Marine microbial diversity: can it be determined?

doi:10.1016/j.tim.2006.04.007

Trends in Microbiology

Volume 14, Issue 6, June 2006, Pages 257-263

https://doi.org/10.1016/j.tim.2006.04.007 Get rights and content

Estimates of the order of magnitude for the total number of microbial species on Earth range from 10³ to 10⁹. Despite global dispersal of microorganisms, this number is probably rather large. The total biodiversity of an ecosystem is composed of two elements: first, a set of abundant taxa that carry out most ecosystem functions, grow actively and suffer intense losses through predation and viral lysis. These taxa are retrievable with molecular techniques but are difficult to grow in culture. Second, there is a seed bank of many rare taxa that are not growing or grow extremely slowly, do not experience viral lysis and predation is reduced. Such taxa are seldom retrieved by molecular techniques but many can be grown in culture, which explains the dictum ‘everything is everywhere’.

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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View full text

Trends in Microbiology

Marine microbial diversity: can it be determined?

Section snippets

How many species?

The known and the unknown

Diversity and biodiversity

Delights of a diluted life

What portion of the unknown can be determined?

Concluding remarks and future perspectives

Acknowledgements

Glossary

Trends Ecol. Evol.

FEMS Microbiol. Ecol.

Trends Ecol. Evol.

Protist

The census of marine life: goals, scope and strategy

Sci. Mar.

Ubiquitous dispersal of free-living microorganisms

Microbial endemisms and biogeography

Biogeography: is everything everywhere?

Science

Prokaryotes: the unseen majority

Proc. Natl. Acad. Sci. U. S. A.

Ecology – marine bugs and carbon flow

Science

All at sea

Nature

Hidden in a sea of microbes

Nature

The deep roots of eukaryotes

Science

Genetic diversity in Sargasso Sea bacterioplankton

Nature

Novel major archaebacterial group from marine plankton

Nature

Archaea in coastal marine environments

Proc. Natl. Acad. Sci. U. S. A.

Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencing

Appl. Environ. Microbiol.

Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton

Nature

Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity

Nature

Use of 16S ribosomal DNA for delineation of marine bacterioplankton species

Appl. Environ. Microbiol.

Biogeographic analysis of ribosomal RNA clusters from marine bacterioplankton

Aquat. Microb. Ecol.

Estimating prokaryotic diversity and its limits

Proc. Natl. Acad. Sci. U. S. A.

Santa Rosalia revisited: why are there so many species of bacteria?

Antonie Van Leeuwenhoek

Global dispersal of free-living microbial eukaryote species

Science

Where are all the species?

Environ. Microbiol.

Cosmopolitan microbes and their ‘cryptic’ species

Aquat. Microb. Ecol.

Assortative mating as a mechanism for rapid evolution of a migratory divide

Science