These scripts (IM#: LLNL-CODE-831991) document the code used to analyze the Pond B (Savannah River Site, South Carolina) microbial community for a manuscript titled "Microbial dynamics impact plutonium and iron biogeochemical cycles in a seasonally stratified pond" (in prep). The R packages used for this manuscript can be found in the file "Packages_and_Paths_microbe.r". The associated scripts for figures/tables in the manuscript are:

• 01.Geochem.r : Figure 2, Figure S2, Figure S3, Table S1, Table S2, Table S3
  
• 02.Dada2.r : Table S6
  
• 03.FilteringOTUs.r : Table S6, Table S9, Table S12, Figure S1
  
• 04.PhylogeneticTree.sh : None
  
• 05.Barplots.r : Figure 3a, Figure 5a, Figure S4
  
• 06.AlphaDiversity.r : Figure 3b, Figure 5b, Figure S5, Figure S9
  
• 07.BetaDiversity.r : Figure 3c, Figure 5c, Figure S6, Figure S10
  
• 08.Songbird_OTUs.r : Figure 4, Figure 7, Figure S7, Figure S8, Table S10, Table S11
  
• 09.Picrust2_Songbird.r : Figure 6, Table S13, Table S14, Table S15
  

Nancy Merino, Naomi Wasserman, Fanny Coutelot, Dan Kaplan, Brian Powell, Yongqin Jiao, Annie Kersting, Mavrik Zavarin

Open Source Distribution, under the terms of the BSD-3 license.
These code will not be updated once the manuscript has been accepted.