Physico-chemical characteristics of topsoil for contrasted forest, agricultural, urban and industrial land uses in France.

Soil quality is related to soil characteristics such as fertility and contamination. The aim of this study is to assess the effect of land use on these soil characteristics and to confirm the following anthropisation gradient: (i) forest, (ii) grassland, (iii) cultivated, (iv) orchard and vineyard, (v) urban vegetable garden, and (vi) SUITMA (urban, industrial, traffic, mining and military areas). A database comprising the characteristics of 2451 soils has been constituted. In order to compare the topsoils from six contrasting land uses, a principal components analysis (PCA) was performed on nine geochemical variables (C, N, pH, POlsen, total Cd, Cu, Ni, Pb, Zn). The first axis of the PCA is interpreted as a global increase of topsoil metallic elements along the anthropisation gradient. Axis 2 reflects the variability of fertility levels. Human activity increases the pressure on soils along the proposed gradient according to six different distribution patterns. This better knowledge of topsoil quality and its dependence on current land use should therefore help to manage and preserve the soil mantle.

Improving soil bacterial taxa-area relationships assessment using DNA meta-barcoding.

The evaluation of the taxa-area relationship (TAR) with molecular fingerprinting data demonstrated the spatial structuration of soil microorganisms and provided insights into the processes shaping their diversity. The increasing use of massive sequencing technologies in biodiversity investigations has now raised the question of the advantages of such technologies over the fingerprinting approach for elucidation of the determinism of soil microbial community assembly in broad-scale biogeographic studies. Our objectives in this study were to compare DNA fingerprinting and meta-barcoding approaches for evaluating soil bacterial TAR and the determinism of soil bacterial community assembly on a broad scale. This comparison was performed on 392 soil samples from four French geographic regions with different levels of environmental heterogeneity. Both molecular approaches demonstrated a TAR with a significant slope but, because of its more sensitive description of soil bacterial community richness, meta-barcoding provided significantly higher and more accurate estimates of turnover rates. Both approaches were useful in evidencing the processes shaping bacterial diversity variations on a broad scale. When different taxonomic resolutions were considered for meta-barcoding data, they significantly influenced the estimation of turnover rates but not the relative importance of each component process. Altogether, DNA meta-barcoding provides a more accurate evaluation of the TAR and may lead to re-examination of the processes shaping soil bacterial community assembly. This should provide new insights into soil microbial ecology in the context of sustainable use of soil resources.

Detection and enumeration of Pseudomonas aeruginosa in soil and manure assessed by an ecfX qPCR assay.

AIMS: To develop a qPCR approach for the detection of Pseudomonas aeruginosa in soil and manure and explore its efficacy and limitations compared with that of a classical culture-dependent approach. METHODS AND RESULTS: A Ps. aeruginosa ecfX qPCR assay was developed. This assay was optimized for soils of contrasting physico-chemical properties and evidenced a three-log dynamic range of detection [5 × 10(4)  - 5 × 10(6) cells (g drywt soil)(-1) ] in inoculated microcosms. Sensitivity was determined to be around 5 × 10(4)  cells (g drywt soil)(-1) . In parallel, the minimum detection limit was estimated in the range of 10-100 CFU (g drywt soil)(-1) using a culture-dependent approach based on the use of a selective medium (cetrimide agar base medium supplemented with nalidixic acid), coupled to ecfX gene amplification to confirm isolate identity. These soil samples led to the growth of abundant non-Ps. aeruginosa colonies mainly belonging to other Pseudomonas species but also some beta-Proteobacteria. These bacteria strongly impacted the detection threshold of this approach. Efficacy of these approaches was compared for Ps. aeruginosa enumeration among manure and agricultural soil samples from various sites in France, Tunisia and Burkina Faso. CONCLUSIONS: The developed qPCR assay enabled a specific detection of Ps. aeruginosa in soil and manure samples. The culture-based approach was usually found more sensitive than the qPCR assay. However, abundance of non-Ps. aeruginosa species among the indigenous communities able to grow on the selective medium affected the sensitivity of this latter approach. SIGNIFICANCE AND IMPACT OF THE STUDY: This study describes the first specific and sensitive qPCR assay for the detection and enumeration of Ps. aeruginosa in soil and manure and shows its complementarity with a culture-based approach.

