer of sugars and amino acids, N-acetyle glucosamine and N-acetyl muramic acid
34
What is a gram positive cell?
Has a thick cell wall (20-80nm)
The cell reinforces the peptidoglycan with teichoic acids
Gram stained purple
Stephlococcus aureus
35
What are the pros of a Gram positive cell?
Resistant to lysis
The teichoic acids are very strong
Several shapes (rod, coccoid, spiral)
36
What are the cons of a gram positive cell?
Kept away from lysozyme
| Sensitive to antibiotics
37
What is a gram negative cell?
Thin cell wall (1-2 sheets of peptidoglycan), then a periplasm space, then an outer membrane with lipopolysaccharide attached to it
Gram stained red
E.Coli
38
What is a lipopolysaccharide?
Contains lipid A which anchors it into the membrane but is also an endotoxin for humans
Then has an inner and outer core and an O antigen
39
What are the pros of a gram negative cell?
can defend against a wide range of toxic molecules
has a built in storage compartment
resistant to lysis
40
What are the cons of a gram negative cell?
toxic if not handled properly
| requires a bigger genome for more complex cell wall
41
Describe in general the mycobacterial cell envelope
Very complex and has unusual membrane lipids (myolic acids), forms a thick, waxy surface (hydrophobic and chemical resistant)
Acid Fast bacili stain (carbonsulfate?)- stained red
M. tuberculosis
42
What is a con of the mycobacterial cell envelope
Often slow growing due to extreme environmental resistance and complexity of cell wall
43
What is an S-Layer
Stands for surface layer
Additional protective layer about 5-25nm thick
Crystalline layer of thick subunits (protein/glycoprotein)
Allows movement of molecules, flexible
44
Where is the S-Layer situated
In gram negative- outside of LPS
| In gram positive- ouside of cell wall/large layer
45
What is a capsule?
Slime layer
Slippery coat of loosely bound polysaccharides
Difficult to stain and appears as clear halos
prevents phagocytosis/innate immune system activation for pathogens
46
Where is the capsule located?
In both G+ and G- strains, outside of S-Layer
47
What is a thylakoid?
Extended folded lamellae (sheets) of membranes that contain photosynthetic proteins with electron carriers
Help to maximize photosythesis in cell
48
Where are thylakoids found?
They are found in G- phototrophs only
49
What is a carboxyzome?
Contains enzymes used to fix CO2
Polyhedral shape
Large structures with a lot of storage space
50
Where are carboxyzomes found?
G- bacteria only, all cyanobacteria, some chemotrophs
51
What are gas vesicles?
Balloons o hydrophobic protein
| Allow microbe to maintain optimal buyoncy in water to its preferred conditions
52
Where are gas vesicles found?
In aquatic photosynthetic bacteria and some heterotrophs
53
What are storage granules?
During optimal growth period, bacteria store excess energy here and consume later as needed
Sotres as glycogen, PHA, PHB
54
Where are storage granules found>
G+ and G- bacteria. usually in cytoplasm but can store sulfur on membrane
55
What is another use for PHB?
biodegradable plastic
| -water insolube, biocompactible, heavier than water
56
What are magnetosomes?
Bound crystals of magnetite, bound on membrane
Allow motile bacteria to orient itself with Earth's magnetic field (MAGNETOTAXIS)
allows to find optimal conditions
57
Where are magnetosomes?
Found on membranes of G- aquatic species
58
How can they be used in medicine?
advantages over nanocrystals
| way to deliver targeted drugs?
59
What is a pili?
Bacterial adhesion
Found on outside of bacterial cell, can come in many forms
Some can be used for bacterial conjugation
Some can be used for special motility (twitching motility)
60
Where are pili found>
In G+ bacteria, found anchored in cell wall
| In G- bacteria, found anchored in outer membrane
61
What is a stalk?
Embedded extension of the cytoplasm
secretes factors called HOLDFASTS
antenna to seek out nutrients
allow bacterium to stay in favourable location
62
What happens with daughter cells when the mother cell has a stalk?
When they divide they have a flagella instead of a stalk, which allows it move to a new location
63
Where are stalks found?
