Chapter 1: Microbial Life: Origin and Discovery Current Research Highlight Procholorococcus is a bacteria that fixes carbon dioxide

e and produces Earths oxygen. In 2010, it was found that UV rays mutate their DNA; and these UV rays are same that cause cancer in humans

Introduction In 2008, Phoneix Mars lander was sent to examine Martian soil for carbon, nitrogen, phosphorous and hydrogen to inspect any sign of living. This is because knowing that life exists beyond Earth will give us a perception on our own standing in the universe. However, much of it is unknown to us; we are even unaware of the microbes residing in our digestive tract. Escherichia Coli lives in our intestinal tract, while algae and cynobacteria turn pond green. Microbes generate much of the air we breathe oxygen, carbon- dioxide and nitrogen

1.1 From Gene to Genome: What is a Microbe? - The study of microbe has deepened through two major research tools o Advanced microscopy o Sequencing of genomic DNA

A Microbe is a Microscopic Organism A microbe any living organism that requires a microscope to be seen. Its size ranges from millimeters to 0.2 micrometer Is virus a microbe? Microbe Description Approximate size Varicella-zoster virus Causes chicken pox and shingles 100 nanometer Prochlorococcus Photosynthetic marine bacteria 500 nanometer Rhizobium Nitrogen fixing bacteria in 1 micrometer symbiotic relationship with leguminous plants Spirogyra Filamentous algae found in 40 micrometer aquatic habitat Pelomyxa (an ameoba) Protists found in solid or aquatic 5 millimeter habitat Exceptions within the definition of microbial cells: 1. Super size microbial cells: some microbial cells grow large enough to be een with a naked eye. For example, thiomagarita namibiensis, is a marine sulfur bacterium that grow as large as a fruit flys head. Another example, the killer alga, Caulerpa taxifolia grows across waters of California 2. Microbial communities: some microbes are multicellular such as mushrooms, kelps and biofilms and imitate multicellular as they have differentiated cells to accommodate differential functions. Yet there are some multicellular organisms such as worms and antropods that require microscope to be seen but are not considered microbes 3. Viruses: some viruses such as mimivirus which infect amebas act as fully functional cells Definition of microbe includes: prokaryotes bacteria and archaea and some forms of eukaryotic cells fungi, algae and protists. o Aside: 3 domains are bacteria, archaea and eukarya

Microbial Genomes are sequenced GENOME all the genetic information in DNA Studying the genome of microbe is important because it allows us to understand as to how microbes grow and associate with other species. o Comparing genomes allows explore relatedness between microbes and other species as they diverged from the same ancestor First genome to be sequenced was of virus (bacteriophage) First cellular microbe to be sequenced was: Haemophilus influenza causes meningitis in children by TIGR (the institute of genomic research) devised a special computational

strategy for assembly large amounts of sequence data; which was later use to sequence human genome - Metagenome: is the sequence collection from an environmental sample because it contain the genome of different individuals in that sample. - Comparative genomics: is a field that compares the genomes of living species, from microbes to Homo Sapiens, providing further evidence that species on Earth share common ancestry. 1.2 Microbes Shape Human History - Microbes in human history o Yeasts and bacteria: in making of bread o In alcoholic beverages o Rock eating bacteria called lithotrophs leached metals such as copper o Microbial leaching leaches ancient monuments Microbial Disease Devastates Human Populations Examples of microbial diseases: tuberculosis and leprosy 18th century: Yersinia pestis, caused by rats 19th century: Mycobacterium tuberculosis was so common that it became symbolic tragic youth in European literature - HIV/AIDS: also a microbial diseases. - In human history microbes are important because more soldiers have died of microbial infection than of battles. - Florence Nightingale, founder of medical statistics was the first one to analyze the important of infections, which led Britishers to improve their soldiers living conditions. This is the polar bear chart that Florence Nightingale made to depict the causes of death, with blue being infection, red being battle and black being others

Microscopes Reveal the Microbial World Robert Hooke observes the microscopic world: with his microscope he observed: mites, mold an published it in Micrographia, the first publication what illustrated objects observed under microscope o Was the first to observe cells. o Never observed single celled because his magnification only went upto 30x

