Wikipedia:Peer review/Bacteria/archive1

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Note Article is now a FAC, its candidacy page is here

A core topic in biology, medicine, biochemistry and biotechnology. The article is intended to be a wide introduction and comments on both content and formatting for a future FA candidacy are very welcome. Thank you. TimVickers 23:19, 24 November 2006 (UTC)

  • A few first thoughts:
    • Maybe two more electron micrographs; I googled for streptococcus to get an idea for what's out there. It should be possible to get an image published under an open license.
    • Also, a size comparison would be good - typical baterium vs. typical diameter of fungus hyphae, and vs. typical virus (I know they vary hugely, maybe use the biggest and smallest known in each category?) - Samsara (talk  contribs) 13:49, 25 November 2006 (UTC)
Added images of Bacillus anthracis and Helicobacter pylori, expanded the information on size is at the start of the morphology section. TimVickers 19:55, 25 November 2006 (UTC)
Good job so far. I was thinking of something more for the kids, along the lines of Image:Trex1.png - Samsara (talk  contribs) 13:13, 26 November 2006 (UTC)
I made a new cartoon and added it to the Morphology section. TimVickers 19:26, 26 November 2006 (UTC)
  • History: "the history of bacteriology is generally described as the history of microbiology" This is not the article on bacteriology but on bacteria. I think the section should be renamed "Bacteriology" I found the sentances on Koch's postulates to stray off-topic. In the lead you said the terminology regarding bacteria scientifically has changed. If this is important enought for the lead I believe the details of this change should be explained.
Koch condensed and two-domain section added. TimVickers 19:55, 25 November 2006 (UTC)
This section holds together better after those changes. I still think the heading should be changed as the text is not the History of Bacteria. The History of Bacteria would be something like "Millions of years ago . . ." I also think the information Only about half of the known bacterial phyla have species that can be cultured in the laboratory and our knowledge of bacteria as a whole is biased towards those organisms that can be isolated in this way. should be moved here as imagine this is true of the whole article not just "Growth and Reproduction". --Birgitte§β ʈ Talk 19:46, 26 November 2006 (UTC)
Section renamed and uncultured majority info added to introduction. TimVickers 21:32, 26 November 2006 (UTC)
Section on "Origin and early evolution" added. Called "early evolution" as these organisms are still evolving rapidly. TimVickers 02:49, 27 November 2006 (UTC)
  • Morphology: I don't understand the paragraph on hydrogen transfer. Is it a close association between bacteria? I thought Archaea were not bacteria? Are mitochondria and chloroplasts still bacteria or do they simply have a common ancestor with some/all bacteria? (I hate when people describe something extant being descended from another extant group; I find it to be an inaccurate portrayal of evolution) If they are not technically bacteria anymore what characteristics to they lack?
Hydrogen transfer association between a bacteria and an archaean. Reword ancestry and define mutualism and parasitism with links.
Added space as a better example and rephrased Clostridium example. TimVickers 19:55, 25 November 2006 (UTC)
This section is much easier to understand now. There is one sentance Each bacterial species tends to display a characteristic morphology. which is so weakly worded I am not sure what it means. Does this means some species have a variety of shapes while most do not? Or is setting up the exception of complex groups with fruiting bodies which posibly involve some individual bacteria changing shapes?--Birgitte§β ʈ Talk 19:46, 26 November 2006 (UTC)
Reworded. TimVickers 21:55, 26 November 2006 (UTC)
  • Spores: Is a rusty nail a particularly hostile environment? Maybe there is better example of something more obviously hard to survive, or you can explain why the reader should be impressed with rust.
  • Metabolism: This section need a stronger structure. I am left confused. After reading that paragraph I wonder if heterotrophic and autotrophic bacteria have varieties that are electron donors and electron acceptors or are autrphic more limited. Is "energy metabolism" the same as electron donating or accepting? If the hetero/autotropic stuff is not "energy metabolism" what kind of metabolism is it? Also what does respitory mean in terms of bacteria?
Structure improved to give more clarity, energy metabolism is the capture of energy from either oxidation/reduction reactions or sunlight, and then the use of this energy for metabolic processes.
This is much clearer but it still loses me in places. Such as: To use chemical compounds as a source of energy, electrons are taken from the reduced substrate and transferred to a terminal electron acceptor.(what is the "reduced substrate? Is a terminal electron acceptor some structure of the bacteria?) and In addition to carbon, some bacteria also fix nitrogen gas (nitrogen fixation) using the enzyme nitrogenase. ("fix" carbon? This does not match earlier terminology so I don't know what you are comparing this to?) --Birgitte§β ʈ Talk 19:46, 26 November 2006 (UTC)
Reworded for more clarity and same terms used throughout. TimVickers 21:55, 26 November 2006 (UTC)
  • Growth and reproduction: Aren't you using these two words to mean reproduction throughout this section. Does bacteria really grow separately from reproducing?
They do, otherwise they would get smaller each time they divide. This section deals with both processes, but never defines them properly. I've added this in the start of this section. TimVickers 22:39, 25 November 2006 (UTC)
This is clearer with that definition. The section talks a great deals about growing bacteria in labratories but nothing at all about their growth within biofilms. --Birgitte§β ʈ Talk 19:46, 26 November 2006 (UTC)