In G- bacteria only, aquatic bacteria
64
What is a bacterial flagella?
organelles of motility
Rigid, long, helical, protein structures
Work with chemoreceptors to propel the cell in the right direction "runs" and "tumbles"
65
Describe the bacterial flagella motor
Almost 100% efficient, almost like a propellar
| Fueled by ionic gradient across membrane
66
Describe chemotaxis with regards to bacterial flagellum
movement towards a chemical gradient using chemoreceptors
Clockwise- stops forward motion, change direction "tumbles"
Counter Clockwise- attraction, moves cell towards it "runs"
67
Describe a monotrichous flagellum
one flagella coming out of one end
68
Describe a lophotrichous flagellum
multiple/tuft of flagella coming out of one end
69
Describe a amphitrichous flagellum
One flagellum coming out of each end
70
Peritrichous flagellum
Multiple flagella coming out of multiple places. Octopus looking
71
What is nanotube?
Extensions of cell envelope that connects cytoplasm or periplasm between two different cells, allows material transmissions; especially biofilm forming microbes
72
What is a thermophile?
An archaea that can only survive at high temperatures >70C
| anaerobe that metabolizes sulfur to H2S, deep sea
73
What is a psychrophile?
Anaerobic heterotrophs, sulfate reducers/nitrite reducing methanotrophs, live in deep permanently cold water
74
What is a halophile?
Hypersaline pools, extreme salt pools, phototroph that forms fragile sheets and floats near surface (gas-filled vesicles)
75
What is an acidophile?
Oxidizes sulfur formm FeS2 to H2SO4, extreme acidic environments, acid mine tailings, no cell wall
76
What is a methanogen?
Generate methane from CO2 H2 and small molecules
| make clean methane
77
What are some applications of methanogens?
Making clean methane
Generated from electrical currents
methane produced is carbon neutral
Can be harnessed to make fuel potentially
78
Difference between bacterial and archaeal cell wall
Bacteria-
D-glycerol fatty acids linked by ESTER links
Archaea-
L-glycerol fatty acids linked by ETHER links
79
Archaea cell wall overview
Lack lipids found in other domains but had side chains with repeating units of ISOPRENE which form together to make isoprenoid
80
How can archael cell walls get stronger
Some isoprene links are covalently bonded to each other which increases their rigidness/strength
81
What are some differences in archaeal cell walls
Cell wall can be very similar to bacteria but pseudopeptidoglycan is used instead
not affected by lysozyme or penicillin
82
what is phototrophic archaea
Do not use chlorophyll are not photosynthetic
Use retinal-based ion pump on membrane (Bacteriorhodopsin)- gives a purple colour
Coupled with ATP synthesis for cell
Still needs to supplement energy needs with carbon
83
Archaea in biotechnology
- Extremophiles make extremozymes
- Arachael make good vaccine adjuvents
- A source of novel antibiotic classes
- bacteriorhodopsin nanoswitch
- treatment of wastewater
84
What are Opisthokonts
Strech of DNA present in fungi and animals but no other clade so they become one clade
85
What are eukaryotic flagella?
They are bigger and contain microtubules, are more flexible and wave instead instead of turning
86
What is the closest relative to humans?
Chanoflagellate
87
What are some evidence points to show that chanoflagellate could be related to humans
Have immunoglobin genes but no immune system
collagen, adherin, integrin domains but no skeleton
Tyrosine kinase genes but do not signal or communicate
88
What are some defining features of fungi?
```
Eukaryotic
Reproduce using spores
heterotrophic (absorptive)
Cell wall with chitin
Cell membrane with ergosterol
Nature's recyclers
```
89
What are some defining features of yeast?
Unicellular fungi
Do not use hyphae to obtain nutrients
used in food manufacture
good models of eukaryotic biology
90
How do yeast reproduce?
Reproduces by budding, where a smaller part of the yeast molecule buds off to another cell asexually and leaves behind a bud scar on the original molecule
91
What is the yeast life cycle?
Alternates between haploid and diploid stages, haploid to gametes to 2n zygote to meiosis to haploid
Haploid in unfavourable conditions
Diploid for genetic diversity
92
How does hyphae growth work?
Chitin allows fungi to penetrate tough food sources
1. Cytoplasm moves towards tip of apical growth zone, driven by turgor pressure
2. regulated by uptake of K+ ions and h+ pumped out
3 septa form as walls across the hypha so that the cytoplasm is in different compartments
93
What is mycelium? What if it is apart of the roots system?
