Tuesday, 5 November 2013

In situ activity of a Prochlorococcus ecotype (eHL-11) from rRNA content and cell size

Prochlorococcus, a genus of unicellular cyanobacteria, is ubiquitous throughout the open ocean ecosystem. Many clades coexist, yet the genetic and physiological diversity found between clades allows them to occupy a range of different ecological niches thus resulting in different ecotypes, biogeographically structured along environmental gradients. Whilst community activity (comprising of different ecotypes) has previously been estimated, very little research has been conducted on individual ecotypes, though they are presumed to differ in their in situ activity.
The authors have used a novel molecular based approach, using cellular ribosomal RNA (rRNA), to measure specific in situ activity of two strains of eHL-11 clade.  By measuring side scatter (SSC), as an operational index of cell size, at different light levels specific growth rates was found. Using this data and plotting it against rRNA cell content (rRNA cell⁻¹) resulted in a linear correlation, a clade eHL-11 specific response. Though the correlation differed between strains, once data was normalised for cell size both strains showed the same slope thus showing a conserved relationship between rRNA cell⁻¹ SSC⁻¹ and growth rate (rRNA content and activity). From this the authors were able to assess the strain specific in situ activity and the response to environmental factors.

Diel variation
The patterns found are consistent with other Prochlorococcus strains in that many cell responses, both genetic and physiological, are tightly coupled with light intensity, showing a substantial diel cycle in order to optimise growth. Cell division was found to occur at night whilst both rRNA synthesis and biomass accumulation increased during the day owing to the observed increase in SSC and rRNA cell⁻¹ (similar in magnitude as driven by same mechanisms). The accumulation of biomass requires more ribosomes for protein synthesis, the energy for which is provided by photosynthesis, requiring light.

Effect of environmental variables
The authors sampled two geographically close stations, yet each with a distinct combination of environmental variables. At both sites: eHL-11 was the dominant clade of Prochlorococcus, the number of cells decreased rapidly once below the mixed layer (despite depth differences of the mixed layer), the cell size was small and constant within the mixed layer and growth rates were similar and ranged from 0.2-0.4 day⁻¹ within the upper 50m.
Though no subpopulation of Prochlorococcus were found throughout both of the water columns vertical trends in specific activity (rRNA cell⁻¹ SSC⁻¹) and inferred growth rates vary substantially between sites and do not follow the same trend as with cell concentrations. These differences could be attributed by many mechanisms including temperature, light and nutrient availability. It has been suggested by the authors that the variability in specific activity despite relatively constant cell counts may be due to the distribution of cells due to mixing, or abiotic pressures of viral lysis and grazing that specifically target fast growing or highly active cells.

I believe this approach has potential, particularly in it’s application on other clades as the rRNA sequences of bacteria are conservative and sufficiently diverse allowing for oligoprimers targeting specific clades. However there are certain limitations e.g. 1) the authors state that linear relationship between rRNA cell⁻¹ and specific growth rate is clade specific to eHL-11 in which case, would this impede the use of this method on other clades? 2) rRNA content can be affected by environmental variations and cellular physiological characteristics. The clade tested is relatively well understood yet many inferences and presumptions have been made from the observed in situ activity due to the variability in the responses to several environmental factors. For that, whilst useful for measuring in situ activity within this clade, I feel it’s difficult to deduce any rational behind the observed activity.

Lin Y., Gazsi K., Lance V. P., Larkin A. A., Chandler J. W., Zinser E. R. and Johnson Z. I. (2013) In situ activity of a dominant Prochlorococcus ecotype (eHL-11) from rRNA content and cell size. Environmental Microbiology, 15(10), 2736-2747

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