Why were Jewish ghettos set up in Nazi occupied territories 1939-41?

Ghettos were established in Poland in 1940/41 for a multitude of reasons. Millions more Jews came under German control after the invasions of Poland and the Soviet Union. Nazi ideology, specifically antisemitic prejudice, contributed to the establishment of the ghettos, firstly because they believed in the necessity of segregation of Jewish populations from Aryan ones, and secondly because the Jews as enemies to the German war effort and therefore needed to be contained and their activities regulated. The Nazis lack of clear and coherent plan for the Jewish populations under their control also contributed to the establishment of the ghettos, as they were often led by Jewish elders in the region, evidencing the reliance of the German government on local Jewish authorities. It is important in answering this question to understand the interrelatedness of the factors, such as the long-term prejudices against Jews that fed into immediate concerns about the war, both from the perceived threat of the Jews to the German war effort as well as the opportunity to economically exploit them for German benefit.