Oil Biodegradation and Bioremediation: A Tale of the Two Worst Spills in U.S. History

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“Oil Biodegradation and Bioremediation: A Tale of the Two Worst Spills in U.S. History”

Atlas, R. M., & Hazen, T. C. (2011). Oil biodegradation and bioremediation: A tale of the two worst spills in U.S. history.  Environmental Science and Technology,  45(16), 6709—6715. https://doi.org/10.1021/es2013227

Abstract
“The devastating environmental impacts of the Exxon Valdez spill in 1989 and its media notoriety made it a frequent comparison to the BP Deepwater Horizon spill in the popular press in 2010, even though the nature of the two spills and the environments impacted were vastly different. Fortunately, unlike higher organisms that are adversely impacted by oil spills, microorganisms are able to consume petroleum hydrocarbons. These oil degrading indigenous microorganisms played a significant role in reducing the overall environmental impact of both the Exxon Valdez and BP Deepwater Horizon oil spills.”

Justification
This is a cool feature, it summarizes the bioremediation efforts for both the Exxon Valdez and Deepwater Horizon oil spills. We have discussed story format a lot this semester and this article claims that it is presenting a “tale”, so we could assess the quality of storytelling.

The Ferrous Wheel: A Perspective on the Iron Cycle

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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?

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.

 

Coal Mine Wastewater Microbial Communities

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“Identification of the microbial community composition and structure of coal-mine wastewater treatment plants”

 

Abstract

The wastewater from coal-mine industry varies greatly and is resistant to biodegradation for containing large quantities of inorganic and organic pollutants. Microorganisms in activated sludge are responsible for the pollutants’ removal, whereas the microbial community composition and structure are far from understood. In the present study, the sludges from five coal-mine wastewater treatment plants were collected and the microbial communities were analyzed by Illumina high-throughput sequencing. The diversities of these sludges were lower than that of the municipal wastewater treatment systems. The most abundant phylum was Proteobacteria ranging from 63.64% to 96.10%, followed by Bacteroidetes (7.26%), Firmicutes (5.12%), Nitrospira (2.02%), Acidobacteria (1.31%), Actinobacteria (1.30%) and Planctomycetes (0.95%). At genus level, Thiobacillus and Comamonas were the two primary genera in all sludges, other major genera included Azoarcus, Thauera, Pseudomonas, Ohtaekwangia, Nitrosomonas and Nitrospira. Most of these core genera were closely related with aromatic hydrocarbon degradation and denitrification processes. Identification of the microbial communities in coal-mine wastewater treatment plants will be helpful for wastewater management and control.

Citation

Ma, Q., Qu, Y. Y., Zhang, X. W., Shen, W. L., Liu, Z. Y., Wang, J. W., … Zhou, J. T. (2015). Identification of the microbial community composition and structure of coal-mine wastewater treatment plants.  Microbiological Research,  175, 1—5. https://doi.org/10.1016/j.micres.2014.12.013

link

Justification

Interesting industrial perspective of wastewater. Paper applies some of the microbial community methods we have discussed in class.

Biogeochemical Cycling of Gold [Repost]

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“Bacterial biofilms on gold grains–implications for geomicrobial transformations of gold”

ABSTRACT

The biogeochemical cycling of gold (Au), i.e. its solubilization, transport and re-precipitation, leading to the (trans)formation of Au grains and nuggets has been demonstrated under a range of environmental conditions. Biogenic (trans)formations of Au grains are driven by (geo)biochemical processes mediated by distinct biofilm consortia living on these grains. This review summarizes the current knowledge concerning the composition and functional capabilities of Au-grain communities, and identifies contributions of key-species involved in Au-cycling. To date, community data are available from grains collected at 10 sites in Australia, New Zealand and South America. The majority of detected operational taxonomic units detected belong to the α-, β- and γ -Proteobacteria and the Actinobacteria. A range of organisms appears to contribute predominantly to biofilm establishment and nutrient cycling, some affect the mobilization of Au via excretion of Au-complexing ligands, e.g. organic acids, thiosulfate and cyanide, while a range of resident Proteobacteria, especially Cupriavidus metallidurans and Delftia acidovorans, have developed Au-specific biochemical responses to deal with Au-toxicity and reductively precipitate mobile Au-complexes. This leads to the biomineralization of secondary Au and drives the environmental cycle of Au.

 

CITATION

Rea, M. A., Zammit, C. M., & Reith, F. (2016, June 1). Bacterial biofilms on gold grains-implications for geomicrobial transformations of gold.  FEMS Microbiology Ecology. Oxford University Press. https://doi.org/10.1093/femsec/fiw082.

Link

 

JUSTIFICATION

Gold- a precious metal, revered since antiquity, mined on every continent (except Antartica)- is important to society. Previously, gold was thought to be biologically inactive but this is now known to be untrue. Discover more about what microbes can do with gold.

