Genetic diversity in cultured and wild marine cyanomyoviruses reveals phosphorus stress as a strong selective agent

Kelly, Libusha; Ding, Huiming; Huang, Katherine; Osburne, Marcia S.; Chisholm, Sallie W.

doi:10.1038/ismej.2013.58

Cited by 76 publications

(90 citation statements)

References 68 publications

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“…This finding hints at the relative selective pressures these two key nutrients exert. The idea that limitation of a given nutrient leads to the gain of genes for uptake and assimilation of that nutrient is supported by numerous studies (Coleman and Chisholm, 2010;Kelly et al, 2013;Thompson et al, 2013). Here, we extend that idea to the quantitative explanatory power of the nutrient's concentration for predicting KO relative abundance.…”

Section: Resultsmentioning

confidence: 64%

“…Several studies have shown that genes for nutrient acquisition are enriched in waters limited for those nutrients, for example, phosphate acquisition in the low-phosphate Mediterranean and Sargasso Seas (Coleman and Chisholm, 2010;Kelly et al, 2013;Thompson et al, 2013). Across the gradients of the Red Sea, numerous KOs for nutrient transport and assimilation were differentially distributed between nutrient-poor (surface and non-GAIW) and nutrientrich (deep and GAIW) samples.…”

Section: Environmental Covariation Patterns Of Individual Kosmentioning

confidence: 99%

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Metagenomic covariation along densely sampled environmental gradients in the Red Sea

et al. 2016

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Oceanic microbial diversity covaries with physicochemical parameters. Temperature, for example, explains approximately half of global variation in surface taxonomic abundance. It is unknown, however, whether covariation patterns hold over narrower parameter gradients and spatial scales, and extending to mesopelagic depths. We collected and sequenced 45 epipelagic and mesopelagic microbial metagenomes on a meridional transect through the eastern Red Sea. We asked which environmental parameters explain the most variation in relative abundances of taxonomic groups, gene ortholog groups, and pathways-at a spatial scale of o2000 km, along narrow but well-defined latitudinal and depth-dependent gradients. We also asked how microbes are adapted to gradients and extremes in irradiance, temperature, salinity, and nutrients, examining the responses of individual gene ortholog groups to these parameters. Functional and taxonomic metrics were equally well explained (75-79%) by environmental parameters. However, only functional and not taxonomic covariation patterns were conserved when comparing with an intruding water mass with different physicochemical properties. Temperature explained the most variation in each metric, followed by nitrate, chlorophyll, phosphate, and salinity. That nitrate explained more variation than phosphate suggested nitrogen limitation, consistent with low surface N:P ratios. Covariation of gene ortholog groups with environmental parameters revealed patterns of functional adaptation to the challenging Red Sea environment: high irradiance, temperature, salinity, and low nutrients. Nutrient-acquisition gene ortholog groups were anti-correlated with concentrations of their respective nutrient species, recapturing trends previously observed across much larger distances and environmental gradients. This dataset of metagenomic covariation along densely sampled environmental gradients includes online data exploration supplements, serving as a community resource for marine microbial ecology.

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Section: Resultsmentioning

confidence: 64%

Section: Environmental Covariation Patterns Of Individual Kosmentioning

confidence: 99%

Metagenomic covariation along densely sampled environmental gradients in the Red Sea

et al. 2016

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“…Recently, Maat et al (2014) have evaluated the outcome of P limitation on viral infection in picoeukaryote Micromonas pusilla, reporting a prolongation of the latent period from 6 to 12 h, and an 80% reduction in viral burst sizes compared to P-replete conditions. Phosphorus stress has been pointed out as a strong selective agent, with some phage having in their genome host-like phosphorus assimilation genes that are upregulated when the host is phosphorous starved, thus promoting P acquisition necessary for phage dispersion (Kelly et al, 2013). In a similar way, it has been reported the presence of host-like photosynthesis genes in phage along with the capacity to express them and actively contribute to primary production during the infection (Sullivan et al, 2006).…”

Section: Viruses and Phytoplankton Mortalitymentioning

confidence: 88%

Bridging the Gap between Knowing and Modeling Viruses in Marine Systems—An Upcoming Frontier

Mateus

2017

Front. Mar. Sci.

