Fungal Bioremediation of Acidic Radioactive Waste Sites- Reposted!

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

 

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Abstract:

“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.”  

Citation:

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.

https://www.frontiersin.org/article/10.3389/fmicb.2017.02528

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.

 

Bioremediation of Uranium-Bearing Wastewater: Biochemical and Chemical Factors Influencing Bioprocess Application

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Abstract:

A biotechnological process for the removal of heavy metals from aqueous solution utilizes enzymatically liberated phosphate ligand which precipitates with heavy metals (M) as cell’bound MHPO4. The enzyme, a phosphatase, obeys Michaelis’Menten kinetics in resting and immobilized cells; an integrated form of the Michaelis’Menten equation was used to calculate the apparent  Km  (Km app.) as operating in immobilized cells in flow’through columns by a ratio method based on the use of two enzyme loadings (Eo1,  Eo2) or two input substrate concentrations (So1,  So2). The calculated  Km app.  (4.08 mM) was substituted into an equation to describe the removal of metals by immobilized cells. In operation the activity of the bioreactor was in accordance with that predicted mathematically, within 10%. The initial tests were done at neutral pH, whereas the pH of industrial wastewaters is often low; an increase in the  Km app.  at low pH was found in previous studies. Immobilized cells were challenged with acidic mine drainage wastewaters, where the limiting factors were chemical and not biochemical. Bioreactors initially lost activity in this water, but recovered to remove uranyl ion with more than 70% efficiency under steady’state conditions in the presence of competing cations and anions. Possible reasons for the bioreactor recovery are chemical crystallization factors.

Link:  https://onlinelibrary.wiley.com/doi/epdf/10.1002/%28SICI%291097-0290%2819970105%2953%3A1%3C100%3A%3AAID-BIT13%3E3.0.CO%3B2-S

Citation:  Fernando I. Ramírez-Paredes,  Teresa Manzano-Muñoz,  Juan C. Garcia-Prieto,  Galina G. Zhadan,  Valery L. Shnyrov,  John F. Kennedy and  Manuel G. Roig,  Biosorption of heavy metals from acid mine drainage onto biopolymers (chitin and α (1,3) β-D-glucan) from industrial biowaste exhausted brewer’s yeasts (Saccharomyces cerevisiae L.),  Biotechnology and Bioprocess Engineering,16, 6,  (1262)

 

This is an old paper from mid 90’s that gives us an insight on how heavy metals are removed from wastewater by immobilized cells. I found this paper interesting because it explained the chemistry of enzymes secreted by microbes pretty well.

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Biodegradation and removal of pharmaceuticals and personal care products in treatment systems: a review

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Abstract:
Pharmaceuticals and personal care products (PPCPs) have been the focus of much recent research as concerns rise about their occurrence in bodies of water worldwide. In an effort to characterize the risk and determine the prevalence of these micropollutants in lakes and rivers, many researchers are examining PPCP removal from impaired water during wastewater treatment and water recycling (soil passage) processes. Biodegradation studies and projects considering combinations of biodegradation and other removal processes have been conducted over a wide range of compound categories and therapeutic classes, as well as across different systems and scales of study. This review summarizes the extent of PPCP removal observed in these various systems.

Link:  https://link.springer.com/article/10.1007%2Fs10532-008-9237-8

Citation:

Ladislav Mandaric, Elena Diamantini, Elisa Stella, Karina Cano-Paoli, Jennifer Valle-Sistac, Daniel Molins-Delgado, Alberto Bellin, Gabriele Chiogna, Bruno Majone, M. Silvia Diaz-Cruz, Sergi Sabater, Damia Barcelo and Mira Petrovic

Journal:  Science of The Total Environment, 2017, Volume 590-591, Page 484

DOI:  10.1016/j.scitotenv.2017.02.185

I chose this article because in our recent trip to WWTP, we discussed about these micropollutants present in water and the challenges that WWTP has to face in removing them.

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Effects of storage of a mature compost on its potential for biodegradation of plastics

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Yang, H. S., Yoon, J. S., & Kim, M. N. (2004). Effects of storage of a mature compost on its potential for biodegradation of plastics. Polymer Degradation and Stability, 84(3), 411—417.

