Disclosed herein are methods of increasing, enhancing, or accelerating root nodulation in a plant, accelerating growth of nitrogen fixing bacteria in nodules of a plant, increasing protein content in a plant, increasing yield of a plant, improving water retention of a plant, or reducing water use of a plant, the method comprising identifying a plant in need of root nodulation, and applying to the plant a composition comprising a protein component comprising yeast stress proteins resulting from subjecting a mixture obtained from the yeast fermentation to stress.