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1.2.1: Types of Microorganisms - Biology


Microorganisms make up a large part of the planet’s living material and play a major role in maintaining the Earth’s ecosystem.

Learning Objectives

  • Define the differences between microbial organisms.

Key Points

  • Microorganisms are divided into seven types: bacteria, archaea, protozoa, algae, fungi, viruses, and multicellular animal parasites ( helminths ).
  • Each type has a characteristic cellular composition, morphology, mean of locomotion, 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.

Key Terms

  • Gram stain: A method of differentiating bacterial species into two large groups (Gram-positive and Gram-negative).
  • peptidoglycan: A polymer of glycan and peptides found in bacterial cell walls.

Microorganisms or microbes are microscopic organisms that exist as unicellular, multicellular, or cell clusters. Microorganims are widespread in nature and are beneficial to life, but some can cause serious harm. They can be divided into six major types: bacteria, archaea, fungi, protozoa, algae, and viruses.

Bacteria

Bacteria are unicellular organisms. The cells are described as prokaryotic because they lack a nucleus. They exist in four major shapes: bacillus (rod shape), coccus (spherical shape), spirilla (spiral shape), and vibrio (curved shape). Most bacteria have a peptidoglycan cell wall; they divide by binary fission; and they may possess flagella for motility. The difference in their cell wall structure is a major feature used in classifying these organisms.

According to the way their cell wall structure stains, bacteria can be classified as either Gram-positive or Gram-negative when using the Gram staining. Bacteria can be further divided based on their response to gaseous oxygen into the following groups: aerobic (living in the presence of oxygen), anaerobic (living without oxygen), and facultative anaerobes (can live in both environments).

According to the way they obtain energy, bacteria are classified as heterotrophs or autotrophs. Autotrophs make their own food by using the energy of sunlight or chemical reactions, in which case they are called chemoautotrophs. Heterotrophs obtain their energy by consuming other organisms. Bacteria that use decaying life forms as a source of energy are called saprophytes.

Archaea

Archaea or Archaebacteria differ from true bacteria in their cell wall structure and lack peptidoglycans. They are prokaryotic cells with avidity to extreme environmental conditions. Based on their habitat, all Archaeans can be divided into the following groups: methanogens (methane-producing organisms), halophiles (archaeans that live in salty environments), thermophiles (archaeans that live at extremely hot temperatures), and psychrophiles (cold-temperature Archaeans). Archaeans use different energy sources like hydrogen gas, carbon dioxide, and sulphur. Some of them use sunlight to make energy, but not the same way plants do. They absorb sunlight using their membrane pigment, bacteriorhodopsin. This reacts with light, leading to the formation of the energy molecule adenosine triphosphate (ATP).

Fungi

Fungi (mushroom, molds, and yeasts) are eukaryotic cells (with a true nucleus). Most fungi are multicellular and their cell wall is composed of chitin. They obtain nutrients by absorbing organic material from their environment (decomposers), through symbiotic relationships with plants (symbionts), or harmful relationships with a host (parasites). They form characteristic filamentous tubes called hyphae that help absorb material. The collection of hyphae is called mycelium. Fungi reproduce by releasing spores.

Protozoa

Protozoa are unicellular aerobic eukaryotes. They have a nucleus, complex organelles, and obtain nourishment by absorption or ingestion through specialized structures. They make up the largest group of organisms in the world in terms of numbers, biomass, and diversity. Their cell walls are made up of cellulose. Protozoa have been traditionally divided based on their mode of locomotion: flagellates produce their own food and use their whip-like structure to propel forward, ciliates have tiny hair that beat to produce movement, amoeboids have false feet or pseudopodia used for feeding and locomotion, and sporozoans are non-motile. They also have different means of nutrition, which groups them as autotrophs or heterotrophs.

Algae

Algae, also called cyanobacteria or blue-green algae, are unicellular or multicellular eukaryotes that obtain nourishment by photosynthesis. They live in water, damp soil, and rocks and produce oxygen and carbohydrates used by other organisms. It is believed that cyanobacteria are the origins of green land plants.

Viruses

Viruses are noncellular entities that consist of a nucleic acid core (DNA or RNA) surrounded by a protein coat. Although viruses are classified as microorganisms, they are not considered living organisms. Viruses cannot reproduce outside a host cell and cannot metabolize on their own. Viruses often infest prokaryotic and eukaryotic cells causing diseases.