Turnover of soil bacterial diversity driven by wide-scale environmental heterogeneity.

Spatial scaling and determinism of the wide-scale distribution of macroorganism diversity has been largely demonstrated over a century. For microorganisms, and especially for soil bacteria, this fundamental question requires more thorough investigation, as little information has been reported to date. Here by applying the taxa-area relationship to the largest spatially explicit soil sampling available in France (2,085 soils, area covered ~5.3 × 10(5) km(2)) and developing an innovative evaluation of the habitat-area relationship, we show that the turnover rate of bacterial diversity in soils on a wide scale is highly significant and strongly correlated with the turnover rate of soil habitat. As the diversity of micro- and macroorganisms appears to be driven by similar processes (dispersal and selection), maintaining diverse and spatially structured habitats is essential for soil biological patrimony and the resulting ecosystem services.

Molecular and quantitative signatures of biparental inbreeding depression in the self-incompatible tree species Prunus avium.

Genetic diversity strongly influences populations' adaptability to changing environments and therefore survival. Sustainable forest management practices have multiple roles including conservation of genetic resources and timber production. In this study, we aimed at better understanding the variation in genetic diversity among adult and offspring individuals, and the effects of mating system on offspring survival and growth in wild cherry, Prunus avium. We analysed adult trees and open pollinated seed-families from three stands in Germany at eight microsatellite loci and one incompatibility system locus and conducted paternity analyses. Seed viability testing and seed sowing in a nursery allowed further testing for the effects of pollen donor diversity and genetic similarity between mates on the offspring performance at the seed and seedling stages. Our results were contrasting across stands. Loss of genetic diversity from adult to seedling stages and positive effect of mate diversity on offspring performance occurred in one stand only, whereas biparental inbreeding depression and significant decrease in fixation index from adults to seedlings was detected in two stands. We discussed the effects of stand genetic diversity on the magnitude of biparental inbreeding depression at several life-stages and its consequences on the management of genetic resources in P. avium.

Spatial distribution of Lindane concentration in topsoil across France.

Lindane [γ-hexachlorocyclohexane (γ-HCH)] is an organochlorine pesticide with toxic effects on humans. It is bioaccumulative and can remain in soils for long periods, and although its use for crop spraying was banned in France in 1998, it is possible that residues from before this time remain in the soil. The RMQS soil monitoring network consists of soil samples from 2200 sites on a 16 km regular grid across France, collected between 2002 and 2009. We use 726 measurements of the Lindane concentration in these samples to (i) investigate the main explanatory factors for its spatial distribution across France, and (ii) map this distribution. Geostatistics provides an appropriate framework to analyze our spatial dataset, though two issues regarding the data are worth special consideration: first, the harmonization of two subsets of the data (which were analyzed using different measurement processes), and second, the large proportion of data from one of these subsets that fell below a limit of quantification. We deal with these issues using recent methodological developments in geostatistics. Results demonstrate the importance of land use and rainfall for explaining part of the variability of Lindane across France: land use due to the past direct input of Lindane on cropland and its subsequent persistence in the soil, and rainfall due to the re-deposition of volatilized Lindane. Maps show the concentrations to be generally largest in the north and northwest of France, areas of more intensive agricultural land. We also compare levels to some contamination thresholds taken from the literature, and present maps showing the probability of Lindane concentrations exceeding these thresholds across France. These maps could be used as guidelines for deciding which areas require further sampling before some possible remediation strategy could be applied.

Use of DNA fingerprints to control the origin of sapelli timber (Entandrophragma cylindricum) at the forest concession level in Cameroon.

