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




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

Degradation of Synthetic Azo Dyes of Textile Industry: a Sustainable Approach Using Microbial Enzymes

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SFazal, T., Mushtaq, A., Rehman, F., Khan, A. U., Rashid, N., Farooq, W., … & Xu, J. (2017). Bioremediation of textile wastewater and successive biodiesel production using microalgae.  Renewable and Sustainable Energy Reviews.


Microalgal biodiesel has emerged as an environment friendly alternative to the existing fossil fuels. The commercial production of this biodiesel is still challenging due to several technical and economic issues, which span from mass cultivation of microalgae to the biodiesel production. Mass cultivation is the most critical step in terms of water and nutrient requirement. Industrial wastewater such as textile wastewater (TWW) is a cheap source for water, which additionally contains necessary nutrients (phosphate, nitrates, micronutrients etc.) and organic dyes (potential carbon source) for algae cultivation. The application of microalgae for biodiesel production employing single objective strategy is not sustainable. Microalgae can be effectively employed to bioremediate TWW (dyes and nutrients removal) and to produce biodiesel from grown microalgae. This process integration (bioremediation-biodiesel production) can potentially improve biodiesel production and wastewater treatment. However, this process coupling needs to be thoroughly investigated to identify and optimize critical process factors (algal species, cultivation and harvesting methods, bioremediation mechanism etc.). This study has reviewed the status of TWW as potential source of water and nutrients, role of different algal species in the bioremediation of TWW, different cultivation systems, harvesting and biodiesel production methods. This review also suggests future research and development challenges for coupled textile wastewater treatment and microalgal biodiesel production.



I thought this paper was really interesting! It talks about the biodegradation pathways involved in textile waste water and how the processes can be coupled with other biological processes. This paper discusses a rising problem in today’s world: fast fashion and the textile industry. I think it brings up important topics that address the sustainability of such a large and fast growing industry, and how microbes can potentially be utilized to mediate.

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



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.


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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.

Evidence of microbial regulation of biogeochemical cycles from a study on methane flux and land use change

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Nazaries, L., Pan, Y., Bodrossy, L., Baggs, E. M., Millard, P., Murrell, J. C., & Singh, B. K. (2013). Evidence of Microbial Regulation of Biogeochemical Cycles from a Study on Methane Flux and Land Use Change.  Applied and Environmental Microbiology,  79(13), 4031—4040.


Abstract:  Microbes play an essential role in ecosystem functions, including carrying out biogeochemical cycles, but are currently considered a black box in predictive models and all global biodiversity debates. This is due to (i) perceived temporal and spatial variations in microbial communities and (ii) lack of ecological theory explaining how microbes regulate ecosystem functions. Providing evidence of the microbial regulation of biogeochemical cycles is key for predicting ecosystem functions, including greenhouse gas fluxes, under current and future climate scenarios. Using functional measures, stable-isotope probing, and molecular methods, we show that microbial (community diversity and function) response to land use change is stable over time. We investigated the change in net methane flux and associated microbial communities due to afforestation of bog, grassland, and moorland. Afforestation resulted in the stable and consistent enhancement in sink of atmospheric methane at all sites. This change in function was linked to a niche-specific separation of microbial communities (methanotrophs). The results suggest that ecological theories developed for macroecology may explain the microbial regulation of the methane cycle. Our findings provide support for the explicit consideration of microbial data in ecosystem/climate models to improve predictions of biogeochemical cycles.


Justification: This paper is very relevant to what we’ve been discussing in class, as well as issues scientists are facing today. It explores how microbial communities fluctuate based on changes in their environment, specifically looking at how biogeochemical processes are influenced.


A1 Intro Post

Hi everyone! My name is Taylor, I’m currently majoring in biological science with a concentration in cellular and molecular, with minors in math and marine science. I’m taking this class for a couple reasons–one being that I really enjoyed taking microbiology last year, and the other being that I’m still not really sure what I’m doing after college so I’m trying to explore as many different areas of science as possible!


Microbe haiku:

Supporting so much

microbes quietly exist,

smaller than a speck.