A2: Microbes in the News (Post 2)

Harnessing Soil Microbes to Enhance Crop Performance


March 28, 2019


This article explains that some organizations (the organization they used as an example was the Agriculture and Food Development Authority (TEAGASC)) have been using bacteria to modify different plants’ genome. This has been done for a while using Agrobacterium tumefaciens, but because of limitations, they were looking into alternative bacteria that could perform the same function. They found a bacterium, Ensifer adherens, which can modify a plant’s genome easier than A. tumefaciens. Plants treat A. tumefaciens as something to guard against, which makes modifying certain plants difficult because some plants have a resistance. On the other hand, many plants recognize E. adherens as a symbiotic bacterium. As such, they do not have the same resistance as they do with the A. tumefaciens. The article then discusses some practical applications that E. adherens has been used for already.

We have been covering in class recently how humans control the growth of bacteria with many different antibacterial methods. I found it interesting that even plants have antibacterial methods that make them resilient to certain strains of bacteria. I believe that this story was scientifically accurate, I just would have liked more information on how E. adherens differed from A. tumefaciens to result in more of a symbiotic relationship. Although, I believe that editing out all of the information would make it so a wider variety of audience would be more likely to read the article. All in all, I found this article interesting and informative.

My question is: Is there any other widely-used bacterium that has been identified that can genetically modify plants?


Painting With Microbes: Matt Andrews F03 – Exponential Sunrise

Title: Exponential Sunrise

The intention here was to portray a sunrise over water, with the backdrop of the UAF. We live in an exponential world, whether it is as everyday as the light which lets us see, the sounds we hear, the technology which surrounds us, or even the dirt under our fingernails. The world is built on exponential growth and the education we are developing here at the UAF helps us to understand some small part of it.

I had created this scene on sever plates with Micrococcus luteus (for the golden sun and reflection) and Serratia marcescens (for the red water), I was hoping for a bit more color from the Serratia  but I am still happy with the overall effect.

Painting with Microbes

Samantha Smith F01

Just a wink and a nudge to my favorite book “East of Eden” by John Steinbeck. I have a a pretty cross stitch of this at home, which admittedly looks a lot better. Perhaps I will stick to my day job and leave the microbe painting to those more artistic than myself.

I used the Eosin Methylene Blue Agar plate for this painting, hoping to achieve a stark different in coloration from the two sources I chose. The lettering and the vine were done with Escherichia coli.  This bacteria is gram negative so is not inhibited by the eosin or methylene blue of the medium. It also produced a deep black color with a metallic green sheen as it ferments lactose with strongly acidic end products. (The green sheen is actually quite pretty, though you can’t tell from the photo). The filigree and leaves are colonies of  Enterobacter aerogenes  which is also gram negative. It produces a pink color because it does ferment lactose, but the end products of fermentation are much less acidic than that of  E. coli.

I would like to add that I had a lot of fun in this assignment and seeing the variety of agar art from the ASM Agar Art Contests.


Microbes Can Prevent Potholes…?

Article: “Scientists hope bacteria could be the cure for potholes” by Talia Kirkland


Source:  Fox News

Date Published: Feb. 5, 2019

Summary:   This article/news story explains how bacteria may be an answer to preventing potholes.   Scientists at Drexel University in Philadelphia have found that bacteria (they did not mention a specific species), when mixed with CO2 and calcium, can change the environment around them to self-produce limestone.   When spread out on a road, they can make the road material stronger and more able to withstand damage that would cause potholes.   The technique is not yet being used, but it may be an alternative for better roads in the future.

Connections:    This article relates to what we have been talking about in class because they are introducing CO2 and Ca2+ to the bacteria to (I assume) get them to use a specific metabolic pathway and get the desired product.

