The present invention provides biological fertilizer compositions that comprise yeast cells that have an enhanced ability to fix atmospheric nitrogen, decompose phosphorus minerals and compounds, decompose potassium minerals and compounds, decompose complex carbon compounds, over produce growth factors, and over produce ATP. The biological fertilizer composition of the invention can replace mineral fertilizers in supplying nitrogen, phosphorus, and potassium to crop plants. Methods of manufacturing the biological fertilizer compositions and methods of uses are also encompassed.