Tuesday, March 10, 2009

The Diversity of Nature

With the advent of next-generation sequencing capabilities, many questions that were previously beyond our capabilities to explore are now well within reach. Metagenomic approaches in particular have recently experienced a burst of recognition. One such question that can no be addressed is the extent to which isolated cultures used in laboratory settings represent the true genetic diversity apparent in nature (Tettelin 2005). Pyrosequencing is especially important for such studies in that it is culture-independent. That is, genome sequences can be obtained from a sample even if the species in that sample cannot typically be grown in a laboratory setting. The authors of this paper applied 454 pyrosequencing to marine and coastal samples of cyanobacteria of the genus Synechococcus. This allowed them to identify the levels of diversity present in natural Synechococcus populations and acknowledge the importance of horizontal gene transfer in marine and coastal populations of cyanobacteria.

The authors were able to enrich their samples with Synechococcus by capitalizing on the genus’ natural fluorescence and thereby sorting out the bacteria in the samples using a high-speed flow cytometer. After this enrichment, 454 pyrosequencing was conducted on the two coastal and one open-ocean cyanobacterial populations. These sequences were then compared to the four complete Synechococcus genome sequences available (including representatives from the two most abundant clades-I and IV- as well as clades II and III)( Fuller 2003). Up to 25% of the reads could be mapped to the previously sequenced genomes when the authors used lenient cutoffs (70% identity, 70% sequence length). Of the gene models that had no hits, ca. 48% had atypical trinucleotide content, suggesting that they may have been recently acquired through horizontal gene transfer. Indeed, at least three plasmid families were found in the samples sequenced, again pointing to the potential contribution of horizontal gene transfer to the diversity within marine Synechoccoccus. This is the first reported incidence of plasmid detection in marine, rather than freshwater, cyanobacteria.

In summary, the authors provided this evidence that plasmids play a part in marine cyanobacterial diversity and indicated that, while backbone genes were highly conserved across the metagenome sample, accessory genes were widely varied. Therefore, nature is much more diverse than would be indicated if we only took into account those few cultured representatives that we use in the lab.

Primary article:
B. Palenik, Q. Ren, V. Tai and I. T. Paulsen. (2009) Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity. Environmental Microbiology 11(2):349-359.

Additional Reading:
Fuller, N.J., Marie, D., Partensky, F., Vaulot, D., Post, A.F., and Scanlan, D.J. (2003) Clade-specific 16S ribosomal DNA oligonucleotides reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea. Appl Environ Microbiol 69: 2430–2443.

Glover, H.E. (1985) The physiology and ecology of the marine cyanobacterial genus Synechococcus. Adv Aquat Microbiol 3: 49–107.

Tettelin, H., Masignan, I.V., Cieslewicz, M.J., Donati, C., Medini, D., Ward, N.L., et al. (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial ‘pan-genome’. Proc Natl Aca Sci USA 102: 13950–13955.

By Julie Hughes
Graduate Student
University of Idaho

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