A county fair 4-H crop exhibit where the 4-H'ers bring in 25 to 30 specimens from different fields gives you a good chance to make comparisons. One of the first things that may grab your eye is differences in root systems. At one such fair recently, root systems ranged from well-developed, full of root hairs, with tons of nodules on the roots, to skimpy root systems with very few nodules. The harder part to solve is that the soybeans above ground in both cases looked healthy and productive.
Various factors contribute to rooting. Obviously soil compaction can affect roots, although most soil scientists say it affects soybean yields less than corn. And in a year like this when it keeps raining through the critical period, at least for corn, it may not affect yields much, if at all. Adequate moisture covers up a lot of sins, including soil compaction.
Soil type may also affect rooting. If plants have a hard time emerging in a clay soil, it may affect root formation.
Some fields simply tend to have soybeans with more nodules than others. The nodules are important because the bacteria that live in the nodules pull nitrogen form the air, allowing soybeans to convert it into the nitrogen that they need to grow and produce soybeans. This symbiotic relationship favors both the bacteria and the plant. The unhealthy situation where nematodes attach to soybean roots and feed on the roots is a parasitic situation. The nematode is a parasite because it's the only one that benefits form the two-way arrangement. Soybeans actually lose ground as nematodes zap their root system.
In general, the more nodules on a soybean plant, the better – and it offers a higher likelihood of better yields. Even at this time of year, if nodules are working hard, they should be pink inside. That indicates that they are doing their job for the plant.