 

Microbial Communities: Built Environment Non-Technical Summary

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Non-Technical Summary

Humans spend most of their time inside buildings- that includes the time they spend in the hospital. Hospitals are a hub for not only sick patients, but healthcare workers and visitors. As a high-traffic area, the types of bacteria growing in a hospital are constantly fluctuating. This growth is only exacerbated by the bacteria lent to the environment by the sick patients. The conditions that impact how microbes spread in a hospital are important to understand so a patient doesn’t come down with a new disease while being treated for something unrelated. Researchers from the University of Chicago spent over a year sampling what bacteria were growing throughout a new hospital and on patients- and they found some surprising results.  When a new patient was admitted to the hospital, the bacteria of the room they were staying in quickly came to resemble the patient. This trend was most obvious on surfaces that a patient would often touch- like a bedrail. Results from DNA sequencing showed that antimicrobial resistance was also present. However, bacteria with resistances to drugs were more likely to be found on the hospital surfaces rather than living on the skin of patients or staff. Researchers also found that certain patients had fewer microbes on themselves and their surroundings. In particular, chemotherapy patients had fewer different types of microbes. This study concluded that humans are the biggest factor for what microbes are living in buildings. Further research should spend more time looking for trends in microbial transfer within hospitals and for deciding what can be done to present a healthy hospital.

Source
S. Lax, et al., Bacterial colonization and succession in a newly opened hospital. Sci. Transl. Med. 9, eaah6500, (2017), https://dx.doi.org/10.1126/scitranslmed.aah6500.

Microbial Communities: Built Environment Technical Summary

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Technical Summary  

The microbiome of the built environment has implications for human health. Understanding what influences the presence, spread and colonization of microbes in the built environment is necessary for preventing disease stemming from the microbial population in homes, workplaces, and hospitals. Furthermore, the risk of hospital-acquired infections is a growing concern as effective treatments for antibiotic-resistant bacteria increases. In order to identify the risk and spread of infection in a hospital preliminary research about the hospital microbiome is required. Lax et al. conducted a longitudinal study in a newly- opened hospital. They sampled the hospital surfaces, patients and staff. Abiotic factors, such as light, temperature and humidity, were also tracked for potential influence on bacterial transmission.  Microbial communities from pre-opening and post- opening were highly distinct suggesting that human presence was highly influential of the built environment microbiome. When a patient was admitted, their skin microbiome was transferred to the surfaces in their room. Metagenomic characterization showed that antimicrobial resistance genes were more likely to be found on surfaces than skin. In this study, there were no correlations found between the abiotic factors measured and the transmission of microbes. Researchers correlated chemotherapy treatment in patients with a lower alpha diversity in the patient’s nose, hand, and bedrail. The conclusions from this study showed that patient skin is clearly a vector for the hospital microbiome.

 

Source
S. Lax, et al., Bacterial colonization and succession in a newly opened hospital. Sci. Transl. Med. 9, eaah6500, (2017), https://dx.doi.org/10.1126/scitranslmed.aah6500.

Biogeochemical Cycling of Gold

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“Bacterial biofilms on gold grains–implications for geomicrobial transformations of gold”

ABSTRACT

The biogeochemical cycling of gold (Au), i.e. its solubilization, transport and re-precipitation, leading to the (trans)formation of Au grains and nuggets has been demonstrated under a range of environmental conditions. Biogenic (trans)formations of Au grains are driven by (geo)biochemical processes mediated by distinct biofilm consortia living on these grains. This review summarizes the current knowledge concerning the composition and functional capabilities of Au-grain communities, and identifies contributions of key-species involved in Au-cycling. To date, community data are available from grains collected at 10 sites in Australia, New Zealand and South America. The majority of detected operational taxonomic units detected belong to the α-, β- and γ -Proteobacteria and the Actinobacteria. A range of organisms appears to contribute predominantly to biofilm establishment and nutrient cycling, some affect the mobilization of Au via excretion of Au-complexing ligands, e.g. organic acids, thiosulfate and cyanide, while a range of resident Proteobacteria, especially Cupriavidus metallidurans and Delftia acidovorans, have developed Au-specific biochemical responses to deal with Au-toxicity and reductively precipitate mobile Au-complexes. This leads to the biomineralization of secondary Au and drives the environmental cycle of Au.

 

CITATION

Rea, M. A., Zammit, C. M., & Reith, F. (2016, June 1). Bacterial biofilms on gold grains-implications for geomicrobial transformations of gold.  FEMS Microbiology Ecology. Oxford University Press. https://doi.org/10.1093/femsec/fiw082.

Link

 

JUSTIFICATION

Gold- a precious metal, revered since antiquity, mined on every continent (except Antartica)- is important to society. Previously, gold was thought to be biologically inactive but this is now known to be untrue. Discover more about what microbes can do with gold.

 

Assignment 1: Introduction

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Hot colors explode

Not from the rainbows or rocks

But microbes within

Grand Prismatic Spring, Midway Geyser, Yellowstone via  Ignacio Palacios  

Hi everyone,

My name is Courtney Hill.

My haiku was written with inspiration from the Grand Prismatic Spring (as pictured above). The bright colors are attributed to extremophile microbes that produce different pigments.

I’m a junior and my major is molecular biology. I am looking forward to this course for two main reasons:

  1. The emphasis on interdisciplinary applications of environmental microbiology. I think it is really cool there is a diverse range in the disciplines of students taking this class. It will be interesting to see ideas in biology from a different perspective.
  2. Promoting science communication through creative writing. I don’t spend a lot of time branching outside of technical writing, but creative writing is great. It is something I would like to dedicate more time to.

I’m always impressed by the wide-reaching impacts microbes have on every facet of life and I’m excited to learn even more.