1
Q
Give examples of man-made vs. natural extreme environments.
A
- Man-made thermophilic habitats
- Acid mine drainage
- Biological wastes
- Self-heating compost piles - Natural thermophilic habitats
- Geothermally heated oil
- Geothermal and volcanic areas
- Hydrothermal vents
2
Q
What adaptations have thermophiles developed?
A
- DNA repair proteins
- Saturated lipids maintain structure
- Higher GC content encodes thermostable amino acids
3
Q
What adaptations have acidophiles developed?
A
- DNA repair proteins
- Chaperones
- Potassium accumulation
- Highly H+ impermeable membrane
4
Q
What adaptations halophiles developed?
A
- Osmoprotectants accumulation
- Na+ stabilizes cell wall
- Bacteriorhodopsin pigment absorbs light
- Carotenoids protect cell DNA from UV induced radicals
5
Q
What adaptations for UV resistance have microbes developed?
A
- DNA repair proteins
- Chaperones
- Manganese accumulation
- Reduced iron levels
- Antioxidants
6
Q
What adaptations have psychrophiles developed?
A
- Unsaturated lipids stay fluid
- Higher GC content encodes thermostable amino acids
- Cold shock proteins
- Chaperones
- Anti freeze proteins
7
Q
What adaptations for xeric habitats have microbes developed?
A
- EPS production
- Osmoprotectants accumulation
- DNA repair proteins
- Sporulation
8
Q
What are the characteristics of hydrothermal vents? What does a typical trophic food web look like here?
A
The chemical laden water escaping from cracks in the seafloor around the mid ocean ridges “feed” chemoautotrophic bacteria
9
Q
- What do thalassohaline and athalassohaline mean?
- What type of habitats are they?
- Give examples for both.
A
- Thalassohaline = derived from seawater
Athalassohaline = salts derived from geology of terrestrial habitat - Hypersaline environments
- Ex. solar salterns (thalassohaline) and the Dead Sea (athalassohaline)
10
Q
How would sampling be different for aquatic vs. terrestrial environments?
A
- Aquatic
- Easier than soil/sediments (homogeneous)
- Can get samples remotely
- May have to filter large volumes of water
- Viruses require care - Terrestrial
- Challenges: contamination, compaction, water content
- More heterogeneous (will have to homogenize first)
11
Q
How would you enumerate microbes in aquatic vs. terrestrial environment?
A
- Aquatic (more volume-based)
- Turbidity
- Flow cytometry
- FISH (fluorescent in situ hybridization) - Terrestrial (more area-based)
- See below - Both
- Serial dilution and plating
- Direct counts
- Most probable number
- Molecular methods (PCR, sequencing)
12
Q
What is the advantage of fluorescent microscopy?
A
- Versatility: applicable to a broad spectrum of biological research
- High sensitivity and specificity: can attach to specific biomolecules of interest
- Multiplexing capability: allows for the simultaneous detection of multiple targets within the same sample
13
Q
In what cases would some environmental samples need more preparation before molecular analyses?
A
- Complex matrices: environmental samples like soil, sediment, or wastewater contain a high content of organic and inorganic material that can inhibit molecular reactions
- Microbial diversity: environmental samples with high microbe diversity require selective enrichment or culture-based methods to increase the abundance of specific microbes of interest
14
Q
What is the basic goal of PCR?
A
To amplify DNA/RNA
15
Q
How is PCR limited?
A
- Extraction biases
- Incomplete lysis, degradation, etc. - PCR bias
- Limitations to amplification
- Primer bias (primers not universal) - PCR is not truly quantitative
- One must return to the environment to check
16
Q
Why is a plasmid the preferred vector to make more copies of DNA?
A
- Can be replicated independent of the bacterial genome
- Functional markers added to vectors allow you to insert things into the DNA
17
Q
How might a molecular biologist use FISH (fluorescent in-situ hybridization) to answer microbial ecology driven questions about microbes and their interactions in the environment?
A
???
- Can tag microbial populations with fluorescent probes —> visualize/ID/quantify microbes
- Can track the tagged microbes to see how they interact with each other and their environment
18
Q
How are soil/sediment samples collected?
A
- Coring: piston corer (can get nice stratification)
- Van Veen grab
19
Q
What are some issues to consider in soil/sediment sample collection?
A
- Contamination: hard to decontaminate such a large drill
- Compaction: a portion of sediment might clog your piston
- Water content: sometimes too much water
20
Q
Why is aquatic sampling easier than soil/sediment sampling?
