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Abstract The soil microbiome provides essential services in agroecosystems that can increase plant health and productivity, such as disease suppression and growth promotion. A small number of microbial groups have been proposed as main players behind disease suppression, but the complete picture of the underlying mechanisms remains unclear for both functions in many soil systems. Here, we investigated broad and fine‐scale microbial community features for their contributions to disease suppression and growth promotion for potato plants. In a greenhouse study, we grew potato plants in pots sharing a common background soil and inoculated with living soil microbial communities with or without a separate inoculation with Streptomyces scabiei, the causal agent of potato common scab disease. The suppression of common scab and growth promotion abilities of a variety of soil microbial communities were estimated and related to quantitative patterns in microbial community structure. We found that suppression of common scab was mostly driven by fine‐scale microbial community features, especially the diversity within the Actinomycetota phylum. Even though opposing components of microbial community structure might be related to the two functions, disease suppression did not cause a negative trade‐off in growth promotion. This suggests high functional redundancy in growth promotion. It may be possible to improve the multi‐functionality of soil microbial communities by engineering the communities toward optimized disease suppression and growth promotion ability.

Abstract Microbial communities contribute to many essential ecological functions, from carbon cycling in soil to healthy functioning of the human body. Yet, determining how the make‐up of microbial communities is causally linked to a particular function remains a huge challenge. Despite improved tools for characterizing microbiomes at increasingly finer phylogenetic and functional scales, researchers are still unable to perform direct experimental hypothesis testing as is performed in plant and animal ecology. However, microbial ecology is not the only scientific field tasked with drawing firm causal inferences from correlational data. Here we introduce microbial ecologists to a framework used by epidemiologists: the Bradford Hill Causal Criteria. Hill posited that as a field accrues different types of evidence to support a hypothesis, it increases confidence in claiming that the hypothesized relationship is causal. A set of nine criteria help distinguish different types of evidence. Our goal was to illustrate how these causal criteria can be used in microbial ecology to retrospectively evaluate a body of research to determine the strength of a causal claim and judge the value of future research directions. We illustrate how this framework can help researchers organize their understanding of a body of literature to reveal knowledge gaps and analytical approaches that have been underutilized. We then discuss the types of causality and illustrate how investigating multicausal systems requires an updated application of older frameworks that assume one causal agent is at play for each functional outcome. We also examine analytical approaches that are appropriate for distinguishing the types of causality.

Abstract Soils contain diverse living communities that provide key ecosystem functions in agroecosystems. In many systems, ecosystem functions are positively related to the taxonomic, phylogenetic, and functional diversity of the community. Despite calls to incorporate microbial diversity in measures of soil health, whether increased microbial diversity per se can predict increased crop health and productivity has rarely been documented. Here, we used microbial communities from commercial potato fields varying in diversity and composition, and experimentally assessed their ability to promote crop yield under low or high nutrient conditions and to suppress a soil‐borne pathogen. Across two independent sets of communities, we found that yields under low nutrient conditions were predicted by high initial microbial diversity measured at broad phylogenetic levels, consistent with greater niche complementarity among unrelated taxa leading to greater total resource use. However, disease suppression was inconsistently linked to diversity and was explained as well or better by microbial composition rather than diversity per se. Ecosystem multifunctionality was predicted by high diversity at broad to intermediate phylogenetic scales. These results indicate that the diversity of microbial taxa may influence multiple soil functions; however, the mechanisms underlying the diversity–function relationships may vary.