NEW YORK—Soybeans shot up Thursday, hurtling back toward $16 a bushel on concerns that last month’s flooding in the Midwest will hurt yields and strain already tight U.S. stockpiles. Corn fell to a one-month low.

Other commodities traded mostly higher, with crude oil soaring above $141 a barrel and other energy futures also gaining. Gold and silver rose sharply.

The U.S. Department of Agriculture on Friday will release U.S. inventory estimates for soybeans, corn, wheat and other grains. Analysts expect a significant drop in soybean stockpiles after severe flooding last ...