Pollutants We Put into Our Environment

We may not realize how much we change the environment that we live in. People introduce a large amount of waste and pollutants into the world. We all are aware that we produce trash and that it go into the landfills, however have you ever considered how the wastewater that you produce is cleaned and put into the rivers and oceans around you, or how taking medications can introduce new chemicals into the environment? What about how heavy metals produced from factories and petroleum products are dealt with? Below is our interactive and informative thinglink to learn more.

Fungal Bioremediation of Acidic Radioactive Waste Sites- Reposted!

Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of  Rhodotorula taiwanensis  MD1149


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“Highly concentrated radionuclide waste produced during the Cold War era is stored at US Department of Energy (DOE) production sites. This radioactive waste was often highly acidic and mixed with heavy metals, and has been leaking into the environment since the 1950s. Because of the danger and expense of cleanup of such radioactive sites by physicochemical processes,  in situbioremediation methods are being developed for cleanup of contaminated ground and groundwater. To date, the most developed microbial treatment proposed for high-level radioactive sites employs the radiation-resistant bacterium  Deinococcus radiodurans. However, the use of  Deinococcus  spp. and other bacteria is limited by their sensitivity to low pH. We report the characterization of 27 diverse environmental yeasts for their resistance to ionizing radiation (chronic and acute), heavy metals, pH minima, temperature maxima and optima, and their ability to form biofilms. Remarkably, many yeasts are extremely resistant to ionizing radiation and heavy metals. They also excrete carboxylic acids and are exceptionally tolerant to low pH. A special focus is placed on  Rhodotorula taiwanensis  MD1149, which was the most resistant to acid and gamma radiation. MD1149 is capable of growing under 66 Gy/h at pH 2.3 and in the presence of high concentrations of mercury and chromium compounds, and forming biofilms under high-level chronic radiation and low pH. We present the whole genome sequence and annotation of  R. taiwanensis  strain MD1149, with a comparison to other  Rhodotorula  species. This survey elevates yeasts to the frontier of biology’s most radiation-resistant representatives, presenting a strong rationale for a role of fungi in bioremediation of acidic radioactive waste sites.”  


Tkavc Rok, Matrosova Vera Y., Grichenko Olga E., Gostinčar Cene, Volpe Robert P., Klimenkova Polina, Gaidamakova Elena K., Zhou Carol E., Stewart Benjamin J., Lyman Mathew G., Malfatti Stephanie A., Rubinfeld Bonnee, Courtot Melanie, Singh Jatinder, Dalgard Clifton L., Hamilton Theron, Frey Kenneth G., Gunde-Cimerman Nina, Dugan Lawrence, Daly Michael J. (2018). Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149. Frontiers in Microbiology 8:2528.


I thought this paper would be interesting to look at not only because it deals with fungi, which are not often thought of as microbes, but because of why fungi were chosen. There are distinctive advantages and disadvantages to utilizing different types of microbes in bioremediation, and I think this paper addresses that well. There is also a definite need for something which is able to process the contamination at this site, and bioremediation is an intriguing possibility.


Phenol biodegradation by halophilic archaea


Acikgoz, Eda, and Birgul Ozcan. “Phenol Biodegradation by Halophilic Archaea.’  Internation Biodeterioration & Biodegradation, vol. 107, Feb. 2016, pp. 140 146., doi:https://doi.org/10.1016/j.ibiod.2015.11.016.

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Phenol is a toxic aromatic compound produced as a by-product of industrial activities. Biological treatment of highly saline wastewaters containing phenol can be performed through halophilic  microorganisms. In this study, the ability of halophilic archaeal isolates to degrade phenol was investigated. Among 103 tested isolates, the strain designated A235 was identified as having the highest phenol degradation capacity on solid and liquid media containing 20% (w/v) NaCl and phenol as the sole carbon and energy source. The strain was adapted sequentially to increasing phenol concentrations. The removal of phenol via cross-toluene adaptation was increased by 14% in the medium. The growth kinetics of strain A235 during growth on phenol was found to fit the Monod model. The values of μmax and Ks were calculated to be 0.015  h−1  and 71.4  g  l−1, respectively. For an initial phenol concentration of 100  ppm, the biodegradation by A235 was found to be optimal at pH 7.5, 37   °C and 200  rpm when the culture contained 20% (w/v) NaCl, 0.025% yeast extract and the inoculum size was set at 10%. A preliminary enzyme screening indicated that the degradation of phenol was achieved through a  meta-cleavage pathway involving a catechol 2,3-dioxygenase. Catechol 2,3-dioxygenase displayed its highest catalytic activity at 42   °C, 2  M KCl, and pH 8. To the best of our knowledge, this is the first report showing the ability an extremely halophilic archaeon to metabolize phenol at higher salt concentrations.

