Project 2

TAXONOMY:

Taxonomy is the classification of living organisms. The biologists divide the whole world of living things into six kingdoms.

THE SIX KINGDOMS

1- A) The arrangement of all six kingdoms from the simplest to the most complex:

One: Archaeobacteria
Two: Eubacteria
Three: Protista
Four: Fungi
Five: Plantae
Six: Animalia

Six kingdom classification of life

B) The Kingdoms that meet the criteria for Microorganisms are:

One: Archaeobacteria
Two: Eubacteria
Three: Protista
Four: Fungi  

C) There are two Kingdoms that do not qualify as Microorganisms, they are Plantae and Animalia.They do not fit the criteria to quality as an Microorganism.
 

D) The two characteristics that disqualify each kingdom as Microbes are:

1) Plantae and Animalia Kingdoms have tissue differentiation.
2) Plantae and Animalia can be seen with the unaided human eye while the microbes can be seen only through the lenses of a microscope.

The various cells of the human body

Plant tissue system

DIVERSITY OF MICROBIAL LIFE

      (Why Microbes cannot fit into a single group or Kingdom)

2- A)  Two characteristics Eubacteria and Archaea share are that both are prokaryotic and single celled organisms. Also, they both lack membrane bound organelles such as nuclei and mitochondria. Both of them are also characterized by having a single chromosome and asexual reproduction by binary fission. Therefore both are denominated bacteria in general. 

B) The estimated average sizes of Archaea and Bacteria are 0.2 micrometer in diameter and 2-8 micrometer in length.

3. To characteristics that differentiate the Kingdoms Archaea and Animalia from Eubacteria are the following:

	EUBACTERIA	ARCHAEA	ANIMALIA
Organism	Bacteria, Cyanbacteria, Actinobacteria	Methanogens, Halophiles, Thermophiles Psychrophiles	Amoebia Sponge Mammals Reptiles
Cell Type	Prokaryotic	Prokaryotic	Eukaryotic
Metabolism	Anaerobic Aerobic Facultative	Aerobic	Aerobic
Nutritional Acquisition	Absorption Photosynthesis Chemosynthesis	Absorption Non-photosynthesis Photophosphorylation Chemosynthesis	Absorption
Reproduction	Asexual	Asexual	Sexual

C). The estimated average sizes of human and animal cells differ in many ways and from organ to organ. In Humans, the estimated average sizes and shapes vary. The average cell is between 10 to 100 micrometers. This diversity is due to the cell's primary function. Some cells, for example the nerve cells, are long and can measure up to a meter long while others like a cheek cell is about 50 micrometers or 0.05 millimeters in size. In Animals, most cells range in size between 1 and 100 micrometers and are visible only with the aid of a microscope.

4-A)  The two kingdoms Fungi and Plantae share the following characteristics: both fungi and plants are eukaryotic, the are multicellular, they possess a cell wall, they produce spores and they are non-motile.

B) Fungi and Plants are not grouped into the same Kingdom because they differ in the way the take nutrients. Plants are autotrophs which means that they produce their own food from photosynthesis, while the Fungi are hetertrophs: they take food from other organisms through metabolism.

C) Estimate the average sizes of Plant & Yeast Cells is as follows:

The estimated size of a Plant cell is between 10 μm and 100 μm while the size of a yeast cell is 2-10 µm.

Plant cell:  size 10 to 100µm

Yeast cells of the species Saccharomyces cerevisiae (credit: Jef D. Boeke and Sarah Richardson, Johns Hopkins University)

KINGDOM: PROTISTA

Protista share many characteristics with the other kingdoms but they remain unique.

5- A) The characteristics of the Kingdom Protista are the following:

The protists belong to the Kingdom Protista which are eukaryotic organisms found in aquatic habitats. Although they are mostly unicellular microscopic organisms or microorganisms, they can also be multicellular or colonial. Some have complex life cycle involving multiple organisms. Some are sexual or asexual, some reproduce by mitosis and meiosis.  Protista motility happen thanks to their use their flagella (tail-like whip), their cilia which are extremely thin filament (hair-like projections) and some of these microorganisms are pseudopods, which means the possess (false feet). 

