Box 3: Designing a successful experiment
Manipulating microbes can be challenging, but microbial treatments can be created by isolating some fraction of the plant microbiome, for example isolates of individual taxa, microbial washes, or whole soil inoculum (for a discussion of efficacy see Howard et al. 2017, Fig. 4A). Defining proper controls is also critical. For example, researchers should isolate soil microbial effects without confounding them with soil abiotic effects by using a sterilized soil mixture (either a sterilized field soil mixture; e.g. Petipas et al. 2020 or sterilized potting mix; Howard et al. 2020, Fig. 4B) with a small amount (1-5% soil volume) of live or sterilized inoculum added back. The choice of soil sterilization methods can be taxon specific (e.g. fungicide) or general (autoclaving or gamma irradiation). Each method has advantages and disadvantages, and each method often has effects beyond direct removal of microbes (Trevors 1996). In addition, given that even sterilized treatments are rapidly colonized by weedy microbes, they should be more likely considered low diversity microbial treatments rather than no or low microbial abundance communities (Lau & Lennon 2012).
Transplantation can occur directly in the soil using a mesh (0.45µm) barrier to keep in microbial inoculum and exclude microbial taxa (fungi and some bacterial taxa) from the surrounding soil environment (Mcguire 2007). Alternatively, plants can be transplanted into pots with microbial treatments and placed in aboveground arrays in the two habitats, although aboveground conditions in pots are often warmer and subject to more rapid drying than in ground transplants (Fig. 4C). When transplanting into the field (and even the greenhouse), especially if plants are surrounded by the soil environment, contamination by non-target microbes will always be an issue as mentioned above. For this reason, the duration of the experiment will need to be planned carefully. Since microbe-mediated adaptation experiments are simultaneously manipulating multiple factors, proper planning of sample sizes is important to have the power to detect significant interactive effects.
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Table 1: Hypothetical linear model terms used to understand microbe-mediated adaptation reciprocal transplant experiments. We also include potential interpretations when main effects or interactions are found to be significant and how that interaction type might be interpreted in a quantitative genetics framework.