Deck 18: Methods in Microbial Ecology

Question 1

For microbial biodiversity studies,it is common to identify the ________ rather than the ________ as a measure of biodiversity.

A) organisms themselves / genes
B) genes / organisms themselves
C) cell types / genes
D) cell types / organisms themselves

Answer 1

B

Question 2

Laser tweezers are used for

A) testing the purity of a culture.
B) isolating individual cells.
C) separating aerobes from anaerobes.
D) enhancing the growth of fastidious organisms.

Answer 2

B

Question 3

Winogradsky columns are used primarily for enrichment of

A) aerobic cultures, although occasionally anaerobes do appear.
B) anaerobic cultures, although occasionally aerobes do appear.
C) aerobes, anaerobes, and phototrophs.
D) phototrophs, although occasionally heterotrophs do appear.

Answer 3

C

Question 4

The methodology of microbial ecology includes

A) enrichment and isolation of specific microbes.
B) cell-staining methods.
C) gene, transcript, and protein characterization.
D) enrichment and isolation of specific microbes, cell-staining, and gene, transcript, and protein characterization.

Question 5

When dealing with stable isotopes,enzymes tend to favor

A) the lighter isotope.
B) the heavier isotope.
C) the isotopes in about equal proportions.
D) either the lighter or the heavier isotope, depending on environmental conditions.

Question 6

The science of microbial ecology deals with

A) how microbial communities interact with each other and their environment.
B) microbial activity and biodiversity.
C) microbial gene regulation mechanisms in response to environmental change.
D) how the activity and biodiversity of microbial communities affect microbial interactions with each other and the environment.

Question 7

Which fluorescent molecule enables visualization of living microorganisms?

A) acridine orange
B) DAPI
C) GFP
D) SYBR® Green

Question 8

Which of the following methods do NOT involve nucleic acid hybridization?

A) RACE-FISH
B) FISH-MAR
C) phylochips
D) T-RFLP

Question 9

Which approach would help to identify biologically produced sulfur in a sediment sample?

A) enrichment
B) isotopic fractionation
C) microautoradiography
D) microelectrodes

Question 10

Amplification of chromosomal DNA from a single-cell is accomplished by

A) randomly initiating DNA replication throughout the chromosome.
B) creating thousands of primers that will prime DNA replication throughout the chromosome.
C) creating complementary DNA from transcripts of a single-cell.
D) cloning fragments of the chromosome from the single-cell into a multi-copy plasmid.

Question 11

Which method requires the addition of at least one radioactive chemical?

A) CARD-FISH
B) MAR
C) NanoSIMS
D) SIP

Question 12

Well-designed microbial activity measurements can reveal ________ of major metabolic reactions in a habitat.

A) types
B) rates
C) both types and rates
D) either types or rates (but not both)

Question 13

The biggest limitation of traditional light microscopy and electron microscopy methods is that they are unable to reveal

A) absolute cell concentration.
B) cellular components of small microbes because of the limits of magnification.
C) genetic and functional diversity of microorganisms in the habitat under study.
D) physical microbial interactions as found in nature.

Question 14

In an agar dilution tube,microbial colonies grow

A) at the bottom of the tube.
B) on the sides of the tube, although some may be at the surface.
C) embedded in the agar, rather than growing on the surface.
D) on the surface, but some creep down the sides away from the surface.

Question 15

Staining methods are suitable for obtaining ________ information about the number of cells in natural samples.

A) qualitative
B) quantitative
C) both qualitative and quantitative
D) neither qualitative nor quantitative

Question 16

The term used when an organism is studied in its natural environment is

A) au naturale.
B) in vitro.
C) in situ.
D) in toto.

Question 17

The term axenic is used to describe a(n)

A) anaerobic culture.
B) anoxygenic culture.
C) nutritionally deficient culture.
D) pure culture.

Question 18

Phylogenetic stains,such as those used in FISH,hybridize with

A) ribosomal RNA.
B) mitochondrial DNA.
C) nuclear DNA.
D) RNA polymerase.

Question 19

What technique(s)can be used to characterize the phylogenetic composition of a microbial community without culturing any of the members?

