Contaminants Round 2

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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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Bio-remediation

Posted by On Filed under Biodegradation and bioremediation papers No Comments

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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2nd Biogeo/wastewater paper

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“Clouds are key components in Earth’s functioning. In addition of acting as obstacles to light radiations and chemical reactors, they are possible atmospheric oases for airborne microorganisms, providing water, nutrients and paths to the ground. Microbial activity was previously detected in clouds, but the microbial community that is active  in situ  remains unknown. Here, microbial communities in cloud water collected at puy de Dôme Mountain’s meteorological station (1465 m altitude, France) were fixed upon sampling and examined by high-throughput sequencing from DNA and RNA extracts, so as to identify active species among community members. Communities consisted of ~103−104  bacteria and archaea mL-1and ~102−103  eukaryote cells mL-1. They appeared extremely rich, with more than 28 000 distinct species detected in bacteria and 2 600 in eukaryotes. Proteobacteria and Bacteroidetes largely dominated in bacteria, while eukaryotes were essentially distributed among Fungi, Stramenopiles and Alveolata. Within these complex communities, the active members of cloud microbiota were identified as Alpha- (Sphingomonadales, Rhodospirillales and Rhizobiales), Beta- (Burkholderiales) and Gamma-Proteobacteria (Pseudomonadales). These groups of bacteria usually classified as epiphytic are probably the best candidates for interfering with abiotic chemical processes in clouds, and the most prone to successful aerial dispersion.”

Summary:  We have long known about the microbial presence within clouds but until recently most of our data has been a result of cell culturing which as we all know: may not be representative of the microbial community. This study via the use of 16s amplicon sequencing sought to define both the taxonomic identity and microbial activity via extracted DNA and RNA respectively. Atmospheric samples were taken periodically above France via a modified weather probes. Each sample was screened for the relative amount of industrial contaminants to serve as a comparison to the negative control. This study found that on average 11000 to 21000 distinct OTUs which is comparable to that of a typical soil sample. Prokaryotes made up the majority of the sample with low amounts of eukaryotic fungal populations also being present.  The source of this diversity has been attributed to aerosols particulate products that resulted from saphorytes. The Microbial richness of the aforementioned microbes was more pronounced in the contaminated samples. Between all the samples it was evident that the metabolic functions of these microbes were important for many hydrological mechanisms such as ice nucleation and ion mediated chemistry reactions which aid in both the formation of water droplets and the act of precipitation respectively. The microbiome of the cloud was found to be variable depending on the location and sensitive to changes in resources (such as industrial contaminants, temperature and topography) so further study should be allocated to defining, and in the far future, altering the clouds’ microbiome.

I chose this article because I honestly had never thought about the microbiome of clouds before and I think it is crazy when scientific papers just blow my mind with something I never considered before

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Amato P, Joly M, Besaury L, Oudart A, Taib N, Moné AI, et al. (2017) Active microorganisms thrive among extremely diverse communities in cloud water. PLoS ONE 12(8): e0182869. https://doi.org/10.1371/journal.pone.0182869

Thinglink Ind. Post A.W

Posted by On Filed under Microbial Community Thinglink individual posts No Comments

Technical

We have long known about the microbial presence within clouds but until recently most of our data has been a result of cell culturing which as we all know: may not be representative of the microbial community. This study via the use of 16s amplicon sequencing sought to define both the taxonomic identity and microbial activity via extracted DNA and RNA respectively. Atmospheric samples were taken periodically above France via a modified weather probes. Each sample was screened for the relative amount of industrial contaminants to serve as a comparison to the negative control. This study found that on average 11000 to 21000 distinct OTUs which is comparable to that of a typical soil sample. Prokaryotes made up the majority of the sample with low amounts of eukaryotic fungal populations also being present. The source of this diversity has been attributed to aerosols particulate products that resulted from saphorytes. The Microbial richness of the aforementioned microbes was more pronounced in the contaminated samples. Between all the samples it was evident that the metabolic functions of these microbes were important for many hydrological mechanisms such as ice nucleation and ion mediated chemistry reactions which aid in both the formation of water droplets and the act of precipitation respectively. The microbiome of the cloud was found to be variable depending on the location and sensitive to changes in resources (such as industrial contaminants, temperature and topography) so further study should be allocated to defining, and in the far future, altering the clouds’ microbiome.

