Ecology of the active soil microfauna (Protozoa, Metazoa) of Wilkes Land, East Antarctica

Active ciliates, testate amoebae, nematodes, rotifers and tardigrades were examined in fresh and preserved fellfield, moss and ornithogenic soil samples of Wilkes Land. Direct counting was used to investigate abundances, community structures and protozoan diversity. Twenty-six ciliate species (nine first records for continental Antarctica, one undescribed) and five testacean species (three new records) were found. Two Colpoda species were active, further disproving Smith's hypothesis that this genus is absent in continental Antarctica. Animal frequencies varied between habitats but every group occurred in at least 74% of the samples, rotifers (95%) and testaceans (92%) being most frequent. Highest abundances were recorded in moss: 354 ciliates/g dry soil (19 species), 671 testaceans (5 species), 513 nematodes, 1,311 rotifers and 4,607 tardigrades, which thus dominated. Rotifers were most abundant in the other habitats. The microfauna was not randomly distributed because individual numbers were often strongly intercorrelated. Water and organic matter content were relevant environmental parameters; air temperature and pH probably had indirect effects. Received:28 August 1996 / Accepted:23 November 1996     

Testate amoebae and environmental features of polygon tundra in the Indigirka lowland (East Siberia)

Polygon tundra characterizes large areas of arctic lowlands. The micro-relief pattern within polygons offers differentiated habitats for testate amoeba (testacean) communities. The objective of this study was to relate testacean species distribution within a polygon to the environmental setting. Therefore, testaceans from four cryosol pits dug at different locations within a low-centered polygon were studied in the context of pedological and pedochemical data, while ground temperature and ground moisture were measured over one summer season. The study site is located on the Berelekh River floodplain (Indigirka lowland, East Siberia). The environmental data sets reflect variations along the rim-to-center transect of the polygon and in different horizons of each pit. The testacean species distribution is mainly controlled by the soil moisture regime and pH. Most of the identified testaceans are cosmopolitans; eight species are described from an arctic environment for the first time. Differences in environmental conditions are controlled by the micro-relief of polygon tundra and must be considered in arctic lowland testacean research because they bias species composition and any further (paleo-)ecological interpretation.     

Ecological aspects of development of testacean complexes in nests of Formica lugubris and Formica exsecta (Hymenoptera, Formicidae)

Testacean population in the nests of Formica lugubris and F. exsecta was studied in a spruce forest and in a mixed birch forest. Samples of the nest material (spruce litter and grass fragments) were taken from the surface layers, the inner parts of the nests, and from underlying soil. In all, 33 species of testaceans were identified. The highest species diversity and abundance were observed in the Formica lugubris nests, in the upper layer of the F. exsecta nest, and in the spruce litter. In all the samples, 10 widespread aerophilic and edaphic species (Centropyxis aerophila, C. sylvatica, C. orbicularis, Cyclopyxis kahli, Trinema lineare, and others) were the most common, resulting in a uniform species composition in all the habitats studied. In the presence of the relevant substrate, this group is supplemented by species of appropriate ecological groups (bryophilic, acidophilic, and inhabitants of coarse humus). In the inner part of the Formica lugubris nest, the testacean population is characterized by a very high abundance of Plagiopyxis penardi, whereas the surface layer of the F. exsecta nest is characterized by abundant Cyclopyxis eurystoma and very low species diversity in the inner layers. The initial composition and decree of decomposition of plant remains due to ant activity are considered as the main factors responsible for the testacean species diversity, as well as the availability of substrates suitable for the development of different ecological groups of testaceans.     

