Microbiology Final - chp 19

Analyses of sulfur isotopes have been used as evidence against life on the Moon, because the sulfides in lunar rocks have

an isotope composition most similar to igneous rocks.

By isolating total community RNA, using reverse transcriptase to make cDNA copies of it, and then sequencing the cDNA, ecologists can __________.

determine the community genome expression at the moment of sampling

Which approach would help to identify biologically produced sulfur in a sediment sample?

isotopic fractionation

Which technique would be used to estimate the concentration of naturally occurring Escherichia coli in a wastewater sample?

most probable number (MPN) method

Metatranscriptomics and metaproteomics are favored over metagenomics when ________ is of more interest than ________.

function or gene expression / gene presence

Microarrays are useful for assessing

gene expression and the presence of specific rRNA sequences.

Metagenomics is a more sensitive analysis of community diversity than rRNA-based analyses because __________.

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

Genomic analysis of Prochlorococcus has revealed

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.

13C/12C stable isotope analysis

Which of the following hypotheses could be tested using microautoradiography fluorescence in situ hybridization (MAR-FISH)?

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

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

False

Which fluorescent molecule enables visualization of living microorganisms?

GFP

When measuring microbial community metabolic activity, __________ is always necessary.

a killed control

The element(s) that have proven most useful for stable isotope studies are

carbon, sulfur, and sometimes nitrogen.

In an agar dilution tube, microbial colonies grow

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

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)

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 __________.

is highly conserved over evolutionary time

Staining methods are suitable for obtaining

quantitative information from natural samples.

Phylogenetic stains, such as those used in phylogenetic FISH, hybridize with

ribosomal RNA.

For what purpose would a microbial ecologist use a microsensor?

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

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.

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

Which of the following techniques can link prokaryotic phylogeny and metabolic function?

environmental genomics and stable isotope probing

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 __________.

phylotype

Thirty organisms containing the same phylogenetic marker, with identical or similar orthologous genes, are all considered to be within the same

phylotype.

Enrichment cultures are often effective for isolating bacteria from complex communities in natural samples because they __________.

select both for and against certain bacteria

The overall purpose of DGGE is to

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 probing using 15N labeled ammonia

Genes encoding ________ are widely used as target genes in molecular biodiversity studies.

16S rRNA

What are activity measurements?

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

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

How would you label and separate the DNA of unknown methylotrophs in a sample?

Incubate the sample with 13C-methane.

How do viability stains usually distinguish between living cells and dead cells?

The dye specifically targets intact cytoplasmic membranes.

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.

The sample would need to be collected, fixed, and permeabilized. A functional probe would be used to bind the mRNA of target genes (those involved in toluene metabolic pathway). A reporter enzyme would need to be bound to the probe to amplify the signal to be able to detect gene expression.

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?

They have different conclusions because the original study was based on biochemical characteristics that rely on the ability to accurately mimic the natural environment. This tends to be really difficult to do, and the lab environment tends to favor the growth of bacteria that may not actually be dominant in its natural habitat. The later study is based on actual sequencing of the bacteria. The second is therefore probably most accurate.

Single-cell genomics may help us

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