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Critique: Phototroph[1]

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The history section of the article is extremely barebones. The author indicates that phototrophs used to have a different definition, but there is no sign of what this definition was exactly. The author does not indicate why Lwoff gave phototrophs its current definition. Overall, this section is redundant and should be removed. In the photoheterotroph section, it links to a separate article dedicated to photoheterotrophs. The author should either merge the phototroph article with photoheterotrophs or make a separate article to cover photoautotrophs. The article has very few citations to support its information. However, all the citations come from appropriate, well-respected sources, and the author presented the sources in a neutral manner. The 4th citation is placed in the middle of a sentence, which makes it difficult to determine what exactly is being sourced. The author appears to have paraphrased the citations in an original manner. In the talk page of the article, it is indicated that this article is rated “Start Class” on the quality scale. This indicates that the article is lacking in content and sources. In the talk page, there seems to have been some conversations between multiple editors, and some changes proposed by the editors in the talk page has been implemented in the main article. The revision history page indicates that many people have worked on the article, reducing the risk of the article having individual bias. Jefft97 (talk) 03:46, 18 September 2017 (UTC)

Critique: Rhodococcus[2]

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This article was selected because of its relevance to my current microbiology courses, and because it is considered start class. Rhodococci have the capability to degrade certain hydrocarbons, and they tend to grow naturally in polluted environments, and they have specialized physiological features that allow them to live in niche environments, therefore Rhodococci may have to potential to be used in bioremediation[3]. The article was rated low importance, but I believe that there is a good supply of reliable, relevant sources that can be used to supplement any assertions stated in the article. I am to focus most of my edits on the section regarding the biodegradation of organic pollutants, as that section is most relevant to my studies. The section detailing the biodegradation of organic pollutants relies on too few sources, which may lead to a bias towards a certain viewpoint. I will need to find additional sources that can supplement the article’s claims. One source was published in 1998, and there might be certain information that may have been updated since then, so I will need to verify the accuracy of the information by referencing it with a more up to date source. The first part of the section is a near complete copy of its source, so it must be paraphrased to be more original. There is a poor transition from the claims of the first source to the claims of the second source, so the second claim should probably be placed in a different paragraph to separate the two ideas. The section also does not delve into the specific features that allow Rhodococci to survive harsh conditions, so that is something that I should consider including in the article. The article also does not cover how Rhodococci may be used for industrially significant chemicals such as PCBs.

Jefft97 (talk) 05:25, 28 September 2017 (UTC)

Original - Rhodococcus

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Biodegradation of organic pollutants

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The burgeoning amount of bacterial genomic data provides unparalleled opportunities for understanding the genetic and molecular bases of the microbial biodegradation of organic pollutants. Aromatic compounds are among the most recalcitrant of these pollutants, and lessons can be learned from the recent genomic studies of R. jostii RHA1, one of the largest bacterial genomes completely sequenced to date. These studies have helped expand the understanding of bacterial catabolism, noncatabolic physiological adaptation to organic compounds, and the evolution of large bacterial genomes. A large number of "peripheral aromatic" pathways funnel a range of natural and xenobiotic compounds into a restricted number of "central aromatic" pathways. Some pathways are more widespread than initially thought. The Box and Paa pathways illustrate the prevalence of nonoxygenolytic ring-cleavage strategies in aerobic aromatic degradation processes. Functional genomic studies have been useful in establishing that even organisms harboring high numbers of homologous enzymes apparently contain few examples of true redundancy. For example, the multiplicity of ring-cleaving dioxygenases in certain rhodococcal isolates may be attributed to the cryptic aromatic catabolism of different terpenoids and steroids. The large gene repertoires of pollutant degraders such as R. jostii RHA1 have evolved principally through more ancient processes.[4] Rhodococcus sp. strain Q1 (American Type Culture Collection strain number 49988), isolated from soil and paper mill sludge, is able to degrade quinoline, various pyridine derivatives, catechol, benzoate, and protocatechuic acid.[5]

Edited - Rhodococcus

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Biodegradation of organic pollutants

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Rhodococcus has been greatly researched as a potential agent for the bioremediation of pollutants as it is commonly found in the natural environment, and they possess certain characteristics that allow them to thrive under a variety of conditions, and they have the capability to metabolize many hydrocarbons.[6]

Rhodococci possess many properties that makes them suitable for bioremediation under a range of environments.  Their ability to undergo microaerophilic respiration allows them to survive in environments containing low oxygen concentrations, and their ability to undergo aerobic respiration also allows them to survive in oxygenated environments[7]. They also undergo nitrogen fixation, which allows them to generate their own nutrients in environments with low nutrients.[8]

Rhodococci also contain characteristics that enhances their ability to degrade organic pollutants. Their hydrophobic surface allows for adhesion to hydrocarbons, which enhances its ability to degrade these pollutants.[9] They have a wide variety of catabolic pathways and many unique enzyme functions.[10] This gives them the ability to degrade many recalcitrant, toxic hydrocarbons. Rhodococcus sp. strain Q1, a strain naturally found in soil and paper mill sludge, contains the ability to degrade quinoline, various pyridine derivatives, catechol, benzoate, and protocatechuic acid.[11]

