Structures & Characteristics of Microorganisms for Classification

Introduction

This assignment will explain how the structures and characteristics of microorganisms are used to classify them. It will illustrate the structures of microorganisms observed using a light microscope and an oil immersion lens. Also will include the comparison of the characteristics of microscopes used for classification and include the comparison of the use of different microscopy technique to observe the structures of microorganisms. Finally it will evaluate the use of microscopy technique to observe structures and classify microorganisms

Bacteria

Bacteria are prokaryotic, made up of one cell. Nearly all bacteria are couple micrometers in length. Bacteria have features such as ribosomes which make proteins from mRNA. Flagellums are hair like structure that turns around to make the bacteria move, some bacteria have additional flagellums or none. Cell wall gives the cell strength and structure. The cell membrane has folds called mesosmes. Plasmids are small loops of DNA, plasmids are not in all bacteria cells. The main DNA floats free in the bacteria cell, the long strand is called a bacterial chromosome. A few bacteria have short hair like features called pili. Pili is used in gene transmission as the pili help the bacteria cell stick to another bacteria cell.

How are bacteria classified?

Bacterial classification uses binomial nomenclature two names genus and species. Species can be divided into subspecies because some organisms are too related to each other. Species of bacteria have different variations called serotypes which determine their structure.​

There are five different groups that bacteria can be classified in to, these are spirochaetes, bacilli, vibrios, Spirilla and cocci, from their shapes.

• Spirochaetes- corkscrew
• Bacilli- rod shaped
• Vibrios- comma
• Spirilla- helical
• Cocci- spherical

The different groups of bacteria can live by themselves or in groups.

Scientific Classification

• Domain: Prokaryotes.
• Kingdom: Bacteria.
• Phylum: Firmicutes.
• Class: Bacilli.
• Order: Lactobacillales.
• Family: Streptococcaceae.
• Genus: Streptococcus.
• Species: Streptococcus pyogenes.

Gram Staining

Gram Staining can help to further classify bacteria. By grouping bacteria into two groups’ gram negative and gram positive based on their cell wall. Gram negative is shown when the cell wall of the bacteria don’t keep the crystal violet satin used in the gram staining process. The gram positive is when the cell wall of the bacteria keep the crystal violet satin.

Bacilli

Bacilli is a group of bacteria, which are rod shaped and are gram positive. Species of bacillus form spores in conditions that bacteria don’t grow in. These endospores make this group of bacteria resistant to chemicals and heat. A few bacillus bacteria can harm plants, humans and other microorganisms

An example is B. cereus can cause canned food to go bad, and if eaten can cause food poisoning for a short while.

(The Editors of Encyclopaedia Britannica 2018)

Cocci

Cocci is a group of bacteria, which is spherical in shape and are gram positive. Species of cocci can be used to help in identification. If two cocci cells are present they are called diplococci, more than eight of cocci cells are called staphylococci. Some are arranged like squares or in clusters this is because the reproduction of bacteria affects this.

Spirilla

Spirillum is a group of bacteria, which is helical shaped and are gram negative.

Vibrios

Vibrio is a group of bacteria, which is comma shaped and are gram negative. Species of vibrios are very mobile and don’t need oxygen, and have up to three flagella at one end.

Spirochaetes

Spirochete is a group of bacteria, which are corkscrew shaped, very mobile and are not classified as gram positive or gram negative. This type of bacteria have harmful pathogens which cause diseases such as Lyme disease.

Why are bacteria classified?

Bacteria are classified as it helps professionals who are working with bacteria day to day. A microbiologist at a hospital may want to know which treatment is needed for a patient. A scientist working with cultures might want to know if his strategy is working or not. A hygienist may want to check if the food plant he is looking after contains any harmful microorganisms.

Why are bacteria important in medicine?

Bacteria for a long time have been used to make bacteria vaccinations and the discovery of antibacterial antibiotics, since this bacterial diseases have gone down.

To make these bacteria vaccinations the toxin protein that bacteria make, toxin protein is made inactive, so it will not cause disease.

People with weak immune systems will need to have top up vaccinations if having the inactive vaccination to make sure they can fight the disease.

Why is bacteria important in the industry?

