Abstract
Viruses in aquatic environments play a key role in microbial population dynamics and nutrient cycling. In particular, bacteria of the phylum Bacteriodetes are known to participate in recycling algal blooms. Studies of phage–host interactions involving this phylum are hence important to understand the processes shaping bacterial and viral communities in the ocean as well as nutrient cycling. In this study, we isolated and sequenced three strains of flavobacteria—LMO6, LMO9, LMO8—and 38 virulent phages infecting them. These phages represent 15 species, occupying three novel genera. Additionally, one temperate phage was induced from LMO6 and was found to be competent at infecting LMO9. Functions could be predicted for a limited number of phage genes, mainly representing roles in DNA replication and virus particle formation. No metabolic genes were detected. While the phages isolated on LMO8 could infect all three bacterial strains, the LMO6 and LMO9 phages could not infect LMO8. Of the phages isolated on LMO9, several showed a host-derived reduced efficiency of plating on LMO6, potentially due to differences in DNA methyltransferase genes. Overall, these phage–host systems contribute novel genetic information to our sequence databases and present valuable tools for the study of both virulent and temperate phages.
Highlights
In the majority of aquatic environments, bacteriophages vastly outnumber their bacterial hosts [1] and have a significant impact on the ecosystem as a result [2]
LMO8 had colonies that were retrieved from the agar plates, whereas both LMO6 and LMO9 colonies were sticky and difficult to pick from the agar plates
The proposed names for these phage genera are Muminvirus, Pippivirus, Tantvirus and Labanvirus (Supplementary Table S1). Despite their genetic (Figure 2; Figure 3) and morphological differences (Figure 6), they were quite similar in genome size, ranging between 34 and 43 kb (Supplementary Table S1)
Summary
In the majority of aquatic environments, bacteriophages (phages) vastly outnumber their bacterial hosts [1] and have a significant impact on the ecosystem as a result [2]. The impact on the microbial community depends on a variety of factors, including the host range and efficiency of infection on different strains [3,4], the number and character of metabolic genes carried by the phage [5,6,7], the metabolic reprogramming of the host population [8,9,10], and the replication strategy of the phage [11,12]. In addition to lysing their microbial hosts, temperate phages have the ability to integrate into the genome of their hosts and remain dormant until they are induced to undergo lytic replication. In this way, temperate phages stay protected during times of harsh conditions [15]. Temperate phages can offer benefits to the host, such as homoimmunity that prevents further phage infections [11], toxin production [16], and changes to the host gene expression [17], all of which increases the fitness and competitiveness of the lysogenised bacteria
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