Deck 21: Microbial Ecology

Question 1

The availability of oxygen and other electron acceptors is the most important determinant of the types of metabolism in a habitat. Which of the following is NOT true about anaerobic environments?

A) They have slower rates of assimilation compared to aerobic habitats.
B) Their rates of dissimilation are slower compared to aerobic environments.
C) Microbes sometimes use minerals such as NO to oxidize organic compounds.
D) Anaerobic microbial communities far exceed that of the oxygenated biosphere.
E) Respiration of organic compounds is highly dissimilatory, reducing them to CO₂.

Answer 1

E

Question 2

The relationship among endosymbiotic microbes in the termite gut that results in complex metabolic fluxes with a negative $\bigotimes$ G, and that would NOT happen for individual members, is called:

A) mutualism
B) parasitism
C) exothermic association
D) predation
E) syntrophy

Answer 2

syntrophy

Question 3

The term "metagenome" was coined by Jo Handelsman and colleagues in 1998 to refer to:

A) shotgun cloning
B) screening of libraries for expression of genes
C) the sum of all genomes from a community
D) the sum of all genomes from a colony
E) all uncultured organisms from a community

Answer 3

C

Question 4

Synechococcus, a cyanobacterium, is a free-living marine organism that fixes CO₂ into biomass while producing molecular oxygen utilized by swarms of heterotrophic bacteria. Its biomass provides food for protists and predators. What is the niche of this organism?

A) phototroph in the open ocean
B) base of the food chain
C) nitrogen assimilation for the ocean environment
D) all of the above
E) none of the above

Question 5

Which of the following is NOT true regarding food webs in ecosystems?

A) primary producers assimilate minerals into biomass
B) primary producers absorb energy from outside the ecosystem
C) grazers convert 10% of carbon back to carbon dioxide
D) consumers convert 90% of biomass carbon to atmospheric CO₂
E) all biomass is recycled and eventually converted to heat

Question 6

Cryptogamic "soils" are found in dry, hot deserts. Which of the following is NOT true of cryptogamic crusts?

A) They develop very slowly.
B) They are made of lichens, mosses, and other algae and fungi.
C) They are quite resilient and not easily killed.
D) They play a vital role in protecting seeds for germination.
E) They help to prevent erosion in desert ecosystems.

Question 7

Metagenomics is one of the newer techniques in microbial ecology. It is useful for obtaining data regarding:

A) diversity of microbes within habitats and over time
B) metabolic flux through trophic levels
C) interactions among organisms
D) community gene expression and function
E) ultrastructure of newly discovered bacteria

Question 8

Synechococcus, a cyanobacterium, is a free-living marine organism that fixes CO₂ into biomass while producing molecular oxygen utilized by swarms of heterotrophic bacteria. Which of the following is the most likely habitat of this bacterium?

A) euphotic zone of the pelagic environment
B) the benthos
C) the littoral zone
D) lake sediments
E) aphotic zone

Question 9

Lichens consist of an intimate mutualistic symbiosis between a fungus, an alga, and/or cyanobacteria. What is the primary role of the cyanobacteria in this association?

A) protection of the symbionts
B) production of photosynthate
C) decomposition of toxic compounds
D) recycling of waste products
E) degradation of lignin

Question 10

The Dutch microbiologist Van Niel first demonstrated anoxygenic photosynthesis in soil and water bacteria. He generalized his work by hypothesizing:

A) every molecule in nature can be used as a source of carbon or energy by some microorganism
B) photosynthesis results in oxygen production
C) microbes are found in every environment on Earth
D) both A and B
E) both A and C

Question 11

Various populations of species in their habitats or environment are best described as a(n):

A) niche
B) ecosystem
C) biosphere
D) biomass
E) microbial environment

Question 12

Which of the following is true about lichens in the boreal forests?

A) They cover the majority of the ground.
B) They are a major food source for caribou in the winter.
C) They contain fungi and a photoautotrophic partner.
D) They form part of crytobiotic soil.
E) All of the above.

