User talk:Thomas Dalhuisen/sandbox

Assignment 1
I chose to evaluate the article on EnvZ-OmpR. The first two parts of the article are well referenced using either one or two sources from reliable scientific papers. Although some sources used in these sections might be considered out dated (i.e. the 1990s), they are all backed-up by sources with a more recent publication date. The referencing later in the article is solely based on one source and fewer claims are directly referenced. Especially the sentence that starts with: “Also, the amount” can be backed up by this reference. The article material is relevant to the article topic and the article is written in a neutral scientific tone. If I were to suggest an add to this article, I would create a diagram that shows the processes described in the article in a sequential manner. The diagram used in the article is not very helpful as it is not annotated and it does not give quick overview. The hyperlinks to the citations lead to the right pages and I suspect there is no (direct) evidence of close paraphrasing or plagiarism because the overall writing style seems coherent. Supporting this suspicion is a comment that was posted on the talk page. One member of the Wikipedia community (rightly) pointed out an interpretation mistake by the original author of the Wikipedia article. This supports the claim that the original author of the article did not blindly copy paste, but interpreted the sources and wrote a summary in their own words. Thomas Dalhuisen (talk) 20:18, 17 September 2017 (UTC)

Assignment 2
I chose the topic on denitrifying bacteria as the article I want to edit. This topic is of high noticeability as denitrifying bacteria play an important role in the denitrification process. Denitrifying bacteria are a diverse group of organisms that can be found in many bacterial phyla and environments. This means that the ability to denitrify must have evolved independently multiple times stressing its importance. One might argue that this topic is only of interest for the expert reader interested in microbiology, but I believe that the general public should be informed about this group of bacteria as they can have an economical impact on society. They can for example cause N loss used in fertilizers. The article as it is now, is of low quality and needs significant improvement. This is supported by Wikipedia members who flagged the article as needing expert attention. This has multiple reasons. Firstly, no statements are backed up by a source. Moreover, the article lacks a coherent structure and some statement are incorrect such as the notion that nitrate reductase can convert nitrate to gaseous dinitrogen. I will attempt to reorganize the article by dividing the article into three subheadings, namely: For my edit, I will focus on the first two sections. The original article does not appreciate the wide variety of denitrifying bacteria and their diverse physiological traits. I want to add more information about the diversity of denitrifies using this great resource as my source. The article briefly mentions Pseudomonas as an important denitrifier and I want to elaborate on this by noting that a specific strain of Pseudomonas, P. stuzeri, serves as an important model organism for research into denitrifying bacteria. Using P. stuzeri as an example, I want to elaborate on the denitrification mechanism and the different enzymes involved to get the basic mechanism of denitrification across. For this assignment, I will not focus much on the third subheading, but I will put the environmental issues that the article alludes to under this section. Thomas Dalhuisen (talk) 19:21, 23 September 2017 (UTC)
 * 1) 	Diversity of denitrifying bacteria
 * 2)  	Denitrification mechanism
 * 3)  	Denitrifying bacteria and the environment

Assignment 3
- Original Denitrifying bacteria

Denitrifying bacteria are bacteria capable of performing denitrification as part of the nitrogen cycle. They metabolise nitrogenous compounds using the enzyme nitrate reductase, turning nitrogen oxides back to nitrogen gas or nitrous oxide.

The process of denitrification lowers the fertility rate of reproduction of the soil and thus is less common in areas where the land is rather well-cultivated. But this loss of nitrogen to the atmosphere can eventually be regained via introduced nutrients, as part of the nitrogen cycle. Some nitrogen may also be fixated by species of nitrifying bacteria and the cyanobacteria.

Denitrification also becomes the key pathway for dissimilative nitrate reduction, which is the process in which nitrates are reduced from the soil, the former being highly toxic for living organisms. Denitrification tends to produce large amounts of by-products.

