Dynamics of Viral Abundance and Diversity in a Sphagnum-Dominated Peatland: Temporal Fluctuations Prevail Over Habitat

Ballaud, Flore; Dufresne, Alexis; Francez, André-Jean; Colombet, Jonathan; Sime-Ngando, Télesphore; Quaiser, Achim

doi:10.3389/fmicb.2015.01494

Cited by 13 publications

(15 citation statements)

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“…Description of bacteriophage populations in Sphagnum peatlands is currently limited to the ssDNA viruses of the Microviridae (45) and Caudovirales (46) observed in metagenomics data, although it appears that phages are the most abundant biological entities in the Sphagnum phyllosphere (46). Given this, and the dominance of bacteria in the Sphagnum microbiome as previously described (15), the relatively low abundance of active bacteriophage in our samples was a surprise.…”

Section: Discussionmentioning

confidence: 59%

Diversity of Active Viral Infections within the Sphagnum Microbiome

Stough

Kostka

Weston

et al. 2018

Appl Environ Microbiol

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-dominated peatlands play an important role in global carbon storage and represent significant sources of economic and ecological value. While recent efforts to describe microbial diversity and metabolic potential of the microbiome have demonstrated the importance of its microbial community, little is known about the viral constituents. We used metatranscriptomics to describe the diversity and activity of viruses infecting microbes within the peat bog. The vegetative portions of six plants were obtained from a peatland in northern Minnesota, and the total RNA was extracted and sequenced. Metatranscriptomes were assembled and contigs were screened for the presence of conserved virus marker genes. Using bacteriophage capsid protein gp23 as a marker for phage diversity, we identified 33 contigs representing undocumented phages that were active in the community at the time of sampling. Similarly, RNA-dependent RNA polymerase and the nucleocytoplasmic large DNA virus (NCLDV) major capsid protein were used as markers for single-stranded RNA (ssRNA) viruses and NCLDV, respectively. In total, 114 contigs were identified as originating from undescribed ssRNA viruses, 22 of which represent nearly complete genomes. An additional 64 contigs were identified as being from NCLDVs. Finally, 7 contigs were identified as putative virophage or polinton-like viruses. We developed co-occurrence networks with these markers in relation to the expression of potential-host housekeeping gene to predict virus-host relationships, identifying 13 groups. Together, our approach offers new tools for the identification of virus diversity and interactions in understudied clades and suggests that viruses may play a considerable role in the ecology of the microbiome. -dominated peatlands play an important role in maintaining atmospheric carbon dioxide levels by modifying conditions in the surrounding soil to favor the growth of over that of other plant species. This lowers the rate of decomposition and facilitates the accumulation of fixed carbon in the form of partially decomposed biomass. The unique environment produced by enriches for the growth of a diverse microbial consortia that benefit from and support the moss's growth, while also maintaining the hostile soil conditions. While a growing body of research has begun to characterize the microbial groups that colonize, little is currently known about the ecological factors that constrain community structure and define ecosystem function. Top-down population control by viruses is almost completely undescribed. This study provides insight into the significant viral influence on the microbiome and identifies new potential model systems to study virus-host interactions in the peatland ecosystem.

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Section: Discussionmentioning

confidence: 59%

Diversity of Active Viral Infections within the Sphagnum Microbiome

Stough

Kostka

Weston

et al. 2018

Appl Environ Microbiol

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“…3 ), and this finding is consistent with results in aquatic systems and sediments ( Brum, Schenck & Sullivan, 2013 ). Soil virus literature to date, suggests viral community structure is not different with depth (based on genetic material; Adriaenssens & Cowan, 2014 ), nor does abundance change (comparing 5–10 cm and 10–15 cm from soil pore water; Ballaud et al, 2015 ), but viral abundance was reported to vary seasonally ( Ballaud et al, 2015 ). To this end, we tested storing both shallow and deep soil samples at chilled (4 °C) and frozen temperatures (−80 °C).…”

Section: Resultsmentioning

confidence: 99%

“…Metagenomic studies in rainforest soils indicate that viral species richness is greater than bacterial species richness by an order of magnitude where moisture content and OM are high ( Fierer et al, 2007 ; reviewed in Kimura et al, 2008 ). Additionally, viral diversity may be greater in soils than in marine water column environments, because soil microorganisms are thought to be more diverse than marine microorganisms ( Torsvik, Øvreås & Thingstad, 2002 ; Weinbauer & Rassoulzadegan, 2004 ; Smalla & Van Elsas, 2010 ; Tamames et al, 2010 ; Crump, Amaral-Zettler & Kling, 2012 ), and viral and microbial diversity are correlated ( Maranger & Bird, 1995 ; Anesio et al, 2004 ; Ballaud et al, 2015 ). In addition, soil viruses have clear seasonal population dynamics with different temporal and spatial distributions ( Ashelford et al, 1999 ; Ashelford et al, 2000 ; Ballaud et al, 2015 ), which could act as mechanisms for maintaining the coexistence of a diverse community ( Chesson, 2000 ).…”

Section: Introductionmentioning

confidence: 99%

Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient

Trubl

Solonenko

Chittick

et al. 2016

PeerJ

107

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Permafrost stores approximately 50% of global soil carbon (C) in a frozen form; it is thawing rapidly under climate change, and little is known about viral communities in these soils or their roles in C cycling. In permafrost soils, microorganisms contribute significantly to C cycling, and characterizing them has recently been shown to improve prediction of ecosystem function. In other ecosystems, viruses have broad ecosystem and community impacts ranging from host cell mortality and organic matter cycling to horizontal gene transfer and reprogramming of core microbial metabolisms. Here we developed an optimized protocol to extract viruses from three types of high organic-matter peatland soils across a permafrost thaw gradient (palsa, moss-dominated bog, and sedge-dominated fen). Three separate experiments were used to evaluate the impact of chemical buffers, physical dispersion, storage conditions, and concentration and purification methods on viral yields. The most successful protocol, amended potassium citrate buffer with bead-beating or vortexing and BSA, yielded on average as much as 2-fold more virus-like particles (VLPs) g−1 of soil than other methods tested. All method combinations yielded VLPs g−1 of soil on the 108 order of magnitude across all three soil types. The different storage and concentration methods did not yield significantly more VLPs g−1 of soil among the soil types. This research provides much-needed guidelines for resuspending viruses from soils, specifically carbon-rich soils, paving the way for incorporating viruses into soil ecology studies.

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“…Instead, virus-focused metagenomics studies either concentrate virus-genomes via their virions or enrich for double-stranded RNA that is a broadly shared feature of virus replication. The virus-enriched nucleic acids are then sequenced by shotgun metagenomics methods (Bibby 2013) for the detection of viruses in environmental material, including marine water (Schmidt et al 2014), fresh water (Mohiuddin & Schellhorn 2015), soil (Ballaud et al 2016), crop plants (Aw et al 2016), native plants and weed plant species (Blouin et al 2016). We remain unable to recommend a single molecular approach to comprehensively target all of the diversity of viral material for metabarcoding studies in an unbiased manner, i.e.…”

Section: Recommendationmentioning

confidence: 99%

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Lear¹,

Dickie²,

Banks³

et al. 2018

107

112

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Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil ® and PowerMax ® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil ® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater ® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications.

show abstract

Dynamics of Viral Abundance and Diversity in a Sphagnum-Dominated Peatland: Temporal Fluctuations Prevail Over Habitat

Cited by 13 publications

References 100 publications

Diversity of Active Viral Infections within the Sphagnum Microbiome

Diversity of Active Viral Infections within the Sphagnum Microbiome

Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

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