Tuesday, April 23, 2013


Diatoms are amazing often beautiful microscopical algae whose typical feature is a siliceous coverage, called frustule, extremely diverse in shape. Diatoms live in almost all types of superficial waters. Depending on their habitats, diatoms are either planktonic, benthic, or both planktonic and benthic.
The ecological requirements of many diatom species are known and therefore many diatom-based indexes of water quality have been developed and are used to monitor water quality. However, producing taxonomical inventories for diatom communities is time-consuming, costly, and requires a high level of taxonomic expertise. On the other hand a comprehensive assessment of the taxonomic composition of an environmental community is often essential for studying an ecosystem in order to evaluate the impact of environmental stressors or to establish a baseline that evaluates ecosystem functions.

A group of French researchers has now published the results of a test to evaluate the suitability of Next Generation Sequencing for the taxonomic characterization of freshwater diatom communities. They used three molecular markers targeting the nuclear, chloroplast and mitochondrial genomes (SSU rDNA, rbcL and COI) and three samples of a mock community composed of 30 known diatom strains belonging to 21 species. 454 pyrosequencing was used to produce libraries for each of the three samples and for each marker. Three DNA reference libraries obtained by conventional Sanger sequencing  were used for read assignment and evaluation of accuracy.

Of all the markers tested RbcL showed the highest resolving power in conjunction with a large DNA reference library. The authors conclude: Although needing further optimization, pyrosequencing is suitable for identifying diatom assemblages and may find applications in the field of freshwater biomonitoring.

Diatoms are one of the largest and ecologically most significant groups of organisms on Earth. Because of their abundance they probably account for as much as 20% of global photosynthetic fixation of carbon, which is more than all the world's tropical rainforests. Understanding their community structures is probably a more important task than most of us would think. Maybe it helps to think of it this way:

Another way to appreciate diatoms is to realize that they give us every fifth breath, by the oxygen they liberate during photosynthesis (David Mann, Tree of Life website).

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