Ethanol can be made by using yeast. Yeast have enzymes that in the process of yeast fermentation, the enzymes turn carbohydrates such as sucrose into simple sugars like glucose, then it converts them into ethanol and carbon dioxide.

Why is bacteria important in food?

Bacteria can convert milk in to other products that are widely consumed, such as yoghurt and cheese. Buttermilk is used using a culture of Lactococcus bacteria, yoghurt are made the same way but using a different culture of bacteria. Most cheese are allowed to ripen with the use of microorganisms, this is important because different types of bacteria give the cheese different tastes and textures. To preserve food bacteria fermentation is used for pickled onions, pickled gherkins and olives.

Viruses

Viruses are microorganisms which are nucleic acid surrounded by protein. They are smaller than bacteria. Viruses have features such as containing a center of DNA or RNA. The protein coat around the DNA is called the capsid, some viruses have an extra layer called an envelope, taken from the cell membrane of a previous host cell. Attachment proteins stick out from the edge of the capsid or envelope. These lets viruses attach itself on to a host cell. Some viruses carry proteins inside their capsid.

How are viruses classified?

Viruses are classified by their shape and size. Also chemical composition and how they replicate.

Mode of Replication: The genome of a virus may contain RNA or DNA which maybe single stranded (ss) or double stranded (ds) linear or circle. The genome may occupy either one nucleic acid molecule (monopartite genome) or several nucleic acid segments (multipartite genome). The different types of genome require different replication strategies.

Why are viruses classified?

Viruses don’t share the same classification system as organisms because they are not believed to be living. Viruses do not have metabolism which means they can’t produce their own food and can only reproduce using an infected host cell.

Why are viruses important in medicine?

Majority of vaccinations use weakened viruses, this is because if a non-weakened virus was used it would reproduce rapidly inside the body, but by using a weakened virus there is small chance for it to infect the person with the disease rather than preventing it. Weakened viruses only reproduce usually 10-20 times compared with a non-weakened virus, which reproduces thousands of times when a person is infected. Because weakened viruses reproduce less, it means it still can produce memory B cells for that particular infection for the future.

Why are viruses important in the industry?

Viruses benefit plants for example there are few plants grow in the hot soils surrounding the geysers and Yellowstone National Park. This plant has a relationship that a fungus takes over the plant and a virus then infects the fungus. This happens to make the plant survive in 50 degrees Celsius. (U.S. Department of the Interior 2017)

Fungi

Fungi are eukaryotic they can be unicellular or multicellular. These are heterotrophs, which means they feed on decaying organic matter. The features that are within a fungi cell are a nucleus where DNA is wrapped around proteins, some have free floating loops of DNA called plasmids, this is similar to bacteria cells.

The cells further contain mitochondria which is said to be the power house of a cell, Golgi apparatus is also present in the cell, and endoplasmic reticulum which is seen as the worm shaped. The cell wall of the fungi cell has polysaccharides called chitin and glucans, which gives it rigid layers and prevents the cell wall from losing moisture and protection. Also have plasma membrane.

How is fungi classified?

There are four different groups that fungi can be classified in which are Chytridiomycota, Zygomycota, Ascomycota and the Basidiomycota. They are classified into these groups depending on how they reproduce.

• Chytridiomycota- chytrids
• Zygomycota- bread moalds
• Ascomycota- yeast and sac fungi
• Basidiomycota- club fungi

(CC BY: Attribution 2018)

• Scientific Classification
• Domain: Eukaryote
• Kingdom: Fungi
• Class: Basidio Mycetes
• Order: Agric Ales
• Family: Agricac Eae
• Genus: Agaricus
• Species: Agaricus Campestris L

Chytridiomycota

Chytridiomycota is the most simple of all types of fungi. Nearly all chytrids have chitin in the cell was but a group has chitin and cellulose in the cell wall. A few chytrids are multicellular but majority are unicellular. They reproduce as diploid and gametes cells that have a flagellum to help them move.

Zygomycota

Zygomycetes are the smallest group of fungi, this type of fungi is the fungi that grown on the surface of breads, vegetables and fruit commonly known as mold. They are present on decaying organic matter.

Ascomycota

Ascomycota are the biggest group of fungi, they are used in the industry to make different types of alcohol such as wine and beer and yeast in baking. A certain fungi can cause harm to patients who have AIDS who have a weakened immune system. They also can be harmful to crops which then are not able to eat.