A) green fluorescent protein tagging
B) stable isotope techniques
C) radioisotope experiments
D) fluorescent in situ hybridization

Question 20

Radioisotopes are useful when

A) very high sensitivity is required.
B) turnover rates need to be determined.
C) the fate of portions of particular molecules need to be followed.
D) very high sensitivity is required, turnover rates need to be determined, and the fate of portions of particular molecules need to be followed.

Question 21

Metatranscriptomics and metaproteomics are favored over metagenomics when ________ is of more interest than ________.

A) gene presence / phylogeny
B) phylogeny / gene presence
C) function or gene expression / gene presence
D) gene presence / function or gene expression

Question 22

What unit is isotopic fractionation reported as?

A) parts per billion
B) parts per million
C) parts per thousand
D) parts per trillion

Question 23

How do viability stains usually distinguish between living cells and dead cells?

A) The chemical fluoresces only when bound to ribosomes that are actively synthesizing proteins.
B) The chemical stain is taken up by living cells and once metabolized becomes fluorescent.
C) The dye specifically targets intact cytoplasmic membranes.
D) The dye's fluorescence is quenched by dead cells.

Question 24

Thirty organisms containing the same phylogenetic marker are all considered to be within the same

A) phylotype.
B) species.
C) functional group.
D) phylogenetic tree.

Question 25

Analyses of sulfur isotopes have been used as evidence against life on the Moon,because the sulfides in lunar rocks have

A) an isotope composition similar to marine sulfate, which is enriched in ³⁴S.
B) an isotope composition similar to marine mud, which is depleted in ³⁴S.
C) an isotope composition similar to igneous rocks.
D) exactly equal amounts of ³⁴S and ³²S.

Question 26

Interpreting stable isotopic fractionation depends on the fact that most enzymes preferentially bind ________ isotope substrates over ________ isotope substrates.

A) nonradioactive / radioactive
B) light / heavy
C) heavy / light
D) radioactive / nonradioactive

Question 27

Which of the following techniques can link prokaryotic phylogeny and function?

A) DAPI staining
B) stable isotope probing
C) environmental genomics
D) environmental genomics and stable isotope probing

Question 28

In microbial ecology studies,the FISH technique identifies organisms based on

A) the presence of green fluorescent protein.
B) fluorescence of unique cofactors or pigments under certain wavelengths of UV light.
C) hybridization of a fluorescent probe to specific ribosomal RNA sequences.
D) the presence of luciferase.

Question 29

Genes encoding ________ are widely used as target genes in molecular biodiversity studies.

A) ATPases
B) DNA polymerase III
C) 16S rRNA
D) RNA polymerase

Question 30

Robotic systems used to quickly test thousands of combinations of nutrients for enrichment of a particular prokaryotic species is an example of a(n)________ technology.

A) outdated
B) biased
C) genomic
D) high-throughput

Question 31

When laser tweezers are used,the laser beam traps

A) isolated single-copy genomes.
B) a single microbial cell.
C) a single microbial colony on a plate.
D) multiple cells of the same type.

Question 32

The rolled tube method is most commonly used for isolating which grouping of microorganisms?

A) anaerobes
B) chemolithotrophs
C) chemoorganotrophs
D) aerobes

Question 33

Diversity is often ________ when ARISA or T-RFLP is used.

A) underestimated
B) overestimated
C) not represented
D) biased

Question 34

Collective estimates of the physiological reactions occurring in the entire microbial community are known as ________ measurements.

A) in vitro
B) in situ
C) activity
D) metagenomics

Question 35

For what purpose would a microbial ecologist use a microsensor?

A) to determine the concentration of cells in small increments in a sediment or water column
B) to determine the expression of a particular gene in a microbial community
C) to quantify the uptake of a radioactive material
D) to determine the concentration of O₂, N₂O, or other chemical species in small increments in a sediment or water column

Question 36

Why is it necessary to have a standard for the interpretation of stable isotope ratios?

A) A standard is necessary to calculate how much radioactivity was added to a sample.
B) A standard is necessary to determine the stable isotope ratio in the absence of biological activity.
C) A standard is necessary to determine the weight of each isotopes.
D) A standard is necessary to determine the age of the sample.

