The answer to this question would be: The soil
In Van Helmont's experiment, he measures the weight of a tree and its soil before and after growing it. After growing the tree, the mass of the soil is almost unchanged. whereas the tree is gaining about 75kg of mass. In this experiment, he concludes that the mass is not from the soil but from the water. This experiment result is modified latter because the mass was not only from water but also from the reaction of carbon dioxide.