Microbiology HW Chapters 17-22

Order the events on the geologic timeline.

(Top to bottom: 4.0mya to 1.0 mya) 1. Oldest sedimentary rocks 2. Oldest stromatolites 3. Bacterial hopanoids 4. Colonial organisms 5. Filamentous cyanobacteria 6. Early eukaryotes 7. Early multicellular life

Please label the following image, which outlines the steps by which metagenomic data are obtained from an environment of interest.

(top to bottom) - Obtain sample from target community - Isolate DNA - Construct library for next-generation sequencing - Obtain sequence data - Assemble sequences into partial genomes

Alphaproteobacteria of the genus ______ cause the formation of galls on plants, such as the one seen here. But when free-living in the soil, these same bacteria are subject to predation by the intracellular parasite _______ (also a proteobacterium).

- Agrobacterium - Bdellovibrio

Which of the following approaches are useful for functional annotation after assembly of a partial genome?

- Comparing with previously sequenced metagenomes. - Searching for ORFs that have an upstream promoter and ribosome-binding site. - Searching for motifs characteristic of particular classes of proteins or enzymes.

While microfossils can be compelling evidence of early microbial life, its use has important limitations, including which of the following?

- Conclusions are based on largely subjective interpretations. - Some formations result from abiotic processes.

This illustration models gene flow, as it is believed to have occurred during evolution of E. coli and S. enterica. The black lines represent genes for products such as which of the following?

- RNA polymerase - ribosomal RNA - elongation factors

Many microorganisms, especially those in the Firmicutes phylum, are of great practical importance for industrial, commercial, and/or medical applications. As an example, which of the species listed here may help limit the spread and impact of the emerging Zika virus?

Bacillus thuringiensis

What kinds of information about the microbes can or cannot be deduced by metagenomic analysis?

Can Be Deduced: - growth temperature and pressure - metabolism - nutritional requirements - taxonomy Cannot Be Deduced: - growth rate - morphology (size and shape) - partner organisms - motility

Research conducted by Elizabeth Hansen and colleagues at Washington University in St. Louis, Missouri, suggests that the presence of methanogens in the gut depends on microorganisms of which genus?

Clostridium

How did the excess propane and benzene in the gulf waters lead to a bloom of Colwellia in the Gulf of Mexico during May and June of 2010?

Colwellia can catabolize propane and benzene. When those compounds were depleted, the numbers of Colwellia dropped accordingly.

Which of the following questions would require a metagenomics approach to answer?

- What percentage of organisms within a soil ecosystem possess lignin degradation genes? - Does sleep deprivation cause a shift in the ratio of various bacterial phyla in a human's intestine? - How do microbial communities of freshwater lakes differ from hypersaline ones?

The phylogenetic tree below shows a proposed relationship among various proteobacteria. The molecular clock assumes that a 5% sequence change is equivalent to 500 million years of evolution. Based on this clock, Buchnera seems to have split from the clade containing the intestinal bacteria and Sodalis glossinidius two billion years ago. Which of the following, if present, would suggest that this time may be an overestimate?

- a shorter generation time in Buchnera relative to the other species - an enhanced mutation rate in Buchnera relative to the other species

Which of the following represent mechanisms by which Proteobacteria generate a proton motive force for ATP synthesis?

- aerobic oxidation of H2S - light-driven proton pumps - anaerobic oxidation of glucose

When life first appeared around 3.5 billion years ago, the Earth's oceans were still a steamy 158ºF (70ºC). Which types of microbes may have contributed to Earth's cooling?

- chemoautotrophs - cyanobacteria - denitrifying bacteria

Which of the following symbionts may be found in lichens?

- cyanobacterium - alga - fungus

Emerging organisms are initially characterized by which process(es)?

- electron microscopy - DNA sequencing

Which of the following are considered requirements for the emergence of life?

- essential elements for organic molecules - liquid water - continual source of energy

Which of the following represent issues of great uncertainty regarding early Earth?

- role of methanogens and atmospheric methane - whether early life forms were thermophiles or psychrophiles - whether life evolved here or was of extraplanetary origin

Probabilistic and dichotomous keys for microbial identification would not be used in situations where:

- time is of the essence. - the organism is uncultured.