Question 13

In wetlands, Beggiatoa bacteria oxidize H₂S for energy. Removal of H₂S enables growth of other microbes for which H₂S is toxic. However, Beggiatoa derives no benefit from these microbes. This interaction is an example of:

A) syntrophy
B) mutualism
C) commensalism
D) amensalism
E) synergism

Question 14

What does annotation in metagenomic analysis involve?

A) determining the number of species in the sample
B) calculating the %G+C in the metagenome
C) finding homologs and recurring peptide motifs that infer the function of the sequence
D) making contigs and scaffolds and assembling the sequence
E) analyzing the RNA sequences to see what was transcribed

Question 15

What is a rarefaction curve?

A) the number of sequences generated from a metagenome
B) the number of SSU rRNA sequences in a metagenome
C) the number of SSU rRNA sequences identified as species in a metagenome
D) the number of OTUs from all combined genes in a metagenome
E) none of the above

Question 16

Which of the following are major consumers of the bulk of biomass in the ocean?

A) multicellular organisms
B) fish and tube worms
C) protists and viruses
D) heterotrophic bacteria
E) fungi

Question 17

Climatic changes that adversely impact planktonic phototropic bacteria in the oceans will directly alter the function of which trophic level(s)?

A) the largest biomass producers
B) marine invertebrates
C) the protist grazers
D) the predators
E) marine consumers

Question 18

Which of the following is NOT part of the cryptogamic crust community?

A) heterotrophic bacteria
B) mosses
C) lichens
D) nonlichenous algae
E) nonlichenous fungi

Question 19

The oceans cover __________ of the Earth's surface.

A) 25%
B) more than two-thirds
C) more than 90%
D) about 10%
E) 50%

Question 20

The algal and fungal interaction within a lichen would best be described as:

A) mutualism
B) synergism
C) commensalism
D) amensalism
E) parasitism

Question 21

Which of the following is responsible for the characteristic odor of soil?

A) Vibrio sp.
B) Bacillus sp.
C) Streptomyces sp.
D) Staphylococcus sp.
E) Pseudomonas sp.

Question 22

Which category has the largest microbes?

A) viruses
B) femtoplankton
C) picoplankton
D) nanoplankton
E) microplankton

Question 23

The __________ region of an oligotrophic lake extends to about 10 meters below the surface.

A) neutron
B) benthic
C) epilimnion
D) hypolimnion
E) none of the above

Question 24

All planktonic microbes are:

A) motile
B) smaller than 200 $\mu$ m in size
C) prokaryotes
D) primary producers
E) unicellular

Question 25

A graduate student filtered a liter of seawater using a Millipore filter membrane of 2 $\mu$ m pore size. Which of the following is true about her filtrate?

A) It is sterile.
B) Microplanktons are present.
C) It contains picoplanktons.
D) It contains nanoplanktons.
E) None of the above.

Question 26

Lakes that have low concentrations of organic nutrients are termed:

A) eutrophic
B) syntrophic
C) aphotic
D) oligotrophic
E) atrophic

Question 27

The high biological oxygen demand that accompanies algal bloom in eutrophic lakes increases the span of the __________ zone.

A) oxygenic epilimnion
B) anoxic hypolimnion
C) coastal shelf
D) anoxic benthic
E) oxygenic neuston

Question 28

All of the following may be found among the benthic microbes EXCEPT:

A) barophiles
B) psychrophiles
C) thermophiles
D) phototrophs
E) methanogens

Question 29

Which class of extremophile would you expect to find within rock crystals down to a depth of 3 km?

A) acidophile
B) barophile
C) endolith
D) halophile
E) oligotroph

Question 30

Which region of marine habitat refers to the microscopic interface between water and air?

