Functions of microorganisms in microbial colony
1) Microorganism as pollutants
Salmonella can be found both inside and outside of eggs. Normally, eggs can be infected by fecal contamination when the egg exits the hen's body or by dirt from surroundings. That is why the eggs are washed and sanitized at the processing plant. Bacteria can also be inside an uncracked, whole egg. Contamination of eggs may be due to Salmonella within the hen's ovary or oviduct being transferred into the contents of yolk and white before the shell forms. Over the years, however, scientists have found that Salmonella Enteritidis has the ability to grow both in the egg yolk and white.
Keeping eggs adequately refrigerated prevents any Salmonella present in the eggs from growing to higher numbers, so eggs should be refrigerated until they are needed. Moreover, cooking reduces number of bacteria in eggs due to the use of high temperature.
Symptoms of Salmonella infection: (12-72 hours after consumption of contaminated food)
- Fever
- Abdominal pain
- Diarrhea
Actions that can be taken to reduce Salmonella infection from eggs
- Discard cracked eggs
- Keep eggs from refrigerated
- Avoid consumption of raw eggs.
- Eggs should be fully cooked
2) Microorganism cause of pollution
Methylmercury is a neurotoxin that poses significant health risk to human. It is formed by the action of anaerobic bacteria. They turn inorganic mercury into methyl mercury.
3) Microorganism as indicator of pollution
Dr mentioned that if E. coli is found in water, it has a high possibility that the water is contaminated with faeces.
4) Microorgnism may reduce pollution
For example, Rhodococcus can be used in oil degradation.
Extra information
- If we want to increase the production of microbes, bioreactor is used which the volume is up to 1000L.
- Pesticide such as DDL is toxic in high concentration. It function through interfering the synthesis of chitin. Thus it will disturb the development of insects such as grasshopper since the head, thorax and body is mostly made up by chitin.
- Superbug is resistant to antibody
-Thiram is a fungiside. It is used to prevent fungal disease in seed and crops. Besides, it also acts like an animal repellent to protect fruit trees and ornamental( plant that is grown for its beauty and decorative value) from damage by rabbits and rodents.
Water related disease
- What is Methaemoglobinemia?
Reduction of ability of blood to carry oxygen due to reduced level of haemoglobin.
- Who will be the victim?
Infants are most infected. They may seem healthy, but show the sign of blueness around the mouth, hands and feets. This is why they are given the name 'Blue baby syndrome'.
- What are the syndrome?
These children will have breathing difficulties,continuous vomiting and diarrhoea.
- What is the cause?
High concentration of nitrate in drinking water, especially in bottle fed infants and water from well in rural areas. The source of nitrate comes from manure and fertiliser on agriculture land.
- How does it work?
In human body, nitrates will be converted to nitrites. Nitrites is then react with haemoglobin in red blood cell to form methaemoglobin, affecting the body's ability to carry oxygen.
Sunday, June 7, 2015
Friday, June 5, 2015
Biogeochemical cycles
Carbon cycle
1)
Reduced form of carbon: CH₄, Organic matter [
presence of H]
Oxidized form of carbon: CO, CO₂ [To ease my
memorising, there is presence of O]
2) Organic matter undergo respiration to release CO₂.
Organic matter undergo fermentation to become CH₄, CO₂, H₂.
3) Carbon dioxide will be fixed into organic matter again by plants and photosynthetic bacteria such as cyanobacteria and green algae.
4) Organic matter includes cellulose, lignin, hemicellulose from plant cell wall, starch, hydrocarbon and lipids from animals.
Nitrogen cycle
3 major process:
1) Nitrification (Oxidation)
Ammonium
ion (NH₄⁺) --------------> Nitrite
(NO₂⁻) --------------> Nitrate
(NO₃⁻)
2) Denitrification
Nitrate (NO₃⁻) -----------> Nitrogen gas (N₂) / Nitrite (NO₂⁻)
Reduction of nitrate to ammonium ion by several bacteria such as Geobacter sp. , Clostridium sp. , Desulfovibrio sp.
