Microbial Ecology
Midterm Exam
Course Introduction
Microbial Ecology explores the interactions of microorganisms with each other, their environments, and host organisms. The course covers the diversity, physiology, and metabolic capabilities of bacteria, archaea, fungi, and viruses in various natural and artificial ecosystems. Students will learn about microbial roles in nutrient cycling, biodegradation, pathogenesis, and symbiosis, as well as approaches to studying microbial communities, such as molecular and culture-based techniques. The course emphasizes the ecological significance of microbes in soil, water, extreme environments, and within host organisms, highlighting their impact on global processes and human health.
Recommended Textbook
Microbiology An Evolving Science 4th Edition by John W. Foster
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Page 2
Chapter 1: Microbial Life: Origin and Discovery
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Q1) You have isolated a bacterium that you believe to be the causative agent of a new disease in frogs. How would you test the third of Koch's postulates?
A) Determine the shape of the bacterial cells.
B) Inject the bacteria into a healthy frog.
C) Isolate the bacterium from a sick frog.
D) Show that the bacterium is not present in healthy frogs.
E) Grow a pure culture of the bacterium outside the frog.
Answer: B
Q2) Carl Woese's discovery replaced the classification scheme of five kingdoms with a scheme of three
A) phyla.
B) domains.
C) classes.
D) orders.
E) genera.
Answer: B
Q3) How are prokaryotes and eukaryotes different?
Answer: A prokaryote lacks a nucleus and membrane-bounded organelles, whereas a eukaryote has a nucleus and membrane-bounded organelles.
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Chapter 2: Observing the Microbial Cell
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Q1) Most electron micrographs in microbiology textbooks are in color. Is this normal for an electron micrograph? Why or why not?
Answer: Electron micrographs are not naturally colored, as color is defined by visible light, not electrons. The original image is produced when the electrons bombard a fluorescent screen. The resultant image is processed by a computer to appear as black and white with intensities in the entire range of grays in between. These images are later colorized using computer software (like Photoshop) to improve the aesthetics and provide additional information.
Q2) Give a few reasons why living organisms may not be observed by transmission electron microscopy (TEM) or scanning electron microscopy (SEM).
Answer: In TEM, the specimens are fixed and embedded into a polymer for sectioning. The specimen is then stained with heavy metal to increase contrast. In SEM, the entire organism is shadowed with heavy metal prior to observation. Most importantly, however, the entire optical column of the EM must be maintained under vacuum, and an electron beam would quickly destroy a living specimen.
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Chapter 3: Cell Structure and Function
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Q1) Specific membrane components, particularly ________, determine which substances are transported across the membrane.
A) phospholipids
B) proteins
C) ions
D) polysaccharides
E) leaflets
Answer: B
Q2) Describe any two roles for membrane proteins.
Answer: Answers can include any of the following: membrane proteins are involved in transport of ions and nutrients across the membrane. They provide structural support for the cell by connecting different layers of the cell envelope or anchoring structures that extend from the cell, such as flagella. They also sense external signals such as presence of nutrients or toxins. They are involved in secretion of toxins, proteins, and molecules for communication.
Q3) Describe the types of molecules that can move through a membrane via passive diffusion.
Answer: Small uncharged molecules such as water, oxygen, and carbon dioxide can move through a membrane via passive diffusion.
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Page 5
Chapter 4: Bacterial Culture, Growth, and Development
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Q1) Which of the following prokaryotic transport systems does NOT require the use of cellular energy to bring compounds into the cells?
A) facilitated diffusion
B) ABC transport
C) siderophores
D) group translocation
E) endocytosis
Q2) The time between inoculation and the beginning of growth is usually called the ________ phase.
A) lag
B) early log
C) late log
D) stationary
E) death
Q3) What are some specific problems that biofilms can cause in the medical field, and why are they so difficult to prevent and destroy?
Q4) How does Anabaena overcome the challenge of performing both photosynthesis and nitrogen fixation?
Q5) Discuss some disadvantages of viable counts of microorganisms.
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Chapter 5: Environmental Influences and Control of
Microbial Growth
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Q1) Which of the following have evolved to grow in conditions extremely different from those optimal for humans?