A) pelagic zone
B) neuston
C) euphotic zone
D) aphotic zone
E) benthic zone

Question 31

Lithotrophic bacteria found in between crystals of solid bedrock as deep as 3 km below Earth's surface are specifically called:

A) endophytes
B) symbionts
C) endoliths
D) decomposers
E) saprophytes

Question 32

Which of the following refers to the oxygenated zone of a lake?

A) neuston
B) epilimnion
C) thermocline
D) hypolimnion
E) benthos

Question 33

The vast majority of microbes in the ocean are:

A) psychrophiles
B) thermophiles
C) mesophiles
D) acidophiles
E) osmophiles

Question 34

The best description for the microbial communities in the cold-seep ecosystem is:

A) thermophilic
B) psychrotrophic
C) barophilic thermophiles
D) barophilic psychrophiles
E) barophilic psychrotrophs

Question 35

Compared to eutrophic lakes, the biochemical oxygen demand, or BOD, of oligotrophic lakes is:

A) low
B) similar
C) high
D) unpredictable
E) extremely high

Question 36

Which of the following plays an important role in keeping the water column clear enough for the penetration of light?

A) algae
B) bacteria
C) fish
D) invertebrates
E) viruses

Question 37

Which of the following techniques is most appropriate for rapid detection and differentiation of specific classes of microbes in a drop of seawater?

A) metagenomics
B) viable plate count
C) DNA and RNA sequencing
D) fluorescent microscopy
E) radiography

Question 38

The salt concentration of marine water is about 3.5%. Which of the following is NOT a major ion in seawater?

A) Na+
B) Cl^-
C) SO₄^2-
D) Cu²⁺
E) I^-

Question 39

Eutrophic lakes typically support ten times the microbial concentrations of an oligotrophic lake. Which of the following statements is NOT true of eutrophic lakes?

A) Biochemical oxygen demand is high.
B) Population of consumer aquatic animals is high.
C) Nitrogen and phosphorous levels are usually high.
D) Photosynthetic activities are altered.
E) Algal bloom is a common characteristic.

Question 40

The depth of the photic zone in the coastal shelf of marine habitats is:

A) 100-200 m
B) 10-20 m
C) about 1 m
D) about 0.1 m
E) about 2 m

Question 41

Explain at least three ways in which metagenomes may miss organisms in the environment.

Question 42

You make two different kinds of metagenomes-one to measure diversity from only 16S rRNA DNA sequences, and one from the entire DNA that does not require amplification. You observe 1,000 times more 16S rRNA gene sequences from the first metagenome than the second. However, you find that the number of species according to the 16S rRNA gene sequences is 10 times more in the second metagenome than the first. Why?

Question 43

How do microbes live if their metabolic process to generate energy has a positive $\Delta$ G?

Question 44

What two factors most differentiate aquatic and terrestrial ecosystems? Why?

Question 45

In the Legume-Rhizobium symbiosis, nitrogen fixation is carried out in nodules by:

A) bacteroids that lack a cell wall
B) intact rhizobia in the plant cortex
C) plant cells in the presence of symbiotic bacteria
D) bacteroids in oxygen-rich nodules
E) photosynthetic bacteroids in plants

Question 46

Which of the following do NOT require endosymbiotic bacteria to digest plant material such as cellulose?

A) termites
B) cattle
C) gorillas
D) humans
E) all of the above require endosymbiotic bacteria

Question 47

As much as 90% of forest trees require mycorrhizae for growth, suggesting that:

A) forest soils are rich in phosphorous
B) mycorrhizae are found everywhere
C) the plant-mycorrhizal association is ammensalic
D) mycorrhizae significantly increase the uptake of nutrients
E) forest trees do not have deep roots

Question 48

In which of the following ways do rhizosphere bacteria benefit their host plant?

A) degrade plant lignin
B) attract symbiotic nematodes
C) improve water uptake
D) produce large amounts of photosynthate
E) discourage growth of plant pathogens

Question 49

Fungi play a much larger and more significant role in the decomposition of terrestrial biomass than they do in marine ecosystems. Why?