A
- More homogeneous
- Easier to get samples, even remotely
21
Q
What are some difficulties in aquatic sampling?
A
- May have to filter/concentrate large volumes of water
- Viruses require care
- High volumes
- Adsorption, elution, reconcentration
22
Q
How are aquatic samples collected?
A
- Plankton net tows: to isolate microbes of different sizes
- Niskin bottle
- CTD rosette: measure physical characteristics of water
23
Q
Compare and contrast crossflow filtration and direct flow filtration.
A
- Crossflow (aka tangential flow)
- High permeate rate - Direct flow (aka dead-end)
- Low permeate rate
24
Q
What are the difficulties in the environment in enumeration?
A
- Small size of microbes - hard to see to count
- Hard to determine viability of samples
25
What is enumeration?
Determining how many microbes there are in a sample
26
Explain serial dilution.
27
How do you get the most probably number (MPN)?
- **Serial dilution** of a liquid sample
- Growth in successive dilutions allows estimation of numbers in original sample
28
How is turbidity measured?
Optical density
- Measure how much light passes through the sample
- Use the same media as your blank
29
What tools are used to take direct counts?
1. Microscopic measures
- **Counting chamber**
- **Gridded filters**
2. **Epifluorescence microscopy**
- Fluoresce when you hit them (natural autofluorescence, acridine orange, DAPI)
30
One way gene probes can be applied is in fluorescent in-situ hybridization (FISH). What is FISH?
Lab technique used to **detect and locate a specific DNA sequence** on a chromosome
31
How is FISH done?
1. Cells are **preserved** whole
2. Cells are **permeabilized** with chemicals
3. Cells are **hybridized with labeled with probes** that bind to the cell's DNA or RNA
4. Upon excitation, the **fluorescent probes emit light**
32
What is the hierarchy of organization for ecology and how does it translate to microbial ecology?
???
33
Compare and contrast the microbial ecological niches of some model organisms.
???
34
Which species concepts is most often applied to microbes?
Genetic species concept
35
Explain the genetic species concept.
A genetic species is a group of **genetically compatible organisms**
- Focuses on genetic isolation (as opposed to reproductive isolation)
36
How can horizontal gene transfer result in the blurring of the distinctions between microbial species?
- Makes it hard to categorize species
- Can **replace** existing gene copies
- Can introduce whole **new functions**
37
Define operation taxonomic unit (OTU). How is it used?
- Clusters of organisms **grouped by DNA sequence similarity** of a specific taxonomic marker gene
- Used to classify organisms based on DNA sequence similarity
38
What is the most common OTU definition used to describe microbial species?
97% 16S rRNA sequence identity
39
Explain what happens in resource partitioning and utilization.
- Through time and natural selection, the **two species diverge** in their use of the resource
- A **new species arrives**, and further competition leads to a **narrower range of resource use for all three species**
40
What are fundamental vs. realized niches?
- Fundamental: full range of conditions that an organism could use
- Realized: portion of the fundamental niche actually occupied by that species
41
Explain the consequences of microbial competition.
- **Competitive exclusion**: if there is significant niche overlap and limited resources, one population will drive the other to extinction
- Intraspecific competition will cause the **population to level out**
42
Define competition.
Interaction between populations in which **growth rates decrease for both**
43
What is the shape of a logistic vs. exponential growth curve?
44
What is carrying capacity (K)?
Max population size the environment can sustain
45
What does the Lotka-Volterra model for interspecific competition tell us and what specifically are the alpha and beta in the equation?
???
46
The Lotka-Volterra model of interspecific competition is able to generate a range of possible outcomes. What are they?
1. The predictable exclusion of one species by another
2. Exclusion dependent on initial densities
3. Stable coexistence
47
What factors reduce competition?
**Niche partitioning**
- Microenvironments
- Variability
- Multiplicity of resources
- Other biological interactions (predation, grazing)
48
What is primary vs. secondary succession? Give examples.
1. Primary: new habitat; pioneer species
- Ex. Newborn's gut, lichens
2. Secondary: catastrophe resets clock
- Ex. Forest fire
49
Describe autotrophic succession vs. heterotrophic succession.
1. Autotrophic: primary production --> respiration
- Microbial mat formation
- Slow
2. Heterotrophic: breakdown of complex substrates
- Quick
50
What is facilitation?
Preparation of habitat by primary colonizers can lead to their being displaced by secondary colonizers
51
What is the Intermediate Disturbance Hypothesis and what does it mean for species diversity?
- Periodic, non-disastrous disturbances
- Creates patchiness but also lead to increased diversity
52
How is community structure defined?
