Exam 3 Study Guide
How would you distinguish between a Spirillum and a spirochete? Flagella (polar) Aerobic Rigid cell wall Magnetotactic Endoflagella Mostly anaerobic or facultatively aerobic Flexible cell wall 1.Spirillum 2.Spirochetes
1 1 1 1 2 2 2
Match the description to indicate whether it refers to Planctomyces and Caulobacter. Stalk made of protein; no cell wall or cytoplasm; S layer type with cysteine, proline Broader stalk; cell wall; antibiotic sensitive; no cell compartmentalization 1.Planctomyces 2.Caulobacter
1 2
Do the bacteria listed below have phycobilins? True cyanobacteria Purple sulfur bacteria Purple nonsulfur bacteria Green sulfur bacteria Prochlorophytes Green nonsulfur bacteria 1. Yes 2. No
1 2 2 2 2 2
Match the chlorophylls used by the bacteria listed below. Purple nonsulfur bacteria Prochlorophytes True cyanobacteria Green nonsulfur bacteria Green sulfur bacteria Purple sulfur bacteria 1. Bacteriochlorophylls 2. Chlorophyll a 3. Chlorophyll a and b
1 3 2 1 1 1
Note that GNSB represent the earliest evolution of photosynthesis! (They are the first lineage on the tree to arise that was capable of photosynthesis - see bacterial phylogeny from class.) The early-diverging, hyperthermophilic bacteria. The two key genera in these ancient lineages of bacteria are Thermotoga and Aquifex. These early lineages are hyperthermophiles.
NO ANSWER
What is a major disadvantage of the enrichment culture approach?
There is a likelihood of there being bias in the results as most fit microorganisms in the laboratory will not always represent the most fit organisms in a natural environment
What aspect of the lifestyle of the green non-sulfur bacteria is shared among all of the early diverging lineages of bacteria? Anaerobic Halophilic Thermophilic Multinucleated
Thermophilic
Define/describe baeocytes and state the group(s) (I-V) of true cyanobacteria in which they are found.
These are small, spherical cells that are produced via multiple fission of certain species of cyanobacteria. They are found in Group II
What role might true cyanobacteria play in deserts like the Sonoran desert?
They create a crust on the surfaces where they reside. They could serve a purpose of keeping the dirt and soil compact as well as retaining the moisture of the ground. This could then provide a decent place for seeds to germinate and grow.
GNSB are capable of photoheterotrophy. True False
True
Many true cyanobacteria are capable of gliding motility.
True
Many true cyanobacteria can poison water by secreting neurotoxins.
True
Some true cyanobacteria are symbionts of other organisms, e.g., plants and fungi.
True
Thermotoga are anaerobic and capable of fermentation. True False
True
True cyanobacteria are though to have been the origin of earth's oxygen atmosphere.
True
Viability staining is useful because it allows one to distinguish between live and dead bacterial cells. True False
True
Choose the best description for "Microbial activity" in the microbial ecology. The richness of microorganisms in focal habitats. The composition of microorganism community in focal habitats. What microorganisms are doing in their habitats. The nutrients required for microorganisms.
What microorganisms are doing in their habitats
How can 12C/13C composition of a substance reveal its origin? Due to the enzyme discrimination of isotopes, biological origin has higher 12C Due to the enzyme discrimination of isotopes, biological origin has higher 13C Due to the enzyme discrimination of isotopes, geological origin has higher 12C None of the above
A
What are the advantages of DAPI stain? Select all that apply. Unreactive with inert materials (reduced background staining) Non-specific stain Reasonable estimate of cell numbers present Simple staining techniques
ALL
What medium could you use to isolate these bacteria relative to others? Agar with glucose Agar with cellulose Blood agar
Agar with cellulose
Define consortia.
An association of two members with a chemoorganotrophic bacterium where there is a symbiotic relationship
Define chlorosomes.
An oblong structure that are bounded by a nonunit membrane and contain the bacteriochlorophyll
How have stable isotopes been used in the argument regarding the potential occurrence of life on the Moon? The isotopic composition of sulfides in lunar rocks closely approximates that of the biogenic sulfide and not that of sulfide standard The isotopic composition of sulfides in lunar rocks closely approximates that of the sulfide standard and not that of biogenic sulfide All of the above None of the above
B
Define enrichment. Select all that apply. The process involves teasing the organisms of interest out from a microbial community. A medium and a set of incubation conditions chosen to select for the desired organism. A medium and a set of incubation conditions that are counterselective for undesired organisms. A medium and a set of incubation conditions are good for all organisms.