B) Some Protista that look like Fungi are better known as molds. There are two major mold groups, Slime Molds and Water molds. Slime molds are fungus-like protista that grow as slimy masses on decaying matter. They play an important role in the recycling of nutrients by digesting decayed organic materials. Now let’s move on to Water Molds. Water Molds resembles white fuzz growing on the surface of dead fish, usually in fresh water. They depend on dead and decaying organic matter in the water to survive. Water molds or Oosmycota are decomposers. They reproduce both sexually and asexually; sexual reproduction takes place in specialized structures that are formed by hyphae.  Antheridium produces male nuclei and oogonium produces female nuclei.  Fertilization takes place and spores form a new organism or asexually: asexual reproduction involves hyphae (thin filaments) which develop into zoosporangia (spore cases) flagellated spores swim away in search of food.  Spores develop into hyphae when they find food and grow into a new organism.

C) Several Protista are Animal-like, these protists are unicellular eukaryotic microorganisms. The fact the they do not have chloroplasts or chlorophyll make them separate from plants. They are called protozoa. Proto-meaning first and zoa- meaning animal: thus the protists are a primitive form of life. These tend to be found around freshwater areas. There are four groups of protista. Ciliophora (cilia bearing), zoomastigina (flagella bearing), sporozoa (in fluids as parasites), and sarcodina (with pseudopods).

(D)  Plant-like Protista can be described as an unicellular algae. They contain chlorophyll and are able to carry out photosynthesis. There are four phyla: Euglenophytes, chrysophytes, diatoms, and dinoflagellates. These algae usually have different colors due to the fact that they have accessory pigments which assist them to absorb light. Euglenophytes reside in water. They have flagella which allows motility (ability to move autonomously). They do use chloroplast to perform photosynthesis, but they can become heterotrophs if left in the dark for an extended period of time. 

THE REAL VIRUSES

Unlike every other life-form, Viruses are not classified in any Kingdom; there are even

questions about whether they are living things!

6-A)  Microbiology defines a Virus by many ways. First, a virus is not visible to the unaided human eye. It is so small that it cannot be seen even with a light microscopy. One needs an electron microscope to see the virus. A virus is an infective agent that typically consists of nucleic acid molecule in a protein coat. Unlike bacteria, a virus can only multiply within the living cells of a host, thus it is a parasitic microorganism.

B) By what criteria are Viruses living things?

Let us first define "living things". A living thing is an organismic state characterized by capacity for metabolism, growth, reaction to stimuli, and reproduction. As stated above, the only way a virus can replicate or better said reproduce is in living cells within a host. Hence viruses cannot really reproduce without the help of cells. In a host virus cells start chemically reacting and more viruses start to come up once a the host's cell is infected. Due to the fact that they to reproduce with the help of cells, that would almost make the virus to be considered "living".

Life diversity

References:

     


Case, T. F. (2014). Microbiology: an introduction. (11th ed.). Boston: Pearson.

Kadner, R. J. (2013, September 12). Diversity of structure of bacteria. Encyclopædia Britannica, Inc., Retrieved January 28, 2014, from http://www.britannica.com/EBchecked/topic/48203/bacteria/39334/Diversity-of-structure-of-bacteria

Davidson, M. W. (1995 - 2013). Introduction to cell and virus structure. Florida State University. (© 1995-2013), Retrieved January 28, 2014, from http://micro.magnet.fsu.edu/cells/index.html

Koning, R. E. (1994). Kingdom archaea. Plant Physiology Information Website, Retrieved January 29, 2014, from http://plantphys.info/organismal/lechtml/archaea.shtml

Kaiser, G. E. (1994). The prokaryotic cell: Bacteria. Doc Kaiser's Microbiology Home Page, Retrieved January 29, 2014, from http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit1/shape/shape.html

Biology II Notes: The 6 Kingdoms. (n.d.).Biology II Notes: The 6 Kingdoms. Retrieved January 30, 2014, from http://www.terrebonneonline.com/6kingdoms.htm

The Five Kingdoms Of Life. (n.d.).Kingdoms Of Life. Retrieved January 30, 2014, from http://waynesword.palomar.edu/trfeb98.htm

The Six Kingdoms. (n.d.). The Six Kingdoms. Retrieved January 28, 2014, from http://www.ric.edu/faculty/ptiskus/Six_Kingdoms/Index.htm

The Six Kingdoms of Life. (n.d.). The Kingdoms. Retrieved January 28, 2014, from http://www.paec.org/biologypartnership/assets/classification/6%20Kingdoms.pdf

biology. (n.d.). Encyclopedia Britannica Online. Retrieved January 30, 2014, from http://www.britannica.com/EBchecked/topic/66054/biology

Microorganisms

INTERESTING LINKS

Microbiology link: 
http://www.austincc.edu/rohde/noteref.htm

This is a beautiful rendering of some of the most common pathogens. These viruses are responsible for widespread infectious diseases like influenza, measles, hepatitis, HIV AIDS etc.