1. **Species diversity**: measure of the number of organisms that make up the community
- Species richness
- Species evenness
2. **Trophic diversity**
53
Describe the types of +/- interactions.
1. Predation: one species (predator) kills and eats the other (prey)
2. Herbivory: herbivore eats part of a plant or alga
3. Parasitism: parasite derives nourishment from host, which is harmed
54
What are some examples of +/- interactions involving microbes?
- **Bdellovibrio**: fast moving Gram-negative bacterium attacked other Gram-negative bacteria
- **Myxobacteria**: lyse other bacteria with exoenzymes
- **Legionella**: bacteria inside algae or protozoa
- **Chytrid fungi**: freshwater parasites attack fungi
- Soil fungi attack nematodes
- More traditional predation: ciliate, flagellate, amoeboid protozoa engulfing bacteria
55
How would you describe the difference between cooperation and mutualism?
Cooperation is organisms working together, which benefits them. In contrast mutualism is a direct relationship between two organisms and both of them benefit from something the other does or produces.
56
Define bacterial cooperation (synthrophy).
Larger numbers of bacteria can encourage growth and survival
57
Give an example of cooperation.
***Desulfovibrio* and *Chromatium***
- Organic matter and sulfate needed by *Desulfovibrio* are produced by the *Chromatium*
- *Chromatium* goes through photosynthesis and oxidizes sulfide to sulfate
58
What is quorum sensing? Briefly describe the overall mechanism.
1. Bacterial response to population density
2. Species-specific chemicals (autoinducers) released into the environment
- Communicate within or between species/groups/domains
3. Chemotaxis: release of signals into environment can cue microbes to move together
59
What is one way quorum sensing might be used by bacteria?
Biofilm formation
60
What is commensalism?
One species benefits, one is neither harmed nor helped (unidirectional)
- Symbiont can survive without host
- Ex. *Nitrosomonas* oxidizes ammonium to nitrite, *Nitrobacter* oxidizes nitrite to nitrate
61
What is mutualism?
Both organisms benefit
- Obligatory relationship (+/+)
- Ex. Lichens
62
Give an example of mutualistic symbioses (describe both species’ interactions and contributions).
Hint: obligatory
1. Lichens: alga and fungi
- Alga fixes CO2 and sometimes N2
- Fungi consume carbon from alga and protect and provide nutrients to alga
63
What is the phycobiont vs. mycobiont in lichen?
- Phycobiont: alga
- Mycobiont: fungi
64
Why does parasitism typically involve a relatively long period of contact?
The parasite needs the host to stay alive since it is acquiring nutrients from the host.
65
How would you define microbial parasitism vs. predation? Give an example.
I would define microbial parasitism as a prolonged interaction in which the microbe lives in or on another organism (the host) and benefits while the host is harmed. For example, Legionella pneumophilia are parasites in free-living protozoa. In contrast, I would define microbial predation as one microbe consuming another microbe. For example, Bdellvibrio enters the periplasm of other Gram-negative bacteria and consumes it from the inside out.
66
What defenses against parasitism/predation have microbes developed?
1. Evolution of resistance
- Resistance to **infection**
- Resistance to **antibiotics**
- **Biofilms**
2. **Spore Formation**: resistance to attack
3. Environmental variability, patchiness, heterogeneity
- **Provide refuge**
67
What is *Thiotrix*? What is it can example of?
- A **sulfur-using bacterium**, which is attached to the **surface of a mayfly larva** and which itself contains a parasitic bacterium
- Example of **ectosymbiosis** (Thiotrix on the outside) and endosymbiosis (parasitic bacterium inside)
68
What is a phage?
A virus that only infects bacteria
69
Label the parts of a virus.
70
What is each viral shape called?
71
What are the 3 components of the viral structure? Describe each one.
1. Nucleic acid core
- DNA or RNA
- Double or single stranded
- Circular, linear, segmented, mixed
2. Capsid: protein coat that encases nucleic acids
- May contain lipids
3. Envelope: lipid membrane outside the capside
- Only in some viruses
72
What are coliphages, bacteriophages, and cyanophages?
- Coliphage = type of bacteriophage that infects coliform bacteria such as *E. coli*
- Bacteriophage = viruses that infect bacteria
- Cyanophage = viruses that infect cyanobacteria
73
What are the types of viral life cycles?
- Lytic: lyses host cell
- Lysogenic: viral DNA merges with host DNA
- Chronic
- Pseugolysogeny: stalled development of the bacteriophage in the host cell, usually caused by unfavorable conditions for the host cell
74
What are the 2 stages of the viral life cycle?
