Lecture 1-Midterm Flashcards
(210 cards)
1
Q
Distinguish between culture-dependent and culture independent techniques of studying bacteria (give examples of each)
A
Culture-dependent (ex. streaking a plate) - relies on growing the bacteria in culture before hand
Culture-independent (ex. microscopy) - doesn’t matter if the bacteria or alive or dead, they must simply be there
2
Q
What is “the great plate count anomaly”?
A
The idea that after serial dilution, we still end up with only 10-1000x of what the original cell count was - a very different result than what is seen under the microscope
3
Q
What does it mean to say that microbial research is usually treated as a “black box”?
A
It means that we have no idea what bacteria or how many bacteria perform a process, but instead just measure the reactions themselves (ex. nitrogen fixation) in controlled environments
4
Q
IT is thought that ____% - ____% of bacteria present in a sample can be cultivated
A
0.1% - 1%
5
Q
Sewage is generally ____% cultivatable bacteria whereas soil is more like ____%
A
30%, 0.01%-0.1%
6
Q
What are some advantages of disadvantages of culture dependent analysis of bacteria?
A
Advantages:
Can create pure culture
Can do genetic/biochemical characterization
After isolating species, we can observe rate of biochemical reactions
Disadvantages:
Most of the organisms present cannot be observed in any way
7
Q
What are some advantages and disadvantages of culture independent analysis of bacteria?
A
Advantages: Easy and cheap Many media (Selective, or general purpose - there is no universal medium) Disadvantages: Harder to isolate organisms
8
Q
How do nutrient concentrations in culture media compare to that of the natural environment?
A
Concentration in culture media is thousands of times that of the natural environment
9
Q
Distinguish between oligotrophs and Copiotrophs
A
Oligotrophs - like to live in low nutrient environments (won’t grow in culture)
Copiotrophs - Like to live in high nutrient or polluted environments
10
Q
What lab media can be used to isolate oligotrophs
A
Dilute versions of other lab media.
11
Q
What are different reasons why bacteria may not grow on standard growth media?
A
May have very low growth rate (months to years)
May be oligotrophic
12
Q
What is an “MPN”? How does one used this?
A
Most probable number - statistical technique used to quantify bacteria.
- Large bottles of varying dilutions are prepared from a sample
- Grow 3mL of each sample in 3-5 separate tubes (and a control)
- Observe tubes for turbidity.
- Results are plugged into a table based on turbidity
- Most probable number of bacteria present is calculated
13
Q
How does the use of MPNs allow scientists to obtain pure cultures?
A
At a certain dilution it is highly likely that only 1 bacterium was inoculated into the tube - so if you streak that it results in a pure culture
14
Q
Why is it that bacterial colonies observed on agar after 6 weeks are the same as those observed at 4 weeks?
A
Because bacteria are dormant a lot of the time, usually under nutrient stress. Randomly, bacteria will break dormancy and appear as a colony.
15
Q
Why is it that pyruvate or rare sugars are better energy sources in growth media than glucose?
A
Glucose breakdown results in more toxic by-products that are harmful to oligotrophic bacteria.
16
Q
TRUE OR FALSE: Oligotrophic or nutrient-starved bacteria are more susceptible to toxic by-products of cellular respiration
A
TRUE
17
Q
IF one wants to grow oligotrophic bacteria, what is the best mixture of substances
A
Small (miniscule) amounts of carbohydrates, organic acids, hydrocarbons, amines
18
Q
There are ______ to ________ of different species of bacteria in one gram of soil
A
Thousands to potentially Millions
19
Q
How did scientists find a way to get bacteria to produce “unlimited” antibiotics?
A
Using two hydrophobic plastic layers covered in wells leading to holes slightly smaller than a single bacteria. Between them is a dialysis membrane.
The plastic is added to water and the space between the two layers (containing the dialysis membrane) mimics the atmosphere. Each well should maintain very few bacteria coming from a single bacterial source (in the hole)
Observations are made using a microtiter reader, observing which wells have bacteria.
These bacteria had 40-50% cultivatability.
20
Q
Why is it that a single cell per volume will grow better than multiple cells?
A
It just does. We have no idea why,
21
Q
What is a FACS machine and how does it work?
A
Fluorescence activated cell sorting machine.
