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

Abstract

Summary 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.

Better to light a candle than curse the darkness: illuminating spatial localization and temporal dynamics of rapid microbial growth in the rhizosphere

“…Microbiosensor design is flexible and can be tailored to particular questions via choice of host organism, promoter, and reporter genes (Gage et al, 2008). Here we used a host bacterium that is native to the rhizosphere environment, and a reporter system with a constitutive promoter ( nptII ) fused to the luxCDABE operon.…”

“…Microbial biosensors consist of a host strain (usually bacterial) that contains inserted DNA (on the chromosome or a plasmid), coding for an environmentally controlled promoter, driving expression of an easily assayed reporter gene (e.g., inaZ , gfp , lux ) (Hansen and Sørensen, 2001; Gage et al, 2008). The expression of the reporter molecule is thus tied to the activity of the promoter within the host organism.…”

Plasmids That Insert into the Rhamnose Utilization Locus, <i>rha</i>: A Versatile Tool for Genetic Studies in <i>Sinorhizobium meliloti</i>

“…Strains with a reporter gene under the control of an inducible, or otherwise regulated, promoter are frequently used for gene expression studies as well as for answering questions in microbial ecology [Bringhurst et al, 2001;Gage et al, 2008]. We constructed a strain (CAP69) that expresses GFP in response to ␣ -galactosides by fusing the S. meliloti melA promoter region to gfp S65T (P melA :: gfp S56T).…”

“…For example, in cases in which availability of transcriptional regulators controlling expression from the promoter is low, titration of the regulator by multiple copies of the promoter could potentially affect regulation and its phenotypic manifestation. Reporter strains have been used in complex environments such as the rhizosphere, on plants, or under other conditions where maintaining antibiotic pressure to ensure plasmid presence may be difficult [Cardon and Gage, 2006;Gage et al, 2008]. Loss of labeling can result in significant underestimation of bacterial numbers, which may be inadmissible for certain applications.…”

Towards a predictive understanding of belowground process responses to climate change: have we moved any closer?

“…Arguably, the most important recent advances contributing to improved understanding of belowground processes involve techniques allowing resolution of fine‐scale mechanisms in space and time. An exciting development is the application of genetically engineered microbiosensors to soils, as reviewed in Gage et al . (2008).…”