DNA metabarcoding

Knowledge graph centered on DNA metabarcoding with 76 nodes and 179 connections. Top connected: Rocky Mountain Biological Laboratory, Gothic, Marmota, Yellow-bellied Marmot, Two-form Bumble Bee.

Method synopsis

Surface sterilization of plant tissues followed by DNA extraction and high-throughput sequencing of the ITS region to characterize fungal endophyte communities. Community composition and diversity metrics were calculated from sequence data.

Synthesized from method descriptions across 22 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 — Experimental warming decouples plant-fungal symbiont interactions and leads to a more conservative ecosystem (2026), PNAS. The protocol was originally introduced by Insect herbivory reshapes a native leaf microbiome (2020), Nature Ecology & Evolution. Implementations in other papers (listed below) may differ.

1. Extract and analyze soil microbial communities
   From each collected soil sample, researchers extracted microbial DNA using bead beating extraction followed by a bead-beating technique. They used MiSeq Illumina lane and sequenced 250 PE bases for 20,000 reads/sample. Fungal sequences were taxonomically assigned using the UNITE database as well as sample preparation and analysis pipelines for this ecosystem.
   Quantities: 250 PE bases, 20,000 reads per sampleDuration: Laboratory analysis following field collectionConditions: Laboratory conditions
   Equipment: MiSeq Illumina sequencer, bead-beating extraction equipment

Typical Equipment

• plastic resealable bags
• −20°C freezer
• Qiagen Powersoil Extraction Kit
• 806R and 515F primers
• Qiagen Multiplex PCR kits
• Illumina MiSeq v. 3
• QIIME2 version 2019.9
• DADA2 denoising tool

Output Measurements

• bacterial taxonomic composition
• Shannon-Wiener diversity
• Faith's phylogenetic diversity
• relative abundance

Papers Using This Protocol (22)

Species Studied With This Protocol

Places Where Used