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The study of interactions and feedbacks between plants and soils is a rapidly expanding research area, and a primary tool used in this field is to perform glasshouse experiments where soil biota are manipulated. Recently, there has been vigorous debate regarding the correctness of methods for carrying out these types of experiment, and specifically whether it is legitimate to mix soils from different sites or plots (mixed soil sampling, MSS) or not (independent soil sampling, ISS) to create either soil inoculum treatments or subjects. We performed the first empirical comparison of MSS vs ISS approaches by comparing growth of two boreal tree species (Picea abies and Pinus sylvestris) in soils originating from 10 sites near the boreal forest limit in northern Sweden, and 10 sites in the subarctic region where boreal forests may potentially expand as a result of climate change. We found no consistent differences in the conclusions that we reached whether we used MSS or ISS approaches. We propose that researchers should not choose a soil handling method based on arguments that one method is inherently more correct than the other, but rather that method choice should be based on correct alignment with specific research questions and goals.