Question 1

What are the pros and cons of traditional enrichment culture techniques? What advances in the last decade are improving enrichment culture techniques to aid the cultivation of uncultured microorganisms?

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Question 2

Metaproteomics is a more developed field than metatranscriptomics due to the high sensitivity of mass spectrometry.

Accepted Answer

Metaproteomics and metatranscriptomics are both rapidly developing fields, but the development of one over the other is not solely due to the sensitivity of mass spectrometry. Both fields face unique challenges and advancements, and their development is influenced by a variety of factors including technological advancements, computational methods, and application areas.

Question 3

What prior knowledge is required to use a phylochip to study the abundance of the different microbes present within a microbial community? How does this cause bias when using a phylochip to analyze microbial community structure?

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Question 4

The Winogradsky column is a method for assessing the entire gene complement of a habitat,revealing both the biodiversity and metabolic capabilities of the microbial community at the same time.

Accepted Answer

The Winogradsky column is a simple device for culturing a diverse community of microorganisms. It is used to study the metabolic activities of the microbes in different layers of sediment, not for assessing the entire gene complement of a habitat.

Question 5

We know that that there are over 50 major phyla in Bacteria; however,only about 25 of these phyla have cultured representatives.Why is this? How are scientists attempting to culture representative from the 25 phyla that do not currently have any organisms in culture?

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Question 6

Describe what an ITS region is in the context of prokaryotes,and explain the significance of the ITS region for microbial ecology.

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Question 7

FISH technology can employ only a single phylogenetic probe.

Accepted Answer

FISH technology can employ multiple phylogenetic probes, which can target different regions of the genome and allow for more precise identification of specific species or strains.

Question 8

Phototrophic organisms in SIP experiments are often observed releasing ¹⁴CO₂ as measuring activity.

Accepted Answer

Phototrophic organisms in SIP (Stable Isotope Probing) experiments typically fix ¹⁴CO₂, not release it, as they use it for photosynthesis to incorporate carbon into their biomass.

Question 9

By using simple microscopy techniques,it is possible to determine if a culture is contaminated with another organism.

Accepted Answer

By observing microscopically the morphological characteristics of the microorganisms present in the culture, it is possible to identify if there is any contamination with another organism. For example, if a bacterial culture appears to have both rods and cocci morphology, it might indicate contamination with another species of bacteria.

Question 10

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.

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Question 11

The MPN technique is rarely applied in the food industry because any microbial presence in food is unsafe.

Accepted Answer

The MPN technique, or most probable number technique, is actually commonly used in the food industry to determine the microbial load in food samples. However, the presence of certain types or levels of microbes may indicate unsafe food and further testing and corrective action may be necessary in such cases.

Question 12

Propose an experiment to identify members capable of assimilating monomers of lignin within a microbial community.

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Question 13

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?

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Question 14

Combined with autofluoresence or fluorescent DNA probes,flow cytometry can separate or count populations of cells from aquatic environments.

Accepted Answer

Flow cytometry combined with autofluorescence or fluorescent DNA probes can indeed separate or count populations of cells from aquatic environments.

Question 15

The diversity of microorganisms in culture collections is representative of the diversity of microorganisms found in nature.

Accepted Answer

Culture collections often have a selection bias towards cultivable or easily culturable microorganisms, which may not be representative of the true diversity found in nature. Many microorganisms cannot be cultured under laboratory conditions, and therefore cannot be included in culture collections. Additionally, some microorganisms may have been lost or not yet discovered, which further limits the representativeness of culture collections.

Question 16

DGGE and T-RFLP are both molecular microbial ecology methods that use the polymerase chain reaction to amplify specific genes to assess diversity.

Accepted Answer

Both DGGE and T-RFLP are PCR-based methods used in molecular microbial ecology to amplify specific genes, such as 16S rRNA genes, to assess microbial diversity in environmental samples. DGGE (denaturing gradient gel electrophoresis) separates amplified DNA fragments based on their melting behavior in a denaturing gradient gel, while T-RFLP (terminal restriction fragment length polymorphism) involves digesting the amplified DNA fragments with a restriction enzyme and analyzing the resulting fragment size distribution.

Question 17

In natural samples it is often difficult to differentiate live cells from dead cells or cells from nonliving matter.

Accepted Answer

This is true. In natural samples, live cells can be difficult to differentiate from dead cells or nonliving matter due to similar physical characteristics and the potential for degradation or damage to cells over time. Additional testing may be required to accurately distinguish live cells from nonliving material.

Question 18

How can NanoSIMS be used to determine which Roseobacters most strongly use DMSP as a sulfur source within a coastal marine environment? Explain the NanoSIMS methodology in your answer.

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Question 19

Several fluorogenic dyes can be used simultaneously in a sample as long as they each emit light at a different measurable wavelength.

Accepted Answer

This is true. Fluorogenic dyes can be used simultaneously as long as they emit light at different measurable wavelengths, which allows them to be distinguished from each other. This is often used in multiplex assays, where multiple targets can be detected in a single sample by using different fluorogenic dyes.

Question 20

Using specific examples,when is it appropriate to use CARD-FISH rather than the traditional FISH method and vice-versa?

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Quiz 18: Methods in Microbial Ecology