A) psychrophiles
B) extremophiles
C) halophiles
D) thermophiles
E) acidophiles
Q2) If a disinfectant is added to a culture containing 1 * 10 CFU per milliliter and the D-value of the disinfectant is 2 minutes, how many viable cells are left after 4 minutes of exposure?
Q3) Halophiles require high salt concentrations to survive. Describe a mechanism involving compatible solutes that has evolved to achieve low internal sodium ion concentrations.
Q4) Describe three mechanisms organisms use to reduce osmotic stress.
Q5) Why are many barophiles also psychrophiles, and how are the adaptations for barophiles and psychrophiles similar?
Q6) How does pH affect proteins? Why do proteins have an optimum, minimum, and maximum pH at which they will function?
Q7) Briefly describe three techniques used to culture anaerobes in the laboratory.
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Chapter 6: Viruses
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Q1) Who was distinguished for modifying tissue culture procedure for plaque assays?
A) David Baltimore
B) Renato Dulbecco
C) Xinzheng Zhang
D) Paulo Verardi
E) Howard Temin
Q2) In contrast to animal viruses and bacteriophages, plant viruses infect cells by mechanisms that do NOT involve specific
A) receptors.
B) membranes.
C) envelopes.
D) vectors.
E) hosts.
Q3) The proteins found in animals and plants that can recognize general signs of viral infections are
A) RNA interference.
B) interferons.
C) T-lymphocytes.
D) surface receptors.
E) antibodies.
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Chapter 7: Genomes and Chromosomes
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Q1) Which of the following is a process that involves cell-to-cell contact to move a plasmid from a donor cell to a recipient cell?
A) transformation
B) lysogeny
C) generalized transduction
D) conjugation
E) lysis
Q2) Bacterial type II topoisomerases are the targets of antibiotics such as ________, which has been used to treat ________.
A) ampicillin; urinary tract infections
B) rifamycin; bacterial meningitis
C) tetracycline; Lyme disease
D) ciprofloxacin; anthrax pneumonia
E) streyptomycin; tuberculosis
Q3) What is horizontal gene transfer and how does it differ from vertical gene transfer? Is horizontal gene transfer limited to bacteria and archaea?
Q4) Describe the role of the two RNA polymerases that are involved in the early stages of bacterial DNA replication.
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Chapter 8: Transcription, Translation, and Bioinformatics
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Q1) A researcher is studying transcription and has added a chemical to a transcription experiment using both E. coli and mammalian cells. This chemical inhibits both systems. The chemical is most likely
A) streptomycin.
B) rifamycin.
C) erythromycin.
D) rifampin.
E) actinomycin D.
Q2) Which of the following is NOT an example of a heat-shock protein?
A) trigger factor
B) GroES
C) GroEL
D) Clp protease
E) DnaK
Q3) A variety of online software tools are available to aid with analyzing DNA and protein sequences. Name any three and explain what they can be used for.
Q4) What are the functions of the different types of RNA molecules?
Q5) How do sigma factors in a bacterium such as E. coli regulate major physiological responses?
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Chapter 9: Gene Transfer, Mutations, and Genome
Evolution
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Q1) Mutations that occur even in the absence of an added mutagen are known as ________ mutations.
A) spontaneous
B) silent
C) missense
D) nonsense
E) frameshift
Q2) The following statements about superfamily proteins are true EXCEPT that
A) ABC (ATP-binding cassette) transporters serve as an example.
B) proteins with structural and functional similarity but low sequence homology may be considered superfamilies.
C) superfamily proteins are encoded by genes found on superfamily islands.
D) superfamily proteins are encoded by genes that have been duplicates and then mutated.
E) proteins such as HSP70 that are found in all domains of life are examples.
Q3) Distinguish between generalized and specialized transduction.
Q4) Describe two processes that may happen during the evolution toward pathogenicity.
Q5) Describe the purpose of an Ames revision test and how it is performed.
Q6) Describe the process whereby DNA is transferred from Agrobacterium to plants. Page 11
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Chapter 10: Molecular Regulation
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Q1) One benefit of operons in bacteria is that they
A) allow for alterations in DNA sequence by flipping promoters around.