Machine sends tiny tiny blobs of liquid which may or may not contain bacteria past a laser beam. This excitational laser beam induces fluorescence in bacteria. If beads fluoresce, they are sent down a tube into one container, and if they do not fluoresce they are sent to another, Sorting can be further differentiated by telling the machine to only take beads containing more than one bacterium, or to sort them into 0 bacteria, 1 bacterium, or more than one.
22
Q
Micrococcus sp. contain _______ which results in the production of a peptide that may resuscitate gram positive cells. How can this be used in experimental conditions?
A
Resuscitation factor.
It is produced by stationary cells and pumped into the external environment. This can be extracted by removing cells from the system. This solution full of resuscitation factor can be added to dormant gram positive bacteria (ex. other micrococcus) to get them to grow
23
Q
What is “co-cultivation”?
A
Some bacteria will only grow in the presence of another type of bacteria, but we don’t know why.
One thing we do is streak colonies out in lines, then streak the sample across the lines (crosshatch).
Sometimes at the intersection of two lines the bacteria will be found.
Another method is to grow some bacteria suspended in agar, and the others grown on top of the agar on a dialysis membrane
24
Q
Is direct microscopic counting a culture dependent or culture independent technique?
A
Culture independent
25
What are the advantages and disadvtanges of Microscopy as an analytical method?
Advantanges: inexpensive and easy
Disadvantages: Hard to tell what is bacteria vs eukarya or inorganic water droplets or rock fragments, it's fucking boring, can't tell the difference between live or dead cells
26
What is phase contrast microscopy?
Get better contrast between cells and background
27
Why would one prepare soil and water samples for phase contrast microscopy?
Add dye to water samples, but soils samples require both dilution and dye, run through filter (usually polycarbonate)
28
What is "epifluorescent" microscopy? How does it relate to the black stain found on polycarbonate filters?
Microscope with light bending substance is used to induce fluorescence in bacteria on black-stained filters. This results in a black background but bright bacteria.
29
What are some dyes used in fluorescence microscopy? What are some advantages and disadvantanges?
```
Acridine orange (stains both protein and DNA - usually different colours - may stain things that are not bacteria)
DAPI or Hoechst 33258 (used more commonly - stains DNA more specifically)
```
30
What are some benefits of fluorescence microscopy?
May see bacteria that are too small to be seen with regular light microscopes, and usually can pick up far more bacteria than standard plate counts
31
What are "ultra micro bacteria"?
Bacteria so small that they cannot be seen with standard microscopy. They make up most of the biomass of some ecosystems
32
What is the formazan dye reduction technique?
Oxidized formazan dye can enter living bacteria and can be reduced inside the cell as part of the ETC. As the dye is reduced it precipitates and a red colour is produced. Once the sample is observed under a standard bright field microscope, red cells are alive and uncoloured cells are dead
33
What is a LiveBac stain?
A stain that results in live and dead cells appearing as different colours
34
What is the difference between viable cells and culturable cells? Are viable cells considered alive?
Viable simply means they stain as "live" cells whereas culturable cells can form a colony. Viable cells are often considered alive, but they may be dead, dying, or becoming dormant.
35
What is meant by the term "VBNC"?
Viable but not culturable - Cells are considered alive but may not divide or cause disease
36
How is Vibrio cholerae shown to sometimes be VBNC
If a mouse ingests cholera bacteria, they may not get sick, but when they excrete the V. cholerae, those bacteria may now be pathogenic. Something in the mouse activated these VBNC cells
37
How does TB dormancy result in TB infections late in life?
Early in life someone can be infected with TB, then it can be triggered over 30 years later by some form of stress (ex. absence of tumour necrosis factor)
38
How can one break dormancy of TB in a lab?
Dormant bacteria can be reactivated by living viable bacteria.
39
What are indirect/functional methods of bacterial analysis?
Things that measure/count a property or reaction that is proportional to bacterial population (ex. measure O2 output)
40
How can one measure cell components to observe bacterial ecology?
Usually one can measure DNA or protein (usually Lowry or Bradford methods). The problem is that these methods are not specific to microorganisms
41
How can one measure DNA to observe bacterial ecology?
Measure UV absorbance of DNA using spectrophotometer or use fluorescence. There is sometimes interference from abiotic components.
42
Why is peptidoglycan a great way to measure bacterial components of a sample? How does one do this?