Much more is known! I generalised the last section, since this applies to all bacterial growth. TimVickers 21:55, 26 November 2006 (UTC)
  • Genetic variation: The last paragraph here would fit better with the text in "History" or "Uses in industry" (although the titles of those sections are misnomers IMHO) . --Birgitte§β ʈ Talk 19:46, 26 November 2006 (UTC)
Added to new Technology and industry section (renamed). TimVickers 21:55, 26 November 2006 (UTC)
  • Groups and identification: This repeats a number of points from earlier in the article. Especialty "History" and "Morphology". It should be higher in the article with repeated points only dealt with in one place. --Birgitte§β ʈ Talk 19:46, 26 November 2006 (UTC)
Reworded and condensed. TimVickers 21:55, 26 November 2006 (UTC)
  • Pathogenic bacteria: I question the title of this section. Is there something in inherently pathogenic about these organisms or are they just "Baceteria as pathogens"? When I look at viruses; they must destroy another cell to reproduce which seem inherently pathogenic. But bacteria seem more oppurtunistic to me. I really don't know. If they are inherently pathogenic; what are the attributes that seperate them from other bacteria. Otherwise this section needs more structure. Are they bacteria usually pathogenic only to humans? Most animal? Genera of organisms? Maybe talk about the most common (broadly pathogenic bacteria or ones which act very specifically) and then move towards the opposite end of the spectrum. I also wonder if this section warrants some "bigger picture" talk. About what leads to an "outbreak" of disease rather than baseline of infections. Is these "conditons needed to thrive" any different for bacteria as opposed to other organismal pathogens?
Looks like Tim has now clarified this a lot better. I'm happy with the section title, although I'd also be happy for it to be called something simpler, such as "bacteria and disease". It comes down to the question whether we want laypeople to pick up jargon - they may find it useful. - Samsara (talk  contribs) 13:21, 26 November 2006 (UTC)
  • Pathogenic bacteria/Symbiotic bacteria: I feel like these should be handled differently. Right I get the impression the article really means Bad Bacteria/Good Bacteria. And honestly is just discussing bacteria which hamper or help human efforts. The Symbiotic section should be higher in the article maybe reworked as "Bacterial associations" with part of the current "Morphology and associations" leaving a stand-alone section on "Morphology". Also the discussion of symbosis should focus on the benefit to the bacteria not to humans or ther crops. I would also like to ruminants mentioned here because it is more commonly known and IMHO more complete symbiosis than soybeans (ie. the nitrogen fixation symbiosis). Maybe the range of symbiosis should be discussed. Somethings can help each other (great they thrive) or not (oh well they still survive) others cannont exist without the relationship. Somehow I imagine all bacteria manage to survive without symbiosis while several of their partners cannot.
I've merged these two sections and moved some of the material down from the old "Morphology and associations" section. Also linked to mutualism, parasitism and commensalism at beginning. TimVickers 22:39, 25 November 2006 (UTC)
I'd just like to voice my opinion that the distinction between pathogenic and non-pathogenic bacteria is an old and distinguished one and needs to be treated as such. Much of microbiology was developed in order to assist the isolation and identification of human pathogens. (And there are certainly some bacteria that are obligate intracellular parasites that cannot survive either independently or symbiotically.) - Nunh-huh 01:07, 26 November 2006 (UTC)
Please do not take my suggestions as firm opinions. I do not have any particular knowledge about microbiology. I am sure many of my points are incorrect. I would just suggest that where they are incorrect the article should have it's wording stregthened or its terminology more clearly defined so that a reader could not wonder about such things. --Birgitte§β ʈ Talk 01:47, 26 November 2006 (UTC)
I'm going to add a bit of this into the Groups and Identificaiton portion of the article later tonight. If it doesn't help with your particular concern about the term "pathogens", let me know! - Nunh-huh 01:54, 26 November 2006 (UTC)
I really like the reworking of this information. --Birgitte§β ʈ Talk 19:46, 26 November 2006 (UTC)
  • Uses in industry: This is the weakest section. I think it should be renamed "Cultured bacteria" and should recount the history of people intentionally culturing or promoting bacterial growth for their own benefit. Whether they knew what a bacteria was or not. And also methods used to do this.
I still find this part weak and dislike the heading. Cesspools existed before the industrial revolution and the production of fermented food before Homo sapiens. This is about more than industry. --Birgitte§β ʈ Talk 19:46, 26 November 2006 (UTC)
  • What is missing: Several time you compare bacteria to eukaryote; I would like to see the basic difference between a bacteria and eukaryote mention the first time (i.e. compared to eukaryotes, organisms whose cells have nuculei,). This article need a proper taxonmy box and a discussion of the conflicting opinions over taxonomy. "Eubacteria" should be a bolded synonym. The relationship to what this articles call bacteria needs to detailed to what are called "Prokaryotes". In fact there is not a clear explanation as to what makes one organism a bacteria and another not. Some discussion of evolutionary biology of bacteria would be nice.
Eukaryote/prokaryote now added to start of intro. TimVickers 22:39, 25 November 2006 (UTC)
I still think redirected synomyms need bolding and the infobox should be more like Archaea (Why use "Subgroups" when there is an actual taxonomy). --Birgitte§β ʈ Talk 19:46, 26 November 2006 (UTC)
Synonyms bolded. TimVickers 22:00, 26 November 2006 (UTC)

