Demographics of lytic viral infection of coastal ocean Vibrio

Abstract

Viral predation on bacteria in the ocean liberates carbon from the particulate fraction, where it is accessible to higher trophic levels, and redirects it to the dissolved fraction, where it supports microbial growth. Although viruses are highly abundant in the ocean little is known about how their interactions with bacteria are structured. This challenge arises because the diversity of both bacteria and viruses is exceedingly high and interactions between them are mediated by specific molecular interactions. This thesis uses heterotrophic bacteria of the genus Vibrio as a model to quantify virus-host interactions in light of host population structure and ecology. The methods developed in this thesis include streamlining of standard bacteriophage protocols, such as the agar overlay, and facilitate higher throughput in the isolation and characterization of novel environmental virus-host systems. Here, >1300 newly isolated Vibrio are assayed for infection by viral predators and susceptibility is found to be common, though total concentrations of predators are highly skewed, with most present at low abundance. The largest phylogenetically-resolved host range cross test available to date is conducted, using 260 viruses and 277 bacterial strains, and highly-specific viruses are found to be prevalent, with nearly half infecting only a single host in the panel. Observations of blocks of multiple viruses with nearly identical infection profiles infecting sets of highlysimilar hosts suggest that increases in abundance of particular lineages of bacteria may be important in supporting the replication of highly specific viruses. The identification of highly similar virus genomes deriving from different sampling time points also suggests that interactions for some groups of viruses and hosts may be stable and persisting. Genome sequencing reveals that members of the largest broad host-range viral group recovered in the collection have sequence homology to non-tailed viruses, which have been shown to be dominant in the surface oceans but are underrepresented in culture collections. By integrating host population structure with sequencing of over 250 viral genomes it is found that viral groups are genomically cohesive and that closely-related and co-occurring populations of bacteria are subject to distinct regimes of viral predation.

Environmental vibrios represent a source of antagonistic compounds that inhibit pathogenic Vibrio cholerae and Vibrio parahaemolyticus strains

“…Given the expectation that environmental strains provide optimal sources for isolation of inhibitory compounds (Cordero, Wildschutte, et al., ), we chose to screen a large collection of previously isolated environmental marine vibrios (Kauffman, ) for activity against Vibrio pathogens. This environmental strain collection was sampled from the marine littoral zone of Nahant, MA, USA, on 3 days in late‐summer to early fall of 2010: August 10th (ordinal day 222), September 18th (ordinal day 261), and October 13th (ordinal day 286) when water temperatures were 13.8°C, 16.3°C, and 14.2°C respectively.…”

“…A collection of environmental marine vibrio strains previously isolated at Canoe Cove, Nahant, MA (Kauffman, ) was screened for activity against representative pathogens. This collection was comprised of free‐living and particle‐associated bacterial strains sampled from the marine littoral zone in Nahant, MA, on August 10th, September 18th, and October 13th of 2010 using a size‐fractionation approach (Hunt et al., ), briefly as follows.…”

Identification and biosynthesis of thymidine hypermodifications in the genomic DNA of widespread bacterial viruses

“…enterica serovar Typhi (ATCC 27870), bacteriophage M6 (ATCC BAA-31-B1), and the M6 host Pseudomonas aeruginosa (ATCC BAA-31). Vibrio phage 1.255.O._10N.286.45.F1 (hereafter referred to as 1.255.O) and its host, Vibrio splendidus 10N.286.45.F1, were isolated from littoral zone seawater at Canoe Cove (Nahant, MA) on October 13, 2010 ( 27 ). Bacteriophages CBA6 and CBA120 as well as their host E. coli Serotype O157:H7 National Collection of Type Cultures (NCTC) strain 12900 (also known as ATCC 700728) were provided by Elizabeth Kutter, Evergreen State College, Olympia, WA.…”

Degradation of host translational machinery drives tRNA acquisition in viruses

“…In order to dissect the selective advantages that tRNA carriage may convey, we used phage 2.275.O [NCBI:txid1881285] as a model. This phage is a part of the Nahant Collection, an extensive collection of Vibriophages previously described by Kauffman et al (Kauffman, 2014;Kauffman et al, 2018). At 348,911 bp, it is among the largest known bacteriophage (Figures 1 and S1), and it is capable of infecting hosts of at least two different species, Vibrio cyclitrophicus and V. lentus.…”