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DNA metabarcoding
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Description
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.
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
article
Legacy effects and arbuscular mycorrhizal fungi of Linaria vulgaris invasion in Colorado and Illinois, USA
student_paper
A nectar-inhabiting bacterium may not influence female fitness in Ipomopsis aggregata
article
Warming disrupts plant–fungal endophyte symbiosis more severely in leaves than roots
thesis
The impacts of environmental change on plant and microbial communities: A turf transplant experiment in the Colorado Rocky Mountains
article
The social microbiome: gut microbiome diversity and abundance are negatively associated with sociality in a wild mammal
article
Reactive iron, not fungal community, drives organic carbon oxidation potential in floodplain soils
article
Effects of an introduced mustard, Thlaspi arvense, on soil fungal communities in subalpine meadows
student_paper
The social microbiome: the relationship between the microbiome and sociality in a wild mammal
thesis
<i> Firmicutes </i> and <i> Bacteroidetes </i> explain mass gain variation in an obligate hibernator
article
Effect of elevation, season and accelerated snowmelt on biogeochemical processes during isolated conifer needle litter decomposition
article
Hidden Processes During Seasonal Isolation of a High-Altitude Watershed
article
The Snowmelt Niche Differentiates Three Microbial Life Strategies That Influence Soil Nitrogen Availability During and After Winter
article
Insect herbivory reshapes a native leaf microbiome
article
A comparison of lodgepole and spruce needle chemistry impacts on terrestrial biogeochemical processes during isolated decomposition
article
No evidence that gut microbiota impose a net cost on their butterfly host
article
Hyporheic Zone Microbiome Assembly Is Linked to Dynamic Water Mixing Patterns in Snowmelt-Dominated Headwater Catchments
article
Altitudinal gradients fail to predict fungal symbiont responses to warming
article
Plant Identity Influences Foliar Fungal Symbionts More Than Elevation in the Colorado Rocky Mountains
article