中国东北样带(NECT)东部森林区的植被与表土花粉的定量关系

The eastern forest stands of Northeast China Transect (NECT) were chosen to study the quantitative relationships between vegetation and pollen in surface samples. The indices of A (association index),O(over-representation index),U(under-representation index),C(correlation coefficient) and R(representation coefficient) for each pollen type were calculated. The results indicated that the relationships between vegetation and pollen type in surface samples were significant and the correlation coefficients of 70% pollen types were more than 0.5(α=0.05); the similarity between pollen assemblage and plant community was good and coefficient of similarity was more than 50%. 69 pollen types found in the surface samples could be divided into four groups with TWINSPAN classification and PCA ordination according to A,O,U and C. The four groups reflected the pollination characteristic of plants and the state of pollen conserved in soil. Group 1 was the associative group which could accurately reflect the local vegetation; Group 2 was over-representative group which had high pollen percentage outproportional to vegetation; Group 3 was the under-representative group in which the pollen were hardly obtainable from the soil, and Group 4 was also an under-representative group, in which pollen were easily obtainable in soil where plants directly grow from. The study also showed that A was a parameter to rectify pollen data and it was easier to obtain than parameter R. The parameters A and R have close relation and their regression equation was: A=-0.0421R2+0.2425R+0.3926(r2=0.6021). These groups and indices provide a solid foundation for using pollen data in accurately reinstating vegetation.     

Heterotrophic soil respiration and soil carbon dynamics in the deciduous Hainich forest obtained by three approaches

Three different approaches were used to calculate heterotrophic soil respiration (Rh) and soil carbon dynamics in an old-growth deciduous forest in central Germany. A root and mycorrhiza exclosure experiment in the field separated auto- and heterotrophic soil respiration. It was compared to modeled heterotrophic respiration resulting from two different approaches: a modular component model of soil respiration calculated autotrophic and heterotrophic soil respiration with litter, climate and canopy photosynthesis as input variables. It was calibrated by independent soil respiration measurements in the field. A second model was calibrated by incubation of soil samples from different soil layers in the laboratory. In this case, the annual sum of Rh was calculated by an empirical model including response curves to temperature and a soil moisture. The three approaches showed good accordance during spring and summer and when the annual sums of Rh calculated by the two models were compared. Average Rh for the years 2002–2006 were 436 g C m^?2 year^?1 (field model) and 417 g C m^?2 year^?1 (lab-model), respectively. Differences between the approaches revealed specific limitations of each method. The average carbon balance of the Hainich forest soil was estimated to be between 1 and 35 g C m^?2 year^?1 depending on the model used and the averaging period. A comparison with nighttime data from eddy covariance (EC) showed that EC data were lower than modelled soil respiration in many situations. We conclude that better filter methods for EC nighttime data have to be developed.     

Feasibility of Estimating Cu Contamination in Floodplain Soils using VNIR Spectroscopy—A Case Study in the Le’an River Floodplain,China

Heavy metal accumulation can influence the physical, chemical, and ecological processes in the soil ecosystem, and the accumulation of heavy metals has become a serious environmental issue in China, especially in the floodplains downstream from mining and smelting sites. A novel method of estimating the heavy metal contamination of soil is proposed using visible and near-infrared (VNIR) spectroscopy and partial least squares regression (PLSR). Our study focuses on the Le’an river floodplain, Jiangxi Province, China, which houses the largest copper mining operation in China and has suffered a series of environmental setbacks from the extraction of copper. Our study employs PLSR to summarize the relationship between VNIR reflectance spectra and the copper content of collected soil samples, and then estimates copper contamination of the soil using VNIR spectroscopy and the calibrated model. More specifically, with 71 soil samples collected from the Le’an River floodplain, our study aims at (1) exploring the correlation between VNIR and soil constituents, including soil organic matter, total copper, and iron content; (2) assessing the relationship between VNIR determination of copper and the pre-processing of soil samples; and (3) evaluating the performance of data transformation methods in PLSR. The correlation analysis revealed that the mechanism of estimating Cu content lay in its correlation with Fe content. The PLSR model with logarithmic scale transformed copper content and the standard normal variate spectra was chosen for estimating copper contamination from untreated soil samples; the model with logarithmic scale transformed copper content and reflectance spectra was selected for pretreated soil samples. The correlation analyses and regression results in the PLSR models both suggest that the main mechanism for estimating Cu content in this case study lies in its correlation with Fe content. Therefore, the coupling of VNIR spectroscopy and PLSR could serve as an alternative method of monitoring heavy metal contamination of soil.     