B) allow for coordinated gene expression of related genes on one mRNA controlled by one promoter.
C) do not need ligands and regulatory proteins as single genes would.
D) do not need any modification of the proteins after they are expressed.
E) allow for the bacteria to utilize a wide variety of carbon sources.
Q2) Phase variation in Salmonella enterica involves A) gene inversion.
B) chemotaxis.
C) outer membrane proteins.
D) sRNA.
E) slipped-strand mispairing.
Q3) Explain the process of attenuation in regulating transcription of the tryptophan operon.
Q4) What is diauxic growth and why does it occur?
Q5) How is sigma H degradation controlled by temperature, and why is this important to the cell?
Q6) Explain how small, untranslated RNAs (sRNAs) regulate iron uptake and iron storage.
Page 13
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Chapter 11: Viral Molecular Biology
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Q1) Why do highly virulent strains of the influenza virus appear periodically? Give one example.
Q2) The causative agent of chickenpox is
A) herpes simplex virus 1.
B) herpes simplex virus 2.
C) varicella-zoster virus.
D) Epstein-Barr virus.
E) HIV.
Q3) How many genomes does an HIV particle have and what is their biochemical nature?
A) two RNA molecules
B) eight RNA molecules
C) a DNA/RNA hybrid
D) a single RNA molecule
E) a DNA molecule and a noncomplementary RNA molecule
Q4) The pol open reading frame of HIV encodes
A) reverse transcriptase.
B) integrase.
C) protease.
D) gyrase.
E) ligase.
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Chapter 12: Biotechniques and Synthetic Biology
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Q1) Potential applications of bacterial oscillator switches include all of the following EXCEPT the
A) study of controlled interactions between two feedback genetic loops.
B) design of bacterial genetic circuits to detect toxins.
C) design of bacterial clocks.
D) reduction of noise in biological circuits.
E) reactivity to concentrations of specific molecules such as arabinose.
Q2) The replacement of the genome of Mycoplasma capricolum with the modified genome of M. mycoides is considered to be a significant accomplishment because it
A) demonstrates that genetic manipulation of recalcitrant organisms is impossible.
B) opens the possibility to redesign prokaryotic genomic systems.
C) enables gene editing of species.
D) merges the genomes into a hybrid.
E) creates a riboswitch board.
Q3) What is synthetic biology? Provide an example of its potential applications.
Q4) How can a protein be detected on a western blot?
Q5) Briefly explain how real-time polymerase chain reaction (PCR) works.
Q6) Describe the whole-genome DNA-binding analysis using ChIP-on-chip technology.
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Chapter 13: Energetics and Catabolism
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Q1) Escherichia coli degrades human waste in the colon using mixed-acid fermentation. Why is this a factor of concern in some medical procedures, such as colonoscopy?
Q2) Some bacteria in the human gut microbiota primarily feed on glucose derivatives from mucus secretions. Which of the following is NOT correct with respect to "mucus farming" by bacteria?
A) Bacteroides thetaiotaomicron and other bacteria induce the colon to produce mucus.
B) Mucus-derived sugar acids are metabolized via the Entner-Doudoroff pathway.
C) Sugar acids must be converted to 6-phosphogluconate in order to enter the Entner-Doudoroff pathway.
D) The glucose derivatives are converted to glucose and degraded via the Embden-Meyerhof-Parnas pathway.
E) This metabolism has been studied via genomics and genetic studies.
Q3) Treponema pallidum, the causative agent of syphilis, was shown to be lacking a TCA cycle. Explain the significance of this finding.
Q4) Define the human metagenome. Describe an example to demonstrate the importance of the metagenome.
Q5) Define "organotroph" and "heterotroph." Are these terms equivalent?
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Page 16
Chapter 14: Electron Flow in Organotrophy, Lithotrophy, and Phototrophy
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Q1) In cytochromes, the heme group plays a key role in acquiring and transferring electrons with a(n) __________ transition.
A) Mg0/Mg2+
B) S0/S2-
C) Cu+/Cu2+
D) Fe3+/Fe2+
E) Mn0/MN +
Q2) The reduction of U to U by Geobacter metallireducens is an example of A) assimilatory metal reduction.
