Plant Microbioloy 2 (Caroline)

Question 1

What is the difference between bulk soil and rhizosphere soil

Answer 1

Bulk soil - soil not directly affected by living roots.

Rhizosphere soil - soil surrounding the rhizoplane (immediate surface of root) and affected by root activity.

Question 2

Describe the molecular methods used to study microbial communities

Answer 2

DNA fingerprinting

• Denaturing Gradient Gel Electrophoresis uses gradient of DNA denaturing agents to separate DNA fragments.
• DNA re-association used to determine the number of genomes present.

Genome sequencing using Illumina sequencing

• DNA fragmentation.
• Attach adapters to DNA fragments to create a sequencing library.
• Clonal amplification by solid phase PCR (bridge amplification).
• All DNA fragments are sequenced simultaneously.

Amplicon sequencing using Illumina technology

• Extraction of metagenomic DNA from an environmental sample.
• Amplification of the 16S region.
• Sequencing of 16S region.
• Use of bioinformatics to gather results.

Metagenomics

• Determining which microbes are present by SSU rRNA approaches.
• Use of metatranscriptomics, metaproteomics, and metabonomics to study what the microbes are doing.
• Use of metagenomics to study the genetic potential of the microbes.