Novel phycodnavirus genes amplified from Canadian freshwater environments

Short, Steven M.; Rusanova, Oksana; Staniewski, Michael A.

doi:10.3354/ame01478

Cited by 18 publications

(28 citation statements)

References 26 publications

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“…These viral genotypes may represent viruses infecting other terrestrial hosts, since our annotation was based on translated nucleotide-protein comparisons (i.e., BLASTx) in which average homology to geminiviruses was low. Phycodnaviruses are large double-stranded DNA (dsDNA) viruses that typically infect eukaryotic algae (17,51). Circoviruses, which are circular single-stranded DNA (ssDNA) viruses (48), were large constituents of soil libraries and were less common in freshwater libraries.…”

Section: Discussionmentioning

confidence: 99%

Temporal Dynamics and Decay of Putatively Allochthonous and Autochthonous Viral Genotypes in Contrasting Freshwater Lakes

Hewson

Barbosa

Brown

et al. 2012

Appl Environ Microbiol

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ABSTRACTAquatic viruses play important roles in the biogeochemistry and ecology of lacustrine ecosystems; however, their composition, dynamics, and interactions with viruses of terrestrial origin are less extensively studied. We used a viral shotgun metagenomic approach to elucidate candidate autochthonous (i.e., produced within the lake) and allochthonous (i.e., washed in from other habitats) viral genotypes for a comparative study of their dynamics in lake waters. Based on shotgun metagenomes prepared from catchment soil and freshwater samples from two contrasting lakes (Cayuga Lake and Fayetteville Green Lake), we selected two putatively autochthonous viral genotypes (phycodnaviruses likely infecting algae and cyanomyoviruses likely infecting picocyanobacteria) and two putatively allochthonous viral genotypes (geminiviruses likely infecting terrestrial plants and circoviruses infecting unknown hosts but common in soil libraries) for analysis by genotype-specific quantitative PCR (TaqMan) applied to DNAs from viruses in the viral size fraction of lake plankton, i.e., 0.2 μm > virus > 0.02 μm. The abundance of autochthonous genotypes largely reflected expected host abundance, while the abundance of allochthonous genotypes corresponded with rainfall and storm events in the respective catchments, suggesting that viruses with these genotypes may have been transported to the lake in runoff. The decay rates of allochthonous and autochthonous genotypes, assessed in incubations where all potential hosts were killed, were generally lower (0.13 to 1.50% h−1) than those reported for marine virioplankton but similar to those for freshwater virioplankton. Both allochthonous and autochthonous viral genotypes were detected at higher concentrations in subsurface sediments than at the water-sediment interface. Our data indicate that putatively allochthonous viruses are present in lake plankton and sediments, where their temporal dynamics reflect active transport to the lake during hydrological events and then decay once there.

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Section: Discussionmentioning

confidence: 99%

Temporal Dynamics and Decay of Putatively Allochthonous and Autochthonous Viral Genotypes in Contrasting Freshwater Lakes

Hewson

Barbosa

Brown

et al. 2012

Appl Environ Microbiol

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“…These particular viruses were used in this study because their hosts can be grown in the laboratory and, therefore, titers of infectious viruses can be estimated. Furthermore, close relatives of each of these viruses are known in local freshwaters; CpV-BQ1 was isolated from Ontario waters (Mirza et al, 2015) and DNA polymerase gene sequences closely related to ATCV-1, CVM-1 and CpV-BQ1 have been amplified from the study site (Short et al, 2011b).…”

Section: Introductionmentioning

confidence: 99%

Seasonal determinations of algal virus decay rates reveal overwintering in a temperate freshwater pond

Long

Short

2016

The ISME Journal

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To address questions about algal virus persistence (i.e., continued existence) in the environment, rates of decay of infectivity for two viruses that infect Chlorella-like algae, ATCV-1 and CVM-1, and a virus that infects the prymnesiophyte Chrysochromulina parva, CpV-BQ1, were estimated from in situ incubations in a temperate, seasonally frozen pond. A series of experiments were conducted to estimate rates of decay of infectivity in all four seasons with incubations lasting 21 days in spring, summer and autumn, and 126 days in winter. Decay rates observed across this study were relatively low compared with previous estimates obtained for other algal viruses, and ranged from 0.012 to 11% h − 1 . Overall, the virus CpV-BQ1 decayed most rapidly whereas ATCV-1 decayed most slowly, but for all viruses the highest decay rates were observed during the summer and the lowest were observed during the winter. Furthermore, the winter incubations revealed the ability of each virus to overwinter under ice as ATCV-1, CVM-1 and CpV-BQ1 retained up to 48%, 19% and 9% of their infectivity after 126 days, respectively. The observed resilience of algal viruses in a seasonally frozen freshwater pond provides a mechanism that can support the maintenance of viral seed banks in nature. However, the high rates of decay observed in the summer demonstrate that virus survival and therefore environmental persistence can be subject to seasonal bottlenecks.

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“…Previous work has shown that different algal viruses such as Prymnesioviruses and Chloroviruses occur in the UTM pond [45], and taxon-specific qPCR methods have already been developed to monitor algal viruses in freshwater environments [24,33,45]. Thus, an obvious and promising next step in this work will be to compare viral production to estimates of virus-mediated mortality.…”

Section: Future Directionsmentioning

confidence: 94%

Contrasting Community versus Population-Based Estimates of Grazing and Virus-Induced Mortality of Phytoplankton

Staniewski

Short

2012

Microb Ecol

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In this study, grazing and virus-induced mortality of phytoplankton was investigated in a freshwater pond at the University of Toronto Mississauga, Canada, during September 2009. The modified dilution assay, which partitions phytoplankton mortality into virus and grazing-induced fractions, was used along with newly designed, taxon-specific quantitative polymerase chain reaction (qPCR) assays that target psbA gene fragments to estimate growth and mortality rates for both the entire phytoplankton community and four distinct phytoplankton populations. Community mortality was estimated via fluorometric determination of chlorophyll a (Chl a) concentrations, whereas the relative mortality of individual phytoplankton populations was estimated via qPCR. The sources and amounts of mortality for individual phytoplankton populations differed from those of the whole community, as well as from each other. Grazing was found to be the only significant source of mortality for the community (0.32 day(-1)), and the Prymnesiales (1.65 day(-1)) and Chroococcales (2.79 day(-1)) populations studied. On the other hand, the Chlamydomonadales population examined experienced both significant grazing (1.01 day(-1)) and viral lysis (0.96 day(-1)), while the Chlorellales population only experienced significant mortality as a result of viral lysis (1.38 day(-1)). Our results demonstrate that the combination of qPCR and the modified dilution method can be used to estimate both viral lysis and grazing pressure on several individual phytoplankton populations within a community simultaneously. Further, previously noted limitations of the modified dilution method associated with the dilution of specific phytoplankton populations at low abundances can be overcome with the qPCR-based approach. Most importantly, this study demonstrates that when used alone, whole community-based methods of assessing mortality can overlook valuable information about carbon flow in aquatic microbial food webs.

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Novel phycodnavirus genes amplified from Canadian freshwater environments

Cited by 18 publications

References 26 publications

Temporal Dynamics and Decay of Putatively Allochthonous and Autochthonous Viral Genotypes in Contrasting Freshwater Lakes

Temporal Dynamics and Decay of Putatively Allochthonous and Autochthonous Viral Genotypes in Contrasting Freshwater Lakes

Seasonal determinations of algal virus decay rates reveal overwintering in a temperate freshwater pond

Contrasting Community versus Population-Based Estimates of Grazing and Virus-Induced Mortality of Phytoplankton

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