Microbial Diversity Methods Review Test

Explanation
PLFA (Phospholipid fatty acid analysis), plating counts, and CLPP (Community level physiological profiling) are all biochemical techniques used to assess microbial diversity and community structure in soil. PLFA involves analyzing the fatty acids present in the phospholipids of microbial cell membranes, providing information about the types and quantities of different microbial groups. Plating counts involve culturing microbes from soil samples on agar plates and counting the number of colonies formed, providing information about the abundance of different microbial species. CLPP involves measuring the metabolic activity of microbial communities by analyzing their ability to utilize different carbon sources, providing information about the functional diversity of the community.

Explanation
Plating counts is the correct answer because it is a traditional biochemical technique used to assess soil microbial diversity. However, it has limitations as it can only determine a small proportion (1%) of microorganisms present in the soil.

Explanation
Phospholipids are potentially useful signature molecules to assess microbial diversity because they are important components of membranes in viable microorganisms. They are also rapidly metabolized following cell death, making them a good indicator of recent microbial activity. Additionally, phospholipids make up a fairly constant proportion of the biomass of organisms, allowing for a reliable assessment of microbial diversity.

Explanation
C+G analysis is a quantitative molecular method that is useful when a coarse level of resolution is required. It is not influenced by PCR biases, which makes it a reliable technique for analyzing the distribution of C+G nucleotides in a DNA sequence. By determining the C+G content, researchers can gain insights into the stability, function, and evolution of the DNA. This method is particularly valuable when studying organisms with varying C+G content, such as bacteria or different species.

Explanation
These molecular methods, including DGGE/TGGE, T-RFLP, RISA, and SSCP, are subject to PCR biases. PCR biases refer to the uneven amplification of DNA fragments during the PCR process, leading to inaccurate representation of the original DNA sample. These biases can occur due to variations in primer binding efficiency, template secondary structure, or differences in DNA sequence composition. Therefore, the results obtained from these methods may not accurately reflect the true diversity or abundance of the target DNA molecules in the sample.

Explanation
T-RFLP (Terminal Restriction Fragment Length Polymorphism) is a molecular technique that utilizes DNA polymorphisms to detect only the labelled terminal restriction fragment. In this technique, DNA is digested with restriction enzymes, and the resulting fragments are labeled with a fluorescent dye. The fragments are then separated by size using gel electrophoresis and detected using a fluorescence detector. By comparing the fragment sizes with a reference database, T-RFLP can identify and differentiate between different DNA samples based on their unique patterns of restriction fragment lengths.

Explanation
RISA stands for Ribosomal Intergenic Spacer Analysis, which is a molecular technique used to analyze and compare the diversity of microbial communities. It involves amplifying the PCR products of the intergenic spacer region located between the 16S and 23S rRNA genes. By analyzing the resulting DNA fragments, researchers can identify and compare different microbial species present in a sample. This technique is commonly used in microbial ecology studies to understand the composition and dynamics of microbial communities in various environments.

Explanation
SSCP (Single-Strand Conformation Polymorphism) is a method that relies on the ability of single-stranded DNA molecules to fold into unique secondary structures. This technique is used to detect genetic variations or mutations in DNA samples. By subjecting the DNA to different temperatures, the single-stranded molecules will adopt different conformations depending on their nucleotide sequence. These conformational changes can be visualized by gel electrophoresis, allowing for the identification of genetic differences. SSCP is commonly used in genetic research and diagnostics to study genetic diseases, identify polymorphisms, and analyze DNA samples.

Explanation
This method involves separating DNA clones based on changes in their electrophoretic mobility as they migrate through a gel with a linearly increasing gradient of DNA denaturants. DGGE (Denaturing Gradient Gel Electrophoresis) and TGGE (Temperature Gradient Gel Electrophoresis) are two techniques that utilize this principle. They are commonly used to analyze DNA sequences and detect genetic variations such as point mutations and single nucleotide polymorphisms. These techniques are valuable tools in molecular biology research and have applications in fields such as genetics, genomics, and forensic science.

Explanation
DNA microarrays are a molecular technique that allows the analysis of thousands of genes. Unlike PCR biases, it is not influenced by them. However, DNA microarrays are only accurate in low diversity systems. This means that they may not be as effective in analyzing highly diverse genetic samples.