Question 1

Which of the following best explains the 'Great Plate Count Anomaly' observed in microbial ecology?

Accepted Answer

Plate counts typically underestimate microbial abundance because many microbes cannot be cultured under standard laboratory conditions.

Question 2

What is the primary function of a biomarker in microbial ecology?

Accepted Answer

To indicate the presence of a specific organism or group through a unique macromolecule.

Question 3

Why is the 16S rRNA gene commonly used as a 'barcode' for bacterial identification?

Accepted Answer

It contains both conserved and variable regions, enabling phylogenetic analysis across diverse taxa.

Question 4

Which step in the 16S rRNA gene survey pipeline ensures that only the target gene is amplified?

Accepted Answer

PCR with specific primers

Question 5

A researcher wants to compare the microbial diversity between two soil samples. Which diversity measure should they use?

Accepted Answer

Beta diversity, which compares diversity between different samples.

Question 6

Which of the following is a cultivation-independent method for identifying microorganisms in an environment?

Accepted Answer

Sequencing the 16S rRNA gene directly from environmental DNA.

Question 7

What is the main advantage of metagenomics over traditional cultivation-based methods?

Accepted Answer

It analyzes the genetic complement of all cells present, including unculturable microbes.

Question 8

Which equation represents the Shannon Diversity Index used to measure alpha diversity?

Accepted Answer

$$H' = -\sum_{i=1}^{S} p_i \log p_i$$

Question 9

In stable-isotope probing (SIP), what is the purpose of using a compound labeled with a stable isotope (e.g., $$^{13}C$$)?

Accepted Answer

To trace the incorporation of the isotope into DNA or RNA of metabolically active microbes.

Question 10

Which of the following best describes the concept of 'enrichment bias' in cultivation-independent microbial surveys?

Accepted Answer

Bias introduced by preferential amplification of certain genes during PCR.

Question 11

A scientist is interested in the functional potential of a microbial community. Which meta-omics approach should they use?

Accepted Answer

Metaproteomics, to study the proteins expressed by the community.

Question 12

Which database is commonly used for 16S rRNA gene sequence comparison and taxonomic assignment?

Accepted Answer

SILVA

Question 13

What is the role of primers in PCR-based microbial surveys?

Accepted Answer

They determine which gene is amplified by initiating DNA synthesis at specific sequences.

Question 14

Which of the following is NOT a limitation of using the 16S rRNA gene for phylogenetic analysis?

Accepted Answer

It is present in all eukaryotes.

Question 15

A metagenomic study reveals a high abundance of nitrogenase genes in a soil sample. What does this suggest about the microbial community?

Accepted Answer

The community is likely involved in nitrogen fixation.

Question 16

Which of the following best describes 'binning' in metagenomics?

Accepted Answer

Grouping genes from metagenomic data into genomes based on sequence similarity.

Question 17

Which meta-omics approach would be most appropriate for studying gene expression patterns in a microbial community?

Accepted Answer

Meta-transcriptomics

Question 18

If a researcher wants to study the metabolic products of a microbial community, which approach should they use?

Accepted Answer

Metabolomics

Question 19

Which of the following is a reason why direct microscopic counts are often higher than plate counts in environmental samples?

Accepted Answer

Direct counts include both culturable and unculturable cells.

Question 20

Which of the following statements about alpha diversity is correct?

Accepted Answer

It includes richness, evenness, and integrated diversity measures within a single sample.

Cultivation-independent Genomic Methods in Microbial Ecology: Study Notes

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