Multicellular Animal Parasites

A group of eukaryotic organisms consisting of the flatworms and roundworms, which are collectively referred to as the helminths. Although they are not microorganisms by definition, since they are large enough to be easily seen with the naked eye, they live a part of their life cycle in microscopic form. Since the parasitic helminths are of clinical importance, they are often discussed along with the other groups of microbes.


Different Types of Bacteria

Bacterial classification is more complex than the one based on basic factors like whether they are harmful or helpful to humans or the environment in which they exist. This article will give you a detailed classification of bacteria.

Bacterial classification is more complex than the one based on basic factors like whether they are harmful or helpful to humans or the environment in which they exist. This article will give you a detailed classification of bacteria.

What are bacteria?

Bacteria (singular: bacterium) are single-celled organisms which can only be seen through a microscope. They come in different shapes and sizes, and their sizes are measured in micrometer – which is a millionth part of a meter. There are several different types of bacteria, and they are found everywhere and in all types of environment.

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There are various groups of bacteria, which belong to the same family and have evolved from the same bacteria (ancestoral). However, each of these types possess their own peculiar characteristics – which have evolved after separation from the original species. The classification of bacteria is based on many factors like morphology, DNA sequencing, requirement of oxygen and carbon-dioxide, staining methods, presence of flagellae, cell structure, etc. This article will give you the classification of these micro-organisms based on all these factors, as well as a few other factors.

Classification of Bacteria

Before the invention of the DNA sequencing technique, bacteria were mainly classified based on their shapes – also known as morphology, biochemistry and staining – i.e. either Gram positive or Gram negative staining. Nowadays, along with the morphology, DNA sequencing is also used in order to classify bacteria. DNA sequencing helps in understanding the relationship between two types of bacteria i.e. if they are related to each other despite their different shapes. Along with the shape and DNA sequence, other things such as their metabolic activities, conditions required for their growth, biochemical reactions (i.e., biochemistry as mentioned above), antigenic properties etc. are also helpful in classifying the bacteria.

Based on Morphology, DNA Sequencing, and Biochemistry

Based on the morphology, DNA sequencing, conditions required and biochemistry, scientists have come up with the following classification with 28 different bacterial phyla:

  1. Acidobacteria
  2. Actinobacteria
  3. Aquificae
  4. Bacteroidetes
  5. Caldiserica
  6. Chlamydiae
  7. Chlorobi
  8. Chloroflexi
  9. Chrysiogenetes
  10. Cyanobacteria
  11. Deferribacteres
  12. Deinococcus-Thermus
  13. Dictyoglomi
  14. Elusimicrobia
  15. Fibrobacteres
  16. Firmicutes
  17. Fusobacteria
  18. Gemmatimonadetes
  19. Lentisphaerae
  20. Nitrospira
  21. Planctomycetes
  22. Proteobacteria
  23. Spirochaetes
  24. Synergistetes
  25. Tenericutes
  26. Thermodesulfobacteria
  27. Thermotogae
  28. Verrucomicrobia

Each phylum further corresponds to the number of species and genera of bacteria. In a broad sense, this bacterial classification includes bacteria which are found in various types of environment such as fresh-water bacteria, saline-water bacteria, bacteria that can survive extreme temperatures (as in sulfur-water-spring bacteria and bacteria found in Antarctica ice), bacteria that can survive in highly acidic environment, bacteria that can survive in highly alkaline environment, bacteria that can withstand high radiations, aerobic bacteria, anaerobic bacteria, autotrophic bacteria, heterotrophic bacteria, and so on…


1.2.1: Types of Microorganisms - Biology

You are to become his research assisitants and help him carry out a research investigation into the properties of microbes.

=====

Brother Gregory has been given a series of the microbes and been asked to determine the growth properties of each species to see where it can grow best.

He wants you, his research assistants, to try growing these microbe under a number of different environmental conditions and find out how fast they reproduce.

This investigation concerns the effect of temperature on the rate of growth, its upper and lower limits, and finding out at which temperature the microbes grow best.

Background
Microbes, even if they are supplied with all the necessary nutritional requirements, still may not grow.

Bacteria, single celled eukaryotes and other microbes, can only live and reproduce within a certain range of environmental conditions. Factors that can influence if or how microbes can grow are temperature, pH, dissolved gases, osmotic pressure and water availability.

Microbes, such as bacteria are more tolerant of environmental conditions than other organisms. However, each species has its own characteristic and particular range of values in which it grows and reproduces best.