- Extracellular: inert viral particle in environment
- Intracellular: reproduction stage
75
What are the general steps of the lytic life cycle?
76
Why is the viral genome so small?
Faster replication --> can infect other cells faster
77
What some defenses bacteria have evolved against viruses (before and after infection)?
1. Before infection
- Prevent **absorption** to surface
- **Decoys**
- Prevent phage **DNA entry**
2. After infection
- **Cutting** phage nucleic acids
- **CRISPR-Cas** system
- **Abortive infection**
78
Explain the Baltimore system of classifying viruses. In which class would you expect higher mutation rates?
- Classifies viruses based on the **type of genome and its replication strategy**
- ssRNA
79
Where do find the majority of viral biomass?
Mostly in aquatic/marine environments
80
How do viruses affect all levels of an ecosystem?
81
How would cyanophages carry genes to maintain host photosynthesis?
???
82
Why are viruses so successful? Specifically what adaptations morphologically, physiologically, or behaviorally make them so successful?
1. Morphologically
- Simple to complex **body form**
- **Outnumber** all biological forms
2. Physiologically
- **Grow faster** than eukaryotes and prokaryotes
- Viruses have more **options to pass on genetic material**
3. Behaviorally
- Infection of one cell could **produce thousands of particles per cell**
83
How do we we sample for viruses?
1. Isolated from environmental samples by **filtering** out the larger living organisms
2. Filter size limits the size of viruses that pass through
3. **Plaque assay**
84
Explain a plaque assay.
- Phages are **enumerated and isolated**
- A plaque is a clear area which results from the lysis of bacteria
- Each plaque arises **from a single infectious phage**
85
Define endorhizosphere, rhizoplane, and ectorhizosphere. What is the rhizosphere effect?
1. Endorhizosphere: epidermal and cortical cells
2. Rhizoplane: colonization of the root surface
3. Ectorhizosphere: soil surrounding the root surface
4. Rhizosphere effect: 100x more microbes in that area
86
What is root exudate? What can be found in it?
Organic compounds that improve growth
- Vitamins, amino acids, sugar, tannins, alkaloids
- Secretions, lysates, mucilage, mucigel
87
In what stage of plant development might bacterial colonization be established? Why is this imperative for the plant?
- Bacteria will spread along the root as it growth downward and laterally **before germination**
- Imperative because it has a lot of benefits for the plant
88
What are the the benefits for plants in microbe-root associations?
1. **Nutrient** recycling
2. **Vitamins, amino acids**
3. **Hormones**
4. Exclusion of pathogens
5. Exclusion of other plants by allelopathic substances
89
Would you expect to find more common or rare species in a dry extreme environment?
Rare species
90
What is the pH surrounding the rhizosphere and why is this important?
1. pH <6.0
2. Important for nutrient availability and absorption
- Macronutrients such as nitrogen, potassium, calcium, magnesium, and sulfur are highly available at pH 6.0–6.5
91
What type of microbes would you expect to find in deoxygenated pockets in the rhizosphere?
Anaerobes or facultative anaerobes
92
Which plant hormone would you expect to increase in flooded soils?
Ethylene (regulates growth)
93
What is the equation for nitrogen fixation?
N2 + 8 H+ + 8e- + 16-24 ATP --> 2 NH3 + H2
94
What is the end goal of the nitrogen fixation?
To release **nitrate** (NO3+) and **ammonium** (NH4+) for plants to use
95
What are rhizobia?
**Diazotrophic** bacteria that **fix nitrogen** after becoming established inside the **root nodules** of legumes
96
What are some examples of root nodule-forming hosts?
Legumes
- Peas
- Clover
- Alfalfa
- Soybeans
- Mung bean
97
What genes control root-nodulating associations?
nod and nif genes
98
What is the role of Leghemoglobin?
Protects **nitrogenase** from oxygen
99
What are the stages of nodulation?
1. Plant root hair releases amino acids and flavonoids
2. Rhizobium recognition chemotaxis and attachment
3. nod factors released by bacteria causes curling of root hair
4. **Rhizobium enzymatically enter** root hair cells, but not cytoplasm
5. Root cell membrane invaginates forming an infection thread to enter root
6. Root cortex cells form deformation layer called a **nodule**
7. Continued cell division leads to a bacteroid
8. Bacteroids produce nitrogenase for N2 fixation (can’t tolerate O2)
100
Describe one type of plant pathogen, name it and what does it do?