B C WRONG
Why is this separation step very important when characterizing microbial communities?
Because the separation is what keeps the gene sizes grouped together so that those genes of same sizes can have their differing sequences analyzed.
What are the two main branches in microbial ecology?
Biodiversity & Microbial activity
What do the different bands in a DGGE analysis correspond to? Different size of a given gene Different conformations of a protein Different forms of a given gene that vary in their sequence Different genes
C
What is one of the most distinctive features of Planctomyces cells? In particular, what is a distinctive feature of Gemmata?
Cell compartmentalization The nucleoid is covered by a nuclear envelope
Like some Archaea, Aquifex is a(n) ________ hyperthermophile. Heterotrophic Chemoorganotrophic Chemolithotrophic Autotrophic
Chemolithotrophic WRONG
Thermotoga make a living as.. Chemolithotrophs Autotrophs Chemoorganotrophs Phototrophs
Chemoorganotrophs
Deinococcus radiodurans is incredibly radiation-resistant. Enzymes in this organism are capable of two methods for repairing radiation damage. However, this organism is susceptible to mutagens that cause.. DNA deletions DNA duplications DNA transversions DNA transitions
DNA deletions
Above, you were asked to state a disadvantage of the enrichment culture technique. Such problems are described in some detail starting on p. 618. Let's explore one of these problems (enrichment bias) a bit more. Enrichment bias can be demonstrated by comparing dilution methods. Explain.
Diluting the solution will give a different organism and is said to eliminate those species that are considered to take over in the undiluted inoculums and allows for the other members of the microbial community being sampled to develop
Chlamydias are Gram-positive. True False
False
To culture true cyanobacteria, you will need to give them vitamins.
False They can use organic material as both a carbon and energy source so there is no need for vitamins
Heterocysts are found in all true cyanobacteria.
False They only form in some filamentous cyanobacteria, not all
True cyanobacteria have true flagellae.
False lack true flagellae and only contain filaments to aid in motility
True cyanobacteria are algae.
False more tolerant to environmental extremes than algae
There are five groups of true cyanobacteria. The characteristics of each group are described below (don't worry about % GC content). Select the correct answer to fill in the blanks. Group II. Pleurocapsalean. These are unicellular/colonial, and reproduce by_____________. Group I. Unicellular. These are unicellular and reproduce by___________. Group III. Oscillatorian. These are filamentous and divide by _________________. Group V. Branching. These are filamentous and - as the name suggests - have a __________________. Group IV. Nostocalean. These are filamentous and have ___________. 1. binary fission in a single plane 2. baeocytes (produced through multiple fission) 3. binary fission 4. branching form 5. heterocysts
Group II: 2 Group I: 3 Group III: 1 Group V: 4 Group IV: 5
What is distinctive about the chromosome of Borrelia?
It is linear rather than circular
What disease is caused by Borrelia burgdorferi?
Lyme disease
As a note, there are other biases, too: what if we don't know what conditions to optimize to capture a particular species in culture? Think about all of those phyla represented only by SSU rDNA sequences. We have a long way to go before we figure out how to isolate them using the enrichment culture technique. Following enrichment culture, pure cultures can be obtained in several ways. You are probably familiar with the streak method, in which small amounts of a particular bacterium are repeatedly spread across an agar plate until a pure culture is isolated. In this case, the bacterium of interest is present on the surface of the agar plate.
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Cytophaga
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Defferibacter Defferibacter is described briefly at the end of the chapter. This is a member of the 'seven phyla', but we don't know much about it. They are versatile at anaerobic respiration and use a variety of electron donors, including iron. Now, we'll step outside of the 'seven phyla' and will work our way down the tree. Spirochetes
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Deinococci. The two key genera in this group are Thermus and Deinococcus.
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Finally, some researchers use the so-called laser tweezers method. This method uses the force of a focused laser to move individual cells away from others, which allows those cells to then be flushed into a new medium, and/or replicate in the absence of competitors. This method is important for isolating bacteria that grow slowly relative to others. Sometimes, researchers in microbial ecology are more interested in enumerating (counting) particular microbes, rather than isolating them. There are two ways to do this: staining, and molecular analysis of communities. We'll deal with staining methods first.