Because Eukarya and Archaea don't have peptidoglycan. This is performed by lysing cells and acid hydrolysing peptidoglycan. This is dependent on the proportion of gram negatives and gram positives because they contain different amounts of peptidoglycan
43
What is the benefit of using lipopolysaccharides to quantify microbes in a sample?
It is specific for gram negatives
44
Why is the measurement of ATP one of the most sensitive ways to determine live cells in a bacterial sample? How is this performed? What are some disadvantages?
It allows one to measure only living cells and it is highly sensitive.
Performed using "luciferase", which reacts with O2, luciferin, and ATP to give off small flashes of light.
The ATP must be removed from the cells almost instantly, as it will degrade very quickly.
45
How are Biolog tests performed?
Using 96 well microtiter plates. In some, you have only a carbon source and in others a nitrogen source. Each well has a pH indicator, and each well is inoculated with the sample. Whether the organisms used the substrate is determined. This allows one to observe the biochemical needs of the whole bacterial community
46
How are isotopes used in microbial ecology?
Radioactive isotopes can be used to follow compounds through an organism, ecosystem, or sample.
47
Radioactive isotopes were popularized in the sciences in the _______, after _____
1940s, after World War II
48
What is an "isotopic ratio"
The idea that many elements have multiple isotopes that have varying abundance. The light isotope is nearly always more abundant
49
How can isotopic ratios be used in microbial ecology?
One can substitute an element (ex Hydrogen) for an isotope of that element. The ratios of Hydrogen1 to the isotope can be measured to track Hydrogen progress
50
How can isotopes be used to track Nitrogen?
One can use isotopes of hydrogen to bind to ammonia. Or, radioactive isotopes (Hydrogen3) can be used to "tag" the molecule
51
TRUE OR FALSE: In bacteria, Carbon is fixed by the Calvin cycle
FALSE, there are many ways bacteria fix carbon
52
How can one use radioactive Carbon14 to observe carbon fixation?
CO2 tagged with Carbon14.
Carbon14 can be found along the cycle in varying intermediates along the cycle. measurements taken slightly after one another can show the steps of the cycle.
53
How does one tell the difference between radioactively-tagged bacteria and non-radioactively-tagged bacteria?
Dilute the sample and pour it over X-ray film. Develop the film, and the glowing bacteria are radioactive.
Another way is to filter the bacteria, roll the filter into a tube and use machinery to measure the amount of the radioactive isotope present.
54
In an experiment a scientist adds 14C tagged glucose to a flask containing bacteria. How do they measure the rate of respiration (CO2 produced/unit weight/unit time)
Put solution in erlenmeyer flask with tube leading to alkaline solution. CO2 should bubble off into solution (CO2 trap) and measured.
55
What are "dissimilatory processes"?
Molecule is not incorporated into biomass and instead is released as a waste product
56
Why is dissimilation so important for the Nitrogen cycle in bacteria?
Because N2 in such organisms is reduced to NH3 but not assimilated into the organism. This results in most of our atmospheric N2
57
Distinguish between DOC and DON
Dissolved organic carbon
| Dissolved organic nitrogen
58
Distinguish between POC and PON
Particulate organic carbon
| Particulate organic nitrogen
59
How does one separate primary and secondary productivity measurements in microbes?
label isotopes that are used in both.
60
What is the primary reason that we use radioisotopes in microbial ecology?
Techniques to measure radioisotopes are VERY VERY VERY VERY sensitive, which is necessary because often we are working with less than a micromole of substance
61
____ is the standard laboratory method to quantify the radioactivity of low energy radioisotopes, mostly beta-emitting and alpha-emitting isotopes. The sensitive detection method requires specific cocktails to absorb the energy into detectable light pulses.
Liquid scintillation counting
62
Why is it that we don't need to use radioisotopes in science any more?
We now have analyticial techniques that allow us to observe the ratios of stable isotopes of an element
63
What is GC-IRMS and how can it be used to distinguish between two isotopes?
gas chromatography - ion ratio mass spectroscopy. Allows for very sensitive separation of isotopes of the same element
64
What is "isotopic discrimination"?
The idea that many biological/chemical processes discriminate against one isotope of an element (preferentially use one - usually the lighter one)
65
Why is isotopic discrimination a way to detect the presence of life?