B) fermentation.
C) dissimilatory metal reduction.
D) organotrophy.
E) lithotrophy.
Q3) In anaerobic soils, some yeasts and filamentous fungi can reduce nitrate to nitrite and nitrite to
A) ammonia (NH3).
B) nitric oxide (NO).
C) urea.
D) nitrogen gas (N ).
E) ammonium hydroxide (NH4OH).
Page 17
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Chapter 15: Biosynthesis
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Q1) Describe how modular enzymes function in polyketide biosynthesis. Why might this be of use medically?
Q2) The Calvin cycle is essentially
A) started by the oxygen capture by Rubisco.
B) a reductive pentose phosphate cycle.
C) the reductive, or reverse, tricarboxylic acid cycle.
D) a pathway to synthesize fatty acids but not sugars.
E) a pathway that is used only when light is present.
Q3) Two strains of E. coli were developed, each of which overproduced an amino acid, either histidine or tryptophan. When grown together in medium with adequate amino acids, they grew but did not associate with each other. When these strains were grown together in medium without histidine and tryptophan, they grew and formed ________ in order to ________.
A) carboxysomes; share the excess of the two amino acids
B) carboxysomes; provide ATP to each other to make the missing amino acids
C) nanotubes; share the excess of the two amino acids
D) nanotubes; provide ATP to each other to make the missing amino acids
E) heterocysts; share the excess of the two amino acids
Q4) How is fatty acid biosynthesis regulated in bacteria?
Q5) How do ammonium and oxygen regulate the expression of nitrogen fixation genes?
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Chapter 16: Food and Industrial Microbiology
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Q1) Which of the following is NOT an example of a microbial enzyme used in industrial or commercial applications?
A) cellulase-improvement of fabric's appearance
B) asparaginase-avoidance of acrylamide production
C) rennin-cheese production
D) lipase B-active in a wide range of temperatures
E) protease-removal of food stains on clothes
Q2) Bacteria generally can't be eaten as isolated organisms. Why is Spirulina an exception? What is Spirulina and what are its health benefits?
Q3) An attribute of an industrial microbial strain is
A) genetic stability and manipulation.
B) expensive growth requirements.
C) a low level of product expression.
D) pathogenic strains.
E) the cell is not easily breakable to liberate product.
Q4) Describe how the transportation of milk products by herders led to the formation of cheeses.
Q5) What categories of foods may be spoiled by psychrotrophs? Why are these organisms a problem with fish?
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Chapter 17: Origins and Evolution
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Q1) Rhizobial bacteroids and their plant hosts have evolved to have what type of symbiotic relationship?
A) mutualistic
B) parasitic
C) commensal
D) ammensal
E) predatory
Q2) Based on small subunit rRNA phylogeny studies, the current view is that there are ________ domains of life.
A) two
B) three
C) four
D) five
E) six
Q3) Describe the intracellular endosymbiosis between algae of the genus Chlorella and Paramecium. Why is this symbiosis considered reversible?
Q4) Discuss what horizontal gene transfer is. How does it occur and how might it obscure phylogenetic relationships among taxa?
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Page 20
Chapter 18: Bacterial Diversity
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Q1) Which genus within the spirochetes includes the causative agent of Lyme disease?
A) Treponema
B) Holandina
C) Leptospira
D) Borrelia
E) Spirochaeta
Q2) In order to learn what makes proteins stable in thermophilic bacteria, how should the amino acids or motifs that are involved in conferring thermostability to proteins be explored?
Q3) Which of the following is an extremophile?
A) Bacillus alkalophilus
B) Bacillus thuringiensis
C) Bacillus subtilis
D) Clostridium botulinum
E) Clostridium tetani
Q4) How do Bacteroides fragilis and B. thetaiotaomicron contribute to 15% of human caloric intake? Are there other benefits provided by these microbes to human health? Are they potentially pathogenic?
Q5) Describe the photosynthetic machinery of cyanobacteria.
Q6) Describe the metabolic characteristics of Chlorobium species.
Page 21
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Chapter 19: Archaeal Diversity
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Q1) Nitrosopumilus maritimus is able to oxidize
A) nitrate.
B) ammonia.