A Critical Review of Discrete Soil Sample Data Reliability: Part 1—Field Study Results

Part 1 of this study summarizes data for a field investigation of contaminant concentration variability within individual, discrete soil samples (intra-sample variability) and between closely spaced, “co-located” samples (inter-sample variability). Hundreds of discrete samples were collected from three sites known respectively to be contaminated with arsenic, lead, and polychlorinated biphenyls. Intra-sample variability was assessed by testing soil from ten points within a minimally disturbed sample collected at each of 24 grid points. Inter-sample variability was assessed by testing five co-located samples collected within a 0.5-m diameter of each grid point. Multi Increment soil samples (triplicates) were collected at each study site for comparison. The study data demonstrate that the concentration of a contaminant reported for a given discrete soil sample is largely random within a relatively narrow (max:min <2X) to a very wide (max:min >100X) range of possibilities at any given sample collection point. The magnitude of variability depends in part on the contaminant type and the nature of the release. The study highlights the unavoidable randomness of contaminant concentrations reported in discrete soil samples and the unavoidable error and inefficiency associated with the use of discrete soil sample data for decision making in environmental investigations.     

Anthropogenic impact on the presence of L. monocytogenes in soil, fruits, and vegetables

The aim of this study was to determine the prevalence of Listeria sp. and Listeria monocytogenes in soil samples with reference to type of fertilizers (natural and artificial) and distance from places intensively exploited by men, as well as to determine the relationship between the presence of L. monocytogenes in the soil and in fruits and vegetables. The examined 1,000 soil samples originated from 15 different areas, whilst 140 samples of fruits and 210 samples of vegetables were collected from those areas. L. monocytogenes was isolated only from 5.5 % of all soil samples coming exclusively from meadows intensively grazed by cattle (27.8 %) and areas near food processing plants (25 %) and wild animal forests (24 %). Listeria sp. and L. monocytogenes were not present on artificially fertilized areas and wastelands. L. monocytogenes was detected in 10 % of samples of strawberry, 15 % of potato samples, and 5 % of parsley samples. Our data indicate that Listeria spp. and particularly L. monocytogenes were found in the soil from (1) arable lands fertilized with manure, (2) pasture (the land fertilized with feces of domestic animals), and (3) forests (again, the land fertilized with feces of animals, not domestic but wild). The bacteria were not detected in the soil samples collected at (1) artificially fertilized arable lands and (2) wastelands (the lands that were not fertilized with manure or animal feces). Moreover, a correlation was determined in the presence of L. monocytogenes between soil samples and samples of the examined fruits and vegetables.     

Testaceans (Protozoa: Testacea) in Quaternary Permafrost Sediments of Bykovsky Peninsula, Arctic Yakutia

The results of the first protozoological study in terms of paleoecology of long-term sediments and buried soils formed in the cryolite zone of northeastern Siberia are discussed. The data on testaceans (Protozoa: Testacea) inhabiting various sites of Bykovsky Peninsula, Laptev Sea coast near estuary of Lena, within the last 53000 years (Late Pleistocene and Holocene) are presented.     