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Fluorescent protein: under this method, bacterial cells are genetically altered so that they fluoresce. This is done with GFP, or green-fluorescent protein, which can be inserted into the bacterial genome and expressed. This method can be used in specific habitats (e.g., plant roots). Note that this is not a staining method, per se! Nothing is stained; instead, the bacteria are transformed so that they express a protein that is visible to us.
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For the question 9-16 , indicate True or False in the first box. If false, explain your answer in the second box.
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Green sulfur bacteria Green sulfur bacteria were covered in detail in the table on the last study guide (question 1). I'd like you to remember the following characteristics of green sulfur bacteria: a. Not closely related to purple sulfur bacteria b. Use H2S as an electron donor, but store sulfur outside of the cell c. Anoxygenic phototrophs d. Non-motile, although some species use gas vesicles to regulate buoyancy e. Most species are capable of photoheterotrophy. f. Because of highly efficient photosystems, they can grow at very low light. g. Have chl a and c, d, or e. h. Are unique in possessing chlorosomes. i. Often are found in consortia. Note that epibionts and central cells often divide in synchrony, suggesting that they communicate with each other.
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We didn't mention this in class - but what is distinctive about the membrane lipids of the GNSB? (Select all that apply) Contain 1,2-dialcohols Contain glycerol Have both ester and ether linkages Lack both ester and ether linkages
Yes no no yes
What does DGGE stand for? What is it?
denaturing gradient gel electrophoresis it is a gel that will separate the genes that are the same size and have the differing base sequences
GNSB produce oxygen from photosynthesis. True False
false
Thermotoga, which have a unique sheath around the cell are Gram-
negative
What is the disadvantage of viability staining with regard to environmental samples? Not differentiating between living and dead cells Low sensitivity Complicated staining protocol Nonspecific staining of background material
no ? ? yes
What do members of this phylum share with some proteobacteria? Select all that apply. Formation of cytoplasmic appendages (prostheca) Presence of peptidoglycan in their cell walls Aerobic to facultatively aerobic bacteria Capable of fermenting various sugars
yes yes yes yes
Are the bacteria listed below oxygenic? Choose yes or no. Purple sulfur bacteria Green nonsulfur bacteria Prochlorophytes True cyanobacteria Purple nonsulfur bacteria Green sulfur bacteria 1. Yes 2. No
2 2 1 1 2 2
Select the method to match each description. Also known as the most probable number method. Several types of anaerobic microorganisms, such as phototrophic sulfur bacteria and sulfate-reducing bacteria from Winogradsky columns can be isolated this way. Dilution of an inoculum in a liquid medium until the final tube or tubes in the series show no growth. Involves the dilution of a mixed culture in tubes of molten agar, resulting in colonies embedded in the agar rather than growing on the surface of an agar plate. Estimating the numbers of microorganism in foods, wastewater, and other samples, where cell numbers need to be assessed routinely. 1. Shake-tube method 2. Serial dilution method
2 1 2 1 2
Are the bacteria listed below tolerant to H2S? If yes, indicate high or low. If no, select no. Green nonsulfur bacteria Green sulfur bacteria True cyanobacteria Purple nonsulfur bacteria Prochlorophytes Purple sulfur bacteria 1. Yes/High 2. Yes/Low 3. No
3 1 2 2 3 1 SOME WRONG
Match the phylum with the bacteria listed below. Green nonsulfur bacteria Green sulfur bacteria True cyanobacteria Purple nonsulfur bacteria Purple sulfur bacteria Prochlorophytes 1. Proteobacteria 2. Green sulfur bacteria 3. Green non-sulfur bacteria 4. Cyanobacteria 5. Originally grouped with Cyanobacteria (now their own phylum)
3 2 4 1 1 5
Important genera to know among the true cyanobacteria: Nostoc and Spirulina. Both of these are often sold as health foods! What groups do these belong to? Spirulina Nostoc 1. Group I 2. Group II 3. Group III 4. Group IV 5. Group V
3 4
Match the distinguishing features with their respective organisms. No ribosomes present; DNA or RNA; antibiotic resistant; no glutamate oxidation; no cell wall; no ATP generation system; host machinery used for macromolecular synthesis Ribosomes present; DNA+RNA; antibiotic sensitive; oxidize glutamate; peptidoglycan in cell wall; ATP generating system; macromolecular synthesis Ribosomes present; DNA+RNA; antibiotic sensitive (except penicillin); oxidize glutamate; peptidoglycan in cell wall; ATP generating system; macromolecular synthesis 1. Rickettsia 2. Chlamydia 3. Virus
3, 1, 2 CHECK
Now, we'll turn to measuring microbial activities in nature. There are three major ways that this work is done: using radioisotopes; using microelectrodes; and using stable isotopes. One major disadvantage here is that we don't know who's doing what - we only can measure the collective microbial activity of the entire community. In some cases, direct chemical measurements can be used to examine microbial activity. For a more sensitive analysis, radioisotopes are used. For example, if one were to study photosynthesis, one might place radiolabelled CO2 into the microbial community, and could compare its concentration under light and dark conditions. Controls are very important in this work. In some cases, microelectrodes are used. In this case, tiny electrodes are moved by micromanipulators to particular places or depths in a sample. These are frequently used, for example, in the study of stratified ecological roles in microbial mats (different activities at surface, interior of mat, base of mat), even though the mats may be only a few millimeters thick.