A) Fungi do not thrive in a marine environment.
B) Fungi out-compete bacteria in terrestrial habitats.
C) Fungi can degrade lignin to form humus.
D) Fungi decompose leghemoglobin rapidly.
E) Fungi degrade human waste faster than bacteria.

Question 50

Which of the following organisms forms a specific mutualistic association with legumes?

A) rhizobia
B) agrobacteria
C) E. coli
D) morels
E) truffles

Question 51

Feeding cattle grain generates high rumen acidity, selecting for acid-resistant pathogens such as:

A) Sulfolobus sp.
B) E. coli O157:H7
C) Halobacterium NRC-1
D) fuselloviruses
E) Helicobacter pylori

Question 52

Ominovores or carnivores have different microbial communities than herbivores due to:

A) the presence of a cecum
B) the availability of branched-chain amino acids for cellulolytic bacterial metabolism
C) hindgut fermentation
D) both A and B
E) both B and C

Question 53

Describe the steps in sequencing a metagenome.

Question 54

One of the most important ecological roles of the Florida Everglades is that:

A) it is home to beautiful birds
B) it filters most of the water supply for Floridians
C) many bacteria reside in it
D) nutrients can easily be leached to the lakes
E) tourists come to see it in large numbers

Question 55

What percent of forest trees require mycorrhizae for growth?

A) 10%
B) 25%
C) 50%
D) 75%
E) 90%

Question 56

Bacteroids remain sequestered within a sac of plant-derived membrane known as the:

A) flavonoid
B) infection thread
C) Nod factor
D) nucleosome
E) symbiosome

Question 57

Lignin decomposition forms:

A) arbuscules
B) detritus
C) fruiting bodies
D) humus
E) rhizopus

Question 58

Vascular abuscular mycorrhizae (VAM) are an example of which of the following?

A) ectomycorrhizae
B) endomycorrhizae
C) free-living fungus
D) lignin decomposer
E) nitrogen fixer

Question 59

Which term represents the region of soil directly in contact with the root surface?

A) stele
B) cortex
C) root cap
D) rhizoplane
E) rhizosphere

Question 60

Explain the difference between assimilation and dissimilation.

Question 61

Compare and contrast the photic zones of pelagic and freshwater lake ecosystems.

Question 62

Explain how viruses select for increased diversity of microbial plankton in the oceans.

Question 63

What does it mean when one says that a particular fluorescent dye intercalates into DNA? Provide an example of how epifluorescence has been used.

Question 64

In any environment, pathogens are always outnumbered by a vast community of neutral or helpful microbes. Describe some beneficial as well as devastating incidences of plant pathogens.

Question 65

Define cryptogamic crust and explain its vital role in desert ecosystems.

Question 66

Describe haustorial parasitism.

Question 67

Define BOD, which can be used to measure the pollution level of lakes. Describe how effluents carrying high levels of nutrients can cause eutrophication.

Question 68

Why is it important to restrict the protein content of cattle feed?

Question 69

Explain how endoliths derive energy inside bedrock, where there is no sunlight.

Question 70

What is one major way that wetlands such as the Everglades benefit human communities?

Question 71

Describe the interaction of Vibrio cholerae with copepods. How can saris help decrease the incidence of cholera in Bangladesh?

Question 72

How can one measure biomass production in terms of DNA replication? What are the limitations?

Question 73

What is coral bleaching? What is its possible cause?

Question 74

Describe the technique pioneered by Robert Hungate of the University of California at Davis to study anaerobic microbiology of the rumen. What types of questions can be answered with this technique?

Question 75

Explain how the benthic interface between the ocean floor and water can act as a charged battery to generate electricity.

Question 76

What is responsible for the high species-species specificity of the Legume-Rhizobium symbiosis?

Question 77

The net biomass of a population does not indicate productivity within an ecosystem. Explain.

Question 78

What are endoliths, and what do they feed on inside rocks?

Question 79

How would a high cereal or grain diet for cattle affect the growth of pathogens like E. coli?