基于Landsat系列数据的盐分指数和植被指数对土壤盐度变异性的响应分析——以新疆天山南北典型绿洲为例

基于不同地理区域,借助目前已有或者构建新的盐分和植被指数定量评估研究区的土壤盐度状况。但多数指数并未在盐渍化较为严重的中国新疆地区进行系统性对比分析。因此,以新疆阜北地区(采样数=37),玛纳斯河绿洲(采样数=68)和渭干河-库车河绿洲(采样数=38)为研究区,以灌区农田和盐渍地采样数据和Landsat TM/ETM+/OLI为数据源,利用线性模型和多个非线性模型(10个)测试上述指数(14个指数)和原始波段对于研究区土壤盐度的敏感性。结果显示,阜北地区基于遥感获取的扩展的增强型植被指数Extented Enhanced Vegetation Index(EEVI)在全样本和部分样本(盐渍化样本,土壤盐度0.3%)两种模式下(0—10cm),较其他指数和波段而言较为敏感。在全样本和部分样本(土壤饱和溶液电导率2ds/m)两种模式下,与玛纳斯流域各层土壤盐度最为敏感的为band 2,部分样本模式下土壤盐度变异性显著性探测最大下探深度为30cm。渭干河-库车河绿洲全样本模式下,最大土壤盐度变异性显著性探测深度为40cm,0—10cm和10—20cm深度表现最为敏感的是土壤盐分指数SI-T,20—40cm深度则为植被指数TGDVI。部分样本下(土壤饱和溶液电导率2ds/m),0—10cm深度最为敏感的为band5,10—20cm深度最为敏感的为TGDVI,20—40cm深度则为EEVI。其他指数因地理环境的差异性(气候,土壤盐分类型,土壤类型,采样时间),与土壤盐度之间并未达到显著性(sig=0.05或者0.01)的水平。以上结果只是初步结论,但也暗示其中的某些指数在本区具有一定土壤盐度的识别潜力。此外,由于土壤本身的复杂性,需要采集更多的样本以深入分析不同盐度等级下上述指数的具体表现。     

Mutagenic potency in Salmonella typhimurium of organic extracts of soil samples originating from urban, suburban, agricultural, forest and natural areas

The purpose of the present work was to assess the mutagenic potency of soil samples presumably not contaminated by industrial wastes and discharges. A set of 51 soil samples was collected from areas considered as not contaminated by a known industrial activity: 11 urban samples (collected in cities), 15 suburban samples (collected in villages), 7 agricultural samples, and 18 forest or natural samples. Each soil sample was collected at the surface (0-5cm deep), dried, sieved (2mm), homogenized before organic extraction (dichloromethane/acetone 1/1 (v/v), 37 degrees C, 4h, soil/solvent ratio 1/2, m/v), solvent exchange to DMSO and sterilizing filtration. The micro-method adaptation of the standard bacterial mutagenicity test on Salmonella typhimurium strain TA98 was performed with and without a metabolic activation system (rat-liver homogenate S9), and thus detected the effect of pro-mutagens and direct mutagens, respectively. The use of a pre-incubation method increased the sensitivity of the assay. The results obtained showed a wide range of effect levels, from no effect to clear mutagenicity. In particular, the extract of all 11 urban soil samples demonstrated mutagenic activity, while the extracts of 10 of the 15 suburban samples showed mutagenicity. On the other hand, the extract of only one of the 7 agricultural samples studied induced mutations, and none of the 18 natural or forest-soil samples investigated produced mutagenic extracts. These findings seem to indicate the crucial influence of the diffuse pollution originating from different human activities on the mutagenic potency of urban soil samples. These findings make it possible to classify the soils according to their mutagenic potency. No clear correlation was found between the mutagenicity detected in soil extracts and the measured polycyclic aromatic hydrocarbon (PAH) content of the soils investigated.     

Analysis of Diesel Fuel Contamination in Soils by Near-Infrared Reflectance Spectrometry and Solid Phase Microextraction-Gas Chromatography

A feasibility study was undertaken to determine whether the rapid, nondestructive analytical technology, near-infrared reflectance spectrometry (NIRS) could be used to predict total petroleum hydrocarbon (TPH) in contaminated soil. Hydrocarbon concentrations were determined on samples of diesel-contaminated soils by the solid phase microextraction-gas chromatography (SPME-GC) method. The same samples were then scanned for near-infrared reflectance spectrometry over the wavelength range 1100 to 2498 nm. Calibrations were developed between the NIR spectral data and the reference SPME-GC chemical data using stepwise multiple linear regression. Linear regression relationships between NIR-predicted TPH concentrations and reference data had r² of 0.68 and 0.72. These results indicate that the combination of NIRS and SPME-GC shows promise as a method for rapid estimation of TPH in soil. A major hurdle in the evaluation of methodology for hydrocarbons residues in soil is the challenge posed by the weathering of such residues.     

