Temperate phages are common and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses infecting mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity, and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages reveals at least five distinct prophage-expressed viral defense systems that interfere with infection of lytic and temperate phages that are either closely-related (homotypic defense) or unrelated (heterotypic defense). Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defense systems include a single-subunit restriction system, a heterotypic exclusion system, and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival, and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, that acts as a highly effective counter-defense system. Prophage-mediated viral defense offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defense promotes phage co-evolution.

The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics.

Integrated multi-trophic aquaculture (IMTA) is an exciting alternative approach to mono-culture aquaculture that reduces environmental impacts of commercial aquaculture systems by combining the cultivation of fed aquaculture species (finfish) with extractive aquaculture species (e.g., shellfish and seaweed). This increases the sustainability and profitability of finfish culture as the organic particulate wastes can be removed by the shellfish extractive component and dissolved inorganic nutrients are extracted by the seaweed component. Shellfish play a critical role in an IMTA system by extracting particulate bound organic nutrients; however they may also influence pathogen dynamics by serving as a reservoir or as a barrier for finfish pathogens, depending on pathogen physiologies. The sea louse, Lepeophtheirus salmonis, has recently made a spectacular comeback as a major parasitic pest of farmed Atlantic salmon (Salmo salar L.) in the Northeast of the United States. The re-emergence of this parasite is due to development of louse resistance to SLICE™, the drug of choice for treating L. salmonis infestations over the last decade. Incorporation of mussel crops on salmon farms may be an alternative method to reduce the infectious pressure of sea lice on farms if mussels can consume copepodids, the planktonic and infectious stage of sea lice. Our study demonstrated that mussels can remove copepodids from the water column. Individual mussels were exposed to copepodids (200 copepodids l −1) for 30-and 60-min durations. Copepodids were observed in the buccal cavity and in stomach contents. Molecular analyses confirmed the presence of copepodids in mussel stomach contents.

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Mycobacteriophages – viruses of mycobacterial hosts – are genetically diverse but morphologically are all classified in the Caudovirales with double-stranded DNA and tails. We describe here a group of five closely related mycobacteriophages – Corndog, Catdawg, Dylan, Firecracker, and YungJamal – designated as Cluster O with long flexible tails but with unusual prolate capsids. Proteomic analysis of phage Corndog particles, Catdawg particles, and Corndog-infected cells confirms expression of half of the predicted gene products and indicates a non-canonical mechanism for translation of the Corndog tape measure protein. Bioinformatic analysis identifies 8–9 strongly predicted SigA promoters and all five Cluster O genomes contain more than 30 copies of a 17 bp repeat sequence with dyad symmetry located throughout the genomes. Comparison of the Cluster O phages provides insights into phage genome evolution including the processes of gene flux by horizontal genetic exchange.