Nitrate (NO₃⁻) -----------> Ammonium ion (NH₄⁺)
3) Nitrogen fixation (Reduction)
Nitrogen gas (N₂) ----------> Ammonium ion (NH₄⁺)
Sulfur Cycle
1) Mineralization of organic sulphur to the inorganic form, hydrogen sulphide (H₂S is toxic)
2) Oxidation of sulphide (H₂S) and elemental sulphur (S) to sulphate (SO₄⁻)
3) Reduction of elemental sulphur (S) /sulphate (SO₄⁻) to sulphide (H₂S) (dissimilatory)
4) Reduction of sulphate (SO₄⁻) to organic sulphur. (assimilatory)
Oxidation (Aerobic condition)
Ferrous ion (Fe²⁺) --------> Ferric ion ( Fe ᶟ⁺)
Reduction (Anaerobic condition)
Ferrous ion (Fe²⁺) <-------- Ferric ion ( Fe ᶟ⁺)
Ferric ion ( Fe ᶟ⁺) --------> Fe₃O ₄by magnetotactic bacteria
Manganase cycle
Oxidation
Mangnase ion (Mn²⁺)--------> Manganic ion (MnO₂)(Mn ⁴⁺ )
Reduction
Mangnase ion (Mn²⁺) <-------- Manganic ion (MnO₂)(Mn ⁴⁺ )
Thursday, June 4, 2015
Microbial groups
Microbial groups
This is the info graphic done by Veron in group 1!
Since this info graphic concludes all the details in the notes, I will write about the extra information that Dr gave during lectures.
1) What should we do if we do not know the temperature that microbes grow best?
Answer: Test at different temperature.
2) When we are conducting inoculation, we must use the temperature of natural habitat of the specific microbes in order to achieve the maximum growth. It is because the enzyme present in microbes has already adapted to the temperature of it's surrounding.
3) Biological agent is the use of one living organism to inhibit or kill the other living organism.
4) Fungisites, together with herbicides and insecticides are all pesticides. It is used to inhibit or kill the growth of fungal or their spores to prevent fungal disease. However, when it has been absorbed by fruit, it will become toxicity once ingested into human body.
5) Log phase of fungus is best extract enzyme while secondary metabolites is normally being extracted between log phase and stationery phase.
6) Psychrophiles (optimal at 15°C) > Psychrotrophs (optimal at 20°C) > Mesophiles (optimal at 35°C) > Thermotolerant ( 35°C-40°C) > Thermophiles ( optimal 45°C-50°C)
7) Two Picrophilus species of archaea P.oshimae and P.torridus are of note for their record low of survival at pH 0.
8) Water activity is the amount of water found in substrate that is enough for organism to grow. The highest water activity will be 1.
9) Fungi is xerophilic, which mean they can resist dessication and grow better in lower water amount.
10) Strict anaerobes = obligate anaerobes.
11) Ruminants like cattle, sheep, goats and deer has four chambered stomach. The largest compartment will be rumen where all the obligate anaerobes are located for digestion of plant fibres and starch. Those microbes live in a symbiotic manner where they help ruminants to break down the food and in return the ruminants provide them with shelter and nutrients.
12) Diazotroph are the nitrogen fixing prokaryotes (bacteria and archaea).
13) Example of organisms using r strategist are bacteria and insects while mammals used K strategists.
14) Autochthonous - Native species in an environment
Allochthonous - Transient member (Not origin)
15) Biofilm must has cilia to adhere to surface. They are embedded within a self-produced matrix of extracellular polymeric substance (EPS) which are generally composed of extracellular DNA, proteins and polysaccharide.
16) Lichen and Biofilm are sensitive to environment. Therefore they act as an indicator as presence of them indicates the surroundings is free of contaminants and pollutants.
This is the info graphic done by Veron in group 1!
Since this info graphic concludes all the details in the notes, I will write about the extra information that Dr gave during lectures.
1) What should we do if we do not know the temperature that microbes grow best?
Answer: Test at different temperature.
2) When we are conducting inoculation, we must use the temperature of natural habitat of the specific microbes in order to achieve the maximum growth. It is because the enzyme present in microbes has already adapted to the temperature of it's surrounding.
3) Biological agent is the use of one living organism to inhibit or kill the other living organism.
4) Fungisites, together with herbicides and insecticides are all pesticides. It is used to inhibit or kill the growth of fungal or their spores to prevent fungal disease. However, when it has been absorbed by fruit, it will become toxicity once ingested into human body.
 |
| Dicarboximide fungicide use for control of botrytis bunch rot Botrytis cinerea on grapes (Figure above). |
6) Psychrophiles (optimal at 15°C) > Psychrotrophs (optimal at 20°C) > Mesophiles (optimal at 35°C) > Thermotolerant ( 35°C-40°C) > Thermophiles ( optimal 45°C-50°C)
7) Two Picrophilus species of archaea P.oshimae and P.torridus are of note for their record low of survival at pH 0.
8) Water activity is the amount of water found in substrate that is enough for organism to grow. The highest water activity will be 1.
