Chapter 19 Homework Questions

Which approach would help to identify biologically produced sulfur in a sediment sample? enrichment microelectrodes isotopic fractionation microautoradiography

isotopic fractionation

Metatranscriptomics and metaproteomics are favored over metagenomics when ________ is of more interest than ________. gene presence / function or gene expression gene presence / phylogeny function or gene expression / gene presence phylogeny / gene presence

function or gene expression / gene presence

Microarrays are useful for assessing gene expression only. the presence of specific rRNA sequences only. enzyme activity. gene expression and the presence of specific rRNA sequences.

gene expression and the presence of specific rRNA sequences.

Metagenomics is a more sensitive analysis of community diversity than rRNA-based analyses because __________. more clone libraries can be assembled rRNA genes are not found in all of the organisms present in the environment genes do not have to be amplified by PCR before being sequenced the extraction of the DNA from the environmental samples is more efficient

genes do not have to be amplified by PCR before being sequenced

Genomic analysis of Prochlorococcus has revealed that no regions are shared between cultured representatives and environmental populations. high levels of gene conservation between cultured representatives and environmental populations. the presence of bacteriorhodopsin. complete congruence of genes and genome structure within the same phylotype

high levels of gene conservation between cultured representatives and environmental populations.

A NASA ecologist wants to design an instrument to send to Mars on the next space probe to determine whether living organisms ever carried out carbon fixation on that planet. Suggest an assay that she could use on Martian soil samples. 34S/35S stable isotope analysis 13C/12C stable isotope analysis MAR-FISH NanoSIMS

13C/12C stable isotope analysis

What are activity measurements? Activity measurements are any measurements taken in vitro. Activity measurements are any measurements taken in situ. Activity measurements are collective estimates of the physiological reactions in an entire microbial community. Activity measurements are an example of metagenomics, which can be used when genetic analysis is difficult.

Activity measurements are collective estimates of the physiological reactions in an entire microbial community.

Describe how FISH can be used to determine which cells within a microbial community are actively degrading toluene. Assume the genes involved in the metabolic pathway have been sequenced from several microorganisms and vary only slightly from one another.

FISH can be used to identify an organism of interest by using a phylogenetic stain that targets toluene degraders. The toluene degraders would become stained and those lacking this ability would not. The organisms with this ability would react with the probe and would be visible when fluoresced. ****how would you target toluene degraders? What do you mean by phylogenetic stain? Do you mean a probe to a toluene degradation gene? If so that is a functional probe, not a phylogenetic probe. Stains are dyes. Probes are oligonucleotide sequences that match a target. Make sure you use teh correct terminology. Question asks about cells actively degrading toluene. How would you find active cells?

Phototrophic organisms in SIP experiments are often observed releasing 14CO2 as a way of measuring photosynthetic activity. True False

False

When measuring microbial community metabolic activity, __________ is always necessary. a killed control radioisotopes enrichment culture DNA extraction and sequencing

a killed control

The element(s) that have proven most useful for stable isotope studies are carbon only. sulfur only. nitrogen only. carbon, sulfur, and sometimes nitrogen.

carbon, sulfur, and sometimes nitrogen.

By isolating total community RNA, using reverse transcriptase to make cDNA copies of it, and then sequencing the cDNA, ecologists can __________. determine the community genomic potential at the moment of sampling determine the community metabolic activity at the moment of sampling determine the community genome translation at the moment of sampling determine the community genome expression at the moment of sampling

determine the community genome expression at the moment of sampling

What technique(s) can be used to characterize the phylogenetic composition of a microbial community without culturing any of the members? fluorescent in situ hybridization (FISH) stable isotope techniques radioisotope experiments green fluorescent protein tagging

fluorescent in situ hybridization (FISH)

The phylogenetic diversity analysis of complex microbial communities often targets small subunit (SSU) ribosomal RNA genes. This is because rRNA is found in all organisms and __________. has more genes than mRNA is made by cells only at certain times is easier to extract from samples is highly conserved over evolutionary time

is highly conserved over evolutionary time

Which technique would be used to estimate the concentration of naturally occurring Escherichia coli in a wastewater sample? most probable number (MPN) method cell tagging using GFP method agar dilution tube method laser tweezers method

most probable number (MPN) method

Staining methods are suitable for obtaining phylogenetic information from natural samples. quantitative information from natural samples. information about physiology from natural samples. neither qualitative nor quantitative information from natural samples.

quantitative information from natural samples.