Branched mass of extending hyphae
Mycorrhizae( provides service to plants by extending the network of absorption and provide nutrients outside of immediate zone)
94
What is a mushroom?
fruiting body of some fungi, true mushroom = Basidiomycetes
95
What is an ameba?
Microscopic lumps of jelly,
They have an ectoplasm and an endoplasm
Through production of pseudopods; controlled complex motion
Free-living predators in soil or water (use phagocytosis)
96
How does a pseudopod move?
Polymerization of actin and this polymer rolls over like a tank tread, membrane projections help cell adhere to surface and the contractile vacuole helps control the water content of the cell
97
What is a slime mold?
Have cellulose not chitin in cell walls
| Type of amebas???
98
What is cellular community of amebas?
Swarms come together in response to a signal
99
What is a plasmodial community of amebas?
Swarms come together and fuse into a giant cell with many nuclei
100
What is a radiolarin?
An ameba with shells (tests) made of silican, pseudopods come out of holes in shells
101
What is primary symbiosis?
Prokaryote + Eukaryote= Eukaryote
102
What is secondary symbiosis?
Eukaryote + Eukaryote = Eukaryote
103
what are the main features of algae?
Primary Producers/ phytoplankton
| Can be primary or secondary or more possibly
104
what are the main features of primary algae?
Share lineages with plants
Have two major clades:
Chlorophyta (green algae)
Rhodophyta (red algae)
105
What makes red algae unique?
Coloured red with phycoerythrin and can colonize deeper water columns because they can absorb green and blue light
106
What are Diatoms>
Secondary algae that are unicellular
Have a protective bipartate shell (frustule)
Interesting cell division (keeps getting smaller...)
Dead diatoms become dichotomous earth
107
What are kelps?
brown algae
Store lipids such as leucocin
"Sargassum Weed"
Form floating forests to support ecosystems
108
What are alveolates?
flattened vacuoles "alveoli" withing their outer cortex
Most have cilia or flagella
Are usually predators, reproduce sexually
Type of protist
109
What are dinoflagellates?
```
"Phototrophic alveolates"
Marine phytoplankton
Highly motile with 2 flagella
One flagella wrapped around body in specialized groove
Secondary or tertiary algal symbionts
Supplement photosynthesis with predation
```
110
What the official definition of a virus?
Non cellular particle that must infect a host cell where it reproduces
111
What are giruses?
Larger than some bacteria, very large genomes, difficult to crack, packages ribosome proteins
112
Why can they be useful?
control infections/biofouling
delivery vehicles for gene therapy
used as cloning vectors
filamentous phage particles can be ussed to crytallize conducting nanowires
113
What is the host range?
Each species of virus infects a particular group of host species, most have narrow host range
114
Typical virus contains:
```
virion/virus particle
Genetic material (DNA or RNA)
Capsid (protective protein coat)
Optional glycoprotein coat
surface proteins for attachment
```
115
What is the virus envelope composed of?
Plasma membrane of infected host cell
Tegument( accessory proteins)
Takes a piece of the membrane when it buds out of the cell
116
What is an icosahedral structure?
3-fold or 5-fold
20 triangular faces (largest # possible)
favoured packaging of most material in smallest subunits
117
What is a filamentous structure?
helical symmetry
| RNA genome coiled into helical capsid structure, varies in size
118
What is the multiple helical packages structure?
Several helical genome segments
| Can enable virus to package different number of RNA segments which allows for rapid evolution of new strains
119
What are complex virus structures?
Iscosahedral head coat plus a helical "neck" which is an elaborate delivery device
Tail fibres look for/bind to host, end plate comes into contact
Cytoplasm can go to place in capsid, genetic material quickly shot into the cell
120
What is asymmetrical virus structures?
No symmetrical capside
DNA enclosed by core envelope; double stranded DNA surrounded by an outer membrane
Can have evolved from degenerate proteins
121
What are some characteristics of viral genomes?
Very simple and efficiently packaged
Overlapping genes
Ressembles eukaryotic mRNA
Polypeptides cleaved in different ways to form different proteins
122
Waht are long terminal repeats (LTR)
signature of a viral incorporation event in a host genome
123
What is a viroid?