Continuing with the wastewater treatment section, and about different energy sources/donors for microbes, this article is about how halophilic archaea can help biodegrade pollutants in extra salty wastewater by adapting to high levels of phenol, and using that as the energy source. I like how this article kind of combines many different subjects that we have talked about this semester, and it includes biodegradation (I also think archaea are super cool).

Biodegradation nomination

Link:  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4507529/

Citation: Santisi, S., S. Cappello, M. Catalfamo, G. Mancini, M. Hassanshahian, L. Genovese, L. Giuliano, M. Yakimov. 2015. Biodegradation of crude oil by individual bacteria strains and a mixed bacterial consortium. Brazilian Journal of Microbiology 46: 377-387.


Three bacterial isolates identified as  Alcanivorax borkumensis  SK2,  Rhodococcus erythropolis  HS4 and  Pseudomonas stutzeri  SDM, based on 16S rRNA gene sequences, were isolated from crude oil enrichments of natural seawater. Single strains and four bacterial consortia designed by mixing the single bacterial cultures respectively in the following ratios: (Alcanivorax: Pseudomonas, 1:1), (Alcanivorax:  Rhodococcus,  1:1), (Pseudomonas:  Rhodococcus, 1:1), and (Alcanivorax:  Pseudomonas:  Rhodococcus, 1:1:1), were analyzed in order to evaluate their oil degrading capability. All experiments were carried out in microcosms systems containing seawater (with and without addition of inorganic nutrients) and crude oil (unique carbon source). Measures of total and live bacterial abundance, Card-FISH and quali-, quantitative analysis of hydrocarbons (GC-FID) were carried out in order to elucidate the co-operative action of mixed microbial populations in the process of biodegradation of crude oil. All data obtained confirmed the fundamental role of bacteria belonging to  Alcanivorax  genus in the degradation of linear hydrocarbons in oil polluted environments.


I find biodegradation of oil fascinating because before learning about it in general Microbiology I had no idea that microbes had the ability to break down such a harsh substance such as oil. I think it is relevant for us to learn about because we live in Alaska, where oil is being extracted and has the potential to have oil spills.

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Wastewater treatment journal discussion


P.N. Lens, Poorter, M., Cronenberg, C., Verstraete, W. 1995. Sulfate reducing and methane producing bacteria in aerobic wastewater treatment systems. Elsevier 29:871-880.

A selection of aerobic biofilm reactors and activated sludge plants were investigated for the presence of methane producing bacteria (MPB) and sulfate reducing bacteria (SRB). Detection tests showed that acetotrophic and hydrogenotrophic MPB as well as lactate, acetate and propionate oxidizing SRB were present in all reactor types investigated, except in an activated sludge reactor aerated with pure oxygen. Methane production rates from acetate by biomass samples of aerobic reactors were less than 1% of the rates measured in anaerobic UASB sludge. The presence of SRB was independent of the reactor configuration, the organic loading and the influent sulfate concentration. Aerobic biofilms growing in a trickling filter packed with plastic carrier and in a rotating biological contactor contained between 5.7 × 107  to 1.1 × 108  CFU/g VS of lactate oxidizing SRB and showed a potential sulfate reduction rate using lactate as electron donor of about 10 mg SO2−4/g VS ·h. The latter is comparable to the values found in sludges from typical anaerobic wastewater treatment reactors. In activated sludges, SRB densities were some 103  time lower and the maximum sulfate reduction rate was  ca  3 times lower compared to the aerobic biofilm reactors. In biofilms, high sulfate reduction rates, in combination with the high sulfide removal rates (11.6 to 131.7 mg HS−/g VS ·h) suggest that  in situ  reoxidation of sulfide might sustain the SRB population. The SRB enumeration, together with activity and oxygen microprofile measurements showed that the biomass of aerobic wastewater treatment systems can serve as inoculum or as site for a wide spectrum of redox related biotransformation processes.

I chose this paper because I would like to learn more about how methane contributes to greenhouse gases. I think that both methane and greenhouse effects are super interesting. I was also surprised to see how the distribution of greenhouse gases in the diagram shown in class on Monday and wanted to learn more about it.

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ThingLink cloud microbiology non-technical summary

Non-technical summary:

Science knows a fair amount about the parts of Earth that can be touched by people. However, not very much is known about microbiology in and above the clouds. A few experiments done earlier suggested that there are microbes in clouds since freshly-fallen snow will “grow’ in a petri dish, clouds have enough of the right chemicals to support microbial life, and the clouds drifting past mountaintops have microbes from lower elevations in them. When cooled to freezing, water needs a small particle to begin crystallizing on, known as an ice nucleus. Some bacteria have special proteins coating them that help water crystallize into ice more easily, and since there were bacteria growing from the snow, it would make sense that the bacteria were serving as ice nuclei. If this is the case, then most of the ice nuclei high in the atmosphere may in fact, be bacteria.

