Microorganisms Basics

Created: Sep 2021

These three sub-reports gained full points during assessment, so they can be considered the most reliable out of all the example reports in the Lab Reports section.


Microbiology is the study of organisms that can’t be seen with a naked eye i.e. 0.5- 10 μm is size. Microorganisms are present in a wide range of environments, including extreme environments such as volcanoes, hot springs and deep sea. Moreover, they have the ability to break down various compounds such as sugars, fatty acids, organic acids and even hardly decomposable aromatic compounds and artificially synthetized environmental pollutants into simple compounds such as water and carbon dioxide. Thanks to this ability, microorganisms play an extremely important role in the circulation of materials and purification of the environment.

Mankind had been using microorganisms for several thousand years, notably in the production of foods such as beer, bread, yoghurt, soy sauce etc.. The production of those traditional fermented foods is called the Old Biotechnology. In recent years, however, microbiology has developed greatly and is now used in production of vitamins, amino acids, antibiotics and much more. Microorganisms are also used in the decomposition of pollutants and detoxication of heavy metals. Moreover, they assist in the production of biofuels and biopolymers. The applications of microbiology have been aiding environmental protection, which has become an objective of numerous governments all over the world, in a plethora of ways.

With the development of genetic engineering techniques in 1970, it became possible to analyse and alter microorganisms at a genetic level. As the result, amino acid mutations that strengthen the enzyme functions have been introduced into microorganisms’ genome. Moreover, various improvements to the gene expression system have been made, which resulted in the development of industrial fermentation. Due to further technological developments, in 2010 it became possible to manipulate the microorganisms at the genomic level (entirety of an organism's genetic information), which allowed further modification of their functions and abilities.

The purpose of conducting the experiments outlined in this report is acquiring the knowledge of basic experimental techniques used in handling microorganisms. Moreover, it is to aid the understanding and the appreciation of the role and importance of microbiology in various areas of science and industry.

In the first experiment, microorganism screening will be conducted. It includes an attempt at isolating a single colony from a larger group of microorganisms, which were cultivated using an environmental sample. Second experiment constitutes growing Escherichia coli, which will aid the knowledge of E. coli handling methods that are frequently used in the field of genetic engineering. The last experiment will investigate the enzyme induction. It will serve to acquire the knowledge of the microorganism function induction system and of the enzyme activity measurement method. Over the course of all three experiments, the knowledge of the operation of the clean bench and autoclave, and the handling method of micropipettes and other equipment, will also be acquired.

Carrying out the experiments described in this report will equip the students with the basic knowledge of microbiology experimental methods that will aid them in further years of university education and, possibly, in the future research career.

More on Microorganisms

Metagenome Analysis for Identifying Microorganism Species

In this experiment, you will see that different cultures of microorganisms will grow on different mediums, depending on what compounds those mediums contain (glucose, succinic acid etc.). However, this time the culture types will only be assessed visually, which has severe limitations concerning differentiating between microorganism types. 16S rRNA gene-based metagenomic analysis is a way more reliable and accurate method for determining which microorganism group we are dealing with.

Metagenome is known as the collective genome of microorganisms present in an environmental sample. That is to say, it contains the genome of many individual microorganisms. 16S rRNA is a part of the ribosomal RNA. Ribosomes are found in all living cells, and are made up of 2 subunits. Prokaryotic ribosomes are made up of 30S and 50S subunits. 16S rRNA belongs to the 30S subunit. The important characteristic of 16S rRNA is the presence of hyper variable regions. Because of this characteristic, the 16 rRNA sequence provides species-specific signature, which can be used to differentiate between bacterial species.

Using 16S rRNA gene-based metagenomic analysis, species diversity (mainly in bacteria) and phylogenetic relationships between those species can be assessed. The experimental procedures involve DNA extraction, PCR, electrophoresis, DNA elution, radiolabelling, restriction digestion, southern blotting and, lastly, autoradiography. In the 16S rRNA gene-based metagenomic analysis, the accuracy of identifying microorganisms’ species is significantly greater than the accuracy of the method used in this experiment.

