Talk:Bacteria

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Number of Species suggestion[edit]

This was originally written for the Species page, but was only added in a very abreviated form. I would like to propose inserting it into this article, following the "Classification and identification" section.


Number of Species[edit]

Total number of bacterial species (estimated): 5–10[1], or even 1,000 million[2] (identified and unidentified) bacteria worldwide.

Of the 6,000 to 170,000 identified prokaryotic species there are:

  • 16,000 prokaryotic species "seen by science", based on the number of different 98% unique 16S_ribosomal_RNA sequences in databases as of 2004[2]. This analysis was based on a total of 56,215 16S rRNA gene sequences, the total number of 16S rRNA gene sequences in 2010 was 1,483,016, almost 30 times as many[3].
  • 6,728 bacteria Type_strains that are fully described, currently stored in culture collections, and with a sequenced 16S_ribosomal_RNA gene (as of 2008)[4].
  • 165,676 bacteria species with some genetic sequence known (of which 10,045 were in Microbiological_culture)), as of 2011[5]
  • 4,794 Archaea species with some genetic sequence known (of which 395 were in Microbiological_culture)), as of 2011[5]


Rationale[edit]

Here is my reasoning for the above values:

This paper: The All-Species Living Tree project. Yarza et al. 20008 http://www.ncbi.nlm.nih.gov/pubmed/18692976 [4] provides a lower-bound estimate of 6728, since the Type Species they are describing are a subset of named species, almost all of which have been grown in pure culture and are in collections (see article).

While the estimates of 5–10 million bacteria are still current, and probably better supported (as pointed out elsewhere, the species concept is even more difficult for these organisms) the paper listed below [2] cites a range from 10^7 to 10^9 (10 to 1,000 million) for the estimated number of species on the planet.

There is also published estimates of 35,498 total species richness, based on the 16,000 species that have been "seen by science". This latter value is based on the number of different 16S_ribosomal_RNA or RRNA genes (also see Molecular_phylogenetics) that are 98% or more divergent as described in this paper: Status of the Microbial Census. Schloss and Handelsman. 2004 http://www.ncbi.nlm.nih.gov/pubmed/15590780 [2]. However, the data they were basing their estimate on was much less than is in current databases, so I referenced release 10 to the RDP for a current number.

I've included values from the NCBI GenBank database's Taxonomy section since it is current, and the repository for all sequences. NCBI also has a taxonomic identifier for each sequence. [5]

References[edit]

  1. ^ Sogin ML, Morrison HG, Huber JA et al. (August 2006). "Microbial diversity in the deep sea and the underexplored "rare biosphere"". Proc. Natl. Acad. Sci. U.S.A. 103 (32): 12115–20. doi:10.1073/pnas.0605127103. PMC 1524930. PMID 16880384.  Cheung L (Monday, 31 July 200). "Thousands of microbes in one gulp". BBC.  Check date values in: |date= (help)
  2. ^ a b c d Schloss, P. D.; Handelsman, J (2004). "Status of the microbial census". Microbiology and molecular biology reviews : MMBR 68 (4): 686–91. doi:10.1128/MMBR.68.4.686-691.2004. PMC 539005. PMID 15590780.  edit
  3. ^ Cole, J. R.; Wang, Q.; Cardenas, E.; Fish, J.; Chai, B.; Farris, R. J.; Kulam-Syed-Mohideen, A. S.; McGarrell, D. M.; Marsh, T.; Garrity, G. M.; Tiedje, J. M. (2009). "The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis". Nucleic Acids Research 37 (Database issue): D141–D145. doi:10.1093/nar/gkn879. PMC 2686447. PMID 19004872.  edit
  4. ^ a b Yarza, P.; Richter, M.; Peplies, J. R.; Euzeby, J.; Amann, R.; Schleifer, K. H.; Ludwig, W.; Glöckner, F. O.; Rosselló-Móra, R. (2008). "The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains". Systematic and Applied Microbiology 31 (4): 241–250. doi:10.1016/j.syapm.2008.07.001. PMID 18692976.  edit
  5. ^ a b c "NCBI taxonomy tool". NCBI, NIH. Retrieved 2011-01-08. 