The ratios of isotopic elements can be used to determine whether life is present, because isotopic ratios will typically favour the light isotopes in the presence of life. It is possible to look at mineral profiles to find how farm back in time living organisms have been on the planet
66
The isotopic ratio of sigma13C for atmospheric CO2 is -8 parts per thousand. What is the ratio within plant organic material? What does this mean?
-27 parts per thousand. This means that plants preferentially use Carbon12 (the smaller isotope).
67
If plants have an isotopic carbon ratio of -27 parts per thousand, what do bacteria have? Are all bacteria the same?
Bacteria that consume plant material will have the same isotopic ratio but other types of bacteria have varying ratios. For example, methanogens have a -40 parts per thousand ratio
68
TRUE OR FALSE: There are no abiotic processes that discriminate against certain isotopes
FALSE - certain geologic processes have designated isotopic ratios
69
What is "deep evolution"?
The idea that life can be traced back as far as almost 4.1 billion years ago
70
Prokaryotes can be found as far back as ______
3.7 billion years ago
71
Why are molecular detection methods the preferred method of microbial analysis?
Allows for culture-independent detection, counting, and identification of microorganisms, which in turn enables one to compare bacterial profiles within ecological research
72
Why are molecular methods considered universal to all life?
All cellular organisms contain DNA or RNA
73
PCR was invented in the year _____
1985
74
How do people harvest bacteria from thermal ponds?
Tying a microscope slide to a fishing line and dipping it in the ponds for long periods of time before viewing them under a microscope
75
how was the important bacterial species "Thermus aquaticus" or "Taq" discovered?
By collecting it from a thermal pond in yellowstone national park
76
Why is Taq such a historically important microorganism?
After the thermophilic bacterium Thermus aquaticus was discovered, scientists realized that it must have its own heat-stable DNA polymerase. This is now used in PCR so we do not have to add new polymerase after each cycle
77
When executing PCR, we want our primers to bind with any possible bacterium. How do we accomplish this?
We need to find a piece of DNA that is found in every bacterial species in the world today
78
How can PCR be used to determine the presence/absence of bacteria or the quantity of bacteria in a sample?
Searching for bacteria-specific DNA codes allows us to detect/quantify bacteria
79
How can PCR be used to identify bacteria? Describe this step by step.
16S rRNA is present in all bacteria and there is some variation between each type of bacteria.
1. Take a sample and isolate total DNA
2. Isolate all 16SrRNA genes (PCR product) - this produces a "gene" library (a bunch of the same gene but all from different bacteria)
3. Insert all those genes into different plasmids
4. All the plasmids are inserted organisms (ex. E. coli) - transformation. Each E. coli has a single plasmid in it.
5. The E. coli cells are plated on agar, and a bunch of colonies grow, each from one CFU of E. coli - Each colony has the same variant of the gene
6. Plasmid DNA can be isolate from one clone - you now have multiple copies of the same gene.
80
How can PCR be used to detect viruses (specifically RNA viruses)?
Can convert RNA to DNA using reverse transcriptase
81
How can PCR be used to determine whether a gene is active/expressed?
Get PCR machine to search for mRNA sequence, convert with reverse transcriptase to DNA.
82
In 1 gram of soil there is approximately ______ species of bacteria present
10 000
83
Why is rRNA used to determine relatedness of microorganism?
Because all cellular organisms require ribosomes to produce protein (and therefore have ribosomal RNA)
84
What is the eukaryotic equivalent of 16SrRNA?
18SrRNA
85
Why is 16SrRNA the perfect molecular arrangement for studying differences between bacteria?
There are invariant sections that are the same across all bacteria, interspersed with variable sections that may have minor changes in them
86
How does sample size affect bacterial growth in culture?
Sometimes a larger sample yields less of the bacteria you are looking for, likely because the large sample has more of the dominant bacteria, which can edge out others
87
How does sample size influence culture independent tests on a soil sample?
A large size sample would be more likely to contain the expected microorganisms, simply due to the heterogeneity of soil. Ex. bacteria live in soil micropores whereas fungi live in macropores
88
If you intend to extract DNA from microorganisms in a sample, why are transportation and handling procedures so important?
DNA may be degraded by microorganisms/chemicals/enzymes present in the sample as you transport it from the site to the lab.
89
What methods can be used to preserve DNA after a sample of microorganisms is taken in the field?
