Question 1

Which of the following best explains the 'plate count anomaly' observed in microbial ecology?

Accepted Answer

Only a small fraction of environmental microbes can grow on standard laboratory media, leading to an underestimation of microbial diversity.

Question 2

You are tasked with isolating an autotrophic ammonia-oxidizing bacterium such as Nitrosomonas. Which medium composition would be most appropriate?

Accepted Answer

Medium with no organic carbon, NH$$_3$$, O$$_2$$, and kept in the dark.

Question 3

Which of the following statements about 16S rRNA gene sequencing is correct?

Accepted Answer

The 16S rRNA gene is found in all life forms and contains both conserved and variable regions, making it useful for taxonomic identification.

Question 4

A researcher wants to visualize the spatial distribution of different microbial taxa within a biofilm. Which technique should they use?

Accepted Answer

Fluorescence In Situ Hybridization (FISH) with taxon-specific probes.

Question 5

Which of the following is a key advantage of Illumina high-throughput sequencing over Sanger sequencing for environmental 16S rRNA gene analysis?

Accepted Answer

Illumina sequencing can generate millions of sequences, allowing detection of rare community members.

Question 6

You want to enrich for and isolate methylotrophic bacteria from an environmental sample. Which of the following media compositions is most appropriate?

Accepted Answer

Medium with methane or methanol as the sole carbon source, mineral nutrients, and no organic nitrogen.

Question 7

Which method would allow you to identify and sequence the genomes of methane-assimilating bacteria in an environmental sample, even if they cannot be cultured?

Accepted Answer

Metagenomic sequencing of total community DNA, followed by bioinformatic analysis to identify methane assimilation genes.

Question 8

A scientist wants to quickly compare the number of microbial species and their similarity across 10 soil samples. Which technique is most suitable for this purpose?

Accepted Answer

16S rRNA gene amplicon sequencing using Illumina technology.

Question 9

Which of the following best describes the purpose of using operational taxonomic units (OTUs) in microbial ecology studies?

Accepted Answer

OTUs group sequences by similarity, serving as a proxy for species in diversity analyses.

Question 10

Which of the following is a major challenge in analyzing metagenomic data from complex microbial communities?

Accepted Answer

Difficulty in assembling short DNA reads into complete genomes due to high species diversity and similar gene sequences.

Question 11

Which of the following best describes the process of FISH-MAR (Fluorescence In Situ Hybridization - Microautoradiography)?

Accepted Answer

Incubating samples with a radioactive compound, detecting cells that assimilate the label by autoradiography, and then using FISH to identify the taxa of those cells.

Question 12

A researcher wants to determine which protein-coding genes are important for survival in a microbial community. Which approach should they use?

Accepted Answer

Metagenomic sequencing followed by functional annotation of protein-coding genes.

Question 13

Which of the following is a key step in preparing a 16S rRNA gene library using the Sanger sequencing method?

Accepted Answer

Cloning PCR-amplified 16S rRNA genes into plasmids and transforming them into E. coli.

Question 14

Which of the following best describes the use of rarefaction analysis in microbial ecology?

Accepted Answer

It assesses whether the sampling effort has captured the full diversity of operational taxonomic units (OTUs) in a community.

Question 15

Which of the following scenarios would require the use of co-culturing techniques in the laboratory?

Accepted Answer

Isolating a microbe that is obligately mutualistic with another species.

Question 16

A scientist is interested in the metabolic pathways present in a microbial community from a mine water biofilm. Which method would provide the most comprehensive information?

Accepted Answer

Metagenomic sequencing and annotation of functional genes.

Question 17

Which of the following is a limitation of using culture-based methods to study environmental microbial communities?

Accepted Answer

They fail to recover the vast majority of microbes that cannot grow on standard laboratory media.

Question 18

Which of the following best describes the process of single-cell genome sequencing?

Accepted Answer

Isolating a single cell, amplifying its genome, and sequencing the amplified DNA.

Question 19

Which of the following is a real-world application of metagenomics in environmental microbiology?

Accepted Answer

Identifying antibiotic resistance genes in hospital wastewater.

Methods in Microbial Ecology: Culture-Based and Culture-Independent Approaches Ch 19

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