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BackgroundUnderstanding microbial interactions in engineering bioprocesses is important to enhance and optimize performance outcomes and requires dissection of the multi-layer complexities of microbial communities. However, unraveling microbial interactions as well as substrates involved in complex microbial communities is a challenging task. Here, we demonstrate an integrated approach of metagenomics, metatranscriptomics, and targeted metabolite analysis to identify the substrates involved in interspecies interactions from a potential cross-feeding model community-bisphenol A (BPA)-biodegrading community, aiming to establish an identification method of microbial interactions in engineering or environmental bioprocesses.ResultsThe community-level BPA-metabolic pathway was constructed using integrated metagenomics and targeted metabolite analyses. The dynamics of active functions and metabolism of major community members were identified using metagenomic and metatranscriptomic analyses in concert. Correlating the community BPA biodegradation performance to the individual bacterial activities enabled the discovery of substrates involved in a synergistic interaction of cross-feeding between BPA-degrading Sphingonomas species and intermediate users, Pseudomonas sp. and Pusillimonas sp. This proposed synergistic interaction was confirmed by the co-culture of a Sphingonomas sp. and Pseudomonas sp. isolates, which demonstrated enhanced BPA biodegradation compared to the isolate of Sphingonomas sp. alone.ConclusionThe three types of integrated meta-omics analyses effectively revealed the metabolic capability at both community-wide and individual bacterial levels. The correlation between these two levels revealed the hidden connection between apparent overall community performance and the contributions of individual community members and their interactions in a BPA-degrading microbial community. In addition, we demonstrated that using integrated multi-omics in conjunction with culture-based confirmation approach is effective to elucidate the microbial interactions affecting the performance outcome. We foresee this approach would contribute the future application and operation of environmental bioprocesses on a knowledge-based control.

Flavonoids are pharmacologically active compounds in flowers of Chrysanthemum morifolium 'Boju' (C. morifolium); however, the molecular regulatory network governing flower development remains largely elusive. Flower samples were collected at four stages, namely budding (BD), bud breaking (BB), early blooming (EB), and full blooming (FB), for omics analysis. We revealed distinct transcriptional regulation patterns at these four stages of the flower from the perspective of differentially expressed unigenes (DEGs). There are 152 DEGs shared among the three comparative groups (BD vs. BB, BB vs EB, EB vs FB), wherein the expression of 44 DEGs (including AtADT6, MDL3, and ROMT) continues to be upregulated, and 85 DEGs (including CYP81E, TPS-Cin-1, and TPS-Cin-2) showed persistent downregulation with flower development. Flavonoid-targeted metabolomics identified 118 differentially abundant metabolites (DAMs) in the FB group compared to the BD stage; the top three upregulated and downregulated metabolites are Cyanidin-3-O-(6″-O-malonyl)glucoside-5-O-glucoside, Luteolin-7-O-(6″-caffeoyl)rhamnoside, Kaempferol-3-O-(6″-p-coumaroyl)glucoside and Chrysoeriol-6,8-di-C-glucoside-7-O-glucoside, Kaempferol, Kaempferol-3,7-O-dirhamnoside, respectively. These DAMs were predominantly enriched in "flavonoid biosynthesis", "isoflavonoid biosynthesis", and "flavone and flavonol biosynthesis" pathways. AtADT6, MDL3, ROMT, CYP81E, TPS-Cin-1, and TPS-Cin-2 were correlated with kaempferol. Our findings provide a new idea for interfering with flavonoid production, especially kaempferol, in flowers. [ABSTRACT FROM AUTHOR]