Extremely simple, no capsid, mostly infects plants and are RNA molecules
124
What is a prion>
Protein only, aberrant proteins from host cell which forms an abnormal structure, interaction with normal form results in transformation to prion form and multiple forms aggregate and cause cell death
125
What are the criteria of the International Commitee on taxonomy of viruses
```
Genome composition
Capsid Symmetry
Envelope
Size of virus particle
Host range
```
126
What are the criteria for the Baltimore Virus Classification
Genome classification
| Since all viruses have to make mRNA to produce proteins, how the mRNA is produced is central to the classification
127
Group 1: ds DNA viruses
(ds DNA to +mRNA)
Make their own DNA polymerase or use host's
transcribe genes using RNA polymerase
Bacteriophage T4, Pox, Giruses, Archael virus
128
Group 2; ss DNA viruses
(ss DNA to ds DNA to +mRNA)
Requires host DNA polymerase to generate complementary strand
Is transcribed by host RNA polymerase
Bacteriophage M13, Parovirus, gemini virus
129
Group 3: ds RNA viruses
(+- ds RNA to +mRNA)
Require viral RNA-dependant RNA polymerase for mRNA
Required immediately after infection usually made and packaged in virion
reoviruses
130
Group 4: (+) sense ss RNA viruses
(+RNA to -RNA to +mRNA)
(+) is coding strand
serves directly as mRNA but needs to made (-) strand to make ds intermediate for replication
Poliovirus, rhino virus
131
Group 5: (-) sense ss RNA viruses
```
(-RNA to +mRNA)
Genomes have template RNA
require viral RNA-dependant RNA polymerase for transcription of (-) RNA to (+) mRNA
may be segmented viruses
Influenza, ebola, measles, rabies
```
132
Group 6: Retroviruses
(+RNA to -DNA to +DNA to +mRNA)
(+) strand RNA genomes, RNA reverse transcribing genomes
Package their own reverse transcriptase
RNA to ds DNA which gets incorporated into host genome
HIV, SIV, FLV
133
Group 7: Pararetroviruses
(+mRNA to ds DNA)
Dna reverse transcribing viruses
Requires reverse transcriptase (host or their own)
copy genomes into RNA then reverse transcribe to DNA
hepatitis B, mosaic virus
134
What are human endogenous retroviruses?
8% of human genome
remains of ancient viruses incorporated into genome
become degraded and non funcional supposedly
135
What is the virulent replication pathway>
Lytic pathway,
| inserts DNA, cycle DNA, DNA is replicated, packed into capsids, cell is lysed and its contents are released
136
What is the temperate replication pathway?
Lysogenic pathway,
Inserts DNA, becomes prophage (phage DNA) inserts into host genome, bacteria DNA reproduces with host genome, can enter lytic pathway if there is stress
137
What is the slow release replication pathway>
Replicates using host cell, goes through but does not lyse cell, slows down metabolism
138
Describe parts of the prokaryotic immune system
It is adaptive
Can have short DNA sequences analogous to viral DNA
CRISPR
RNA expressed when attacked by phage, this triggers defensive phage DNA cleavage system
139
Prokaryotic cell growth and replication is:
By binary fission, vertical transmission, asexual
140
Genome replication of prokaryotes involves:
DNA formed into a loop
Semi-conservative replication: one of parental strands is inherited by the daughter cell
DNA unwinds at fixed origin and proceeds in both directions
141
What is bacterial transformation>
UPtake of naked DNA to incorporate into its own genome (taken from cells that have lysed)
Or
uptake of plasmid DNA to replicate in cell
142
What is a plasmid?
Extrachromosal DNA, smaller than a chromosome, encodes accessory function, autonomous replication
143
What is bacterial conjugation?
Cell-cell contact mediated by sex pilus
can even happen with different species
Requires presence of special plasmid to direct process. F+ is a donor and F- is an acceptor
Pilus only facilitates close contact and membrane fusion
144
What is bacterial transduction?
Bacteriophage mediated
Packaging viral DNA into capsids is a sloppy process,
host DNA packaged instead by accident
as bacteriophages are released transfer host DNA to another cell
145
What is generation time>
In an environment with unlimited ressources, bacteria divide at this constant interval (doubling time)
146
What is Lag phase>
Cell adjusting to environment and sensing nutrients, no real growth
147
What is exponential phase?
Early- cells growing at max rate, large cells
| Late- slowing of growth rate due to cell density
148
What is stationary phase?