In this experiment, the scientists rode along on a NASA airplane while it was flying ahead of and behind hurricanes Earl and Karl in 2013 doing many other hurricane- and atmosphere-related experiments. The experimenters used a sensor in the airplane that measured how common particles of different sizes were in the air. They then ran the air through a filter that would catch bacteria and took them back to a lab to analyze. In the lab, they examined SSU rRNA, a gene found in all living things to count the bacteria and to identify what the organisms were.

In the air before the hurricanes passed through, most of the bacteria were hardy varieties that could thrive on the chemicals that clouds brought up from the surface. They largely belonged to the Proteobacteria, a group which has a few members known for whacky lifestyles (such as living in frozen ground or inside other cells). After the hurricanes swept through, they found most of the bacteria were from the ocean, except when the hurricanes went over a city, when the bacteria were mostly human fecal bacteria. Based on these findings, the scientists concluded that storms are able to pick up bacteria from near the ground and carry them up into the upper atmosphere where they can help the next generation of clouds condense and fall back down to Earth.


Paper:  DeLeon-Rodriguez, N., Lathem, T.L., Rodriguez-R, L.M., Barazesh, J.M., Anderson, B.E., Beyersdorf, A.J., Ziemba, L.D., Bergin, M., Nenes, A. and Konstantinidis, K.T., 2013. Microbiome of the upper troposphere: species composition and prevalence, effects of tropical storms, and atmospheric implications.  Proceedings of the National Academy of Sciences,  110(7), pp.2575-2580.


Microbes influence the biogeochemical and optical properties of maritime Antarctic snow

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“Snowmelt in the Antarctic Peninsula region has increased significantly in recent decades, leading to greater liquid water availability across a more expansive area. As a consequence, changes in the biological activity within wet Antarctic snow require consideration if we are to better understand terrestrial carbon cycling on Earth’s coldest continent. This paper therefore examines the relationship between microbial communities and the chemical and physical environment of wet snow habitats on Livingston Island of the maritime Antarctic. In so doing, we reveal a strong reduction in bacterial diversity and autotrophic biomass within a short (<1  km) distance from the coast. Coastal snowpacks, fertilized by greater amounts of nutrients from rock debris and marine fauna, develop obvious, pigmented snow algal communities that control the absorption of visible light to a far greater extent than with the inland glacial snowpacks. Absorption by carotenoid pigments is most influential at the surface, while chlorophyll is most influential beneath it. The coastal snowpacks also indicate higher concentrations of dissolved inorganic carbon and CO2  in interstitial air, as well as a close relationship between chlorophyll and dissolved organic carbon (DOC). As a consequence, the DOC resource available in coastal snow can support a more diverse bacterial community that includes microorganisms from a range of nearby terrestrial and marine habitats. Therefore, since further expansion of the melt zone will influence glacial snowpacks more than coastal ones, care must be taken when considering the types of communities that may be expected to evolve there.”

Hodson, A. J.,  A. Nowak,  J. Cook,  M. Sabacka,  E. S. Wharfe,  D. A. Pearce,  P. Convey, and  G. Vieira(2017),  Microbes influence the biogeochemical and optical properties of maritime Antarctic snow,  J. Geophys. Res. Biogeosci.,  122,  14561470.


I selected this paper as a means to expand what could be considered as an environment while also wanting to learn more about how changes to the global climate might affect different microbial communities, especially in areas expected to undergo notable change.

I wouldn’t think of travelling to Antarctica to study microbial life, yet this paper explores the communities found there and how a warming climate is affecting both carbon emissions and microbial diversity on what most would consider a barren waste. I found it especially fascinating that microbial activity may actually enhance the melt of Antarctic ice!

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.

Hello everyone. I am Ankur Sachan and I am from India. I am currently pursuing M.S. degree in Mining Engineering. My research topic is biodegradation of Alaskan coal to extract rare earth elements. My hobbies include cooking Indian food, driving and travelling (I admit I like flights!!)   to new places.


I realized on flight

I ran tests for a month

Now, the microbes are dying.

This is a beach in Andaman and Nicobar islands in India where I went this winter break. This beach is famous for bioluminescent bacteria and it glows in night when water is disturbed. I do not have the photograph of night, but trust me it is awesome when you look at it in person!!!


Assignment 1: Introduction

Hey everyone!

My name is Karen and I am majoring in biology with a concentration in physiology. I am currently a CNA working in an assisted living home and planning on going to grad school somewhere warm (aka not Alaska) to become a PA. I have been looking forward to this class since I first heard of it, especially the writing intensive part! I have worked in environmental education in the past and I have run several blogs. I have a great interest in making scientific concepts more understandable to the general public while not losing any important content or ideas, and I think that combining traditional scientific writing with more creative ideas is a great way to achieve that.


Here is my haiku from class:


Energy cycles through all

Life into new life


Starvation Gulch 2016