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Planctomyces
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The Flavobacteria or Bacteroidetes
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The green non-sulfur bacteria The key genus in this group is Chloroflexus.
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Until the prochlorophytes were discovered, it was thought that chloroplasts represented the evolutionary acquisition of cyanobacteria. However, this was always a problematic hypothesis, because phycobilins are present in cyanobacteria (chlorophyll a + phycobilins)...but the chloroplast contains chlorophylls a and b, and no phycobilins. Thus, it would seem that prochlorophytes are the ancestors of chloroplasts. However, phylogenetic analyses suggest that instead, it was another descendant of the common ancestor of cyanobacteria and prochlorophytes that led to the chloroplast. Under this scenario, phycobilins and several different chlorophylls were present in the ancestor of prochlorophytes, cyanobacteria, and chloroplasts. Over time, cyanobacteria lost some chlorophylls; prochlorophytes lost phycobilins; and chloroplasts lost phycobilins and some chlorophylls. We'll talk about this in class. Make sure you can describe the relationship of prochlorophytes, true cyanobacteria, and chloroplasts based on our notes and the reading.
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Verrucomicrobia
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We met the Winogradsky column when we talked about the domain bacteria. Familiarize yourself with (1) the methods used to construct one, and (2) one of the major advantages of doing so. You do not need to write anything here.
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Imagine that you have (A) a filamentous cyanobacterium with heterocysts, and (B) one that is filamentous but lacks heterocysts. Which one is Nostoc and which is Spirulina? Nostoc Spirulina 1. A 2. B
Nostoc-1 Spirulina-2
Aquifex is ________to the rest of bacteria. It is the most ancient lineage, and is characterized by the most extreme hyperthermophilic growth in the domain Bacteria. Sister Homologous Paralogous
Paralogous WRONG
Prochlorophytes are the other major lineage in the phylum Cyanobacteria. They may have single-cell or filamentous growth forms. The first one to be discovered, ________ lives as a symbiont in marine invertebrates called sea squirts (ascidians). These have membranes that resemble the chloroplasts of plants.
Prochloron
SG7
SG7-This study guide covers Brock Ch. 12, part IV: the phylum Cyanobacteria, including both the true cyanobacteria and prochlorophytes. Note that the phylum Cyanobacteria is sister to the Gram-Positive bacteria, as depicted in Fig. 12.1. Three groups of bacteria are generally considered to be phototrophic. These include the purple bacteria (including the purple sulfur bacteria and the purple nonsulfur bacteria), which we have discussed already; the green bacteria (including the green sulfur and green non-sulfur bacteria, which each form a distinct phylum and will be discussed later); and the phylum Cyanobacteria, which includes the true cyanobacteria and the prochlorophytes. Use the chapter, our notes, and the information on pages 352-356 to answer questions 1-5.
SG8
SG8- This study guide covers Brock Ch. 12, parts V through XV: the remaining phyla of bacteria. We'll start in the 'seven phyla' group, as defined in class. The Chlyamidias
SG9
SG9
What major product of Thermus has reshaped molecular biology? Magnesium ions Agar Taq DNA polymerase
Taq DNA polymerase
The study of biodiversity includes the ________, ________ and ________ of microorganisms in various habitats. (Choose three words to fill in the blanks) isolation simulation inhibition identification quantification
isolation, identification, quantification
What is special about the cell wall of the GNSB - just like Planctomyces? Contains ether linkages Is resistant to antibiotics Lacks peptidoglycan None of the above
lacks peptidoglycan
Nucleic acid probes are the basis of FISH - fluorescent in situ hybridization. The chapter discusses three methods of FISH. Be familiar with each of these, and the conditions under which you might use them: Phylogenetic staining using FISH; chromosome painting; in situ reverse transcription. You do not need to write anything here. The next class of methods focuses on identifying microbes using molecular tools -- without culturing or directly observing those microbes. Remember that 16S = SSU rDNA (16S is traditionally used when referring to Bacteria). Carefully examine Fig. 18.14. This should remind you of our earlier discussion in class regarding ways to sequence SSU rDNA from environmental samples. Make sure that you can reproduce this figure for Exam 3. Note that at the bottom of the figure, there's the path that we took in class (cloning), and another: DGGE.
no answer?
