CaveMethanotrophs

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An analysis of cave methanotrophic communities from environmental 16S rRNA dna sequece data from caves in the US. This repository contains open-source code, data, and text files to examine how methanotrophic communities vary in caves.

Repo Contents

• CaveMethanotrophData: - Data files used in this research

  • CvMcrb03_20190225.shared - A shared file describing the abundance of an OTU at a particular study site
  • CvMcrb03_20190225.taxonomy - A taxonomy file of the identified sequences
  • MethanotrophSearch.fasta - A FASTA file of methanotroph 16S rRNA sequences from the literature
  • MinAbnMatr.txt - A mineral abundance matrix by site
  • NCBIPutMntrphIDCave_20190616.txt - Matches between OTUs from the shared file and known methanotrophs
  • sample_meta_data+d.txt - A txt file of the collected meta data

• CaveMethanotrophRcode: - Analytical and figure generating code

  • DistDecay_20220617.r - This code examines the distance decay pattern of methanotrophs
  • MethanoExploration_20220616.r - Code to look at the alpha and beta diversity, and the core metanotroph microbiome of caves
  • MethanoMap_20220617.r - This code generates a spatial map of cave methanotroph abundance
  • MethanoMineralCCA_20220617 - Code for cannonical correspondance analysis of cave methanotroph communities against mineral abundance
  • MethanoVsCHConc_20220617.r - This code examines how methanotroph relative abundance changes with CH4 concentration
  • MethanoVsDistEnt_20220620.r - Code for examining how methanotroph relative abundance changes with distance to a cave entrance
  • MetahnoVsSoilGrainSize_20220618.r - Code for examing how methanotroph relative abundance changes with soil grain size
  • Slopetest_20220623.r - Code containing fuctions for distance decay analysis

Contributors

Dr. Kevin Webster: Associate Research Scientist, Planetary Science Institute.

Dr. Jay Lennon: Associate Professor, Department of Biology, Indiana University, Bloomington. Head of the Lennon Lab.