*Agrobacterium tumifaciens*
- Affects fruit trees, beets, and other broad-leafed plants
- Induces **tumor-formation** in plant tissue
101
Explain the protozoan-termite relationship.
+/+
1. Protozoa live in the gut of termites and wood roaches
- **Digest the cellulose** ingested by their host
- **Produces acetate**
2. Termites
- **Oxidize the acetate**
- Don't produce cellulase
102
What do the aphids and *Buchanera aphidicola* each provide for the other in their mutualistic relationship?
1. Aphids
- Feed on phloem sap, which is rich in carbs but poor in most amino acids except glutamine
- Drop **sugar** water feces
2. *Buchanera aphidicola*
- Intracellular endosymbionts (reside in bacteriocytes)
- Can make all **amino acids** for host aphid
- Use the glutamine from aphid to make arginine
103
Describe the mutualistic relationship between mollusca and bacteria.
Snails, clams, and mussels gill tissue have **chemosynthetic symbionts**
104
Phytosymbionts
???
105
What are ruminants?
Herbivorous cud-chewing mammals (ex. goats, deer, cows) with high cellulose diet (indigestible)
106
Describe the rumen.
Organ that lacks cellulases, is anaerobic, near neutral pH
107
Describe the rumen microbiota.
- Complex, dense microbial community
- Bacteria: cellulose fermenters, starch fermenters
- Archaea, protozoa, fungi
108
Explain rumen metabolism.
- **Large production of gas** removed via eructation
- **VFAs produced** and cross into bloodstream
- **Ruminant gains further nutrition** (amino acids and vitamins)
109
What are the characteristics of the rumen microbes?
1. Bacteria
- Cellulose fermenters (e.g., Ruminococcus, Fibrobacter)
- Starch fermenter (e.g., Ruminobacter)
2. Archaea - methanogens
3. Protozoa - primarily ciliates
- Cellulolytic - fermentation
- Prey on bacteria
4. Fungi – cellulolytic
- Often multiple layers of symbiosis
110
What are the likely functions of bioluminescent symbioses?
- Species **recognition** (mating)
- Feeding **lures** (deep sea fish)
- **Counterillumination** (predation, camouflage)
111
What are some examples of human commensalism?
1. ***Lactobacillus*** in human intestines
- They get our extra food but we are not hurt by it
2. ***Corynebacterium*** in human eyes
- Eat our dead skin cells but we are not hurt by it
3. ***Staphylococcus epidermidis***
- Use the dead skin cells of the human skin for nutrients
112
What are the effects of the human gut microbiome on human nutrition?
1. Metabolically most active human organ
2. Microbes makeup ~30% of fecal matter
3. Microbes **help digest food**
4. Fermentation produces **VFAs**
5. Microbes supply **vitamin B12 & K**
6. Modified bile acids - steroid metabolism
7. Gases - CO2, CH4 and H2S
113
What is a fungal garden? Give an example.
1. A fungal garden is a structure maintained my some insects where they cultivate fungi as a nutrition/food source.
2. Ex. Leaf-cutter ants
- This relationship evolved about 60 million years ago
- Ants feed leaves to the fungi growing on their colony
114
What temperatures can white smokers vs. black smokers reach? What is the temperature of sea water?
- White smokers: up to 73ºC
- Black smokers: up to 400ºC
- Sea water: 2ºC
115
What causes the black chimneys in black smokers?
- Black color is caused by the presence of **iron and sulfur**
- When the iron monosulfide solidifies, it creates the black chimneys
116
What causes the white chimneys in white smokers?
- Contain more **barium, calcium, and silicon**
- Create white chimneys, which are usually smaller than black chimneys
Microbial Ecology (BIOL 355)
flashcards
Decks in class (17)
# Cards
-
Lecture 1: Intro13
-
Lecture 2: Early Life24
-
Lecture 3: Ecophysiology26
-
Lecture 4: Soil70
-
Lecture 5: Aquatic33
-
Lecture 6: Extremophiles35
-
Lecture 7: Sampling and Enumeration28
-
Lecture 9: Microbial Population Ecology34
-
Lecture 10: Microbial Interactions13
-
Lecture 11: Viruses29
-
Lecture 8: Molecular Diversity29
-
Lecture 12: Plant-Microbes33
-
Lecture 13: Animal-Microbes22
-
Exam 2116
-
Lecture 14: Metabolism15
-
Lecture 15: Biogeochemical Cycles25
-
Lecture 16: Wastewater and Bioremediation18
