The Awesome Microbe Carnival

Rehearsal day 18/11/15

On that day, everyone was so busy and Dr. Wan looked so worry because there are a lot of things stll not yet settled especially the golden history tunnel. Although we knew all these were rush and crazy, the only way we can do is to go ahead with everything. Secreteriat were dividing our own job on that day and we found that we need the help from the post graduate student to in charged of the exit counter. I straight away called Kak Fatin and she is ok with that. I felt so grateful to Kak Fatin and her friends for their help.

1st day 19/11/15

We had SSK lab at 8am but we still need to reach Panggung Percubaan at 7.30am to set up. Our poster looked so beautiful. We started to decorate our poster booth with some ribbon and balloon. After Lian Sing reached our poster booth, then we only went to our class because Lian Sing will took over our poster booth during our SSK class time. Thanks to our SSK lecturer because she willing to release us earlier to our carnival. At first, we were quite passive. We seldom approached to the visitors. I think this was because we were not yet ready and prepared. Haha. I some more walked way from my poster booth to visit other game booth , of course I knew my group members will be stood in front of our poster booth. I felt like in charged of game booth was more interesting.
After that, May Ling and I then in charged of the registration counter. We found that people kept ignored the registration counter and entered through the exit door. I think this was because we didn't labelled "registration counter" and we also didn't labelled any "entrance" or "exist" at the door. There were no any big problem on the registration counter. The people on the first day was too many and caused the booklets are not enough to distribute.

2nd day 20/11/15

On the second day, our poster booth will be jugded. We felt quite nervous. We kept practising what we are going to present later. Before our judgement, there were quite a lot of visitors come to our booth compared to the first day. This made us more used to what we are going to present later because we kept repeating the content of our poster. Dr. Suriana and Dr.Amalia praised the idea of our poster and video were creative. After the SCL judgement, I will then again in charged of the registration counter. Today visitors were not much compared to yesterday, but our goodies bag are finish distributed. There were few students ask for goodies bag, but we only can apologized. There were also few master students who rejected to write down their name for registration. They only willing to write down their name after we explained to them the purpose of writing down their name is to count the number of visitors.

Throughout this carnival, for my part, I am not doing my best. I will do better in the next carnival because finally I understood the job scope of secreteriat. Thank You Dr Wan, Kak Syaza, Radin, Mokry and everyone who helped me in this carnival. This carnival will not be that successful if without you Dr.Wan. My friends are all amazed by this carnival and they hope for The Awesome Microbes Carnival 2.0 !

Semester 3 Microbial physiology Topic 3

Topic 3: Intracellular structures of prokaryote

Notes:
1) The intracellular structure found in prokaryote are plasma membrane, cytoplasm, the nuclear area, ribosomes, inclusions and endospore.

• Plasma membrane

- Function: selectively permeable barrier, synthesize cell wall components, assists in DNA replication, carries on respiration and captures energy as ATP.

- The movement of materials across membrane: simple diffusion, facilitated diffusion, osmosis, active transport and group translocation.

- Simple diffusion, facilitated diffusion and osmosis do not require energy where active transport and group translocation belong to active transport.

- Group translocation are molecules that chemically modified during passage across cytoplasmic membane. 

• Cytoplasm

- Cytoplasm refers to the substance of the cell inside the plasma membrane,

- contains proteins, carbohydrates, lipids, inorganic ions, DNA, ribosomes and inclusions.

- lacks of cyoskeleton

• The nuclear area

- Single long circular molecule of double-stranded DNA

- do not include histones and not surrounded by nuclear envelope

- In addition to the bacterial chromosome, bacteria often contain small circular, double stranded DNA molecule called plasmid.

• Plasmid

- small circular, double stranded DNA

- do not contain genetic material essential for growth

- contain features that enhance survivability such as gene for drug resistance can be transfer from one bacterial to another

- The characteristic of plasmid: not connected to bacterial chromosome and replicate independently of chromosomal DNA

• Ribosomes

- for protein synthesis

- 70S ribosome

- small subunit - 30S and large subunit - 50S

- Each subunit consists of protein and RNA called ribosomal RNA ot rRNA.