Link:  https://doi.org/10.1016/j.polymdegradstab.2004.01.014

Abstract

Biodegradation of plastics was tested in the compost stored at −20   °C, 4   °C and 20   °C for different periods. Viable cells in the compost stored at −20   °C were expected to be fewer than those in the compost stored at 4   °C and 20   °C, because microbes may be under stress or even be killed due to the formation of ice crystals at the subzero temperature. Mesophilic bacteria and mesophilic actinomycetes were fewer in number in the compost stored at 20   °C than in the compost stored at the other two lower temperatures contrary to expectation. In contrast, both thermophilic bacteria and thermophilic actinomycetes were fewest in the compost stored at −20   °C as was expected, indicating that thermophilic microbes were more susceptible to stress in the freezing conditions than the mesophilic ones. Activity of the exo-enzymes plausibly excreted by the microbes in the compost decreased as a result of the storage. Nevertheless, biodegradation of cellulose in the compost was almost independent of the storage time and temperature. In contrast, biodegradability of both polycaprolactone (PCL) and poly(butylene succinate) (PBS) depended strongly on the storage conditions. From the point of view that the existing standards for biodegradation tests of plastics in compost accept reproducibility of cellulose biodegradability as a criterion for the validity of the biodegradation tests, a new standard of the compost preparation should be provided to guarantee more reliable results on the biodegradability of plastics.

I thought this paper seemed interesting, mostly because I have never thought  of how compost could biodegrade plastic, and I thought it would be an interesting topic to learn more about, because of the large amount of plastic that we use nowadays.

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Phenol biodegradation by halophilic archaea

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https://www.sciencedirect.com/science/article/pii/S0964830515301384

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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ABSTRACT
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.

Justification:
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).

The effects of fluoride based fire-fighting foams on soil microbiota activity and plant growth during natural attenuation of perfluorinated compounds

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Considering the multiple sites around the greater Fairbanks area that have been found to have PFC contamination, I thought it would be of interest to learn  more about  the subject.  PFC’s are an emerging contaminant that do not readily biodegrade.

Abstract: The use of fluoride based foams increases the effectiveness of fire-fighting operations, but they are also accompanied by major drawbacks regarding environmental safety of perfluorinated compounds (PFCs). The main concern with PFCs release is due to their well-known persistence and bioaccumulative potential, as they have been detected in many environmental samples. There is a significant knowledge gap on PFC toxicity to plants, even though such data could be useful towards bioremediation procedures. It is consensus that a realistic assessment of fire-fighting foam toxicity should cover as many test organisms as possible, however, few studies combine the performance of ecotoxicological tests with a detailed study of microbial communities in soil contaminated with firefighting foams. Our research evaluated the effects of natural attenuation of PFCs on the development of arugula and lettuce seeds. The effects of variable PFCs amounts were also observed in soil microbiota using the 2,6 dichlorophenol-indophenol redox dye as microbial metabolism indicator. We aimed to determine whether aqueous film forming foams toxicity increased or decreased over time in a simulated contamination scenario. We argued that the long-term biotransformation of fire-fighting foams should be taken in to account when evaluating toxicity, focusing on a time-based monitoring analysis, since potentially toxic intermediates may be formed though biodegradation. The phyto-toxicity of PFCs to lettuce and arugula was high, increasing as a function of the concentration and decreasing as a function of exposure time to the environment. However, very specific concentrations throughout biodegradation result in the formation of non-inhibiting intermediates. Therefore, variable biodegradation-dependent germination rates may be misleading on non-time-based monitoring approaches. Also, the low phyto-toxicity after 240 days does not exclude the potential for PFC bioaccumulation in plants. We also proposed that the colorimetric data modelling could also establish a novel toxicity parameter to evaluate the release impacts to soil and biota. The combined assays allowed the monitoring of PFCs during long-term exposition to plants as well as their immediate effects on the same soil microbiota.

Citation: Renato Nallin Montagnolli, Paulo Renato Matos Lopes, Jaqueline Matos Cruz, Elis Marina Turini Claro, Gabriela Mercuri Quiterio, Ederio Dino Bidoia,
The effects of fluoride based fire-fighting foams on soil microbiota activity and plant growth during natural attenuation of perfluorinated compounds,
Environmental Toxicology and Pharmacology, Volume 50, 2017, Pages 119-127, ISSN 1382-6689, https://doi.org/10.1016/j.etap.2017.01.017.

Link: https://www.sciencedirect.com/science/article/pii/S138266891730025X

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Biodegradation nomination

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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.