Phylogenetic stains, such as those used in phylogenetic FISH, hybridize with mitochondrial DNA. nuclear DNA. RNA polymerase. ribosomal RNA.

ribosomal RNA.

Enrichment cultures are often effective for isolating bacteria from complex communities in natural samples because they __________. select against certain bacteria select both for and against certain bacteria do not select for or against any bacteria; they help every organism to grow select for certain bacteria

select both for and against certain bacteria

How do viability stains usually distinguish between living cells and dead cells? The dye specifically targets intact cytoplasmic membranes. The dyes fluorescence is quenched by dead cells. The chemical stain is taken up by living cells and once metabolized becomes fluorescent. The chemical fluoresces only when bound to ribosomes that are actively synthesizing proteins.

The dye specifically targets intact cytoplasmic membranes.

In an agar dilution tube, microbial colonies grow embedded in the agar, rather than growing on the surface. at the bottom of the tube. on the surface, but some creep down the sides away from the surface. on the sides of the tube, although some may be at the surface.

embedded in the agar, rather than growing on the surface.

Genes that retain their function yet change over evolutionary time as organisms diverge are called orthologs. Organisms with identical or very similar orthologous genes belong to the same __________. phenotype ribotype phylotype genotype

phylotype

Single-cell genomics may help us understand the physiology of uncultured microbes. predict which microbes will be abundant based on the environmental conditions. understand the physiology of uncultured microbes and develop better enrichment culture methods. develop better enrichment culture method

understand the physiology of uncultured microbes and develop better enrichment culture methods.

Radioisotopes are useful when very high sensitivity is required, turnover rates need to be determined, and the fate of portions of particular molecules need to be followed. the fate of portions of particular molecules need to be followed. very high sensitivity is required. turnover rates need to be determined.

very high sensitivity is required, turnover rates need to be determined, and the fate of portions of particular molecules need to be followed.

Genes encoding ________ are widely used as target genes in molecular biodiversity studies. 16S rRNA RNA polymerase ATPases DNA polymerase III

16S rRNA

Which of the following hypotheses could be tested using microautoradiography fluorescence in situ hybridization (MAR-FISH)? The ammonia monooxygenase gene is present in members of the phylum Verrucomicrobium. The microbial community of agricultural soils is more phylogenetically diverse than the microbial community of native prairie soils. Archaea are the main autotrophs in marine water samples taken 300 m below the surface of the ocean. Bacteriorodopsin uses light energy to translocate protons.

Archaea are the main autotrophs in marine water samples taken 300 m below the surface of the ocean.

When Beijerinck enriched for nitrogen fixers, he inoculated soil into two types of liquid media: one containing mineral salts and mannitol but no nitrogen source (flask A), and one containing mineral salts, mannitol, and an ammonium salt (flask B). After incubation in the presence of air, what types of organisms did he expect to find in each flask? Flask A would contain nitrogen fixers that could not tolerate the presence of ammonium; flask B would contain ammonium utilizers. Flask A would contain ammonium utilizers, and flask B would contain nitrogen fixers that could grow without the presence of ammonium. Flask A would contain nitrogen fixers that could grow both without ammonium; flask B would not contain nitrogen fixers but would contain organisms that could use ammonium. Flask A would contain ammonium utilizers and flask B would contain nitrogen fixers that could not tolerate the presence of ammonium.

Flask A would contain nitrogen fixers that could grow both without ammonium; flask B would not contain nitrogen fixers but would contain organisms that could use ammonium.