Dry ice and liquid nitrogen are options, but they are bulky and outdated. A sucrose lysis buffer can be used to lyse cells and preserve DNA. Another option is to perform experiments almost immediately after sampling, so that temperature and pH of the sample are not affected either.
90
What is the most widely used stain in microbial research?
Gram stain
91
When giving a microscope count of microorganisms in a sample, a minimum of ___ fields must be counted
20
92
How does staining impair one's ability to count microorganisms under a microscope?
Sometimes the background (ex. soil) is stained as well, making it hard to differentiate from the microorganisms.
93
A ____ count uses a microscope whereas a _____ count uses culture-dependent techniques
Total cell count, plate count
94
What does "FISH" stand for and how is this method utilized?
FISH = Fluorescent in situ hybridization. Uses labelled oligonucleotides to reveal the presence of specific organisms/groups of organisms.
95
How does one determine which oligonucleotide sequence to tag using FISH?
There are databases such as "probeBase" which outline varying probes and give guidelines for which probes may be appropriate.
96
How can one get a stronger signal out of a FISH experiment?
Perform CARD-FISH: Catalyzed reported deposition fluorescence in situ hybridization, which labels the oligonucleotide with horseradish peroxidase as well, which binds more strongly to cells.
97
What are some challenges associated with "FISH" method?
If cell membranes are not very permeable, less dye will get in. Sometimes probes do not bind well to fluorescent material either.
98
How can scanning electron microscopy be used to examine microbial communities
Can be used to visualize surface features of a microbial community.
99
What is SEM?
Scanning electron microscopy - electrons are used for imaging. Samples are coated with gold or palladium to make them easier to view
100
What is TEM?
Transmission electron microscopy. Requires very thin slices of samples and allows for viewing the internal parts of cells. Usually samples are stained with permanganate or osmic acid
101
What are some advances in microbiology that have been made using TEM?
The ability to see microbial pesudopilli, Yersinia injectisomes, and microbe-mineral interactions
102
What does it mean to say that our lack of success in culturing microorganisms may be related to the growth medium?
There is growing evidence that we would simply be more successful growing bacteria if we mimicked the natural conditions of their environment better
103
The uptake (consumption) of oxygen as a proxy of microbial respiration is referred to as _____
Respiration index (RI)
104
What is one parameter that can throw a wrench in respiration monitoring?
pH affects accuracy of CO2 monitoring
105
Measuring microbial biomass of a community can indicate what types of parameters?
Decomposition rate, fertility, organic matter content, mineralization of nitrogen, soil fertility, structure/stability in soil ecosystems
106
How can a scientist measure microbial biomass?
Chloroform fumigation - microorganisms are killed with chloroform, and either the substrate is extracted to quantify carbon, or researchers measure carbon dioxide released by microbial spore germination (using carbon from the ones that just died)
107
How can adding glucose to a medium give an estimate of microbial biomass?
It allows scientists to observe how long it took for the glucose to be used up, measuring the metabolically active portion of the biomass.
108
16SrRNA is sometimes known as ____
SSU
109
How is 16S rRNA considered a "molecular chronometer"?
Can be used to measure rate of evolutionary descent through randomly accumulated mutations.
110
How does one develop a phylogenetic tree for bacteria?
Look at the two most related species in the sample and observe their similarities and differences (in 16SrRNA). After that, look at the next most similar species and see if it shares more DNA with species 1 or species 2, determining which one must have diverged first
111
The 16SrRNA gene is about _____ base pairs long
1600 bp
112
Generally there is only about ___% variation in 16SrRNA between all microorganisms
15%
113
To differentiate bacteria into species, they have to have at least a __% difference in 16S rRNA
3%
114
Why do we do PCR on the RNA of bacteria when it is harder to start from RNA?
DNA is found in all sorts of places in the environment but if you start with RNA you know it is coming from live cells
115
How does one remove live bacteria from soil?
It's basically impossible. They are bound so tightly to the soil particles that any method to try to remove the bacteria usually kills them (ex. detergents or centrifugation)
116
After plasmid 16SrRNA is obtained from an agar plate "gene library" and sequenced, what is done with the data?
the varying sequences are lined up and the species identities are investigated.
117
RDB II is a database for only ____ sequences
16S rRNA sequences
118
If, after PCR and 16SrRNA isolation in a sample, there is a 96% similarity to an existing bacterial species, what does that mean?
