BI 305 Exam 4 Chp 18 and 21 Flashcards
1
Q
What is a phylum?
A
Phylum=group of organisms with a common ancestor that diverged early from other bacteria.
2
Q
What are the advantages and disadvantages of akinetes and hormogonia?
A
Akinetes=spores produced by cyanobacteria.
Hormogonia=mobile short chains of cyanobacteria.
Akinetes: Advantage: Can very harsher environments. Disadvantage: Not growing until germinated. Cannot move on its own.
Hormogonia: Advantage: Can continue to grow. Not a free-living cell so can work with others to survive. Allows for differentiation. Can travel. Disadvantage: Can die easier.
3
Q
What is the advantage for Streptomyces to produce antibiotics?
A
Can kill neighboring cells and others that would kill it.
Can use dead cells for nutrients.
Destroys competition.
4
Q
Why did it take so long for scientists to discover bacteria’s ability to form biofilms?
A
Focus on identification and pure culture played a big role.
Bias towards microbes not being complex.
May have decreased funding for looking into the function of bacteria.
Assumed that beyond E. coli, knowing how microbes worked was not important.
5
Q
What are deep-branching taxa?
A
Deep-branching taxa=taxonomic groups that diverged early before well-known phyla were formed.
6
Q
What are Gram-variable organisms?
A
Gram-variable organisms=organisms that do not always have the same results under Gram-staining.
7
Q
What are emerging clades?
A
Emerging clades=recently defined or characterized clades.
8
Q
What is monophyletic?
A
Monophyletic=one clade with a single common ancestor.
9
Q
What is polyphyletic?
A
Polyphyletic=many clades that branch among different genera.
10
Q
What are oligotrophs?
A
Oligotrophs=cells with unusual shapes that enhance nutrient uptake in low nutrient environments.
11
Q
What are thylakoids?
A
Photomembranes in bacteria.
12
Q
How are cyanobacteria different from other phototrophic organisms?
A
Many bacteria can be phototrophic but only cyanobacteria use photosystem 1 + 2, and chlorophyll a and b.
13
Q
What does anoxic mean?
A
Anoxic=without oxygen.
14
Q
What are carboxysomes?
A
Carboxysomes=where dark reactions take place.
15
Q
What are gas vesicles?
A
Gas vesicles help to retain buoyancy in the water.
16
Q
What are hormogonia?
A
Hormogonia=short mobile chains for cyanobacteria.
17
Q
What are akinetes?
A
Spore cells for cyanobacteria.
18
Q
What are baeocytes?
A
Spore cells for cyanobacteria that Myxosacrina produce.
19
Q
What are heterocysts?
A
Nitrogen-fixing cells that differentiate from aerobic cyanobacteria.
20
Q
What does monoderm membrane mean?
A
1 membrane.
21
Q
What does diderm membrane mean?
A
2 membranes.
22
Q
What are methylotrophs?
A
Methyltrophs can metabolize single carbon molecules.
23
Q
What is leghemoglobin?
A
A protective compound that binds oxygen and keeps the rhizobia in an anaerobic environment.
24
Q
What are nitrifers?
A
Nitrifiers=ammonia to nitrite or nitrite to nitrate.
25
What is the life cycle of a bdellovibiro?
Bdellovibrio=deltaproteobacteria.
Finds host cell by chemotaxis.
Binds to host receptors.
Invades periplasm and uses host resources to grow.
Generates enzymes to enter the cytoplasm.
Degrades host macromolecules and makes them available to them.
The entire host cell loses its shape as it becomes an incubator for these bacteria.
Bdellovibrio grows in a spiral chain and fragments and flagellated cells.
Host lyses and bdellovibrio is released.
26
What is the life cycle of a chlamydiae bacterium from the PVC Superphylum?
Life cycle:
The elementary body (a spore) is taken into a host.
Grows into a reticulate body.
Can grow and site for a long time.
Makes a new elementary body.
New elementary bodies lyse cell and find a new host.
27
What are the common characteristics of cyanobacteria?
Uses thylakoid and two photosystems.
Uses chlorophyll a and b.
Only phototrophs that can photolyze water.
Where most of Earth’s oxygen comes from.
Share a common metabolism but differ in shape and environment.