Cell numbers stop rising, lack of nutrients and more waste
Cells become smaller, there is a stress response, sporulation
Shown by a plateau
149
What is Death phase>
Logarithmic, longer than exponential phase as nutrients become available when cells die
150
What is bacterial cell sporulation?
Certain G+ bacteria can place themselves in suspended animation (endospore formation)
Germination returns when optimal conditions return
151
What do cells do if they cannot sporulate>.
Get smaller
cell walls get thicker
glycogen stores are laid down
nutrient transporters and stress response proteins are expressed
152
What are fimbrial jackets>
Bacterial species knit a complex coat of cellulose and fimbrial protein to protect against drying and cold
153
What are biofilms?
Microbes tend to stick together in these specialized structures, a lot in aquatic ecosystems
154
Why can biofilms be bad
Damage equipment, contaminate abiotic substance in body, can cause tooth decay
155
Why can biofilms be good
Allow microbes to work together to metabolize
156
What are the steps of formation of biofilms>
```
Attachment
mIcrocolonies
Exopolysaccharides (EPS) production to bind cells together (inorganic and organic substances)
Mature biofilm
Dissolution
```
157
What is quorum sensing?
prokaryotes have a unique language to sense presence of their friends or enemies to trigger behaviours
158
What is an oligotroph?
An increased growth rate in low nutrient conditions, most bacteria are like this
159
what are phylogenomics>
Nucleic acids
| taxonomic reference genes (snapshot of ecosystem)
160
What are metagenomes?
Sequencing/assembling of entire genomes from ecosystem
161
What are metatranscriptomics?
entire collections of mRNA from ecosystem, take mRNA to find complementary DNA sequence to see genes
162
What are proteomics?
amiino acid sequences and identifying collection of signatures
163
What are lipidomics
identifying lipid signatures in ecosystems
164
What are metabolomics>
detect/identifying molecules from an ecosystem and their overall activity in an ecosystem
165
What is assimilation
Organisms acquire an element to build into cells
| Sometimes can assimilate form inorganic sources (Primary Producers)
166
What is dissimilation
Organisms break down organic nutrients and convert them to inorganic minerals through oxidation
167
What are some services of dissimilation?
Creates minerals for plants
| Wastewater treatment
168
What do primary producers do?
Absorb energy from the outside and assimilate minerals to biomass
169
What is mutualism?
Both species benefit and have trouble being independant from each other
170
What is synergism?
Both species benefit but can grow independant of each other and easily separate
171
What is amensalism?
One benefits by harming another, relationship is not defined
172
What is commensalism?
One benefits and one is neither harmed or benefitted
173
What is parasitism?
One harms the other by being a parasite and invading the host
174
Describe the lichen symbiosis?
Includes fungus, cyanobacteria, algae
Fungus is for protection
cyanobacteria is for fixing nitrogen
Algae is for photosynthesis and to disperse the lichen further with the fungus
175
What are the different types of plankton?
Microplankton (20-200 micrometer)
Nanoplankton (2-20 micrometer)
Picoplankton (0.3-2 micrometer)
Femtoplankton (<0.3 micrometer)
176
What do plankton colonize?
suspended particles called "marine snow"
| Tends to be in thin concentrated layers
177
What is the neuston layer?
The top 10 micrometer thick layer of the ocean, most microbes in this area
178
What is the euphotic zone?
Zone with light available (0-200 m or less in coastal regions)
179
What is the aphotic zone?
Zone where there is no light
180
What did Holger Jannasch discover?
That it takes up to 100x longer to decompose in water than on Earth
181
Describe what a thermal vent is
Where techtonic plates meet, fissures in ground, waater seeps to hot heated by magma in Earth, reacts and becomes full of minerals which are released out of vents as precipitants, not permanent
182
What are some other places that are teeming with life in the Ocean
Wherever there are rich sources of carbon:
Whale falls
Cold Seeps
Shipwreck
183
What is eutrophication?
When there is runoff or fertilizer or other minerals into a lake which causes a surplus of phosphates and other minerals which are eaten up by microbes that use up oxygen which creates an oxygen dead zone and kills off other species
184
What is the Organic horizon in soil?
Fungi/slime molds that are in the process of decomposing decaying matter such as leaves, can still tell what it was originally
185
what is the aerated horizon in soil?
Decomposed organic matter, may not be able to tell what it was before
186
What is the eluviated horizon in soil?
Insoluble particles leached by rain water
187
What is the water table in soil?
