CSI_Dispersal

This repository contains open-source code, data, & text files for

For information regarding the project, please visit:

Project (1) Werba, J.A., A. Stucy, A.L. Peralta, and M.W. McCoy (2020) Effects of diversity and coalescence of species assemblages on ecosystem function at the margins of an environmental shift. PeerJ. 8:e8608 PDF

Project (2) Peralta, A.L. M.E. Muscarella, A. Stucy, J.A. Werba, and M.W. McCoy (In review) Bacterial composition reflects fine-scale salinity changes while phylogenetic diversity exhibits a strong salt divide. bioRxiv LINK

Raw sequence files can be found at NCBI SRA BioProject ID PRJNA615001.

We address the following questions

Project (1)

• Aim): How do the combined effects of salinity and mixing (via dispersal) influence aquatic community composition (zooplankton and bacterioplankton) and ecosystem function (carbon mineralization and litter decomposition) using an experimental salinization approach?

Project (2)

• Aim): How does acute salinization affect microbial taxonomic and phylogenetic diversity and function of freshwater microbial communities as estuarine aquatic communities and saltier conditions move in and persist?

Repo Contents

• analyses:: An R Markdown file that includes R script written by Mario Muscarella, Jo Werba, Alexandra Stucy, and Ariane Peralta containing functions used in analysis of soil and microbial sequence data.

• bin:

  • MothurTools.R: An R script written by Mario Muscarella (Indiana University, now at University of Illinois) containing functions used in the analysis of community sequence data.

• data:: Files associated with soil and microbial data sets.

• figures:: Figures (of zooplankton and bacterioplankton structure and function) generated according to R script located in R Markdown file.

• mothur:: Files containing script for bioinformatic analysis of 16S rRNA gene sequences (Illumina MiSeq platform) using mothur pipeline.

Contributors

Dr. Ariane Peralta: Associate Professor, Department of Biology, East Carolina University. Principal Investigator of the Peralta Lab

Dr. Mario Muscarella: Assistant Professor, Institute or Arctic Biology, University of Alaska Fairbanks. Principal Investigator of the Muscarella Lab.

Alexandra Stucy: MS Student, Department of Biology, East Carolina University

Jo Werba: PhD Candidate, Department of Biology, McMaster University (former MS Student at East Carolina University)

Dr. Mike McCoy: Associate Professor, Department of Biology, East Carolina University. Principal Investigator of the Mike McCoy Lab