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16S rRNA gene sequencing
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Description
Systematic collection of sediment samples from floodplain sites at regular depth intervals followed by DNA extraction and metagenomic sequencing to characterize microbial communities.
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 (11)
article
Metagenome-assembled genomes for oligotrophic nitrifiers From a mountainous gravelbed floodplain
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Borgs are giant genetic elements with potential to expand metabolic capacity
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Borgs are giant genetic elements with potential to expand metabolic capacity
article
Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale
article
Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock
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Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock
article
Modeling transient soil moisture limitations on microbial carbon respiration
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Heterogeneity in Hyporheic Flow, Pore Water Chemistry, and Microbial Community Composition in an Alpine Streambed
article
The East River, Colorado, Watershed: A mountainous community testbed for improving predictive understanding of multiscale hydrological-biogeochemical dynamics
student_paper
Does it stay or does it go: exploring seasonal influences on nutrients across topography in a Colorado mountain watershed
student_paper