Basidiomycota

Basidomycota is a group of fungi which are seen as mushrooms that we eat and the bark on trees, this group includes the most edible fungi but some are very dangerous as they make toxins. For example Crptococcus neformans cause bad respiratory illnesses. (CC BY: Attribution 2018)

Why is fungi classified?

Fungi classification have changed over the years, once they were just thought to be plants but now they have their own kingdom and are in fact more related to animals that plants.

Why is fungi important in medicine?

Fungi are useful to humans they are a part of the nutrient cycle in ecosystems. Fungi can naturally produce antibiotics and stop the growth of bacteria, meaning they don’t have to compete in nature. Penicillin a well-known antibiotic that can be made separating from fungi. After someone has an organ transplant they are likely to reject the organ but a drug called cyclosporine lowers down the risk of rejection. Also a fungi called ergot alkaloids is used to stop bleeding in hospital.

(Boundless Biology 2018)

Why is fungi important in the industry?

The farming industry uses fungi in the root system, this because without in they would not live. Fungal supplements are used as soil additives that can be bought from gardening stores. It is mostly favored for organic farming.

Why is fungi important in food?

Fungi makes up a lot of the human diet such as cheeses the fungi penicillium ripens them, also mushroom the most common one found in many dishes is the meadow mushroom. Truffles are used to garnish dishes and are very expensive. For the making of blue cheese, sheep milk is stacked to get the molds of the genus penicillium for the blue veins and strong taste of the cheese. Fungi is used to ferment wheat to make beer and fruit to make wine. Saccharomyces cerevisiae is an example of yeast that is used in baking. It has been used for thousands of years to make bread which was a staple in people’s diets. They did this by leaving dough to gather yeast from surrounding air for a couple of days.

Protozoa

Protozoa are eukaryotes which are singled celled. They are parasitic that feed on decaying matter. Protozoa can have many shapes due to not having a cell wall. Some protozoa will have features such as a rigid shell and pellicle which is a thick membrane. They come in all different shapes and sizes. The size range is big with 10 micrometers as the smallest and 60 micrometer. The largest protozoa are called xenophyophores, which can measure up to 20 centimeters in diameter.

(Wikimedia Foundation, Inc 2018)

How is protozoa classified?

Protozoa the group has thousands of species, which belong to kingdom Protista. Some protozoan feed on bacteria and algae others are parasites.

They are classified into four groups based on how they move:

• Amoebiod
• Flagllates
• Cilliates
• Sporozoans

Amoebiod

Amoebiods are a group of protozoa that can change its shape, which are in dirt or mud and in water. They travel by using pseudopods, which are located on the edge of the amoebiod, they also use pseudopods to submerge their prey. Amoebiod feed in many different ways.

Flagllates

Flagellates are a group of protozoa that have a flagella on the end of it. They live in many ways one is as parasitic, in intestines or bloodstream of host, the host does not benefit from this relationship. Some flagellates are autotrophic while others are heterotrophs.

Ciliates

The ciliates are a group of protozoans that have hair-like organelles called cilia. Cilia are used in the movement, eating and attaching. Most ciliates are heterotrophs.

Several ciliates feed by osmotrophy which is by absorbing the energy. Whereas some hunt for their sources of energy that are other protozoa

There are different types of ciliate protozoa which are crawling, stalked and swimming ciliates. All of which use ciliates for movement and getting their food.

Sporozoans

Sporozoans are a group of protozoa that are unicellular and consist of parasites.

Why are protozoans important in medicine?

Protozoans are food for a lot of organisms that live in water. Example Zooplankton are small protozoans that live in the sea. This is a part of the diet of blue whales, they consume this as they are taking gulps of water.

Why are protozoans important in the industry?

Protozoans have vital roles with soil fertility. As protozoa eat the bacteria in soil, they keep the number of bacteria low, which would mean a higher fertility of soil. They also produce nitrogen and phosphorus which benefits the soil. As plants such as lentils like to thrive in nitrogen and phosphorus rich soil.

Summary of microorganisms

(PeteJago 2013)

Identifying structures from electron micrographs

The nucleus is a large, circular structure surrounded by a tiny membrane.

