Live reports from the soil grain - the promise and challenge of microbiosensors

Linking microbial activity with ecosystem function is a continuing goal among ecologists focusing their efforts below ground in terrestrial ecosystems. Genomic approaches, using DNA and RNA extracted from soil to characterize types of microbes present and genes expressed in soil, are promising, but, the required destructive harvest confounds spatial and temporal information. Microbiosensors offer a gene-based way to examine microbial perception of, and response to, the soil environment non-destructively, with high spatial and temporal resolution. In this mini-review, we explore the promise, challenges and tradeoffs associated with the design and deployment of microbiosensors in soil, as well as the interpretation of information derived from them 'live from the soil grain'. Both the promises and challenges are caused by the facts that: micro-biosensors are living organisms with specific traits; they come from a phylogenetically diverse but restricted subsample of enormous soil microbial diversity; they are responsive to internal and external influences on multiple cellular processes (not just promoter induction); and they become part of food chains in non-sterile soils. We examine each of these characteristics, and associated blessings and curses, in the context of using microbiosensors to explore microbial soil ecology.