Which of the following traits of bacterial cells differ significantly from the other domains of life?

- type of RNA polymerase - translation elongation factors - peptidoglycan in cell envelope

Organize the taxonomic ranks used to classify the species E. coli, in order of descending rank.

1. (higher) bacteria 2. Proteobacteria 3. Gammaproteobacteria 4. Enterobacteriales 5. Enterobacteriaceae 6. Escherichia

Based on the flow cytometry data shown below, rank the following from low intracellular complexity to high.

1. (low complexity) Synechococcus 2. Picoeukaryotes 3. (high complexity) cryptophytes

Place the microbial types in order of where they grow in stromatolites, going from the ocean-facing exterior to the interior.

1. (ocean-exposed side) photosynthetic microbes 2. bacteria that photolyse H2S 3. (interior of stromatolite) sulfate-reducing microbes

Imagine you are designing a probe for fluorescent in situ hybridization (FISH) detection of Ruminococcus albus within a sample of ruminal contents. You have decided to target bases 1390-1404 of its 16S rRNA gene that has the nucloleotide sequence 5'-CCTGTGTTCTAACCG-3'. When conjugated to your chosen fluorophore, which of the sequences shown will produce the strongest signal?

5'-CGGTTAGAACACAGG-3'

Corals with multiple diverse species of Symbiodinium survive environmental stresses better than corals with only one or a few species. What best explains this pattern?

A greater variety of endosymbionts poses a greater likelihood that at least one can survive in the stressful environment.

Many synthetic polymers, such as polyester and plastics, persist in the environment because microorganisms naturally lack the pathways for their degradation. However, microbes can acquire the ability to break down these products. What is the most likely mechanism for how microbes evolve this ability?

A missense mutation in a catabolic gene for a related polymer changes its substrate specificity.

Given the extreme environment of the black smoker vent, how is information about the archaea living there gathered?

A special submersible device with a robotic arm retrieves samples.

Sort the features of genome structure into the correct category of organisms.

Archaea/Bacteria: - operons - circular chromosome - uninterrupted protein coding sequences Archaea/Eukaryotes: - histones - introns within tRNA gene sequences - TATA-binding protein Bacteria/Eukaryotes: - queusine

Members of the Actinobacteria often have unique patterns of cellular growth. Which of the following genera includes species that grow as irregularly shaped branched rods (as shown here) but are coccoid shaped when nutrient limited?

Arthrobacter

Please sort the following items as examples of either assimilatory or dissimilatory processes.

Assimilatory: - Photosynthesis - Chemoautotrophy - Nitrogen fixation Dissimilatory: - Decomposition - Nitrification - Aerobic respiration of organic compounds

The phylogenetic tree of Archaea currently describes four large groups: DPANN, Asgard, TACK, and Euryarchaeota. Match each group with its major characteristics.

DPANN: - deepest branching; likely to have reduced genomes that suggest symbiotic lifestyles Asgard: - found in deep-sea vents; possible ancestors of eukaryotes TACK: - diverse metabolism; hyperthermophiles and mesophiles Euryarchaeota: - diverse metabolism; includes halophiles and many methanogens

Which of the following statements is NOT true regarding the relationship of oxygen to microbial ecology?

In the absence of oxygen, prokaryotes are restricted to fermentation of organic substrates.

According to the graph above, which habitat's species diversity is best represented by the existing clone sequence library?

Indoor air-2

Once inside the host, how does Listeria evade phagocyte-mediated killing?

It uses a toxin to escape the phagosome.

Why are Lokiarchaeota believed to be the prokaryotic lineage most closely related to eukaryotes?

Lokiarchaeota encode certain proteins shared only by eukaryotes.

Which of the following represents a major challenge for accurately defining the phylogeny of Archaea?

Many archaeal genomes show evidence of extensive horizontal gene transfer.

Cyanobacteria provide important environmental functions such as generating oxygen and fixing inorganic carbon (CO2) and nitrogen (N2) into biomass. However, some species, primarily those of the genus _______ , produce toxic compounds that can contaminate water supplies for entire cities.