What is distinctive about the 'feeding' habits of Cytophaga relative to other bacteria? No production of soluble, extracellular cellulases Exceptionally halotolerant Aerotolerant anaerobes Thermophilic and grow well on acidic media
no production of soluble, extracellular cellulases
What are the disadvantages of DAPI stain? Select all that apply. High background stain Not differentiating between living and dead cells Not allowing for tracking specific organisms in an environment Complicated staining protocol
no yes yes no
What is meant by isotopic fractionation? Select all that apply. Biochemical reactions tend to favor the heavier isotope. The heavier isotope is discriminated against relative to the lighter isotope when the elements are acted on by enzymes. The difference in natural abundance of these isotopes changes when C or S is metabolized by organisms. A given enzyme has no preference for isotope.
no yes yes no
Stable isotopes are used in the third set of methods. What are stable isotopes?
non radioactive isotopes that are used to analyze microbial transformations that occur in nature
What does DAPI stain bind to? Cell wall Protein Cell membrane Nucleic acid
nucleic acid
What unique cell wall component do Thermus and Deinococcus share? Ornithine Cholesterol Ergosterol
ornithine
Fluorescent antibodies are highly _______ . This is the main advantage to this method; the disadvantage is that specific antibodies must be prepared, which can be time- and labor-consuming. active specific stable manageable
specific
What disease is caused by Treponema pallidum?
syphilis
To what does the name of this phylum refer?
warty
What are characteristics of Bacteroides? Select all that apply. Numerically dominant bacteria in human large intestine Most important aerobic bacteria associated with human infections Can be pathogenic Most important anaerobic bacteria associated with human infections
yes no yes yes
What are the three main characteristics of the Chlamydias? Select all that apply. Obligate parasites Limited biosynthetic capacity Gene encodes FtsZ Very small genome
yes yes no yes
Which diseases are caused by Chlamydia sp.? Select all that apply. Psittacosis Trachoma Meningococcal disease Respiratory syndromes
yes yes no yes
Which are the correct descriptions of heterocysts? Select all that apply. Heterocysts are rounded, seemingly empty cells, usually distributed regularly along a filament or at one end of a filament Heterocysts arise from differentiation of vegetative cells and are the sole sites of nitrogen fixation in heterocystous cyanobacteria Heterocysts are surrounded by a thickened cell wall which can maintain an anoxic environment Heterocysts are low in phycobilin pigments and lack photosystem II They occur in the true cyanobacteria Group IV
yes yes yes yes yes
Describe the morphology and Gram-stain characteristics of Spirochetes. Select all that apply. : Gram-negative Tightly coiled Motile Slender and flexous Outer sheath surrounds protoplasmic cylinder and endoflagella
yes yes yes yes yes
The next set of methods refers to nucleic acid probes. What are these, and how do they work? Select all that are true. The term refers to DNA or RNA oligonucleotide complementary to a sequence in a target gene. The probe can be used to identify organisms containing a nucleic acid sequence complementary to the probe. Oligonucleotide probes can be made fluorescent with certain dyes. The probes can be used in the method called FISH.
yes yes yes yes
Note that these are all important methods. However, there are some major limitations to microscopy-based approaches to enumerating microbes. What are the limitations? Select all that apply.: Very small prokaryotes may be overlooked. It's difficult to differentiate live cells from dead cells and cells from nonliving matter. The method limits your ability to assess the genetic diversity of microorganisms in a natural habitat. You have to prepare samples in large quantity.
yes yes yes ?
What major lesson(s) has/have been learned thus far from PCR-based exploration of microbial communities (both via DGGE and cloning)? Select all that apply. PCR-based explorations are sufficient to study the microbial communities. Our knowledge of microbial diversity from enrichment culture studies is still very incomplete. Enrichment bias is likely a serious problem in biodiversity studies. By using these methods, our understanding of microbial diversity is complete.
yes yes yes no