Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression

Abstract

Phage integrase genes often play a role in the establishment of lysogeny in temperate phage by catalyzing the integration of the phage into one of the host's replicons. To investigate temperate phage gene expression, an induced viral metagenome from Tampa Bay was sequenced by 454/Pyrosequencing. The sequencing yielded 294,068 reads with 6.6% identifiable. One hundred-three sequences had significant similarity to integrases by BLASTX analysis (e≤0.001). Four sequences with strongest amino-acid level similarity to integrases were selected and real-time PCR primers and probes were designed. Initial testing with microbial fraction DNA from Tampa Bay revealed 1.9×107, and 1300 gene copies of Vibrio-like integrase and Oceanicola-like integrase L−1 respectively. The other two integrases were not detected. The integrase assay was then tested on microbial fraction RNA extracted from 200 ml of Tampa Bay water sampled biweekly over a 12 month time series. Vibrio-like integrase gene expression was detected in three samples, with estimated copy numbers of 2.4-1280 L−1. Clostridium-like integrase gene expression was detected in 6 samples, with estimated copy numbers of 37 to 265 L−1. In all cases, detection of integrase gene expression corresponded to the occurrence of lysogeny as detected by prophage induction. Investigation of the environmental distribution of the two expressed integrases in the Global Ocean Survey Database found the Vibrio-like integrase was present in genome equivalents of 3.14% of microbial libraries and all four viral metagenomes. There were two similar genes in the library from British Columbia and one similar gene was detected in both the Gulf of Mexico and Sargasso Sea libraries. In contrast, in the Arctic library eleven similar genes were observed. The Clostridium-like integrase was less prevalent, being found in 0.58% of the microbial and none of the viral libraries. These results underscore the value of metagenomic data in discovering signature genes that play important roles in the environment through their expression, as demonstrated by integrases in lysogeny.

A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes

“…First, it is essential to extend the current model to link increasingly strain-resolved information on microbial and viral diversity (Breitbart et al, 2002;Edwards and Rohwer, 2005;Allen et al, 2011) and interactions between viruses and their hosts (Flores et al, 2011;Deng et al, 2012;Weitz et al, 2013) the aggregated representation of virus-host interactions and nutrient feedbacks presented here (see the example of a calibrated model for dynamics including viruses of the algae Phaeocystis globosa; Ruardij et al, 2005). Strain-specific interactions also include the change in host physiology that occurs during infection, whether preceding lysis (Lindell et al, 2007;Ankrah et al, 2014) or during long-term associations with hosts, for example, lysogeny (McDaniel et al, 2008). Such extensions are analogous to the expanded representations of phytoplankton and zooplankton in terms of size-structured and/ or functional type groups (Follows et al, 2007;Stock et al, 2014).…”

Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1

“…Five marine virus metagenomes were retrieved from NCBI, representing pooled viromes from the Arctic, British Columbia (Strait of Georgia estuary), Gulf of Mexico, Sargasso Sea and a coastal Tampa Bay community, the integrated prophages of which were induced to undergo lysis (gpids: 18 225 and 28 619; Supplementary Material S2) (Angly et al, 2006;McDaniel et al, 2008). Specialized tblastn (BLOSUM62 substitution matrix) of predicted Phage H105/1 proteins and of nine other marine phages was carried out against all six reading frames of virome nucleotide reads using Decypher hardware (TimeLogic, Inc., Carlsbad, CA, USA).…”

“…As the public sequence databases are insufficient to grasp phage protein diversity, traditional approaches to genome analysis, which rely on similarity searches (blast (Altschul et al, 1990) against NCBI-nr), or protein family classification (Pfam (Finn et al, 2010)), reveal little about phage evolution. We expanded the similarity searches of Phage H105/1 to include the Global Ocean Sampling data set (GOS) (Rusch et al, 2007) and five globally distributed marine viral metagenomes missing from NCBI-nr and -env (Angly et al, 2006;McDaniel et al, 2008). Such an approach lends itself to 'ecogenomic' interpretations, whereby ecological inferences about Phage H105/1 can be made on the basis of genomic patterns and their respective environmental contextual data (Kottmann et al, 2010).…”

Virus genes in Arctic marine bacteria identified by metagenomic analysis

“…However, no study has systematically surveyed virus DNA in genomes of uncultivated bacteria. One study in Tampa Bay, Florida, waters detected a Vibrio phage-like and a Clostridium phage-like integrase gene, which enables virus DNA to be integrated into the host genome, in only 3% and 0.5%, respectively, of the bacterial genomes in the GOS data set (McDaniel et al 2008). Other viral genes were not examined.…”

“…The GOS project did not sample the Arctic Ocean (www. jcvi.org/cms/research/projects/gos/overview/), and no clear relationship has yet emerged between environment and integrase gene phylotype or frequency (McDaniel et al 2008).…”