What Kind of Life Wood You See in Fairbanks?

This is my abstract interpretation of the decomposition of spruce and the interacting systems in a subarctic climate such as Fairbanks, with a focus on the fungi you may find on a piece of decomposing (as well as  living) spruce (left to right: lichens, slime mold, and turkey tails). The array of color in the background serves as a reminder of the diversity of the interacting systems, both biotic and abiotic. The plants on this piece represent the living features in an  healthy ecosystem, such as the different plants, animals, fungi, bacteria, archaea, and viruses that  inhabit that ecosystem. The soil on this  piece  is in reference  to  nutrient cycling within a system of decomposition, as well as the soil the wood will ultimately become part of and that many decomposing microbes  inhabit.    The symmetry and mixture of media serve to show the balance between the biotic/abiotic factors in a healthy subarctic habitat.

I chose this as my project because the there are so many components that go into the decomposition [of wood] that I had previously underestimated. Also, when you typically  envision   “nature” in Fairbanks, you may think: birch, spruce, squirrels, ravens, fireweed, etc., but the   great diversity of microbes within  the environment is typically less prominent. I felt it was important to highlight the interactions and results of microbes in a forest system.

I picked these fungi because as I was choosing a log from my wood pile to cut for this project, I saw 2/3 of these fungi on some of the logs. All of the plants in this piece are were found outside of my house.

**After painting this I found out slime molds(middle log)  are no longer categorized as fungi, but eukaryotes… so it’s really the interactions of fungi and eukaryotes.

Microbes in the News: Post #2

Article and link: “The Mycobiome” — https://www.the-scientist.com/?articles.view/articleNo/45153/title/The-Mycobiome/

 

Summary: This article discusses the commonly overlooked mycobiome, which is those fungi which are in and on our bodies. In recent years the microbiome has gained much more attention in both health and human medicine, but the mycobiome is still very much understudied. This article characterizes the human mycobiome and asserts that it is similarly important to human health, and even influences microbial communities. The researchers explored the presence of many different fungi in the oral cavity. As of yet, this field is still in need of scientific development and research.

 

Connections: I connected this to our brief lectures on fungi, and also to the attention on the human microbiome.

 

Critical Analysis: I found the idea of the human mycobiome to be interesting. The author ascertains that most people, scientists included, often overlook it. I had never thought of a mycobiome until reading this article myself. I think that the article is well written. It is more directed to readers who have some scientific background, as he provides a detailed outline of his research involving the mycobiome.

 

Question: What are the implications of the mycobiome, and how much influence does it have on the microbiome and overall human health?

A2: Microbes in the News!

Fungi have enormous potential for new antibiotics

https://www.eurekalert.org/pub_releases/2017-04/cuot-fhe041917.php

Summary: This article explores recent research into the genome of 24 different fungal species in order to identify antibiotic and other bioactive compound production genes. This study has resulted in the discovery of over 1000 pathways for generation of bioactive compounds with pharmaceutical application.

Connection:  The article could be characterized as part history of the use of antibiotics and the rise of antibiotic resistance. We have at length discussed the prevalence and mechanisms for bacterial antibiotic resistance as well as the known pathways for antibiotic production in microbes like fungi.

Critical Analysis:  The studied referenced in the article shows the promise of new antibiotic and even anti-cancer medications as a result of identifying these genomic pathways in fungi. The researchers believe that the knowledge gained from these sequences will also improve the efficiency of production and efficacy of existing antibiotics. At one point in the article, they refer to the predictive capability of the researchers experiments with the new sequencing data, claiming that not only could they predict the chemicals these fungi were capable of making, but identifying new versions of the same antibiotic chemicals. The reader must infer from the phrasing of this part that the researchers were able to trace the gene and find fungi that were previously unknown to have the ability to produce that particular antibiotic. The implications of information like that open the door wide to not only new means of production, but new variants of chemicals that have otherwise been fighting an uphill battle against antibiotic resistance.

Question:  If it is true that the researchers found antibiotic production previously undiscovered in some fungi, they use the example of the chemical yanuthone, are these inactive genes that must be activated, and how are they accurately and consistently activating these genes to produce this chemical?

Abandoned Toxic Pit Might Have Next Antibiotic

Article Title:  Fungal duo isolated from toxic lake produce novel antibiotic

Source:  C&En

Date: 4-19-17

Link:  https://cen.acs.org/articles/95/i17/Fungal-duo-isolated-toxic-lake-produce-novel-antibiotic.html

Summary: In Montana there is an abandoned mining pit called  Berkeley Pit. Since it was abandoned in 1983 water has leaked in and make it into a toxic pool with a pH of 2.5. It is so toxic that thousands of snow geese died last winter after they landed in it. However microbes love the pit. Two scientist from the University of Montana Andrea A. Stierleand  and Donald B. Sterile who have been studying the fungus in the lake have found that two  Penicillium fungus together make a new antibiotic. The antibiotic isn’t really a super new shape but it seems to act differently from know antibiotics.