The most common denitrification process is basically outlined below, with the nitrogen oxides being converted back to gaseous nitrogen (as opposed to that of nitrifying bacteria):


 * 2 NO3− + 10 e− + 12 H+ → N2 + 6 H2O

The result is one molecule of nitrogen (consisting of two atoms) and six molecules of water. Denitrifying bacteria are a part of the N cycle, and consists of sending the N back into the atmosphere

Denitrifying bacteria themselves include several species of Pseudomonas, Alkaligenes, Bacillus and others. By their activity the losses of nitrogen into the atmosphere is roughly balanced by that which is released into the soil by nitrifying bacteria, forming a relatively balanced cycle.

Diversity of denitrifying bacteria
There is a great diversity in bacteria capable of performing denitrification. Members of this group encompass most bacterial phyla and therefore posses a wide variety of physiological traits. Denitrifying bacteria have been identified in over 50 genera with over 125 different species and are estimated to represent 10-15% of bacteria population in water, soil and sediment. Denitrifying include for example several species of Pseudomonas, Alkaligenes, Bacillus and others. The majority of denitrifying bacteria are facultative aerobic heterotrophs that switch from aerobic respiration to denitrification when oxygen as an available terminal electron acceptor (TEA) runs out. This forces the organism to use nitrate to be used as a TEA. For the diversity of denitrifying bacteria is so large, this group can thrive in a wide range of habitats including some extreme environments such as environments that are high in saline and high in temperature.

Denitrification mechanism
Denitrifying bacteria use denitrification to generate ATP.

The most common denitrification process is outlined below, with the nitrogen oxides being converted back to gaseous nitrogen

2 NO3− + 10 e- + 12 H+ → N2 + 6 H2O

The result is one molecule of nitrogen and six molecules of water. Denitrifying bacteria are a part of the N cycle, and consists of sending the N back into the atmosphere. The reaction above is the overall half reaction of the process of denitrification. The reaction can be further divided into different half reactions each requiring a specific enzyme. The transformation from nitrate to nitrite is performed by nitrate reductase (Nar)

NO3- + 2 H+ +2 e- → NO2- + H2O

Nitrite reductase (Nir) then converts nitrite into nitric oxide

2 NO2- + 4 H+ + 2 e- → 2 NO + 2 H2O Nitric oxide reductase (Nor) then converts nitric oxide into nitrous oxide

2 NO + 2 H+ +2 e- → N2O + H2O

Nitrous oxide reductase (Nos) terminates the reaction by converting nitrous oxide into dinitrogen N2O + 2 H+ + 2 e- → N2 + H2O

It is important to note that any of the products produced at any step can be exchanged with the soil environment.

Denitrifying bacteria and the environment
The process of denitrification lowers the fertility rate of reproduction of the soil and thus is less common in areas where the land is rather well-cultivated. But this loss of nitrogen to the atmosphere can eventually be regained via introduced nutrients, as part of the nitrogen cycle. Some nitrogen may also be fixated by species of nitrifying bacteria and the cyanobacteria.

Denitrification also becomes the key pathway for dissimilative nitrate reduction, which is the process in which nitrates are reduced from the soil, the former being highly toxic for living organisms. Denitrification tends to produce large amounts of by-products. Thomas Dalhuisen (talk) 18:35, 4 October 2017 (UTC)

Thoma's Peer Review
The edited version of “Denitrification” has much improved structure. The original passage which encompassed too many aspects of denitrification has now been separated into appropriate and relevant subsections, allowing readers to easily find the information about who does what, and where, as well as making the article easier to read. The structure does not need changing.

Content-wise, important information was added about the diversity of organisms that perform denitrification and includes more detail into the mechanism of denitrification and its environmental effects, especially in “Denitrification Mechanism” where denitrification is very systematically explained. All content is given equal and appropriate length and priority. However, “Denitrifying Bacteria and the Environment” should mention the impact of released N2O as a greenhouse gas and NO as an ozone depleting species, an important global phenomenon that should be mentioned considering the talk surrounding global warming today.

