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rpS3 marker gene analysis

Subcategory: taxonomic classification
Standard reference: Anantharaman et al. (2016)
Papers: 1 | Mentions: 2

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Knowledge graph centered on rpS3 marker gene analysis with 37 nodes and 121 connections. Top connected: leaf water content, carbon cycling, biogeochemical reactions, nitrogen retention, elevation gradient.

Description

Taxonomic classification of microbial communities using ribosomal protein S3 (rpS3) marker genes identified through Hidden Markov Models and phylogenetic analysis.

Typical Equipment

  • Hidden Markov Models (HMM)
  • MAFFT alignment software

Output Measurements

  • taxonomic abundance
  • phylogenetic relationships

Papers Using This Protocol (1)

article

Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock

2019Ecology and Evolutionmodifying

Species Studied With This Protocol

Nitrososphaera sp.

1 paper

Desulfobacca acetoxidans

Syntrophaceae1 paper

Geobacter spp.

1 paper

Desulfuromonas sp.

1 paper

Thaumarchaeota

1 paper

Bathyarchaeota

1 paper

Euryarchaeota

1 paper

Alphaproteobacteria

1 paper

Gammaproteobacteria

1 paper

Shewanella oneidensis

1 paper

Places Where Used

Colorado River

stream1 paper

Gunnison

study site1 paper

Gunnison River Basin

watershed1 paper

Crested Butte

study site1 paper

Boulder

region1 paper

south-central Colorado

region1 paper

San Joaquin Valley

valley1 paper

Uncompahgre River Basins

watershed1 paper

eastern Tibetan plateau

region1 paper

PLM

study site1 paper