Soil microorganisms determine the sorption of radionuclides within organic soil systems.

The potential of soil microorganisms to enhance the retention of (137)Cs and (85)Sr in organic systems was assessed in a series of experiments. A biologically active, 'mineral-free', organic material, produced under laboratory conditions from leaves, was used as the uptake matrix in all experiments to minimise potential interference from competing clay minerals. Biological uptake and release were differentiated from abiotic processes by comparing the sorption of radionuclides in sterilised organic material with sterile material inoculated with soil extracts or single fungal strains. Our results show conclusively that living components of soil systems are of primary importance in the uptake of radionuclides in organic material. The presence of soil microorganisms significantly enhanced the retention of Cs in organic systems and approximately 70% of the Cs spike was strongly (irreversibly) bound (remained non-extractable) in the presence of microorganisms compared to only approximately 10% in abiotic systems. Sorption of (85)Sr was not significantly influenced by the presence of soil microorganisms. A non-linear temperature response was observed for the retention in biotic systems with increased uptake at between 10 and 30 degrees C and lower retention at temperatures above or below the optimum range. The optimum temperatures for biological uptake were between 15 and 20 degrees C for Cs, and 25 and 30 degrees C for Sr. Our results indicate that single strains of soil and saprotrophic fungi make an important contribution to the sorption of Cs and Sr in organic systems, but can only account for part of the strong, irreversible binding observed in biotic systems. Single strains of soil fungi increased the amount of non-extractable (137)Cs (by approximately 30%) and (85)Sr (by approximately 20%) in the organic systems as compared to abiotic systems, but the major fraction of (137)Cs and (85)Sr sorbed in systems inoculated with saprotrophic fungi remained extractable.

Detection and classification of atmospheric methane oxidizing bacteria in soil.

Well-drained non-agricultural soils mediate the oxidation of methane directly from the atmosphere, contributing 5 to 10% towards the global methane sink. Studies of methane oxidation kinetics in soil infer the activity of two methanotrophic populations: one that is only active at high methane concentrations (low affinity) and another that tolerates atmospheric levels of methane (high affinity). The activity of the latter has not been demonstrated by cultured laboratory strains of methanotrophs, leaving the microbiology of methane oxidation at atmospheric concentrations unclear. Here we describe a new pulse-chase experiment using long-term enrichment with 12CH4 followed by short-term exposure to 13CH4 to isotopically label methanotrophs in a soil from a temperate forest. Analysis of labelled phospholipid fatty acids (PLFAs) provided unambiguous evidence of methane assimilation at true atmospheric concentrations (1.8-3.6 p.p.m.v.). High proportions of 13C-labelled C18 fatty acids and the co-occurrence of a labelled, branched C17 fatty acid indicated that a new methanotroph, similar at the PLFA level to known type II methanotrophs, was the predominant soil micro-organism responsible for atmospheric methane oxidation.

Rapid degradation of the triazinone herbicide metamitron by a Rhodococcus sp. isolated from treated soil.

Seven bacterial isolates which degraded the herbicide metamitron (3-methyl-4-amino-6-phenyl-1,2,4-triazin-5-one) were obtained from field-enhanced soil by liquid enrichment culture. All isolates appeared to be identical and a representative, 0246b, was identified as a Rhodococcus sp. by cell wall and fatty acid analyses. This isolate degraded metamitron as the sole source of carbon within 24 h at 25 degrees C and this is the first report of a bacterium capable of growing with metamitron as the sole source of carbon. Metamitron was degraded less rapidly when it was the sole source of both carbon and nitrogen. The rate and extent of degradation was affected by the presence and type of additional sources of carbon and nitrogen in the culture medium. In studies with [14C]-phenyl-labelled metamitron Rhodococcus sp. 0246b partly mineralized the phenyl ring.

Stable-isotope probing as a tool in microbial ecology.