Antonie van Leeuwenhoek observes bacteria with a single lens: reported pages of microbes describing their shapes and sizes, accurately enough to allow others to identify the species he looked at. o he found out that heat killed microbes when he examined animals in his teeth before and after drinking hot coffee. o Another problem at that time: it was hard to distinguish between human cells such as blood cells and microbes - Spontaneous generation: do Microbes have Parents? o In 18th century many priests debated on theory of spontaneous generations to explain the origination of microbes. Two priests disapproved of this theory: Priest Redi as he proved that meat only produced maggot when in contact with flies, suggesting that maggots were offspring of flies Priest Lazzaro Spallanzani: noticed that microbes appeared in pairs. Demonstrated cell fission, process by which cells arise by splitting in two. He also demonstrated that heat sterilization can prevent microbial growth. o Louis Pasteur revealed the biochemical basis of microbial growth: showed that providing oxygen does not enable spontaneous generation. Fermentation: is a process by which microbes gain energy by converting sugars into alcohol. Pasteur said that when oxygen in not present, yeast produce alcohol as a waste product. However, in the presence of oxygen culture is contaminated, giving rise to bacteria, which outgrow yeast and produce acetic acid instead. Attempted a swan flask that let air in but was filtered for any microbes o John Tyndall attempted the same swan flask experiment: showed that repeated cycles of were necessary to eliminated spores formed by certain kind of bacteria. This is because heat resistant bacteria called endospores contaminate the flask. Later, we found out that endospores can be eliminated by boiling under pressure like pressure cooker. The steam pressure device called autoclave was used to sterilize tools for controlled study. 1.3 Medical Microbiology - Germ theory of diseases: states that many diseases are caused by microbes. - Robert Koch: was the first scientist to deduce that a specific microbe causes a certain disease. o Developed the pure culture technique and Kochs postulates for identifying the causative agent of a disease.

Growth of Microbes in Pure Culture Koch studied Anthrax: o To study whether anthrax was transmissible disease Used blood from an anthrax- infected carcass(dead body) to infect a rabbit, which died and then used its blood to infect others, which also died. This way Koch introduced a concept called: chain of infection or transmission of a diseases. o To study tuberculosis, he used pure culture of microorganisms (solid substrate culture)To isolate a pure culture, he added serum heated it to solidify it Improvement: gelatin to defined liquid medium which he then chilled to form a solid medium in a glass dish covered version of glass dish petri dish Further improvement: replacing gelatin with something that is viable at higher temperature such as agar

Koch's Postulates: was awarded noble prize for figuring out that Mycobacterium tuberculosis causes tuberculosis His 4 criteria that explain the link between an infectious agent and a disease o Microbe is not found in healthy and is found in all the other cases of the disease

o The microbe is isolated from the diseased host and grown in pure culture

o When the disease is introduced into a healthy host, the same disease occurs.

o The same stain of microbe is obtained from the newly diseased host. When cultured, the stain shows the same characteristics as before.

o Modern example of microbe causing disease that have determined using Kochs postulates are: Lyme disease, hantaviral pneumonia However, some exceptions to the postulates are tuberculosis and AIDS as the virus in infected people is not easily detectable Immunization Prevents Disease The concept of vaccination came in to light due to extreme case of smallpox in Europe. What some people did was they vaccinated themselves with small pox virus because small pox virus, outside the host loses some of its molecular integrity, which gives you a small pox that is less virulent to the actual virus o However, a much robust method that later came into light, was to vaccinate with cowpox, a much milder disease Pasteur was the first to realize that weaker (attenuated )virus acts as immunity as it eliminates the viruss potency to cause the disease. Furthermore, he extended his principle to other pathogens; which forms the modern belief of vaccinating with attenuated virus to achieve immunity. o Method of weakening a virus: heat, aging Pasteur found the cure for rabies caused by a rabid dog he used heat treatment and repeated inoculation to achieve. The university named after him, found that HIV causes AIDS

Antiseptics and Antibiotics Before Pasteur and Koch, many patients died of the disease from their own doctor. Ignaz Semmelweis was the first to see chlorine as an anti-septic agent (Pg. 24) Joseph Lister developed the use of antiseptic agents, such as carbolic acid, to treat wounds and surgical instruments.

