Synthetic biology-assisted fungus-assembling beads for regulating rhizosphere microbiome and improving plant growth in saline soil

Soil salinization seriously reduces crop yields and threatens food security. Microbial inoculants have a wide prospect in the improvement of saline soil quality, while their soil colonization is frequently compromised. We previously isolated Trichoderma atroviride 1607 from the moss Brachythecium piligerum capable of reducing environmental salinity, while its efficiency in crop rhizosphere colonization was quite low. To improve its activity in enhancing crop salt tolerance, we introduced the synthetic Escherichia coli strain EcCMC, which exposed artificial glucan-binding protein to provide physical contacts between the fungal hyphae. During the co-incubation of EcCMC, 1607 and the solid substance perlite, the fungus exhibited dense hyphae both on the surface and within the pores of perlite, forming the well-developed fungus-assembling beads 1607Ec. In both the pot and field experiments of cabbage cultivation, the 1607Ec beads reduced the soil salinity obviously, improved the levels of soil enzyme activity levels and organic matter content, together with the leaf chlorophyll contents and plant weights. Rhizosphere microbiome analysis further revealed that the 1607Ec beads increased the relative abundance of Hypocreaceae, particularly the genus Trichoderma. Moreover, 1607Ec increased the Simpson index of the rhizosphere bacterial compositions. The bacteria involved in polysaccharide production, e.g., Sphingomonadaceae, Flavobacteriaceae, and Xanthomonadaceae, exhibited the increased abundance in the 1607Ec group. Similarly, 1607Ec showed the growth-promoting effect on the Poaceae crops in saline soil. This study provides a synthetic biology-based strategy to facilitate the rhizosphere colonization of functional fungi for regulating rhizosphere microbiome and enhancing plant tolerance against saline stress.