Trends in Microbiology
Marine microbial diversity: can it be determined?
Section snippets
How many species?
Ecologist Robert May remarked that “we have a catalog of all the celestial bodies our instruments can detect in the universe, but we ignore how many living beings share the Earth with us” (ISME meeting, Barcelona, 1992). This ignorance is particularly large for life in the oceans. Thus, the international initiative ‘Census of Marine Life’ [1] was launched to “assess and explain the changing diversity, distribution and abundance of marine species from the past to the present, and to project
The known and the unknown
Approximately 6000 species of prokaryotes (http://www.bacterio.cict.fr/number.html) and 100 000 species of protists [17] have been formally described. This is the known diversity. Most information about these microorganisms comes from the study of pure cultures, at least in the case of prokaryotes, in which a strain deposited in a culture collection is necessary to describe a new species.
The unknown diversity is currently being explored with molecular techniques, particularly cloning and
Diversity and biodiversity
A way out can be found in the distinction between diversity and biodiversity proposed by Margalef 39, 40. Biodiversity would be the total genetic information on Earth or in any part of it. Diversity, in turn, would be the components that are active and abundant at one particular time and place. A literary analogy would equate biodiversity with a dictionary of all the words in a language, whereas diversity would be the particular set of words (and their frequency of use) chosen for a particular
Delights of a diluted life
The rare taxa are recruited through immigration, which is dependent on dispersal from other ecosystems. It has already been argued that because of their small size and large numbers, microbes should be easily dispersed everywhere 2, 3, 6, 23, 26, thus, immigration rates are expected to be large. By contrast, death and subsequent loss will eliminate taxa from the rare part of the curve, however, these taxa can be expected to have extremely low loss rates. The two main loss factors for
What portion of the unknown can be determined?
Rare taxa will seldom be retrieved by cloning and sequencing with universal primers. PCR primers will predominantly hybridize with the common taxa and the rare ones will remain unknown for the same reasons that viruses cannot find rare bacterial taxa in a reasonable amount of time. The situation can be improved by using primers specific for some groups of bacteria (such as ammonia oxidizers [46]) by techniques such as nested PCR [47] and by shotgun cloning, in which PCR is not used 48, 49.
Concluding remarks and future perspectives
Studies of bacterial diversity within this framework make sense from an ecological point of view. Thus, for example, latitudinal patterns in the distribution of the bacterial taxa that form the diversity have been found by cloning and sequencing large clone libraries from different oceans (T. Pommier et al., unpublished). If the seed bank from such samples could have been analyzed simultaneously, it is likely that ‘everything would be found everywhere’.
Some rare taxa will eventually be
Acknowledgements
My work is currently supported by grant CTM2004–02586/MAR from the Spanish Ministry of Education and Science and the EU network of excellence ‘Marine Genomics Europe’ EU-FP6–505403. Ramon Massana, Josep M. Gasol, Jarone Pinhassi, Thomas Pommier and three anonymous reviewers provided useful comments on earlier versions of the manuscript.
Glossary
- Allopatric speciation:
- the origin of two or more species resulting from divergent evolution of populations that live in geographical isolation.
- Biodiversity:
- the total, specific, taxonomic or genetic richness contained in nature or in any local or taxonomic part of it. The repository of genotypes. The actual richness of ‘nature's dictionary’ [39,40], which could be also named ‘global diversity.’
- Biological species concept:
- two populations are considered to belong to the same species if they can
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