Abstract
Viruses are ubiquitous in the oceans and critical components of marine microbial communities, regulating nutrient transfer to higher trophic levels or to the dissolved organic pool through lysis of host cells. Hydrothermal vent systems are oases of biological activity in the deep oceans, for which knowledge of biodiversity and its impact on global ocean biogeochemical cycling is still in its infancy. In order to gain biological insight into viral communities present in hydrothermal vent systems, we developed a method based on deep-sequencing of pulsed field gel electrophoretic bands representing key viral fractions present in seawater within and surrounding a hydrothermal plume derived from Loki's Castle vent field at the Arctic Mid-Ocean Ridge. The reduction in virus community complexity afforded by this novel approach enabled the near-complete reconstruction of a lambda-like phage genome from the virus fraction of the plume. Phylogenetic examination of distinct gene regions in this lambdoid phage genome unveiled diversity at loci encoding superinfection exclusion- and integrase-like proteins. This suggests the importance of fine-tuning lyosgenic conversion as a viral survival strategy, and provides insights into the nature of host-virus and virus-virus interactions, within hydrothermal plumes. By reducing the complexity of the viral community through targeted sequencing of prominent dsDNA viral fractions, this method has selectively mimicked virus dominance approaching that hitherto achieved only through culturing, thus enabling bioinformatic analysis to locate a lambdoid viral “needle" within the greater viral community “haystack". Such targeted analyses have great potential for accelerating the extraction of biological knowledge from diverse and poorly understood environmental viral communities.
Highlights
IntroductionViruses are the most numerous and diverse biological entities in the oceans [1,2,3,4] with important roles in biochemical cycling and in structuring microbial communities [5,6,7]
Blurb Targeted metagenome analysis identifies lambdoid virus and reveals sub-genomic viral diversity in an Arctic hydrothermal plume.Viruses are the most numerous and diverse biological entities in the oceans [1,2,3,4] with important roles in biochemical cycling and in structuring microbial communities [5,6,7]
Analysis of viral community composition The pulsed field gel electrophoresis (PFGE) analysis revealed that the genome size of the prominent members of the viral community from both sample sites was between 31 and 48 kb (Figure S1)
Summary
Viruses are the most numerous and diverse biological entities in the oceans [1,2,3,4] with important roles in biochemical cycling and in structuring microbial communities [5,6,7]. The geothermal reducing power of vent fluid is dispersed from the vent source in plumes that may travel hundreds of kilometres from their source [19]. In these plumes, biological productivity is primarily driven by chemolithoautotrophs, but a considerable portion of the microbial biomass is likely to consist of heterotrophic prokaryotes [17,20,21,22,23]. Significant efforts have been made to describe the diversity and function of plume-derived prokaryotic communities [24,25,26,27], little focus has been given to the viral component in these systems
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