Physiological and Genetic Identification of Micrococcus luteus Isolated from the Hind Foot of a Chinchilla
Here is the link to my Lab Report. Thanks for a wonderful semester! Wishing everyone a great summer!
Art Project: “Extreme Environments”
My name is Kjersten Williams. For my art project, I decided to go with mixed media. I constructed the microbes’ background environments out of paper and colored pencil, and made the microbes themselves out of modeling clay, giving the project a bit of visual depth. For my subject, I decided to focus on a specific group of microbes: the temperature extremophiles. I wanted to showcase the variety of different morphologies and habitats of these microbes (through the relatively accurate depiction of the microbes and their respective environments), while also making a statement against the general belief that all microbes are “bad’ (hence, the added shaky eyes to make them cuter and more personable). These microbes live in environments which would be deemed uninhabitable to the majority of life forms on Earth. Due to their resilience and adaptability, they represent the type of organism which astrobiologists may be most likely to find on other planets!
There are a couple mesophiles included for the sake of contrast. The microbes represented are: Chloroflexus aurantiacus (the red snake-like thermophilic bacterium represented against the background of a hot spring area), Methanopyrus kandleri (the blue, rod-shaped hyperthermophilic archaea set against the background of hydrothermal vents), Deinococcus radiodurans (a mesophilic bacteria represented by the green tetrad set against the forest background), Acidithiobacillus thiooxidans (a mesophilic bacterium represented by the purple, rod-shaped microbe with the pink flagellum), Psychrobacter arcticus (the blue diploid psychrophilic coccobacillus bacterium with pink spots, which is set against the aquatic background underneath the ice layers), and Planococcus halocryophilus (the blue-green diploid cocci bacterium set against the polar background).
Microbes in the News Assignment: Post #3
— Article and link: “Too Clean for Our Children’s Good? The Checkup’ by Perri Klass, MD, The New York Times, April 17, 2017.
— Summary: This article talks about the many various ways in which our children are protected from interaction with microbes, including giving birth by caesarian section, bottle-feeding, and possible exposure to antibiotics. Such protection on the one hand affords protection from disease but on the other hand offers greater risk that children may experience complications of the “built environment.’ It is a concern that living in such a clean, controlled environment could lead to an underdeveloped immune system and subsequent health problems which may have otherwise been avoidable had the body been exposed to a diverse array of microbes at a young age. In order to combat this problem, it is recommended that young children be introduced to these microbes in the outside environment through “controlled exposures’ in the form of either “natural exposure’ consisting of interaction with their environment or through a type of vaccine yet to be developed.
— Connections: This article include discussion of the development of the human microbiome, its importance in the overall health of an individual, the avenues by which children are typically first exposed to microbes, and also the concept of vaccination with microbes in order to improve health. All of these are topics which have been mentioned or discussed over the course of the semester.
— Critical analysis: I liked the contrast that the author provided between the microbes found outdoors as opposed to those found within the “built environment.’ While I had naturally assumed that the inside of a house or apartment may be “cleaner’ than the outside world, I had not given much thought to the members of the microbial populations to be found in each of the two environments; in reality, the inside of a dwelling is not necessarily any more microbe-free than the outside, it is instead simply inhabited by a different, and possibly narrower, variety of microbes. I did not detect anything scientifically inaccurate or confusing in this article, and think that it did perform an adequate job in relaying this information to the public. The author did not get too technical in any of their explanations, yet clearly stated the anticipated problem, reasons behind that belief, and also the possible solutions to the problem.
— Question: Are researchers suspecting that the health problems mentioned are primarily due to inadequate exposure to pathogenic bacteria? Or do interactions with the non-pathogenic bacteria also play a role in shaping the immune system of children? What kinds of “natural exposures’ are parents advised to pursue in order to assist their child’s immune system to develop properly?
Microbes in the News Assignment: Post #1
— Article and link: “Zika-Fighting Sterile Mosquitoes Released Near Key West’, NBC News, April 19, 2017.
