Week 13 : Recalcitrant molecules

This is our last class of Microbial Ecology for this sem. We learnt about recalcitrant molecules which means materials that difficult to degrade and therefore using microbes to help with the process of degrading the recalcitrant compounds. There are many terms that we need to know and remember such as bioremediation, biomagnification, biostimulation, phytoremediation, mycoremediation and many others. I think I need to make a flashcard by using Quizlet to make it easier to understand, remember and not to confuse.

Lastly, I would like to thank to Dr. Wan Zuhainis for all the knowledge, advice, support and new experience during this semester. See you again in the next semester. 

Thank you Dr. Wan!  :)

Week 12 : Nitrogen Fixation

On Monday, we learn about nitrogen fixation. As usual, before class we must do the flipped classroom materials prepared by group 6. In this topic, I can learn about nitrogen fixation, importance of nitrogen and type of nitrogen fixation microbes involve.

Nitrogen cycle.

This week also we have done an awesome event with the students from SMK Warisan Puteri, Seremban. This "Life Without Microbes" event went very well and we manage to handle the event successfully. In this event, we held an exhibition about "Life Without Microbes". Then, we have some activities in the DKU which involve the students. Besides, we also have been interviewed by the students from Biochemistry and Biocell courses that also came to our event. But I do not really agree with the way and time they interview us because at that time we are all busy with the activities and students. In my opinion, they should interviews when the exhibition is ongoing so that the activities do not interfere with the interview. 

I would like to take this opportunity to thank Dr. Wan Zuhainis for the spirit and support given. Thank you Dr. Wan!  :)

Week 11

Topic : Food Spoilage 

On Monday, I learnt about food spoilage that is not the same as foodborne disease. This topic is very interesting as I can know the type of food spoilage microbes, how the microbes can cause the food spoilage and also the factors the can promote their growth. Group 1 has done the flipped classroom about this topic. So, before entering the class we need to do some quizzes and of course, to answer the questions we need to look for the materials provided by group 1. Click here to view the video and mindmap.

Topic : Waste Pollution and Waste Water Management

This topic was covered on Thursday. Group 5 had prepared the flipped classroom materials and they also present the slide in the class. Their presentation is quite interesting and I like the video as it explained very clearly about the  waste water management and also easy to understand. We also have to do some quizzes based on this topic before the class. 

As soon as we enter the class on Friday, we were asked to do the crossword puzzle based on topic waste water management. Some of the question are quite challenging but I manage to answer all the questions well. After crossword puzzle, we do quiz on Socrative based on the topic food spoilage. I really like these activities because I can know how much that I really know or understand about the topics. However, internet connection problem still cannot be avoided while these activities is conducted.

All right, that's all for now. 

Week 10

Topic : Human Microbiome

This week we finish the topic human microbiome. We learnt about pathogenesis in pathogen where it have five mechanism; entry, specific adherence, invasion, colonization and growth, and host damage. Pathogenic organisms must have mechanisms in place to evade attack by the immune system.  The promotion of disease is characterized by the ability of pathogenic organism to enter a host, inflict damage and destruction into the host cell. Diphtheria is a disease of the upper respiratory tract caused by a toxin secreted by Corynebacterium diptheriae.

We also do some revision for each topic that included in test 2. I think this test is quite hard for me as we need to relate what we learnt from each topic with other topic and there are so many terms to remember.

That's all for this week. :)

Week 9

Topic : Human Microbiome

On Monday, we continued the topic human microbiome. From this class I have been able to differentiate between parasites, pathogen, pathogenicity, disease and infection. Pathogen is a biological agent that causes disease or illness to its host while pathogenicity is the ability of parasite to inflict damage on the host and on the resistance of the host to the parasite. However not all pathogen are parasites but parasites can be pathogenic to the host.

It is interesting to learn about microorganism in our body. The body contains 10 times more bacteria and other microorganisms than human cells. Some of the microbes are beneficial for us and some may be pathogenic.

Here I share some videos about human microbiome and lets meet your microbiome.

Week 8

Topic : Atmospheric Habitat & Human Microbiome

This week we learn about the topic atmospheric habitat. Before the class on Thursday, we need to do quiz that have been prepared by group 7 on topic atmospheric habitat. They also provide a video and mindmap about this topic. I like the video because each point is well explained and easy to understand. From what I learnt, atmosphere consist of  6 regions ; troposphere, stratosphere, mesosphere, thermosphere, exosphere and ionosphere. Troposphere is nearest to the earth and lower troposphere contain high number of microorganisms. There are 3 stages of dispersal of airborne particles ; liberation --> dispersion in air currents --> deposition. We also have done some quizzes related to this topic in the class. 