9) Fungi is xerophilic, which mean they can resist dessication and grow better in lower water amount.
10) Strict anaerobes = obligate anaerobes.
11) Ruminants like cattle, sheep, goats and deer has four chambered stomach. The largest compartment will be rumen where all the obligate anaerobes are located for digestion of plant fibres and starch. Those microbes live in a symbiotic manner where they help ruminants to break down the food and in return the ruminants provide them with shelter and nutrients.
12) Diazotroph are the nitrogen fixing prokaryotes (bacteria and archaea).
13) Example of organisms using r strategist are bacteria and insects while mammals used K strategists.
14) Autochthonous - Native species in an environment
Allochthonous - Transient member (Not origin)
15) Biofilm must has cilia to adhere to surface. They are embedded within a self-produced matrix of extracellular polymeric substance (EPS) which are generally composed of extracellular DNA, proteins and polysaccharide.
16) Lichen and Biofilm are sensitive to environment. Therefore they act as an indicator as presence of them indicates the surroundings is free of contaminants and pollutants.
Principles of Ecology
Principles of Ecology
There are few main points here:
1) Cellulolytic microbes are found in cattle and termites to hydrolyze cellulose.
2) Ecology is the study of interactions between organism with organism and organism with their environment.
3) Hierarchy in Ecology:
4) Negative interaction includes competition, parasitic and prey and predator.
Positive interaction includes commensalism and mutualism.
5) Community is made up of many populations. But when it includes the abiotic (non living) factor it is called ecosystem. Abiotic factors are temperature, water, wind, sun light and etc. It can act as a limiting factor as well.
6) Homeostasis is the balancing of waste and nutrient of organism through flow of energy.
7) In marine food chain, after the dead of photoautotroph like phytoplankton, it became dissolved organic matter. Then, it is digested by protozoa. Protozoa will be ingested by zooplankton which is tiny fishes. Finally, fish or prawn will eat zooplankton.
8) The hydrosphere is the liquid water component of Earth. It includes oceans, seas, lakes, ponds, rivers and streams. The hydrosphere covers 70% of the surface of the Earth and is the habitat of many organisms.
9) Lithosphere is the outer hard surface of earth. It includes soil and the land.
10) Energy flows in the form of C-C bonds. C-C bonds can be found in molecules such as glucose and proteins.
11) Ultimate fate of energy: Lost as heat
Ultimate source of energy: Sun
12) Examples of microbes that act as oxygen producer is blue green algae.
Also, nitrogen fixation bacteria such as Nitrosomonas sp. is responsible to turn nitrogen compound into usable form.
Cyanobacteria and protozoa are source of food in food chain.
13) There are few approaches to effective ecosystem management. For example, stakeholder needs to have diversity of knowledge about the nature. Next, landscape level conservation is conducted to protect wildlife. Lastly, Laws, contracts and agreement have to be implemented.
There are few main points here:
1) Cellulolytic microbes are found in cattle and termites to hydrolyze cellulose.
2) Ecology is the study of interactions between organism with organism and organism with their environment.
3) Hierarchy in Ecology:
Positive interaction includes commensalism and mutualism.
5) Community is made up of many populations. But when it includes the abiotic (non living) factor it is called ecosystem. Abiotic factors are temperature, water, wind, sun light and etc. It can act as a limiting factor as well.
6) Homeostasis is the balancing of waste and nutrient of organism through flow of energy.
7) In marine food chain, after the dead of photoautotroph like phytoplankton, it became dissolved organic matter. Then, it is digested by protozoa. Protozoa will be ingested by zooplankton which is tiny fishes. Finally, fish or prawn will eat zooplankton.
8) The hydrosphere is the liquid water component of Earth. It includes oceans, seas, lakes, ponds, rivers and streams. The hydrosphere covers 70% of the surface of the Earth and is the habitat of many organisms.
9) Lithosphere is the outer hard surface of earth. It includes soil and the land.
10) Energy flows in the form of C-C bonds. C-C bonds can be found in molecules such as glucose and proteins.
11) Ultimate fate of energy: Lost as heat
Ultimate source of energy: Sun
12) Examples of microbes that act as oxygen producer is blue green algae.
Also, nitrogen fixation bacteria such as Nitrosomonas sp. is responsible to turn nitrogen compound into usable form.
Cyanobacteria and protozoa are source of food in food chain.
13) There are few approaches to effective ecosystem management. For example, stakeholder needs to have diversity of knowledge about the nature. Next, landscape level conservation is conducted to protect wildlife. Lastly, Laws, contracts and agreement have to be implemented.
