Quantifying aquatic viral community change associated with stormwater runoff in a wet retention pond using metagenomic time series data

Green, Jasmin C.; Rahman, Faraz; Saxton, Matthew; Williamson, Kurt E.

doi:10.3354/ame01856

“…On the other hand, some phage particles can exceed 0.2 μm [33], although the majority of phages examined by electron microscopy so far belong to the caudovirales order, with capsid sizes < 0.22 μm [34]. However, whether Caudovirales are predominant in soil is unclear [35][36][37][38]. Our TEM analysis confirms the integrity of phages in both PS1 and PS2 filtered suspensions, as well as the presence of Caudovirales phages (Additional file 2: Fig.…”

Section: Discussionsupporting

confidence: 66%

Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios

Braga¹,

Spor²,

Kot³

et al. 2020

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Background: Bacteriophages, the viruses infecting bacteria, are biological entities that can control their host populations. The ecological relevance of phages for microbial systems has been widely explored in aquatic environments, but the current understanding of the role of phages in terrestrial ecosystems remains limited. Here, our objective was to quantify the extent to which phages drive the assembly and functioning of soil bacterial communities. We performed a reciprocal transplant experiment using natural and sterilized soil incubated with different combinations of two soil microbial communities, challenged against native and non-native phage suspensions as well as against a cocktail of phage isolates. We tested three different community assembly scenarios by adding phages: (a) during soil colonization, (b) after colonization, and (c) in natural soil communities. One month after inoculation with phage suspensions, bacterial communities were assessed by 16S rRNA amplicon gene sequencing. Results: By comparing the treatments inoculated with active versus autoclaved phages, our results show that changes in phage pressure have the potential to impact soil bacterial community composition and diversity. We also found a positive effect of active phages on the soil ammonium concentration in a few treatments, which indicates that increased phage pressure may also be important for soil functions. Conclusions: Overall, the present work contributes to expand the current knowledge about soil phages and provide some empirical evidence supporting their relevance for soil bacterial community assembly and functioning.

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“…Previous viromic studies have been limited to describing dsDNA viruses or using MDA to describe ssDNA viruses, but with the onset of the Accel-NGS 1S Plus kit, we leveraged the quantitatively-amplified viromics data produced here to investigate the diversity and relative abundance of ssDNA viruses in our soil samples. Culture collections have revealed ssDNA viruses commonly infect plants as opposed to bacteria, but their distributions in soils remain poorly explored outside a handful of papers which suggest they are highly diverse (Kim et al, 2008; Reavy et al, 2015; Green et al, 2018). Notably, the first quantitative ssDNA/dsDNA viromes suggested that identifiable ssDNA viruses represent a few percent of the viruses observed in marine and freshwater systems (Roux et al, 2016).…”

Section: Resultsmentioning

confidence: 99%

“…For these reasons, most soil viral work is limited to direct counts and morphological analyses (i.e., microscopy observations), from which we have learned (i) there are 10 7 –10 9 virus-like particles/g soil, (ii) viral morphotype richness is generally higher in soils than in aquatic ecosystems, and (iii) viral abundance correlates with soil moisture, organic matter content, pH, and microbial abundance (reviewed in Williamson et al, 2017; Narr et al, 2017). The minimal collective metagenomic data for soils suggests that genetic diversity of soil viruses far exceeds that of other environments for which virome data are available and these viral communities are localized in that viruses form habitat-specific groups (Fierer et al, 2007; Kim et al, 2008; Srinivasiah et al, 2015; Reavy et al, 2015; Zablocki, Adriaenssens & Cowan, 2016; Trubl et al, 2018; Emerson et al, 2018; Green et al, 2018). Thus, while sequencing data for soil viruses is not as robust as it is in aquatic environments, such high particle counts and patterns suggest that viruses also play important ecosystems roles in soils.…”

