User talk:Ayserdo/sandbox

Critique of the article "Microbial Loop"

The article provided substantial amount of information on the topic, and contradictory to the lack of comments on the ‘talk’ page of the article there was many editions made, according to the history of the page, but nonetheless was rated as a 'start class' article, according to WikiProject Environment and WikiProject Microbiology, which indicates that the articles quality is not the best that it can be and needs more alterations to improve errors related to grammar and spelling errors. The style of in-text citations used by the author is different than the usual way wikipedia recommends its authors to use, and also was missing from several paragraphs to guide the readers to the source of the claims being made. There is mention of several processes such as viral infection and lytic pathway, which lack hyperlinks, making it challenging for readers to access the information to fully comprehend the article. The author also mentioned phenomena such as sloopy feeding and mucilaginous exopolymer in the first sentence of the 2nd paragraph, which he directly plagiarized from the book: 'Prescott's Principles of Microbiology', and did not even include it in the bibliography section. The figure used to visually represent the microbial loop include organisms such as mesoplankton, microplankton, nanoplankton and picoplanton, none of which mentioned in the article and for none of them links were provided for the author to learn about them.

Ayserdo (talk) 00:56, 17 September 2017 (UTC)

Assignment 2 - Article chosen: Co-metabolism
Co-metabolism is the term for the biological phenomena that occurs when an enzyme which is normally (intended to be) used to degrade a substrate to provide energy and/or use as a carbon source, is also able to transform another substrate which it cannot utilize as a carbon and/or energy source.

As some of the molecules that are the substrates of these reactions xenobiotic, persistent compounds, such as PCE, TCE and MTBE, that have harmful effects on several types of environments; it is important for the article to deliver accurate, updated information on how co-metabolism can be used as a bioremediation tool for it's ability to neutralize the toxicity of such compounds.

Although it is accurate like the article suggests that the presence of a primary molecule catabolism is necessary for a second compound to also go under reaction, this definition alone is ambiguous and does not explain enough about the process.

The article has several sentences with foul structures, and unexplained or loosely explained several biological phenomena such as ‘simultaneous metabolism’ ‘reductive chlorination’ and ‘commensal growth’.The present form of the article also lacks the information of where most of the statements made came from; thus making it hard for the readers to reach the source and confirm the validity of the assertions made.

Elucidating these phenomena both by giving specific examples of bacteria species and the types of hazardous molecules they co-metabolically transform, if this process is carried out using oxygen as a terminal electron acceptor or not, would help the readers get a better grasp of the subject. Ayserdo (talk) 00:02, 28 September 2017 (UTC)

Assignment 3 - Editing a Wikipedia Article: Co-metabolism
Original- "Cometabolism"

Co-metabolism is defined as the simultaneous degradation of two compounds, in which the degradation of the second compound (the secondary substrate) depends on the presence of the first compound (the primary substrate). This is in contrast to simultaneous catabolism, where each substrate is catabolized. For example, in the process of metabolizing methane, propane or simple sugars, some bacteria, such as Pseudomonas stutzeri OX1, can degrade hazardous chlorinated solvents, such as tetrachloroethylene and trichloroethylene, that they would otherwise be unable to attack. They do this by producing methane monooxygenase, an enzyme which is known to oxidize numerous compounds, including pollutants such as chlorinated solvents, via co-metabolism. Co-metabolism is thus used as an approach to biological degradation of hazardous solvents.

Another example is Mycobacterium vaccae, which uses an enzyme to oxidize propane. Accidentally, this enzyme also oxidizes, at no additional cost for M. vaccae, cyclohexane into cyclohexanol. Thus, cyclohexane is co-metabolized in the presence of propane. This allows for the commensal growth of Pseudomonas on cyclohexane. The latter can metabolize cyclohexanol, but not cyclohexane.

Another promising method of bioremediation of chlorinated solvents involves co-metabolism of the contaminants by aerobic microorganisms in groundwater and soils. Several aerobic microorganisms have been demonstrated to be capable of doing this, including methane oxidizers, phenol-degraders, and toluene-degraders. Unlike reductive dechlorination, the chlorinated compounds are completely mineralized to CO2 and chloride with no intermediates making co-metabolism an attractive alternative where it can be sustained. However, the microorganisms gain no energy from these processes, limiting the ability of cells to co-metabolize chlorinated compounds. This, together with the difficulties and high costs of maintaining substrate and an oxic environment, have led to limited field-scale application of co-metabolism for solvent degradation. Recently, this method of remediation has been improved by the substitution of cheap, nontoxic plant secondary metabolites in the place of synthetic, toxic aromatics like toluene .

Edit- “Cometabolism"

Cometabolism is defined as the simultaneous degradation of two compounds, in which the degradation of the second compound (the secondary substrate) depends on the presence of the first compound (the primary substrate). This shouldn’t be confused with simultaneous catabolism, where each substrate is catabolized concomitantly by different enzymes. Cometabolism occurs when an enzyme produced by an organism to catalyze the degradation of it's growth substrate to derive energy and carbon from it is also capable of degrading additional compounds. The fortituous degradation of these additional compounds does not support the growth of the bacteria, and some of these compounds can even be toxic in certain concentrations and limit the growth of the bacteria.