— Summary: This article aims to describe the testing of new experimental methods for the reduction of Aedes aegypti mosquito populations, a species which has been previously linked to the spread of multiple diseases, including the Zika virus. The ultimate goal of this testing is to control the spread of the Zika virus through controlling these insect vector populations. One such method has recently been tested in Key West, Florida, where lab-raised male mosquitoes infected with Wolbachia spp. of bacterium were released into habitats known to harbor populations of Aedes aegypti. The lab-raised male mosquitoes will breed with the wild female mosquitoes; however, due to the Wolbachia spp. carried by the male parent, the young produced by this coupling cannot survive to adulthood. While this method involves the use of microbes, there is another technique mentioned which instead involves genetic modification of lab-raised male mosquitoes to obtain a similar result.
— Connections: This article related to the material in class through its association with Zika virus, which was covered both in our course material and also in the guest lecture given by Dan Stinchcomb. The use of these microbes by humans to alter a detrimental aspect of an environment is also an example of microbes functioning in environmental bioremediation, another topic covered in class.
— Critical analysis: I found this method for mosquito population control extremely interesting. We had learned in class that certain microbes can be used to confer certain health benefits to a host organism through the transfer of particular genes, but I had not yet heard much of this particular strategy involving using members of a population as hosts for the microbe with the aim of stopping the spread of a disease from an insect vector to a human population. Both this method as well as the genetic engineering process mentioned towards the end of the article, if such methods prove effective in their goal and also harmless to the environment, would be extremely useful in inhibiting the spread of the Zika virus and thereby preventing further human infections.
This article was written in such a way as to inform the general public. As such, the scientific details and mechanisms behind the ideas discussed are not mentioned in great detail. In terms of the limited scientific details provided, I believe the article was scientifically accurate, though somewhat vague. The explanation of the science involved was somewhat simplified, and I did not detect any confusing aspects. While I personally feel that they could have included more detail behind the processes mentioned, I can see that the inclusion of too much detail could have been confusing to someone not well-versed in biological concepts. I think the article adequately communicated the highlights of the science to the public, as it stuck to the main ideas and results of the testing in an attempt to be clear and to communicate their ideas effectively.
— Question: What is the mechanism by which Wolbachia spp. inhibits the development of the next generation of mosquito? Would the inhibition of mosquito populations through such methods reduce their numbers to the point where other organisms in the food chain might be affected (most specifically those organisms in the food chain which utilize mosquitoes as a food source)? In reference to the genetic engineering method for the control of mosquito population, what is altered or added in the genome of the mosquitoes in order to obtain the desired effect?
A2: Microbes in the News
Article: 7 Alien ‘Earths’ May Be Swapping Life via Meteorites
Link: National Geographic, Mar 22, https://news.nationalgeographic.com/2017/03/earth-planets-aliens-life-panspermia-space-science/
Summary: On Feb 23, NASA reported that they found other solar system about 39 light years away from our solar system, called TRAPPIST-1 and some of planets in TRAPPIST-1 have liquid water. This release gave a shock to the world and someone may think that extraterrestrial life is existing now. According to the new research from Manasvi Lingam and Abraham Loeb of the Harvard-Smithsonian Center for Astrophysics released on Mar 15 that seven planets in TRAPPIST-1 is condensed around the stellar host so that the seeds of life can jump from one planet to other planet by debris. This research support the theory of panspermia, which maintains the origin of life came from the space to Earth. In TRAPPIST-1, all planets are located close to each other and distance between them is much shorter than the distance between Earth and Mars, so it’s easy to approach to other planets in TRAPPIST-1. Also, three planets out of seven planets may have liquid water and is located in habitable zone, so they think if they have moderate temperature and atmosphere, life can exist there. However, some astronomers are suspicious of this because they think life can’t stand the harsh condition while they are traveling. In the space, there are lots of cosmic rays and they can be exposed for more than million years. In addition, they receive a huge shock when they land on some planets. Though some member in the team says it’s really difficult to survive in the harsh condition, but some organism like extremophiles can overcome it. They don’t find plausible evidence yet, but it is a good chance for us to think about what is panspermia theory and where life come from.
Connection: The idea of ubiquitous is relate to this article. It is also relate to the origin of life(LUCA).
Critical analysis: Discovering of the TRAPPIST-1 was amazing. However, I’m wondering how microbes can jump from one planet to the other. This news said some researchers thinks it’s difficult for some microbes to survive in the space for long time due to UV or cosmic rays. While, other researchers says extremophiles can survive because some has tolerance for UV or heat. I’m suspect for this idea. If microbes can jump to other planet, we can find microbes from meteorites which come to the earth. Inside the meteorites, there are lots of Carbon sources, but their shock when land on some planet or heat can sterile them. However, the distance between one planet to the other is shorter than the distance between the Earth and Mars. Therefore, maybe, if their travel is short, some may survive and land on other planet, but it’s rarely happened.
