Microbial analysis of soil and groundwater from a gasworks site and comparison to a sequenced biological reactive barrier remediation process (SEREBAR)

Aims: To investigate the distribution of a polymicrobial community of biodegradative bacteria in (i) soil and groundwater at a former manufactured gas plant (FMGP) site and (ii) in a novel SEquential REactive BARrier (SEREBAR) bioremediation process designed to bioremediate the contaminated groundwater. Methods and Results: Culture-dependent and culture-independent analyses using denaturing gradient gel electrophoresis (DGGE) and polymerase chain reaction (PCR) for the detection of 16S ribosomal RNA gene and naphthalene dioxygenase (NDO) genes of free-living (planktonic groundwater) and attached (soil biofilm) samples from across the site and from the SEREBAR process was applied. Naphthalene arising from groundwater was effectively degraded early in the process and the microbiological analysis indicated a dominant role for Pseudomonas and Comamonas in its degradation. The microbial communities appeared highly complex and diverse across both the sites and in the SEREBAR process. An increased population of naphthalene degraders was associated with naphthalene removal. Conclusion: The distribution of micro-organisms in general and naphthalene degraders across the site was highly heterogeneous. Comparisons made between areas contaminated with polycyclic aromatic hydrocarbons (PAH) and those not contaminated, revealed differences in the microbial community profile. The likelihood of noncultured bacteria being dominant in mediating naphthalene removal was evident. Significance and Impact of the Study: This work further emphasizes the importance of both traditional and molecular-based tools in determining the microbial ecology of contaminated sites and highlights the role of noncultured bacteria in the process.

A finite element solution scheme for an elastic–viscoplastic soil model

A Newton–Raphson solution scheme with a stress point algorithm is presented for the implementation of an elastic–viscoplastic soilmodel in a finite element program. Viscoplastic strain rates are calculated using the stress and volumetric states of the soil. Sub-incrementsof time are defined for each iterative calculation of elastic–viscoplastic stress changes so that their sum adds up to the time incrementfor the load step. This carefully defined ‘iterative time’ ensures that the correct amount of viscoplastic straining is accumulated overthe applied load step. The algorithms and assumptions required to implement the solution scheme are provided. Verification of the solutionscheme is achieved by using it to analyze typical boundary value problems.

Contrasting effects of a nonionic surfactant on the biotransformation of polycyclic aromatic hydrocarbons to cis-dihydrodiols by soil bacteria

The biotransformation of the polycyclic aromatic hydrocarbons (PAHs) naphthalene and phenanthrene was investigated by using two dioxygenase-expressing bacteria, Pseudomonas sp. strain 9816/11 and Sphingomonas yanoikuyae B8/36, under conditions which facilitate mass-transfer limited substrate oxidation. Both of these strains are mutants that accumulate cis-dihydrodiol metabolites under the reaction conditions used. The effects of the nonpolar solvent 2,2,4,4,6,8,8-heptamethylnonane (HMN) and the nonionic surfactant Triton X-100 on the rate of accumulation of these metabolites were determined. HMN increased the rate of accumulation of metabolites for both microorganisms, with both substrates. The enhancement effect was most noticeable with phenanthrene, which has a lower aqueous solubility than naphthalene. Triton X-100 increased the rate of oxidation of the PAHs with strain 9816/11 with the effect being most noticeable when phenanthrene was used as a substrate. However, the surfactant inhibited the biotransformation of both naphthalene and phenanthrene with strain B8/36 under the same conditions. The observation that a nonionic surfactant could have such contrasting effects on PAH oxidation by different bacteria, which are known to be important for the degradation of these compounds in the environment, may explain why previous research on the application of the surfactants to PAH bioremediation has yielded inconclusive results. The surfactant inhibited growth of the wild-type strain S. yanoikuyae B1 on aromatic compounds but did not inhibit B8/36 dioxygenase enzyme activity in vitro.

Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms

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 (CO2)-C-13 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 C-13-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 C-13 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 C-12 and C-13 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.

The legacy of past manuring practices on soil contamination in remote rural areas

This paper demonstrates that there can be a legacy of contamination on former arable land in remote rural areas as a result of past manuring practices. In the first part of the study four farms abandoned in the late 19th to mid-20th century were investigated with samples collected from residual material in domestic hearths, the midden heaps, kailyards (walled garden for vegetables), infields (intensively managed arable land) and outfields (less intensively managed land for cropping or grazing). Consistent sequences in concentration values were found for such elements as Pb, Zn, Cu and P in the order hearth>midden>kailyard>infield>outfield. Such patterns can in part be explained in terms of atmospheric deposition on peat and turf which were subsequently burnt in hearths to result in enhanced elemental concentrations. The ash then was deposited in midden heaps and subsequently on kailyards or infields. In the second part, microanalytical results from St. Kilda are discussed. Enhanced loadings of Pb and Zn were found in the old arable land. The highest levels of Zn were found in small fragments of carbonised and humified material and bone fragments; in contrast Pb tended to be more uniformly distributed. Seabird waste was extensively applied to the arable land and some of the Zn may have accumulated in the soil by this pathway. The retention of Zn in bone is likely to have been very minor given the rarity of bone fragments as evident in thin sections (0.3%); this compares with 6.8% for black carbonised particles which are likely to provide the main storage sites for Zn.

