Microbial ecology is currently undergoing a revolution, with repercussions spreading throughout microbiology, ecology and ecosystem science. The rapid accumulation of molecular data is uncovering vast diversity, abundant uncultivated microbial groups and novel microbial functions. This accumulation of data requires the application of theory to provide organization, structure, mechanistic insight and, ultimately, predictive power that is of practical value, but the application of theory in microbial ecology is currently very limited. Here we argue that the full potential of the ongoing revolution will not be realized if research is not directed and driven by theory, and that the generality of established ecological theory must be tested using microbial systems.

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The bioluminescence response of a genetically modified (lux‐marked) bacterium to potentially toxic elements (PTEs) was monitored using an in vitro assay. Washed cells of Pseudomonas fiuorescens were added to solutions containing various concentrations of metal salts. Bioluminescence, involving either plasmid or chromosomally encoded lux genes, declined as the metal concentration increased. The plasmid marked construct was significantly more sensitive to all metals except Cr. The order of metal sensitivity was found to be Cu = Zn > Cd > Cr > Ni for the chromosomally marked construct and Cu = Zn > Cd > Ni > Cr for the plasmid marked construct. The very sensitive response of lux‐marked terrestrial bacteria to PTEs identified the potential for a rapid and flexible ecotoxicity assay for assessing the pollution of soil or fresh water environments.

Rhizosphere microorganisms play an important role in soil carbon flow, through turnover of root exudates, but there is little information on which organisms are actively involved or on the influence of environmental conditions on active communities. In this study, a 13CO2 pulse labelling field experiment was performed in an upland grassland soil, followed by RNA-stable isotope probing (SIP) analysis, to determine the effect of liming on the structure of the rhizosphere microbial community metabolizing root exudates. The lower limit of detection for SIP was determined in soil samples inoculated with a range of concentrations of 13C-labelled Pseudomonas fluorescens and was found to lie between 10(5) and 10(6) cells per gram of soil. The technique was capable of detecting microbial communities actively assimilating root exudates derived from recent photo-assimilate in the field. Denaturing gradient gel electrophoresis (DGGE) profiles of bacteria, archaea and fungi derived from fractions obtained from caesium trifluoroacetate (CsTFA) density gradient ultracentrifugation indicated that active communities in limed soils were more complex than those in unlimed soils and were more active in utilization of recently exuded 13C compounds. In limed soils, the majority of the community detected by standard RNA-DGGE analysis appeared to be utilizing root exudates. In unlimed soils, DGGE profiles from 12C and 13C RNA fractions differed, suggesting that a proportion of the active community was utilizing other sources of organic carbon. These differences may reflect differences in the amount of root exudation under the different conditions.

Aim: To determine the persistence of Escherichia coli O157 in contrasting organic wastes spread to land and to assess the potential environmental risk associated with the disposal of these wastes to land. Methods and Results: Twenty-seven organic wastes originating from slaughterhouses, wastewater treatment plants (raw and treated sewage), creameries and farms (bovine slurry), were inoculated with E. coli O157:H7 and incubated at 10°C. Although pathogen numbers gradually declined in all the wastes, albeit at different rates even in the same waste type, E. coli O157:H7 was still viable in 77% of organic wastes tested after 2 months. Conclusions: Long-term storage of organic wastes led to a significant and gradual decline in E. coli O157:H7 numbers. Consequently, storage may be a useful means of reducing the pathogen load of wastes destined for land application. However, in most cases, long-term storage cannot be expected to completely eliminate E. coli O157:H7 from waste. Significance and Impact of the Study: Our results indicate that current legislation may be insufficient to protect the environment from E. coli O157:H7 contamination from untreated wastes spread to land.