Jefft97 (talk) 06:31, 9 October 2017 (UTC)

Peer Review

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This is an excellent edit of the article because the author provided only relevant information and avoided using unnecessary scientific jargon. The original version was hard to read because all the information is crammed into one paragraph and contains numerous scientific jargon that may not be comprehensive to many readers. On the contrary, the edited version is divided into three paragraphs; the first paragraph gives the overview of the content and the following paragraphs provide support to the main points. The content flows smoothly through the three paragraphs. The author used comprehensive words and included all the relevant information about the biodegradation of organic pollutants by Rhodococcus in a concise manner. For example, the author mentioned that Rhodococci are capable of different respirations, which gives them the ability to degrade recalcitrant hydrocarbon pollutant under a wide range of environments. The article shows no bias and represents all viewpoints equally. Each paragraph has at least one citation and all the sources are properly cited from reputable and reliable scientific journals. After examining each citation, there is no evidence of plagiarism and close-paraphrasing, which indicates that the author has sufficient understanding of the topic.

To further improve the article, I would suggest that the author to go more in-depth on the various catabolic pathways that Rhodococci utilize to degrade recalcitrant toxic hydrocarbon. The original article states that Rhodococci express dioxygenases that play a big role in the degradation process. The author failed to include this crucial information. This improvement will allow the readers to understand how Rhodococci is different from other bacteria that are capable of biodegradation. Moreover, I would provide examples on how Rhodococci can be utilized on an industrial scale for the bioremediation of contaminated environment. For example, Rhodococci can be used for the cleanup of polluted groundwater and soil [12]. Overall, this is an outstanding edit that is well-structured. Micb301student (talk) 05:58, 9 November 2017 (UTC)


Final Edit - Rhodococcus

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Biodegradation of organic pollutants

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Rhodococcus has been greatly researched as a potential agent for the bioremediation of pollutants as it is commonly found in the natural environment, and they possess certain characteristics that allow them to thrive under a variety of conditions, and they have the capability to metabolize many hydrocarbons.[13]

Rhodococci possess many properties that makes them suitable for bioremediation under a range of environments. Their ability to undergo microaerophilic respiration allows them to survive in environments containing low oxygen concentrations, and their ability to undergo aerobic respiration also allows them to survive in oxygenated environments[14]. They also undergo nitrogen fixation, which allows them to generate their own nutrients in environments with low nutrients.[15]

Rhodococci also contain characteristics that enhances their ability to degrade organic pollutants. Their hydrophobic surface allows for adhesion to hydrocarbons, which enhances its ability to degrade these pollutants.[16] They have a wide variety of catabolic pathways and many unique enzyme functions.[17] This gives them the ability to degrade many recalcitrant, toxic hydrocarbons. For example, Rhodococci expresses dioxygenases, which can be used to degrade benzotrifluoride, a recalcitrant pollutant.[18] Rhodococcus sp. strain Q1, a strain naturally found in soil and paper mill sludge, contains the ability to degrade quinoline, various pyridine derivatives, catechol, benzoate, and protocatechuic acid.[19] Rhodococci are also capable of accumulating heavy metal ions, such as radioactive caesium, allowing for easier removal from the environment.[20] Other pollutants, such as azo dyes[21], pesticides[22] and polychlorinated biphenyls[23] can also be degraded by Rhodococci. Jefft97 (talk) 05:35, 20 November 2017 (UTC)