Upper and Lower Values, and Temperature Range Some species of microorganism can grow at temperatures as low as -10 o C, and others at temperatures as high as 100 o C - or higher. These upper and lower values are a function of cell metabolism. At lower temperatures molecules move slower, enzymes cannot mediate in chemical reactions, and eventually the viscosity of the cell interior brings all activity to a halt.

As the temperature increases, molecules move faster, enzymes speed up metabolism and cells rapidly increase in size. But, above a certain value all of these activities are proceeding at such high rates, enzymes start to denature, and the total effect is detrimental. Cellular growth ceases.

These boundary values define the maximum and minimum temperature at which life can exist (and grow). Each species of microbe has its own, unique upper and lower limit, which is a defining characteristic for that species.

Optimum Values
Somewhere between its characteristic upper and lower temperature limits, each species of microbe has a particular temperature at which it grows best. At this temperature all aspects of the cell metabolism function at their optimum values, the cell is able to rapidly increase in size and divide. When members of a species find themselves living at their optimum temperature, their growth rate is at its maximum value.

Bacteria that grow at temperatures in the range of -5 o C to 30 o C, with optimum temperatures between 10 o C and 20 o C, are called psychrophiles . These microbes have enzymes that catalyze best when the conditions are cold, and have cell membranes that remain fluid at these lower temperatures.

Sea water near the poles of the earth are rich in algae that can live below 0 o C, and the psychrophilic bacteria that spoil milk, meat, vegetables and fruit are perfectly happy growing in a refrigerator. Although refrigeration is a good way of slowing down food spoilage, it cannot stop the growth of these bacteria.

Microbes that grow at optimal temperatures in the range 20 o C to 40 o C, are called mesophilic . Important members of this group are those that live in and on warm blooded creatures, such as humans. Pathogenic bacteria and included here, as are symbiotic bacteria that live in the human body without harming it.

Certain bacteria can live and grow at temperatures that exceed 50 o C. These are thermophilic microbes that can tolerate the very harsh conditions decomposing organic material, the hot springs at Yellowstone National Park (where temperatures are at least 80 o C to 85 o C), or deep in the oceans by thermal vents bubbling up from the hot rocks just below the earth's crust.

Tools of the Trade
In these investigations, a tiny group of each microbe species are placed into a liquid, nutrient filled broth that has been sterilized (so no other bacteria will compete!). Usually this is in a special flask (called an "Erlenmeyer flask"), which is slowly shaken (to keep the microbes and nutrient at uniform distributions).

Each growing culture is carefully kept at the appropriate, and constant, temperature for the length of the experiment.

At regular intervals of time, small samples of the growing culture are taken from the flask and all reproduction of the microbes stopped by some poison or inhibitor (they can also be chilled or frozen). The size of the population at each time point is then determined.

M endel's M other shows you --- -- how bacteria grow.

Recording Results

CLICK HERE,
print out, and use this
Table of Results
to record your data

The results of each of your investigations should be recorded as a table (a Table of Results ). In these tables you should indicate the name of the microbe being studied, the temperature growth, and make an accurate record of either the growth data (growth curve), or the value of the generation time (generations per minute), as required.

The logatithmic value of the generations per hour should also be recorded on your table of results.

CLICK HERE,
print out, and use this
Presenting the Results
sheet to graph your data

The results of each investigation should then be presented as a graph.

The horizontal axis of the graph should be the intervals of the different temperatures at which the microbes were grown. The vertical axis should represent the logarithmic value of the generations per hour determined for that sample.

This is called a Arrhenius plot .

The shape of these graphs or plots is characteristic for each species of microbe, but each organism will show an optimum temperature where growth proceeds most rapidly, and as the temperatures either exceed, or fall below that optimum, growth slows down. Above or below the maximum and minimum permissive temperatures, all growth stops.

Conditions
Each investigation is carried out under a specific set of growth conditions .

A species of microbe is chosen first.

It is then necessary to chose a temperature. Use the thermometer sliding scale to set the chosen temperature. The value chosen will appear in the box.

For each temperature, click on "GROWTH" and record your results. In some investigations you will need to record the entire growth curve (data on extreme right), but for most investigations you only need to record the "generations per minute" and "log. value of the generations per hour".

Record all the temperatures and all the values where you see that the microbial species could grow at all. It is not necessary to record those values that occur when there is not microbial growth.


