User talk:Micb301student/sandbox

Peptidoglycan critique
This is a flawed article that contains a couple unreliable sources and lacks adequate information.

The article contains mostly reliable sources. It cited academic presses from prestigious institution. Other sources also come from reliable and unbiased scientific journals as well as a variety of microbiology textbooks. However, the article contains two unreliable references. The first reference on the “References” section is an amateur education website, which the author closely paraphrased from. This website cited their sources from two microbiology textbooks. Therefore, to avoid close paraphrasing and citing unreliable sources, one can examine the sources provided in this website and rewrite the article. Another inappropriate reference is the ninth one because its hyperlink cannot be reached.

The article is divided into appropriate subheadings that explains the structure and synthesis of peptidoglycan. Each section presented all important information equally from a neutral scientific viewpoint. However, the article lacks some relevant information that can be added to make the more satisfactory. The author can explain in detail more about the molecular difference in the structure of peptidoglycan in gram negative and gram positive bacteria and provide suitable diagram that demonstrate the difference. Moreover, a new subheading “Function”, should be added describe the function of peptidoglycan and how it prevents bacteria from osmotic lysis in a hypotonic environment.

In the “talk” page, one Wikipedian suggested that more detailed molecular structure diagrams can aids visualization. However, no new diagram has been updated. Micb301student (talk) 07:49, 17 September 2017 (UTC)

Reflection
I had trouble starting the assignment because I do not usually read Wikipedia articles critically and question their sources. After completing the assignment, I learned to be a more critical reader and examine the everything on Wikipedia articles thoroughly. Micb301student (talk) 07:49, 17 September 2017 (UTC)

Green sulfur bacteria critique and improvements
This is a below satisfactory article that contains unreliable source and lacks many relevant information.

The article cited sources from reputable scientific journals written by experts. The article also derived information from a textbook on photosynthesis. These sources were appropriated cited and there is no sign of close paraphrasing and plagiarism. However, the reliability of the 6th reference is questionable because the link cannot be reached. As a result, the content of the taxonomy portion of the article is unreliable.

The article is also poorly organized. The first portion of the article should contain a general overview of the topic, but all the information is tightly packed into this portion. Although the content is neutral, many facts are underrepresented and missing. The contents of the article only go into detail about the phylogeny and taxonomy of green sulfur bacteria. Relevant information, such as the carbon fixing mechanism and habitats are missing. The information about the electron transport chain, and sulfur oxidation is not adequate for deep understanding.

There was discussion in the talk page of this article. One user suggested for more in-depth explanation of the roles of photosystems and pigments. One other user suggested that the author should provide information about the significance of the habitat of green sulfur bacteria. Despite these suggestions, there is no edit to improve the article.

This is a highly notable article that deserve extensive edit. Green sulfur bacteria are important in the understanding the evolution of eukaryotic phototrophs, which is why the article needs to cover more facts and findings. To improve on the article, I will add two subtopics, autotrophy and habitats, in order to go into detail on carbon fixation through reverse TCA cycle and the marine habitats of green sulfur bacteria. This additional information will allow readers to understand the autotrophic mechanisms of green sulfur bacteria and their roles in the marine habitats. Since the image provided in the article does not show the structure and organelles of green sulfur bacteria, I would also add a microscopic image of a single green sulfur bacterium to depict important bacterial components. Micb301student (talk) 06:36, 28 September 2017 (UTC)

Original- "Green sulfur bacteria"
The green sulfur bacteria (Chlorobiaceae) are a family of obligately anaerobic photoautotrophic bacteria. Together with the non-photosynthetic Ignavibacteriaceae, they form the phylum Chlorobi. Most closely related to the distant Bacteroidetes, they are accordingly assigned their own phylum.

Green sulfur bacteria are nonmotile (except Chloroherpeton thalassium, which may glide). Photosynthesis is achieved using a Type 1 reaction centre using bacteriochlorophyll (BChl) a and in chlorosomes which employ BChl c, d, or e; in addition chlorophyll a is also present. They use sulfide ions, hydrogen or ferrous iron as an electron donor and the process is mediated by the type I reaction centre and Fenna-Matthews-Olson complex. Elemental sulfur deposited outside the cell may be further oxidized. By contrast, the photosynthesis in plants uses water as the electron donor and produces oxygen.