Question: Why it support panspermia theory? How to jump to other planet from the ocean in the planets in TRAPPIST-1?
A2: Microbes in the News
Article: 60,000-year-old microbes found in Mexican mine: NASA scientist
Link: PHYS, https://phys.org/news/2017-02-year-old-microbes-mexican-nasa-scientist.html
Summary: The research team from NASA found some microbes which is 60,000-year-old in the Naica mine in Mexico and revived them. Penelope Boston of NASA’s Astrobiology Institute said that in that mine, they found some crystals and inside of that, they found lots of microbes and viruses and they were alive, but they were locked by the crystal. Naika is the mine region and inside the mine, temperature is so high, so those area is extreme environment. When the researchers conducted research, they wore a spacesuit and an ice bag. Then, those microbes and viruses were picked up. They are really different from other well known microbes in terms of genome. It’s 10% difference between them and some microbes which has the closest genome sequence and this difference is like between humans and mushrooms. Those microbes lay dormant in the layer of minerals. Penelope said they adapted to their harsh environment and this discovery is just an one example how organisms in the earth are strong.
Connections: It’s relate to microbial ubiquitous and some extrememophiles.
Critical analysis: This mine is really hot and dark and nutrient are limited, so for almost all of organisms, it’s absolutely extreme environment. However, some microbes and viruses can exist in those environment. I was surprised when I read this article, but I am wondering why genome became different from others due to living inside crystals? This article said they are different like human to mushrooms. However, human and mushrooms are completely different from the shape, complexity, habitat and foods etc and they are microbes, but genome is different at 10%, so I’m confused.
Question: How to survive in the crystal even they can’t move? Why they are totally different from other microbes in terms of genome?
A2: Microbes in the News- Using tropical microbes to improve the environment
Article Title: Using tropical microbes to improve the environment
Source: phys.org
Date: 4-12-17
Link: https://phys.org/news/2017-04-tropical-microbes-environment.html
Summary: Researchers have been investigating ways to use the rich and diverse microbiome of the tropic region to help advance farming and agriculture, often finding ways to use them to protect against disease or increase efficiency in some way. For example, the scientists cultured the bacterium found in the guts of tropical fish, which can possibly be probiotics for commercially grown fish by inducing it into their guts through their food. This would protect them from the same diseases that the bacterium prevent in the tropical fish, enhancing survivability and resistance to diseases that could otherwise wreak havoc on the fish. A similar method is also used to protect banana crops, using the Streptomyces bacteria as an antifungal and antibacterial in the soil.
Connections: This is similar to what we have studied about both oil spills and microbiomes, as they are using microbes to reduce man made chemical use and are introducing these bacteria to the microbiomes of the fish and the plants.
Critical Analysis: I thought it was interesting to see how microbes can be used to protect against disease and how introducing them to the guts of the fish is almost like a vaccine for the fish. Although the article is about a developing way of helping agriculture and farming, there is a good amount of depth and explanation to the story to explain what is going on to the reader. It provides what may otherwise be a little technical to read for the general public into an interesting read that explains what it is saying well.
Question: In hat other ways could this be applied? Could it be used in place of certain vaccinations in humans? Even if it is just temporary, it would be interesting to see if this could be used for things like traveling. Because different people, especially of different cultures, have different microbiomes, could this method make it easier to travel and tolerate things such as drinking water and foods in different countries?
A2: Microbes in the news
Article title: Behind the iron curtain: How the methan-making microbes kept early Earth warm Behind the iron curtain: How methane-making microbes kept the early Earth warm
Date: Arpil 17, 2017
Article author was not listed but the research’s author was: m S. Bray. The article was provided by the Georgia institute of Technology.