For topic human microbiome, my group (group 2) have done the flipped classroom. Through the midsem break, we were busy preparing our flipped classroom. We have prepared some online materials such as infographics, video, mindmap and quiz. As usual before the class, we need to view the materials and do the online quiz. I like this topic because I get to know the role of microbes in our body and the interaction. Besides, I can distinguish between normal flora and pathogenic microbes.

This week also we need to submit our thinglink. Click here to  view my thinglink about soil habitat.

That's all from me for this week :)

Week 7

Topic : Microorganisms in terrestrial ecosystem 

This week we continue with the topic soil population. Bacteria is the numerous microbes in the soil and they can be found on the surfaces of soil particles. Soil bacteria function as decomposers, mutualists, pathogens, and lithotrophs or chemoautotrophs. Besides bacteria, fungi also play important roles in soil as decomposers, mutualists and pathogens or parasites. Verticillium, Phytium and Rhizoctonia are the examples of fungi soil pathogens. Other than bacteria and fungi, there is minority of protozoa which is exposed outer surface of surface particle, only 15 cm from top soil. Soil protozoa function as mineralizing nutrients, regulating bacteria populations and food source.

Microbe plant interaction.

Mycorrhizae can be described as a symbiotic relationship between a fungus and a plant. Due to the fact that this is a symbiotic relationship, both the fungus and the plant benefit from this interaction (mutualistic). Mycorrhizae provide enhanced nutrient uptake for plant. Mycorrhizal associations consists of endomycorrhizae and ectomycorrhizae. 

Endomycorrhizae (left) and ectomycorrhizae (right).

In ectomycorrhizae, nutrients taken up by rhizomorphs pass through hypal sheath then into Hartig net filaments which have numerous contact with root cells.

The most common type of mycorrhizae is arbuscular mycorrhizae (AM). This type of mycorrhizae provide plant host with protection from disease, drought, nematodes and other pests. It also transfer phosphorus to roots and provides ammonium to host. This natural attraction of phosphorus has lead to its ability to become widespread and very comon. Nutrient transport occurs through symbiotic structures inside plant root cells known as arbuscules. 

Arbuscular mycorrhizae (AM).

Topic : Hydrosphere

Before the class on topic hydrosphere, we have to look for the flipped classroom that prepared by group 3. They make a good effort to make the ways of presentation attractive but simple. They had prepared the thinglink for freshwater and marine environment, presentation in videos and also crossword puzzle. And of course before answering the crossword puzzle, I need to study and understand the topic on the link given.

Thinglink on marine environment.

 Crossword puzzle about hydrosphere.

Video presentation about hydrosphere.

Apart from learning about the hydrosphere, I can also find out and learn new application to make our presentation attractive and informative.  

On Friday, we were asked by Dr. Wan to answer a few question based on hydrosphere topic. We need to draw a digram that describe the nutrient cycle in the aquatic environment. I managed to draw the microbial loop diagram although not all correct. Second question is differentiate between oligotrophic and eutrophic lakes. For this question, I was able to state one differences only. :(

microbial loop.

differences between oligotrophic and eutrophic.

From this activity I can know how much that I really know and understand, and which part that I don't understand or maybe I don't really focus on that.

The lecture continued on the zones of lakes or pond based on light penetration and temperature. Littoral zone and limnetic zone get full light penetration while profundal zone which is near the benthic zone get very low penetration of sunlight. Zonation of lakes based on temperature consists of epilimnion, thermocline and hypolimnion. The lowest temperature and light penetration is hypolimnion.

Thats all for this week. :)

Week 6
Topic : Microbial Interaction and         Lithosphere

On Monday, the class is continued with the topic on microbial interaction. We learn about others interaction types ; cooperation, commensalism, predation, parasitism, amensalism and competition. 

Cooperation give benefits to both organisms in relationship but it differs from mutualism because cooperative relationship is not obligatory. Examples of cooperation are the relationships between sulfide-oxidizing bacteria and a variety of animals. Commensalism is one organism benefits and the other is neither harmed nor helped. Example of commensalism is nitrification which carried out by two different bacteria; Nitrosomonas and Nitrobacter. 

Next is predation among microbes which involves a predator species that attack, usually killing its prey. Vampirococcus, Bdellovibrio and Daptobacter are examples of predator where  Vampirococcus have epibiotic mode of attacking prey, Bdellovibrio penetrates cell wall but grows outside plasma membrane and Daptobacter penetrates prey then directly consumes the cytoplasmic contents.

Microbial predators.