Chlorobium tepidum has emerged as a model organism for the group; although only 10 genomes have been sequenced, these are quite comprehensive of the family's biodiversity. Their 2-3 Mb genomes encode 1750-2800 genes, 1400-1500 of which are common to all strains. The apparent absence of two-component histidine-kinases and response regulators suggest limited phenotypic plasticity. Their small dependence on organic molecule transporters and transcription factors also indicate these organisms are adapted to a narrow range of energy-limited conditions, an ecology shared with the simpler cyanobacteria, Prochlorococcus and Synechococcus.

A species of green sulfur bacteria has been found living near a black smoker off the coast of Mexico at a depth of 2,500 m in the Pacific Ocean. At this depth, the bacterium, designated GSB1, lives off the dim glow of the thermal vent since no sunlight can penetrate to that depth.

Green sulfur bacteria appear in Lake Matano, Indonesia, at a depth of about 110–120 m. The population may include the species Chlorobium ferrooxidans.

Edits- "Green sulfur bacteria"
The green sulfur bacteria (Chlorobiaceae) are a family of obligately anaerobic photoautotrophic bacteria. Together with the non-photosynthetic Ignavibacteriaceae, they form the phylum Chlorobi. Most closely related to the distant Bacteroidetes, they are accordingly assigned their own phylum.

Green sulfur bacteria are nonmotile (except Chloroherpeton thalassium, which may glide). Photosynthesis is achieved using a Type 1 reaction centre, which contains bacteriochlorophyll (BChl) a, and is taken place in chlorosomes, which employ BChl c, d, or e in addition to chlorophyll a. Type 1 reaction centre is equivalent to photosystem I found in plants and cyanobacteria. Green sulfur bacteria use sulfide ions, hydrogen or ferrous iron as an electron donor and the process is mediated by the type I reaction centre and Fenna-Matthews-Olson complex. Reaction centre contains bacteriochlorophylls, P840, which donates electrons to cytochorome c-551 when it is excited by light. Cytochrome c-551 then passes the electrons down the electron chain. P840 is returned to its reduced state by the oxidation of sulfide. Sulfide donates two electrons to yield elemental sulfur. Elemental sulfur is deposited in globules on the extracellular side of the outer membrane. When sulfide is depleted, the sulfur globules are consumed and oxidized to sulfate. However, the pathway of sulfur oxidation is not well-understood. By contrast, the photosynthesis in plants uses water as the electron donor and produces oxygen.

Green sulfur bacteria are anoxygenic. These autotrophs fix carbon dioxide using the reverse tricarboxylic acid (RTCA) cycle. Energy is consumed to incorporate carbon dioxide in order to assimilate pyruvate and acetate. Chlorobium tepidum, a member of green sulfur bacteria were found to be mixotrophs due to their ability to use inorganic and organic carbon sources. They can assimilate acetate through the oxidative (forward) TCA (OTCA) cycle in addition to RTCA. In contrast to the RTCA cycle, energy is generated in the OTCA cycle, which may contribute to better growth. However, the capacity of the OTCA cycle is limited because gene that code for enzymes of the OTCA cycle are down-regulated when the bacteria is growing phototrophically.

Chlorobium tepidum has emerged as a model organism for the group; although only 10 genomes have been sequenced, these are quite comprehensive of the family's biodiversity. Their 2-3 Mb genomes encode 1750-2800 genes, 1400-1500 of which are common to all strains. The apparent absence of two-component histidine-kinases and response regulators suggest limited phenotypic plasticity. Their small dependence on organic molecule transporters and transcription factors also indicate these organisms are adapted to a narrow range of energy-limited conditions, an ecology shared with the simpler cyanobacteria, Prochlorococcus and Synechococcus.

The Black Sea, an extremely anoxic environment, was found to house a large population of green sulfur bacteria at about 100 m depth. Due to the lack of light available in this region of the sea, most bacteria were photosynthetically inactive. The photosynthetic activity detected in the chemocline suggests that the bacteria need very little energy for cellular maintenance.

A species of green sulfur bacteria has been found living near a black smoker off the coast of Mexico at a depth of 2,500 m in the Pacific Ocean. At this depth, the bacterium, designated GSB1, lives off the dim glow of the thermal vent since no sunlight can penetrate to that depth.

Green sulfur bacteria appear in Lake Matano, Indonesia, at a depth of about 110–120 m. The population may include the species Chlorobium ferrooxidans.

Yi-Cheng Tsai's Peer Review (done by Thomas Soroski)
The edited text contains detailed information about Green Sulfur Bacteria's biochemical pathways. This information is placed into the lead (the first section) of the Wikipedia article. This information is misplaced. WikiEdu training teaches that “good leads don't get too bogged down in detail”. Therefore, the Wikipedia article would be more logical and comprehensive if these edits were moved out of the lead and into a different section of the article.

