In Situ engineering of Bacterial Communities

Plants are colonized by complex microbial communities that can promote plant growth, increase disease resistance, and improve environmental stress tolerance. The bacteria associated with plants are often difficult to manipulate genetically, which limits scientific studies and microbiome engineering. We constructed a versatile Bacillus subtilis donor strain to deliver an engineered Integrative Conjugative Element (ICEBs1) to complex communities of bacteria in situ. We demonstrate that ICEBs1 can be used to deliver heterologous DNA to >17 Gram-positive bacterial species isolated from human and soil microbiomes (e.g., Bacillus sp., Paenibacillus sp., Enterococcus sp., Staphylococcus sp.). Then, ICEBs1 is used to create synthetic diazatrophs by transforming soil bacteria with nitrogenase (nif) gene clusters.