Temporal dynamics and decay of putatively allochthonous and autochthonous viral genotypes in contrasting freshwater lakes - PubMed (original) (raw)

Temporal dynamics and decay of putatively allochthonous and autochthonous viral genotypes in contrasting freshwater lakes

Ian Hewson et al. Appl Environ Microbiol. 2012 Sep.

Abstract

Aquatic 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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Figures

Fig 1

Fig 1

(A) Map of sampling locations in the Finger Lakes region of upstate New York. Samples were collected from two contrasting lakes: Fayetteville Green Lake, within the Green Lakes State Park, at the boathouse for plankton and sediments and on agricultural land nearby for soil (B); and Cayuga Lake, in Stewart Park and at site LC3 for plankton and at the equine research park for soil (C).

Fig 2

Fig 2

Phylogenetic annotation of metaviromes of sequence reads (A and B) and contiguous sequences (C). The read annotations were performed using the VIROME pipeline (

http://virome.diagcomputing.org/

), while the contig annotation was performed based on BLASTx searches of contig ORFs against viral, bacterial, archaeal, and eukaryotic databases at CAMERA (

http://camera.calit2.net

), using an E value cutoff of 10−3. (A) Affiliation of reads by kingdom. (B) Viral read annotation by family. (C) Viral contig affiliation by family.

Fig 3

Fig 3

Catchment precipitation (A) and viral genotype abundances in Fayetteville Green Lake (FGL) (B) and Cayuga Lake (CL) (C) during summer 2011. Error bars show SE for duplicate samples. Autochthonous viral genotypes are indicated by open symbols, while allochthonous viral genotypes are indicated by closed symbols. Precipitation data were obtained for Ithaca and Syracuse weather stations from the National Climatic Data Service. Missing data at any time point indicate that abundances were below the detection threshold.

Fig 4

Fig 4

Abundance of viral genotypes in surface and deep sediments and within net plankton (>64 μm) in Fayetteville Green Lake. Error bars show SE for duplicate samples.

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