Phylogenetic Diversity of Sequences of Cyanophage Photosynthetic Gene
            <i>psbA</i>
            in Marine and Freshwaters

Chénard, Caroline; Suttle, Curtis A.

doi:10.1128/aem.02480-07

Cited by 86 publications

(93 citation statements)

References 31 publications

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“…For example, bacteriophage structural proteins g20 (portal vertex protein) (Short and Suttle 2005;Sullivan et al, 2008) and gp23 (major capsid protein) (Filee et al, 2005;Jamindar et al, 2012) have been used to identify the diversity and distribution of cyanomyoviruses and T4-like phages. Functional genes like DNA polymerase A (Labonté et al, 2009;Huang et al, 2010) and photosystem genes psbA and psbD (Bench et al, 2007;Chenard and Suttle 2008) have been used as proxies of T7-like podoviruses and cyanophage diversity, respectively. These marker genes, which have been examined in both cultivated phages and environmental amplicon sequence data, have yielded key insights into the diversity and distribution of their respective phage targets.…”

Section: Discussionmentioning

confidence: 99%

Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton

et al. 2013

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Virioplankton have a significant role in marine ecosystems, yet we know little of the predominant biological characteristics of aquatic viruses that influence the flow of nutrients and energy through microbial communities. Family A DNA polymerases, critical to DNA replication and repair in prokaryotes, are found in many tailed bacteriophages. The essential role of DNA polymerase in viral replication makes it a useful target for connecting viral diversity with an important biological feature of viruses. Capturing the full diversity of this polymorphic gene by targeted approaches has been difficult; thus, full-length DNA polymerase genes were assembled out of virioplankton shotgun metagenomic sequence libraries (viromes). Within the viromes novel DNA polymerases were common and found in both double-stranded (ds) DNA and single-stranded (ss) DNA libraries. Finding DNA polymerase genes in ssDNA viral libraries was unexpected, as no such genes have been previously reported from ssDNA phage. Surprisingly, the most common virioplankton DNA polymerases were related to a siphovirus infecting an a-proteobacterial symbiont of a marine sponge and not the podoviral T7-like polymerases seen in many other studies. Amino acids predictive of catalytic efficiency and fidelity linked perfectly to the environmental clades, indicating that most DNA polymerase-carrying virioplankton utilize a lower efficiency, higher fidelity enzyme. Comparisons with previously reported, PCR-amplified DNA polymerase sequences indicated that the most common virioplankton metagenomic DNA polymerases formed a new group that included siphoviruses. These data indicate that slower-replicating, lytic or lysogenic phage populations rather than fast-replicating, highly lytic phages may predominate within the virioplankton.

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Section: Discussionmentioning

confidence: 99%

Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton

et al. 2013

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“…Other studies, however, have identified compositional variation among locations. In these cases, the patterns appear to be related to salinity, whereby freshwaters harbor cyanophage taxa not found in marine habitats (Short & Suttle 2005, Chénard & Suttle 2008, Sullivan et al 2008, Wang et al 2010. Indeed, we know of only 1 study that found evidence for genetically distinct cyanophage communities across relatively small (<100 km) scales within a marine system (Frederickson et al 2003).…”

Section: Introductionmentioning

confidence: 98%

“…Patterns over horizontal space are less consistent, however. Some studies suggest that cyanophage composition exhibits little horizontal spatial variation, given that nearly identical cyanophage gene sequences have been identified in surface marine samples collected from distant locations (Zhong et al 2002, Breitbart et al 2004, Short & Suttle 2005, Chénard & Suttle 2008. Other studies, however, have identified compositional variation among locations.…”

Section: Introductionmentioning

confidence: 99%

“…We successfully amplified psbA from 95% of the cyanophage isolates using primers developed by Wang & Chen (2008 Phylogenetic 'Mar1' group refers to the marine cyanobacteria-infecting myovirus clade according to Chénard & Suttle (2008). Bootstrap values are indicated at the nodes 517 of these sequences fell into a single OTU (OTU-1), 20 of the OTUs were composed of only 1 sequence (Table 1, Fig.…”

Section: Psba Sequence Diversitymentioning

confidence: 99%

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Diversity and temporal dynamics of Southern California coastal marine cyanophage isolates

Clasen¹,

Hanson²,

Ibrahim³

et al. 2013

Aquat. Microb. Ecol.

