A Bioremediation fairy tale

Interested in microbial bioremediation? Want to teach your children about it? You’re in luck! Follow the link here to read a children’s story about a small bacterial population who uses the power of plasmids to remediate their island from petroleum pollution!

Pseudomona and the Tale of Bioremediation follows the story of Psuedomona, the daughter of the leader of a population of bacteria, who must travel a great distance to find Psueodmonas putida, the fabled microbe who eats petroleum. Will they be able to save the island together? Find out here!

The Brothers Microbes: Microbial Fairy Tales

The Earth today is riddled with environmental contaminants. While humans have been figuring out ways to clean up our messes, we are not alone in our efforts. Join us on a journey into a far away land where microbes live! Explore how microbes deal with tasks involving biodegradation of contaminants. Each story below shares a problem and how microbes are able to tackle them. Click on the titles to read.


Lord PAH of Aerobia,  written by Presley Coryell

Aesop’s Butter Battle Book: PCBs The Great Race,  written by Alex Wynne

The Benzene Curse,  written by Sophie Weaver

The Princess and the PCBs,  written by Taylor Seitz




The Clean Up Adventures of Pseuda & Mona


Follow along with Pseuda & Mona as they try to clean up a heating fuel spill in Pseuda’s yard. Pseuda and Mona try several techniques to clean up the mess, but with each technique they learn more about heating fuel, bioremediation techniques, and that there is nothing “simple” about cleaning up an oil spill.

Table of Contents:
pg 2: Meet Pseuda
pg 4: B.TEX
pg 8: Mona to the rescue!
pg 8-10: Soil Excavation – Aasne
pg 12-15: Land farming – Ankur
pg 16-19: Ground water remediation – Tonya
pg 20-21: Phytoremediation – Kim
pg 22-23: Clean & green

Presence of microbes on utensils.

Layman’s Terms:

Microscopic organisms are everywhere, even in places where you would think they wouldn’t be, such as on clean clothes, clean kitchen counters or even washed utensils. Do you remember those advertisements for disinfectants that claim they can kill 99.9% of bacteria? You might think that 0.1% are left there even after using these antibacterial disinfectants. In Ontario, they have a standard that on a cleaned utensil there should not be more than 100 bacterial cells! Imagine what happens to utensils cleaned in dishwashers without such effective disinfectants! A study was done by scientists in Ontario, Canada on the dishwashers which did not handle a lot of utensils at an instance, such as those in residential care homes. Along with disinfectants, high temperature is also needed to kill microorganisms which is a strategy that dishwashers actually use. But in establishments that have relatively few utensils, household dishwashers are sometimes used instead of commercial dishwashers. The household dishwashers cannot always achieve such high temperatures which means that they need to use sanitizers to treat utensils. The sanitizer has to be used at a set time and concentration but normal dishwashers do not have this function. The study found that 83% of these dishwashers actually worked within the prescribed limits but still there are 17%, that is, more than 1 out of 6 instances that your utensils actually contain a lot of microbes. So the next time you take the utensils out from the dishwasher, think again if they are clean or not. Also, if you live in residential care facilities or places that use common dishwashers then you might ask that they install a commercial sized dishwasher instead of domestic dishwasher.

Technical Explanation:

The researchers aimed to study cleaning ability of domestic dishwashers employed in residential care homes. The researchers focused on these places because they know that dishwashers do not work that well if there are fewer utensils cleaned at a time. This happens due to low temperature that water reaches when cleaning occurs. A temperature of 82oC for 10 seconds or chemical sanitization at 24oC is required to properly sanitize the utensils. For samples, they chose 4 establishments with different numbers of dishwashing units to a total of 103 units. Four different types of utensils were selected for the study and were swabbed after one full cycle was over. Standard operating procedures laid out by United States Public Health Service’s (USPHS) were followed. Of the 103 domestic dishwashers evaluated, 85 (83%) yielded results that fell within the prescribed limit of no more than 100 bacterial colonies per utensil as determined by heterotrophic plate count (HPC). Dishwashers that contained utensils classified as somewhat soiled or very soiled before washing were more likely to fail (P < 0.05) than those that were classified as very clean or somewhat clean before washing when all other characteristics and operating parameters and the number of plastic items were controlled for. With increasing maximum rinse temperature, dishwashers were less likely to fail (P < 0.05) while the same characteristics were controlled for. Also, dishwashers were more likely to fail when chlorinated detergents were used (P < 0.05). So even after using a dishwasher on dirty utensils, there is a 16% chance that it will not be as clean as the required standards and we have to use sanitizer in the dishwasher to get the desired results.