  1. ^ "Phototroph - Wikipedia".
  2. ^ "Rhodococcus- Wikipedia".
  3. ^ Bell, K. S.; Philp, J. C.; Aw, D.W.J.; Christofi, N. (1 August 1998). "The genus Rhodococcus". Journal of Applied Microbiology. 85 (2): 195–210. doi:10.1046/j.1365-2672.1998.00525.x. ISSN 1365-2672. PMID 9750292. S2CID 44605726.
  4. ^ McLeod MP, Eltis LD (2008). "Genomic Insights Into the Aerobic Pathways for Degradation of Organic Pollutants". Microbial Biodegradation: Genomics and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-17-2.
  5. ^ O'Loughlin, E.J.; Kehrmeyer, S.R.; Sims, G.K. (1996). "Isolation, characterization, and substrate utilization of a quinoline degrading bacterium". International Biodeterioration and Biodegradation. 38 (2): 107–118. doi:10.1016/S0964-8305(96)00032-7.
  6. ^ Alvarez, Héctor (2010). Biology of Rhodococcus. Springer Science & Business Media. pp. 231–256. ISBN 9783642129377.
  7. ^ Fuller, M.E.; Perreault, N. (July 8, 2010). "Microaerophilic degradation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by three Rhodococcus strains". Letters in Applied Microbiology. 51 (3): 313–318. doi:10.1111/j.1472-765X.2010.02897.x. PMID 20666987. S2CID 46159929 – via Wiley.
  8. ^ Blasco, Rafael (2001). "Rhodococcus sp. RB1 grows in the presence of high nitrate and nitrite concentrations and assimilates nitrate in moderately saline environments". Archives of Microbiology. 175 (6): 435–440. doi:10.1007/s002030100285. PMID 11491084. S2CID 864067 – via Springer.
  9. ^ Mendez-Volas, A. (2012). Microbes in applied research; current advances and challenges; proceedings. World Scientific. pp. 197–200. ISBN 9789814405034.
  10. ^ Laczi, Krisztián; Kis, Ágnes; Horváth, Balázs; Maróti, Gergely; Hegedüs, Botond (November 2015). "Metabolic responses of Rhodococcus erythropolis PR4 grown on diesel oil and various hydrocarbons" (PDF). Applied Microbiology and Biotechnology. 99 (22): 9745–9759. doi:10.1007/s00253-015-6936-z. PMID 26346267. S2CID 9213608.
  11. ^ O'Loughlin, E.J.; Kehrmeyer, S.R.; Sims, G.K. (1996). "Isolation, characterization, and substrate utilization of a quinoline degrading bacterium". International Biodeterioration and Biodegradation. 38 (2): 107–118. doi:10.1016/S0964-8305(96)00032-7.
  12. ^ Kuyukina, Maria S.; Ivshina, Irena B. (2010). "Application of Rhodococcus in Bioremediation of Contaminated Environments". Biology of Rhodococcus. Microbiology Monographs. 16. Springer, Berlin, Heidelberg: 231–262. doi:10.1007/978-3-642-12937-7_9. ISBN 978-3-642-12936-0.
  13. ^ Alvarez, Héctor (2010). Biology of Rhodococcus. Springer Science & Business Media. pp. 231–256. ISBN 9783642129377.
  14. ^ Fuller, M.E.; Perreault, N. (July 8, 2010). "Microaerophilic degradation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by three Rhodococcus strains". Letters in Applied Microbiology. 51 (3): 313–318. doi:10.1111/j.1472-765X.2010.02897.x. PMID 20666987. S2CID 46159929 – via Wiley.
  15. ^ Blasco, Rafael (2001). "Rhodococcus sp. RB1 grows in the presence of high nitrate and nitrite concentrations and assimilates nitrate in moderately saline environments". Archives of Microbiology. 175 (6): 435–440. doi:10.1007/s002030100285. PMID 11491084. S2CID 864067 – via Springer.
  16. ^ Mendez-Volas, A. (2012). Microbes in applied research; current advances and challenges; proceedings. World Scientific. pp. 197–200. ISBN 9789814405034.
  17. ^ Laczi, Krisztián; Kis, Ágnes; Horváth, Balázs; Maróti, Gergely; Hegedüs, Botond (November 2015). "Metabolic responses of Rhodococcus erythropolis PR4 grown on diesel oil and various hydrocarbons" (PDF). Applied Microbiology and Biotechnology. 99 (22): 9745–9759. doi:10.1007/s00253-015-6936-z. PMID 26346267. S2CID 9213608.
  18. ^ Yano, Kenichi; Wachi, Masaaki; Tsuchida, Sakiko; Kitazume, Tomoya; Iwai, Noritaka (2015). "Degradation of benzotrifluoride via the dioxygenase pathway in Rhodococcus sp. 065240". Bioscience, Biotechnology, and Biochemistry. 79 (3): 496–504. doi:10.1080/09168451.2014.982502. ISSN 1347-6947. PMID 25412819. S2CID 205616972.
  19. ^ O'Loughlin, E.J.; Kehrmeyer, S.R.; Sims, G.K. (1996). "Isolation, characterization, and substrate utilization of a quinoline degrading bacterium". International Biodeterioration and Biodegradation. 38 (2): 107–118. doi:10.1016/S0964-8305(96)00032-7.
  20. ^ Takei, Takayuki; Yamasaki, Mika; Yoshida, Masahiro (2014-04-01). "Cesium accumulation of Rhodococcus erythropolis CS98 strain immobilized in hydrogel matrices". Journal of Bioscience and Bioengineering. 117 (4): 497–500. doi:10.1016/j.jbiosc.2013.09.013. PMID 24183457.
  21. ^ Heiss, G. S.; Gowan, B.; Dabbs, E. R. (1992-12-01). "Cloning of DNA from a Rhodococcus strain conferring the ability to decolorize sulfonated azo dyes". FEMS Microbiology Letters. 78 (2–3): 221–226. doi:10.1016/0378-1097(92)90030-r. ISSN 0378-1097. PMID 1490602.
  22. ^ Parekh, N. R.; Walker, A.; Roberts, S. J.; Welch, S. J. (November 1994). "Rapid degradation of the triazinone herbicide metamitron by a Rhodococcus sp. isolated from treated soil". The Journal of Applied Bacteriology. 77 (5): 467–475. doi:10.1111/j.1365-2672.1994.tb04389.x. ISSN 0021-8847. PMID 8002472.
  23. ^ Boyle, Alfred W.; Silvin, Christopher J.; Hassett, John P.; Nakas, James P.; Tanenbaum, S. W. (1992-06-01). "Bacterial PCB biodegradation". Biodegradation. 3 (2–3): 285–298. doi:10.1007/BF00129089. ISSN 0923-9820. S2CID 7272347.
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