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Marine ecosystems contain an immense diversity of phages, many of which infect the cyanobacteria responsible for a portion of oceanic primary productivity. To add to the growing body of research on the dynamics and diversity of these cyanophages, we measured cyanophage abundance, diversity, and community composition monthly for 15 mo at 3 coastal locations in Southern California, USA. We characterized over 900 individual cyanophages, isolated on Synechococcus sp. WH7803, by amplifying and sequencing 2 different genes from each isolate: g20 (the portal protein gene) and psbA (a host-derived gene involved in photosynthesis). The taxonomic composition and diversity of isolated cyanophages were highly variable over time, with little variation across the 3 locations. Particular taxa dominated the community at distinct times of year, with more rapid turnover of dominant types and higher overall abundance and diversity during spring and summer. These temporal patterns as well as taxonomic designations were highly congruent for both genes, based on operational taxonomic units (OTUs) defined at 99% nucleotide similarity, despite a greater level of amino acid conservation within psbA as compared to g20. Overall, this suggests that either gene can serve as a useful marker for cyanophage diversity. However, we detected 1 myovirus taxon (representing about 2.5% of the isolates) of uncertain phylogenetic affiliation that was negative for psbA amplification. Further sampling is necessary to assess whether these temporal dynamics in cyanophage composition, diversity, and abundance are seasonally recurring.

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“…In the ocean, the cyanobacteria Synechococcus and Prochlorococcus are the major phytoplankton fixing carbons via photosynthesis (Waterbury et al, 1986;Partensky et al, 1999;DeLong and Karl, 2005;Jardillier et al, 2010), and marine cyanophages reportedly participate in the process by carrying the ratelimiting photosystem II protein D1 in their genomes (Sullivan et al, 2006). Because cyanophage D1 protein were reportedly detectable in other freshwater lakes (Chenard and Suttle, 2008), we tried homology search and also detected D1 proteins in our metaviromes. However, any homology search is highly database-dependent.…”

Section: Viral Community In Ftrmentioning

confidence: 99%

Microbial and viral metagenomes of a subtropical freshwater reservoir subject to climatic disturbances

Tseng¹,

Chiang

Shiah

et al. 2013

The ISME Journal

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Extreme climatic activities, such as typhoons, are widely known to disrupt our natural environment. In particular, studies have revealed that typhoon-induced perturbations can result in several long-term effects on various ecosystems. In this study, we have conducted a 2-year metagenomic survey to investigate the microbial and viral community dynamics associated with environmental changes and seasonal variations in an enclosed freshwater reservoir subject to episodic typhoons. We found that the microbial community structure and the associated metagenomes continuously changed, where microbial richness increased after typhoon events and decreased during winter. Among the environmental factors that influenced changes in the microbial community, precipitation was considered to be the most significant. Similarly, the viral community regularly showed higher relative abundances and diversity during summer in comparison to winter, with major variations happening in several viral families including Siphoviridae, Myoviridae, Podoviridae and Microviridae. Interestingly, we also found that the precipitation level was associated with the terrestrial viral abundance in the reservoir. In contrast to the dynamic microbial community (L-divergence 0.73 ± 0.25), we found that microbial metabolic profiles were relatively less divergent (L-divergence 0.24±0.04) at the finest metabolic resolution. This study provides for the first time a glimpse at the microbial and viral community dynamics of a subtropical freshwater ecosystem, adding a comprehensive set of new knowledge to aquatic environments.

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Phylogenetic Diversity of Sequences of Cyanophage Photosynthetic Gene psbA in Marine and Freshwaters

Cited by 86 publications

References 31 publications

Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton

Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton

Diversity and temporal dynamics of Southern California coastal marine cyanophage isolates

Microbial and viral metagenomes of a subtropical freshwater reservoir subject to climatic disturbances

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