Contrasting Life Strategies of Viruses That Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging

Deng, Li; Gregory, Ann C.; Yilmaz, Suzan; Poulos, Bonnie T.; Hugenholtz, Philip

doi:10.1128/mbio.00516-12

Cited by 21 publications

(26 citation statements)

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“…metagenomics, enable the sequencing of wild viral assemblages with unprecedented depth and resolution, due to an incredibly high diversity of viral genomes, the majority of viral sequences are not yet found in databases, which prevents their complete characterization when relying on sequence homology-based identification. Therefore, further genetic analysis of gene contents of the identified phage contigs should provide more information about their lifestyle, and investigations with methods such as viral tagging (Deng et al, 2012) or digital PCR (Tadmor et al, 2011) will be required to expand our knowledge on the interactions between viruses and their hosts in AD environments.…”

Section: Discussionmentioning

confidence: 99%

Analysis of dsDNA and RNA viromes in methanogenic digesters reveals novel viral genetic diversity

Całusińska

Marynowska

Goux

et al. 2016

Environmental Microbiology

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SummaryAlthough viruses are not the key players of the anaerobic digestion process, they may affect the dynamics of bacterial and archaeal populations involved in biogas production. Until now viruses have received very little attention in this specific habitat; therefore, as a first step towards their characterization, we optimized a virus filtration protocol from anaerobic sludge. Afterwards, to assess dsDNA and RNA viral diversity in sludge samples from nine different reactors fed either with waste water, agricultural residues or solid municipal waste plus agro-food residues, we performed metagenomic analyses. As a result we showed that, while the dsDNA viromes (21 assigned families in total) were dominated by dsDNA phages of the order Caudovirales, RNA viruses (14 assigned families in total) were less diverse and were for the main part plant-infecting viruses. Interestingly, less than 2% of annotated contigs were assigned as putative human and animal pathogens. Our study greatly extends the existing view of viral genetic diversity in methanogenic reactors and shows that these viral assemblages are distinct not only among the reactor types but also from nearly 30 other environments already studied, including the human gut, fermented food, deep sea sediments and other aquatic habitats.

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Section: Discussionmentioning

confidence: 99%

Analysis of dsDNA and RNA viromes in methanogenic digesters reveals novel viral genetic diversity

Całusińska

Marynowska

Goux

et al. 2016

Environmental Microbiology

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“…Viruses, however, appear to retain their potential to infect bacteria at low temperatures (Wilcox and Fuhrman, 1994). Also, viruses are reportedly more infective and replicate faster if matched with rapidly growing cells (Deng et al, 2012), whereas BALOs prefer prey in a slowly growing or stationary state. The low growth rate of the prey in our experiments may have accounted for the low viral activity observed in this study, which was conducted in NW microcosms with no added nutrients to support bacterial growth.…”

Section: Discussionmentioning

confidence: 99%

Halobacteriovorax, an underestimated predator on bacteria: potential impact relative to viruses on bacterial mortality

et al. 2015

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Predation on bacteria and accompanying mortality are important mechanisms in controlling bacterial populations and recycling of nutrients through the microbial loop. The agents most investigated and seen as responsible for bacterial mortality are viruses and protists. However, a body of evidence suggests that predatory bacteria such as the Halobacteriovorax (formerly Bacteriovorax), a Bdellovibrio-like organism, contribute substantially to bacterial death. Until now, conclusive evidence has been lacking. The goal of this study was to better understand the contributors to bacterial mortality by addressing the poorly understood role of Halobacteriovorax and how their role compares with that of viruses. The results revealed that when a concentrated suspension of Vibrio parahaemolyticus was added into microcosms of estuarine waters, the native Halobacteriovorax were the predators that responded first and most rapidly. Their numbers increased by four orders of magnitude, whereas V. parahaemolyticus prey numbers decreased by three orders of magnitude. In contrast, the extant virus population showed little increase and produced little change in the prey density. An independent experiment with stable isotope probing confirmed that Halobacteriovorax were the predators primarily responsible for the mortality of the V. parahaemolyticus. The results show that Halobacteriovorax have the potential to be significant contributors to bacterial mortality, and in such cases, predation by Halobacteriovorax may be an important mechanism of nutrient recycling. These conclusions add another dimension to bacterial mortality and the recycling of nutrients.

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“…Several existing and emerging approaches will likely help identify and characterize non-tailed marine viruses. These include culture-based approaches (for example, targeted isolations with existing and new marine bacterial, archaeal and eukaryotic cultures), as well as new methods that either require only the host to be in culture (for example, viral tagging; Deng et al, 2012) or are completely cultivation-independent (for example, physical fractionation of viral assemblages; Bergeron et al, 2007;Steward and Rappé, 2007;Brum and Steward, 2011;Brum et al, 2013). The abundance and distribution of genetically characterized, non-tailed viruses could also be explored using phageFISH (Allers et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses

2013

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Viruses influence oceanic ecosystems by causing mortality of microorganisms, altering nutrient and organic matter flux via lysis and auxiliary metabolic gene expression and changing the trajectory of microbial evolution through horizontal gene transfer. Limited host range and differing genetic potential of individual virus types mean that investigations into the types of viruses that exist in the ocean and their spatial distribution throughout the world’s oceans are critical to understanding the global impacts of marine viruses. Here we evaluate viral morphological characteristics (morphotype, capsid diameter and tail length) using a quantitative transmission electron microscopy (qTEM) method across six of the world’s oceans and seas sampled through the Tara Oceans Expedition. Extensive experimental validation of the qTEM method shows that neither sample preservation nor preparation significantly alters natural viral morphological characteristics. The global sampling analysis demonstrated that morphological characteristics did not vary consistently with depth (surface versus deep chlorophyll maximum waters) or oceanic region. Instead, temperature, salinity and oxygen concentration, but not chlorophyll a concentration, were more explanatory in evaluating differences in viral assemblage morphological characteristics. Surprisingly, given that the majority of cultivated bacterial viruses are tailed, non-tailed viruses appear to numerically dominate the upper oceans as they comprised 51–92% of the viral particles observed. Together, these results document global marine viral morphological characteristics, show that their minimal variability is more explained by environmental conditions than geography and suggest that non-tailed viruses might represent the most ecologically important targets for future research.

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Contrasting Life Strategies of Viruses That Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging

Cited by 21 publications

References 0 publications

Analysis of dsDNA and RNA viromes in methanogenic digesters reveals novel viral genetic diversity

Analysis of dsDNA and RNA viromes in methanogenic digesters reveals novel viral genetic diversity

Halobacteriovorax, an underestimated predator on bacteria: potential impact relative to viruses on bacterial mortality

Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses

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