Wednesday, June 3, 2015
Protozoa
Protozoa
1) Ectoplasm and endoplasm
One of the unique features of protozoa is the presence of ectoplasm and endoplasm. Ectoplasm is the gelatinous cytoplasm right under plasma membrane while endoplasm is surrounded by ectoplasm. The fluid which most organelles located.
2) Pellicle
1) Ectoplasm and endoplasm
One of the unique features of protozoa is the presence of ectoplasm and endoplasm. Ectoplasm is the gelatinous cytoplasm right under plasma membrane while endoplasm is surrounded by ectoplasm. The fluid which most organelles located.
2) Pellicle
In addition, protozoa has pellicle which is the thin layer supporting the cell membrane. It is embedded in ectoplasm.
3) 2 types of nucleus.
Protozoa has macronucleus and micronucleus. The larger nucleus, macronucleus performs normal cell functions like respiration, protein synthesis and digestion while the smaller micronucleus is responsible for cell division and used only during reproduction.
| Characteristic | Micronucleus | Maconucleus |
| Polidy | 2n | ~1000n |
| Genome size | 100-120 megabases | 80-90% micronuclear complexity |
| Number of chromosomes | ~50 | ~350 |
| Chromosome size | ~2 megabases | ~300(50-1000) kilobases |
4) Vacuoles
Contractile vacuole is for osmoregulatory. In other words it controls the amount of water enter and leaving the cell to prevent bursting of cell.
5) Chemoheterotrophic
Protozoa can either be holozoic nutrition or saprozoic nutrition. Holozoic nutrition is the intake of solid nutrients through phagocytosis while saprozoic nutrition is the intake of soluble nutrients through pinocytosis.
Moreover, there are three types of locomotory organelles for protozoa. The first one will be pseudopodia, the false foot in amoeba. Next is flagella and cilia.
Asexual reproduction in protozoa is binary fission while sexual reproduction is conjugation.
Protozoa classifies according to
I. Type of nuclei II. Mode of reproduction III. Mechanism of locomotion
For instance, Phylum Sarcomastigophora has only single type of nucleus. Subphylum Mastigophora has flagella while subphylum Sarcodina has pseudopodia.
Subphylum Mastigophora has two types. Phytoflagellates with the presence of chlorophyll while zooflagellates without the presence of chlorophyll.
Besides, apicomplexa has it's unique feature which is apical complex.
Lastly, Phylum Ciliophora is the largest phylum in protozoa. It is unicellular and has cilia as its locomotory organelle. It has two macronucleus and micronucleus.
Virus & Algae
Virus
Virus is an obligate intracellular parasites. It means that they will only be activated inside living host cells. It only contain one single type of nucleic acid, either DNA or RNA but not BOTH. Based on Internstional Committee on Taxonomy of Viruses (ICTV). It is grouped based on three aspects, the nucleic acid type, strategy of replication and lastly morphology. Host range means the type of organism that can be infected by virus. Outer surface of virus will form hydrogen bond with specific receptor sites on host cell. In addition, nucleic acid is protected by protein coat called capsid made up of capsomeres. In certain virus, capsid will be covered by envelope. Envelope may or may not have spikes. Lastly, there are 4 general morphology of virus:
(I) Helical viruses
(II) Polyhedral viruses
(III) Enveloped viruses
(IV) Complex viruses
Algae
Algae can be found in aquatic or terrestrial environment. In algae, there are 7 divisions from 2 kingdoms which is kingdom Protista and kingdom Plantae based on a few things:
In isogamy, the morphology of gametes is similar. They got the similar shape and size which makes us difficult to differentiate whether it is male or female. They are only differs in allele expression. With the touching of flagella poles, pairs of isogametes fused to form diploid zygote. It is either non motile gamete fused with non motile gamete or motile gamete fused with motile gamete. The motility of both isogametes will be the same.
In anisogamy, gametes of different shape and size will fuse together. The smaller gamete (sperm) will be male while the larger gamete (egg cell) will be representing female. Oogamy is a form of anisogamy. However, it only involves the fusion of non motile egg cell and highly motile sperm cell. Motile sperm cell needs to compete for fertilisation of non motile egg cell.
Figure above shows the characteristic of algae from different division.