- Cells that have high rates of protein synthesis, have a large number of ribosomes.

• Inclusions

- divided into granules and vesicles

- Metachromatic granules are large inclusion. Volutin granules are an intracytoplasmic (inside the cytoplasm of a cell) storage form of complexed inorganic polyphosphate, the production of which is used as one of the identifying criteria when attempting to isolate Corynebacterium diphtheriae on Löffler's medium. They appear red when stained with methylene blue and gives a metachromatic effect.

- Sulfur granules serve a an energy reserve, derive energy by oxidising sulfur and sulfur-containing compounds. The bacteria that contain sulfur granules is sulfur bacteria.

- Carboxysomes contain the enzyme ribulose 1,5 - diphosphate carboxylase. It used for carbon dioxide fixation during photosynthesis.

- Magnetosomes contain iron oxide that act like magnets. Their main function is to protect the cell against hydrogen peroxide accumulation.

- Lipid inclusions store polymer poly-beta-hydroxybutric acid. It revealed by Sudan eyes and the example of bacteria that contain lipid inclusion is Mycobacterium, Bacillus, Azotobacter and Sprillum.

- Gas vesicles are normally found in photosynthetic group such as cyanobacteria, proteobacteria and green sulfur bacteria. The function of gas vesicle is to provide buoyancy for aquatic prokaryotes and to receive sufficient amount of oxygen, light and nutrients.

• Endospores

- resting structure formed by some bacteria for survival during adverse environemental conditions

- germination results in leaving the dormant stage and once again becoming a typical, multiplying cell (vegetative cell)

- high resistant differentiated bacterial cell

- enable the organism to endure extreme environmental conditions

- The structure of spore is more complex than vegetative cell:

- The presence of dipicolinic acid which located in core wall give the resistance properties of endospore because intercalate in DNA and stabilizing it to prevent heat denaturation.

- Genus Bacillus and Clostridium are two common disease causing bacteria that produce endospores as needed.

My own explorace：

1) In group translocation, the substance is chemically altered during transport, preventing it from escaping the cell after it is transported inside. This process requires high-energy phosphate compounds like phosphoenolpyruvic acid (PEP) to phosphorylate the ransported molecule, preventing its movement out of the cell. 

2) The magnetotactic bacteria can be subdivided into two categories, according to whether they produce particles of magnetite or of greigite, although some species are capable of producing both. Magnetite possesses a magnetic moment three times that of greigite.

3) The formation of endospores may help maintain the symbiotic association between these Epulopiscium-like symbionts and their surgeonfish hosts. Since endospore formation coincides with periods in which the host surgeonfish is not actively feeding, the cells do not need to compete for the limited nutrients present in the gut at night. The protective properties of the endospores also allow them to survive passage to new surgeonfish hosts. The fish may also benefit from this relationship because it is able to maintain stable microbial populations that assist in digestion and may receive a nutritional gain from microbial products released during mother cell death and spore germination.

Reflection:

I would like to know the benefit of endospore to the environment.  People always think that endospore maximize the chance of spreading disease. Actually endospore is not just spreading disease, but it help to maintain the symbiotic association between Epulopiscium-like symbionts and their surgeonfish hosts. Besides that, Bacillus subtilis spores are useful for the expression of recombinant proteins and in particular for the surface display of peptides and proteins. Therefore, everything have their good side and bad side include endospore, bacteria or even virus.

Semester 3 Microbial Physiology Topic 2

Topic 2: Cell Wall and Membrane Structure of Prokaryotes

Notes:
1) There are four structure external to the cell wall:

• Glycocalyx

- substances that surround cell

- it is made inside the cell and excreted to the cell surface

- capsule is called if the substance is organised and is firmly attached to the cell wall

- slime layer is called if the substance is unorganized 

- Functions: protection from phygocytosis, attachement to various surfaces, source of nutrients, and protect a cell against dehydration.