28
What are Nostoc?
Nostoc=cyanobacteria with thyalkoids distributed throughout the cell.
29
What are Prochlorococcus?
Prochlorococcus=cyanobacteria with concentric circles of thylakoids.
30
What is Prochlorococcus marinus?
Prochlorococcus marinus is a cyanobacteria and the smallest and most abundant oxygen producer.
31
What is Microcystis?
Microcystis=cyanobacterial genus that produces microcystins, a toxin.
Becomes more abundant during nitrogen and phosphorous runoffs.
32
What are Oscillatora?
Oscillatoria=cyanobacteria that can form hormogonia.
33
What are Anabaena?
Anabaena=cyanobacteria that can form spore cells called akinetes.
34
What are Myxosacrina?
Myxosacrina=cyanobacteria that can form large cell aggregates and release baeocytes to reproduce.
35
What are common characteristics of Firmicutes, Tenericutes, and Actinobacteria?
Gram-positive.
1 membrane
Except for mycobacterium.
36
What are common characteristics of Firmicutes?
Thick peptidoglycan cell wall.
Low GC content.
Well-developed S layer of glycoproteins.
37
What are Bacillus?
Bacillus=spore producing firmicutes.
38
What is Bacillus thuringiensis?
Bacillus thuringiensis= firmicutes of great economic importance as an insecticide.
During sporulation, it forms a diamond-shaped endotoxin.
Activated by high pH in insect tracts.
Is not activated in the human digestive tracts.
39
What are Clostridium?
Clostridium=spore producing firmicute.
Polyphyletic spore-forming anaerobes.
More than one ancestor.
C. tetani.
40
What are Clostridium botulinum?
Under Clostridium, a spore-producing firmicute.
C. botulinum is commercially and medically important for the botulinum toxin.
Botox paralyzes muscles.
41
What are Lactobacillales?
Lactobacillales=non-spore-producing aerotolerant firmicutes that produce lactic acid and are used to produce sauerkraut and cheese.
42
What are Listeria and Streptococcus?
Listeria and Streptococcus=firmicutes that are well-known human pathogens.
43
What is Listeria monocytogenes?
Listeria monocytogenes= firmicutes; can survive phagocytic vesicles and multiply in the cytoplasm.
Generates actin tails that project it into neighboring cells.
Uses the actin cytoskeleton of the host to move.
44
What are common characteristics of tenericutes?
Lack cell wall, and require an animal host.
Holds shape via the cytoskeleton.
Tenericutes=Mycoplasms=Mollicutes.
45
What are mycoplasma?
Mycoplasma=tenericute that can lead to human pneumonia and meningitis.
46
What are actinobacteria?
Thick peptidoglycan cell wall.
| High GC content.
47
What are mycobacterium?
Mycobacterium= actinobacteria with a waxy cell covering and more than 1 membrane.
Cell covering includes mycolic acids.
Waxy outer covering.
Harder to get things across the covering.
This includes nutrients too so that’s why they are slow-growing.
Very defensive.
48
What is M. tuberculosis?
M. tuberculosis=actinobacteria mycobacterium that causes tuberculosis.
49
What are Streptomyces?
Streptomyces=actinobacteria; filamentous spore formers.
50
What are Corynebacterium?
Corynebacterium=non-mycelial actinobacteria.
| Unusually shaped rods that divide by a hinge half-snapping measure where the cells remain attached at one side.
51
What are common chatacteristics of Proteobacteria?
Gram-negative.
Porins have evolved to take in nutrients and exclude antibiotics.
Wide range of metabolism.
52
What are common characteristics of alphaproteobacteria?
Can use phototrophy or heterotroph and which is used depends on the environment.
53
What is Rhodospirillum rubrum?
Rhodospirillum rubrum=spiraled alphaproteobacteria.
54
What is Rhodobacter sphaeriodes?
Rhodobacter sphaeriodes=alphaproteobacteria with rounded rods.
Has photomembranes as invaginated vesicles from the membrane.
These membranes disappear when oxygen is present.
55
What is Caulobacter crescentus?
Alphaproteobacteria; nonphototropic heterotroph.
| The shape can differ based on the environment.
56
What is Bartonella henslae?
