Dominic Standing

Meeting the challenge of scaling up processes in the plant–soil–microbe system

The scaling up of processes in the plant–soil–microbe system represents one of the greatest challenges facing environmental scientists and yet is essential for sustainable land management worldwide. The latter encompasses, for example, the mitigation of and adaptation to anthropogenic climate change, the bioremediation of industrially contaminated sites, catchment management of human pathogens such as Escherichia coli O157 and integrated crop management on the farm. Scaling up is also essential for the regional and global biogeochemical modelling that will inform policy-makers of the critical environmental factors driving climate change. Despite increasing understanding of the links between gene expression and process on a microscale, there is still much progress to be made when relating this to processes at the macroscale. In this paper, we explore the challenges this poses and examine key case studies of successful up-scaling.

A tripartite microbial reporter gene system for real-time assays of soil nutrient status

Plant-derived carbon is the substrate which drives the rate of microbial assimilation and turnover of nutrients, in particular N and P, within the rhizosphere. To develop a better understanding of rhizosphere dynamics, a tripartite reporter gene system has been developed. We used three lux-marked Pseudomonas fluorescens strains to report on soil (1) assimilable carbon, (2) N-status, and (3) P-status. In vivo studies using soil water, spiked with C, N and P to simulate rhizosphere conditions, showed that the tripartite reporter system can provide real-time assessment of carbon and nutrient status. Good quantitative agreement for bioluminescence output between reference material and soil water samples was found for the C and P reporters. With regard to soil nitrate, the minimum bioavailable concentration was found to be greater than that analytically detectable in soil water. This is the first time that bioavailable soil C, N and P have been quantified using a tripartite reporter gene system.

Novel Screen for Investigating In Situ Rhizosphere Production of the Antibiotic 2,4‐Diacetylphloroglucinol by Bacterial Inocula

Abstract The rhizosphere is a complex zone of multitrophic interactions comprising plant roots, associated bacteria, fungi, and micro‐, meso‐, and macro‐fauna. Of considerable importance in this system is the production of antibiotics by root‐associated or “rhizo” bacteria. This is a widespread phenomenon of which a much‐studied exemplar is the production by pseudomonads of 2,4‐diacetylphloroglucinol (DAPG), known to be effective in the suppression of soil‐borne fungal pathogens. Rapid advances in understanding the molecular and biochemical bases of antibiotic (particularly DAPG) production have been made. However, our understanding of in situ antibiotic production currently lags behind this. There is therefore a need for a rapid soil‐based screen with which to identify antibiotic producers under rhizosphere C‐flow conditions. Here, a novel “rhizocosm,” comprising porous pipe and Rhizon sampler®, was superior to a simple, nonperfusing incubation‐type microcosm with respect to supporting a rhizobacterial inoculum. Its use as a screening tool is illustrated by screening known DAPG‐producing inocula in soil continuously supplied with simulated rhizosphere carbon flow. The DAPG was then extracted from soil using acetone and quantified by high‐performance liquid chromatography (HPLC). Simple sugars (glucose and fructose) stimulated the greatest DAPG production, while glucose with an additional organic or amino acid, or with a signal molecule, resulted in strongly variable DAPG expression.

Ecotoxicological screening of Kenyan tannery dust using a luminescent-based bacterial biosensor

Abstract Ecotoxicological screening of dust sampled throughout a Kenyan tannery was conducted using a luminescence (lux)-based bacterial biosensor for both solid and liquid assays. This was complemented by chemical analysis in an attempt to identify possible causative toxic components. The biosensor results showed a highly significant (p < 0.001) difference in both solid and liquid phase toxicity in samples collected from various identified sampling points in the tannery. A positive correlation was observed between results of the solid and liquid phase techniques, for most of the sampling points indicating that the toxic contaminants were bioavailable both in the solid and liquid state. However, the results generally indicated toxicity associated with liquid phase except certain areas in solid phase such as chemical handling, buffing area and weighing. The most toxic tannery area identified was the weighing area (p < 0.001), showing the lowest bioluminescence for both the solid (0.38 ± 2.21) and liquid phases (0.01 ± 0.001). Chromium was the metal present in the highest concentration indicating levels higher than the stipulated regulatory requirement of 0.5 mg Cr/m3 for total Cr (highest Cr concentration was at chemical handling at 209.24 mg l−1) in all dust samples. The weighing area had the highest Ni concentration (1.87 mg l−1) and the chemical handling area showed the highest Zn concentration (31.9 mg l−1). These results raise environmental health concerns, as occupational exposure to dust samples from this site has been shown to give rise to elevated concentrations (above the stipulated levels) of chromium in blood, urine and some body tissues, with inhalation being the main route. Health and Safety Executive (HSE), UK, and American Conference of Governmental Industrial Hygienist (ACGIH) and National Institute for Occupational Safety and Health (NIOSH), USA stipulates an occupational exposure limit of 0.5 mg Cr/m3 (8 h TWA) for total chromium. However, schedule 1 of Controls of substances hazardous to health (COSHH) regulations developed by HSE, indicate 0.05 mg m3 (8 h TWA reference periods) to be the limit for Cr (VI) exposure. The exposure limit for individual (e.g., Cr, Zn, Ni etc.) contaminants (homogeneity) was not exceeded, but potential impact of heterogeneity (multi-element synergistic effect) on toxicity requires application of the precautionary principle.