Biological diversity and Taxonomy

[iansmith]

For bacterial species, it is hypothesised that only 1% of the species have been identified. Fewer species have been isolated are culturable. Most bacterial species are not culturable. Also you to include all other unicellular organism which includes, archea, some species of fungi, and protozoan. Also, it is hypothesized that virtually all insects have an bacterial endosymbionts.

The living is more unicellular than multicellular.

 

[Phobos]

ryokan - I'll see if I can find some more statistics for you. For now, a quick Google search says there are about 900,000 species of insects (http://www.encyclopedia.com/html/section/insect_InsectSpecies.asp ) and there are believed to be around 3,000,000 species of bacteria (http://www.tiscali.co.uk/reference/encyclopaedia/hutchinson/m0007824.html).

Bacterial populations certainly outnumber everything else! (e.g., there can be as many as 2.5 billion bacteria in one gram of fertile soil...http://www.encyclopedia.com/html/b1/bacteria.asp )

You may be interested to read Stephen Jay Gould's book "Full House" on this subject.

 

[ryokan]

ryokan - I'll see if I can find some more statistics for you. For now, a quick Google search says there are about 900,000 species of insects (http://www.encyclopedia.com/html/section/insect_InsectSpecies.asp ) and there are believed to be around 3,000,000 species of bacteria (http://www.tiscali.co.uk/reference/encyclopaedia/hutchinson/m0007824.html).

Bacterial populations certainly outnumber everything else! (e.g., there can be as many as 2.5 billion bacteria in one gram of fertile soil...http://www.encyclopedia.com/html/b1/bacteria.asp )

You may be interested to read Stephen Jay Gould's book "Full House" on this subject.

Phobos, thank you for your interesting links. But my doubts remain.
First, in one of your links I read: "Only 4,000 species of bacteria are known (1998), although bacteriologists believe that around 3 million species may actually exist" . That is a great numerical difference (three magnitude orders)
On the other hand, it is difficult to make a comparison because different concepts are being used for bacteria and metazoans.

Bacterial systematics has not yet reached a consensus for defining the species (Annual Review of Microbiology 2002;56:457-487)

I believe that a phylogenetic approach is being used in bacteria. Following a report in the International Journal of Systematic Bacteriology 1987;37:463-464 a bacterial species is defined as a group of strains (including the type strain) sharing 70% or greater DNA-DNA relatedness with 5 degrees C or less difference of melting temperature (Delta Tm).

Sex has an important role in the definition of species in insects.
It is possible that, whereas an unified concept of species don't be in use, we cannot stablish if insect's diversity is greater than bacterial variety.

 

[iansmith]

First, in one of your links I read: "Only 4,000 species of bacteria are known (1998), although bacteriologists believe that around 3 million species may actually exist" . That is a great numerical difference (three magnitude orders)

As I said before, only a small percentage of the bacteria are cultivable and those are usually the one that are associated with disease in farms animals and human. One of the lab in my old department was looking at the bacterial community of artic soil based on 16 rRNA. They more often identify archea and bacteria that have not been characterized. The a small portion of the bacterial community was identified.

a lot of the study on unculturable bacteria is based on DNA isolated from the environment and Winogradsky colums and its derivative.

Bacterial systematics has not yet reached a consensus for defining the species (Annual Review of Microbiology 2002;56:457-487)

Have you read the paper?

Just out of the abstract

These molecular methods suggest that a typical named species contains many ecotypes, each with the universal attributes of species. A named bacterial species is thus more like a genus than a species.

http://www.ncbi.nlm.nih.gov/entrez/...ve&db=pubmed&dopt=Abstract&list_uids=12142474

So the author is suggesting that bacterial diversity is greater than that of the multicellular world.

For microbiologists, the new systematics has been particularly fruitful. Microbial systematists have built a universal tree of life, such that any newly discovered organism can be placed near its closest relatives (18,104). Sequence surveys have fostered discovery of new bacterial taxa at all levels. Sequence data have frequently turned up organisms with no known close relatives; these organisms represent new divisions within the bacterial world (18). At the other extreme, sequence surveys have fostered the discovery of new species. For example, sequence data revealed the Lyme disease spirochete Borrelia burgdorferi (sensu lato) to consist of several species, each with its own etiology (7,8). Sequence-based approaches have allowed systematists to characterize the species diversity even among uncultured bacteria, and species names have now been given to many uncultured organisms, pending further characterization (62). ...