Microcystis

Imagine that a physician is treating a case of meningitis in a high school student. The responsible organism is proving difficult to culture, but preliminary DNA sequence analysis shows that it is a member of the Firmicutes phylum. The doctor confidently prescribes penicillin, and later vancomycin, neither of which result in any improvement in the patient's condition. Based on these results, the causative agent is most probably a species of ________ .

Mycoplasma

The production of _______ by cyanobacteria is believed to have resulted in one of Earth's earliest mass extinctions.

O2

Which of the following is true of both parasitism and amensalism?

One partner is harmed or suffers.

The first step in PCB degradation requires an unusual dechlorination reaction. Imagine that you are conducting a long-term study of a PCB-affected site and detect organisms capable of PCB dechlorination. This is intriguing because none had been detected at the same site 20 years earlier. What is the best explanation for your finding?

PCB dechlorinators were always present in very small (i.e., nondetectable) numbers but became selectively enriched over time.

How do Prochlorococcus cells survive in the presence of hydrogen peroxide without a catalase gene?

Prochlorococcus relies on other microbes in their habitat that do produce catalase.

What benefit does Prochlorococcus gain from losing its catalase gene?

Prochlorococcus saves energy by not producing the catalase enzyme.

Which Gram-negative phylum contains the most metabolic diversity of any phylum and the largest number of described species?

Proteobacteria

Which of the following is NOT a disease caused by spirochetes?

Rocky Mountain spotted fever

S-layer proteins replace the cell wall found in most bacteria in many extremophiles such as Sulfolobus. Other archaea, such as Methanothermus, have both a cell wall as well as a glycoprotein S-layer. In general, what is the function of the S-layer?

S-layers provide protection against osmotic stress.

How did scientists study the succession of microbes in the gulf of Mexico before and after the Deepwater Horizon blowout in 2010?

Scientists used metagenomic studies to identify 16S RNA gene sequences.

Which of the following is not true regarding the sensory rhodopsins I and II?

Sensory rhodopsin I directs the cell to swim toward blue light, and sensory rhodopsin II directs the cell to swim toward red/orange light.

Your text describes five phyla of Gram-negative bacteria that are only distantly related to the Proteobacteria. These deep-branching phyla have diverse lifestyles and habitats. Sort the phyla below according to whether they are associated with human health and disease, or whether they function primarily in nutrient cycling in the environment.

Soil and Water: - Chlorobi - Acidobacteria - Nitrospirae Humans: - Fusobacteria - Bacteroidetes

Imagine you are studying an ancient stromatolite-like formation which contains what appear to be microfossils. Intrigued, you conduct δ34S analysis on some pyrite (FeS) contained in the formation and find that the sample is depleted in 34S relative to 32S. This result provides good evidence for which of the following hypotheses?

Some bacteria in this ancient microbial mat used SO42- as a terminal electron acceptor in respiration.

Which of the following characteristics is not shared by both methanogens and bacteria?

Some methanogens have cell walls composed of peptidoglycan.

What characteristic of stromatolites accounts for their abundance in the fossil record as compared with fossils of individual microbes?

Stromatolites are easily fossilized because silicate grains (sand) are major components of the structures.

Place the characteristics of Crenarchaeota with the correct genus to which they belong.

Sulfolobus: - acidophile - O2 respiration on S0 Pyrodictium: - cannulae - anaerobic oxidation of H2 by S0 Desulfurococcus: - flagellated cocci - anaerobic S0 respiration All Three Genera: - S-layer - hyperthermophile

Match each description to its corresponding TACK clade.

Thaumarchaeota: - widespread; includes ammonia oxidizers and animal symbionts Bathyarchaeota: - widespread in temperate marine and soil environments; some methanogens Korarchaeota: - found only in hydrothermal vents and hot springs Crenarchaeota: - hyperthermo-philes, psychrophiles, acidophiles, and mesophiles

Corals and dinoflagellates of the genus Symbiodinium form a mutualism that is essential for the health of coral reefs. Coral bleaching is a process in which heat causes the mutualism between corals and their endosymbionts to fail. The endosymbionts are sensitive to high temperatures, so they weaken and are expelled from the corals. What does each partner gain by the relationship?