Section: Introductionmentioning

confidence: 99%

Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils

Trubl

¹

,

Roux

²

,

Solonenko

³

et al. 2019

PeerJ

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Soils impact global carbon cycling and their resident microbes are critical to their biogeochemical processing and ecosystem outputs. Based on studies in marine systems, viruses infecting soil microbes likely modulate host activities via mortality, horizontal gene transfer, and metabolic control. However, their roles remain largely unexplored due to technical challenges with separating, isolating, and extracting DNA from viruses in soils. Some of these challenges have been overcome by using whole genome amplification methods and while these have allowed insights into the identities of soil viruses and their genomes, their inherit biases have prevented meaningful ecological interpretations. Here we experimentally optimized steps for generating quantitatively-amplified viral metagenomes to better capture both ssDNA and dsDNA viruses across three distinct soil habitats along a permafrost thaw gradient. First, we assessed differing DNA extraction methods (PowerSoil, Wizard mini columns, and cetyl trimethylammonium bromide) for quantity and quality of viral DNA. This established PowerSoil as best for yield and quality of DNA from our samples, though ∼1/3 of the viral populations captured by each extraction kit were unique, suggesting appreciable differential biases among DNA extraction kits. Second, we evaluated the impact of purifying viral particles after resuspension (by cesium chloride gradients; CsCl) and of viral lysis method (heat vs bead-beating) on the resultant viromes. DNA yields after CsCl particle-purification were largely non-detectable, while unpurified samples yielded 1–2-fold more DNA after lysis by heat than by bead-beating. Virome quality was assessed by the number and size of metagenome-assembled viral contigs, which showed no increase after CsCl-purification, but did from heat lysis relative to bead-beating. We also evaluated sample preparation protocols for ssDNA virus recovery. In both CsCl-purified and non-purified samples, ssDNA viruses were successfully recovered by using the Accel-NGS 1S Plus Library Kit. While ssDNA viruses were identified in all three soil types, none were identified in the samples that used bead-beating, suggesting this lysis method may impact recovery. Further, 13 ssDNA vOTUs were identified compared to 582 dsDNA vOTUs, and the ssDNA vOTUs only accounted for ∼4% of the assembled reads, implying dsDNA viruses were dominant in these samples. This optimized approach was combined with the previously published viral resuspension protocol into a sample-to-virome protocol for soils now available at protocols.io, where community feedback creates ‘living’ protocols. This collective approach will be particularly valuable given the high physicochemical variability of soils, which will may require considerable soil type-specific optimization. This optimized protocol provides a starting place for developing quantitatively-amplified viromic datasets and will help enable viral ecogenomic studies on organic-rich soils.

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“…ssDNA viruses are recovered in all 3 habitats Previous viromic studies have been limited to describing dsDNA viruses or using MDA to describe ssDNA viruses, but with the onset of the Accel-NGS 1S Plus kit, we leveraged the quantitatively-amplified viromics data produced here to investigate the diversity and relative abundance of ssDNA viruses in our soil samples. Culture collections have revealed ssDNA viruses commonly infect plants as opposed to bacteria, but their distributions in soils remain poorly explored outside a handful of papers which suggest they are highly diverse (Kim et al 2008;Reavy et al 2015;Green et al 2018). Notably, the first quantitative ssDNA/dsDNA viromes suggested that identifiable ssDNA viruses represent a few percent of the viruses observed in marine and freshwater systems (Roux et al 2016).…”

Section: Experiments 2: Heat-based Lysis Of Non-cscl-purified Virus Pamentioning

confidence: 99%

“…microscopy observations), from which we have learned (i) there are 10 7 -10 9 virus-like particles/g soil, (ii) viral morphotype richness is generally higher in soils than in aquatic ecosystems, and (iii) viral abundance correlates with soil moisture, organic matter content, pH, and microbial abundance (reviewed in Williamson 2017; Narr et al 2017). The minimal collective metagenomic data for soils suggests that genetic diversity of soil viruses far exceeds that of other environments for which virome data are available and these viral communities are localized in that viruses form habitat-specific groups (Fierer et al 2007;Kim et al 2008;Srinivasiah et al 2015;Reavy et al 2015;Zablocki et al 2016;Trubl et al 2018;Emerson et al 2018;Green et al 2018). Thus, while sequencing data for soil viruses is not as robust as it is in aquatic environments, such high particle counts and patterns suggest that viruses also play important ecosystems roles in soils.…”

Section: Introductionmentioning

confidence: 99%

Peer Review #1 of "Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils (v0.1)"

2019

0

View full text Add to dashboard Cite

Soils impact global carbon cycling and their resident microbes are critical to their biogeochemical processing and ecosystem outputs. Based on studies in marine systems, viruses infecting soil microbes likely modulate host activities via mortality, horizontal gene transfer, and metabolic control. However, their roles remain largely unexplored due to technical challenges with separating, isolating, and extracting DNA from viruses in soils. Some of these challenges have been overcome by using whole genome amplification methods and while these have allowed insights into the identities of soil viruses and their genomes, their inherit biases have prevented meaningful ecological interpretations. Here we experimentally optimized steps for generating quantitatively-amplified viral metagenomes to better capture both ssDNA and dsDNA viruses across three distinct soil habitats along a permafrost thaw gradient. First, we assessed differing DNA extraction methods (PowerSoil, Wizard mini columns, and cetyl trimethylammonium bromide) for quantity and quality of viral DNA. This established PowerSoil as best for yield and quality of DNA from our samples, though ~1/3 of the viral populations captured by each extraction kit were unique, suggesting appreciable differential biases among DNA extraction kits. Second, we evaluated the impact of purifying viral particles after resuspension (by cesium chloride gradients; CsCl) and of viral lysis method (heat vs bead-beating) on the resultant viromes. DNA yields after CsCl particle-purification were largely non-detectable, while unpurified samples yielded 1-2-fold more DNA after lysis by heat than by bead-beating. Virome quality was assessed by the number and size of metagenome-assembled viral contigs, which showed no increase after CsCl-purification, but did from heat lysis relative to bead-beating. We also evaluated sample preparation protocols for ssDNA virus recovery. In both CsCl-purified and non-purified samples, ssDNA viruses were successfully

show abstract

Quantifying aquatic viral community change associated with stormwater runoff in a wet retention pond using metagenomic time series data

Cited by 9 publications

References 42 publications

Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios

Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios

Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils

Peer Review #1 of "Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils (v0.1)"

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