The winogradsky column is as an artificial microbial ecosystem that serve a short term source of bacteria for isolating a pure culture.

Mud is supplemented with Calcium Sulphate as a buffer and Calcium Carbonate as a source of Carbon

Air is not prohibited in the Winogradsky column since the anaerobic microorganism could live below the surface where the Oxygen is not available. The column could be packed loosely but should be covered by different source of water.

Agar dilution tubes is a mixed culture diluted in molten agar for purifying anaerobic microorganisms.

DAPI, AO, and SYBR Green stain will be fluorescent under UV, but unable to be used to measure the quantity of microorganism in the sample.

In the Winogradsky Column, the up-most layer in the water column is oxic because algae and cyanobacteria produces O2 by photosynthesis. Decomposition process happens in the mud, leading to the production of organic acid, alcoholes, and H2 that provides a good environment for non-sulfate-reducing bacteria. These bacteria then produce H2S, triggering the growth of purple and green bacteria. These bacteria grow in the shape of layers and may bloom due to the lack of oxygen and/or oxygenic phototrophs.

Winogradsky columns have been used to enrich only the aerobic prokaryotes since the anaerobic ones are inhibited by anaerobic bacteria. The other purpose of using this columns is to test the hypothesis that an organism in the inoculum is able to degrade the specific compound that supplemented in the column. Using this column as a supply source of inocula for enrichment cultures is impossible.

Agar Dilution Tubes method uses a serial dilution in a molten agar to isolate a single colony of aerobic microorganism.

MPN (Most Probable Number) technique is used to estimate the number of microorganism in samples that have to be assessed regularly like food, wastewater, etc.

Since DNA Staining such as DAPI and AO is highly specific, the viability of the cells could be assessed and measure the living cells. Thus, this technique is desirable to track species of microorganism in the environment.

The basis of differentiating between living and dead cells is whether or not the endoplasmic reticulum is intact. Dyes that fluoresce green and red are used, green for all bacteria, and red only stains dead bacteria. Viability staining like this could instantly give an information about the abundance and viability of microorganism observed.

The more specific fluorescent staining possible is by using fluorescent antibodies. This antibody provides a great information about the microorganism observed. However, this technique is rather expensive and time-consuming.

gfp gene is able to be used on both oxic and anoxic environment because the need of O2 is optional for GFP protein to fluoresce. That is the reason why gfp method is widely used in many fields to track microorganism and its life cycle.

A reporter gene is a gene that able to report an activity of translation.