Bartonella henslae=actinobacteria that causes cat scratch fever.
57
What are Hyphomicrobium?
Hyphomicrobium=alphaproteobacterium methylotroph that lives in a wide range of environments from wastewater treatment facilities to Antartica.
58
What are Rhizobium?
Rhizobium=alphaproteobacteria that gives nitrogen to plants and receives nutrients and leghemoglobin.
59
What is Rickettsia rickettsii?
Rickettsia rickettsii=alphaproteobacterium; causes Rocky Mountain spotted fever.
Can only live inside of the host cell.
Survives phagocytosis.
60
What is Agrobacterium tumefaciens?
Agrobacterium tumefaciens is an alphaproteobacterium and can inject its DNA and can cause Crown gall.
61
What are the common characteristics of betaproteobacterium?
Lithotrophs and nitrifiers.
62
What are Nitrosomonas?
Nitrosomonas=betaproteobacteria; are essential for water treatment to oxidize ammonia and conduct electron transport through extensive membrane invaginations.
63
What are N. gonorrhoeae?
N. gonorrhoeae=betaproteobacteria; microaerophiles that need to grow on blood.
64
What are N. meningtidis?
N. meningtidis=betaproteobacteria; may only be in a quarter of the population and it rarely causes meningitis.
Only causes meningitis if the immune system is down or if it doesn’t get to where it needs to be.
65
What are the common characteristics of gammaproteobacterium?
Includes species that do phototrophy with iron and sulfur.
66
What are Acidothiobacillus?
Acidithiobacillus, gammaproteobacteria, and a sulfur lithotroph oxidizes sulfur and make the environment acidic enough to leach iron, copper, and lead.
67
What are Enterobacter and what are some species in this group?
Enterobacteriaceae=gammaproteobacteria; facultative aerobes.
Enterobacter and Klebsiella are two gut gammaproteobacteria that can become opportunistic pathogens if they get to where they shouldn’t be.
E. coli=gammaproteobacteria.
68
What are Pseudomonadaceae?
Pseudomonadaceae=gammaproteobacteria; can catabolize almost anything and use it as a carbon source.
Includes Pseudomonas.
Respire on oxygen and nitrate.
Caused many infections acquired in the hospitals.
69
What is Legionella pneumophila?
Legionella pneumophila=gammaproteobacterium pathogen that survives and is aerosolized in AC units.
Causes Legionnaire’s disease.
70
What are the common characteristics of deltaproteobacterium?
Includes sulfur and iron-reducing bacteria.
71
What is Myxobacteria xanthus?
Myxobacteria xanthus=deltaproteobacteria; forms multicellular fruiting bodies.
Fruiting body releases myxospores.
72
What are bdellovirbrio?
Bdellovibrio=deltaproteobacteria that parasitizes other bacteria.
The host loses shape and becomes an incubator (bdelloplast).
Enters periplasm and steals host nutrients.
73
What are common characteristics of epsilonproteobacteria?
Gram-negative helical pathogens and marine sulfur bacteria.
74
What is Heliobacteria pylori?
Helicobacter pylori=epsilonproteobacteria.
Moves like a corkscrew.
Digs into stomach mucus.
Cause of gastritis and ulcers.
Produces urease enzyme to neutralize local environment so it doesn’t die from high acid number.
75
What are Nautilia and Hydrogenimonas?
Nautilia and Hydrogenimonas epsilonproteobacteria oxidize H2 using sulfur or nitrate at hydrothermal vents, and enriches the marine habitat by helping with carbon, nitrogen, and sulfur cycling.
76
What are the common characteristics of Deep Branching Gram-Negative Phyla?
Gram-negative.
77
What are spirochetes?
Spirochetes=deep-branching gram-negative bacterium with a flexible, extended spiral shape.
Cytoplasm and cell membrane are contained in an outer membrane called a sheath.
Contain flagella that twist and move the bacteria using chemotaxis.
Have LPS and protein layer like other Gram-negative bacteria.
78
What is Treponema pallidum?
Treponema pallidum=spirochete; cause of syphilis.
Cannot be cultured.
The only system of ATP production is glycolysis.
79
What is Borrelia burgdorferi?
