Lysogeny in the oceans: Lessons from cultivated model systems and a reanalysis of its prevalence

Abstract

In the oceans, viruses that infect bacteria (phages) influence a variety of microbially mediated processes that drive global biogeochemical cycles. The nature of their influence is dependent upon infection mode, be it lytic or lysogenic. Temperate phages are predicted to be prevalent in marine systems where they are expected to execute both types of infection modes. Understanding the range and outcomes of temperate phage-host interactions is fundamental for evaluating their ecological impact. Here, we (i) review phage-mediated rewiring of host metabolism, with a focus on marine systems, (ii) consider the range and nature of temperate phage-host interactions, and (iii) draw on studies of cultivated model systems to examine the consequences of lysogeny among several dominant marine bacterial lineages. We also readdress the prevalence of lysogeny among marine bacteria by probing a collection of 1239 publicly available bacterial genomes, representing cultured and uncultivated strains, for evidence of complete prophages. Our conservative analysis, anticipated to underestimate true prevalence, predicts 18% of the genomes examined contain at least one prophage, the majority (97%) were found within genomes of cultured isolates. These results highlight the need for cultivation of additional model systems to better capture the diversity of temperate phagehost interactions in the oceans.

Phage-plasmids spread antibiotic resistance genes through infection and lysogenic conversion

“…Numbers indicated above non-homologous cassettes represent different types of ARGs: [1,14]:ant(2'')-Ia, [2]:aac(6')-33, [3,13,19]:qacEΔ1, [4]:aac(3)-Ib, [5]:dfrA15, [6]:arr-2, [7]:group II intron reverse transcriptase/maturase, [8]:aac(6')-Ib, [9]:blaCARB-2, [10,17,25]:aadA2, [11]:cmlA6, [12]:catB11, [15,20]:dfrA12, [16,21,24]:DUF1010 protein, [18]:aac(3)-VIa, [22]:blaGES-1, [23]:arr-6.…”

“…All these processes have been shown to result in the transfer of ARGs in the lab, but there is extensive controversy on the extent and pertinence of this process in natural environments (15)(16)(17)(18)(19). In contrast, lysogeny is common in nature (20)(21)(22). In this case, the phage remains mostly silent in the cell (as prophage), but accessory genes can be expressed and change the host phenotype.…”

The landscape of lysogeny across microbial community density, diversity and energetics

“…Changes in bacterial cell metabolism can modify ecological interactions between the lysogen (bacterial host encoding a prophage) and other bacteria and eukaryotes, with cascading effects on the whole community (Brüssow, 2007; Rabinovich et al ., 2012; Haaber et al ., 2016). Despite lysogeny's impacts on microbial community functioning, the environmental cues that drive the lysis–lysogeny decision remain unclear (Luque and Silveira, 2020; Tuttle and Buchan, 2020).…”

Plasmid-Mediated Stabilization of Prophages

“…At least 15 isolated roseophages encode integrase genes, suggestive of a temperate lifestyle ( 26 , 27 ). Moreover, prophage detection within publicly available genomes also reveals a high incidence of lysogeny within roseobacters (estimated at 26 to 80% [ 28 , 29 ]).…”