Jia-Xiu/dispersal_experiment_2018

Dispersal experiment performed in March-August 2018

Dispersal_experiment

The dispersal microcosom experiment was performed in March-August 2018. The following is the scripts related to this manuscript: Dispersal by inundation differentially alters bacterial communities along a primary succession, authored by Xiu Jia, Cas Cornet and Joana Falcão Salles (in preparation)

Analysis 16S rRNA gene sequences

Work at QIIME2/2019.10 environment, using the following script

• script_dispersal_xiu_5-11-2019.sh

Community and statistic analysis

• alpha & beta-diversity analysis:

  • alpha_diversity_dispersal_scatterplot.R
  • richness_dispersal_gls_glm.Rmd
  • beta_diversity_dispersal.R

• Analyze the rare biopphere:

  • define_rare_common_biospheres.R
  • rare_biosphere_analysis_dispersal.R

• Metagenome prediction by PICRUSt2

  • Use full pipeline script

   # load module in HPC
   module load PICRUSt2/2.3.0b
   # run script with default settings (<30min)
   picrust2_pipeline.py -s rep-seqs-cleaned-0-year.fasta -i table_0_year.biom -o picrust2_out_pipeline -p 4
   picrust2_pipeline.py -s rep-seqs-cleaned-70-year.fasta -i table_70_year.biom -o picrust2_out_pipeline -p 4
  

  • Overall pattern PICRUST2_PCoA_dispersal.R
  • Heatmap for "flight" and "fight" traits (Dini-Andreote, 2018) PICRUST2_heatmap_dispersal.R

Author

• Jia, Xiu