Borrelia burgdorferi=spirochete; the causative agent of Lyme disease.
Has a multipart genome.
Lyme disease is hard to get rid of.
80
What are bacteriodes?
Bacteriodes=gut and soil deep-branching gram-negative bacteria.
Many are obligate anaerobes.
Live in the human gut and help digest indigestible and potentially toxic parts of plants.
Major inhabitants of the human colon with envelope polysaccharides that help it evade the immune system.
Provides fermentation products for the host.
Is an opportunistic pathogen outside of the colon.
The most common cause of abscesses in humans.
81
What are fusobacterium?
Fusobacteria=deep-branching G- bacterium; includes some human pathogens.
Highly virulent pathogens that form dental plaques.
2nd most common cause of abscesses, especially in the mouth.
82
What are chlorobi?
Chlorobi=deep-branching G- bacterium; Known as green sulfur bacteria.
Obligate anaerobes incapable of heterotrophy.
Photolithotrophs.
Sulfur granules are deposited extracellularly.
83
What are nitrospirae?
Nitrospirae=deep branching G- bacteria; oxidize nitrite to nitrate.
84
What are acidobacteria?
Acidobacteria=deep-branching G- bacteria; important for soil bacteria.
Extremophiles.
85
What are the common characteristics of the PVC Superphylum?
Compartmentalized cells with diminished cell walls.
86
What are Planctomyces?
Part of PVC Superphyla.
Planctomycetes have a double membrane around their nucleoid.
Analogous evolution with the nucleus in eukaryotes.
Can move its membrane a lot due to reduced cell wall.
Can complete phagocytosis.
87
What are Verrucomicorbia?
Part of PVC Superphylum.
Verrucomicrobia has wrinkled bumps.
Bumps are made out of tubulin protein, which was thought to be eukaryotic only.
Tubulin is part of the cytoskeleton.
May have been a horizontal gene transfer to this organism.
88
What are Chlamydiae?
Part of PVC Superphyla.
| Chlamydiae are intracellular parasites.
89
What is Chlamydia trachomatis?
Chlamydia trachomatis is the most common STI.
| Part of Chlamydiae section of PVC Superphyla.
90
What is Chlamydia pneumoniae?
Part of Chlamydiae section of PVC Superphyla.
| Chlamydia pneumoniae causes pneumonia and possibly cell disease.
91
What are the general steps in analyzing a metagenome?
```
Identify target population.
Isolate DNA
Preliminary scan for diversity.
Sequence DNA via library construction.
Bin organisms into the approximate taxonomic groups.
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92
What is a niche?
Niche=specific conditions that allow for organisms to grow and reproduce.
Niches are made by physical environmental limits and chemical limits which can be made by other organisms.
93
Is assimilated anabolic or catabolic?
Assimilated=anabolic.
| Carbon fixation, nitrogen fixation.
94
Is dissimilated anabolic or catabolic?
Catabolic.
| Ex: Fermentation and cellular aerobic respiration.
95
What is symbiosis?
Symbiosis=initimate relationship between two partners.
96
What is mutualism?
Mutualism=both partners benefit and cannot grow independently.
97
What are -omics?
Omics=collections of tools including genomics, proteomics, and metagenomics.
These tools help find, identify, and understand uncultured microbes and microbial communities.
98
Why are microbes everywhere?
If an energy-yielding reaction exists, some microbe will evolve to use it.
99
What is detritus?
Detritus=discarded biomass such as branches and leaves that are decomposed by fungi and bacteria.
100
How can you tell if a relationship is mutualism?
Removal of one partner leads to death or decreased growth of the other.
The microbial genome shows reductive evolution for normal essential genes for metabolism.
Now, it must get those nutrients from a partner.
Isotype labeling shows that each partner is using resources from the other.
101
What is synergism?
Synergism=both partners benefit but they can live on their own.
102
What is commensalism?
Commensalism=one partner benefits and the other is neutral or not harmed.
103
What is amenalism?
Amensalism=one species benefits by harming the other.
| Nonspecific relationship.
104
What is parasitism?
Parasitism=obligatory relationship for parasites to harm the host.
105
Why can it be hard to tell the difference between parasitism and mutualism?
The same 3 criteria for the definition apply to both.
| One can't grow without the other and they share resources.