They are in the same genus
119
If, after PCR and 16SrRNA isolation in a sample, there is a 97.3% similarity to an existing bacterial species, what does that mean?
They are probably the same species
120
What purpose does it serve to compare a full 16S rRNA set from one sample with that from a sample taken elsewhere, or at a different time of year
To quantify the amount of different genes between the two areas or two times of the year. Basically, you are measuring changes in composition of the microbial community. This does not allow you to observe the actual species-by-species differences, just an entire community.
121
What term is used to describe two similar bacterial groups that may or may not be a proper "species"?
"Operational Taxonomic Unit"
122
OTUs or groups of bacteria defined by 16S rRNA genes or similar techniques are called ___
phylotypes
123
Out of one round of PCR replication from 1g of soil, you may get 1000 gene sequences. Does each sequence belong to a different species?
No, it's more likely that the more abundant species will have 200-300, and less abundant more like 10. Each sequence belongs to a different organism (not species)
124
How is a hybridization curve developed?
By obtaining DNA/RNA renaturation data (rates)
125
How is renaturation of DNA tracked?
DNA is quickly heated up, and OD260 is taken using a spectrophotometer. Continuous spectrophotometer readings will show how quickly the DNA renatures (binds together again) because single stranded DNA absorbs more light than double stranded
126
The more *different* pieces of DNA you have in a sample, the ____ (longer/shorter) time it will take to renature
longer
127
How can DNA renaturation/hybridization curves be used to determine the amount of different types of DNA in a sample?
One can create a calibration curve using known amounts of different types of DNA and denaturing the DNA. The more different sequences (species) that are present the slower the renaturation process.
128
How is DNA generally separated after PCR?
Using gel electrophoresis - separated by size
129
What is DGGE and what does it contain?
Denaturing gradient gel electrophoresis. It contains compounds that can denature DNA: urea, formamide in increasing concentrations as you go down the gel
130
As DNA moves down DGGE gel, what happens?
As the DNA moves down the gel it eventually reaches the concentration of denaturation compounds that will denature it (make it single stranded). This results in a series of bands in the gel that results in different sequences of the same sized gene. Each band should then represent a species of bacteria.
131
At what point is DGGE used?
Usually after regular gel electrophoresis, using one band of equal length chunks of DNA
132
What is needed to perform massively parallel sequencing?
An Illumina machine, a 454sequencing machine, a pyro sequencing machine.
133
What are MPS machines and what do they do?
Massively Parallel Sequencing machines, used to sequence hundreds of thousands to millions of genes from a sample (called short reads because each sequence is very short - 100-200bp in length)
134
Using conventional read methods of DNA sequencing, what length of sequence can be read?
Almost an entire gene (ex. 16SrRNA), over 800bp
135
Why is MPS not used often?
Chips that are needed for 1 experiment cost 8000 to 10 0000 dollars and the machines themselves are 150-250 thousand dollars
136
What is one way to run several experiments on the same MPS chip?
barcode each strip on the chip, indicating which sample is which.
137
How do you figure out what fatty acids are present in a bacterial sample?
Isolate fatty acids, perform gas chromatography, and observe the output. The output can sometimes be enough to determine what species it is
138
How does one extract fatty acids from a sample?
Use a mixture of chloroform and methanol, which when evaporated off leaves all the lipids. Eventually you send up with the total fatty acids from the sample
139
What is the one culture independent microbiology method that does not use DNA?
Fatty acid analysis (extraction and gas chromatography)
140
How can fatty acid analysis of bacterial samples indicate what species it is?
Some fatty acids are distinctive of certain types of organisms. Ex. gram positives, or cyanobacteria
141
Some "signature fatty acids" can be used to indicate what stresses are being applied to bacteria. What are some examples of stressful situations?
Starving bacteria, bacteria under temperature stress, etc.
142
The new way to look at ecology, based on food webs, was developed by ____ in the 1920s
Charles Elton
143
How is "the first ecologist" Charles Elton's work related to Manitoba?
He used Hudson Bay Trading Company Records to track the furs of hares, lemmings, voles, and wolves. Based on year-to-year sales records he determined population levels of these animals.
144
How did A.G. Tansley define the word "ecosystem"?
