Biodiversity - "barcoding" of taxa

MARK BLAXTER Molecular systematics: Counting angels with DNA. Nature 421, 122 - 124 (2003)

How many species of prokaryotes are there in the ocean ?

Until recently only as many as 0.01% of cells in mid-ocean could be cultured.

Many cells in mid-ocean are < 0.2 µm in diameter

How many of the cells we see by epifluorescent microscopy are viable?

Are most cells we see under the microscope dead but not yet degraded?

Washing stained cells removes the stain from many but most cells still retain stain.

Until recently most work on prokaryoticplankton treated it as a single trophic department because we were unable to accurately resolve the composition of the community. Molecular studies are now opening up this hidden world. Archaea are now known to dominate Bacteria in some oceanic water samples. DeLong, E.F.; Wu, Ke Ying; Prezelin, B.B.; Jovine, R.V.M. 1994 High abundance of Archaea in Antarctic marine picoplankton. Nature; vol. 371, no. 6499, pp. 695-697; 1994

Archaea
These organisms are microscopic prokaryotes. When the first ones were discovered (in 1977), they were considered bacteria. However, when their ribosomal RNA was sequenced, it became obvious that they were more closely related to the eukaryotes (including ourselves!)
The Archaea have been divided into three groups on the basis of r-RNA:
Euryarchaeota
Crenarchaeota
Korarchaeota
Euryarchaeota - there are three main subgroups:
Methanogens
Halophiles
Thermocidophiles
Crenarchaeota
The first members of this group to be discovered like it really hot and so are called hyperthermophiles. One, Pyrolobus fumaris, lives at 113°C. Other members of this group seem to make up a large portion of the plankton in cool, marine waters. As yet, none of these has been isolated and cultivated in the
laboratory.
Korarchaeota
only their nucleic acids have been detected, and no organisms have been isolated or cultured

How can mid-ocean bacteria be grown?

1. Reduce phosphate to 0.005 µM

2. Pass sea water through Chelex resin to remove metals

3. Incubate sonicated water samples on membrane filters
and count dividing cells

This gives a count of doubling cells > 20 % of direct counts

SAR 11, possibly the most numerous bacterium in the world, has now named as Pelagibacter ubique

SAR11 was first identified from a study of r-RNA genes in a sample of bacteria fom the Sargasso Sea in 1990. It was finally isolated last year:

Michael S. Rappé, Stephanie A. Connon, Kevin L. Vergin, Stephen J. Giovannoni Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418: 630-633 (2002).

This bacterium has a world-wide distribution. It is a vibrio 0.37-0.89 µm long, 0.12-0.20 µm diameter and cell volume as small as 0.01µm3 This makes it one of the smallest self-replicating cells known.

R. M. Morris et al. SAR11 clade dominates ocean surface bacterioplankton communities Nature 420, 806 - 810 (2002)

Iron fertilization - can it solve the 'greenhouse' problem

Schiermeier, Q. (2003) Climate change the oresmen. Nature 421: 109-110.