Microbial Communities in Long-Term Heavy Metal Contaminated Ombrotrophic Peats

High concentrations of heavy metals are known to be toxic to many soil organisms. The effects of long-term exposure to lower levels of metals on the soil microbial community are, however, less well understood. The southern Pennines of the U.K. are characterised by expanses of ombrotrophic peat soils that have experienced deposition of high levels of heavy metals since the mid to late 1800s. Concentrations of metals in the peat remain high but the effect of the contamination on the in-situ microbial communities is unknown. Geochemical and molecular polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and sequencing techniques were used to derive new information on the metal chemistry and microbial populations in peat soils from six locations in the southern Pennines. All sites were highly acidic (pH 3.00–3.14) with high concentrations of potentially toxic heavy metals, particularly porewater Zn and particulate-associated Pb. The results also reveal a split in site characteristics between the most polluted sites with the highest levels of bioavailable metals (Bleaklow, FeatherBed Moss and White Hill) and those with much lower bioavailable metals (Cowms Moor, Holme Moss and Round Hill). There was no difference in the number of dominant bacterial species between the sites but there were significant differences in the species composition. At the three sites with the highest levels of bioavailable metals, bacterial species with a high similarity to acidophilic sulphur- and iron-oxidizing bacteria and those from high metal environments were detected. The transformations carried out by these metal mobilising and acid producing bacteria may make heavy metals more bioavailable and therefore more toxic to higher organisms. Bacteria with similarity to those typically found in forest and grassland soils were documented at the three sites with the lowest levels of bioavailable metals. The data highlight the need for further studies to elucidate the species diversity and functionality of bacteria in heavy metal contaminated peats in order to assess implications for moorland restoration.     

Near‐infrared spectroscopy can predict the composition of organic matter in soil and litter

The usefulness and limitations of near‐infrared reflectance spectroscopy (NIRS) for the assessment of several soil characteristics are still not sufficiently explored. The objective of this study was to evaluate the ability of visible and near‐infrared reflectance (VIS‐NIR) spectroscopy to predict the composition of organic matter in soils and litter. Reflectance spectra of the VIS‐NIR region (400–2500 nm) were recorded for 56 soil and litter samples from agricultural and forest sites. Spectra were used to predict general and biological characteristics of the samples as well as the C composition which was measured by ¹³C‐CPMAS‐NMR spectroscopy. A modified partial least‐square method and cross‐validation were used to develop equations for the different constituents over the whole spectrum (1st to 3rd derivation). Near‐infrared spectroscopy predicted well the C : N ratios, the percentages of O‐alkyl C and alkyl C, the ratio of alkyl C to O‐alkyl C, and the sum of phenolic oxidation products: the ratios of standard deviation of the laboratory results to standard error of cross‐validation (RSC) were greater than 2, the regression coefficients (a) of a linear regression (measured against predicted values) ranged from 0.9 to 1.1, and the correlation coefficients (r) were greater than 0.9. Satisfactorily (0.8 ≤ a ≤ 1.2, r ≥ 0.8, and 1.4 ≤ RSC ≤ 2.0) assessed were the contents of C, N, and production of DOC, the percentages of carbonyl C and aromatic C and the ratio of alkyl C to aromatic C. However, the N‐mineralization rate and the microbial biomass were predicted unsatisfactorily (RSC < 1.4). The good and satisfactory predictions reported above indicate a marked usefulness of NIRS in the assessment of biological and chemical characteristics of soils and litter.     

Purification and identification of linoleic acid hydroperoxides generated by soybean seed lipoxygenases 2 and 3

It has been known that lipoxygenase (LOX) isozymes exhibit differences in product formation, but most product information to date is for LOX 1 among soybean (Glycine max) LOX isozymes. In this study, LOXs 2 and 3 were purified and used to generate hydroperoxide (HPOD) products in an in vitro system using linoleic acid as a substrate in the presence of either air or O2. The products were analyzed to determine their stereoisomeric characteristics. The control (no enzyme) showed only low levels of hydroperoxide production and no stereoisomeric specificity. LOX 2 shows high specificity in product formation, producing roughly 4 times more 13-HPOD than 9-HPOD, nearly all of which was 13-S(Z,E)-HPOD. LOX 3 produced more 9-HPOD than 13-HPOD at approximately a 2:1 ratio. No single stereoisomer was predominant among LOX 3 products. These results demonstrate that different isozymes of LOX have characteristic product profiles in in vitro reactions.     