• Flagella

- Long filamentous appendages that propel bacteria

- There are four arrangement of flagella: Monotrichious, Amphitrichous, Lophotrichous and Peritrichous. 

- There are three basic parts in a flagellum:

Filament(contain the globular protein flagellin) , Hook, Basal body(gram-negative bacteria contains two pairs of rings and gram-positive bacteria contains only the inner pair)

• Axial Filaments

- bundles of fibrils that arise at the ends of the cell beneath the outer sheath.
- spiral around the cell
- present in the spirochetes group of bacteria
- e.g. Treponema pallidum and Borrelia burgdorferi

• Fimbriae and Pili

- Hairlike appendages that are shorter, straighter and thinner than flagella

-consist of pilin

- used for motility rather than for motility

- There are two types of fimbriae and pili: Fimbriae can occur at the poles, evenly distributed over the entire surface, and can number anywhere from a few to several hunfred per cell.

- Pili are longer than bimbriae and joint bacterial fells in the perparation for the transfer of 

DNA from on cell to another. 

Pili is used for the transfer of extrachromosomal

2) Cell wall component: Gram-negative and gram positive bacteria

Gram-negative and gram positive bacteria are structurally different and this differences cause them to have different characteristics. Gram-negative bacteria are resistant to antibiotics due to the presence of outer membrane.

3) Archaea have cell walls consisting of polysaccharide, glycoprotein but not peptidoglycan.

They contain a substance similar to peptidoglycan called pseudopeptidoglycan (pseudomurein).

Their cell wall type is S layer which protects against osmotic stress, pH and enzymes.

Archaea are naturally resistant to lysozyme and penicillin.

4) The unique feature found in cell wall of archae is the presence of L-amino acid instead of D-amino acid, the presence of N-acetyltalosaminuronic acid but not N-acetylmuramic acid and the presence of beta(1,3) glycosidic bond instead of beta(1,4)glycosidic bond.

My own exlporace：

1) Mycobacterium does not have any glycocalyx because they do not have cell wall or very little cell wall material.

2) Capsules give better protection than slime layer because capsule is organised and is firmly attached to the cell wall.

3) A spheroplast is a cell from which the cell wall has been almost completely removed, as by the action of penicillin. Spheroplasts are osmotically fragile, and will lyse if transferred to a hypotonic solution.

4) Septic shock is what happens as a complication of an infection where toxins can initiate a full-body inflammatory response. It often occurs in people who are elderly or have a weakened immune system. It is thought that the inflammation resulting from sepsis causes tiny blood clots to form, which can block oxygen and nutrients from reaching vital organs. As a result, the organs fail, causing a profound septic shock. 

Reflection:
Although cell wall and membrane structure of prokaryotes have learned in last two semester, there are few terms that I am not familiar with. Septic shock and spheroplast are new for me. I think to differentiate gram negative and gram positive bacteria have to be very specific to avoid any error since this is the important step to identify the bacteria.

Semester 3 Microbial physiology Topic 1

Topic 1: Introduction to Prokaryotes

Notes:

1) Prokaryotes divided into two domains which are bacteria and archaea.
2) Definition of prokaryote: Organisms that lack a cell nucleus or any other membrane-bound organelles.
3) They are unicellular, but a few prokaryotes such as myxobacteria have multicellular stages in their life cycles.
4) Prokaryotic diversity include proteobacteria, cyanobacteria, gram positive bacteria, spirochetes with unique morphology, green sulfur and green nonsulfur bacteria.

- Proteobacteria are a major group (phylum) of gram-negative bacteria.
a. Alphaproteobacteria - They grow at very low nutrient area and are agriculturally important because they able to induce nitrogen fixation.
b. Epsilonproteobacteria - They are microaerophilic and they are the most common cause in stomach cancer.
c. Gammaproteobacteria - They are medically important and a large group of pathogen belong to this group such as Salmonella spp.
d. Betaproteobacteria - They play a role in nitrogen fixation in various types of plants, oxidizing ammonium to produce nitrite.
e. Deltaproteobacteia - They are predators on other bacteria and are important contributors to the sulfur cycle.