C) sulfide.
D) sulfate.
E) methane.
Q2) Which of the following is unique to archaea?
A) pseudopeptidoglycan
B) S-layers
C) supercoiled DNA
D) infection by double-stranded DNA viruses
E) methanotrophs
Q3) The Sulfolobales includes species that respire by oxidizing A) sulfate.
B) carbon dioxide.
C) ammonia.
D) methane.
E) sulfur.
Q4) Describe the physiological adaptations found in haloarchaea that compensate for the high internal potassium chloride concentrations.
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Chapter 20: Eukaryotic Diversity
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Q1) What are protists? What is the current status of the classification of protists? What is the difference between protozoa and protists?
Q2) What are choanoflagellates and what is their importance in evolutionary studies?
Q3) Which of the following statements regarding pseudopods is NOT correct?
A) The term "pseudopods" means "false feet."
B) Amoebozoa have lobe-shaped pseudopods.
C) Lamellar pseudopods of amebas are similar to those generated by human leukocytes.
D) Needlelike pseudopods are thin extensions reinforced by myosin polymers.
E) The tip of a pseudopod contains a gel of polymerized actin beneath its cell membrane.
Q4) One of the smallest eukaryotes recently discovered, the green alga Ostreococcus tauri, measures less than ________ across and its genome (8 Mb) is ________ the size of that of Escherichia coli.
A) 2 mm; barely twice
B) 500 nm; half
C) 10 mm; about
D) 1 mm; three times
E) 100 mm; five times
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Chapter 21: Microbial Ecology
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Q1) Which step is NOT common for metagenomic processing and analysis?
A) FISH
B) binning
C) functional annotation
D) contig assembly
E) scaffold assembly
Q2) Name two factors that differentiate aquatic and terrestrial ecosystems and explain how they affect food cycles in these systems.
Q3) The depth of the photic zone at 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.
Q4) The net biomass of a population does not indicate productivity within an ecosystem. Explain.
Q5) Compare and contrast the photic zones of freshwater lake and pelagic ecosystems.
Q6) Describe the initiation process for legume-rhizobium symbiosis.
Q7) Propose a method to measure biomass production in terms of DNA synthesis. What are the limitations?
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Chapter 22: Microbes in Global Elemental Cycles
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Q1) In the marine photic zone, the rate of photosynthesis
A) is equal to the amount of CO released from the niche.
B) exceeds the rate of respiration.
C) is less than the respiration rate.
D) does not affect carbon cycling.
E) is inversely related to rate of respiration.
Q2) During wastewater treatment, the secondary treatment requires continual aeration to
A) suppress microbial growth.
B) select for anaerobic heterotrophs.
C) stimulate abiotic degradation.
D) increase microaerophilic filamentous bacteria.
E) maximize breakdown of molecules to CO and nitrates.
Q3) Which of the following is an anaerobic respiration reaction?
A) conversion of phosphine to phosphate
B) methanogenesis
C) photolysis of hydrogen sulfide to sulfur
D) precipitation of ferric iron with hydroxide
E) nitrogen fixation
Q4) Describe the difference between a source, sink, and reservoir of an element.
Page 25
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Chapter 23: Human Microbiota and Innate Immunity
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Q1) Which of the following types of cells are antigen-presenting cells?
A) only eosinophils
B) platelets and macrophages
C) only macrophages
D) only neutrophils
E) macrophages and dendritic cells
Q2) Interferons are
A) antibacterial agents produced by skin, GI-tract, and lung cells.
B) secreted by eukaryotic cells in response to intracellular infection.
C) only produced by activated phagocytes.
D) host specific and virus specific.
E) able to block bacterial replication.
Q3) Much of the ________ is normally free from microbes in a healthy individual.
A) nose
B) mouth
C) skin
D) respiratory tract
E) genitourinary tract
Q4) Why is the alternative complement cascade not considered a part of adaptive immunity?
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Chapter 24: The Adaptive Immune Response
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Q1) A surgical patient infected with a blood-borne Staphylococcus would initially produce an anti-staphylococcal antibody of the IgM class. Why is that?
Q2) Why is type AB blood considered to be the "universal recipient"? Explain what this means in terms of the antigens and antibodies present in blood types.
