Abstract

The use of cultivation-independent approaches to map microbial diversity, including recent work published in BMC Biology, has now shown that protists, like bacteria/archaea, are much more diverse than had been realized. Uncovering eukaryotic diversity may now be limited not by access to samples or cost but rather by the availability of full-length reference sequence data.See research article http://www.biomedcentral.com/1741-7007/7/72

Highlights

  • It may seem astounding to some that we could be unaware of phylum-level protistan taxa, the discovery of novel eukaryotic SSU rRNA genes in natural environmental samples mirrors the gaps in our understanding of bacterial and archaeal diversity

  • Every time we have surveyed an environment using SSU rRNA cultivation-independent methods, we have found that it contains more protistan species than we know from our culture collections or sequence databases

  • How many protistan species have we missed? In their analysis of two marine anoxic environments using massively parallel pyrosequencing recently published in BMC Biology, Stoeck and colleagues [5] conclude we have missed considerable protistan diversity

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Summary

The extent of protistan diversity

How many protistan species have we missed? In their analysis of two marine anoxic environments using massively parallel pyrosequencing recently published in BMC Biology, Stoeck and colleagues [5] conclude we have missed considerable protistan diversity. To determine the extent of a possible protistan ‘rare biosphere’, Stoeck et al [5] sequenced about 250,000 eukaryoticspecific V9 variable regions of the SSU rRNA Previous surveys of these two anoxic environments were limited to Sanger sequencing of SSU rRNA clone libraries. Deep sequencing allows the extensive characterization of SSU RNA PCR amplicons, and the authors [5] thereby determined that over 90% of the SSU rRNA sequence diversity was derived from individual rare sequences, each of which was identified less than ten times. They have revealed the existence of a protistan ‘rare biosphere’. The authors [5] detected eukaryotic microbes from all major protistan groups in their anoxic sediment samples, indicating that these environments harbor the same types of eukaryotic microbes as more familiar oxic environments

Defining and quantifying eukaryotic microbial diversity using rRNA
Findings
Further challenges in assessing eukaryotic microbial diversity
Full Text
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