- Cyanobacteria are aquatic and photosynthesic. They have live on earth for 3.5 billion years. Therefore, they important in shaping the course of evolution and ecological change throughout earth's history.
- Gram positive bacteria have specifc membrane structure. Their structure consist of thick peptidoglycan layer, teichoic acids and gram-positive bacteria are more receptive to antibiotics than gram-negative, due to the absence of the outer membrane.
- Spirochetes are helical in shape They are tightly coiled, and so look like miniature springs or telephone cords.These filaments run along the outside of the protoplasm, but inside an outer sheath; they enable the bacterium to move by rotating in place. Spirochetes causes syphilis and lyme disease.
- Green sulfur bacteria and green nonsulfur bacteria are autotrophs. They produce energy from light and are named for their green pigment, usually found in photosynthetic bodies called chlorosomes.
- Deinococcus radiodurans are extremophilic bacteria where they can survive cold, dehydration, vacuum and acid. Deinococcus radiodurans has a unique quality in which it can repair both single- and double-stranded DNA. When a damage is apparent to the cell, it brings it into a compartmental ring-like structure, where the DNA is repaired and then is able to fuse the nucleoids from the outside of the compartment with the damaged DNA. They are the toughest bacterium in the world.

5) Archaea, the another domain of prokaryote. They are known as extremophiles, halophiles and thermoacidophiles. Their can survice in harsd environement because of their specific cell structure. They are chemotrophic and chemolithotrophics. The example of archaea is Pyrolobus and Halobacterium.

The differences between Bacteria and Archaea:



My own Explorace:
1)  Deinococcus radiodurans can withstand large amounts of radiation, can live in a vacuum for up to six weeks and live, can live dehydrated, and live through fluctuations in pH. This bacteria is so special that it was the first be in the phylum "Deinococcus". This is one of the only organisms in the world that can withstand 5,000 GYs of radiation. It can repair itself completely within 12-24 hours and can survive on Mars.

2) Crenarchaeota are Archaea that have been classified as a phylum of the Archaea kingdom.The Crenarchaeota were thought to be sulfur-dependent extremophiles but recent studies have identified characteristic Crenarchaeota environmental rRNA indicating the organism may be the most abundant archaea in the marine environment. Until recently all cultured Crenarchaea had been thermophilic or hyperthermophilic organisms, some of which have the ability to grow at up to 113 °C. These organisms stain Gram negative and are morphologically diverse having rod, cocci, filamentous and oddly shaped cells.

3) E. coli O157:H7’s ability to induce injury in humans is a result of its ability to produce numerous virulence factors, most notably Shiga toxin, which is one of the most potent toxins known to man.

4) Shiga toxin has multiple variants and acts like the plant toxin ricin by inhibiting protein synthesis in endothelial and other cells. Endothelial cells line the interior surface of blood vessels, and are known to be extremely sensitive to E. coli O157:H7, which is cytotoxigenic to these cells.

Reflection:
Deinococcus radiodurans are such a strong bacteria, I can't imagine how they can withstand so high radiation that even can't stand by a person. This is my first time heard proteobacteria in the class. Proteobacteria are gram negative bacteria but it has divided into five classes.

10th Lecture: 1/6/15

Topic: Biogeochemical cycle and Aspects of Biotechnology of Microbial Ecology

Notes:
1) Biogeochemical cycles is which mechanisms by which recycling nutrient occur.

2) The characteristics of biogeochemical cycles are transformed and cycled through oxidation-reduction reactions and all cycles are linked.

3) Carbon cycle
- The final product of aerobic respiration in carbon cycle is oxidized products: H20, NO3-, SO42- and carbon dioxide.
- The final product of anaerobic respiration in carbon cycle is reduced products: NH4+, H2S. H2 and CH4.

