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

• Published in: PeerJ
• Main Authors: Gareth Trubl, Simon Roux, Natalie Solonenko, Yueh-Fen Li, Benjamin Bolduc, Josué Rodríguez-Ramos, Emiley A. Eloe-Fadrosh, Virginia I. Rich, Matthew B. Sullivan
• Format: Article in Journal/Newspaper
• Language: English
• Published: PeerJ Inc. 2019
• Subjects: Soil viruses; Viromes; DNA extraction; Organics; Microbiology; ssDNA viruses; Medicine; R; Biology (General); QH301-705.5; permafrost
• Online Access: https://doi.org/10.7717/peerj.7265; https://doaj.org/article/36ba41b4e0d44090970f5e501b79f697

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 ...