Variance, locality and structure: Three experimental challenges in the study of the response of soil microbial communities to multiple perturbations

Abstract There is an increasing interest in understanding how soil microbial communities respond to perturbations associated with global change. Much of the currently available knowledge is based on controlled laboratory experiments, large scale surveys and manipulative studies in which one perturbation, for example drought, is applied under a range of conditions. Until now, emphasis has been on spatial replication of experimental units and the quantification of variation in soil microbial community structure, and its correlation to ecosystem-level variables such as gas fluxes. But microbial communities naturally fluctuate over time, their response to perturbations is temporal, and they generally experience multiple perturbations simultaneously and/or in a variable sequence, such as spells of drought alternating with flooding events. Furthermore, variation in the soil microbial community in response to perturbations may not directly reflect the overall expression of functions of a microbial community. Here, we identify three experimental challenges that we refer to as the variance, locality and structure challenge. We briefly synthesise the state of the art around these three challenges to open a discussion on the many experimental issues ecologists face when measuring the effects of perturbations on the structure and functions of soil microbial communities in time and space. We propose experimental, sampling and modelling strategies that can help resolve the experimental challenges discussed in this paper.