4) Nitogen cycle

• Nitrification

- Nitrification carry out in aerobic condition where ammonium ion (NH4+) undergo oxidation to form Nitrite (NO2-), followed by oxidation of nitrite (NO2-) to form Nitrate (NO3-).

- The example of microorganisms that oxidized ammonium (Nh4+) to nitrite (NO2-) is Nitrosomonas and Nitrococcus. The example of microorganisms that oxidized nitrite (NO2-) to nitrate (NO3-) is Nitrobacter.

• Denitrification

- Denitrification carry out in anaerobic condition where nitrate (NO3-)  is reduced to nitrite (NO2-), nitrogen gas (N2) or nitrous oxide (N2O). 

- Dissimilatory process (use nitrate NO3- as the electron acceptor to produce ATP)

- Nitrate (NO3-) as oxidant.

- The example of microorganisms is Pseudomonas.

- Nitrate (NO3-) can reduced to ammonia (NH3) by Geobacter, Desulfovibrio and Clostridium.

• Nitrogen fixation

- Nitrogen fixation is a process in which nitrogen (N2) in the atmosphere is converted into ammonium (NH4+) or nitrogen dioxide (NO2).

- Reductive processes

- Ammonia is the product

- must occur in anaerobic condition even in aerobic microorganisms

- Anammox process: anaerobic oxidation of NH4+ and reduction of NO2- to produce nitrogen gas by some microorganisms.

5) Sulfur cycle

• Sulfur Oxidation

- Sulfur is oxidized to sulfate (SO42-) by using Sulfide (H2S) as electron acceptor.

- The example of microorganisms are Thiothrix, Beggiatoa and Thiobacillus.

• Sulfur Reduction

-Sulfur is reduced to sulfide (H2S) .

• Sulfate Reduction (Dissimilatory process)

- Sulfate (SO42-) is reduced to sulfide (H2S) by Desulfovibrio and Desulfuromonas.

- Sulfite (SO32-) is reduced to sulfide (H2S) by Alteromonas, Clostridium, Desulfovibrio and Desulfotomaculum.

• Sulfate Reduction (Assimilatory process)

- Sulfate (SO42-) is reduced to organic sulfur for use in amino acid and protein biosynthesis.

- Mineralization is the process where the sulfhydryl (-SH) groups in protein of dead animals converted to sulfide (H2S).

6) Iron cycle

• Ferrous ion (Fe2+) is oxidized to Ferric ion (Fe3+) in aerobic condition. The example of microorganisms are Thiobacillus ferrooxidans, Gallionella,Sulfolobus.
• Ferric ion (Fe3+) is reduced to Ferroous ion (Fe2+) in anaerobic condition. The example of microorganisms are Geobacter, Ferribacterium and Shewanella.

7) Manganase cycle

• Manganase ion ( Mn2+) is oxidized to manganic ion (Mn4+) in aerobic condition. the examples of microorganisms are Leptothrix, Arthrobacter and Pedomicrobium.
• Manganic ion (Mn4+) is reduced to Managnase ion (Mn2+)in anaerobic condition. The examples of Shewanella and Geobacter,

8) The function of microorganisms in microbial ecology:

• Microorganisms as pollutants - Food borne and water borne pathogens, massive growth of pathogens causes eutrophication
• Microorganisms as cause of pollution - Mercury will combine with the organic methyl group that found in aerobic microorganisms and form  Methyt mercury. Methyl mercury will totally absorbed by body and retained in the body longer than elemental mercury.
• Microorganisms as an indicator of pollution - colliform group of bactera and biofilm can test for pollution
• Microorganisms may reduce pollution - Biodegradation and Bioremediation

9) Biodegradation is the natural decomposition or breakdown of molecules by microorganisms. All natural organic compounds are degradable. Recalcitrant are non-biodegradable because they are synthetic molecules.