Source: Phys.org
Link: https://phys.org/news/2017-04-iron-curtain-methane-making-microbes-early.html
Assignment author: Morgen Southwood
Summary-
Marcy Bray and his team simulated early earth conditions to try and explain why the oceans could be liquid in the first two billion years. The prevailing theory is that methanogens provided enough methane for the green house effect to maintain liquid oceans. The problem with this theory is that, as we learned in class, methanogenesis is an inefficient system, and can be out competed when alternatives are possible. One major competitor in this time period was the rust-breathing microbes, they would dominate any environment when iron was available. The term iron curtain, refers to the potential for rust-breathing microbes to repress methane emissions when rust is plentiful. If methane was completely suppressed then the planet would likely have cooled. The microbiologists simulated early earth to study microbial diversity and methane emissions in varying conditions. They found that in iron free pockets of the oceans, methanogens could have thrived and been enough of a source of methane for keeping early Earth warm.
Connections-
This article strongly related to our lectures on the methane cycle It also related to some exam 1 material, when we learned about the ferrous and ferric iron signatures that signaled changes in early earth microbial diversity.
Critical analysis-
This article could have used some more explanations. I understood the conclusions it drew, but I wouldn’t have been able to without material I learned in this class. I would have needed someone to fill in the blanks for me. It was important to understand why rust-breathing microbes would have outcompeted methanogens, and the significance of shifts in microbial diversity with different conditions etc. The article assumed/required the reader to know this supplementary information, and therefore it was not accessible to the general public. I think the article was scientifically accurate in the way it described the idea proposed by the results of the study, however the title is misleading. The title seems portray that the study was a confirmation, when it was only supportive of the idea.
Since I did have some background information, this article was very interesting to me. When I thought about the major shifts in microbial diversity of the planet , I always thought about microbes relating to oxygen. These rust breathing microbes and methanogens were just as important stepping stones in shaping the Earth.
Question-
The conclusion of the article is that methane emissions could have come from microbial communities that were in rust free patches of the ocean. I thought that the ocean was well mixed. How could there be sections of the early ocean that were so poorly mixed that they lacked iron, while other areas had high levels of iron?
A2: Microbes in the News Assignment
Microbes in the News !
Over the course of the semester, post 3 different stories involving microbes from the popular media and then read and comment on 3 posts by other students.
Points: Total possible = 30 points. Earn up to 8 pts for making a post and 2 points for posting a comment. Create 3 posts and 3 comments over the course of the semester.
Deadline: All posts and comments must be made by April 24 to receive credit.
Learning Objectives:
– Increase your awareness of microbiology and its role in society
– Expand and apply your knowledge of microbiology
– Practice critical thinking by analyzing popular news media for scientific accuracy
– Develop questions about microbiology
– Help your peers and yourself understand microbiology by answering their questions
Instructions:
Over the course of the semester, create 3 separate Microbes in the News posts on the course website, and then read and comment on 3 Microbes in the News posts by other students. Be sure to follow the guidelines below in order to qualify for full credit.
Guidelines for creating a post:
– Article and link: Enter the title, source, and date of the article and create a link to it. Articles should be from any popular media source (newspaper, magazine, podcast, blog, etc.) that others can access without hitting a paywall. Any relevant story is acceptable, but challenge yourself to find stories that are current (~within the last 3 months) and that haven’t yet been posted by your peers, whenever possible.
– Summary: Write a short summary of the story (just a few sentences is sufficient).
– Connections: Explain briefly how this connects to what we’ve covered in class.
– Critical analysis: Explain what you found interesting about this story, and what (if anything) you learned. Comment on whether you think the story was scientifically accurate or not. If you noticed any factual inaccuracies or aspects of the story that might inadvertently confuse or misinform readers, identify those and provide a more accurate explanation. Also comment on how this was written. Do you think it did a good job of communicating science to the public? Why or why not?
– Question: Write a question about microbiology that you had as a result of reading this story.
– Categorize: Categorize your post as “A2: Microbes in the News’ using the categories menu on the right. This will ensure I can find it and give you credit.
– Tag: Tag your post based on any relevant microbiological themes by choosing from the tag menu (below categories on the right). Use existing tags when possible, but you can add new ones if needed by clicking “+Add New Category’ link just below the list of tags. This will help us find stories on relevant themes. You can also use these tags to search for other students’ stories on themes that interest you.
Guidelines for commenting on a post:
– Read the news story and the students’ post about it
– Create a comment and write a response to their critical analysis. Do you agree, disagree, or have more to add?
– In your comment, answer their question to the best of your ability. This might require some independent research.