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rpS3 marker gene analysis

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

Local Knowledge Graph (37 entities)

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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