Abstract:

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.

Justification:

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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Bio-remediation

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The purpose of this paper was to illustrate the effectiveness of anoxic bioremediation of tanker fuel in anoxic marine sediments. The consumption of hydrocarbons and other aromatic compounds is typically an oxic process an is quickly limited as oxygen is consumed as a terminal electron acceptor. After a period of time naturally induced bioremediation ceases, typically around nine weeks. Using a tank modeling anoxic sludge and a Modular Slurry System for aeration, this study continued to process of bioremediation. Not surprisingly samples that were treated with the MSS were substantially closer to the original microbiota as opposed to the samples that were not aerated.

I chose this paper because I thought it would be interesting to find cases of anoxic bioremediation. However most papers were not free and I did not have access to any of them. Ironically the only free paper I could find is misleading because it is aerating anoxic environments. That being said, while this paper does not bring anything crazy to the table, I am a sucker for completion and I appreciated seeing the limitations of current bioremedation methods as well as how we can circumvent them.

 

https://www.frontiersin.org/articles/10.3389/fmicb.2014.00162/full

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Biodegradation of imidazolium ionic liquids by activated sludge microorganisms

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Biodegradation of imidazolium ionic liquids by activated sludge microorganisms
Abstract
Biological properties of ionic liquids (ILs) have been usually tested with the help of standard biodegradation or ecotoxicity tests. So far, several articles on the identification of intermediate metabolites of microbiological decay of ILs have been published. Simultaneously, the number of novel ILs with unrecognized characteristics regarding biodegradability and effect on organisms and environment is still increasing. In this work, seven imidazolium ionic liquids of different chemical structure were studied. Three of them are 1-alkyl-3-methyl-imidazolium bromides, while the other four are tetra- or completely substituted imidazolium iodides. This study focused on the identification of intermediate metabolites of the aforementioned ionic liquids subjected to biodegradation in a laboratory activated sludge system. Both fully substituted ionic liquids and 1-ethyl-3-methyl-imidazolium bromide were barely biodegradable. In the case of two of them, no biotransformation products were detected. The elongation of the alkyl side chain made the IL more susceptible for microbiological decomposition. 1-Decyl-3-methyl-imidazolium bromide was biotransformed most easily. Its primary biodegradation up to 100 % could be achieved. Nevertheless, the cleavage of the imidazolium ring has not been observed.
I thought that this paper would be fun to examine since the methods of wastewater treatment is such an important topic to society.
Liwarska-Bizukojc E, Maton C, Stevens CV. Biodegradation of imidazolium ionic liquids by activated sludge microorganisms. Biodegradation. 2015;26(6):453-463. doi:10.1007/s10532-015-9747-0.

Fungal- Driven Biodegradation

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“A New Perspective on Sustainable Soil Remediation–Case Study Suggests Novel Fungal Genera Could Facilitate  in situ  Biodegradation of Hazardous Contaminants”

Citation

Czaplicki, L. M., Cooper, E., Ferguson, P. L., Stapleton, H. M., Vilgalys, R., & Gunsch, C. K. (2016). A New Perspective on Sustainable Soil Remediation-Case Study Suggests Novel Fungal Genera Could Facilitate in situ Biodegradation of Hazardous Contaminants.  Remediation,  26(2), 59—72. https://doi.org/10.1002/rem.21458

Abstract

“Deciding upon a cost effective and sustainable method to address soil pollution is a challenge for many remedial project managers. High pressure to quickly achieve cleanup goals pushes for energy-intensive remedies that rapidly address the contaminants of concern with established technologies, often leaving little room for research and development especially for slower treatment technologies, such as bioremediation, for the more heavily polluted sites. In the present case study, new genomic approaches have been leveraged to assess fungal biostimulation potential in soils polluted with particularly persistent hydrophobic contaminants. This new approach provides insights into the genetic functions available at a given site in a way never before possible. In particular, this article presents a case study where next generation sequencing (NGS) has been used to categorize fungi in soils from the Atlantic Wood Industries Superfund site in Portsmouth, Virginia. Data suggest that original attempts to harness fungi for bioremediation may have focused on fungal genera poorly suited to survive under heavily polluted site conditions, and that more targeted approaches relying on native indigenous fungi which are better equipped to survive under site specific conditions may be more appropriate.”

Justification

I thought this was unique because we haven’t had any papers discussing fungi this semester.