Q3) If a person was unable to undergo negative selection during T-cell education, what is T-cell education, and why would this be a severe immune problem?
Q4) The difference between antibody allotypes and isotypes is that isotypes are ________ and allotypes are ________.
A) the differences in constant regions; differences within isotypes
B) differences within allotypes; the differences in constant regions
C) the differences in constant regions; alternations in the hypervariable regions
D) alternations in the hypervariable regions; differences within isotypes
E) alternations in the hypervariable regions of one person; alternations in the hypervariable regions among a species
Q5) Would taking probiotic health supplements be good for the average person's immunity?
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Chapter 25: Microbial Pathogenesis
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Q1) Briefly describe three classic modes of action of bacterial toxins. How are they similar? How are they different?
Q2) Which of the following protein secretory systems injects effector molecules directly from the bacterial cytoplasm into the host cytoplasm?
A) type I
B) type II
C) type III
D) type IV
E) types I, II, III, and IV
Q3) How does a pathogenicity island increase the "fitness" of a microorganism (pathogen) to interact with a host and cause disease?
Q4) What type of toxin is the alpha hemolysin of Staphylococcus aureus?
A) protein synthesis inhibitor
B) protease
C) superantigen
D) cell membrane disruptor
E) second messenger pathway disruptor
Q5) Define a fomite and give at least two specific examples.
Q6) Diphtheria toxin is a classic AB exotoxin. How does it cause host cell damage?
Page 28
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Chapter 26: Microbial Diseases
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Q1) What is the reservoir for Trichomonas vaginalis? Explain how it causes disease in the acidic vagina of females.
Q2) Why is antibiotic treatment NOT recommended for the enterohemorrhagic E. coli O157:H7, or EHEC?
Q3) Predict how a chest X-ray and blood counts differ for a fungal versus bacterial lung infection in children and adults.
Q4) Which of the following respiratory infections is caused by a viral pathogen?
A) diphtheria
B) whooping cough
C) tuberculosis
D) Legionnaires' disease
E) severe acute respiratory syndrome
Q5) Chlamydia employs ________ for spreading within and between hosts.
A) elementary body
B) rapidly replicating reticulate body
C) microspore
D) conidia
E) actin polymer
Q6) Describe the replication cycle of Chlamydia.
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Chapter 27: Antimicrobial Therapy
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Q1) The multidrug resistance, or MDR, efflux pumps found in organisms such as resistant strains of Escherichia coli work most similarly to A) ABC transporters.
B) facilitated diffusion.
C) reverse osmosis.
D) electron transport.
E) phospholipid flip-flop.
Q2) Why is it that the organism that produces penicillin, Penicillin notatum, is not affected by the production of this molecule, but Staphylococcus aureus is? Of what benefit is the antibiotic in the organism that created it?
Q3) The antiviral nucleoside inhibitor zidovudine, used in treating HIV infection, works by A) fooling reverse transcriptase to incorporate it, causing a chain termination reaction.
B) disabling protease and preventing HIV protein folding.
C) blocking gag and pol genes from transcription.
D) binding directly to reverse transcriptase and allosterically inactivating the enzyme.
E) sterically hindering integrase from cutting into the host nuclear DNA.
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Chapter 28: Clinical Microbiology and Epidemiology
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Sample Questions
Q1) A hemolysis reaction (on a blood agar plate) with an unidentified colony that results in a green zone due to oxidized iron in nonlysed red blood cells would be called
A) beta-hemolytic.
B) nonhemolytic.
C) gamma-hemolytic.
D) alpha-hemolytic.
E) epsilon-hemolytic.
Q2) The following are all concerns of the influence of global climate change on infectious diseases EXCEPT that
A) global climate change will increase the incidence of antibiotic resistance.
B) the habitat of insect vectors increases in size as temperatures rise.
C) extending ranges of vectors may bring them in contact with new hosts.
D) climate change may bring more flooding, thus increasing the spread of gastrointestinal illness.
E) infectious disease cycles may speed up or extend through longer portions of the year.
Q3) Compare and contrast the dichotomous key approach to bacterial determination with the seven-digit-number approach when using the API strip system.
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