Virus is an obligate intracellular parasites. It means that they will only be activated inside living host cells. It only contain one single type of nucleic acid, either DNA or RNA but not BOTH. Based on Internstional Committee on Taxonomy of Viruses (ICTV). It is grouped based on three aspects, the nucleic acid type, strategy of replication and lastly morphology. Host range means the type of organism that can be infected by virus. Outer surface of virus will form hydrogen bond with specific receptor sites on host cell. In addition, nucleic acid is protected by protein coat called capsid made up of capsomeres. In certain virus, capsid will be covered by envelope. Envelope may or may not have spikes. Lastly, there are 4 general morphology of virus:
(I) Helical viruses
(II) Polyhedral viruses
(III) Enveloped viruses
(IV) Complex viruses
Algae
Algae can be found in aquatic or terrestrial environment. In algae, there are 7 divisions from 2 kingdoms which is kingdom Protista and kingdom Plantae based on a few things:
- the living habitat
- presence of cell wall
- reproductive structure
- type of chlorophyll present
- morphology of cells
- flagella number and location
- form of food and assimilatory products stored in pyrenoids
In isogamy, the morphology of gametes is similar. They got the similar shape and size which makes us difficult to differentiate whether it is male or female. They are only differs in allele expression. With the touching of flagella poles, pairs of isogametes fused to form diploid zygote. It is either non motile gamete fused with non motile gamete or motile gamete fused with motile gamete. The motility of both isogametes will be the same.
In anisogamy, gametes of different shape and size will fuse together. The smaller gamete (sperm) will be male while the larger gamete (egg cell) will be representing female. Oogamy is a form of anisogamy. However, it only involves the fusion of non motile egg cell and highly motile sperm cell. Motile sperm cell needs to compete for fertilisation of non motile egg cell.
Figure above shows the characteristic of algae from different division.
Fungi
Fungi
There are a few things that I highlighted in the notes of Fungi.
1) Disease caused by fungi is called mycosis.
2) Lung is the first organ that will come into contact with spores through inhalation.
3) Potato dextrose agar is used for the cultivation of fungi.
4) During diagnosis for infection of lungs, there is a possibility where fungi will be mixed up with Mycobacterium tuberculosis as they are both found in lungs.
5) Mycorhizae is the mutualistic relationship between plant root and fungi. Fungi enhance the absorption of mineral ions in plant roots while it benefits through obtaining soluble organic nutrients from root cells. Example of mycorhizae is truffles.
6) Lichen is the mutualistic relationship between algae and fungi(usually Ascomycota). Algae provide food while fungi provide protection. Lichen may live in a very cold condition. Besides, lichen act as an environmental indicator because it is sensitive to toxin .
7) Microsporidia is an obligate intracellular fungal parasites that infect fish, humans and insects. It is structurally similar to fungi, but lack of mitochondria and centrioles.
8) Plasmodial slime mold will produce 2 types of spores. Non flagellated amoeboid myxamoeba and flagellated swarm cells.
9) Myxomycota is acellular while acrasiomycota is cellular.
10) Oomycota is also known as water mold. It's cell wall is made up of cellulose which is different from fungi.
11) Deuteromycota is known as second fungi or fungi imperfecti. It is due to lack of sexual reproduction and causes it's 'imperfection'.
12) Mycoremediation is the use of fungi for bioremediation while phytoremediation is the use of plant for bioremediation.
There are a few things that I highlighted in the notes of Fungi.
1) Disease caused by fungi is called mycosis.
2) Lung is the first organ that will come into contact with spores through inhalation.
3) Potato dextrose agar is used for the cultivation of fungi.
4) During diagnosis for infection of lungs, there is a possibility where fungi will be mixed up with Mycobacterium tuberculosis as they are both found in lungs.
5) Mycorhizae is the mutualistic relationship between plant root and fungi. Fungi enhance the absorption of mineral ions in plant roots while it benefits through obtaining soluble organic nutrients from root cells. Example of mycorhizae is truffles.
6) Lichen is the mutualistic relationship between algae and fungi(usually Ascomycota). Algae provide food while fungi provide protection. Lichen may live in a very cold condition. Besides, lichen act as an environmental indicator because it is sensitive to toxin .
7) Microsporidia is an obligate intracellular fungal parasites that infect fish, humans and insects. It is structurally similar to fungi, but lack of mitochondria and centrioles.
8) Plasmodial slime mold will produce 2 types of spores. Non flagellated amoeboid myxamoeba and flagellated swarm cells.
9) Myxomycota is acellular while acrasiomycota is cellular.
10) Oomycota is also known as water mold. It's cell wall is made up of cellulose which is different from fungi.
11) Deuteromycota is known as second fungi or fungi imperfecti. It is due to lack of sexual reproduction and causes it's 'imperfection'.
12) Mycoremediation is the use of fungi for bioremediation while phytoremediation is the use of plant for bioremediation.
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