Check here >>> VIRUSES

Project 1

PIONEERS OF MICROBIOLOGY:

The scientists who came with a major contribution to the development of microbiology:


PROJECT PART I

Leeuwenhoek

        Antonie van Leeuwenhoek (1632-1723) was born and lived in Delft, Netherlands. He was from a modest family of tradesmen. He himself made his living as a draper and a minor city officer. Antonie did not receive a high education degree, nor academic training. But his insatiable curiosity and his tenacious assiduity and rigor allowed him to make some among the most important scientific findings in the field of biology: the discovery of microorganisms. 

Leeuwenhoek's microscope, Deft.

After he read a copy of Hooke’s work Micrographia, Leeuwenhook started to make his own microscopes and he used them to observe things. He is credited to have been the first to observe bacteria. The tiny organisms he saw through his lenses he called “animalcules” (little animals). His microscopes were magnifying glass mounted on a small brass structure. These were rudimentary microscopes but they were magnifying enough to allow him to observe the blood cells and sperm cell among many other living thing like Spirogyra and Vorticella. Leeweenhoek sent his discoveries with drawings what he saw and his comments to the Royal Society of London, an institution of which he became a fellow. A specimen of Leeuween’s microscope is conserved at the Delft University of Technology, Netherlands.

Tyndall

        John Tyndall (1820-1893) was an Irish scientist. His work has been fundamental to the development of microbiology, especially the research surrounding the “germ theory”. In 1877, Tyndall demonstrated that dust did carry germs and that if dust was absent, broth remained sterile even if directly exposed to air.  Providing a blow to spontaneous generation. He also created a process to destroy heat-resistant bacteria by eradicating bacteria spores. He used a set up to preserve broth in “optically pure” air, which means he isolated the broth from direct exposure to air a way to avoid any contamination by the germs from the dust in the air, and the result was that the meat he kept in “optically pure” air did not decompose. During the 1870s Tyndall was in frequent communication with Pasteur. This technique explained above is still know as Tyndalization.

Cohn

        Ferdinand Cohn (1828-1898), was a German biologist. His studies concerned the bacteria, and fungi and the algae. Cohn described the physiological processes in microorganisms. In 1849 at the university of Breslau, using his Plössl microscope he studied with scrutiny the unicellular protozoa and other bacteria. During his observation he described the developmental and sexual  cycles of algae Protococcus pluvialis among other microorganisms. He studies led to the system of classifying the bacteria. He divided bacteria into four groups based on morphology. These groups are: sphericals, short rods or cylinder, long rods or threads and spirals. This classification is still used today. Cohn is considered one of the founders of modern bacteriology.

Needham

        John Turberville Needham (1713–1781) was an English biologist. He studied in London and Paris. During his studies he conducted experiments that made him to become an advocate of spontaneous generation. In his experiment he briefly boiled broth and sealed it with cork lids and discovered that microorganisms proliferated in the broth. He then believed that life could arise from inanimate things and “spontaneously” appear under the form of microorganisms. This theory descredited by Spallanzani and Pasteur.

Lister

        Joseph Lister (1827-1912) British Surgeon. He was professor of Surgery at Glasgow University. During his years as surgeon at Glasgow Royal Infirmary, he became aware that many patient who underwent surgical operations felt well, then they surprisingly died afterwards. In 1865, Lister read about the work done by Louis Pasteur on how wine was soured. Lister believed that it was microbes carried in the air that caused diseases to be spread in wards. To cope with the problem of “ward fever” he introduced new principles of cleanliness that transformed the surgical practice in the late 1800s. He used antiseptic methods to limit the propagation of germs in the clinical environment. Lister also experimented with hand-washing, clean gloves and gowns, sterilising instruments and spraying carbolic (phenol) in the operation room and soaked the instrument in phenol to kill germs. For his revolutionary ideas, he is known as the ‘Father of Antiseptic Surgery’.