The nucleolus is contained within the nucleus, and it is responsible for creating rDNA, the ribosomal genome that translates mRNA to proteins.

Mitochondria structures are accountable for making the adenosine triphosphate (cellular energy) for metabolism and chemical reactions inside cells. They are recognizable by the cristae formations that zigzag within the mitochondria cell.

The Golgi complex is the packaging center for the cell. It adds the final compounds on biomolecules such as proteins and fatty acids and transports them to other parts of the cell or into the blood stream

Chromosomes hold the genome of the cell. They are only visible during cell division. They are little, worm-like structures contained inside the nucleus in animal cells.

How the structure of microorganisms is viewed using light microscopes with and without oil immersion?

Light microscopes use lenses and light to magnify a sample, the sample is extremely close to the lens and small, so light can pass through easily.

Oil immersion is a method where the image will look bigger, as it makes the resolving power of the light microscope higher.

Compared to stereo microscopes light microscopes are cheap to purchase and use, small and portable, natural colour of specimen can be observed, living as well as dead matter can be viewed, to set up is quick and simple, requiring little knowledge and not affected by magnetic field.

Fungi- Penicillium 100x magnification not oil immersion

The penicillium is not clear compared to the oil immersion 1000x magnification.

Fungi- Penicillium 1000x magnification with oil immersion

The penicillium is very clear compared to the light microscope without oil immersion and at 100x magnification.

How the structure of microorganism is viewed using stereo microscope?

A stereo microscope is used to observe something that requires a low magnification, it is done when light is reflected of the sample. The magnification is 100x magnification, it is quite low compared to light microscopes that can go up to 1000x magnification when using oil immersion.

Skin and nail 100x magnification which is the highest is magnify to.

There isn’t much detail when using a stereo microscope as the magnification is quite low, only hair and skin indents are seen when a hand is put under a stereo microscope but this is because it is purposely designed to.

Importance of light microscopes and stereo microscopes in medicine and industry

In medicine stereo microscopes are used in pathology labs to view tissue specimens, as it provides accurate observation, which would provide with other information that would not be able to see with the naked eye, the stereo microscope gives a correct final diagnosis.

In industry stereo microscopes are used a lot in factories that make electronic devices, where soldering would take place. Also to see the quality of products, if they are consistent and inspection of delicate product. The reason why they are used is because the high can easily be adjusted and can be moved out of the way if needed by swinging it.

In medicine light microscopes are used because organisms that cause diseases can best seen under a microscope are therefore microscopic. Because of this when a sample is taken from a patient to identify the microorganisms, this allows the patients to receive the right treatment or medicated drugs.

Gram Staining helps scientists to further classify different types of bacteria. By grouping bacteria into two groups’ gram negative and gram positive based on their cell wall. Gram negative is shown when the cell wall of the bacteria don’t keep the crystal violet satin used in the gram staining process. The gram positive is when the cell wall of the bacteria keep the crystal violet satin. These method needed the use of a light microscope.

In industry light microscopes mineralogists use light microscopes to identify what minerals are present in rocks. Mineralogist have a process called thin section. Rocks are cut into thin sections, thin enough for light to pass through from the light source to the mineralogist’s eye. Different crystal grains will be seen because the rock is so thin. Then the shapes seen will let the microbiologist identify what minerals are present.

Reason microorganisms are placed in different groups and why is there such division

I argue that microorganisms are placed in their different groups as microorganisms are divided into seven types: bacteria, archaea, protozoa, algae, fungi, viruses, and multicellular animal parasites. Each type has a unique characteristic cellular composition, morphology, mean of movement, and reproduction. Microorganisms are beneficial in producing oxygen, decomposing organic material, providing nutrients for plants, and maintaining human health, but some can be pathogenic and cause diseases in plants and humans.

Examples of why microorganisms and infectious agents are placed in different groups

Bacteria

Bacteria are prokaryotic, made up of one cell and have no nucleus. There are five different groups that bacteria can be classified in to, these are spirochaetes, bacilli, vibrios, Spirilla and cocci, from their shapes.