Overall this is a strong article on subject that is so broad it is difficult. I think a better job could be done identifying daughter articles but maybe they do not exist yet. I think when you are done this will be a great blue-print for other empires/kingdoms/domains and I hope someone tackles the other six articles as they are important core topics. --Birgitte§β ʈ Talk 16:20, 25 November 2006 (UTC)

Excellent review, thank you. TimVickers 22:39, 25 November 2006 (UTC)
  • A section for interesting info: I think trivia sections are kind of lame but there are a lot of inteseting feats that bacteria perform that are worth mentioning. For instance the only occurance of D-amino acids in nature (that I know of) is in the peptidoglycan of gram negative bacteria, would there be a place for nick-nacks of trivia like this?
  • Someone have a reference for bacteria storing glycogen in granules (as this article suggests)? I was under the influence that glycogen was an animal storage method?—Preceding unsigned comment added by Adenosine (talkcontribs)
Added D-amino acids to cell wall section and referenced glycogen. TimVickers 21:58, 25 November 2006 (UTC)
Wow, learned something cool. Thanks Tim, this is a preimer article on wikipedia.. (sorry I didn't sign before) Adenosine | Talk 10:38, 26 November 2006 (UTC)
  • Please see automated peer review suggestions here. Thanks, AZ t 16:49, 26 November 2006 (UTC)
Suggestions incorporated, thank you. TimVickers 18:47, 26 November 2006 (UTC)

I'd like to double-check that it makes sense to treat the 3-domain system as authoritative. I haven't read anything particularly recent about prokaryotic relationships, but some of the most recent I have seen were skeptical. Gupta (1998)[1] and Cavalier-Smith (2002)[2] for instance argue that archaebacteria more likely developed from Gram-positive bacteria instead of forming a separate domain; Palaeos has a quick discussion of some objections. Obviously this is a minority point of view, but is it one that has since been discredited, or is it something we should acknowledge as a possibility?

All of the articles I read while researching this treated the archaea/bacteria division as a settled fact. I wasn't aware of this alternative viewpoint but at the moment the article reflects the majority view on this. TimVickers 03:49, 28 November 2006 (UTC)
There's nothing wrong with reflecting the majority view, but if it's still based on the idea that rRNA trees are authoritative I think we should at least mention the newer alternative. I'd like to change the text in Groups and Identification to something like the following:
The term "bacteria" was traditionally applied to all microscopic, single-celled prokaryotes. However, evolutionary trees based on rRNA showed prokaryotic life to consist of two separate domains, originally called Eubacteria and Archaebacteria, but now called Bacteria and Archaea. Nowadays this is the generally accepted system of classification, though a few biologists have argued that Archaebacteria are more likely specialized Gram-positive bacteria.[1][2]
Does that seem fair, without putting too much weight on the minority position? It'd be nice to add more about prokaryotic origins and relationships, but as I said, I haven't seen any newer material. Josh 06:37, 28 November 2006 (UTC)
Sounds good. Text added. Thank you. TimVickers 14:30, 28 November 2006 (UTC)
I support the notion that these references this takes a minority view and give it too much weight. The three domain system is the working model that is used by bacterial taxonomists and an encyclopedia article should reflect this. The 3 domains system was developed based on 16S rRNA gene comparison but is also supported by other conserved traits in the domains such as cell wall structure and composition, features of the RNA transcription and translation mechanisms (see three-domain system). The references cited are "works in progress" reflecting minority views that, though they may prove to be correct in the long run, pale into insignificance when compared with the volume of sources that use the three domain classification. If we look hard we can find exceptions for everything in an article as broad as this topic but that does not mean that these exceptions should be detailed. --Azaroonus 10:47, 29 November 2006 (UTC).

In any case we should make sure none of the examples are Archaea. Right now Thermoproteus is mentioned, and it sounds like it's meant as a representative bacterium. I don't know if any bacteria are comparable, but if one exists it should be used instead, or the sentence should be changed. Josh 01:36, 28 November 2006 (UTC)

Sentence changed to use a bacterial example. TimVickers 03:49, 28 November 2006 (UTC)
    • ^ a b Radhey S. Gupta (1998). "Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes". Microbiology and Molecular Biology Reviews. 62: 1435–1491. 
    • ^ a b T. Cavalier-Smith (2002). "The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification". International Journal of Systematic and Evolutionary Microbiology. 52: 7–76.