Semi-protected edit request on 16 January 2014[edit]

I thought the discovery of bacteria occurred in 1676 not 1683. 68.111.75.96 (talk) 05:30, 16 January 2014 (UTC)

Not done: please provide reliable sources that support the change you want to be made. --Anon126 (talk - contribs) 23:12, 16 January 2014 (UTC)
Done. The cited source says 1676. --Anon126 (talk - contribs) 23:14, 16 January 2014 (UTC)

Fungi is smelly stuff that grew on your Nan. — Preceding unsigned comment added by 5.64.243.207 (talk) 19:55, 13 May 2014 (UTC)

Bacteria also live in symbiotic and parasitic relationships with plants and animals.[edit]

This sentence from the first paragraph maybe should be re-written. Parasitism is a type of symbiosis. I would suggest "Bacteria also live in mutualistic, commensualistic, and parasitic relationships with plants, animals, and other organisms." — Preceding unsigned comment added by 50.149.237.104 (talk) 14:53, 17 May 2014 (UTC)

Bacteria also live in symbiotic and parasitic relationships with plants and animals.[edit]

This sentence from the first paragraph maybe should be re-written. Parasitism is a type of symbiosis. I would suggest "Bacteria also live in mutualistic, commensualistic, and parasitic relationships with plants, animals, and other organisms." — Preceding unsigned comment added by 50.149.237.104 (talk) 14:58, 17 May 2014 (UTC)

Semi-protected edit request on 25 July 2014[edit]

I suggest a small grammar change in the section Classification and Identification. In the sentence "Once a pathogenic organism has been isolated, it can be further characterised by its morphology, growth patterns such as (aerobic or anaerobic growth, patterns of hemolysis) and staining." the open parentheses needs to be moved to replace the comma currently inside it, and another comma added after the end of the parentheses. This is the last sentence in the second to last paragraph in the section. 155.41.91.189 (talk) 17:45, 25 July 2014 (UTC)

Yes check.svg Done Anon126 (notify me of responses! / talk / contribs) 05:33, 26 July 2014 (UTC)

Copyright violation and incorrect information about Gram stain type[edit]

Braineeee (talk) 20:32, 11 October 2014 (UTC)I'm in a Biology course in post secondary school (ie. College) and I needed to find some information about Gram staining. I found a page with the exact same image (from a published book) only a different color. Its the image claimed to have been made by LadyOfHats and uploaded by NI74 in 2006 on this page. Changing 10% of an image (ie. its color) or other copyrighted work does not make it yours to release for free on the internet or in the public domain. That is a violation of copyright law as well. The correct Gram stain for this type of bacteria is Gram negative (using a red/pink Safranin or Fuchsine) dye. The image on this page is blue, and that is completely incorrect, it should be pink. I'm just a tad bit upset that I had to add this comment, and I had to waste my time double checking this for a homework assignment. Other Wikipedia pages about bacteria have conflicting information with this one. My sources are: http://amrita.vlab.co.in/?sub=3&brch=73&sim=208&cnt=1 and http://en.wikipedia.org/wiki/Gram_staining.

Number 1
Number 2
Hi @Braineeee: Thanks for your post. Is Number 1 the image you refer to first? If it is then it's almost certain that the book you read copied the image from Wikipedia rather than the other way around. User:LadyofHats makes amazing illustrations and releases them into the public domain so that anyone can republish them wherever they like.
I think you also refer to number 2 which was taken from p4. of this paper and I agree that it is a little different to the original. The image is in the public domain however as it was created by employees of the Centre for Disease Control. Unfortunately it is difficult to find good images for us to use and in this case this might be the best that we can find and we need someone with a good microscope to donate a better one. SmartSE (talk) 21:37, 11 October 2014 (UTC)

DNA and RNA[edit]

This is a very useful source on bacteria. My thanks to to all who put it together .

I am confused about one thing. The text refers to bacteria having RNA in its chromosome whereas the diagram of a bacterium refers to DNA. is there an error in the diagram or am I missing something? Andrew Morris andrewmorris@msn.com — Preceding unsigned comment added by 82.6.237.86 (talk) 15:12, 1 April 2015 (UTC)

I think you mean these two sentences: "Most bacteria do not have a membrane-bound nucleus, and their genetic material is typically a single circular chromosome located in the cytoplasm in an irregularly shaped body called the nucleoid. The nucleoid contains the chromosome with its associated proteins and RNA." This means that the chromosome is made of DNA, but the nucleoid also contains RNA and proteins. Clarified here. Opabinia regalis (talk) 19:47, 1 April 2015 (UTC)

Metabolism Section -- Table[edit]

The table in the metabolism section list three energy sources: phototrophs, lithotroph, and organotroph. Technically, this is not correct, as lithotroph and organotroph refer to source of reducing equivalents. Lithotrophs can be photolithotrophs or chemolithotrophs. ~~Glucono — Preceding unsigned comment added by 50.149.237.104 (talk) 12:33, 18 April 2015 (UTC)

Semi-protected edit request on 13 July 2015[edit]

Please add to the "Further reading section" the following reference: Ogunseitan, O.A. (2005) Microbial Diversity: Form and Function in Prokaryotes. 312 pages. Wiley-Blackwell. ISBN: 978-1-4051-4448-3.

Plebeiansix (talk) 18:19, 13 July 2015 (UTC)

Yes check.svg Done Sorry about the not done earlier. I was mistaken. I will add it in now.