Diving into chilly California waters, understanding genomic differentiation and the role of gene transfer in marine cyanophages

At this point, it’s clear: microbes are everywhere, there are a lot of them, and they are important. In fact, they are more abundant, more diverse and older than any other organism we have on this planet. In particular, cyanobacteria are pretty amazing, and contribute to the majority of the oxygen we breathe (2 of every 3 breaths).
Gregory et al., (2016) Figure 1.The most abundant marine cyanobacteria are Synechococcus and Prochlorococcus, the main representatives of oceanic phytoplankton, which contribute to about half of the world’s primary production. The forces driving population structure and ecotype differentiation in Synechococcus and Prochlorococcus are diverse (including light, temperature, nutrients) as well as cyanophages.

Gregory et al., (2016) Figure 3.Genomes are complicated. They are not set in stone, but instead shift around and change. Phages are viruses that infect bacteria, and can influence their genomes, in particular, they’ve been found to mediate horizontal gene transfer (HGT). There are different drivers of genomic evolution, and the genomes that persist are likely those that lead to higher fitness for the organism they encode. The mechanisms leading to big genomic shifts include mutation and HGT.

Understanding how recombination impacts the cohesion and dissolution of individual whole genomes within viral sequence space is poorly understood across double-stranded DNA bacteriophages (a.k.a phages) due to the challenges of obtaining appropriately scaled genomic datasets.   

Gregory et al., (2016) Figure 4.From viruses to elephants everyone’s got a genome and as a recent paper by Gregory et al., in BMC Genomics notes, it was long believed that for viruses – evolution was thought to be driven by mutation, which had rates that were found to be pretty dang high in RNA viruses. On the other hand, in the case of dsDNA viruses (double stranded that is) recombination might be the key driver of population structure.
Gregory and colleagues isolated 142 cyanophages a Synechococcus strain after growth in two different water samples, and then sequenced all of their genomes. They focused on 51 core genes found in all the genomes to generate a phylogenetic tree, which revealed distinct populations. Since the authors examined genomes from two distinct sites, they were also able to examine what role biogeography might have on diversity.

The cyanophage data presented here provide a first look at gene flow in ocean viruses, and are consistent with recent observations that “everything is everywhere, and the environment selects” derived from patterns observed in global ocean surveys using viral population genome fragments.

Gregory et al., (2016) Figure 5.There is much still to learn about cyanophages, and figuring out what role recombination versus mutation in these little guys likely depends on their preferred host and environment. The study suggests that recombination maintains distinct cyanophage populations, however, teasing apart this data is tricky since the genomes are so very closely related. The authors have presented an interesting look at selection and recombination in a specific group of cyanophages, and although there is plenty more to be done, it is a step towards a better understanding of key players driving oceanic microbial community populations.
Gregory, A.C., Solonenko, S.A., Ignacio-Espinoza, J.C., LaButti, K., Copeland, A., Sudek, S., Maitland, A., Chittick, L., dos Santos, F., Weitz, J.S. and Worden, A.Z., 2016. Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer. BMC genomics, 17(1), p.930.
Biller, S.J., Berube, P.M., Lindell, D. and Chisholm, S.W., 2015. Prochlorococcus: the structure and function of collective diversity. Nature Reviews Microbiology13(1), pp.13-27.
Flombaum, P., Gallegos, J.L., Gordillo, R.A., Rincón, J., Zabala, L.L., Jiao, N., Karl, D.M., Li, W.K., Lomas, M.W., Veneziano, D. and Vera, C.S., 2013. Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus. Proceedings of the National Academy of Sciences110(24), pp.9824-9829.
Sullivan, M.B., Coleman, M.L., Weigele, P., Rohwer, F. and Chisholm, S.W., 2005. Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations. PLoS Biol3(5), p.e144.

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