Question 37

Which technique would be used to estimate the concentration of naturally occurring Escherichia coli in a wastewater sample?

A) agar dilution tube method
B) laser tweezers method
C) most probable number (MPN) method
D) cell tagging using GFP method

Question 38

Microarrays are useful for assessing

A) gene expression.
B) enzyme activity.
C) the presence of specific rRNA sequences.
D) gene expression and the presence of specific rRNA sequences.

Question 39

Which molecular method allows for the detection of a specific organism within a diverse microbial community?

A) fluorescent DNA staining using DAPI
B) viability staining
C) enrichment techniques
D) fluorescent in situ hybridization

Question 40

Genomic analysis of Prochlorococcus has revealed

A) the presence of bacteriorhodopsin.
B) variations in ribosomal genes within the same phylotype.
C) complete congruence of genes and genome structure within the same phylotype.
D) variation in functional genes within phylotypes, but high levels of gene conservation between cultured representatives and environmental populations.

Question 41

If properly constructed,a Winogradsky column can be used to isolate pure cultures.

Question 42

Strict anaerobic organisms are not suited for GFP reporters due to the protein requiring oxygen to fluoresce.

Question 43

How would you label and separate the DNA of unknown methylotrophs in a sample?

A) Incubate the sample with ¹³C-methane.
B) Hybridize the DNA to FISH probes.
C) Use DGGE to separate the strands of DNA in the sample.
D) Use T-RFLP to identify the methylotroph DNA in the sample.

Question 44

The goal of environmental genomics is to detect as many genes as possible and then,if possible,to determine to the phylogeny of the organisms to which the genes belong.

Question 45

Which of the following hypotheses could be tested using microautoradiography fluorescence in situ hybridization (MAR-FISH)?

A) Bacteriorodopsin uses light energy to translocate protons.
B) Archaea are the main autotrophs in marine water samples taken 300m below the surface of the ocean.
C) The microbial community of agricultural soils is more phylogenetically diverse than the microbial community of native prairie soils.
D) The ammonia monooxygenase gene is present in members of the phylum Verrucomicrobium.

Question 46

Organisms in natural environments can be detected by assaying for the presence of their genes.

Question 47

Once a putative pure culture has been obtained from the environment,it is no longer necessary to check its purity.

Question 48

Single-cell genomics may help us

A) predict which microbes will be abundant based on the environmental conditions.
B) understand the physiology of uncultured microbes.
C) develop better enrichment culture methods.
D) understand the physiology of uncultured microbes and develop better enrichment culture methods.

Question 49

Traditional enrichment culturing circumvents issues associated with "weed" species from overcoming the population.

Question 50

The ¹³C/¹²C isotopic ratio of geological rocks of different ages has been used as evidence for or against past biological activity,because compounds of biological origin

A) do NOT contain ¹³C.
B) have a higher proportion of ¹³C that compounds of geological origin.
C) have a lower proportion of ¹³C that compounds of geological origin.
D) are not well preserved in geological samples.

Question 51

The element(s)that have proven useful for stable isotope studies are

A) carbon.
B) nitrogen.
C) sulfur.
D) carbon, nitrogen, and sulfur.

Question 52

Stable isotope probing (SIP)is a method that

A) causes cells that hybridize with a fluorescent probe to fluoresce under UV light.
B) compares the isotopic ratios of different compounds in the environment to determine whether they are of biological or geological origin.
C) uses substrates containing heavy isotopes to label the DNA of organisms that use those substrates.
D) compares the transcription of specific isotope labeled genes under different conditions.

Question 53

Which of the following statements is FALSE concerning enrichment bias?

A) Dilution of the inoculum may help to avoid enrichment bias in some cases.
B) Enrichment bias is impossible to overcome in some oligotrophic environments.
C) Enrichment bias resulted in the underestimation of prokaryotic diversity.
D) Enrichment bias favors organisms that grow quickly.

Question 54

Transcription of various genes under particular environmental conditions can be studied by

A) CARD-FISH.
B) using a reporter gene that encodes for green fluorescent protein (GFP).
C) T-RFLP.
D) using a reporter gene that encodes for green fluorescent protein (GFP) or CARD-FISH.