Source-wise, all references are cited well and appear to be from reliable peer-reviewed sources for the first two of three subsections with sources attributed to them. However, the source from A. Eldor doesn’t receive enough representation in the article as it is only found once in the second paragraph and information from it can be expanded further, such as by adding to “Denitrifying Bacteria and the Environment” that each denitrifying enzyme is inhibited by oxygen and rainfall helps to increase rate and strength of denitrification due to low oxygen solubility in water. There are no sources found in the section “Denitrifying bacteria and the environment”, and I highly suggest that they be added to legitimize the section’s information.

Writing-wise, the edits are concisely-written, with ideas that flow well and no disjointed or run-on sentences. No close paraphrasing is noted and content is written neutrally and in an objective manner. Watch out for some spelling errors – “Denitryfing” occurs in the first two subsections.Lincolnp8 (talk) 05:57, 9 November 2017 (UTC)

Edited text based on peer review
Denitrifying bacteria are a diverse group of bacteria that encompass many different phyla. This group of bacteria, together with denitrifying fungi and archaea, is capable of performing denitrification as part of the nitrogen cycle. They metabolise nitrogenous compounds using various enzymes, turning nitrogen oxides back to nitrogen gas or nitrous oxide.

Diversity of denitrifying bacteria
There is a great diversity in bacteria capable of performing denitrification. Members of this group encompass most bacterial phyla and therefore posses a wide variety of physiological traits. Denitrifying bacteria have been identified in over 50 genera with over 125 different species and are estimated to represent 10-15% of bacteria population in water, soil and sediment. Denitrifying include for example several species of Pseudomonas, Alkaligenes, Bacillus and others. The majority of denitrifying bacteria are facultative aerobic heterotrophs that switch from aerobic respiration to denitrification when oxygen as an available terminal electron acceptor (TEA) runs out. This forces the organism to use nitrate to be used as a TEA. For the diversity of denitrifying bacteria is so large, this group can thrive in a wide range of habitats including some extreme environments such as environments that are high in saline and high in temperature.

Denitrification mechanism
Denitrifying bacteria use denitrification to generate ATP.

The most common denitrification process is outlined below, with the nitrogen oxides being converted back to gaseous nitrogen:

2 NO3− + 10 e- + 12 H+ → N2 + 6 H2O

The result is one molecule of nitrogen and six molecules of water. Denitrifying bacteria are a part of the N cycle, and consists of sending the N back into the atmosphere. The reaction above is the overall half reaction of the process of denitrification. The reaction can be further divided into different half reactions each requiring a specific enzyme. The transformation from nitrate to nitrite is performed by nitrate reductase (Nar)

NO3- + 2 H+ +2 e- → NO2- + H2O

Nitrite reductase (Nir) then converts nitrite into nitric oxide

2 NO2- + 4 H+ + 2 e- → 2 NO + 2 H2O Nitric oxide reductase (Nor) then converts nitric oxide into nitrous oxide

2 NO + 2 H+ +2 e- → N2O + H2O

Nitrous oxide reductase (Nos) terminates the reaction by converting nitrous oxide into dinitrogen N2O + 2 H+ + 2 e- → N2 + H2O

It is important to note that any of the products produced at any step can be exchanged with the soil environment.

Denitrifying bacteria and the environment
The process of denitrification can lower the fertility of soil as nitrogen, a growth-limiting factor, is removed from the soil and lost to the atmosphere. This loss of nitrogen to the atmosphere can eventually be regained via introduced nutrients, as part of the nitrogen cycle. Some nitrogen may also be fixated by species of nitrifying bacteria and the cyanobacteria. Another important environmental issue concerning denitrification is the fact that the process tends to produce large amounts of by-products. Examples of by-products are nitric oxide (NO) and nitrous oxide (N2O). NO is an ozone depleting species and NO2 is a potent greenhouse gas which can contribute to global warming.

Thomas Dalhuisen (talk) 22:34, 14 November 2017 (UTC)