Flux and turnover of fixed carbon in soil microbial biomass of limed and unlimed plots of an upland grassland ecosystem

The influence of liming on rhizosphere microbial biomass C and incorporation of root exudates was studied in the field by in situ pulse labelling of temperate grassland vegetation with (13)CO(2) for a 3-day period. In plots that had been limed (CaCO(3) amended) annually for 3 years, incorporation into shoots and roots was, respectively, greater and lower than in unlimed plots. Analysis of chloroform-labile C demonstrated lower levels of (13)C incorporation into microbial biomass in limed soils compared to unlimed soils. The turnover of the recently assimilated (13)C compounds was faster in microbial biomass from limed than that from unlimed soils, suggesting that liming increases incorporation by microbial communities of root exudates. An exponential decay model of (13)C in total microbial biomass in limed soils indicated that the half-life of the tracer within this carbon pool was 4.7 days. Results are presented and discussed in relation to the absolute values of (13)C fixed and allocated within the plant-soil system.

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.

Relative role of deterministic and stochastic determinants of soil animal community: a spatially explicit analysis of oribatid mites

1. Ecologists are debating the relative role of deterministic and stochastic determinants of community structure. Although the high diversity and strong spatial structure of soil animal assemblages could provide ecologists with an ideal ecological scenario, surprisingly little information is available on these assemblages.
2. We studied species-rich soil oribatid mite assemblages from a Mediterranean beech forest and a grassland. We applied multivariate regression approaches and analysed spatial autocorrelation at multiple spatial scales using Moran's eigenvectors. Results were used to partition community variance in terms of the amount of variation uniquely accounted for by environmental correlates (e.g. organic matter) and geographical position. Estimated neutral diversity and immigration parameters were also applied to a soil animal group for the first time to simulate patterns of community dissimilarity expected under neutrality, thereby testing neutral predictions.
3. After accounting for spatial autocorrelation, the correlation between community structure and key environmental parameters disappeared: about 40% of community variation consisted of spatial patterns independent of measured environmental variables such as organic matter. Environmentally independent spatial patterns encompassed the entire range of scales accounted for by the sampling design (from tens of cm to 100 m). This spatial variation could be due to either unmeasured but spatially structured variables or stochastic drift mediated by dispersal. Observed levels of community dissimilarity were significantly different from those predicted by neutral models.
4. Oribatid mite assemblages are dominated by processes involving both deterministic and stochastic components and operating at multiple scales. Spatial patterns independent of the measured environmental variables are a prominent feature of the targeted assemblages, but patterns of community dissimilarity do not match neutral predictions. This suggests that either niche-mediated competition or environmental filtering or both are contributing to the core structure of the community. This study indicates new lines of investigation for understanding the mechanisms that determine the signature of the deterministic component of animal community assembly.

Dietary switching of collembola in grassland soil food webs

Soil food webs are characterised by complex direct and indirect effects among the organisms. Consumption of microorganisms by soil animals is considered as an important factor that contributes to the stability of communities, though cascading effects within the food web can be difficult to detect. In a greenhouse experiment, an addition of a high number the fungal feeding collembola Folsomia quadrioculata was applied to grassland soil food webs in monocultures of three plant species: Plantago lanceolato (forb), Lotus corniculatus (legume) and Holcus lanatus (grass). The abundance of microorganisms, determined as the abundances of phospholipid fatty acids (PLFAs) and the abundances of resident invertebrates, nematodes and collembolans, did not change due to the addition of E quadrioculata. Trophic positions of collembolans were determined by analyses of natural abundances of N-15 stable isotopes. The use of food resources by microorganisms and collembolans was determined by C-13 analysis of microbial PLFAs and solid samples of collembolans. delta C-13 values of the resident collembola Folsomia fimetaria were lower in the presence of E quadrioculata than in the control food webs indicating a use of more depleted C-13 food resources by E fimetaria. The delta N-15 values of E fimetaria did not change at the addition of E quadrioculata thus no change of trophic levels was detected. The switch of E fimetaria to a different food resource could be due to indirect interactions in the food web as the two collembolan species were positioned on different trophic positions, according to different delta N-15 values. (c) 2008 Elsevier Ltd. All rights reserved.

Inorganic species of arsenic in soil solution determined by microcartridges and ferrihydrite-based diffusive gradient in thin films

The bioavailability of soil arsenic (As) is determined by its speciation in soil solution, i.e., arsenite [As(III)] or arsenate [As(V)]. Soil bioavailability studies require suitable methods to cope with small volumes of soil solution that can be speciated directly after sampling, and thereby minimise any As speciation change during sample collection. In this study, we tested a self-made microcartridge to separate both As species and compared it to a commercially available cartridge. In addition, the diffusive gradient in thin films technique (DGT), in combination with the microcartridges, was applied to synthetic solutions and to a soil spiked with As. This combination was used to improve the assessment of available inorganic As species with ferrihydrite(FH)-DGT, in order to validate the technique for environmental analysis, mainly in soils. The self-made microcartridge was effective in separating As(III) from As(V) in solution with detection by inductively coupled plasma optical emission spectrometry (ICP-OES) in volumes of only 3 ml. The DGT study also showed that the FH-based binding gels are effective for As(III) and As(V) assessment, in solutions with As and P concentrations and ionic strength commonly found in soils. The FH-DGT was tested on flooded and unflooded As spiked soils and recoveries of As(III) and As(V) were 85–104% of the total dissolved As. This study shows that the DGT with FH-based binding gel is robust for assessing inorganic species of As in soils.