Connection:  Antibiotics we learned we discovered  from a penicillin fungus by Alexander Fleming, so I thought it was really cool that we still find antibacterials like that. Could it be that fungus are adapting their antibacterials to fight resistant bacteria? This article also connects to the section on what bacteria use as energy sources, as finding life in an inhospitable place like an abandoned mining pit with pH2.5 is incredible and show how microbes can adapt to use almost anything.

Critical Analysis:  The article doesn’t give much on the antibacterial agent it’s self, however it does provide us with a picture of the its chemical structure and a link to the article that the scientists published. The purpose of the post must have been to inform the public of a new discovery in science and I think it does this very well. How the article starts by describing the location of the discovery really draws readers and helps the mission of the article.

Question:  We have learned a bit about how bacteria survive in inhospitable places like this pit, but how do fungus do it? How do fungus deal with low pH and high concentrations of heavy metals? Also what do the fungus use as an energy source?

Researchers Discover Antifungal Agent from Pathogen Box Project

Article:Researchers Discover Antifungal Agent from Pathogen Box Project                

Source: American Society for Microbiology

https://www.asm.org/index.php/mbiosphere/item/6334-scientists-identify-promising-new-compound-for-deadly-fungal-pathogens

Summary:

The pathogen box, which is  an open-source drug discovery project, is seeking to find/create solutions to under-researched/neglected diseases. Researchers can receive this pathogen box, which is composed of 96 well plates with different compounds (thought to be anti-microbial agents, or known to have certain effects on microbes), for free as long as they report any findings within 2 years. In recent tests, a compound targeting cell walls and membranes in fungi (with low toxicity to humans) could potentially be used to treat common fungal infections Cryptococcus neoformans and Candida albicans.

Connections:

In class we have discussed finding different antibiotic targets for fungi, and the difficulty with doing so due to the physiological similarities between  humans and fungi.

Critical Analysis:

I found it interesting that there is an ongoing project like this, with seemingly high potential, that is actually providing a vast amount of knowledge on antibacterial targets. This is actually a really great idea, the fact that the boxes are free to researchers as long as data is shared in order to add to a database is really creative and cool. I feel like techniques like this could really be used to stimulate interest and action in certain subfields and topics. This article was well written, interesting and pertinent to bio students, but simple enough  for non-bio folk to have no problems reading and comprehending.

Question:

I would like to know how popular the pathogen box is (as far as how many people are using it) and what data they have gathered thus far (since its start in 2015).

Neanderthal Tooth Plaque Hints at Meals and Kisses

Neanderthal Tooth Plaque Hints at Meals-and Kisses

Nature 08 March 2017

doi:10.1038/543163a

https://www.nature.com/news/neanderthal-tooth-plaque-hints-at-meals-and-kisses-1.21593

Summary: The plaque of teeth from Neanderthal remains discovered in  El Sidrón cave in northern Spain, which are estimated to have been from 50,000 years ago, were used to reconstruct the first microbiomes from extinct species. The researchers were able to determine their diet consisted of mushrooms and plants while Neanderthals from Spy cave ate wooly rhinoceros and mushrooms all from sequencing of the DNA from the plaque. The data also suggests that Penicillium mold was consumed along with aspirin from poplar trees to treat infections. The genetic analysis also suggests that Neanderthals and humans were kissing or sharing food as well since they both shared the same species of microbe in their mouths as modern humans. This is supported by the fact the strains did not split off until Neanderthals went extinct.

Connections: In lab we tested for some of the types of bacteria often found in the mouth using a variety of differential and selective agars. Though we were testing specifically for opportunistic pathogens, we discussed the amount of bacteria that is found in the mouth. In class we discussed the necessity and dangers of the bacteria that live in and on us and also the transfer of bacteria between people such as mother and baby. In addition, we learned about using penicillin as an antibiotic.

Critical Analysis: I found it very interesting that they could sequence DNA from such a long time ago. I thought the DNA would have degraded too much to get whole reads. It is amazing that they learned more about the social behavior of Neanderthals and humans just by the transfer of microbes. Since kissing means an intimacy during mating instead of the aggressive way they thought Neanderthals mated, the relationship between the two species is now considered different than what archaeologists previously thought.

Question: How did they track the split of the bacterial strain found in the ancient Neanderthals and humans from the same species of bacteria found in modern humans?

A Microbe Hunter Plies Her Trade In Space

Title: A Microbe Hunter Plies her Trade in Space

Date: March 14, 2017

Link: https://www.npr.org/sections/health-shots/2017/03/14/511891419/a-microbe-hunter-plies-her-trade-in-space

Summary: Microbiologist Kate Rubins has been investigating the unique microbiome of the International Space Station and establishing a microbiology lab in space. There has been 16 years of accumulation of the microbes brought by varying crews up from Earth, and microbes tend to stick around. While most of the microbes are harmless, some do have the potential to cause problems for crew, varying from infection to mold growing on the wall panels of the Space Station.

