Transcriptomics integrated with metabolomics reveal the competitive relationship between co-cultured Trichoderma asperellum HG1 and Bacillus subtilis Tpb55.

Microbial co-culture has proven to be an effective way to improve the ability of microorganisms to biocontrol. However, the interactive mechanisms of co-cultural microbes, especially between fungi and bacteria, have rarely been studied. By comparative analysis of morphology, transcriptomics and metabolomics, the interactive mechanisms of a sequential co-culture system of Trichoderma asperellum HG1 and Bacillus subtilis Tpb55 was explored in this study. The results revealed that co- culture has no significant effect on the growth and cell morphology of the two strains, but lead to mycelium wrinkling of HG1. RNA-seq analysis showed that co-culture significantly upregulated the HG1 genes concerning amino acid degradation and metabolism, proteolysis, resisting environmental stress, cell homeostasis, glycolysis, the glyoxylate cycle, and the citric acid (TCA) cycle, while Tpb55 genes related to cell homeostasis, spore formation and membrane fluidization were significantly upregulated, but genes associating to TCA, glycolytic cycles and fatty acid β-oxidation were significantly downregulated. Metabolomic results revealed that some amino acids related to energy metabolism were significantly altered in HG1, whereas palmitic acid, which is related to cell membrane functions, was upregulated in Tpb55. These results indicated that HG1 could interfere with carbon metabolism and cell membrane fluidity, but accelerate spore formation of Tpb55. Biophysical assays further convinced that co-culture could decrease ATP content and inhibit ATPase activity in HG1, and could promote spore formation and reduce the cell membrane fluidity of Tpb55. In addition, co-culture also accelerated the production of intracellular anti-oomycete compound octhilinone. The above results indicate that HG1 and Tpb55 are mainly in a competitive relationship in the co culture system. These findings provide new insights for understanding the interaction mechanism between co cultured microbes.