A method to assess whether ‘preferential use’ occurs after N ammonium addition; implication for the N isotope dilution technique

The robustness of the assumption of equilibrium between native and added N during ¹⁵N isotope dilution has recently been questioned by Watson et al. (Soil Biol Biochem 32 (2000) 2019-2030). We re-analyzed their raw data using equations that consider the added and native NH₄⁺ and NO₃⁻ pools as separate state variables. Gross mineralization rates and first-order rate constants for NH₄⁺ and NO₃⁻ consumption were obtained by combining analytical integration of the differential equations with a non-linear fitting procedure. The first-order rate constants for NH₄⁺ consumption and NO₃⁻ immobilization for the added NH₄⁺ and NO₃⁻ pool were used to estimate gross mineralization rates and first-order rate constants for nitrification of native NH₄⁺. The latter were 2-4 times lower than the first-order rate constants derived from the added N pool. This discrepancy between first-order rate constants for nitrification implies that one or more process rates estimated for the added N pools cannot be applied to the native N pools. Preferential use of the added N resulted in an overestimation of the gross mineralization by 1.5-2.5-fold, emphasizing the need for critical evaluation of the assumption of equilibrium before gross mineralization rates are calculated.     

Morphogenesis and erodibility of soil-saprolite complexes from magmatic rocks in Swaziland (Southern Africa)

The Kingdom of Swaziland in Southern Africa is affected by diverse forms of severe soil erosion as a consequence of population growth, deforestation, and overgrazing of the grass savanna. The physical, chemical and mineralogical properties of soil-saprolite complexes show that the presence of relict saprolite underlying the soils is an essential precondition for the development and rapid expansion of deep incising erosion gullies in areas with magmatic rocks. The polygenetic isovolumetric weathering of saprolite led to mass losses of more than 50 vol.-% due to the formation of solution cavities by leaching in warm and humid climatic phases. Therefore, the saprolite is highly susceptible to erosion. Low structure stability of the saprolite, indicated by shear strength values < 5 kPa, results from a silty texture, absence of organic matter, and low contents of Fe- and Al-oxides and exchangeable Al-ions. On the contrary, the clay-rich ferrallitic soils developed from saprolite are comparatively stable against erosion. The relatively high structure stability of the soil, indicated by shear strength values ranging from 7 to 12 kPa, results from the organic matter content of about 3 wt.-% C_org in the topsoil, up to 7 wt.-% pedogenic Fe- and Al-oxides, pH(KCI)-values around 4, and Al-saturations above 50 %. Concerning the genesis and the susceptibility to erosion, the results show a distinct bipartition of the weathering mantle. Therefore, it is necessary to investigate the site properties and spatial distribution of complete soil-saprolite complexes from magmatic rocks as a basis of soil erosion control, land evaluation, and land use planning.     

Porous tubing for use in monitoring soil CO2 concentrations

The composition of the soil atmosphere is an indicator of biological processes, and soil CO₂ gradients have been used to estimate CO₂ efflux from the surface. Soil atmosphere samplers, constructed with gas-permeable materials, have been used to quantify soil CO₂ concentrations. The type of material used can influence the perceived real-time concentrations of CO₂ in the soil. Previous works have not directly compared different types of materials under the same conditions. The objective of this study was to determine the diffusion coefficient (D) and time of 95% equilibrium (t_eq) of CO₂ through several materials, and to evaluate the effect of long-term soil burial (183 days) on diffusion characteristics. Materials tested included silicone, expanded Teflon (ePTFE), and ultra high molecular weight polyethylene (PE) tubing. The D of each material was determined using a closed-loop system consisting of a CO₂-enriched (7800 ppm) chamber, a CO₂ analyzer and an inner tube (experimental tubing) placed inside the chamber. Air was re-circulated through the inner tube, and as CO₂ diffused from the chamber into the tubing, the analyzer recorded the increase in concentration. The silicone tubes had values of D ranging from 8.64 to 5.80×10⁻⁶ cm² s⁻¹ with corresponding t_eq between 3.9 and 9.7 h. Diffusion coefficients of the ePTFE (1.25×10⁻⁴ cm² s⁻¹) and PE (7.70×10⁻⁴ cm² s⁻¹) materials were 2 orders of magnitude greater, with t_eq<6 min. Exposure to the soil environment for 183 days did not visibly deteriorate the materials or significantly affect the D or t_eq values. Use of the ePTFE or PE materials, over the silicone materials, may allow for better characterization of dynamic CO₂ concentrations in the soil based on the greater D and lesser t_eq values of these materials.     

