Water column stratification structures viral community composition in the Sargasso Sea

Goldsmith, Dawn B.; Brum, Jennifer R.; Hopkins, Max; Carlson, Craig A.; Breitbart, Mya

doi:10.3354/ame01768

Cited by 16 publications

(22 citation statements)

References 67 publications

(72 reference statements)

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“…Evident seasonal succession patterns of microbial communities have been previously described in the Gulf of Aqaba (44,59,60), largely driven by its oligotrophic nature and annual stratification-mixing cycles (59,61,62). Additionally, changes in viral communities have also been observed between different seasons and and between stratified and mixed water column (30,(63)(64)(65)(66).…”

Section: Extended Informationmentioning

confidence: 78%

Rising through the Ranks: Seasonal and Diel Patterns of Marine Viruses

Hevroni

Flores‐Uribe²,

Béjà

et al. 2020

Preprint

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Virus-microbe interactions have been studied in great molecular details for many years in cultured model systems, yielding a plethora of knowledge on how viruses use and manipulate host machinery. Since the advent of molecular techniques and high-throughput sequencing, viruses have been deemed the most abundant organisms on earth and methods such as cooccurrence, nucleotide composition and other statistical frameworks have been widely used to infer virus-microbe interactions, overcoming the limitations of culturing methods. However, their accuracy and relevance is still debatable, as co-occurrence does not necessarily mean interaction. Here, we introduce an ecological perspective of marine viral communities and potential interaction with their hosts, using analyses that make no prior assumptions on specific virus-host pairs. By size fractioning water samples into "free viruses" and "microbes" (i.e. also viruses inside or attached to their hosts) and looking at how viral groups abundance changes over time along both fractions, we show that the viral community is undergoing a change in rank abundance across seasons, suggesting a seasonal succession of viruses in the Red Sea. We use abundance patterns in the different size fractions to classify viral populations, indicating potential diverse interactions with their hosts and potential differences in life history traits between major viral groups. Finally, we show hourly resolved variations of intracellular abundance of similar viral groups, which might indicate differences in their infection cycles or metabolic capacities. marine viruses | seasonal succession | virus-host interaction | diel oscillation

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Section: Extended Informationmentioning

confidence: 78%

Rising through the Ranks: Seasonal and Diel Patterns of Marine Viruses

Hevroni

Flores‐Uribe²,

Béjà

et al. 2020

Preprint

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“…Previous studies showed that the composition of viral phoH sequences not only varied throughout the water column but also changed throughout the year in the Sargasso Sea232627. In addition, the composition of viral phoH sequences was also different among six worldwide oceans23.…”

Section: Discussionmentioning

confidence: 99%

“…They found that viral phoH sequences in marine waters were highly diverse, and they identified six novel groups of phoH sequences. Subsequently, they further investigated the viral community composition throughout the water column both in summer and in winter across three years at the Bermuda Atlantic Time-series Study site in the Sargasso Sea, and this study revealed that the distribution patterns of viral communities varied not only with depth but also with time2627. Their findings indicated that phoH is an effective signature gene for examining phage diversity in marine environments.…”

mentioning

confidence: 99%

Novel groups and unique distribution of phage phoH genes in paddy waters in northeast China

Wang

Liu

Jin

et al. 2016

Sci Rep

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Although bacteriophages are ubiquitous in various environments, their genetic diversity is primarily investigated in pelagic marine environments. Corresponding studies in terrestrial environments are few. In this study, we conducted the first survey of phage diversity in the paddy ecosystem by targeting a new viral biomarker gene, phoH. A total of 424 phoH sequences were obtained from four paddy waters generated from a pot experiment with different soils collected from open paddy fields in northeast China. The majority of phoH sequences in paddy waters were novel, with the highest identity of ≤70% with known phoH sequences. Four unique groups (Group α, Group β, Group γ and Group δ) and seven new subgroups (Group 2b, Group 3d, Group 3e, Group 6a, Group 6b, Group 6c and Group 6d) were formed exclusively with the clones from the paddy waters, suggesting novel phage phoH groups exist in the paddy ecosystem. Additionally, the distribution proportions of phoH clones in different groups varied among paddy water samples, suggesting the phage community in paddy fields is biogeographically distributed. Furthermore, non-metric multidimensional scaling analysis indicated that phage phoH assemblages in paddy waters were distinct from those in marine waters.

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“…In both cases, after resuspension in ascorbic-EDTA buffer (0.1 M EDTA, 0.2 M Mg, 0.2 M ascorbic acid, pH 6.0), viral particles were concentrated using Amicon Ultra 100 kDa centrifugal devices (Millipore), treated with DNase I (100 U/mL) followed by the addition of 0.1 M EDTA and 0.1 M EGTA to halt enzyme activity, and extracted with the QIAamp DNA Mini Kit (Qiagen 51304). The two remaining water samples were collected from 0 m and 100 m depths at the Bermuda Atlantic Time-series Study site in March 2011, where approximately 180L of seawater were concentrated using a 100kDa tangential flow filter, 0.22 µm-filtered, PEG precipitated, cesium chloride purified, and DNA was extracted using formamide (Goldsmith et al, 2015). All samples were sequenced on an Illumina MiSeq platform at the University of Arizona Genetics Core.…”

Section: Methodsmentioning

confidence: 99%

Towards quantitative viromics for both double-stranded and single-stranded DNA viruses

Roux

Solonenko

Vinh

et al. 2016

PeerJ

176

226

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BackgroundViruses strongly influence microbial population dynamics and ecosystem functions. However, our ability to quantitatively evaluate those viral impacts is limited to the few cultivated viruses and double-stranded DNA (dsDNA) viral genomes captured in quantitative viral metagenomes (viromes). This leaves the ecology of non-dsDNA viruses nearly unknown, including single-stranded DNA (ssDNA) viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation).MethodsHere we designed mock viral communities including both ssDNA and dsDNA viruses to evaluate the capability of a sequencing library preparation approach including an Adaptase step prior to Linker Amplification for quantitative amplification of both dsDNA and ssDNA templates. We then surveyed aquatic samples to provide first estimates of the abundance of ssDNA viruses.ResultsMock community experiments confirmed the biased nature of existing library preparation methods for ssDNA templates (either largely enriched or selected against) and showed that the protocol using Adaptase plus Linker Amplification yielded viromes that were ±1.8-fold quantitative for ssDNA and dsDNA viruses. Application of this protocol to community virus DNA from three freshwater and three marine samples revealed that ssDNA viruses as a whole represent only a minor fraction (<5%) of DNA virus communities, though individual ssDNA genomes, both eukaryote-infecting Circular Rep-Encoding Single-Stranded DNA (CRESS-DNA) viruses and bacteriophages from the Microviridae family, can be among the most abundant viral genomes in a sample.DiscussionTogether these findings provide empirical data for a new virome library preparation protocol, and a first estimate of ssDNA virus abundance in aquatic systems.

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Water column stratification structures viral community composition in the Sargasso Sea

Abstract: Sargasso Sea viral communities at 0 and 100 m are similar in the well-mixed winter, but differ during summer watercolumn stratification.Image: Mya Breitbart and Dawn B. Goldsmith

Cited by 16 publications

References 67 publications

Rising through the Ranks: Seasonal and Diel Patterns of Marine Viruses

Rising through the Ranks: Seasonal and Diel Patterns of Marine Viruses

Novel groups and unique distribution of phage phoH genes in paddy waters in northeast China

Towards quantitative viromics for both double-stranded and single-stranded DNA viruses

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