Wide distribution of phage that infect freshwater SAR11 bacteria

Abstract

Fonsibacter (LD12 subclade) are among the most abundant bacterioplankton in freshwater ecosystems. These bacteria belong to the order Pelagibacterales (SAR11) and are related to Pelagibacter (marine SAR11) that dominate many marine habitats. Although a handful of Pelagibacter phage (Pelagiphage) have been described, no phage that infect Fonsibacter have been reported. In this study, a complete Fonsibacter genome containing a prophage was reconstructed from metagenomic data. A circularized and complete genome related to the prophage, referred to as uv-Fonsiphage-EPL, shows high similarity to marine Pelagiphage HTVC025P. Additionally, we reconstructed three complete and one draft genome of phage related to marine Pelagiphage HTVC010P, and predicted a lytic strategy. The similarity in codon usage and co-occurrence patterns of HTVC010P-related phage and Fonsibacter suggested that these phage infect Fonsibacter . Similar phage were detected in Lake Mendota, Wisconsin, where Fonsibacter is also present. A search of related phage revealed the worldwide distribution of some genotypes in freshwater ecosystems, suggesting their substantial role in shaping indigenous microbial assemblages and influence on biogeochemical cycling. However, the uv-Fonsiphage-EPL and one lineage of HTVC010P-related phage have a more limited distribution in freshwater ecosystems. Based on this, and their close phylogenetic relatedness with Pelagiphage, we predict that they transitioned from saline into freshwater ecosystems comparatively recently. Overall, the findings provide insights into the genomic features of phage that infect Fonsibacter , and expand understanding of the ecology and evolution of these important bacteria.

Expanding the diversity of bacterioplankton isolates and modeling isolation efficacy with large scale dilution-to-extinction cultivation

“…One possibility is as an effective defense mechanism against abundant viruses. Viruses infecting SAR11 have been shown to be extremely abundant in both marine (115, 116) and freshwater (117) systems. Indeed, the paradox of high viral abundances and high host abundances in SAR11 has led to a refining of negative density dependent selection through Lokta-Volterra predator-prey dynamics (118) to include heterogeneous susceptibility at the strain level (119, 120) and positive density dependent selection through intraspecific proliferation of defense mechanisms (121).…”

Genomic diversity, life strategies and ecology of marine HTVC010P-type pelagiphages

“…Quantitative PCR and digital droplet PCR techniques have been employed to investigate the absolute abundance of the isolate HTVC010P, which have revealed that the abundance of HTVC010P was within the range of 10 3 -10 4 virus ml −1 in various oceanic regions [27,28]. To date, only two HTVC010P-type isolates [12,16], HTVC010P-type SAR11 prophage PNP1 [20], one HTVC010P-related contig from Western English Channel viral metagenome [29] and three reconstructed HTVC010Prelated freshwater SAR11 phages (fonsiphages) [30] have been reported, limiting our understanding of this important phage group. Therefore, more HTVC010P-type pelagiphages need to be analysed to better understand their diversity and ecology.…”

Lysogenic host–virus interactions in SAR11 marine bacteria

“…4 ). Recent evidence of prophages in freshwater SAR11 41 and other temperate phages in marine SAR11 42 point to a mechanism capable of mediating significant horizontal gene transfer in the environment.…”