The article goes into detail about the bacteria's photosynthesis pathway. The cited scientific article discusses bacterial photosynthesis at length using a high amount of jargon. The edited text provides a comprehensive summary of the source, reducing jargon use to a minimum. As well, the edits compare the bacteria’s photosynthesis with plant photosynthesis. This allows readers put the information into perspective, and contributes to overall understanding. The article also discusses the TCA cycles that the bacteria are capable of. The source is long-winded and full of jargon. The Wikipedia article boils down the scientific article and presents it in a very accessible way. The article mentions that acetate and pyruvate are assimilated, and that the bacteria undergoes different TCA cycles, but does not explain why. The cited source explains that the bacteria use these chemicals as carbon and energy sources, and that the cycles contribute to bacterial growth. The final edit should include these explanations to allow the reader to get a better understanding of the content.

The source about the Black Sea habitat is well-chosen, as it applies directly to the bacteria, and is recent (2010). The edits mention the Black Sea chemocline, however, it does not explain what kind of chemical gradient is in the chemocline, nor does it explain what a chemocline is. The journal article explains that it is a sulfide chemocline, and that a chemocline is a vertical chemical gradient. Adding this information would greatly contribute to the clarity of the content.

Overall, the tone is neutral and succinct. This is demonstrated in the easily-understood and logical explanations of photosynthesis, the TCA cycle, and the bacteria’s habitats.

Tsoroski (talk) 02:46, 9 November 2017 (UTC)

Green Sulfur Bacteria
The green sulfur bacteria (Chlorobiaceae) are a family of obligately anaerobic photoautotrophic bacteria. Together with the non-photosynthetic Ignavibacteriaceae, they form the phylum Chlorobi. Most closely related to the distant Bacteroidetes, they are accordingly assigned their own phylum.

Green sulfur bacteria are nonmotile (except Chloroherpeton thalassium, which may glide) and capable of anoxygenic photosynthesis. In contrast to plants, green sulfur bacteria mainly use sulfide ions as electron donors. They are autotrophs that utilize the reverse tricarboxylic acid cycle to fix carbon dioxide. Green sulfur bacteria are often found in the deep sea, which has low light availability.

Catabolism
Photosynthesis is achieved using a Type 1 reaction centre, which contains bacteriochlorophyll a, and is taken place in chlorosomes. Type 1 reaction centre is equivalent to photosystem I found in plants and cyanobacteria. Green sulfur bacteria use sulfide ions, hydrogen or ferrous iron as electron donors and the process is mediated by the Type I reaction centre and Fenna-Matthews-Olson complex. Reaction centre contains bacteriochlorophylls, P840, which donates electrons to cytochrome c-551 when it is excited by light. Cytochrome c-551 then passes the electrons down the electron chain. P840 is returned to its reduced state by the oxidation of sulfide. Sulfide donates two electrons to yield elemental sulfur. Elemental sulfur is deposited in globules on the extracellular side of the outer membrane. When sulfide is depleted, the sulfur globules are consumed and oxidized to sulfate. However, the pathway of sulfur oxidation is not well-understood.

Anabolism
These autotrophs fix carbon dioxide using the reverse tricarboxylic acid (RTCA) cycle. Energy is consumed to incorporate carbon dioxide in order to assimilate pyruvate and acetate and generate macromolecules. Chlorobium tepidum, a member of green sulfur bacteria was found to be mixotroph due to its ability to use inorganic and organic carbon sources. They can assimilate acetate through the oxidative (forward) TCA (OTCA) cycle in addition to RTCA. In contrast to the RTCA cycle, energy is generated in the OTCA cycle, which may contribute to better growth. However, the capacity of the OTCA cycle is limited because gene that code for enzymes of the OTCA cycle are down-regulated when the bacteria is growing phototrophically.

Habitat
The Black Sea, an extremely anoxic environment, was found to house a large population of green sulfur bacteria at about 100 m depth. Due to the lack of light available in this region of the sea, most bacteria were photosynthetically inactive. The photosynthetic activity detected in the sulfide chemocline suggests that the bacteria need very little energy for cellular maintenance.

A species of green sulfur bacteria has been found living near a black smoker off the coast of Mexico at a depth of 2,500 m in the Pacific Ocean. At this depth, the bacterium, designated GSB1, lives off the dim glow of the thermal vent since no sunlight can penetrate to that depth.

Green sulfur bacteria appear in Lake Matano, Indonesia, at a depth of about 110–120 m. The population may include the species Chlorobium ferrooxidans.