Deck 22: Methods in Microbial Ecology

Question 1

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

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

Answer 1

D

Question 2

Analyses of _ isotopes have been used as evidence against life on the Moon.

A) sulfur
B) carbon
C) hydrogen
D) oxygen

Answer 2

A

Question 3

In an agar dilution tube, microbial colonies grow

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

Answer 3

D

Question 4

The science of microbial ecology deals with

A) how microbial communities interact with each other.
B) microbial communities.
C) how microbial communities interact with their environment.
D) all of the above.

Question 5

The methodology of microbial ecology includes

A) gene isolation and characterization.
B) general and specific cell- staining methods.
C) enrichment and isolation.
D) all of the above.

Question 6

Which of the following fluorescent molecules does NOT kill microorganisms?

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

Question 7

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

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

Question 8

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

A) viability staining
B) enrichment techniques
C) fluorescent antibodies
D) fluorescent staining using DAPI

Question 9

When dealing with stable isotopes, enzymes tend to favor

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

Question 10

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

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

Question 11

Formalin at a concentration of is commonly used as a chemical sterilant in microbial ecology studies.

A) 6%
B) 4%
C) 8%
D) 2%

Question 12

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

A) quantitative
B) qualitative
C) both qualitative and quantitative
D) none of the above

Question 13

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

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

Question 14

Laser tweezers are used for

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

Question 15

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

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

Question 16

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

A) in situ.
B) in toto.
C) in vivo.
D) in vitro.

Question 17

What kind of polymerase is used in multiple displacement amplification (MDA) of a cell's genome?

A) RNA polymerase from a bacteriophage
B) DNA polymerase from an archaeon
C) RNA polymerase from an archaeon
D) DNA polymerase from a bacteriophage

Question 18

Winogradsky columns are used primarily for enrichment of

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

Question 19

What unit is isotopic decay reported as?

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

Question 20

The biggest limitation with the microscopic methods used in today's ecological studies is that they are unable to reveal

A) phylogenic diversity of the microorganisms in the habitat under study.
B) oxygen requirements related to the microbes' location in given samples.
C) cellular components of the smaller microbes because of the limits of magnification.
D) microbial interactions as found in nature.

Question 21

An international standard used as a carbon isotope standard is

A) Troilite.
B) V- SMOW.
C) atmospheric air.
D) PeeDee belmnite.

Question 22

Radioisotopes are useful when

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

Question 23

As a microbial examination technique, FISH stands for _ .

Question 24

In the T- RFLP method, only the digested amplicons are labeled with a that are detected.

Question 25

To trap a specific organism in a capillary tube when using laser tweezers, it is necessary to
.

Question 26

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

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

Question 27

The six measurements for which microelectrodes have been developed are ,
, , , , and .

Question 28

Two _ are hybridized to a complementary sequence in a target gene in PCR technology.

Question 29

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

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

Question 30

Culture independent approaches circumvent issues associated with .

Question 31

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

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

Question 32

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

Question 33

DGGE stands for .

Question 34

When laser tweezers are used, the laser beam traps .

Question 35

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

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

Question 36

Microarrays are useful for assessing

A) protein folding.
B) the presence of any DNA sequence.
C) gene expression.
D) the presence of specific rRNA sequences.

Question 37

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

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

Question 38

The term axenic is used to describe a(n)

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

Question 39

For what purpose would a microbial ecologist use a microelectrode?

A) to quantify cell concentration
B) to determine the concentration of NO3-
C) to quantify dissolved organic carbon
D) to determine energy potential of a solution

Question 40

Transcription of various genes can be studied using a reporter gene that encodes for
.

Question 41

The overall purpose of DGGE is to .

Question 42

Detection of 14CO2 from a community fed 14C- glucose suggests _.

Question 43

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

Question 44

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

Question 45

An artificial microbial ecosystem that serves as a long- term source of bacteria for enrichment cultures is called a(n) .

Question 46

Two elements that have proven the most useful for stable isotope studies are _ and
.

Question 47

FISH technology makes use of probes directed against , whereas environmental genomics studies the presence of certain .

Question 48

Robotic systems used to quickly test thousands of combinations of nutrients for growth of organisms capable of growth is an example of a(n) technology.

Question 49

The genus of the most abundant phototrophic organism on Earth is .

Question 50

The biodiversity metric depends on both and of organisms present within a community.

Question 51

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

Question 52

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

Question 53

Metatranscriptomics and metaproteomics involve studying the total community of
and , respectively. These are favored over metagenomics when
is of more interest than gene presence.

Question 54

Before detecting peptides in a metaproteome, the peptides must first be based on their chemical properties.

Question 55

An important consideration in enzymology and isotope probing involves the recognition that enzymes prefer metabolizing isotope substrates over _ isotope substrates.

Question 56

The 13C/12C isotopic ratio of geological rocks of different ages has been used as evidence for or against past biological activity, because the biological and geological origins of these two isotopes .

Question 57

ARISA is a favored method over T- RFLP when the phylogenetic marker of interest is the
.

Question 58

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

Question 59

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

Question 60

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

Question 61

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

Question 62

DGGE and T- RFLP are both powerful molecular microbial ecology methods that use multiple genes to look at diversity.

Question 63

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 64

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

Question 65

The goal of environmental genomics is to detect as many genes as possible and then if possible to determine to which phylogenetic groups(s) they belong.

Question 66

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

Question 67

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

Question 68

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

Question 69

Identify Martinus Beijerinck and explain his importance to microbiology.

Question 70

Organisms in culture are generally representative of those found in nature.

Question 71

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

Question 72

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 73

Describe the procedures involved in sequencing an individual cell's genome present in seawater.

Question 74

Due to the precise cell sorting capabilities of a flow cytometer, it can take several hours to sort 1 ml of ocean water.

Question 75

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

Question 76

FISH technology can employ only a single phylogenetic probe.

Question 77

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

Question 78

What prior knowledge is required to use a phylochip to study the abundances of the microbes present within a microbial community?

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

A purpose of the enrichment culture technique is to separate different organisms from the microbial community.