As "all the plants and animals together with the physical factors of their environment"
145
Alfred J. Lotka was a chemist who described ecosystems/populations/communities in what way? What did he recognize about ecological interactions and thermodynamics?
As a set of equations of energy and matter exchanges among constituent organisms. Basically biomass = energy. He recognized that ecological interactions obey thermodynamic laws
146
Ecologist Raymond Lindeman took ideas from Elton, Tansley, and Lotka and did what?
Wrote a textbook synthesizing these ideas - the idea of trophic levels, with an emphasis on energy passing through the ecosystem (pyramidal food chain)
147
Eugene Odum is known for "quantifying" ecology - what does this mean?
He depicted ecosystems by energy flow diagrams, with "energy" being equivalent to carbon or other elements passing through a food chain.
148
Ecological efficiencies range between __% and __%
5% and 20%
149
Total energy available in an ecosystem is dependent on what trophic level?
The primary producers
150
What is the main difference between microbial primary producers and primary producers in other communities
Microbial primary producers can obtain carbon without photosynthesis - the two are mutually exclusive
151
What is referred to as "assimilation efficiency"
Ratio of assimilation to ingestion (ingested energy - egested/excreted energy = assimilated energy)
152
Why is measuring assimilation efficiency easier in eukaryotes?
Easier because they "eat" stuff and excrete undigestible components
153
What is the net production efficiency in an ecosystem?
Ratio of the energy contained in new biomass production to the total assimilated energy
154
What is "gross production efficiency" in an ecosystem?
Ratio of energy contained in new biomass production to the total ingested energy. includes total energy transferred from one trophic level to the next
155
Gross production efficiency ranges from __% in mammals to __% in insects
1%, 20%
156
TRUE OR FALSE: As a resource increases, the population increases
False, the GROWTH RATE of the population increases
157
Generally there are ___ limiting nutrient(s) in a community
1 limiting nutrient
158
What is considered to be the only carbon limited environment?
The bottom of the ocean - most carbon is near the surface
159
What is "Liebig's Law of the Minimum"?
A population will increase until one resource becomes too low to support further growth - this is the limiting resource
160
What is an example of a place where there is a lot of biological productivity, but limiting nutrients prevent algal blooms?
Greenish-parts of the ocean have large amounts of algal cells, with very high nitrate concentrations but they still do not form blooms - why? This is because there is iron limitation.
161
Why did Liebig say that the dumping iron into the right parts of the ocean would cause an ice age?
Iron is a limiting nutrient in a lot of algae-heavy parts of the ocean. This would cause large blooms to build up, then subsequently die and lock CO2 into the bottom of the ocean for a couple hundred years. This could drop CO2 levels to the point that one could cause an ice age.
162
What is Gause's principle or "the competitive exclusion principle"?
Two species cannot coexist indefinitely while using the same limiting resource - can derive a mathematical model where 2 or more species can coexist stably
163
A ___ classification of bacteria is based on testable properties
Phenetic
164
What is the most commonly used classification of bacteria?
Phylogenetic taxonomy
165
What is "species richness" in a community?
Number of species in the community.
166
Differentiate between species richness and species evenness
Species richness is the number of species in a community, whereas species evenness is how much of the population is made of one species
167
In a standard log normal distribution graph of microbial environments, what is the format? Why is it plotted on semi log plot?
Species are arranged from left to right by their abundance, with the species with the most individuals on the left followed by species with the second greatest number of individuals and so on. called "rank order". Usually semi log because microbial communities can vary by several orders of magnitude.
168
Why is it assumed that microbial species will follow a log normal distribution?
Because we have no data to the contrary, generally it does
169
What is the jackknife estimate?
```
S = s + (n-1/n)^k
S = jackknife estimate of diversity
s = observed number of species
n = number of samples
k =
```
170
Describe Simpson's Index: D = 1/sumofpi^2?
pi = proportion of species i
| Higher D means more species diversity but less common species contribute less diversity than more common
171
How is Simpson's Index used in microbial ecology?
Gives us the opportunity to compare two different samples for species diversity/distribution
172
What is the idea of the Shannon-Weaver Index: H = -sumofpi(logepi)
ughhh I'm so sick school is so hard - this is important because its popular or some shit
173
Local diversity/number of species in a small, homogenous habitat is called ___ diversity
alpha
174
Taking samples from a field near Boissevain and a field near Morris is an example of ____ diversity sampling
Beta
175
What is gamma diversity?