Ground water, has organic materials and minerals, is anoxic
188
What is the bedrock in soil>
Crust/rocks in the earth, only endoliths are found here (rock eaters)
189
What are streptomyces?
Soil microbes that make their own antibiotics and contribute to the smell of soil
190
What are nematodes>
Microscopic worms in the top of the soil
191
What is the rhizosphere?
Area just outside of plant roots that is rich with nutrients and microbes
192
What do microbes in the rhizosphere do?
Help to protect plant from pathogens
May fix nitrogen
Feed off nutrients of the plant
193
What is endomycorrhizae?
Fungi that invade the root cells and form arbuscules
| Completely dependant on plant host
194
What are endophytes?
Grow within plant tissue
form nitrogen fixing organ for the host plant
need anaerobic root nodule pigment that removes O2
e.g. plant roots and rhizobia (bacteria)
195
What are the majority of microbes in humans?
Bacteria or bacteriophage
196
What are the body defenses
Non specific
| and adaptive/non-adaptive immune system
197
what is a commensal?
A bacteria found at a non sterile site in the body
198
What is the microbiome?
Genetic potential of constortium (microbes their genes and the molecules they produce)
199
What is the microbiota?
Cell consortium of colonizing microbes
200
What can happen if a microbiota switches location?
Can cause abnormal function and disease
201
Describes skin microbes
Difficult to colonize the skin but are a lot more in moist areas
Mostly gram positive because of thick cell wall
Staphlycoccus aureus, propionibacterium acnes
202
Describe mouth microbes
First colonized by non pathogenic Neiser spp. (gram -) and streptococcus, lactobacillius (gram +)
As teeth emerge more bacteria emerge in gums and enamel
Most common site of infection
203
Describe nose and oropharynx microbes
Dominated by Firmicutes and Actinomycetes (usually one more than the other)
Nasophorynx- staphlycoccus aureus and s. epidermis
Oropharynx- similar composition of microbes to saliva
204
Describe lung microbes
Mainly anaerobes
| Microbiota in lung diseases seem to be distinct for each condition
205
Describe genitourinary tract microbes
kidneys and bladder usually sterile
urethra contain s.epidermis and enterobacteraceae (UTIs)
Vaginal microbiota composition changes with menstrual cycle
Acidic secretions are Lactobacillius
206
Describe stomach microbes
low pH so few microbes
| H. pylori
207
What is hypochlorydia?
When stomach acidity decreases usually due to malnutrition which leads to disease most likely
208
Describe intestine microbes
Many microbes in feces
Most important place for microbes is the colon
Has the same metabolic activity as the liver
209
What happens with high gut diversity>
Healthy, balance, functional redundancy, resistance to damage
210
What happens with low gut diversity
sink ecosystem, imbalance, functional disability, susceptible to damage
211
What are metabolic uses of gut microbes?
```
Fermentation
vitamin production
removal of toxins
IEC differentiation
Energy
Antimicrobial secretion
Competition for sites and nutrients
```
212
What are protective uses of gut microbes
```
Colonization resistance
Innate/adaptive immunity
Inflammatory cytokine oversight
Immune system/barrier
Competition for sites and nutrients
Antimicrobial secretion
```
213
What are structural uses of gut microbes
```
Intestinal villi and crypts
tight junctions
Slg A production
mucus secretion
Immune system/barrier
Energy
Competition for sites and nutrients
```
214
How are microbes protective against pathogens in the gut?
Competitve exclusion
environment modification
host stimulation
215
what are gnotobiotic animals
Animal where associated microbes are known
216
What are some characteristics of gnotobiotic animals
```
Poor immune system
low cardiac output
More calories needed
Thin intestinal wall
abnormal ceae
odd behaviour
misshapen mitochondria
```
217
Who is David Vetter?
The boy in the bubble
218
What is a microbial mat?
floating islands of biodiversity that support multiple trophic levels in neat layers
219
What is the typical composition of a microbial mat?
Cyanobacteria
Aerobic bacteria and archaea
Anoxic layers (purple sulfur and sulfate reducing)
220
What microbes are cold and dry environments home to?
Rock eaters or endoliths
| also have cyanobacteria
221
Archaeal viruses
Sulfolobus (low pH and heat)
| Resemble bacteriophage in size and behaviour but have spindle-shaped capsule with turrets
