16S rRNA gene sequencing

Knowledge graph centered on 16S rRNA gene sequencing with 76 nodes and 217 connections. Top connected: Rocky Mountain Biological Laboratory, Gothic, Crested Butte, Engelmann Spruce, Pekania pennanti.

Method synopsis

Systematic collection of sediment samples from floodplain sites at regular depth intervals followed by DNA extraction and metagenomic sequencing to characterize microbial communities.

Synthesized from method descriptions across 12 papers using this protocol.

Procedure from a recent peer-reviewed implementation

Steps below were extracted from the most recent peer-reviewed implementation of this protocol in the corpus — Metagenome-assembled genomes for oligotrophic nitrifiers From a mountainous gravelbed floodplain (2025), Environmental Microbiology. The protocol was originally introduced by Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock (2019), Ecology and Evolution. Implementations in other papers (listed below) may differ.

1. Field sampling of floodplain sediments
   Samples were collected from 2 floodplain locations (OBJ1 and OBJ2) below the confluence of Oh-Be-Joyful Creek and Slate River at coordinates 38°54'34.59'' N, 107°1'43.40'' W. Sediment cores were collected every 20 cm from 50-150 cm below the ground surface.
   Quantities: 2 locations, samples every 20 cm depth intervals from 50-150 cm depthDuration: June 18, 2018 (OBJ2) and June 20, 2018 (OBJ1)Conditions: After peak water table height in early June, during late spring conditions
   Equipment: sediment coring equipment
2. DNA extraction from sediment samples
   DNA was extracted from 4.76-5.29 g of frozen soil using the DNeasy PowerMax Soil Kit (Qiagen) with an added incubation step at 80°C for 40 min immediately after bead beating to improve yields. DNA was eluted in 5 mL solution C6, and concentrated down to ~1 mL with a VivaSpin Turbo 15 column (Sartorius).
   Quantities: 4.76-5.29 g sediment per sample, eluted to ~1 mL final volumeDuration: 40 min incubation step added to standard protocolConditions: Frozen soil samples processed
   Equipment: DNeasy PowerMax Soil Kit (Qiagen), VivaSpin Turbo 15 column (Sartorius)

Typical Equipment

• sediment coring equipment
• DNeasy PowerMax Soil Kit (Qiagen)
• VivaSpin Turbo 15 column (Sartorius)
• Illumina NovaSeq S4

Output Measurements

• sediment samples
• extracted DNA
• metagenomic sequence data

Papers Using This Protocol (12)

Species Studied With This Protocol

Places Where Used