10) The example of biodegradation:

• Biodegradation of oil spills

- fungi, bacteria especially Pseudomonas oxidized hydrocarbon to carbon dioxide

- Slow because low nutrients and low population. We can improve by using bioremediation and genetic engeneering. Nutrient sprayed to encourage microbial growth. 

•  Microorganisms in Landfills

- The microorganisms found in landfills are mostly anaerobic and they are methanogens and cellulose digesters. The major product of fermentation is carbon dioxide, methanem organic acids and alcohols. The products will leached out from landfills so landfills have to far from water source.

• Microbial application as pesticides 

-Bt protein that produced naturally by Bacillus thuringiensis used to spray on plants. Bt protein won't harm plants but will attack specific stages of insects only and solve the problem of pesticides.

11) Bioremediation is the use of living organisms to promote the degradation of environmental pollutants cartificiallyby increase the growth of naturally occuring microorganisms. Bioremediation only carry out when biodegradation processes not at a desired rate. Microorganisms use the contaminant as nutrient for reproduction and converts contaminant to less harmful form and release to the environment.

12) Cometabolism is defined as the simultaneous degradation of two compounds, in which the degradation of the second compound (the secondary substrate) depends on the presence of the first compound (the primary substrate). For example: trichloroethylene (TCE) is groundwater pollutant. Methane and oxygen is added to encourage methanotrophs. TCE not a substrate for methanotrophs but methanotrophs produce methane monooxygenase to degrade TCE.

13) Source of microorganisms is contaminated sites, culture collection and genetically engineered "superbug". Unfortunately, superbug are less effective due to the attractiveness of laboratory-grown microorganisms as the food source for predators, inability to contact the compounds to be degraded and failure to survive and compete with indigenous microorganisms.

14) In general, bioremediation is the addition of microorganisms to accelerate the growth of indigenous microorganisms.

15) Phytoremediation is the use of plant  to stimulate the degradation, transformation or removal of compounds, either directly or in conjunction with microorganisms.

16) The advantages of plants with microorganisms in bioremediation are extensive root system, higher ability for storage and easy to harvest.

17) The types of phytoremediation are phytoextraction, phytodegradation, rhizofiltration, phytostabilization and phytovolatilization.

Activity:
No other activity except for teaching....^^

My own Explorace:
1) In nature, nitrogen not only fixed by microorganisms but also by lighting.

2) Fritz Haber undertook the work on the fixation of nitrogen from the air for which he was given the Nobel Prize in Chemistry for 1918 (awarded in 1919).

3) In biology, the opposite of assimilation in the process of metabolism, consisting in the decomposition of organic compounds and conversion of protein, nucleic acids, fats, and carbohydrates (including those ingested) into simple substances.

4) The definition of biotechnology is the use of living organisms and biomolecular process to develop, make or modify product to improve our human lives.

5) Blue baby syndrome occurs when newborn babies have cyanotic heart defects. Th reason cause blue baby is methemoglobinemia. Methemoglobinema is caused by nitrate contamination in groundwater resulting in decreased oxygen carrying capacity of hemoglobin in babies leading to death.

6) Endotoxin only released when the cells or microorganisms are lysed and exotoxin is more pathogenic compared to endotoxin because exotoxin can released without the lysis of cells.

7) Superbugs are strains of bacteria that are resistant to several types of antibiotics.

Reflection:
Today is the last class of Microbiology 2 . The things we learnt getting harder and harder. I felt that the use of Bt protein as pesticides is a great discovery. This really help farmer to solve their problem. To avoid blue baby, the landfill sites need to far away from water source. The biogeochemical cycle made me confused but Dr Wan said we gonna learn more detail about biogeochemical cycle during physiology miicrobiology. @.@
Dr Wan, thanks for teaching us this semester~~~ See You~~~ ^^

9th Lecture: 21/5/15

Topic: Principles of ecology

Notes:
1) Ecology is the study of the systematic study of organisms and their interactions with environment. It reveals the relationship between living and non living parts of the environment.

2) Niches is a place where the organisms perform the best.