Antibiotics Antibiotics anything that inhibits the growth of or destroy bacteria that cause infection. They do not work against virus because, biotic means living and virus are not living. An important step in developing antibiotics was realizing that microbes themselves produce antibiotic compounds; this conclusion was derived from the accidental discovery of Penicillin, when Fleming noticed the area contaminated by Penicillium mold was free of Staphylococcus colonies. Antibiotics are not effective anymore, because it selects antibiotic resistant pathogens, which become a bigger pain in ass. For example, mycobacterium tuberculosis is a serious threat now.

The Discovery of Viruses Viruses require hosts to be cultured.

Martinus Beijerinck was the first to deduce viruses as pathogens

1.4 Microbial Ecology - Microbes make up majority of the Earths biosphere Microbes Support Natural Ecosystems Early suspicion on existence of microbial organisms o Soil samples oxidized hydrogen gas and treatment of soil with acid or heat eliminated this activity o Ammonia in sewage was oxidized to form nitrogen Russian Scientist Sergei Winogradsky was the first scientist to study microbes in their natural habitat. He studied, chemolithotrophs or lithorops, that solely rely on inorganic mineral as their food source. He studied Beggiatoa, a microbe that fixes carbon dioxide into biomass, without consuming any organic compounds. A problem that Winogradsky encountered was that he could grow most of the lithotrophs on agar plate. For example, nitrifers. Therefore, to accommodate this, he prepared an inorganic solution with ammonia and silica gel, which was the root model for enrichment culture medium to grow other microbes, which require selective media, supporting only certain classes of microbial species.

Winogradsky Column: It was used to prove that Earth is like a cell. He made glass model tube, containing mud, newsprint, and calcium salts of sulfate and carbonate. After weeks of light exposure, different layers and colours of mineral metabolizing bacteria developed. On top cynobacteria that need light to conduct photosynthesis, then below we have purple that use oxygen split hydrogen sulfide. At the bottom, we have oxygen exhausted bacteria fulfilling the deficient end of oxygen, as sulfide produced by purple bacteria, is used to produce hydrogen sulfide and iron as precipitate. The gradient from oxygen rich conditions at the surface to highly reduced conditions below generates a voltage potential, like a battery cell. Why cant you grow lithotrophs on agar plate?

Bacterial Endosymbiosis with Plants and Animals jiij

Summary and important contributions - Microbes affected human civilization for centuries before humans guessed their existence through their contribution to our environment, food and drink production, and infectious diseases - Robert Hooke and Antonie van Leeuwenhoek were the first to record observations of microbes through simple microscopes - Spontaneous generation is the theory that microbes arise spontaneously, without parental organisms. Lazzaro Spallanzani showed that microbes arise from pre-existing microbes and demonstrated that heat sterilization can prevent microbial growth - John Tyndall showed that repeated cycles of heat were necessary to eliminate spores formed by certain kinds of bacteria - Florence Nightingale statistically quantified the impact of infectious disease on human population. - Robert Koch devised techniques of pure culture to study a single species of microbe in isolation. A key technique is culture on solid medium using agar, as developed by Angelina and Walther Hesse, in a double dish container devised by Julius Petri. - Kochs postulates provide a set of criteria to establish a causative link between an infectious agent and a disease - Edward Jenner established the practice of vaccination, inoculation of cowpox to prevent smallpox. Jenners discovery was based on earlier observation by Lady Mary Montagu and other that a mild case of smallpox could prevent future cases.

- Louis Pasteur discovered that microbial basis of fermentation. He also showed that providing oxygen does not enable spontaneous generation. He developed the first vaccines based on attenuated strains, such as the rabies vaccine - Ignaz Semmelweiz and Joseph Lister showed that antiseptics could prevent transmission of pathogens from doctor to patient - Alexander Fleming discovered that the Penicillium mold generated a substance that kills bacteria. Howard Florey and Ernst Chain purified the substance penicillin, the first commercial antibiotic to save human lives. - Martius Beijerinck discovered viruses as filterable infective particles.