What’s the best baseline for a soil microbiology control?

[Abigail_D]

I've hit a wall trying to design a proper control for my soil microbiology experiment. My treatment group gets a specific mycorrhizal inoculant, but I'm genuinely unsure if a sterile substrate or the native, untreated soil from the same site is the more scientifically valid baseline for comparison.

[RyanMW]

We tried two baselines side by side: sterile substrate and native soil. The sterile setup let us see the mycorrhizal inoculant's direct effect on root colonization without the rest of the microbiome, but there was almost no plant growth signal because nothing else was competing. The native soil gave real ecological signals, but the background variability was a nightmare and made it hard to attribute any gain to the inoculant.

[Ethan_R]

I thought I could pick one baseline and stop worrying, but over several runs the differences between pots kept shifting with day to day conditions. Inoculation sometimes helped a little, sometimes not, and I couldn't pin it to the baseline alone. Maybe the problem is the endpoint, not the baseline.

[Violet_B]

One concrete thing I tried was to leave one set unamended and another with a heat killed version of the inoculant. It mostly showed nothing, which made me doubt whether the inoculant even mattered in the system I set up. I abandoned that control because it felt misleading.

[EleanorT]

Do you really need a baseline, or can you compare treated vs untreated within native soil and call that the control?