The Symbiodinium receive protection from predators, while the coral receives photosynthetic products.

Why do scientists think members of the DPANN group of archaea are likely obligate symbionts of other organisms?

The genomes of these archaea are much smaller than those of other archaea.

In 2001, a newly discovered archaeon, Altiarchaeum hamiconexum, was discovered living in a "string of pearls" community with filamentous bacteria in marsh water rich in sulfides in the Sippenauer Moor, Germany. The Altiarchaeum hamiconexum cells possess a unique appendage not previously seen: pilus-like grappling hooks called "hami," shown in the following illustration. What function might this unique structure provide for the archaea?

The hami allow the formation of a matrix composed of Altiarchaeum hamiconexum and sulfide-oxidizing bacteria.

What is the significance of the Cit+ phenotype in Lenski's Long-Term Evolution Experiment?

The precipitating genetic duplication event of citT would have been of no effect except for a previous mutation in the strain's lineage.

Which hypothesis regarding benzene-degrading bacteria is supported by the data in this figure?

They are catabolizing substrates other than benzene in the contaminated sites.

Which is true of bacteriorhodopsin and halorhodopsin?

They are homologs that contribute to the generation of a proton motive force.

In an archaeal variation of the Entner-Doudoroff (ED) pathway, which statement about Sulfolobus and Thermoplasma is correct?

They do not produce any ATP.

Why is it so difficult to arrive at a simple species definition for prokaryotes?

They engage in extensive horizontal gene transfer.

Select the unusual shared feature of the archaeal species Thermoplasma acidophilum and Ferroplasma acidarmanus.

They lack cell walls and S-layers.

Which is true about the halophilic Halobacterium species?

They require an initial input of one ATP prior to entering the bacterial ED pathway.

Imagine that you have isolated what appears to be a new species of thermophile from a microbial mat at Yellowstone National Park. This organism can grow up to 90ºC and contains ether-linked lipids in its plasma membrane. Using whole-genome sequence data, your team pieces together a single circular chromosome—about half the size of the one in E. coli. About 54% of its genes have functional assignments, but there is an interesting pattern in their biological roles. Specifically, genes required for transcription and translation are most like bacterial orthologues, while genes encoding nutrient transporters and electron transport proteins are most similar to thermophilic archaea. What is the best interpretation of your data?

This is a bacterium which has acquired a surprisingly large number of archaeal genes.

A molecular clock is best described as what?

a biomolecule (such as DNA) whose sequence can be used to deduce ancestry

The gamma class of the Proteobacteria includes many medically important genera in the families Enterobacteriaceae and Pseudomonadaceae. Which of the following characteristics allows differentiation between these two groups?

ability to grow anaerobically

A bacterial phylum is generally defined based on:

ancestry and key traits.

On a phylogenetic tree, an organism that has undergone genetic reduction would be positioned where?

at the end of a long branch

Which protein(s) aggregate in complexes called purple patches?

bacteriorhodopsin

Which is the most distinctive cellular structure found in archaea?

cell membrane

Which of the following microbial groups are associated with the bovine, but NOT human, gut microbiome?

chytridiomycetes

Nowhere is the damage from people more apparent than in the once-beautiful Morning Glory Pool, a hot spring in Yellowstone National Park. This pool, named after the blue flower of the same name, is now referred to as "Fading Glory" or "Garbage Can," because early visitors and vandals threw trash, coins, and even, reportedly, a couch into the baby blue water. Some also removed the delicate scalloped border for souvenirs. What specific feature of hot springs is being affected by the accumulation of garbage?

consistent high temperature as one moves toward the edge of the pool

Methanogens increase the efficiency of bacterial fermentation in the mammalian gut by

consuming fermentation end products.