Soil analysis by means of a 1:2 volume extract

Summary The use of the 1:5 weight extract in soil analysis presents some difficulties. Conductivity determinations as a means of assessing the salt status are unreliable for those soils containing appreciable amounts of gypsum, and it is also desirable that the soil organic matter content be known when interpreting the analytical data. These objections are largely overcome by using saturation extracts. The principal drawback with this method is, however, its laborious procedure. In an investigation at the Experiment Station at Naaldwijk very good results were obtained using an extract made by adding sufficient field-moist soil to two parts of water until the total volume had increased by one part (1:2 volume extract). The analytical data for conductivity, chloride, nitrogen, phosphate, potassium and magnesium in this extract were very closely related to data obtained by the saturation extract. The correlation coefficientes being between 0.943 and 0.982. The weight ratio water: soil of the 1:2 volume extract was highly correlated with the organic matter content. In soils low in organic matter the ratio was about 1:1, and with very peaty soils (40 per cent organic matter) about 3 1/2:1. For precise preparation of the 1:2 volume extract it is necessary to use soil samples at field capacity. A visual check on this condition appeared to be possible.     

Detection and quantification of copper-denitrifying bacteria by quantitative competitive PCR

We developed a quantitative competitive PCR (QC-PCR) system to detect and quantify copper-denitrifying bacteria in environmental samples. The primers were specific to copper-dependent nitrite reductase gene (nirK). We were able to detect about 200 copeis of nirK in the presence of abundant non-specific target DNA and about 1.2 x 10(3)Pseudomonas sp. G-179 cells from one gram of sterilized soil by PCR amplification. A 312-bp nirK internal standard (IS) was constructed, which showed very similar amplification efficiency with the target nirKfragment (349 bp) over 4 orders of magnitude (10(3)-10(6)). The accuracy of this system was evaluated by quantifying various known amount of nirK DNA. The linear regressions were obtained with a R(2) of 0.9867 for 10(3)copies of nirK, 0.9917 for 10(4) copies of nirK, 0.9899 for 10(5) copies of nirK and 0.9846 for 10(6) copies of nirK. A high correlation between measured nirK and calculated nirK (slope of 1.0398, R(2)=0.9992) demonstrated that an accurate measurement could be achieved with this system. Using this method, we quantified nirK in several A-horizon and stream sediment samples from eastern Tennessee. In general, the abundance of nirK was in the range of 10(8)-10(9) copies g soil(-1) dry weight. The nirK content in the soil samples appeared correlated with NH(4)(N) content in the soil. The activities of copper-denitrifying bacteria were evaluated by quantifying cDNA of nirK. In most of sample examined, the content of nirK cDNA was less than 10(5) copies g soil(-1) dry weight. Higher nirK cDNA content (>10(6) copies g soil(-1) dry weight) was detected from both sediment samples at Rattlebox Creek and the Walker Branch West Ridge. Although the stream sediment samples at the Walker Branch West Ridge contained less half of the nirK gene content as compared to A-horizon sample, the activities of copper-denitrifying bacteria were almost 600 times higher than in the A-horizon sample.     

Spatial analysis of archaeal community structure in grassland soil

The complex structure of soil and the heterogeneity of resources available to microorganisms have implications for sampling regimens when the structure and diversity of microbial communities are analyzed. To assess the heterogeneity in community structure, archaeal communities, which typically contain sequences belonging to the nonthermophilic Crenarchaeota, were examined at two contrasting spatial scales by using PCR-denaturing gradient gel electrophoresis (DGGE) analysis followed by unweighted pair group method with arithmetic mean analysis of 16S rRNA- and ribosomal DNA-derived profiles. A macroscale analysis was carried out with soil cores taken at 2-m intervals along triplicate 8-m transects from both managed (improved) and natural (unimproved) grassland rhizosphere soils. A microscale analysis was carried out with a single soil core by assessing the effects of both sample size (10, 1, and 0.1 g) and distance between samples. The much reduced complexity of archaeal profiles compared to the complexity typical of the bacterial community facilitated visual comparison of profiles based on band presence and revealed different levels of heterogeneity between sets of samples. At the macroscale level, heterogeneity over the transect could not be related to grassland type. Substantial heterogeneity was observed across both improved and unimproved transects, except for one improved transect that exhibited substantial homogeneity, so that profiles for a single core were largely representative of the entire transect. At the smaller scale, the heterogeneity of the archaeal community structure varied with sample size within a single 8- by 8-cm core. The archaeal DGGE profiles for replicate 10-g soil samples were similar, while those for 1-g samples and 0.1-g samples showed greater heterogeneity. In addition, there was no relationship between the archaeal profiles and the distance between 1- or 0.1-g samples, although relationships between community structure and distance of separation may occur at a smaller scale. Our findings demonstrate the care required when workers attempt to obtain a representative picture of microbial community structure in the soil environment.     

