Seasonal soil viral metagenomics (Asteraceae)

Knowledge graph centered on Seasonal soil viral metagenomics (Asteraceae) with 32 nodes and 111 connections. Top connected: Rocky Mountain Biological Laboratory, Crested Butte, Potentilla gracilis, Potentilla pulcherrima, Potentilla.

Method synopsis

Systematic collection of soil samples across seasonal transitions in a mountainous watershed to capture viral community dynamics during snowmelt and plant phenological changes.

Synthesized from method descriptions across 1 paper using this protocol.

Procedure as described in the canonical source

Steps below were extracted from the paper that introduces this protocol — Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem (2023), Microbiome. Implementations in other papers (listed below) may differ.

1. Soil sampling from transects
   Soils were sampled from upland hillslope-to-riparian floodplain transect adjacent to the main stem of the East River using a 4-cm diameter soil bulk density corer. Samples were collected at locations separated by approximately 10 m at the upslope and downslope.
   Quantities: 48 total soil samples split into three discrete depth increments: 0-5 cm, 5-15 cm, and 15+ cm below soil surface. ~10 g subsample from each soil core at each depth.Duration: Four sampling dates: March 7, 2017 (peak winter snow depth), May 9, 2017 (snowmelt period), June 9, 2017 (complete loss of snowpack, start of plant growing season), and September 15, 2017 (autumn after plant senescence)Conditions: Winter snow cover typically persists 4 to 6 months (November through May). During snow-free times, soil sampling at upslope and downslope while during winter snow cover, snow-pits were dug down to soil surface at locations adjacent to previous sampling sites.
   Equipment: 4-cm diameter soil bulk density corer
2. Sample preservation
   Each soil core at each depth was frozen immediately with dry ice in the field and archived at −80 °C for metagenome and metatranscriptome analyses.
   Quantities: Samples frozen at -80°CDuration: Immediate freezing, long-term storage at -80°CConditions: Frozen storage conditions maintained throughout
   Equipment: dry ice, -80°C freezer

Typical Equipment

• 4-cm diameter soil bulk density corer
• dry ice
• -80°C freezer

Output Measurements

• soil samples across seasons
• depth profiles
• viral DNA and RNA

Papers Using This Protocol (1)

Species Studied With This Protocol

Places Where Used