Total diversity seen in all habitats in a larger region (more long range)
176
How did Pasteur and Koch's ideas lead to pure culture ideas within microbiology?
They identified primarily pure cultures - just through the experimental means they chose
177
What are some of the main contributions of Sergei Winogradsky to the field of Microbial ecology?
Discovered hemolithotrophy, autotrophic growth with CO2, nitrogen fixation
178
What did Martinus Beijerinck contribute to the field of Microbial ecology?
Created enrichment cultures - things that select for certain "types" of bacteria.
179
How does one create an enrichment culture for Nitrogen fixers?
Remove the nitrogen source so that only nitrogen fixers can grow
180
What is considered to be one of the oldest branches of bacteria?
Hyperthermophiles
181
Approx __/___ of the biomass on Earth is prokaryotes
2/3rds
182
At least __/___ of all carbon fixed by photosynthesis on Earth is done by prokaryotes
1/4th
183
What is the maximum ocean depth at which plant photosynthesis would occur
30 meters
184
A large proportion of fixed carbon is mineralized to _____ by microorganisms
CO2
185
Why is the conversion of fixed carbon to CO2 so imporant?
CO2 is nedded for plants
186
What are the primary storage molecules of organic carbon?
Mostly cellulose
187
What is an "endophyte"?
A microorganisms that lives within a plant and forms a symbiotic relationship
188
How does the presence/absence of oxygen on the planet influence life/metabolism on earth?
No oxygen = no ozone = penetrating UV light:
this means that dry land and the upper layers of the ocean would be irradiated. Therefore, metabolism that would develop would have nothing to do with photosynthesis
189
Have we found fossils of bacteria to aid explanations of microorganisms development on earth?
We have found "microfossils" that are roughly the size and shape of filamentous (probably cyano)bacteria. Many would argue that these are too ambiguous and might not be fossils at al
190
What are "stromatolites"?
In shallow water, cyanobacteria form little mounds of carbonates (as a waste product), which slowly grow more and more carbonates until they become strange limestone rocks
191
What is one way to determine whether cyanobacteria existed around 3.5 billion years ago
Identified by the presence of fossilized stromatolites
192
What happened during the great oxygenation event?
Went from anaerobic environment on earth to aerobic. from
193
What is a rarefaction curve?
A plot of the number of individuals (x axis) vs species number (y axis)
194
What is a bootstrap estimate within ecology?
A random re-sampling of data to see if it gives the same results as using entire data - can be used to estimate species in a sample
195
What is an "allochthonous" microorganism?
Considered to be "passing through" the environment - do not show adaptation to the environment and cannot compete successfully with other organisms
196
Are there bacteria native to air? Why or why not?
No, likely not. The pressure is very low, it's dry, cold, and high UV
197
How are spores (ex fungal) considered to be adapted for aerosolization?
Light - low density, small size and shape
| Thick walls to prevent dessication, have pigmentation to resist radiation - millions are released
198
What is "darwin's dust"?
The samples Darwin collected off the sails of the HMS Beagle when he realized it was getting dusty in the middle of the ocean. They found it was made of spores - which are still viable to this day
199
Why is water necessary for microorganisms?
They take up their nutrients from water (must be a dissolved substance)
200
What is another term for freshwater?
Limnetic
201
Distinguish between lotic and lentic habitats
Lentic - still water
| Lotic - runnign water
202
the _____ zone is the bottom of a body of water which is sun lit
Littoral zone
203
The zone where light penetrates a lake is the ____ zone, below that is the ____ zone
Euphotic zone, profundal zone
204
What are "microbial mats"
Mats of microbes occurring on the bottom of the lake (usually full of photosynthesizers)
205
What is the light comensation limit?
Depth in limnetic zone where net photosynthesis ends (where respiration equals photosynthesis)
206
How is light intensity used to measure the light compensation limit?
MEasure light intensity in the lake and the point at which 1% of the incident light intensity at the surface
207
What does it mean if you run into a black layer of sediments in a lake?
It means you have run into a sulphide reduction zone (anoxic)
208
Where do most nutrients come from in freshwater environments?
Mostly from plants rather than single celled organisms
209
What is the most common nutrient in lake
Carbon
210
What is the primary difference between dissolved and particulate matter?
>0.22 micrometers, Particulate.