Spatial Analysis of Archaeal Community Structure in Grassland Soil

The complex structure of soil and the heterogeneity of resources available to microorganisms have implications for sampling regimens when the structure and diversity of microbial communities are analyzed. To assess the heterogeneity in community structure, archaeal communities, which typically contain sequences belonging to the nonthermophilic Crenarchaeota, were examined at two contrasting spatial scales by using PCR-denaturing gradient gel electrophoresis (DGGE) analysis followed by unweighted pair group method with arithmetic mean analysis of 16S rRNA- and ribosomal DNA-derived profiles. A macroscale analysis was carried out with soil cores taken at 2-m intervals along triplicate 8-m transects from both managed (improved) and natural (unimproved) grassland rhizosphere soils. A microscale analysis was carried out with a single soil core by assessing the effects of both sample size (10, 1, and 0.1 g) and distance between samples. The much reduced complexity of archaeal profiles compared to the complexity typical of the bacterial community facilitated visual comparison of profiles based on band presence and revealed different levels of heterogeneity between sets of samples. At the macroscale level, heterogeneity over the transect could not be related to grassland type. Substantial heterogeneity was observed across both improved and unimproved transects, except for one improved transect that exhibited substantial homogeneity, so that profiles for a single core were largely representative of the entire transect. At the smaller scale, the heterogeneity of the archaeal community structure varied with sample size within a single 8- by 8-cm core. The archaeal DGGE profiles for replicate 10-g soil samples were similar, while those for 1-g samples and 0.1-g samples showed greater heterogeneity. In addition, there was no relationship between the archaeal profiles and the distance between 1- or 0.1-g samples, although relationships between community structure and distance of separation may occur at a smaller scale. Our findings demonstrate the care required when workers attempt to obtain a representative picture of microbial community structure in the soil environment.     

Spatial Analysis of Soil Organic Carbon in Zhifanggou Catchment of the Loess Plateau

Soil organic carbon (SOC) reflects soil quality and plays a critical role in soil protection, food safety, and global climate changes. This study involved grid sampling at different depths (6 layers) between 0 and 100 cm in a catchment. A total of 1282 soil samples were collected from 215 plots over 8.27 km². A combination of conventional analytical methods and geostatistical methods were used to analyze the data for spatial variability and soil carbon content patterns. The mean SOC content in the 1282 samples from the study field was 3.08 g·kg⁻¹. The SOC content of each layer decreased with increasing soil depth by a power function relationship. The SOC content of each layer was moderately variable and followed a lognormal distribution. The semi-variograms of the SOC contents of the six different layers were fit with the following models: exponential, spherical, exponential, Gaussian, exponential, and exponential, respectively. A moderate spatial dependence was observed in the 0–10 and 10–20 cm layers, which resulted from stochastic and structural factors. The spatial distribution of SOC content in the four layers between 20 and 100 cm exhibit were mainly restricted by structural factors. Correlations within each layer were observed between 234 and 562 m. A classical Kriging interpolation was used to directly visualize the spatial distribution of SOC in the catchment. The variability in spatial distribution was related to topography, land use type, and human activity. Finally, the vertical distribution of SOC decreased. Our results suggest that the ordinary Kriging interpolation can directly reveal the spatial distribution of SOC and the sample distance about this study is sufficient for interpolation or plotting. More research is needed, however, to clarify the spatial variability on the bigger scale and better understand the factors controlling spatial variability of soil carbon in the Loess Plateau region.     

