Genomic island variability facilitates Prochlorococcus–virus coexistence

Abstract

Prochlorococcus cyanobacteria are extremely abundant in the oceans, as are the viruses that infect them. How hosts and viruses coexist in nature remains unclear, although the presence of both susceptible and resistant cells may allow this coexistence. Combined whole-genome sequencing and PCR screening technology now enables us to investigate the effect of resistance on genome evolution and the genomic mechanisms behind the long-term coexistence of Prochlorococcus and their viruses. Here we present a genome analysis of 77 substrains selected for resistance to ten viruses, revealing mutations primarily in non-conserved, horizontally transferred genes that localize to a single hypervariable genomic island. Mutations affected viral attachment to the cell surface and imposed a fitness cost to the host, manifested by significantly lower growth rates or a previously unknown mechanism of more rapid infection by other viruses. The mutant genes are generally uncommon in nature yet some carry polymorphisms matching those found experimentally. These data are empirical evidence indicating that viral-attachment genes are preferentially located in genomic islands and that viruses are a selective pressure enhancing the diversity of both island genes and island gene content. This diversity emerges as a genomic mechanism that reduces the effective host population size for infection by a given virus, thus facilitating long-term coexistence between viruses and their hosts in nature.

Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils

“…Whole-genome phylogeny analysis was performed as previously described (Avrani et al, 2011) using custom python scripts. The predicted protein sequences of each genome were compared with those of the other genomes using BLASTP (Altschul et al, 1997); reciprocal best blast hits of ⩾ 50% identity, aligned over ⩾ 70% of the length of both Non-symbiotic Bradyrhizobia dominate forest soils D VanInsberghe et al query and subject sequences were defined as orthologous genes.…”

Cyanobacterial defense mechanisms against foreign DNA transfer and their impact on genetic engineering

“…are under a constant threat of phage infection (Mann 2003, Avrani et al, 2011. Cyanophages infecting fi lamentous heterocystous cyanobacteria seem to be less frequent (Hu et al, 1981).…”

Transcriptional response of Prochlorococcus to co-culture with a marine Alteromonas: differences between strains and the involvement of putative infochemicals

“…Thus, like other phytoplankton, the life and death of Prochlorococcus are intimately coupled with that of co-occurring microbes. Although significant advances have been made in understanding 'top down' control of Prochlorococcus populations by phage and grazers (for example, Worden and Binder, 2003;Avrani et al, 2011;Pasulka et al, 2015), as well as 'bottom up' control by nutrients, temperature and light (for example, Bouman et al, 2006;Johnson et al, 2006;Saito et al, 2014), studying how co-occurring heterotrophic microbes affect Prochlorococcus is still in its infancy. Several recent studies have shown that co-occurring heterotrophic bacteria can both enhance and inhibit the growth of Prochlorococcus in laboratory co-cultures (Morris et al, 2008;Sher et al, 2011).…”