Methods and compositions for improving plant traits

A method of decreasing an amount of nitrogen-containing fertilizer required for producing a yield of a crop, the method comprising:

• a) inoculating soil of a field with a plurality of genetically engineered bacteria that fix atmospheric nitrogen, wherein the genetically engineered bacteria comprise at least one genetic variation introduced into at least one gene, or non-coding polynucleotide, of a nitrogen fixation or assimilation genetic regulatory network, such that the genetically engineered bacteria are capable of fixing atmospheric nitrogen in the presence of exogenous nitrogen, wherein said plurality of genetically engineered bacteria:
• i. have an average colonization ability per unit of plant root tissue of at least about 1.0×104 bacterial cells per gram of fresh weight of plant root tissue;
• and
• ii. produce fixed N at a rate of at least about 1×10−17 mmol N per bacterial cell per hour,
• b) planting a crop in said inoculated soil;
• and
• c) applying a nitrogen-containing fertilizer, wherein the applied nitrogen-containing fertilizer corresponds to no more than 90% of a dose of said nitrogen-containing fertilizer, wherein said yield of said crop is the same as if 100% of the dose of nitrogen-containing fertilizer is applied under similar conditions between planting and harvesting said crop in the absence of said plurality of genetically engineered bacteria.