Abstract
Dissolved organic matter (DOM) is a complex mixture of thousands of molecules and plays crucial roles in aquatic and terrestrial ecosystems. The study of DOM has been advanced and accelerated by developments of instrumental and statistical approaches over the last decade. Due to the complexity of molecular data and underlying ecological mechanisms, there are substantial challenges for statistical analysis, visualization, and theoretical interpretation. Here, we developed an R package iDOM with functions for the basic and advanced statistical analyses and the visualization of DOM derived from Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS). The iDOMpackage could handle various data types of DOM, including molecular compositional data, molecular traits, and unclassified molecules (that is, dark matter). It integrates additional explanatory data types such as environmental and microbial data to explore the interactions of DOM with abiotic and biotic drivers. To illustrate its use, we presented case studies with an example dataset of DOM under experimental warming. We included the case studies of basic functions for molecular trait calculation, molecular class assignment, and the compositional analyses of chemical diversity and dissimilarity. We further showed case studies with advanced functions for DOM assemblages, such as quantifying and exploring their assembly processes, the effects of dark matter on their ecological networks, and the associations between DOM and microbes under warming. We expect that iDOM will serve as a comprehensive pipeline for DOM statistical analyses and bridge the gap between chemical characterization and ecological interpretation.