Microbiology in space is incredibly important to the future of space travel, be it for identifying alien life, preventing disease while in orbit, or simply improving the quality of life for spacefaring explorers.

Connections: We have been working to identify microbes from various environments and biomes, just as Rubins has, albeit from a less prestigious location. Being able to quickly and accurately identify microbes in all scenarios is something emphasized through the course, and Rubins is putting what we are learning to practical application whilst in orbit.

Critical Analysis: This article was actually a transcript of an NPR broadcast, and so read a little bit differently than most traditional news articles. It was filled with interview blurbs from Rubins, recollections of her time in space, and easy-to-follow explanations of her work. I know NPR works to tell stories as well as news, and this article was an interesting and engaging story. However, if you want the hard details about what Rubins was doing, or the specific microbial work done in the International Space Station, this is not the article for you. This is, more than anything, a story, and is not meant for conveying details. However, as a springboard for ideas, or an interesting illustration that your job can sometimes take you in strange and exciting directions, this is a good read or listen.

Questions: What other positions has NASA been searching for since it has stopped focusing on pilots? Rubins is a microbiologist, but what other branches of the sciences or other professions have gone to space?

Candida auris Outbreak in the U.S.

Title: “Deadly Drug Resistant Fungal Infection Outbreak Causing Concern In U.S.”

Source: ReliaWire

Date:  March 12, 2017

Link:  https://reliawire.com/candida-auris/

Summary:  Candida auris  has led to almost 30 infections in the United States. The outbreak is troubling because the fungal strain happens to be multi-drug resistant and is linked to a high death rate.  Even though that the outbreak is fairly new, researchers are confident that there may be a way to work against it.

Connections: We’ve talked about antimicrobial resistance in class and this is an example of a drug resistant fungus. This also incorporates with the overarching theme that public health and science are intertwined.

Critical Analysis: I find it interesting that this fungus has been able to cause an outbreak despite how many downfalls it has. For example, C. auris cannot produce spores. This is surprising considering that it has been able to spread and infect  patients so easily in hospitals. Also, not every strain even has the enzymes that allow for infections in body tissues. It is strange that the fungus has been able to be so successful considering these things. This article seems to be factually correct. It quotes both the CDC and a professor at the Center for Medical Mycology at Case Western Reserve School of Medicine. The article may have had some scientific terms that could be tough to understand for someone that is unfamiliar with medicine or biology. Despite that, it was not written to be misleading and does not describe the infection in a way that would cause panic in the public. Instead, it describes what has happened to cause the outbreak and what researchers and healthcare workers are doing to prevent spread.

Question: The article mentioned that combatting this fungus is an issue because it can be especially hard to identify in labs. What could be a method to properly identify the pathogen?

What’s Going on With Our Phones?

Title: Scientists Discover 3 New Species of Microbes Growing on Mobile Phones

Source: Press Trust of India from Gadgets

Date: March 6, 2017

https://gadgets.ndtv.com/science/news/scientists-discover-3-new-species-of-microbes-growing-on-mobile-phones-1666732

Summary: A lot of people have their cell phones attached to their hands wherever they go, but what researchers have recently found is that phones are starting to become a home for a diverse array of microbes. In the midst of their research, scientists came across three new species of bacteria, as well as one new species of fungi. Not only that, but the researchers found that people’s phones contain more species of microbes than what they found on toilet seats. On the plus side, these scientists found that from the phones that they sampled, there were no dangerous bacteria species.

Connections: The microbial world is extremely diverse between the different species of bacteria, fungi, and archaea. Bacteria and fungi can flourish in any place that provides them with the optimal growing conditions, like temperature or amount of light. We have briefly explored how diverse the Bacteria domain is, as well as discussed different types of environmental conditions that assist with the growth and survival of bacteria based on their composition.

Critical Analysis: Reading through this article, I was surprised about how many species of bacteria and fungi grew on the surfaces of our phones. Not only that, but the fact that the researchers behind this study discovered 3 new species of bacteria and 1 new fungal species just further proves how diverse microbes can be. The article presented the findings from the study that would stand out and catch the audience’s attention, so I feel as though the article was scientifically accurate, even briefly including some of the methods used to obtain samples. The author even pointed out where the researchers could enhance the study by taking samples from phones that belong to those who work in the medical field. This article was easy to read and was written in a way that was somewhat entertaining and attention grabbing, which helps the audience stay interested in the material presented. I also liked how I was expecting the article to be all doom-and-gloom, but the authors had a positive tone.

Question: How would the microbial diversity be on phones that were sampled from people that work in healthcare locations, like a hospital? Would there be deadly bacterial strains and would this effect the sterility of an environment that is supposed to be completely sterile?

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.