106
What is a holobiont?
Holobiont=great beneficial benefits from a microbial partner.
They should be considered one organism because of the close association.
107
Explain the rumen of a cow.
Allows animals to obtain nutrients from complex plant fibers with the aid of a complex community of microorganisms.
Ex: Cows do not have the digestive enzymes to break down cellulose.
Microbes do this for them.
Firmicutes such as Ruminococcus, Megasphaera, and Clostridium break down cellulose and plant fibers.
The released hydrogen and CO2 support Methanobrevibacter and Methanosarcina.
The reason why cattle release a lot of methane.
108
What are the 3 short-chain fatty acid (SCFA) products?
Butyrate, propionate, and acetate.
109
What are some ways to culture uncultured microbes?
Grow fecal sample on plates with different antibiotics.
| Grow fecal sample on different media.
110
What are some benefits of the gut microbiome?
Bacteriodes and Prevotella that release short-chain fatty acids provide up to 15% of caloric intake.
Our cells use amino acids synthesized by gut bacteria.
The gut microbiome provides interaction with the immune system.
They help prime the immune system.
The gut microbiome releases peptides that signal the brain.
Genome capacity is 100X what human gene capacity is.
More genes in the gut than in our own genome.
Influence our actions.
Release peptides that signal feelings of satiation.
Keep pathogens away by acting as competition.
111
What is marine snow?
Marine snow=microplankton can form biofilms on algae (usually macro) and inorganic particles.
Constantly filtering down.
112
What is microplankton?
Microplankton=members of all 3 domains and include motile and nonmotile members.
113
What is metatranscriptomics?
Metatranscriptomes can give information on what genes microbes have, what is being expressed, and what genes are in organisms you don’t know about.
If a gene is expressed a lot but makes up little of the genome you know about, that indicates that there are microbes expressing these genes that are unknown.
114
What are the problems with eutrophic water?
Eutrophic water causing algal blooms are detrimental to animal life.
Microbes produce toxins and deplete oxygen from the water as heterotrophic microbes digest dead fish.
115
How can population size in the ocean be measured?
Population size in the ocean can be measured by:
The number of individual reproduction units.
Biomass.
Assimilation rate of key nutrients.
116
How do rhizobia form associations with plants?
How rhizobia get into legumes:
Flavonoids=the legume exuding signaling molecules into the area that act as hormones.
Attracts rhizobia.
Rhizobia come by chemotaxis.
Flavonoids then induce rhizobia to produce nod factors composed of chitin with lipid attachments.
Nod factors communicate with host plants and form plant-bacteria specificity.
Root hair curls around rhizobia covering it with a plant cell envelope.
Rhizobia grow into an infection chain that penetrates other cells.
Rhizobia differentiate into bacteroids.
Bacteroids are in a sac in the plant cell called a symbiosome.
117
What is special about the Bacteroides, the rhizobia inside the plant?
Oxygen delivery is controlled so it doesn't poison nitrogenase. Leghemoglobin stops oxygen from entering the symbiosome.
Bacteroides do not replicate.
They need amino acids delivered from plants.
Nitrogen fixation is controlled using negative feedback loops.
No cell wall.
Receive nutrients such as malate for TCA.
118
What is soil?
Soil=complex mixture of decaying organic and mineral matter.
119
How do viruses increase the diversity of microbial plankton?
Contributes to nutrient cycling through the marine shunt.
By killing off certain microbes, it lowers competition for other microbes to establish their place and niche in the environment.
Contributes to evolution and allows for variation.
120
What is the rhizosphere?
Rhizosphere=region surrounding the roots of a plant contains sugar and proteins that feed bacteria.
121
Explain the difference between ectomycorrhizae and endomycorrhizae.
Endomycorrhizae penetrates cell walls while ectomycorrhizae colonize the surface of rootlets, the rhizoplane.
Ectomycorrhizae extend the plant's reach for nutrients.
Endomycorrhizae have an obligate relationship with plants and give resources in exchange for photosynthetic products.
122
What are proteobacterial phototrophs?
Proteobacterial phototrophs=G- phototrophs that are often named purple sulfur or nonsulfur bacteria even though there are many colors.