• Spirochaetes- corkscrew
• Bacilli- rod shaped
• Vibrios- comma
• Spirilla- helical
• Cocci- spherical

Gram Staining can help to further classify bacteria. By groping bacteria into two groups’ gram negative and gram positive based on their cell wall. Gram negative is shown when the cell wall of the bacteria don’t keep the crystal violet satin used in the gram staining process. The gram positive is when the cell wall of the bacteria keep the crystal violet satin. Bacteria can be split again depending on how they react to oxygen, which are anaerobic, aerobic and both.

Depending on the way they get energy, they are called chemoautotrophs as they get there energy from chemical processes, also heterotrophs as bacteria use decaying matter to get energy are named saprophytes.

Example

Staphylococcus saprophyticus is a Gram-positive coccus belonging to the coagulase-negative genus Staphylococcus.

Scientific Classification

• Kingdom: Bacteria
• Phylum: Firmicutes
• Class: Bacilli
• Order: Bacillales
• Family: Staphylococcaceae
• Genus: Staphylococcus
• Species: S. saprophyticus

Binomial name

Staphylococcus saprophyticus

 (Wikimedia Foundation Inc 2018)

Fungi

Fungi are eukaryotic they can be unicellular or multicellular. These are heterotrophs, which means they feed on decaying organic matter and they have co-opertave relationships with plants, this means both the fungi and the plant benefit. The features that are within a fungi cell are a nucleus where DNA is wrapped around proteins, some have free floating loops of DNA called plasmids, this is similar to bacteria cells.

Example

Penicillium albocoremium is a fungus species in the genus Penicillium.

Scientific Classification

• Kingdom: Fungi
• Division: Ascomycota
• Class: Eurotiomycetes
• Order: Eurotiales
• Family: Trichocomaceae
• Genus: Penicillium
• Species: P. albocoremium

Binomial name

Penicillium albocoremium

(Wikimedia Foundation Inc 2018)

Protozoa

Protozoa are eukaryotes which are singled celled. They are parasitic that feed on decaying matter. Protozoa can have many shapes due to not having a cell wall. Some protozoa will have features such as a rigid shell and pellicle which is a thick membrane. They come in all different shapes and sizes. The size range is big with 10 micrometers as the smallest and 60 micrometer. The largest protozoa are called xenophyophores, which can measure up to 20 centimeters in diameter.

Example

Plasmodium falciparum is plasmodium that causes malaria, which can cause death in humans. This species of plasmodium is unicellular

Scientific Classification

• Domain: Eukaryota
• (unranked): SAR
• (unranked): Alveolata
• Phylum: Apicomplexa
• Class: Aconoidasida
• Order: Haemosporida
• Family: Plasmodiidae
• Genus: Plasmodium
• Species: P. falciparum

Binomial name

Plasmodium falciparum

(Wikimedia Foundation, Inc 2018)

Viruses

Viruses are classified as microorganisms (that are not classed as living) which are nucleic acid surrounded by protein. Viruses have features such as containing a center of DNA or RNA. The protein coat around the DNA is called the capsid. Virus have to live inside a host as they can’t reproduce without a host, which are usually eukaryotic cells and prokaryotic cells. This then leads to diseases.

Example

Ebola virus (which used to be known as Zaire ebolavirus) is a virus within in the genus Ebolavirus

Scientific Classification

• Group: Group V ((−)ssRNA)
• Order: Mononegavirales
• Family: Filoviridae
• Genus: Ebolavirus
• Species: Zaire ebolavirus

Binomial name

Zaire ebolavirus

(Wikimedia Foundation, Inc 2018)

Reference List

Images

• H S Pathology Private Limited, (2018), Microbiology [ONLINE]. Available at: http://www.hsppl.com/Images/PathologySevices/microbiology.jpg [Accessed 18 October 2018].
• Jackom, (2018), Bacterial Cell Anatomy and Internal Structure [ONLINE]. Available at: https://www.thoughtco.com/thmb/qdm2YliznfZS9qo1pjaQ2JZhTrc=/1500×0/filters:no_upscale():max_bytes(150000):strip_icc():format(webp)/bacteria_cell_drawing-5786db0a5f9b5831b54f017c.jpg [Accessed 17 October 2018].
• Study.com, (2018), Structure of an enveloped virus [ONLINE]. Available at: https://study.com/cimages/multimages/16/340px-viral_tegument.svg.png [Accessed 17 October 2018].
• Mike Adkins, (2018), Fungal Cell Diagram [ONLINE]. Available at: http://mikeadkinsguitar.com/fungal-cell-diagram.html [Accessed 17 October 2018].
• Biology Wise, (2018), Ciliates [ONLINE]. Available at: https://biologywise.com/protozoa-classification-characteristics [Accessed 17 October 2018].

