Group Post: Single Cells Show Massive Microbial Diversity

Prochlorococcus a small photosynthetic phytoplankton, in fact the smallest known photosynthetic organism, is widely distributed and most abundant in the upper surface layer down to 200m. Prochlorococcus has been previously split into a number of different ecotypes which are defined by the intergeneric transcribed spacer (ITS) section of the ribosomal RNA genes. They show great diversity in physiology, seasonality, depth and geographic patterns in their pheno- and genotype. Recently, Kashtan et al. (2014) further investigated the diversity of Prochlorococcus by using single-cell genomics and revealed hundreds of coexisting subpopulations.

Samples of wild Prochlorococcus were collected from 60 m depth at three time points throughout the year. To explore cell by cell genomic composition, flow sorting and DNA amplification of more than 1000 co-occurring cells was used. As mentioned earlier, ecotypes are defined by the ITS-area. Further ITS-rRNA sequencing showed a presence of finely resolved clusters within broadly defined ecotypes. To look at fine scale genomic variation, this was followed by sequencing partial genomes (70%) from the three largest clusters found in the ITS-rRNA sequencing. Topologies of ITS and genomic trees were found to be highly congruent. ITS sequences can therefore be considered as a proxy for genome sequences at much finer level of resolution than previously demonstrated. A key stengeth of the work was the use of a diverse array of methods, with each being followed up, which created an extremely comprehensive study. However if would also be intresting to examine phenotypic traits as well.

To understand the evolutionary forces that shaped these clades as described, differences in nucleotide sequences within and between clades were investigated. Using novo assemblies it was discovered that clade subpopulations have distinct 'genomic backbones', i.e. a set of core genes, which is linked to a set of flexible gene cassettes. These are used in interactions between the cell and environmental stimuli and possibly includes phage attachment, recognition by grazers, cell to cell communication and interaction with bacteria. Individual cells within a clade also possess a minimum of one unique cassette, an amazing level of individual variation. In some cases, a few closely related cells within backbones share distinct cassettes. Surprisingly some cells in different subpopulations also share cassettes.

The abundance of the largest backbone sub-populations was found to fluctuate seasonally, while maintaining their genomic composition. This indicates that the fitness of groups changes throughout the year. But how many sub-populations co-exist? Use of the ITS-ribotype cluster as a proxy to estimate the diversity of these groups showed that hundreds of these genetically distinct groups coexist and have done for the last few million years, presumably by occupying distinct niches and due to selective phage and grazer predation. The size of these populations is likely to be extremely large, which suggests that natural selection is the key driver in the differentiation of backbone populations. If these findings are typical of other species, this indicates a mind-boggling level of diversity. Clearly bacterial species are not equivalent to those of eukaryotes and this is important to bear in mind when comparing biodiversity between domains.

But how do such subpopulations arise? It may be that new genomic backbone populations appear when they acquire a beneficial flexible gene cassette, which allows shift to a new niche. This is followed by a slower adjustment of the core genes. This population structure may allow Prochlorococcus as a whole to retain a stable population size via adjustments in the abundance of the different sub-populations over time. But over decades to millennia, the collective may responded to shifting selective pressures by the evolution of the backbones and by sharing gene cassettes between populations.

Ref: Kashtan, N., Roggensack, S., Rodrigue, S., Thompson, J., Biller, S., Coe, A., Ding, H., Marttinen, P., Malmstrom, R., Stocker, R., Follows, M., Stepanuskas, R., Chisholm, S. (2014). Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus. Science. 344 416-420.