1.2.1: Types of Microorganisms - Biology

Negative stained transmission electron microscopy (TEM) image of the Poliovirus (Enterovirus C). This virus belongs to the Picornaviridae family and causes poliomyelitis also known as polio. Polio is a crippling and potentially deadly disease. It is very contagious and spreads from individual to individual infecting the brain and spinal cord causing paralysis. Most people will not show any visible symptoms but a small proportion will develop serious symptoms. Symptoms may include meningitis, paresthesia and paralysis. Children are 99% protected via vaccination which prepares the body to fight the virus. Image courtesy of the Centers for Disease Control and Prevention (CDC / Dr. Fred Murphy J. J. Esposito).

Mucor spp., fruiting structure with spores. Magnification 400, scanning electron microscopy. The fruiting structure (condiophore) has matured and its outer membrane is disintegrating allowing the spores (conidia) to be released. Mucor is a common fungus found in many environments. It is a Zygomycetes fungus which may be allergenic and is often found as saprobes in soils, dead plant material (such as hay), horse dung, and fruits. Mucor is in house dust, air samples, and old dirty carpets, especially in water damaged moist building materials. Accumulated dust in ventilation ducts may contain high concentrations of viable Mucor spores giving rise to allergic or asthmatic reactions. It is an opportunistic pathogen and may cause mucorosis in immunocompromised individuals. The sites of infections are the lung, nasal sinus, brain, eye, and skin. Few species have been isolated from cases of zygomycosis, but the term mucormycosis has often been used. Zygomycosis includes mucocutaneous and rhinocerebral infections, as well as renal infections, gastritis, and pulmonary infections. Courtesy of Dennis Kunkel.


Bacterial Skin Infections

Bacterial skin infections are usually caused by gram-positive strains of Staphylococcus and Streptococcus or other organisms. Common bacterial skin infections include:

  • Cellulitis causes a painful, red infection that is usually warm to the touch. Cellulitis occurs most often on the legs, but it can appear anywhere on the body.
  • Folliculitis is an infection of the hair follicles that causes red, swollen bumps that look like pimples. Improperly treated pools or hot tubs can harbor bacteria that cause folliculitis.
  • Impetigo causes oozing sores, usually in preschool-aged children. The bullous form of impetigo causes large blisters while the non-bullous form has a yellow, crusted appearance.
  • Boils are deep skin infections that start in hair follicles. Boils are firm, red, tender bumps that progress until pus accumulates underneath the skin.

Bacterial skin infections are treated with oral or topical antibiotics depending on the strain causing the infection.


The Science of Sauerkraut: Bacterial Fermentation, Yum!

Last week my husband needed some jars for cooking purposes. Tesco sell jars for somewhere around £3 each. However they also sell large jars full of sauerkraut for £1 each.

Last week my husband needed some jars for cooking purposes. Tesco sell jars for somewhere around ?3 each. However they also sell large jars full of sauerkraut for ?1 each. Which means that last weekend we had an awful lot of sauerkraut to try and get through.

I’m not a great fan of sauerkraut, which is a pity because most of the taste comes from the action of bacteria. Not just one bacteria either, but a whole range of different species are involved in the fermentation process. The bacteria don’t even need to be added to the sauerkraut, as they live naturally on the cabbage leaves. All that is required to start the process off is shredded cabbage and salt.

The first stage of sauerkraut fermentation involves anaerobic bacteria, which is why the shredded cabbage and salt need to be packed in an airtight container. At this stage the surrounding environment is not acidic, just cabbagey. The bacteria, mostly Leuconostoc species, produce carbon dioxide (replacing the last vestiges of oxygen in the jar) and lactic acid, which is a natural byproduct of anaerobic respiration. Eventually, the conditions within the jar become too acidic for these bacteria to survive and they die out, replaced with bacteria that can better handle the acidic conditions such as Lactobacillus species.

The lactobacillus further ferment any sugars remaining in the cabbage, using anaerobic respiration. This produces more lactic acid, until the sauerkraut reaches a pH of about 3. These bacteria are inhibited by high salt concentrations (so most sauerkraut contains around 2-3% salt) and low temperatures, which is why the fermenting jars should be left at room temperature rather than in the fridge. At pH3 the lactobacillus stop fermenting and the sauerkraut can be stored until needed.

All the these bacteria help to create the tangy acidic taste, however there are ways that microbial growth can go wrong. Overgrowth of the lactobacillus, for example if the jar is stored at too high a temperature during fermentation, can cause the sauerkraut to form the wrong consistency. Likewise if the sauerkraut gets too acidic too early the lactobacillus get in on the action early leading to soft sauerkraut. Although the finished sauerkraut is far too acidic for pathogens to live in, fungal spores may settle on the surface and spread, spoiling the food.

