Organic molecular network analysis reveals transformation signatures of dissolved organic matter during anaerobic...

Identifying the transformation types, i.e., syntheses or decompositions, of organic molecules in complex environmental systems remains a significant challenge. To address this, we propose a new analytical framework, Transformation-based Organic Molecular Ecological Network Analysis (TOMENA) for the systematic recognition and analysis of molecular transformations according to the measurement of high-resolution mass spectrometry (FT-ICR MS) through time-series data. Applying the TOMENA framework, we systematically investigated transformation signatures of dissolved organic matter (DOM) during anaerobic digestion processes. We found a close relationship between molecular transformation and molecular weight in the biodegradation system. A total of 129 transformations were identified, involving carbon numbers ranging from 0 to 24, with 59 of these transformations concentrated in small molecular weight changes involving 1-3 carbons. As the molecular weight corresponding to transformations increased, the proportion of bio-transformations used for decomposition decreased linearly. Simultaneously, large molecules were decomposed and small molecules synthesized, indicating a system tendency to transform molecules towards a medium mass range. Topological analysis of the transformation network further expanded our understanding. We discovered that molecular transformations did not follow the shortest path, as the path distance was significantly longer than in random networks (2.558 vs. 2.383). We identified that N-containing transformations were centrally located in the system through edge analysis. However, the transformations' position did not coincide with functional importance. A comprehensive indicator of irreplaceability and usage frequency revealed that C(+1)H(+3)O(+2)N(-1), C(+1)H(+2), O(+1), C(+3)H(+4)O(+2), and H(-2)O(+1) are critical transformation pathways in the system, showing the top 5 efficiency contributions. Our developed TOMENA workflow provides novel insights and robust methodological support for future research, advancing our understanding of molecular transformations in complex biodegradation system.