The Ins and Outs of a Septic System

How often to do you think about where the water goes when you flush your toilet? Maybe never until the toilet doesn’t flush or there is wastewater backing up into the tub. Many homes throughout the U.S. are connected to a utility but onsite wastewater disposal systems are also common. According to the Environmental Protection Agency (EPA), an estimated 4 billion gallons of wastewater nationwide is collected, treated, and released from onsite wastewater systems per day.

Onsite wastewater disposal systems can be effective in the removal of pathogens (bacteria and viruses) but can also be major contributors of nitrogen and phosphorous to groundwater and surface waters; a potential problem that is propagated due to septic systems not always being correctly sited, installed, or maintained. Groundwater represents about 97 percent of the earth’s fresh water resource and needs to be protected from potential sources of contamination. Nitrates in drinking water supplies may adversely affect public health and are linked with methemoglobinemia (blue-baby syndrome), increased risk of cancer, and other possible health effects. Excessive nutrients, such as phosphorous and nitrogen, in surface waters can lead to eutrophication and decreased dissolved oxygen leading to adverse effects on aquatic species.

The most common type of onsite wastewater system is a septic system which generally consists of a septic tank and soil absorption system. If a septic system fails to treat wastewater properly, namely complete denitrification, this may lead to contamination of groundwater and surface water. The focus of our Coggle is on nitrogen cycling through a septic system and the ultimate fate of nitrogen released to the environment.

After exploring the coggle, you should be able to answer the following questions: ?

What are the sources of nitrogen input to wastewater?
What makes the septic tank and anaerobic environment?
What types of microbes transform ammonia or ammonium to nitrite, and what do they gain from it?
What happens to nitrogen present in wastewater? Can it pollute groundwater?

Brought to you by Kimberly Fitzgerald, Aasne Hoveid, Ankur Sachan, and Tonya Bear  



It’s More than just Rotten Eggs, It’s the Sulfur Cycle!

The sulfur cycle is made up of 4 steps: mineralization, oxidation, reduction and incorporation.  Sulfur is one of the main constituents of many proteins, vitamins and hormones. Sulfur is   often found in oxidation states that can range from Sulfates to In the soil environment, sulfur can be produced in either an organic or inorganic form. The sulfur cycle contains both atmospheric and terrestrial processes. In the inside of the terrestrial portion, the cycle begins with the weathering of rocks, which is what releases the stored sulfur. It is imperative to learn about how exactly the sulfur undergoes mineralization in the sulfur cycle. For this case, sulfur is mainly cycled throughout the soil environment and sea water in the marine environment.
Oxidation is the process of losing an electron from an element or compound. In the sulfur cycle there is a sulfide oxidation and a sulfur oxidation, each of these processes are performed by microbes in anaerobic environments such as a hotspring.  Sulfate reduction is a process carried out by anaerobic microbes which transforms sulfate into sulfide. These microbes are a diverse and varied group both genetically and physiologically, and are typically found in aquatic environments, where they act as decomposers. However, they are also present in great numbers within sulfur springs, such as those in Yellowstone, where sulfate is abundant and continually replenished. Incorporation involves the process of changing sulfide into organic compounds. This can include metal-containing derivatives. Microorganisms have the ability to immobilize sulfur compounds, which ultimately results in subsequent incorporation of these sulfur compounds into the organic form of sulfur.. The sulfur cycle is important because of how abundant it is in our environment. Take a look at our interactive coggle to learn about each of these parts more in depth.