Microorganisms are responsible for driving the biogeochemical cycling of elements on Earth. Despite their importance and vast diversity, the taxonomic identity of the microorganisms involved in any specific process has usually been confined to that small fraction of the microbiota that has been isolated and cultivated. The recent coupling of molecular biological methods with stable-isotope abundance in biomarkers has provided a cultivation-independent means of linking the identity of bacteria with their function in the environment. Here we show that 13C-DNA, produced during the growth of metabolically distinct microbial groups on a 13C-enriched carbon source, can be resolved from 12C-DNA by density-gradient centrifugation. DNA isolated from the target group of microorganisms can be characterized taxonomically and functionally by gene probing and sequence analysis. Application of this technique to investigate methanol-utilizing microorganisms in soil demonstrated the involvement of members of two phylogenetically distinct groups of eubacteria; the alpha-proteobacterial and Acidobacterium lineages. Stable-isotope probing thus offers a powerful new technique for identifying microorganisms that are actively involved in specific metabolic processes under conditions which approach those occurring in situ.

Carbofuran-degrading bacteria from previously treated field soils.

Laboratory incubation studies were made on soils collected from five field sites with different histories of treatment with carbofuran. All soils treated earlier with carbofuran degraded the compound more rapidly than untreated samples of the same soils. Reduced rates of degradation in the presence of chloramphenicol imply that soil bacteria are primarily responsible for the breakdown of carbofuran in these soils. Sixty-eight bacteria, capable of degrading carbofuran as the sole source of carbon and nitrogen, were isolated from liquid cultures of treated soils. The concentration of carbofuran in the liquid medium used for isolation and subsequent culture of carbofuran-degrading isolates appeared to affect the stability of their ability to degrade. Similar types of carbofuran-degrading bacteria were isolated from different soils and several different types were isolated from one soil. All carbofuran-degrading isolates were Gram-negative, aerobic rods which hydrolysed the insecticide to carbofuran phenol. They were separated into four groups on the basis of a limited number of phenotypic characters. There was a good correlation between the phenotype of carbofuran-degrading isolates and the stability of their ability to degrade. Fourteen isolates were placed in phenotypic group I and 13 of these did not degrade carbofuran after one subculture in liquid medium. Phenotypic groups II, III and IV consisted of 54 isolates in total (3, 46 and 5 isolates respectively) and 52 of these retained their ability to degrade carbofuran when subcultured.

(13)C incorporation into DNA as a means of identifying the active components of ammonia-oxidizer populations.

AIMS: To identify active CO2-assimilating species of ammonia-oxidizing bacteria in fresh water sediment. METHODS AND RESULTS: Enrichment cultures were incubated in the presence of 13C labelled CO2, and 13C-DNA successfully resolved from 12C-DNA by caesium chloride density gradient ultracentrifugation of DNA extracts. Ammonia-oxidizer DNA recovered from these gradients was amplified and characterised by Temporal Temperature Gradient Gel Electrophoresis (TTGE), with confirmatory sequence analysis to identify the metabolically active components of the population. CONCLUSION: The 12C-DNA fraction was dominated by nitrosospiras, in contrast to the 13C-DNA fraction which was largely nitrosomonad DNA, in support of the hypothesis that nitrosomonads out-compete nitrosospiras in laboratory culture. SIGNIFICANCE AND IMPACT OF THE STUDY: The use of stable isotype incorporation into ammonia-oxidizer DNA could therefore circumvent the problems associated with RNA detection to identify metabolically active species in situ.

Assessing soil biodiversity across Great Britain: national trends in the occurrence of heterotrophic bacteria and invertebrates in soil.

An assessment of the biodiversity of soils was a component of the Countryside Survey 2000 (CS2000). This was the first integrated survey of soil biota and chemical properties at a national scale. A total of 1052 soil samples were collected across Great Britain during CS2000 and analysed for a range of soil microbial and invertebrate characteristics resulting in the production of a series of robust datasets. A principal objective was to use these datasets to investigate relationships between soil biota and environmental factors such as geographical location, vegetation, land use, land cover, soil type and pollutant levels as first stages in characterising the inherent biodiversity of British soils and investigating the potential of soil biodiversity as indicators of soil health at a regional or national scale. Preliminary results for culturable heterotrophic, invertebrate taxa, Acari, Collembola and Oribatid mites are presented here to illustrate the nature of the data collected and the patterns of soil biodiversity in relation to large-scale regional, vegetation and soil characteristics across the British countryside.