In parasitism, one organism gains (parasite) and the other is harmed (host) while in ammensalism, negative impact of one organism on another based on release of a specific compound. Competition occurs when two organism try to acquire or use the same resources. We also have some quizzes based on this topic. In my opinion, this quiz shows how many that we understand about this topic and how we concentrate during lecture. :)

Before class on Thursday, we need to sign up for Voicethread and give comment on the video that presented by group 4 for flipped classroom about the topic microorganism in terrestrial ecosystems. Basically, they did a good job and they explore a new way to present their work. From that I get to know the overview of this topic before entering the class on Thursday. 

This topic is about soil as microbial habitat, microbe plant interactions, soil conditions and microorganism in the soil. Then, we have class activity in group discussion. We need to discuss about microbial habitat in the soil at different depth or layer. My group has find some article and video, and share it in Blendspace.

From this activity, I get to know more about microbial habitat of soil as we have to find some information from article or video. By putting all the information from other groups in Blendspace, we can have more informations about different depths of each layer of the soil.

So, thats all for this week.. (^_^)

Week 5
Topic : Microbial Interaction

This week, I learned about microbial interactions which may be parasitism, one organism benefits at the cost of another; mutualism, both organisms benefit; commensalism, one organism benefits at no cost or benefit to the other; or amensalism, one species is inhibited or completely obliterated and one is unaffected. Mycorrhizae, protozoan-termite relationship and zooxanthellae are examples of the mutualistic interaction.

Mycorrhizae can be described as a symbiotic relationship between a fungus and a plant. Due to the fact that this is a symbiotic relationship, both the fungus and the plant benefit from this interaction. The mycorrhizae aid the plant with growth, yield, improved fitness, increase the root absorption area of nutrients, while the fungus receives carbon from the associated plant. Endomycorrhizae and ectomycorrhizae are the two main types of mycorrhizae that produce the same overall results, but with different fungal characteristics.

In protozoa-termite relationship, the termite provide food for protozoa while protozoa digests cellulose in wood particles and provide nutrients for termite. The symbioses in the termite gut are often beneficial to both partners and so are called a mutualistic relationship. 

Species within Aphidoidea have established mutualistic relationships with the obligate intracellular endosymbiont Buchnera aphidicola to overcome nutritional deficiency of such unbalanced diets. Buchnera are grown within specialized cells known as bacteriocytes. They produce nutrients (essential amino acids) that are not synthesized by insects or obtained sufficiently from plant saps. In return, aphids provide Buchnera with other nutrients required to survive. 

Pea aphid (Acyrthosiphon pisum) living with their endosymbiont Buchnera aphidicola. 

This topic is very interesting as I get to know the various interactions between two or more different species of organisms. Who would have thought that the interaction of microbes not only cause one organism benefits at the cost of another but can benefit both organism or one organism benefits at no cost or benefit to the other.

During the class on Thursday (26 March 2015), we were given a task to find materials that related to the topic microbial interactions. Every person is required to find and share with class members through padlet.

This is an article that I found about the role of bacteria and mycorrhiza in plant sulfur supply.

Week 4
Topic : Microbial Nutrition

Nutrients are necessary for microbial growth and play a vital role in the proper cultivation of microorganisms in the laboratory and for proper growth in their natural environments. In regard to required nutrients for proper growth, there are often limiting factors involved. The limiting factor or limiting nutrient effects and controls growth. When all requirements are present, microorganisms will thrive. In circumstances where there are lack of specific requirements, the growth process is affected.

Microbial nutrition summary.

Lecture on Monday (16 March 2015) began with the topic of microbial nutrition. We learn about water activity, nutrient, pH and temperature effects on growth of microorganisms. Then, the lecture was continued with the topic Distribution of Microorganism. From this topic I learnt about the factors affecting the microbial distribution and able to distinguish the microbes according to the categories. 

We finished these topics on Monday because these topics will come out on test 1 microbial ecology. The test was held on Thursday (19 March 2015) located in BK1.4. This test takes about an hour.

After the test, which only takes about an hour, Dr. wan has explain more clearly about our SCL which include, Life Without Microbes, Thinglink, Flipped classroom and Infographics. 

Week 3
Topic : Microbial groups

As for the introduction, microorganism or microbes play a very important role in our lives. Some microbes cause disease but the majority are completely harmless. In fact we couldn't live without them, but they could live without us. These microscopic organisms play a key role in maintaining life on earth, fixing gases and breaking down dead plant and animal matter into simpler substances that are used at the beginning of the food chain. Biotechnologists can also exploit the activities of microbes to benefit humans, such as in the production of medicines, enzymes and food. They are also used to breakdown sewage and other toxic wastes into safe matter. This process is called bioremediation.

There are three major forms of life; eucaryotes, procaryotes and viruses. Fungi, slime/water molds, algae and protozoa are classified as eucaryotic microbes. 

