Dimensions: Collaborative Research: Microbial seed banks: processes and patterns of dormancy-driven biodiversity

This repository contains open-source code, data, & text files for research projects related to a National Science Foundation Dimensions of Biodiversity grant (#1442246) awarded to Dr.'s Jay Lennon and Ken Locey of Indiana University (Bloomington) and to Dr. Stuart Jones of the University of Notre Dame (#...).

http://www.nsf.gov/awardsearch/showAward?AWD_ID=1442246&HistoricalAwards=false

Goals

To identify key ecological and evolutionary processes that generate and maintain microbial biodiversity, and to understand how this diversity in turn influences ecosystem processes. These goals will be addressed by focusing on how and why dormancy varies among microbes as a result of life history trade-offs. Combined with novel insight into dormancy-driven communication networks, the research will determine how seed bank dynamics affect the function and geographic patterns of microbial diversity. Three major objectives pertaining to dormancy and the diversity of microbial communities will be addressed:

• Aim 1.) Test for life history tradeoffs between dormancy and physiological and genomic characteristics by comparing survivorship during prolonged dormancy across a phylogenetically diverse collection of soil bacteria using a traits-based approach,

• Aim 2.) Test predictions regarding the nature of dormancy as a cell-cell communicated response that affects pathogen suppression, plant-soil feedbacks, and ecosystem processes using signaling molecules to directly manipulate microbial seed banks,

• Aim 3.) Develop and test theoretical predictions regarding the contribution of seed banks to geographic patterns of taxonomic and phylogenetic diversity using communities of soil bacteria from systems with contrasting disturbance histories.

Aim 1:

Contents

Aim 2:

Contents

Aim 3:

Contents

• bin:

  • MothurTools.R: An R script written by Mario Muscarella (Indiana University) containing functions used in the analysis of 16S rRNA sequence data post mothur analysis.

• DATA:

  • CurrentData: Files containing taxonomic data by site from samples obtained by ... from more than 50 ponds in central Indiana.
  • OldDataVersion: Contains previous versions of data files that are no longer used but are kept on permanent record.

• DocsForMeetings:

  • Contains R Markdown files and .pdf's detailing findings, the date of which is contained in the filename.

• GIS:

  • BrownCoData_GeoEco:

  • LandCover: contains GIS shapefiles and associated files for a GIS layer of percent landcover in south and central Indiana. Obtained from the IndianaMap geographical layer gallery: http://maps.indiana.edu/layerGallery.html.

  • Water: contains GIS shapefiles and associated files for a GIS layer of water bodies in south and central Indiana. Obtained from the IndianaMap geographical layer gallery: http://maps.indiana.edu/layerGallery.html.

  • RGIS2.Rmd: A tutorial for using various GIS tools through R/RStudio

• TARs:

  • IBMs: Contains Python files for exploring the species/taxa area relationship with individual-based models
  • MI_Ag: Contains R files, data, and plots resulting from analysis of Michigan agricultural soils

Contributors

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

Dr. Ken Locey: co-Principle Investigator, Postdoctoral Fellow in the Lennon Lab

Dr. Stuart Jones: co-Principle Investigator, Assistant Professor, Department of Biological Sciences, University of Notre Dame.

Dr. Sarah Bray: Collaborator, Associate Professor of Biology, Transylvania University

Mario Muscarella: Ph.D. candidate in the Lennon Lab

Megan Larsen: Ph.D. candidate in the Lennon Lab

Kayla Miller: Ph.D. Student, Indiana University, Bloomington.