Finding a Needle in the Virus Metagenome Haystack - Micro-Metagenome Analysis Captures a Snapshot of the Diversity of a Bacteriophage Armoire

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.

Selective isolation of bacteria for metagenomic analysis: Impact of membrane characteristics on bacterial filterability

“…Only 1% of the sequences were attributed to the presence of eukaryote (fungal-probably from spores) and viruses, which compares favorably to other reports. 157,160 In most studies DNA is isolated directly from the environment 159 or from microorganisms in aquatic 46,160 or soil environments. 161 No reports at all exist on the selective isolation of bacterial populations from wood.…”

Learned and unlearned concepts in periodontal diagnostics: a 50‐year perspective

“…(203–205) demonstrated evidence of a robust bacteriophage population in periodontally healthy subjects and reported that only about 7–22% of the streptococcal populations of saliva are stable over time. As is the case in other ecosystems in nature, viruses appear to be one of the main driving forces behind changes in the microbial populations (208, 214, 255, 256).…”

The influence of vent systems on pelagic eukaryotic micro-organism composition in the Nordic Seas

“…The pre-filter samples were fixated in 96 % ethanol and stored at -80°C, while the rest of the filters were instantly placed in sterile 1.5 mL cryo-tubes and frozen in liquid nitrogen before storage at -80°C for further analysis. The water samples were further filtered using 0.22-lm Sterivex TM filters (Millipore TM , Merck KGaA Darmstadt, Germany) to extract prokaryote DNA (unpublished data), and finally, viruses were analysed and described in Ray et al (2012).…”