Talk:Bacteria

Number of Species suggestion

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

Total number of bacterial species (estimated): 5–10, or even 1,000 million (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. 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.
• 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).
• 165,676 bacteria species with some genetic sequence known (of which 10,045 were in Microbiological_culture)), as of 2011
• 4,794 Archaea species with some genetic sequence known (of which 395 were in Microbiological_culture)), as of 2011

Number of Species suggestion rational

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 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 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 . 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.

Habitat

The introduction suggests that bacteria only live on planet Earth. Is this true? Are there no bacteria on the Moon or on Mars, e.g.? 196.215.32.190 (talk) 13:42, 14 August 2010 (UTC)1 Geografiskt läge

If you have any reliable sources which tell us there are bacteria (or life) outside planet Earth, please provide them. Crum375 (talk) 14:06, 14 August 2010 (UTC)

Most people believe that there is no such thing as bacteria outside of Earth. That would be equivalent to extra-terrestrial life i.e. aliens (but not in the common sense of the word). However, there have been claims made by scientists regarding possible outer space bacteria (http://archives.cnn.com/2000/TECH/space/11/24/alien.microbe.claim/index.html) or fossils of these bacteria but there are no definitive results. I guess the article should have mentioned that this fact has not been established yet and plenty of speculation remains. Occamsrazorwit (talk) 08:58, 20 August 2010 (UTC)

The article does not say that there are extra-terrestrial bacteria, the only statement close to this is in the section on endospores, which states that "endospores even allow bacteria to survive exposure to the vacuum and radiation in space" (PMID 15748651), which deals with the problem of contaminating other planets with Earth bacteria during space exploration. The putative fossilised extraterrestrial microbes can't be classified as bacteria or archaea (they might be an entirely different form of life or not the remains of living things at all) so including them in this article based solely on morphological similarity would be very misleading. Tim Vickers (talk) 16:45, 20 August 2010 (UTC)

Origin and early evolution

The "Origin and early evolution section" says:

"The most recent common ancestor of bacteria and archaea was probably a hyperthermophile that lived about 2.5 billion–3.2 billion years ago."

It supports this statement by quoting two references:

1. Di Giulio M (2003). "The universal ancestor and the ancestor of bacteria were hyperthermophiles". J Mol Evol 57 (6): 721–30. doi:10.1007/s00239-003-2522-6. PMID 14745541.

2. Battistuzzi FU, Feijao A, Hedges SB (November 2004). "A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land". BMC Evolutionary Biology 4: 44. doi:10.1186/1471-2148-4-44. PMID 15535883.

However, the references do not support this statement. For example, the second article (the one by Battistuzzi and Hedges) says:

Divergence time estimates for the major groups of eubacteria are between 2.5–3.2 billion years ago (Ga) while those for archaebacteria are mostly between 3.1–4.1 Ga. The time estimates suggest a Hadean origin of life (prior to 4.1 Ga), an early origin of methanogenesis (3.8–4.1 Ga), an origin of anaerobic methanotrophy after 3.1 Ga, an origin of phototrophy prior to 3.2 Ga, an early colonization of land 2.8–3.1 Ga, and an origin of aerobic methanotrophy 2.5–2.8 Ga.

What they are saying is that the divergence date for the 3 major groups of eubacteria (Actinobacteria, Deinococcus, and Cyanobacteria) are between 2.5 and 3.2 billion years ago. This is not the same as saying "The most recent common ancestor of bacteria and archaea was probably a hyperthermophile that lived about 2.5 billion–3.2 billion years ago".

It stands to reason that if the 3 major groups of eubacteria diverged from each other at 2.5-3.2 billion years ago, then eubacteria must have diverged from archea even earlier.

As they say later in the article, this is a guess, since a date for the common ancestor of eubacteria and archaebacteria has not been calculated. There are only various minimum estimates. Their estimates are <4 billion years, as stated here:

"Neither the time for the origin of life, nor the divergence of archaebacteria and eubacteria, was estimated directly in this study. Nonetheless, one divergence within archaebacteria was estimated to be as old as 4.11 Ga (Node P), suggesting even earlier dates for the last common ancestor of living organisms and the origin of life."

In fact, this is reiterated in a more recent publication by the same group. The publication is "The Timetree of Life" by S. Blair Hedges and Sudhir Kumar (Oxford Press). Quoting from this:

"An initial split (~4200 Ma) led to the Superkingdoms Eubacteria and Archaebacteria."

I haven't ever directly edited any Wikipedia page, and am unsure whether this is a good idea for a Wikipedia newbie like me. Therefore, I am putting my comments on the talk page. I hope someone will confirm the details I have provided and correct the article.

Xen1977 (talk) 21:05, 29 September 2010 (UTC) Xenofon

Thanks for pointing that out, apologies it's taken so long for someone to respond! I'm not sure how to correct it, but have asked some other people to take a look. If you see errors again, don't be afraid to be BOLD and fix them. SmartSE (talk) 21:28, 10 November 2010 (UTC)

Rcats needed

{{editprotected}} The following redirects need redirect categories/category parameters added:

• Bacterium

#REDIRECT [[Bacteria]]{{R to plural|printworthy}}{{R from move}}

That will subdue the Unprintworthy cat and add the redirect to Category:Printworthy redirects.