Critical Analysis:   I think it is really interesting that it only requires two simple ingredients (CO2 and Ca2+) to get these bacteria to produce limestone.   There may be other underlying factors that contribute to the production of the limestone, but the fact that they figured this out with these simple ingredients that are extremely common is pretty impressive.   The information seemed to be scientifically accurate since they actually interviewed the scientists who did the research; it makes the article a little more credible.   One thing that I found misleading, and a bit frustrating, was that within the article, they kept using the terms pavement and concrete interchangeably, but concrete and asphalt are different materials that are made in different ways.   I don’t know if they actually tested this bacteria mixture on actual roads or not, but I think there would be a difference if they tested them on concrete versus asphalt.   The scientist kept saying “concrete”, which leads me to believe that they experimented with concrete, which is not the same material that roads are usually made out of, as far as I know (I would be surprised if roads in Philadelphia are made out of concrete, although it is possible).   If that is the case, then this mixture may not actually work on pavement (asphalt) to fix potholes, as they are claiming.   It is also possible that they were actually working with pavement and are just using ‘concrete’ incorrectly, which would be confusing to people who know the difference between the two materials!   Other than that, I think the author did a really good job at keeping the information simple enough for any person to understand it.   I think someone who knows nothing about biology would still be able to follow along and understand what they are talking about.

Question:    The scientists say that the bacteria are changing the microenvironment around them to self-produce limestone, which made me wonder- are the bacteria that they are adding the ones who are actually producing the limestone?   If not, then what changes are they making that cause other organisms to produce limestone?

A2 Microbes in the News

Article and link

“Gene expression study sheds new light on African Salmonella’
Science Daily, January 15, 2019 https://www.sciencedaily.com/releases/2019/01/190115144045.htm

Further Reading: https://www.ncbi.nlm.nih.gov/pubmed/30645593



A variant of Salmonella typhimurium (ST) 313 is responsible for the deaths of approximately 400,000 persons ever year in sub-Saharan Africa. Researchers at the University of Liverpool are attempting to understand how the genome of African S. typhimurium, which enters the bloodstream and spreads through the body, differs from the global strains of S. typhimurium which causes gastroenteritis.

By culturing the different Salmonella strains in different environments they could simulate differences of stages within the human infectious timeline. They then analyzed the transcriptome of these two strains and found a multitude of gene expression variations as well as RNA variations. These coincided with metabolic and plasmid differences within the two strains.


This correlates with the information that we have learned about variations in culture mediums in class. As well as what we will be going over in lab. The ability to culture this bacterium in different environments allowed for the researchers to study the gene expression at essentially different time frames in the bacterial life cycle. Say, from an environment similar to that outside of the human body, and then an environment within the human body.

Critical Analysis

What I found interesting in this article is that the phenotypic expression of genes within one strain has caused such a different in its ability to act as a pathogen. I also never thought of culturing microbes in different environments to simulate gene expression. I just thought you would culture them in their ideal environment and study them as such. Thinking about it now, it makes a great deal of sense to do this, not only to study the activity of pathogens, but to perhaps study microbes and why they fit into their respective niches.

The forum for this article is a scientific forum, and though it is technical it is written in a way that someone who isn’t specifically a microbiologist (such as myself) can understand what is being studied and the accomplishments that this group of researchers have made.


The question that I have is a technical one. How is it that they were able to find out the gene expression of these bacterium from culture? I know that the genome can be sequenced using various methods, but how would one know or ascertain which portions of that genome are being expressed at any given time.

-Samantha Smith

A2: Microbes in the News- Deep Sea Japan

Extreme Microbes Found in Crystals Buried 200 Feet Beneath the Sea of Japan

source: https://www.livescience.com/64532-microbes-inside-gas-hydrate-crystals

January 17, 2019.


Recently, In the depths of the ocean off the coast of Japan, with extremely cold temperatures and high pressure, microbes were discovered inside of small mineral grains sealed into crystals. These were discovered during an expedition sampling gas hydrates.

Its pretty incredible to find microbes in such extreme conditions such as this. In fact, we touched on the topic in class, they are often known as “Extremeophiles.” These are organisms that are able to live in otherwise uninhabitable environments.

I think its pretty neat that even though the researchers were originally searching for something else, they found this incredible discovery. Being from a pretty cool and efficiently sourced scientific website, I believe this article to be accurate. The microbes were effectively “sealed” into a environment perfect for them, within these crystals. No other organisms were introduced, this makes for a really incredible historical discovery as well, seeing as these organisms have been in a protected environment for hundreds if not thousands of years.

What I wanted to know, was could these organisms tell us a little about the past for sure? Being in an enclosed system, possibly could have halted any sort of evolution.