Which fluorescent molecule enables visualization of living microorganisms? acridine orange SYBR® Green DAPI GFP

GFP

How would you label and separate the DNA of unknown methylotrophs in a sample? Incubate the sample with 13C-methane. Hybridize the DNA to FISH probes. Use DGGE to separate the strands of DNA in the sample. Use T-RFLP to identify the methylotroph DNA in the sample

Incubate the sample with 13C-methane.

A study of the human gut performed in 1982 used various types of plates under different growth conditions to describe and enumerate the microbes in the human gut. They concluded that the majority of the microbes in the human gut are Gammaproteobacteria. A study conducted in 2010 using next-generation sequencing to characterize 16S rRNA sequences concluded that the majority of the microbes in the human gut are Firmicutes and Bacteriodetes. Why did these studies have different conclusions? Which study do you think is most accurate?

The techniques in 1982 relied on the construction of clone libraries to separate individual amplified DNA molecules. Each clone in the library had a unique sequence which was used as a template for sequence determination. Since the amplified target gene was from a mixture of different cells, the different phylotypes in the single band have to be sorted out before they're sequenced. Next generation sequences are more advanced and do not require a cloning step. The individual DNA fragments are separated and amplified on the sequencing device itself, so the PCR products are now used directly for sequencing. The amplification reactions occur simultaneously which means the total number of sequencing reads are much larger than what can be done when you sequence an individual clone. Next generation sequencing gives massive amounts of data which means that minor phylotypes which were most likely missed with the clone library method are now revealed. There were different results because the clone library method missed the minor phylotypes that the next generation sequencing method was able to detect. I believe the next generation sequencing method would be most accurate for reasons previously described. ***The key is that the media used in the lab were likely suitable for growth of only some of the gut microbiota and did not provide appropriate growth conditions for all the species in the gut. NGS skips cultivation and is therefore likely to give us a more accurate picture of gut microbiome diversity. They don't say that cloning or sequencing was done in the 1982 study. Return to Current Item

Analyses of sulfur isotopes have been used as evidence against life on the Moon, because the sulfides in lunar rocks have exactly equal amounts of 34S and 32S. an isotope composition most similar to marine mud, which is enriched in 34S. an isotope composition most similar to igneous rocks. an isotope composition most similar to marine sulfate, which is enriched in 34S.

an isotope composition most similar to igneous rocks.

Phylogenetic analysis of microbial communities in nature using various PCR techniques has revealed that only a minority of phylotypes have been cultured from the environment and the most common phylotypes have not been grown in in the laboratory. This is due in part to __________. enrichment bias the uncultured organisms' being rare in the community poor technique lack of sufficient sampling of the community

enrichment bias

Which of the following techniques can link prokaryotic phylogeny and metabolic function? DAPI staining stable isotope probing only environmental genomics and stable isotope probing environmental genomics only

environmental genomics and stable isotope probing

Thirty organisms containing the same phylogenetic marker, with identical or similar orthologous genes, are all considered to be within the same species. functional group. phylogenetic tree. phylotype.

phylotype.

The overall purpose of DGGE is to measure the activity of cells that use DGGE as an energy source. detect cells that utilize a specific radiolabeled substrate. separate genes that differ in length. separate genes of the same length that have different sequences, resulting in different denaturation profiles.

separate genes of the same length that have different sequences, resulting in different denaturation profiles.

You would like to test the hypothesis that ammonia-oxidizing Archaea are more active and abundant than ammonia-oxidizing Bacteria in coastal marine water. What technique(s) or experiment(s) could you use to test this hypothesis? stable isotope ratios of ammonia and nitrite stable isotope probing using 15N labeled ammonia fluorescent in situ hybridization (FISH) environmental proteomics

stable isotope probing using 15N labeled ammonia

For what purpose would a microbial ecologist use a microsensor? to determine the expression of a particular gene in a microbial community to determine the concentration of cells in small increments in a sediment or water column to quantify the uptake of a radioactive material to determine the concentration of O2, N2O, or other chemical species in small increments in a sediment or water column

to determine the concentration of O2, N2O, or other chemical species in small increments in a sediment or water column