Increased emergence of spring wheat after inoculation with Pseudomonas chlororaphis isolate 2E3 under field and laboratory conditions

Inoculation at the time of planting with Pseudomonas chlororaphis strain 2E3 increased the emergence of spring wheat by 8% and 6% at two different sites in northern Utah. Isolate 2E3 strongly inhibited the growth of the wheat pathogen Fusarium culmorum on artificial media. A second isolate of P. chlororaphis (strain O6) also inhibited fungal growth on artifical media but did not increase emergence of the spring wheat at the same field sites. Inoculation of winter wheat by 2E3 did not promote emergence when planted into field soil sterilized by fumigation with methyl bromide. Under laboratory conditions, emergence of spring wheat in sterilized soils from both sites was at least 90%. In the soils that were not sterilized, emergence was below 25% in soil from one site and below 50% in soil from the other. Treating seeds with 2E3 significantly improved emergence in a sterile soil-containing matrix that had been inoculated with the wheat pathogen Fusarium culmorum. Consequently, we propose that increases in wheat emergence can be attributed to the suppression by 2E3 of pathogenic organisms present in the native field soils. A strain of Rhizoctonia solani, shown to the pathogenic on winter wheat, was isolated from one of these soils.     

Spatial structure of multispecies distributions in southern California, USA

Analysis of the spatial distribution of all species of conservation importance within a region is necessary to augment reserve selection strategies and habitat management in biodiversity conservation. In this study, we analyzed the spatial aggregation, spatial association, and vegetation types of point occurrence data collected from museum and herbaria records for rare, special concern, threatened, and endangered species of plants, reptiles, mammals, and birds in western Riverside County in southern California, USA. All taxa showed clumped distributions, with aggregation evident below 14 km for plants, 12 km for reptiles, 2 km for mammals, and 10 km for birds. In addition, all combinations of the different species groups showed high positive spatial association. The Santa Rosa Plateau exhibited the highest number of rare, special concern, threatened, and endangered species, and shrubland (coastal sage and chaparral) was the vegetation type inhabited by the most species. Local land use planning, zoning and reserve design should consider the spatial aggregation within and between species to determine the appropriate scale for conservation planning. The higher spatial association between species groups in this study may indicate interdependence between different species groups or shared habitat requirements. It is important to maintain diverse communities due to potential interdependence. The results of the study indicate that concentrating preservation efforts on areas with the highest number of species of concern and the restoration of native shrublands are the most appropriate actions for multiple species habitat conservation in this area.     

Degradation and binding of atrazine in surface and subsurface soils

Understanding the dissipation rates of chemicals in unsaturated and saturated zones of subsurface soils will help determine if reductions of concentrations to acceptable levels will occur. Chemical properties and microbial biomass and activity were determined for the surface (0-15 cm), lower root (50-105 cm), and vadose (175-220 cm) zones in a Huntington silty clay loam (Fluventic Hapludoll) collected from an agricultural field near Piketon, OH. The rates of sorption, mineralization, and transformation (formation of bound residues and metabolites) of atrazine were determined. Microbial activity was estimated from the mineralization of (14)C-benzoate. We observed decreased levels of nutrients (total organic carbon, N, and P) and microbial biomass with depth, while activity as measured with benzoate metabolism was higher in the vadose zone than in either the surface or the root zones. Sorption coefficients (K(f)) declined from 8.17 in the surface to 3.31 in the vadose zone. Sorption was positively correlated with organic C content. Rates of atrazine mineralization and bound residues formation were, respectively, 12-2.3-fold lower in the vadose than in the surface soil. Estimated half-lives of atrazine ranged from 77 to 101 days in the surface soil, but increased to over 900 days in the subsurface soils. The decreased dissipation of atrazine with increasing depth in the profile is the result of decreased microbial activity toward atrazine, measured either as total biomass or as populations of atrazine-degrading microorganisms. The combination of reduced dissipation and low sorption indicates that there is potential for atrazine movement in the subsurface soils.