Purification of environmental pollution (Bioremediation) using microorganisms

Microorganism have the ability to break down a wide range of organic compounds. They are able to degrade pollutants into non-toxic substances, which is why they are often used in pollution clean-up. Removing the pollutants using microorganisms is called bioremediation. Bioremediation can be used for treatment of contaminated soil and groundwater and biofiltration of air.

In case of contaminated soil, the pollution can occur due to chemical spillage, heavy metal accumulation or pesticide use. The example of such contaminated land is London’s Olympic Park, which has been heavily contaminated due to industrial activity. Before the 2012 Olympics, 1.7 million cubic metres of heavily polluted soil has been cleaned using bioremediation. In that case, biostimulation techniques have been used to stimulate the growth of microbes present in the contaminated soil. Biostimulation overcomes the limitations to the growth of the microbes (nutrient availability, moisture content etc.) by providing various resources. As the microbes in the soil increase in number, the pollutant degradation rate also increases. In alternative to biostimulation using chemicals, poultry droppings can also be used as a biostimulating agent, providing microbes with nitrogen and phosphorus that increases their growth rate.

If the air becomes polluted due to industrial processes, biofiltering techniques are employed to counteract the pollution. The polluted air is passed over a replaceable culture medium that contains organisms which are able to degrade the pollutants into non-toxic compounds such as water, salts and carbon dioxide.

Bioremediation can also be used to treat polluted water, especially sewage. Sewage water is first aerated, which grants oxygen to microorganisms that break down the organic matter and pollutants. Microbes metabolise the organic contaminants and bind the less soluble compounds, which can be filtered off afterwards. Ammonia in the sewage water is turned into harmless nitrogen gas. Groundwater polluted with ammonia can also be cleaned using this method.

As the research continues, new, more effective bioremediation methods are being developed. They help to decrease the negative environmental impacts of industrial activities, promoting clean enrivorment.

Medium for isolating microorganisms from seawater

To isolate microorganisms from the sea, mediums of similar makeup to that of the seawater are often used. The mediums need to be rich in nutrients and salts in order to mimic the marine environment.

Sea water with agar is frequently used as the culture medium for marine microorganisms, as it already contains all the nutrients present in the microorganism’s natural environment. To make sea water agar plates, bacto agar is mixed with sea water. Alternatively, filtered sea water (of the same salinity as the seawater the microorganisms were collected from) can be used as a liquid culture medium. If the sea water is not available, Glycerol Artificial Sea Water Agar etc. can be used[4].

However, microorganisms that are abundant in the sea often prove difficult to be cultured by standard microbiological procedures. One possible explanation is that the laboratory cultures do not allow cell‐to‐cell communication that occurs in the marine environment, which impedes the growth of marine microorganisms in laboratory conditions.

Bibliography for this section (including sub-reports):

[1] Biology Discussion. 2018. Difference between Constitutive and Inductive Enzymes. http://www.biologydiscussion.com/enzymes/difference-between-constitutive-and-inductive-enzymes/22905. [Accessed 24 December 2018].

[2] Rebecca Philp. 2015. Bioremediation: the Pollution Solution? https://microbiologysociety.org/blog/bioremediation-the-pollution-solution.html. [Accessed 24 December 2018].

[3] Research Gate. 2016. How to isolate marine microorganisms? https://www.researchgate.net/post/how_to_isolate_marine_microorganisms. [Accessed 24 December 2018].

[4] Ian Joint, Martin Mühling and Joël Querellou. 2010. Culturing marine bacteria – an essential prerequisite for biodiscovery. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3815769/. [Accessed 24 December 2018].

[5] Nature. 2018. Metagenomics. https://www.nature.com/subjects/metagenomics. [Accessed 24 December 2018].

[6] Your Dictionary. 2018. Metagenome. https://www.yourdictionary.com/metagenome. [Accessed 24 December 2018].

[7] Virtual Amrita Laboratories Universalizing Education. 2016. 16S Ribosomal RNA Sequencing. http://vlab.amrita.edu/?sub=3&brch=76&sim=1421&cnt=1. [Accessed 24 December 2018].

[8] Khan Academy. 2018. The lac operon. https://www.khanacademy.org/science/biology/gene-regulation/gene-regulation-in-bacteria/a/the-lac-operon. [Accessed 24 December 2018].

[9] J. Parker. 2001. Lac Operon. https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/lac-operon. [Accessed 24 December 2018].