3) Hierarchy in ecology :
- species : organisms with common genetic makeup, behaviour and physical characteristics.
- population: a group of individuals belonging in the same species inhabiting a particular geographical area.
- community: all organisms inhabiting a particular area
- ecosystems: include all abiotic factor and biotic factor of a habitat.
- biosphere: all ecosystems on earth

4) Abiotic factors are the non living parts of the environment where include temperature, water, sunligh, wind, rock and soil and periodic disturbances.

5) Homeostasis is the dynamic balance of processes materials and organisms in the ecosystem and biosphere.

6) Homeostasis og the ecosystem invlove the interaction between organisms and organisms and also interaction between organisms and habitat.

7) Energy and nutrient are absorbed from one stage of organisms to another stage of organisms but part of the energy will lost as heat.

8) Energy itself does not recycle but the energy only recycle in the form of C-C bond. Ultimate fate of energy are lost as heat while the ultimate source of energy is sun.

9) Microbes play important roles in the ecosystem. Microbes can act as:
- oxygen producer
- environment nitrogen fixer
- recyclers of dead material
- source of food in food chain
- weak species remover

10) The factors that may affect the stability of the environment are:
- increase the frequency of natural or unnatural disturbances
- abrupt change in species diversity
- a change in the rate of nutrient and energy consumption

11) There are few ways we can do to manage our ecosystem :

• Stakeholders

- develop knowledge about the values of nature to open negotiations to develop mutual beneficial partnerships

• Adaptive management

- implement and analyse hypotheses based on their previous implemented management strategies

• Natural resource management

- deal with the particular resource but not the whole ecosystem.

- fulfill and take care of demands without causing harm to the ecosystem

• Strategic management

- encourages establishment of goals that will benefit the ecosystem while keeping the socioeconomic and politically relevant issues in mind.

• Landscape level conservation

- considers wildlife needs to identify the best option for protecting their ecosystem.

• Command and control management

- perceived problems solved through controlling devices such as laws, contracts or agreements.

Activity: Submit kubbu that is prepared by group 3 and padleting for the topic of biogeochemical cycle.

My own explorace:

1) The example of negative interaction are competition, prey and predator, parasitic relationship.

2) Microbial loop describes dissolved organic carbon is introduced to marine food web via its incorporation into bacterial biomass, and then coupled with the classic food chain formed by phytoplankton-zooplankton-nekton.

3) The dossolved organic materials will first absorbed by bacteria. When the bacteria died, the bacteria will be digested by protozoa and protozoa digested by zooplankton. Zooplankton will consumed by fished or other marine animals.

Reflection:

Today Dr Wan was talked about ghost story in the class and everyone was awake at this moment. Hahahahaha. The study of principles of ecology is important because we need to understand their habitat and how they work with the environment if we want to further study about them. For example, we need to know the habitat of the microorganisms when we want to isolate a certain microorganisms. The relationship of microorganisms with their habitat is important in the study of roles of microbes in the ecosystems.

8th Lecture: 20/5/15

Topic: Microbial group

Notes:
1) Microbial growth is based on the growth of population and not individual growth.
2) There are four physical growth requirements of microbial growth:

- light

-temperature
(Mesophiles 25 degree celcius to 40 degree celcius, Psychrophiles 0 degree celcius to 20 degree celcius, psychrotrophs 20 degree celcius to 30 degree celcius, thermophiles 45 degree celcius to 50 degree celcius)

-pH
(most bacteria pH 5-9, most fungi pH 2-9)

- water activity and water pressure
(water activity is the amount of water found in substrate for the microorganisms to grow)
(maximum water activity for biomolecules is 1)
(bacteria live in higher water activity habitat 0.91 while fungi live in lower water activity habitat is 0.7 )

3) There are six chemical growth requirements:

- water

- carbon

- oxygen
(microaerophiles - need little amount of oxygen, facultative anaerobes -can live with oxygen or without oxygen, aerotolerant - can live in with oxygen and without oxygen)