• Talk:Bacterium

#REDIRECT [[Talk:Bacteria]]{{R to talk}}

Thank you in advance for making these code modifications.  —  Paine Ellsworth ( CLIMAX )  19:19, 16 February 2011 (UTC)

Y Done. Also unprotected that talk page. — Martin (MSGJ · talk) 11:56, 17 February 2011 (UTC)

Once again, I thank you very much, Martin! Just curious as to why the full protection on the singular redirect? The target is only semi-protected, if I'm not mistaken.  —  Paine Ellsworth ( CLIMAX )  15:57, 17 February 2011 (UTC)

• PS. Never mind. I was able to receive the kind help of the administrator who had added full protection to modify it to semi. Cheers!  — Paine Ellsworth ( CLIMAX ) 

Plasma membrane

In the section, "Cellular structure", the term "plasma membrane" is introduced with no explanation: "However, in many photosynthetic bacteria the plasma membrane is highly folded". Is it the same as the "cell membrane" or different? AndreasLotheOpdahl (talk) 07:37, 6 April 2011 (UTC)

Toxin-producing bacteria>

In the modern Darwinian model of evolution, what survival/evolutionary benefit does it confer to the bacteria to produce toxin(s) that kill the host (take your pick: cholera, bubonic plague, etc, etc, etc)? There must be some; the article says that these are very ancient bacteria. Old_Wombat (talk) 09:26, 11 October 2011 (UTC)

Bacteria have not evolved to kill people. Bacteria have evolved to multiply and spread. Toxicity that helps the bacteria spread to new hosts (by inducing diarrhea, for example) confers a survival benefit. When or if the host dies is not relevant if the bacteria can successfully spread to new hosts. -- Donald Albury 10:43, 11 October 2011 (UTC)

See the article Optimal virulence, which discusses this topic in detail. Peter coxhead (talk) 11:00, 11 October 2011 (UTC)

Ahh, two good answers. That Optimal virulence article answers my question exactly and I would not have thought to even look for such a title on my own. Dumbass me. Thank you all. Old_Wombat (talk) 09:07, 12 October 2011 (UTC)

Not "dumbass" at all. This illustrates the paradox of large amounts of information being available, but without more intelligent search agents, not being findable. I happened to know that there is a field called "evolutionary medicine" which covers this topic; from the article on this I found "optimal virulence". I don't see how you would find this unless you first knew where to look... Peter coxhead (talk) 10:43, 12 October 2011 (UTC)

Indeed. I knew that the topic has been studied, but my (admittedly quick and sloppy) search didn't find a relevant article. -- Donald Albury 12:37, 12 October 2011 (UTC)

Number of species (redux)

Some observations. Cyanophytes are Bacteria. Under the three-domain system, all Bacteria are prokaryotes, but not all prokaryotes are Bacteria (some are Archaea). We do not add together the number of cyanophytes and the number of prokaryotes to get the number of Bacteria. The source at http://www.bacterio.cict.fr/number.html gives a figure of 9,278 species of prokaryotes. This would include all Bacteria (including all cyanobateria) and all Archaea. This source from 2006, Staley, James T. (2006 November 29). "The bacterial species dilemma and the genomic-phylogenetic species concept". Philosophical transactions of the Royal Society B Biological Sciences 361 (1475): 1899-1909. doi:10.1098/rstb.2006.1914. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1857736/. Retrieved 13 December 2011. , states that there were then about 5,000 named species of Bacteria and Archaea. A 1990s source I saw stated there were then about 4,000 described species of bacteria (presumably including Archaea). I will change the article back to reflect this. -- Donald Albury 22:03, 13 December 2011 (UTC)

I agree. Graham Colm (talk) 22:06, 13 December 2011 (UTC)

Uhm... I think the problem with Cyanobacteria is not that it was not part of Monera in many schemes —incessant Christian vandalisms to Monera apart—, but that the vast majority of cyanobacterial species are not validly described, even "Nostoc" and "Acharyochloris". However, the more fundamental problem of "bacterial species" is not addressed. In my mishmash Bacterial taxonomy I have a section (Bacterial taxonomy#Species concept) that briefly touches upon it, Species problem does not talk about non-animal, so to the best of my knowledge, there is not article in Wikipedia about Bacterial species problem (along with many other pages). I think the take-home message should be that the definition of species is near meaningless for Bacteria and that only 5,000 or so species have so far been properly classified (by properly I mean validly, but properly is more legible in layman English). Regarding the exact figure —I thought 5,000 too—, Euzeby's site (http://www.bacterio.cict.fr/number.html) may the most accurate source of species number, although this page in particular is not: there is not only the Archaea issue, but also an issue with basonyms (ie. if it changed name, it will have be counted twice). It is a shame as all other sources will be out of date or estimates, but maybe it should be switched with a paper. On a side comment, 700 new species a year is a cool figure, shame those tables in LPSN are not also in graph form... Digressions apart, I think the sentence should have a different message. --Squidonius (talk) 06:01, 14 December 2011 (UTC)

The Staley article I linked to above discusses the problem of defining species of bacteria. There are surely enough reliable sources out there to support a good article/section on the problem. The species concept is a bit blurred, even in mammals (see Talk:Red Wolf). -- Donald Albury 12:17, 14 December 2011 (UTC)

Extra (

Just working on a PowerPoint for my high school biology class and noticed an extra open parenthesis '(' in the growth and development section. Since the article was locked, I did not think I could do anything. Thanks and keep up the good work wikipedia!

Axc201 (talk) 04:33, 27 January 2012 (UTC)

Fixed, thanks. Materialscientist (talk) 04:37, 27 January 2012 (UTC)