Optimization of viral profiling approaches reveals strong links between viral and bacterial communities in a eutrophic freshwater lake

Hardbower, Dana M.; Dolman, Jessica L.; Glasner, Dustin R.; Kendra, Joseph A.; Williamson, Kurt E.

doi:10.3354/ame01582

Cited by 9 publications

(22 citation statements)

References 78 publications

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“…The VLP values from El Neusa reservoir were within the same order of magnitude as those observed in lentic ecosystems of temperate and tropical latitudes with different trophic states, especially those with moderate to high levels of nutrients and biological productivity (Wilhelm & Smith, 2000;Bettarel et al, 2003;Liu et al, 2006;De Araújo & Godinho, 2009;Ram et al, 2011;Hardbower et al, 2012;Almeida et al, 2015). However, the variability of this study was relatively higher than in other studies, probably due to differences in temporal and spatial scales of the sampling design.…”

Section: Discussioncontrasting

confidence: 53%

Spatial and temporal dynamics of virioplankton in a high mountain tropical reservoir, El Neusa (Cundinamarca, Colombia)

Hakspiel-Segura¹,

Rosso-Londoño²,

Canosa-Torrado

et al. 2017

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Section: Discussioncontrasting

confidence: 53%

Spatial and temporal dynamics of virioplankton in a high mountain tropical reservoir, El Neusa (Cundinamarca, Colombia)

Hakspiel-Segura¹,

Rosso-Londoño²,

Canosa-Torrado

et al. 2017

lajar

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“…Bacterial and viral abundance were determined in duplicate subsamples from each pond via epifluorescence microscopy using a method adapted from N oble & Fuhrman (1998) as has been described previously (Hardbower et al 2012). …”

Section: Bacterial and Viral Enumerationmentioning

confidence: 99%

“…A 1 µl aliquot of virus concentrate, diluted to contain 10 5 virus particles, was used to provide template DN A, as previously described (Hardbower et al 2012). RAPD-PCR products from the complete 25 µl reaction were separated by gel electrophoresis on 13 × 16 cm 1.8% metaphor agarose gels (Lonza) in 0.5× TBE buffer, run at 4 V cm −1 .…”

Section: Viral Community Profile Analysis Via Random Amplified Polymomentioning

confidence: 99%

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Site-specific environmental factors control bacterial and viral diversity in stormwater retention ponds

Saxton¹,

Naqvi²,

Rahman³

et al. 2016

Aquat. Microb. Ecol.

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Stormwater retention ponds are ubiquitous in urban and suburban landscapes of the United States. Most studies of the microbiology of these ponds have focused on the abundance and removal efficiency of fecal indicator bacteria. Here we provide the first comprehensive study of microbial community diversity and activity in these ponds, and assess how different environmental and engineering factors influence these communities. Watershed land-use had no grouping effect on pond geochemistry or biology. Instead, we found that microbial community composition and activity were best explained by site-specific environmental variables. 16S rRNA gene sequence analysis indicated that bacterial community structure varied greatly across sampled ponds, and appeared to be the result of autochthonous bacterial growth and not simply surface runoff. Metagenomic sequencing of pond viral communities suggested that viral taxa were influenced by external inputs, with viromes composed of bacteriophage that infect environmental bacteria, as well as viruses that infect eukaryotes and phages that infect bacteria pathogenic to eukaryotes. Collectively, our results indicate that the environmental conditions and microbial communities of these ponds vary greatly, even among ponds in close spatial proximity, and that pond microbial communities appear to be shaped by site-specific environmental factors.

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“…Viral and bacterial abundance was determined using SYBR Gold-epifluorescence microscopy from triplicate subsamples (Noble & Fuhrman 1998, Hardbower et al 2012. Virus-to-bacterium ratios were calculated based on averages of both viral and bacterial abundances for each sample.…”

Section: Environmental Metadatamentioning

confidence: 99%

Metagenomic assessment of viral diversity in Lake Matoaka, a temperate, eutrophic freshwater lake in southeastern Virginia, USA

Green¹,

Rahman²,

Saxton³

et al. 2015

Aquat. Microb. Ecol.

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Little is known about the composition and diversity of temperate freshwater viral communities. This study presents a metagenomic analysis of viral community composition, taxonomic and functional diversity of temperate, eutrophic Lake Matoaka in southeastern Virginia (USA). Three sampling sites were chosen to represent differences in anthropogenic impacts: the Crim Dell Creek mouth (impacted), the Pogonia Creek mouth (less impacted) and the main body of the lake (mixed). Sequences belonging to tailed bacteriophages were the most abundant at all 3 sites, with Podoviridae predominating. The main lake body harbored the highest virus genotype richness and included cyanophage and eukaryotic algal virus sequences not found at the other 2 sites, while the impacted Crim Dell Creek mouth showed the lowest richness. Cross-contig comparisons indicated that similar virus genotypes were found at all 3 sites, but at different rankabundances. Hierarchical cluster analysis of multiple viral metagenomes indicated high genetic similarity between viral communities of related environments, with freshwater, marine, hypersaline, and eukaryote-associated environments forming into clear groups despite large geographic distances between sampling locations within each environment type. These results support the conclusion that freshwater viral communities are genetically distinct from virus assemblages in other environments.KEY WORDS: Virus · Freshwater · Lake · Temperate · Metagenome · Sequencing · Virome Resale or republication not permitted without written consent of the publisher

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Optimization of viral profiling approaches reveals strong links between viral and bacterial communities in a eutrophic freshwater lake

Cited by 9 publications

References 78 publications

Spatial and temporal dynamics of virioplankton in a high mountain tropical reservoir, El Neusa (Cundinamarca, Colombia)

Spatial and temporal dynamics of virioplankton in a high mountain tropical reservoir, El Neusa (Cundinamarca, Colombia)

Site-specific environmental factors control bacterial and viral diversity in stormwater retention ponds

Metagenomic assessment of viral diversity in Lake Matoaka, a temperate, eutrophic freshwater lake in southeastern Virginia, USA

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