Basic

Recent studies have suggested that clouds could could act as a catalyst for environmental change. In fact the sheer abundance of microbes housed within a typical cloud is comparable to your everyday sample of dirt. Many of these microbes are important for key functions of the water cycle such as: aiding in the formation of water droplets, the initiation of precipitation and others. In fact, some of these microbial players have been shown to be partly responsible for the acceleration of climate change via the depletion of ozone. Indeed even bacteria which are responsible for creating methane, a potent greenhouse gas, were found in the clouds themselves, further aggravating climate change. While we have always known that there are microbes in the air, and by extension the clouds, we were ignorant as a species to the sheer magnitude and richness of the cloud microbiome. Above us in the skies are basically wastewater treatment plants that filter and control the flow of Earth’s lifeblood: water. Equipped with a better understanding of the microbial presence and hydrological implication there-in, mankind has made a significant step towards altering our weather and water cycles and perhaps in the far future this research could serve as the backbone of space exploration as we flush out variables involved in terraforming.

Pictures on my thing-link: compliments of Sophie

Biogeo. cycle A.W

Posted by On Filed under Biogeochemical cycling papers No Comments

“Clouds are key components in Earth’s functioning. In addition of acting as obstacles to light radiations and chemical reactors, they are possible atmospheric oases for airborne microorganisms, providing water, nutrients and paths to the ground. Microbial activity was previously detected in clouds, but the microbial community that is active  in situ  remains unknown. Here, microbial communities in cloud water collected at puy de Dôme Mountain’s meteorological station (1465 m altitude, France) were fixed upon sampling and examined by high-throughput sequencing from DNA and RNA extracts, so as to identify active species among community members. Communities consisted of ~103−104  bacteria and archaea mL-1and ~102−103  eukaryote cells mL-1. They appeared extremely rich, with more than 28 000 distinct species detected in bacteria and 2 600 in eukaryotes. Proteobacteria and Bacteroidetes largely dominated in bacteria, while eukaryotes were essentially distributed among Fungi, Stramenopiles and Alveolata. Within these complex communities, the active members of cloud microbiota were identified as Alpha- (Sphingomonadales, Rhodospirillales and Rhizobiales), Beta- (Burkholderiales) and Gamma-Proteobacteria (Pseudomonadales). These groups of bacteria usually classified as epiphytic are probably the best candidates for interfering with abiotic chemical processes in clouds, and the most prone to successful aerial dispersion.”

Summary:  We have long known about the microbial presence within clouds but until recently most of our data has been a result of cell culturing which as we all know: may not be representative of the microbial community. This study via the use of 16s amplicon sequencing sought to define both the taxonomic identity and microbial activity via extracted DNA and RNA respectively. Atmospheric samples were taken periodically above France via a modified weather probes. Each sample was screened for the relative amount of industrial contaminants to serve as a comparison to the negative control. This study found that on average 11000 to 21000 distinct OTUs which is comparable to that of a typical soil sample. Prokaryotes made up the majority of the sample with low amounts of eukaryotic fungal populations also being present.  The source of this diversity has been attributed to aerosols particulate products that resulted from saphorytes. The Microbial richness of the aforementioned microbes was more pronounced in the contaminated samples. Between all the samples it was evident that the metabolic functions of these microbes were important for many hydrological mechanisms such as ice nucleation and ion mediated chemistry reactions which aid in both the formation of water droplets and the act of precipitation respectively. The microbiome of the cloud was found to be variable depending on the location and sensitive to changes in resources (such as industrial contaminants, temperature and topography) so further study should be allocated to defining, and in the far future, altering the clouds’ microbiome.    

Amato P, Joly M, Besaury L, Oudart A, Taib N, Moné AI, et al. (2017) Active microorganisms thrive among extremely diverse communities in cloud water. PLoS ONE 12(8): e0182869. https://doi.org/10.1371/journal.pone.0182869

Assignment Al Intro Post A.W

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Frozen Deep Beneath

Ancient Microbes Slumber Deep

Waiting To Be Free

Image result for microbe jokes

My name is Alex Wynne, I am a senior studying molecular biology. I love Hawaii and all the things you can do there (I was born there; on a coffee farm actually) but seeing that I am here, I lack the colloquial hobbies that should be expected from an Alaskan making me, as a result, rather dull. This is where science comes in; I do not know what I am going to do with my career but flushing out the finer points of reality seems a good a cause as any (plus its pretty exciting). In the past I have researched the interaction between the permafrost gradient and its respective microbial population in response to the changing seasons. Microbes can provide novel solutions to disasters but also cause devastating harm. Understanding how microbes, which interact with everything around-and inside of us, is important. So that is why I am here and I look forward to having class with all of you.