 

Joblot         
Louis Joblot was born on  August 9, 1645 and died on April 27, 1723 at the age of 78. Louis Joblot was the first French Microscopist. Between the years of 1710 -1716 Joblot describes and illustrated a number of new types of Protozoa. He was the first to picture the larva of hydrachnid and the nymph of Unioicola ypsilophorus, a parasite of the pond mussel.

Linnaeus

        Carolus Linnaeus (Swedish Carl von Linné) was a Swedish scientist. He was born on 23 May 1707 and died 10 January 1778 at the age of 91. Linnaeus lays the basic formation of the formal system of classification system of the binomial nomenclature. This classification system grouped organism based on ancestral relationships. 

The value of the binomial nomenclature system derives primarily from its economy, its widespread use, and the uniqueness and stability of names it generally favors. It generally speaking allows us to see the order of life. Linnaeus is the inventor of the modern taxonomy.
 

Appert

Nicolas Appert was born 17 November 1749 and died on 1 June 1841 at the age 91. Appert was the French inventor of airtight food preservation. In 1810, after 15 years of experimenting with how to preserve new food he published The Art of Preserving Animal and Vegetable Substances.  By boiling the food you kill the bacteria and seal it. Preserving it allows people to better store there food and for a much longer period of time.

Schleiden

Matthias Jakob Schleiden was born 5 April 1804 and died 23 June 1881 at the age of 77. He wrote Contributions to Phytogenesis in 1838, in which he stated that the different parts of the plant organism are composed of cells. Because of this Schleiden and his partner Schwann became the first to formulate what was then an informal belief as a principle of biology equal in importance to the atomic theory of chemistry.

Koch

Robert Koch was born 11 December 1843 and died on 7 May 1910 at the age of 67. He is called the founder of modern bacteriology. He is known for his role in identifying the specific causative agents of tuberculosis cholera and anthrax. He his research also led to the creation of Koch’s postulates. Due to the scientist where able to give the scientific support for the concept of infectious disease and link specific organisms to certain diseases. He put forward the "Koch Postulates" a unanimously accepted process to determine the relationship between germs and diseases.  

Koch's Postulates

Four criteria that were established by Robert Koch to identify the causative agent of a particular disease, these include:

1.      the microorganism or other pathogen must be present in all cases of the disease

2.      the pathogen can be isolated from the diseased host and grown in a pure culture

3.      the pathogen from the pure culture must cause the disease when inoculated into a healthy, susceptible organism

4.      the pathogen must be re-isolated from the new host and shown to be the same as the originally inoculated pathogen.

Koch's Postulates diagram

Haeckel

Ernst Haeckel was a German zoologist (1834-1919). He was very well known in the field of science due to him combining two theories cell theory with evolution theory. As well as his explanation of the initial state of multi-cellular organisms from colonies of single-cell protists that play a very significant role in biology. One of Haeckel’s main points, is to prove that organism can be systemically arranged according to a classification system from the most complicated to the most basic levels of individuality. They can be organized any which way. From single-cell organisms to higher animals and animal societies while evolution can explain the existence of these organisms.

Spallanzani

      Lazzaro Spallanzani was an Italian Physiologist (1729-1799). Spallanzani contributed a very important finding to biology. He proved that “Spontaneous Generation” did not exist. He also confirmed that John Needham’s experiment was flawed. Needham boiled broth and heated the flask, but did not take into consideration that air was a factor in his experiment. The air caused bacteria to grow in the broth, hence he thought that spontaneous generation existed. On the other hand, Spallanzani took two flask one sealed airtight, while the other was sealed after it was exposed to air. The conclusion was that the one with air got the same results as Needham. The one that was sealed initially was not growing any life in it. Even though it was proven that spontaneous generation does not exist, many still doubt Spallanzani’s findings.

Redi

Francesco Redi , an Italian physician and poet, was  born on February 18, 1626 in Arezzo, Italy and died March 1, 1697, Pisa. He demonstrated that the presence of maggots in decomposed meat does not result from spontaneous generation but from eggs placed on the meat by flies. 