Ammonia-oxidizing archaea (AOA) are found in marine environments, where they play an important role in which of the following?

converting nonusable ammonia to nitrite

Under which conditions would expression of glutamate decarboxylase increase the relative fitness of E. coli?

during death phase at pH 3 with excess glutamate

The association shown in this photo is a good example of which of the following? (green thing with chlorella labeled)

endosymbiosis

Verrucomicrobia contain cytoskeletal elements whose genes were likely acquired by transfer from what?

eukaryotes

Complete the following sentence with the correct pairs of terms. "Long branch attraction is most likely to infer a __________ sister relationship between sequences with __________ mutation rates."

false, increased

The process of methanogenesis uses a series of specific cofactors to carry each carbon from CO2 (or another substrate) as it becomes progressively reduced by hydrogen. Which of the following is not a cofactor unique to methanogens?

flavin adenine dinucleotide (FAD+)

There is now sufficient bioinformatic evidence to state with some certainty that eukaryotic cells share a common ancestor with the Asgard branch of the archaea. Aside from sequence similarity, what feature of the Asgard group suggests that it likely shares a common ancestor with the first eukaryote?

genes for an actin cytoskeleton and for phagocytosis

Imagine that a strain of E. coli acquires a silent point mutation in its gene for DNA photolyase. After isolating this mutant, you expose a mixed culture, containing equal numbers of parent and mutant cells, to UV light. You then transfer an inoculum of this mixed culture into fresh media and let it grow (a subculture). The next morning you make a transfer from the subculture, and continue this practice daily. After months of successive sub-culturing, you discover that the population exists entirely of the mutant strain. What is the best explanation for loss of the parental genotype?

genetic drift

An organism's phylogeny describes what?

genetic relatedness to other species

Imagine that you are examining a culture of Anabaena and observe clusters of bacteria surrounding the larger differentiated cells that occur at regular intervals along the filaments. These bacteria are probably:

growing on organic compounds leaked from the cyanobacterium.

Which evidence best supports the hypothesis that modern viruses are derived from an ancient form that originated prior to the existence of the three domains of life?

homology between capsid proteins of archaea, bacteria, and eukaryotes

The bacterium Listeria monocytogenes enters a new host by:

ingestion of contaminated food.

The hyperthermophilic archaeon Pyrodictium possesses cannulae that are believed to facilitate

intraspecies metabolite exchange.

A mutant strain of Listeria that failed to polymerize actin would be less able to:

invade neighboring cells.

Which feature of Nanoarchaeum equitans is most suggestive of its obligate dependence on Ignicoccus hospitalis?

its very small genome

The two major genera of Gram-positive bacteria include the _______________ , which contains the endospore-forming genera (e.g., Bacillus and Clostridium), and the _______________, which contains some filamentous forms (e.g., Streptomyces) that produce exospores.

low GC Firmicutes ; high GC Actinobacteria

Which eukaryote-like organelles have been observed in Planctomycete cells?

membrane-bound "nucleus" containing DNA

Which group of archaea are present in the human gut and may contribute to obesity?

methanogens

A position in a phylogenetic tree where two clades diverge is referred to as a _____ .

node

Prochlorococcus spp. are highly abundant in the surface waters of Earth's oceans where their concentrations may exceed 105 cells ml-1. Although they are free-living, they are not completely independent. Instead, they are reliant on other members of the picoplankton (specifically the closely related Synechococcus) to protect them from which of the following?

oxidative stress

Experimental mice reared in the absence of segmented filamentous bacteria (SFB) would likely be:

prone to infectious disease.

Consider the following sequence of events where the blue lines represent a nucleic acid and the brown shapes are proteins The nucleic acid is not necessarily eliminated at the end, but may be enclosed by protein components. Which of the following might have evolved by the process shown here?

ribosomes

Ammonia-oxidizing archaea (AOA) comprise a significant part of which human system?

skin

What term best describes the relationship between bacterial fermenters and M. smithii in the human gut?

syntrophy

As demonstrated in the photo of Morning Glory Pool, the bright blue at the center now fades into greens, oranges, and ultimately yellows in the outer edges of the pool. What can these colors be attributed to?

the presence of a range of thermophilic organisms due to the current temperature gradient

Life on Earth relies on the production, consumption, and recycling of nutrients. The position that an organism occupies within a food web is referred to as its ______.

trophic level