Books

• Parsons R  2015. A-Level Biology Edexcel A (Salters-Nuffield). 1st ed. Newcastel upton Tyne: Coordination Group Publications Ltd.

Websites

• LibreTexts. 2018. 24.1B: Fungi Cell Structure and Function. [ONLINE] Available at: https://bio.libretexts.org/TextMaps/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/24%3A_Fungi/24.1%3A_Characteristics_of_Fungi/24.1B%3A_Fungi_Cell_Structure_and_Function. [Accessed 17 October 2018].
• Biology Wise. 2018. The Major Classification and Characteristics of Protozoa. [ONLINE] Available at: https://biologywise.com/protozoa-classification-characteristics. [Accessed 17 October 2018].
• The Editors of Encyclopaedia Britannica. 2018. Bacillus Bacteria. [ONLINE] Available at: https://www.britannica.com/science/bacillus-bacteria. [Accessed 18 October 2018].
• Gelderblom, H. 2018. Structure and Classification of Viruses. [ONLINE] Available at: https://www.ncbi.nlm.nih.gov/books/NBK8174/ [Accessed 18 October 2018].
• BioNinga. 2018. Virus Classification. [ONLINE] Available at: http://ib.bioninja.com.au/standard-level/topic-5-evolution-and-biodi/53-classification-of-biodiv/virus-classification.html. [Accessed 18 October 2018].
• American Society For Microbiology. 2018. Viruses: You’ve Heard the Bad. Here’s the Good. [ONLINE] Available at: https://www.asm.org/index.php/asm-newsroom2/press-releases/93495-viruses-you-ve-heard-the-bad-here-s-the-good. [Accessed 18 October 2018].
• Biology II. 2018. Classification of Fungi. [ONLINE] Available at: https://courses.lumenlearning.com/suny-mcc-biology2/chapter/classification-of-fungi/. [Accessed 18 October 2018].
• Cliffs Notes. 2018. A Kingdom Separate from Plants. [ONLINE] Available at: https://www.cliffsnotes.com/study-guides/biology/plant-biology/fungi-not-plants/a-kingdom-separate-from-plants. [Accessed 19 October 2018].
• Boundless Biology. 2018. Importance of Fungi in Human Life. [ONLINE] Available at: https://courses.lumenlearning.com/boundless-biology/chapter/importance-of-fungi-in-human-life/. [Accessed 18 October 2018].
• Study.com. 2018. Light Microscope: Definition, Uses & Parts. [ONLINE] Available at: https://study.com/academy/lesson/light-microscope-definition-uses-parts.html. [Accessed 22 October 2018].
• Wikimedia Foundation Inc. 2018. Staphylococcus. [ONLINE] Available at: https://en.wikipedia.org/wiki/Staphylococcus. [Accessed 7 November 2018].
• MICROSCOPE WORLD. 2018. Industrial Stereo Microscopes. [ONLINE] Available at: https://www.microscopeworld.com/t-industrial_stereo_microscopes.aspx. [Accessed 23 October 2018].
• U.S. Department of Health & Human Services. 2018. Efficacy of stereomicroscope as an aid to histopathological diagnosis. [ONLINE] Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4409178/. [Accessed 24 October 2018].
• PBworks. 2018. Why Do Hospitals Use Microscopes?. [ONLINE] Available at: http://confocalmanawatu.pbworks.com/w/page/78944981/Why%20Do%20Hospitals%20Use%20Microscopes. [Accessed 24 October 2018].
• Leaf Group Ltd. 2018. How to identify cell structures. [ONLINE] Available at: https://sciencing.com/identify-cell-structures-5106648.html. [Accessed 5 November 2018].
• Boundless Microbiology. 2018. Microbes and the World. [ONLINE] Available at: https://courses.lumenlearning.com/boundless-microbiology/chapter/microbes-and-the-world/. [Accessed 7 November 2018].