Redi's experiment

In 1668 he shared a series of experiments named as Esperienze Intorno alla Generazione degl'Insetti (Experiments on the Generation of Insects) which was one of the first theories refuting "spontaneous generation", Redi set up a series of jars containing different meats, some of the jars were covered and some of the jars were exposed to open air. Then he repeated the experiment but, instead of sealing the containers, he covered half of them with gauze so that air could go inside the jars. Even though the meat in all of the jars putrefied, he found that only in the open and uncovered ones, in which flies had entered freely, the meat had maggots. Leading to the conclusion that the maggots came from the eggs left on the meat by the flies; however, Redi still believed that the process of spontaneous generation was possible in cases such as: gall flies and intestinal worms.

Schwann

The German biologist Theodor Schwann (1810-1882) is best known as the founder of the cell theory. He also was responsible for the discovery of pepsin which the first digestive enzyme prepared from animal tissue, and last but not least, he discredited the theory of spontaneous generation. In 1834 he decided to take boiled broth to heated air in a glass tube, resulting in the fact that no micro-organisms were detectable and no chemical change or decomposition occurred in the broth. He was convinced that the idea of spontaneous generation was false. In 1838 after studying Matthias Schleiden's microscopic research on plants who basically proposed a  plant cells’ theory which was the key to plant anatomy and growth; Schwann decided to focus his  research on animal tissues, theory that actually proved the existence of cells and the development of mature tissue from its very first stage as an embryo; furthermore, animals and plants are made of cells and the fluids that come out of them, cells have its own life and finally, without cells there is no organism. Every cell can be placed into groups: Those that together are formed by molecules and those by chemical changes, this gave birth to classification of tissues into five big groups, the ones formed by individual cells like blood and skin; formed by blended cells as cartilage and bones, large cells that formed fibers like tendons and ligaments and the those that form muscles from fused cells.

Hooke

     Robert Hooke was an English philosopher, mathematician and scientist of the 17^th Century who was born on July 18, 1635. Although he was mainly educated at home by his father, he managed to enter Westminister School at age thirteen and went on to Oxford University, where some of the best scientist in England worked at the time.  Robert Hooke is remembered in the history of microbiology for his 1665 publication  of the book “Micrographia”.

Hooke's microscope

In this book he inspired use  and introduced the microscopes for the first time for scientific exploration,  thrugh his amazing drawings, he was able to illustrate what he had discovered, in a thin piece of cork, he saw honeycomb-like structures which later he called a Cell. He was the first person to use the term “Cell” to describe a basic unit of life.Hooke was an early advocate of biological evolution. Hooke is also credited with the invention of microscope.

   

Metchnikoff

Elie Metchnikoff, whose original name was llya llich Mechnikoff was a Russian scientist born on May 16, 1845. He was a brilliant man who studied Zoology and Microbiology . In 1883, he presented  “The Curative Forces of the Organism,"  Metchnikoff's theory of phagocytes. Phagocytes (eating/Cells), such as leukocytes or white blood cells work as our front line defense against infections.  According to Metchnikoff, under appropriate conditions, protector cells within an organism would engulf, mount, attack and ingest foreign bodies, such as bacteria to protect us from invading matters. . This phenomenon known as Phagocytes would become a fundamental part of our immune response system. This discovery honored Mechnikovff  to receive the Nobel Prize in 1908. Elie Metchnikoff made significant contributions to biology, life science and medicine.

       

von Dusch

Von Dusch and Schroeder

Theodor von Dusch was born on Spetember 17, 1824  and was a German physician. In 1850’s He, along with Heinrich Schroder revealed that a filter made of cotton-wool was effective in removing microbes, such as bacteria from the air. In 1854,  Georg Schroeder and von Dusch performed a convincing experiment to disprove the theory of spontaneous generation. Schroeder and von Dusch were the first to present the idea of using cotton plugs for plugging microbial culture tubes. Dusch was the author of influential works such as thrombosis of cerebral sinuses, heart disease and diseases of endocardium and myocardium. Georg Schoeder worked with von Dusch and both introduced a technique that consists of filtering the air trapping the microbes.  

