MicroEcoTools: an R package for comprehensive theoretical microbial ecology analysis

Abstract

BackgroundEcological theory aids in understanding how disturbances affect ecosystems. However, experimental data are often complex, with multiple post-disturbance theories potentially applying simultaneously to the same ecosystem. This emphasizes the need for tools to experimentally test these theoretical predictions. ResultsWe introduce MicroEcoTools, an R package designed to test ecological framework predictions using microbial community data. It assesses microbial diversity and evaluates the relative impacts of stochastic and deterministic assembly mechanisms through a taxa-based null model approach for replicated designs. Specifically, the package allows application of Grimes trait-based life-history categories--competitor, stress-tolerant, and ruderal (CSR)-- to taxa, functional traits, and ecosystem functions within microbial communities. MicroEcoTools also includes relevant statistical tests, numeric simulations, and publicly available datasets for demonstration. ConclusionsIn conclusion, MicroEcoTools facilitates the application of ecological frameworks, including community assembly mechanisms, diversity analysis, and life-history strategies, to microbial ecosystems under disturbance. This R package, along with its source code, can be freely accessed on GitHub at https://www.github.com/Soheil-A-Neshat/MicroEcoTools.