Although sauerkraut is a German word, the dish is thought to have originated in China with cabbage fermented in rice wine or brine. This spread to Europe by way of Ghengis Khan’s invaders where the cabbage was dry cured with salt. As sauerkraut keeps for long periods, and is a source of vitamin C, it was favoured by the Dutch sailors, who took it with them when they travelled to America. Captain Cook also travelled with it to Australia, as sauerkraut contains a range of vitamins and minerals that are difficult to obtain when travelling for long periods at sea.

As the bacteria required for sauerkraut fermentation are found on the cabbage leaves, it’s a very easy and healthy dish to produce. All you need is cabbage! By exploiting the actions of bacteria simple ingredients such as cabbage and salty water can be used to produce a healthy dish that can be stored long past the time when raw fruit and vegetables will have begun to spoil.

The views expressed are those of the author(s) and are not necessarily those of Scientific American.

ABOUT THE AUTHOR(S)

A biochemist with a love of microbiology, the Lab Rat enjoys exploring, reading about and writing about bacteria. Having finally managed to tear herself away from university, she now works for a small company in Cambridge where she turns data into manageable words and awesome graphs.


Plant growth-promoting microbes for abiotic stress tolerance in plants

Abstract

Microorganisms play a major role in the growth and development of plants. Plants interact with these microorganisms found in soil, on the surface of plants, or within the plant tissue. Plant growth-promoting microorganisms (PGPM) composed groups of microbes, mostly bacteria, fungi, and actinomycetes, that are rhizospheric, endophytic, or mycorrhizal in nature. Many biotic and abiotic factors affect the health of plants and eventually their yields. This chapter discusses the effects of major abiotic stresses on plants including the role of different PGPM in the management of stress tolerance of plants.


1.2.1: Types of Microorganisms - Biology

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As we said, not all protists are bad for the world. In the bacteria section we already told you about a species that lives in the digestive system in cows. These bacteria help cows break down the cellulose in plants. Similar bacteria live in all sorts of grazing animals, helping them survive off plant material. Many ecosystems are based on creatures that are called herbivores.

Scientists have even discovered fungi that will help you battle bacterial diseases. So you get sick, the doctor looks at you and says you have a bacterial infection, maybe bronchitis. He prescribes an antibiotic to help you get better. Antibiotics are drugs designed to destroy bacteria by weakening their cell walls. When the bacterial cell walls are weak, your immune cells can go in and destroy the bacteria. Although there are many types now, one of the first antibiotics was called penicillin. It was developed from a fungus (a fungus named Penicillium found on an orange, to be exact).

1.2.1: Types of Microorganisms - Biology

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All foods are continually assaulted by many kinds of microorganisms, racing to eat as much as possible. When you pickle vegetables by fermentation, you help one type of microbe win this "race."

More specifically, you create special conditions in your pickle crock that keep away "bad" spoilage-causing microorganisms, and that allow a unique class of "good" bacteria, called lactic acid bacteria, to colonize your cucumbers.

Why are lactic acid bacteria good?

As lactic acid bacteria grow in your pickle crock, they digest sugars in the cucumbers and produce lactic acid. Not only does this acid give the pickles their characteristic sour tang, it controls the spread of spoilage microbes. Also, by gobbling up the sugars, lactic acid bacteria remove a potential food source for bad bacteria.

Salt gives the good guys an edge.

Adding salt to your pickling brine is one important way to help lactic acid bacteria win the microbial race. At a certain salt concentration, lactic acid bacteria grow more quickly than other microbes, and have a competitive advantage. Below this "right" concentration, bad bacteria may survive and spread more easily, possibly out-competing lactic acid bacteria and spoiling your pickles.

Too much salt is also a problem: Lactic acid bacteria cannot thrive, leaving your vegetables unpickled. What’s more, salt-tolerant yeasts can spread more quickly. By consuming lactic acid, yeasts make the pickles less acidic—and more hospitable to spoilage microbes.

Oxygen gives the bad guys one leg up.

During fermentation, it’s important to keep your crock covered to seal out the air. That’s because oxygen encourages the spread of spoilage microbes. Any exposed pickle or brine becomes a breeding ground for the bad microbes, which can spread to spoil the entire batch.

Too hot . . . too cold . . . just right.

A pickle-maker can also control the microbial garden in a pickle crock by adjusting the temperature. The ideal temperature range for lactic acid bacteria—and successful fermentation—is 70° F㫣° F. If it’s too chilly or too toasty in the room, other microbes may gain a competitive advantage over lactic acid bacteria.


Watch the video: Classes of Microorganisms (December 2021).