Pasteur

Louis Pasteur was born on December 27, 1822 in Dole France. He was a doctor, chemist and inventor who is known for the “germ theory of disease”. Perhaps since three of his children died of typhoid fever, that could have been the drive to save people from dying. Pasteur discovered that most infections are caused by germs and bacteria, he figured that if germs was the cause of fermentation, then germs had to be cause of contagious diseases. He fought with hospitals to change their practice and pasteurize all medical equipment to minimize the spread of germs.  

Pasteur's swan neck flask experiment

Pasteur’s pasteurization process killed germs and prevented the spread of diseases. In 1879, Pasteur’s created the first vaccine for Chicken Cholera, he demonstrated that they become resistant to the actual virus, and soon after, he developed vaccination for diseases such as anthrax, Cholera, TB and smallpox and rabies. He is the reason antibiotics and vaccines exist today.

Gram

Hans Christian Joachim Gram was a Danish bacteriologist that is remembered for his development of the “Gram Stain”. In 1884, Gram accidentally came across a method on how to distinguish between two major classes of bacteria to make them more visible under the microscope. The gram stain consists of a primary stain of Crystal Violet and a counterstain of Safranin, bacteria that turn purple are called “Gram positive” and these that turn red are “Gram Negative. 

Gram's Staining

 Identifying and characterizing bacteria is widely used in microbiology, it reflects essential differences in biochemical and structural properties of bacteria.

PROJECT PART II

Major microbiologists' position regarding the opposing theories: spontaneous generation and biogenesis.

#	NAME OF SCIENTIST	THEORY		TITLE OF EXPERIMENT
		SPONTANEOUS GENERATION	BIOGENESIS
1	Leeuwenhoek	N/A	N/A	Microscope
2	Tyndall		x	Tyndallization
3	Cohn	N/A	N/A	Germ Theory
4	Needham	x		Germ Theory
5	Lister	N/A	N/A	Germ Theory
6	Joblot		x	Germ Theory
7	Linnaeus			N/A
8	Appert		x	Germ Theory
9	Schleiden			Cell Theory
10	Koch			Germ Theory of Disease
11	Haeckel		x	Cell Theory
12	Redi		x	Germ Theory
13	Schroeder			Germ Theory
14	Schwann		x	Cell Theory
15	Spallanzani		x	Germ Theory
16	Hooke			Microscope
17	Metchnikoff		x	Immunology
18	Von Dusch		x	Filtration of microbes
19	Pasteur		x	Germ Theory of Disease
20	Gram	N/A	N/A	Gram Stain

What is the theory of ‘SPONTANEOUS GENERATION’?

According to the Biology Online Dictionary and other online sources, the term spontaneous generation was a popular hypothesis that stated that previous organisms develop from nonliving matter. The theory dates back to Aristotle and ancient Greek philosophy and continued to have support in Western scholarship until the 19th century. Abiogenesis, which is the term used nowadays, basically held that certain complex, living organisms were generated by decaying organic substances. It was believed back in the days that aphids arose from the dew which fell on plants. Also that flies developed from putrid matter as mice did from dirty hay and crocodiles from rotting logs at the bottom of bodies of water, and so on.

Many microbiologist of the era such a Hooke and Van Leeuwenhoek felt that the existence of microorganisms was evidence necessary to support spontaneous generation, since microorganisms seemed too simplistic for sexual reproduction, and asexual reproduction through cell division had not yet been observed. It wasn't until 1668, when Francesco Redi showed with a simple experiment (the sealed and unsealed flask) that no maggots appeared in meat when flies were prevented from laying eggs. Thus, a new era was created, the era of biogenesis; where many other experiments were carried out by other microbiologists of major importance who proved the presence of microorganisms in the air, and added other important milestones to the history of science: the introduction of aseptic techniques to the medical field and the discovery of causative agents of infectious diseases and their treatment.

BIOGENESIS

Biogenesis is the principle or theory that living organisms develop only from other living organisms, and not from nonliving matter as defined by the online dictionary organization. The theory was attributed to Louis Pasteur, who demonstrated that fermentation is caused by the growth of micro-organisms, and the emergent growth of bacteria in nutrient broths is due not to spontaneous generation, but rather to biogenesis. This is summarized in the phrase Omne vivum ex vivo, Latin for "all life [is] from life." A related statement is Omnis cellula e cellula, "all cells [are] from cells;" this observation is one of the central statements of cell theory.

REFERENCES

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