Fungi

Algae

Protozoa

Bacteria are classified into 5 groups according to their basic shapes: spherical (cocci), rod (bacilli), spiral (spirilla), comma (vibrios) or corkscrew (spirochaetes). They can exist as single cells, in pairs, chains or clusters.

Viruses are the smallest of all the microbes.  The virus particle attaches to the host cell before penetrating it. The virus then uses the host cell’s machinery to replicate its own genetic material. Once replication has been completed the virus particles leave the host by either budding or bursting out of the cell (lysis).

Before the class started, we were ask to read first about microbial groups topic and summarize it using our own way. Then, we need to upload it in the LMS. 

We also share our work to the others class members in Blendspace. They really do a good job as most of them share interesting videos related to the topic. It is good to share our works and findings with the rest of class members in order to increase our knowledge. 

During the one hour class, we were asked to sit in groups and discuss about the topic. We need to summarize the topic using Popplet.

Lecture on Thursday began with the topic microbial group. After that, Dr. Wan make online quiz activity using Kahoot.it. It was really interesting and fun ! The quiz got timer and we need to answer within the time allocated. It is simple but we need to focus and answer the question very fast. Yet so, I really enjoyed this activity.

Topic 3 : Microbial Nutrition and Metabolism

As usual, we need to prepare before entering the class. There will be an individual task in Quizlet. We have to write 50 terms and their definition that related to the microbial nutrition and metabolism topic. 

After completing the 50-terms assignments, we were asked to do the test in Quizlet based on terms that have been written and upload the result in LMS. We also need to upload and share the 50 terms in the Blendspace. 

The following day (Friday), we have the replacement class for 2 hours. We continued the topic on microbial groups. After finishing this topic, we proceed with the microbial nutrition and metabolism topic. 

Before the class ended, Dr. Wan once again create online quiz based on the topic microbial nutrition and metabolism and surely makes everyone excited. I found that this activity very fun and exciting. :)

Introducing.... Microbial Ecology

Assalamualaikum.. 

Ever since I decided to take microbial ecology course, I was curious about what we are going to learn and the activities we are going to do. Especially when I found out that the lecturer who will teach this subject is Dr. Wan Zuhainis because she has lots of ideas for activities that will be conducted to attract students in this subject, next assist the students for better understand about this subject.

Week 1  (26 Februari 2015)

The first task given was to look for an article or journal from scientific journal publisher or website related to the topic on principle of microbial ecology and share with the other class members by uploading it in Edmodo. Each of us is need to comment on one or more article that may interest us.

This is the article that I found about principle of microbial ecology.

This article is interesting as it tell us about how the principle of microbial ecology being search through experiment and lot of research by microbiologists.

On the first day of class, we were briefed on the activities and SCL that will be carried out during this semester which include PoBL (life without microbes), infographic or newspaper, thinglink, flipped classroom and reflective journal. For life without microbe, flipped classroom, and infographics are held in groups while thinglink and reflective journal individually. Each group has six members and for the topic of life without microbes, my group (Group 2) has chosen the title about "Ruminant Free-microbes".

Interesting topic choosen by the others group.

Oh ya then, we were asked to discuss with the group members on the article that we found interesting and relevant to the topic of principle of microbial ecology, which has been shared in Edmodo. So, we have chosen the article titled "Principles of Microbial Ecology and Their Application to Xerostomia - Associated Opportunistic Infections of the Oral Cavity". This article is very interesting ! It tell us about the myriad bacterial interactions between innocuous and potentially pathogenic species that prevent the growth of sufficient number of bacteria to initiate the xerostomia. By using the principle of microbial ecology, it can prevent the particular disease prevalent in xerostomia patient. On top of that, this article is easy to understand.

Our view about the chosen article.

Week 2 (5 March 2015)

On the second week, which is actually our first lecture on the first topic which is Principle of Microbial Ecology. From this topic, I learn about the definition of ecology which is the study of relationships among organism and the environments, and between other organism. I also can list the hierarchy in ecology ( species > population > community > ecosystem > biosphere ). The main factor of distribution of organism is nutrient. From this lecture I got to know that microorganisms have two strategists which are r strategist and k strategist to remain survive. k strategist is the most stable because organism can adapt to the new environment and reproduce slower but r strategist growth rapidly and high reproduction.

Other than that, I also learn about two types of succession which are autogenic and allogenic. Autogenic is microorganism that alter the habitat to adapt in the environment and produce new population, for example biofilm. Allogenic is microorganism that change in environment.

In this topic, I also learn about the contribution factors leading to homeostasis. Homeostasis is the dynamic balance between process, materials and organisms in the ecosystem and biosphere. Homeostasis is measured by photosynthesis (P) and respiration (R). 
At the end of this lecture, I learnt about environmental change and ecological crisis.

This is the summary of principle of microbial ecology =)