A palaeoecological model for the interpretation of wild plant species

The interpretation of subfossil records of wild plant species with respect to both environmental conditions and past vegetation is complicated by the following: (1) production and dispersal of plant remains including diaspores, (2) the formation of the soil flora, (3) taphonomic processes and differential preservation that act on subfossil assemblages and (4) methods applied to produce subfossil records. Whereas the similarity between recent plant communities and seed banks is often weak, the relationship between past vegetation and subfossil assemblages is still more complicated. It is therefore unlikely that macrofossil assemblages derived from soil samples can be considered as pure samples representing particular palaeobiocoenoses. The assumption that plant communities, in the past, may have been in some way aberrant with respect to composition and that the ecological ranges of species varied during the Quaternary has to be rejected, if not based on well considered assumptions or evidence from pure samples. Only if a sufficient number of suitable studies is available, which enable evaluation between all kinds of plant communities and their respective seed floras, can progress be made with regard to the reconstruction of past vegetation and environmental conditions. As long as these data are not available, the ecological interpretation of particular subfossil assemblages isolated from soil samples has to be carefully evaluated within their particular context.     

Habitat associations of two entomopathogenic nematodes: a quantitative study using real-time quantitative polymerase chain reactions

1. Despite nematodes being the most abundant animals on earth, very few animal ecologists study them, probably because of the difficulties of identifying them to species by morphological methods. 2. A group of nematodes that are important both ecologically and economically is the entomopathogenic nematodes, which play a key role in regulating soil food webs and are sold throughout the world as biological insecticides, yet for which very little is known of their population ecology. 3. A novel detection and quantification method was developed for soil nematodes using real-time polymerase chain reaction (PCR), and the technique was used to estimate numbers of two closely related species of entomopathogenic nematodes, Steinernema kraussei and S. affine in 50 soil samples from 10 sites in Scotland representing two distinct habitats (woodland and grassland). 4. There was a high degree of correlation between our molecular and traditional morphological estimates of population size and our data clearly showed that Steinernema affine occurred only in grassland areas, whereas S. kraussei was found in grassland and woodland samples to a similar degree. 5. Real-time PCR offers a rapid and accurate method of detecting individual nematode species from soil samples without the need for a specialist taxonomist, and has much potential for use in studies of nematode population ecology.     

Detection and quantification of Escherichia coli O157:H7 in environmental samples by real-time PCR

AIMS: To apply the real-time Polymerase chain reaction (PCR) method to detect and quantify Escherichia coli O157:H7 in soil, manure, faeces and dairy waste washwater. METHODS AND RESULTS: Soil samples were spiked with E. coli O157:H7 and subjected to a single enrichment step prior to multiplex PCR. Other environmental samples suspected of harbouring E.coli O157:H7 were also analysed. The sensitivity of the primers was confirmed with DNA from E.coli O157:H7 strain 3081 spiked into soil by multiplex PCR assay. A linear relationship was measured between the fluorescence threshold cycle (C T ) value and colony counts (CFU ml(-1)) in spiked soil and other environmental samples. The detection limit for E.coli O157:H7 in the real-time PCR assay was 3.5 x 10(3) CFU ml(-1) in pure culture and 2.6 x 10(4) CFU g(-1) in the environmental samples. Use of a 16-h enrichment step for spiked samples enabled detection of <10 CFU g(-1) soil. E. coli colony counts as determined by the real-time PCR assay, were in the range of 2.0 x 10(2) to 6.0 x 10(5) CFU PCR (-1) in manure, faeces and waste washwater. CONCLUSIONS: The real-time PCR-based assay enabled sensitive and rapid quantification of E. coli O157:H7 in soil and other environmental samples. SIGNIFICANCE AND IMPACT OF THE STUDY: The ability to quantitatively determine cell counts of E.coli O157:H7 in large numbers of environmental samples, represents considerable advancement in the area of pathogen quantification for risk assessment and transport studies.