DNA metabarcoding

Local Knowledge Graph (Top 76 entities)

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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 20 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.

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 (20)

article

Experimental warming decouples plant-fungal symbiont interactions and leads to a more conservative ecosystem

2026PNASusing

article

Legacy effects and arbuscular mycorrhizal fungi of Linaria vulgaris invasion in Colorado and Illinois, USA

2025Invasive Plant Science and Managementusing

student_paper

A nectar-inhabiting bacterium may not influence female fitness in Ipomopsis aggregata

2025using

article

Warming disrupts plant–fungal endophyte symbiosis more severely in leaves than roots

2025Global Change Biologyusing

thesis

The impacts of environmental change on plant and microbial communities: A turf transplant experiment in the Colorado Rocky Mountains

2025using

article

The social microbiome: gut microbiome diversity and abundance are negatively associated with sociality in a wild mammal

2023Royal Society Open Scienceusing

article

Reactive iron, not fungal community, drives organic carbon oxidation potential in floodplain soils

2023Soil Biology and Biochemistryusing

article

Effects of an introduced mustard, Thlaspi arvense, on soil fungal communities in subalpine meadows

Species Studied With This Protocol

DNA metabarcoding

Local Knowledge Graph (Top 76 entities)

Method synopsis

Procedure from a recent peer-reviewed implementation

Typical Equipment

Output Measurements

Papers Using This Protocol (20)

Experimental warming decouples plant-fungal symbiont interactions and leads to a more conservative ecosystem

Legacy effects and arbuscular mycorrhizal fungi of Linaria vulgaris invasion in Colorado and Illinois, USA

A nectar-inhabiting bacterium may not influence female fitness in Ipomopsis aggregata

Warming disrupts plant–fungal endophyte symbiosis more severely in leaves than roots

The impacts of environmental change on plant and microbial communities: A turf transplant experiment in the Colorado Rocky Mountains

The social microbiome: gut microbiome diversity and abundance are negatively associated with sociality in a wild mammal

Reactive iron, not fungal community, drives organic carbon oxidation potential in floodplain soils

Effects of an introduced mustard, Thlaspi arvense, on soil fungal communities in subalpine meadows

Species Studied With This Protocol

Bacteria

Ascomycota

Ligusticum porteri

Festuca

Bacteroidetes

mycorrhizal fungi

Firmicutes

Basidiomycota

Marmota flaviventris

Rushes

The social microbiome: the relationship between the microbiome and sociality in a wild mammal

<i> Firmicutes </i> and <i> Bacteroidetes </i> explain mass gain variation in an obligate hibernator

Effect of elevation, season and accelerated snowmelt on biogeochemical processes during isolated conifer needle litter decomposition

Hidden Processes During Seasonal Isolation of a High-Altitude Watershed

The Snowmelt Niche Differentiates Three Microbial Life Strategies That Influence Soil Nitrogen Availability During and After Winter

Insect herbivory reshapes a native leaf microbiome

A comparison of lodgepole and spruce needle chemistry impacts on terrestrial biogeochemical processes during isolated decomposition

No evidence that gut microbiota impose a net cost on their butterfly host

Hyporheic Zone Microbiome Assembly Is Linked to Dynamic Water Mixing Patterns in Snowmelt-Dominated Headwater Catchments

Altitudinal gradients fail to predict fungal symbiont responses to warming

Plant Identity Influences Foliar Fungal Symbionts More Than Elevation in the Colorado Rocky Mountains

Using geochemical indicators to distinguish high biogeochemical activitiy in floodplain soils and sediments