Scavenger Hunt-Find the answers to the following questions in the coggle

  1. What is one practical application for sulfate reducers?
  2. Where does oxidation in the environment occur?
  3. What exactly would happen to sulfide if it were to be incorporated after oxidation and reduction?
  4. What are the three major processes that control the amount of sulfate in the oceans?

Scavenger Hunt Answers click here

To go to the coggle click here  

Collaborators: Kirsten Veech, Connor Ito, Alisa Thiede, Zachary Snelson

Phosphorus Cycle in Soil

Phosphorus, an essential nutrient, is a key component of molecules necessary for life, including energy (e.g. ATP), lipids, and DNA. Phosphorus exists in both organic and inorganic forms in the environment, initially entering ecosystems through weathering of bedrock and then cycling through soil, water, and organisms. Microbes are integral to the cycling of phosphorus, as they mediate transformations many within the phosphorus cycle, including immobilization, mineralization, and solubilization. Within this interactive Coggle, we present the various transformations of phosphorus between inorganic and organic forms and describe how these are mediated by microbes. Multiple mechanisms can be behind each transformation, and there is an abundance of literature available for you to dive deeper and explore each process!

You might be wondering: why it is so important to learn about the role that microbes play in phosphorus cycling? In addition to being an essential nutrient that all organisms need to live, phosphorus in high concentrations can have negative impacts on biota within freshwater ecosystems, causing harmful algal blooms and eutrophication. With increasing food demand due to a growing human population, the use of fertilizers containing phosphorus has increased in recent times, impacting surrounding ecosystems. Use the scavenger hunt questions below to help guide your exploration of the phosphorus cycle.


Scavenger hunt questions:

  1. What process in the phosphorus cycle is the opposite of mineralization?
  2. What are three factors that can influence phosphate mineralization in soil?
  3. What kind of phosphite oxidation (BPO or APO) would occur in the following environments? (Top later of loosely packed soil? Lake sediments?)
  4. What is the main limitation of phosphate-solubilizing microorganisms?

Collaborators: Presley Coryell, Sophie Weaver, Taylor Seitz, Alex Wynne

The Ferrous Wheel: A Perspective on the Iron Cycle

While you won’t find the ferris wheel that is a staple of the county fair, this coggle will introduce you to a different kind of ferrous wheel- the cycle of the transition metal, iron. Iron naturally exists in two states: ferrous iron, Fe(II), and ferric iron (III). These forms can exist as ions, or minerals, where they are bound to oxides. Iron is not only important to human life where it serves as cofactors in chemical reactions, but also to many microbes, where it drives their metabolism. It is prevalent in terrestrial environments, in oceans, and even the atmosphere. Preservation of the iron cycle is critical to the fluidity of geochemical cycling, as it plays a role in nitrogen cycling and limits phytoplankton’s ability to perform photosynthesis.

In this coggle we describe how microbes facilitate the anaerobic transition between ferric and ferrous iron, how microbes covert ions to minerals, and how iron enters the cycle. We presented this research in the framework iron cycling in the ocean, (including the role of phytoplankton), but the microbial iron cycle is diverse, and one step can happen via multiple mechanisms. This leaves much more to learn and explore, and we urge you to use this project as your first step into the ferrous wheel.

Begin on the left side with the entry “Mineral Iron II Flux”, and follow the blue arrows around the ferrous wheel. Click and drag to view different parts of the coggle


Team: Ben Hedges, Bayli Mohl, Karen Biondich, Courtney Hill and Mark Velasco

Scavenger Hunt: challenge yourself to complete these by reviewing all of the posts

  1. What method of iron oxidation was likely the first, evolving in ancient oceans?
  2. How can diatoms uptake iron into their cell bodies?
  3. Do anaerobic iron reducers need to import the iron?
  4. What is it about sea water that allows for the rapid oxidation of iron?
  5. Which ocean experiences the greatest input of aerial dust from the Earth’s major deserts?