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Viruses are the most abundant biological entities in the world's oceans. Their potential control on the dynamics and diversity of bacterioplankton and some phytoplankton groups, and consequent effect on the flow of energy and matter in food webs, may be argued as beyond dispute. Paradoxically, their importance seems to be persistently underestimated by marine modelers, frequently by exclusion, despite the uninterrupted volume of knowledge advanced during the past decades. Bridging the gap between knowing and modeling the role of viruses is, undoubtedly, one of the upcoming frontiers to be crossed in modeling the plankton. This paper has a two-fold objective: (1) review the knowledge on the roles of viruses in marine systems that has been put forward over the past decades, and (2) see how viruses have been incorporated into marine ecosystem models, along with the factors that are limiting their inclusion.

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“…Interestingly, the pho4 gene, found in six OlVs, also has been found in many other marine eukaryotes and viruses (56). Similarly, a gene that encodes PstS, a protein that is involved in phosphate metabolism, is found in many prokaryotes and cyanophages (57). Multiple independent pho4 gene transfer events (with retention) have been proposed to occur between marine viruses and their hosts.…”

Section: Discussionmentioning

confidence: 99%

Diversity of Viruses Infecting the Green Microalga Ostreococcus lucimarinus

Derelle

Monier

Cooke

et al. 2015

J Virol

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The functional diversity of eukaryotic viruses infecting a single host strain from seawater samples originating from distant marine locations is unknown. To estimate this diversity, we used lysis plaque assays to detect viruses that infect the widespread species Ostreococcus lucimarinus, which is found in coastal and mesotrophic systems, and O. tauri, which was isolated from coastal and lagoon sites from the northwest Mediterranean Sea. Detection of viral lytic activities against O. tauri was not observed using seawater from most sites, except those close to the area where the host strain was isolated. In contrast, the more cosmopolitan O. lucimarinus species recovered viruses from locations in the Atlantic and Pacific Oceans and the Mediterranean Sea. Six new O. lucimarinus viruses (OlVs) then were characterized and their genomes sequenced. Two subgroups of OlVs were distinguished based on their genetic distances and on the inversion of a central 32-kb-long DNA fragment, but overall their genomes displayed a high level of synteny. The two groups did not correspond to proximity of isolation sites, and the phylogenetic distance between these subgroups was higher than the distances observed among viruses infecting O. tauri. Our study demonstrates that viruses originating from very distant sites are able to infect the same algal host strain and can be more diverse than those infecting different species of the same genus. Finally, distinctive features and evolutionary distances between these different viral subgroups does not appear to be linked to biogeography of the viral isolates. IMPORTANCEMarine eukaryotic phytoplankton virus diversity has yet to be addressed, and more specifically, it is unclear whether diversity is connected to geographical distance and whether differential infection and lysis patterns exist among such viruses that infect the same host strain. Here, we assessed the genetic distance of geographically segregated viruses that infect the ubiquitous green microalga Ostreococcus. This study provides the first glimpse into the diversity of predicted gene functions in Ostreococcus viruses originating from distant sites and provides new insights into potential host distributions and restrictions in the world oceans.

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Genetic diversity in cultured and wild marine cyanomyoviruses reveals phosphorus stress as a strong selective agent

Cited by 76 publications

References 68 publications

Metagenomic covariation along densely sampled environmental gradients in the Red Sea

Metagenomic covariation along densely sampled environmental gradients in the Red Sea

Bridging the Gap between Knowing and Modeling Viruses in Marine Systems—An Upcoming Frontier

Diversity of Viruses Infecting the Green Microalga Ostreococcus lucimarinus

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