Question 55

The purpose of the enrichment culture technique is to enrich for organisms with specific physiological properties from a microbial community.

Question 56

One way to study a microbial ecosystem is to isolate microorganisms from it and study their properties in laboratory culture.

Question 57

The overall purpose of DGGE is to

A) separate genomes that are less than 95% similar.
B) measure activity of cells that use DGGE as an energy source.
C) detect cells that utilize a specific radiolabeled substrate.
D) separate genes of the same length that differ in their denaturing profile due to sequence variation.

Question 58

Culture-independent approaches avoid issues associated with

A) detecting very rare phylotypes.
B) conflating phylogenetic and functional diversity.
C) growing organisms in the lab.
D) next generation sequencing.

Question 59

Enrichment cultures can be established by placing the inoculum into selective media and incubating under specific conditions.

Question 60

You would like to test the hypothesis that ammonia-oxidizing Archaea are more active and abundant than ammonia-oxidizing Bacteria in coastal marine water.What technique(s)or experiment(s)could you use to test this hypothesis?

A) environmental proteomics
B) fluorescent in situ hybridization (FISH)
C) stable isotope probing using ¹⁵N labeled ammonia
D) stable isotope ratios of ammonia and nitrite

Question 61

What are the pros and cons of traditional enrichment culture techniques? What advances in the last decade are improving enrichment culture techniques to aid the cultivation of uncultured microorganisms?

Question 62

Metaproteomics is a more developed field than metatranscriptomics due to the high sensitivity of mass spectrometry.

Question 63

What prior knowledge is required to use a phylochip to study the abundance of the different microbes present within a microbial community? How does this cause bias when using a phylochip to analyze microbial community structure?

Question 64

The Winogradsky column is a method for assessing the entire gene complement of a habitat,revealing both the biodiversity and metabolic capabilities of the microbial community at the same time.

Question 65

We know that that there are over 50 major phyla in Bacteria; however,only about 25 of these phyla have cultured representatives.Why is this? How are scientists attempting to culture representative from the 25 phyla that do not currently have any organisms in culture?

Question 66

Describe what an ITS region is in the context of prokaryotes,and explain the significance of the ITS region for microbial ecology.

Question 67

FISH technology can employ only a single phylogenetic probe.

Question 68

Phototrophic organisms in SIP experiments are often observed releasing ¹⁴CO₂ as measuring activity.

Question 69

By using simple microscopy techniques,it is possible to determine if a culture is contaminated with another organism.

Question 70

Describe how FISH can be used to determine which cells within a microbial community are actively degrading toluene.Assume the genes involved in the metabolic pathway have been sequenced from several microorganisms and vary only slightly from one another.

Question 71

The MPN technique is rarely applied in the food industry because any microbial presence in food is unsafe.

Question 72

Propose an experiment to identify members capable of assimilating monomers of lignin within a microbial community.

Question 73

A study of the human gut performed in 1982 used various types of plates under different growth conditions to describe and enumerate the microbes in the human gut.They concluded that the majority of the microbes in the human gut are Gammaproteobacteria.A study conducted in 2010 using next-generation sequencing to characterize 16S rRNA sequences concluded that the majority of the microbes in the human gut are Firmicutes and Bacteriodetes.Why did these studies have different conclusions? Which study do you think is most accurate?

Question 74

Combined with autofluoresence or fluorescent DNA probes,flow cytometry can separate or count populations of cells from aquatic environments.

Question 75

The diversity of microorganisms in culture collections is representative of the diversity of microorganisms found in nature.

Question 76

DGGE and T-RFLP are both molecular microbial ecology methods that use the polymerase chain reaction to amplify specific genes to assess diversity.

Question 77

In natural samples it is often difficult to differentiate live cells from dead cells or cells from nonliving matter.

Question 78

How can NanoSIMS be used to determine which Roseobacters most strongly use DMSP as a sulfur source within a coastal marine environment? Explain the NanoSIMS methodology in your answer.

Question 79

Several fluorogenic dyes can be used simultaneously in a sample as long as they each emit light at a different measurable wavelength.

Question 80

Using specific examples,when is it appropriate to use CARD-FISH rather than the traditional FISH method and vice-versa?