The first report of this phenomena was the degredation of ethene by the species Pseudomonas methanica.These bacteria degrade their growth-substrate methane with the enzyme methane monooxygenase(MMO). MMO was discovered to be capable of catalyzing the degradation ethene and propene, although the bacteria were unable to use these compounds as energy and carbon sources to grow.

Another example is Mycobacterium vaccae, which uses an alkane monooxygenase enzyme to oxidize propane. Accidentally, this enzyme also oxidizes, at no additional cost for M. vaccae, cyclohexane into cyclohexanol. Thus, cyclohexane is co-metabolized in the presence of propane. This allows for the commensal growth of Pseudomonas on cyclohexane. The latter can metabolize cyclohexanol, but not cyclohexane.

Cometabolism in Bioremediation
Some of the molecules that are cometabolically degraded by bacteria are xenobiotic, persistent compounds, such as PCE, TCE, and MTBE, that have harmful effects on several types of environments. Co-metabolism is thus used as an approach to biologically degrade hazardous solvents.

For instance, cometabolism can be used for the biodegradation of the pollutant methyl-tert-butyl ether (MTBE): a chemical synthesized by the use of fossil fuels and that is toxic to both ground and underground aqueous environments. Pseudomonas aeruginosa and Pseudomonas citronellolis were shown to be able to carry out the cometabolic degradation of MTBE and fully degrade it by using their enzymes that have a physiological role of oxidizing, n-alkane (e.g. methane, propane) to utilize them as growth sources.

Additionally, a promising method of bioremediation of chlorinated solvents involves cometabolism of the contaminants by aerobic microorganisms in groundwater and soils. Several aerobic microorganisms have been demonstrated to be capable of doing this, including n-alkane, aromatic compound (e.g. toluene, phenol) and ammonium oxidizers.

One example is Pseudomonas stutzeri OX1, which can degrade a hazardous, and water soluble water-soluble compound tetrachloroethylene (PCE). PCE, one of the major underground water contaminants, was regarded as being undegradable under aerobic conditions and only degraded by reductive dehalogenation to be used as a growth substrate by organisms. Reductive dehalogenation often results in the partial dechlorination of the PCE, which results in toxic and/or carcinogenic compounds such as TCE, DCE, and Vinyl Chloride. Pseudomonas st. OX1, on the other hand, degrade PCE by using toluene-o-xylene monooxygenase (ToMO), an enzyme they produce to degrade toluene and several other aromatic compounds to derive energy and carbon from them. Thus, cometabolism poses as an potential pathway to remove PCE from polluted sites.

The difficulties and high costs of maintaining the growth-substrates of the organisms capable of cometabolising these hazardous compounds and providing them an aerobic environment have led to the limited field-scale application of co-metabolism for pollutant solvent degradation. Recently, this method of remediation has been proposed to be improved by the substitution of the synthetic aromatic growth-substrates (e.g. toluene) of these bacteria with cheap, non-toxic plant secondary metabolites. This would allow the cometabolism of the pollutant cDCE (cis-1,2-dichloroethene) while taking away the requirement of adding toxic growth-substrates of the bacteria to the environment in the need of bioremediation.

Ayserdo (talk) 23:54, 18 November 2017 (UTC)

Ayse's Peer Review
The edited article is generally structured well. The choice to create an additional subheading for co metabolism in bioremediation improves the flow of the article and makes it easier to follow. Also breaking the lead paragraph into two makes sense as it did make sense to have them in the same paragraph.

The structure could be improved by moving the last paragraph about hazardous solvents into the bio remediation section. Not only does this fit better in that section but the paragraph also acts as good introduction for the following content.

The added content does a good job of providing more examples of using co metabolism to degrade hazardous chemicals. However, in the paragraph about P. Stutzeri OX1, the article states the enzyme used is methane monooxygenase but the cited source says the enzyme used is toluene-o-xylene monooxygenase and does not mention oxidation of methane at all. This should be changed to represent the cited literature accurately. Also it would be good to mention that the process occurs aerobically to give the reader a better idea of how the process works.

The references used are from reliable journals and are equally represented in the content. The content from reference 14 talks about replacing toluene with cheap plant secondary metabolites but not much context is provided about using toluene and other aromatics. The article should elaborate on the use of these compounds and their limitations before talking about better alternatives.

Finally, there are several sentences that are confusing and should be reworded. For example, in the first paragraph the second last sentence could be reworded as such: “Co-metabolism occurs when an organism produces an enzyme that can degrade a second compound in addition to the original substrate that is used as an energy and carbon source.” The second paragraph under bio remediation can also be made more concise. The last sentence of the third paragraph also needs rewording as the last part of it is confusing.

Malhar97 (talk) 05:37, 9 November 2017 (UTC)