A day in the life of wild planktonic microbial species

Planktonic microbial communities are able to adjust to environmental fluctuations by regulation gene expression in response to nutrient availability. However, detailed patterns of the dynamic responses of planktonic communities in situ are not well-described. Here Ottesen et al. face the challenge to study activities of a discrete picoplankton community over a time period of two days off the coast of California. They had to find a way to monitor gene expression of a diverse community over time, while taking into account the spatial heterogeneity of the ocean resulting from hydrodynamic processes, because samples from a fixed location may not represent the same coherent microbial population over time through the action of ocean currents. 

A robotic sampler, attached to a buoy, allowed drifting over 50 km with the currents and results confirmed that samples showed greater overall similarity in taxonomic composition to one another than did samples collected at a fixed station.  Every 4 hours samples for community RNA sequencing were collected and preserved. This analysis allows creating genome-wide transcriptome profiles of co-occurring taxa within a microbial assemblage; so basically, by matching gene sequences to a adequate database and by using various statistics (cluster analysis) and software packages (geneARMA), you are able to identify the genes expressed by each taxon and to create profiles showing the expression of those genes over time. 

Ottesen et al. focused on five microbial populations representing ecologically important clades of marine picoplankton:  Ostreococcus, Synechococcus, Pelagibacter,SAR86 cluster  Gammaproteobacteria (SAR86), and marine group II Euryarchaea (MGII). Consistent with previous laboratory studies, the photosynthetic Ostrococcus and Synechococcus exhibited strong diel rhythms over thousands of gene transcripts. For instance genes regulating carbon fixation, photosynthesis, oxidative phosphorylation, and respiration had periodic trends in transcript abundance, which relates to the photoautotrophic lifestyle of these organisms.

In contrast, none of the transcript from the heterotrophic populations was identified to be periodic. Instead Ottesen et al. observed “well-orchestrated”, genome-wide transcriptional regulation (particularly of genes involved in growth and nutrient acquisition) with strong correlation between some major metabolic pathways in Pelagibacter. Interestingly, SAR86 and MGII showed the same patterns of gene regulation, which seemed to reflect synchronous responses to the same environmental signal. Either each species population responds independently to the same environmental cues, or the transcriptional patterns are the result of interspecific communication and signalling e.g. by using auto-inducer molecules. Possibly, only one species senses the cues, which are then indirectly broadcast to others. But more transcriptional studies are required to determine the mechanism of these synchronised patterns. 

This study provides an insight into daily patterns of gene expression of dominant members of the picoplankton community and puts it into a temporal context. I was surprised by the high level of gene regulation occurring on a daily basis and in such a short period of time and it just shows how rapidly these organisms can respond to environmental changes. The suggestion that specific cues elicit cross-species coordination of gene expression among diverse microbial groups sounds promising and is worth following up. 

The study of these short time-scale microbe-environment and microbe-microbe interactions are crucial to understand the large scale patterns observed within populations and communities. 

Ottesen, E. A., Young, C. R., Eppley, J. M., Ryan, J. P., Chavez, F. P., Scholin, C. A. & DeLong, E. F. 2013. Pattern and synchrony of gene expression among sympatric marine microbial populations. Proceedings of the National Academy of Sciences, 1–10. Available at: http://www.pnas.org/cgi/doi/10.1073/pnas.1222099110