- nitrogen, phosphorus and sulfur
(nitrogen can obtained from atmosphere, phosphorus can obtained from inorganic source, sulfur can obtained from organic or inorganic molecules)

- special growth factors
(Legionella pneumophila require L-cystein and iron to grow and L-cystein are provided by algae and amoebas)

- trace elements

4) Nutritional types:
- Photoautotrophs (E:light, C: CO2)
- Photochemotrophs (E:light, C: organic molecules)
- Chemoautotrophs (E:light, C:inorganic molecules)
- Chemoheterotrophs (E: organic molecules, C: organic molecules)

5) Population strategies are either r strategists or K strategists.
- r strategists have high rate of reproduction rate, short generation time, population are subject to extreme fluctuation
- K strategists have low rate or reproduction, large size, large storage, successful in resource limited environments and they are more stable populations

6) They are four types of succession:

- Preemptive colonization - pioneer organisms alters condition in a way that discourages further succession
- Autogenic succession - microorganisms modify the habitat in a way that permits in a new population to develop
- Allogenic population - Microbial species succession occurs because the habitat is altered by environmental factors.
- Climax community - achieved when succession ends however it is rarely achieved.

7) Biofilm composed of living. reproducing microorganisms, such as bacteria that exist as a community. Biofilm can trap nutrient and prevent detachment from surfaces. The disadvantages of biofilm are unavailable for attack by immune system, dental caries, slow the flow of water through pipelines and accelerate the corrosion of pipes.

Activity:
No other activity except for teaching...^^

My own explorace:

1) Biology control agent is the use of natural enemies to reduce the populations of pests such as insects and weeds.

2) We can know the temperature where the microorganisms used to grow based on the temperature of their habitat.

3) To isolate a microorganisms, we need to know the habitat of the microorganisms. Suitable media need to prepare and dilution pf the culture is necessary before we incubate in the media. After verify the cingle colony of the target microorganisms, we need to do sub culture to transfer the microorganisms to a fresh new media for them to grow.

4) We need to test at different temperature is the isolated microorganisms didn't grow well in the expected temperature.

5) Gnotobiotic animals are animals in which only certain known strains of bacteria and other microorganisms are present. They are only exposed to those microorganisms that the researchers wish to have present in the animal. Animals reared in a gnotobiotic colony often have poorly developed immune systems, lower cardiac output, thin intestinal walls and high susceptibility to infectious pathogens.

6) Diazotrophs are bacteria and archaea that fix atmospheric oxygen into a more usable form such as ammonia. Even within a species that can fix nitrogen there may be strains that do not fix nitrogen. Fixation is shut off when other sources of nitrogen are available, and, for many species, when oxygen is at high partial pressure.  Azotobacter vinelandii is one of the diazotroph that can fix nitrogen while growing aerobically.

7) Biofilm can act as indicator ( same with the function of lichens) because the habitat of biofilm is always unpolluted.

8) We can obtain the enzymes at the lag phase of bacterial growth while we can obtain the secondary metabolites at between log phase and stationary phase.

9) Termite gut exhibits complex microbial community as in rumen. Since termite feed on diet that is rich in carbon but poor in nitrogen, therefore nitrogen fixers is essential to supply a sufficient amount of nitrogen in termite gut. Treponema, Citobacter, Enterobacter, and Spirochaeta are some of the responsible nitrogen fixers. The prokayotes in termite guts usually associated with protists as symbionts. Treponema spirochete bacteria attached to the plasma membrane of mixotricha and contributes the movement of mixotricha. Treponema also benefits on living within mixotricha where hydrogen and carbon dioxide nutrients are easily to access by the production from mixotricha.

Reflection:
Amazing microbial community! I can't imagine the small termite gut contain so many microorganisms. I think we really can't live without microbes. My friends from the department of biomolecules created an article for the event "life without microbes" and the title of the articles is MICRO-AVENGERS. I like this title because people will know that human can't live without microbes based on this title.