Elucidating the impact of microbial community biodiversity on pharmaceutical biotransformation during wastewater treatment

Link:  https://onlinelibrary.wiley.com/doi/10.1111/1751-7915.12870/full


Stadler, L. B., Vela, J. D., Jain, S., Dick, G. J., & Love, N. G. (2017). Elucidating the impact of microbial community biodiversity on pharmaceutical biotransformation during wastewater treatment.  Microbial Biotechnology,10(6). doi:10.1111/1751-7915.12870


In addition to removing organics and other nutrients, the microorganisms in wastewater treatment plants (WWTPs) biotransform many pharmaceuticals present in wastewater. The objective of this study was to examine the relationship between pharmaceutical biotransformation and biodiversity in WWTP bioreactor microbial communities and identify taxa and functional genes that were strongly associated with biotransformation. Dilution-to-extinction of an activated sludge microbial community was performed to establish cultures with a gradient of microbial biodiversity. Batch experiments were performed using the dilution cultures to determine biotransformation extents of several environmentally relevant pharmaceuticals. With this approach, because the communities were all established from the same original community, and using sequencing of the 16S rRNA and metatranscriptome, we identified candidate taxa and genes whose activity and transcript abundances associated with the extent of individual pharmaceutical biotransformation and were lost across the biodiversity gradient. Metabolic genes such as dehydrogenases, amidases and monooxygenases were significantly associated with pharmaceutical biotransformation, and five genera were identified whose activity significantly associated with pharmaceutical biotransformation. Understanding how biotransformation relates to biodiversity will inform the design of biological WWTPs for enhanced removal of chemicals that negatively impact environmental health.


I thought this paper was relevant to what we recently discussed in class, especially with chemical and pharmaceutical contaminants becoming so prevalent in our waste water.


down voteup vote (+1 rating, 1 votes)

Microbial communities of Mt. Prindle, AK-canine oral microbiome


Non-technical summary

Have you ever heard the idea that your dog’s mouth is cleaner than yours? Well that very well may not be true. A dog’s mouth, similar to yours and other humans’, has its own diverse array of microbes living inside; all of these microbes living together is known as a microbiome. Microbiomes are known to be influenced by many factors including genetics of the host and the environment, with perhaps the most important environmental factor being what we eat. Human microbiomes have been a popular area of study for scientists in recent times, and although a fair amount is known about the human microbiome, very little is known about microbiomes of other mammals. Many scientists are interested in what microbes are living in a dog’s mouth for two reasons: first, to see how similar the microbes are to those living in humans, and second, to allow veterinarians and doctors to learn more about how disease and health problems are related to the dog’s microbiome. This paper set out to compare and discover distinctions and similarities in bacteria colonizing dog and human mouths. By collecting plaque from the teeth of over 50 dogs, scientists were able to extract and analyze DNA samples from the microbial creatures living in the plaque. This study compared specific DNA sequences of the microbes from dogs to those in humans, and found a very small amount of overlap in microbiomes–only 16.4%! In this study scientists found thousands of   of bacteria that have not been already identified to the species level, but are known not to be found in humans. More research on this topic could help scientists discover new microbes and possibly even learn about how they affect your dog’s health, and maybe even yours!


Technical summary

Over recent years, interest has grown in the field of analyzing interactions and fluxes of microbes living in specific environments. Scientists have conducted ground-breaking research in the microbiomes of humans and are beginning to expand into research of other mammals. This paper aimed to discover similarities and distinctions between human and canine oral microbiomes. This study offers a unique comparison between two divergent mammalian species and the microbiomes associated. Scientists, as well as veterinarians and medical professionals, are interested in the bacterial communities of canines, in order to investigate their relations to disease and health issues. This was done by first determining the diversity and abundance of microbial life existing in the canine oral cavity. By using 16S rRNA sequence comparison they were able to analyze 5,958 rRNA gene sequences from 353 different bacterial taxa found in the canine oral cavity. Of those 353 taxa, over 80% are currently unnamed. In order to compare between human and canine microbiomes a similarity cutoff of 98.5% was used, resulting in only 16.4% similarity between the two oral microbiomes. These results are significant for they offer a basis for continued study of canine oral microbiome diversity. Since a large majority of the discovered taxa remain unnamed, future research can focus on further categorization and identification.