I argue that there are bacterial taxa called "ecotypes" (15), which share the quintessential set of dynamic properties held by all eukaryotic species. I demonstrate that, alas, the species generally recognized in bacterial systematics do not have these universal properties: Each named "species" appears to contain many ecotypes, each with the dynamic properties of a species. I present several universal sequence-based approaches for discovering ecotypes and recommend a means of incorporating ecotypes into bacterial taxonomy.

http://proquest.umi.com.ezproxy.lib...&VName=PQD&TS=1100979044&clientId=15814&aid=1

I believe that a phylogenetic approach is being used in bacteria. Following a report in the International Journal of Systematic Bacteriology 1987;37:463-464 a bacterial species is defined as a group of strains (including the type strain) sharing 70% or greater DNA-DNA relatedness with 5 degrees C or less difference of melting temperature (Delta Tm).

That is an old report and does hold true most of the time nowadays. This concept of species is starting to lose grip on classification because new techniques and test are being developped and the scientific community is aging and new blood is coming in.

Sex has an important role in the definition of species in insects. It is possible that, whereas an unified concept of species don't be in use, we cannot stablish if insect's diversity is greater than bacterial variety.

The problem here might that the role of sex might not be of concept to identify a species. Arthropoda as a group probably one of the greatest diversity in the animal kingdom. I also agree that it is hard to compare diversity when you are not using the same concept of classification. However, the microbial world has colononized every possible niche on Earth's which includes arthropoda digestive system. It is hypotheised that every arthropoda digestive system have at least a unique bacterial, archeal or protozan specie. Some of which have been sequenced.

 

[ryokan]

The problem here might that the role of sex might not be of concept to identify a species. Arthropoda as a group probably one of the greatest diversity in the animal kingdom. I also agree that it is hard to compare diversity when you are not using the same concept of classification. However, the microbial world has colononized every possible niche on Earth's which includes arthropoda digestive system. It is hypotheised that every arthropoda digestive system have at least a unique bacterial, archeal or protozan specie. Some of which have been sequenced.

What would be a good, universal, definition of species ? I don't know if there is already such definition.
If DNA or RNA homologies are an essential component of definition, it would be possible that one insect species, for example, were also rather a genus. And, could we talk on species with reference to cells in a multicellular organism? Of course, in this case, genotype is the same, but gene expression differ. Furthermore, there are changes in genotype by somatic mutations in cancer. Make it sense talk about species of cancerous cells?

 

[iansmith]

As far as I know, there no universal definition for a species but a lot of reoganization are being done. Highly conserved genes and morphology are being used to classified insect species. I personnaly think that genetic and morphology is the way to go. Sexual behavior is sometimes missleading. If you used genetic, then you use the same level for bacteria. Although, some bacterial species have been separated for medical purpose. The best example is Shigella and E. coli. They are both the same species but cause distinctive clinical symptomes. I personally think it's silly.

Different gene expression in bacteria only results in different strain name or group rather than a new species. For cancer, the highly conserved genotype is unchange, it is only the genes regulating cell division that usually mutates and are usually not used in systematics. You can also tell the site of origin of the cancer. There is classification for cancer based on the site of origin but it is not a new specie.

 

[ryokan]

As far as I know, there no universal definition for a species but a lot of reoganization are being done. Highly conserved genes and morphology are being used to classified insect species. I personnaly think that genetic and morphology is the way to go.

With quantitative or qualitative criteria?
What would be important: % of homology in genomes or rather homology in selected regions?

For cancer, the highly conserved genotype is unchange, it is only the genes regulating cell division that usually mutates and are usually not used in systematics. You can also tell the site of origin of the cancer. There is classification for cancer based on the site of origin but it is not a new specie.

But sometimes changes in cancerous cells are enough important to be seen at cytological level (structural and numeric chromosomal aberrations).
Site of origin is only one characteristic in one cancer. Histological differentiation grade is also important and clinically, as you know, criteria as TNM are very useful to make the prognosis in a lot of cancers. Now, the differentiation in expression patterns by means of microarrays is a promising way to make a best prognosis and election of therapy.
In some form, we can talk from different species of cancer, even for a common anatomic origin, although in this case, the concept species be unrelated to the traditional concept.

 

[iansmith]

We were having a discussion in other thread about complexity, which I split and merge with this one, and started to discuss diversity.

We are trying to answer these questions

I do we measure biological diversity? What should we used to measure biological diversity?

I do we classify species and I do we group them?