Illegal logging and associated trade are the cause of many economic and ecological problems both in producer and in consumer countries. There are an increasing number of national and international regulations in place that call for efficient timber tracking systems. We present results of a pilot study of a DNA-based method to control the geographical origin of timber in forest concessions in Cameroon. We addressed genetic differentiation at five nuclear microsatellite loci in seven sapelli (Entandrophragma cylindricum, Meliaceae) populations located in three forest concessions in Eastern Cameroon. In the framework of a blind test, seven anonymous timber sample sets were analysed at three microsatellite loci and compared to the genetic reference data of the forest concessions in Cameroon. Our results show that genetic differentiation was low within and among concessions. Combining the results of Bayesian genetic assignment method and exclusion test, we could determine that the timber stemmed or did not stem from the focus forest concession in six out of the seven blind sample sets. We further discuss the accuracy of the presented method and draw conclusions for a better sampling and genotyping strategy. Our work provides clear evidence that the use of genetic fingerprints is a useful tool to fight against illegal logging.

Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale.

Little information is available regarding the landscape-scale distribution of microbial communities and its environmental determinants. However, a landscape perspective is needed to understand the relative importance of local and regional factors and land management for the microbial communities and the ecosystem services they provide. In the most comprehensive analysis of spatial patterns of microbial communities to date, we investigated the distribution of functional microbial communities involved in N-cycling and of the total bacterial and crenarchaeal communities over 107 sites in Burgundy, a 31,500 km(2) region of France, using a 16 × 16 km(2) sampling grid. At each sampling site, the abundance of total bacteria, crenarchaea, nitrate reducers, denitrifiers- and ammonia oxidizers were estimated by quantitative PCR and 42 soil physico-chemical properties were measured. The relative contributions of land use, spatial distance, climatic conditions, time, and soil physico-chemical properties to the spatial distribution of the different communities were analyzed by canonical variation partitioning. Our results indicate that 43-85% of the spatial variation in community abundances could be explained by the measured environmental parameters, with soil chemical properties (mostly pH) being the main driver. We found spatial autocorrelation up to 739 km and used geostatistical modelling to generate predictive maps of the distribution of microbial communities at the landscape scale. The present study highlights the potential of a spatially explicit approach for microbial ecology to identify the overarching factors driving the spatial heterogeneity of microbial communities even at the landscape scale.

Low levels of realized seed and pollen gene flow and strong spatial genetic structure in a small, isolated and fragmented population of the tropical tree Copaifera langsdorffii Desf.

Over the past century, the Brazilian Atlantic forest has been reduced to small, isolated fragments of forest. Reproductive isolation theories predict a loss of genetic diversity and increases in inbreeding and spatial genetic structure (SGS) in such populations. We analysed eight microsatellite loci to investigate the pollen and seed dispersal patterns, genetic diversity, inbreeding and SGS of the tropical tree Copaifera langsdorffii in a small (4.8 ha), isolated population. All 112 adult trees and 128 seedlings found in the stand were sampled, mapped and genotyped. Seedlings had significantly lower levels of genetic diversity (A=16.5±0.45, mean±95% s.e.; H(e)=0.838±0.006) than did adult trees (A=23.2±0.81; H(e)=0.893±0.030). Parentage analysis did not indicate any seed immigration (m(seeds)=0) and the pollen immigration rate was very low (m(pollen)=0.047). The average distance of realized pollen dispersal within the stand was 94 m, with 81% of the pollen travelling <150 m. A significant negative correlation was found between the frequency and distance of pollen dispersal (r=-0.79, P<0.01), indicating that short-distance pollinations were more frequent. A significant SGS for both adults (∼50 m) and seedlings (∼20 m) was also found, indicating that most of the seeds were dispersed over short distances. The results suggested that the spatial isolation of populations by habitat fragmentation can restrict seed and pollen gene flow, increase SGS and affect the genetic diversity of future generations.

Multivariate analysis of the spatial patterns of 8 trace elements using the French soil monitoring network data.

Geostatistical and spatially constrained multivariate analysis methods (MULTISPATI-PCA) have been applied at the scale of France to differentiate the influence of natural background from the pollution due to human activities on the content of 8 trace elements in the topsoil. The results of MULTISPATI-PCA evidence strong spatial structures attributed to different natural and artificial processes. The first axis can be interpreted as an axis of global richness in trace elements. Axis 2 reflects geochemical anomalies in Tl and Pb. Axis 3 exhibits on one hand natural pedogeogenic anomalies and on the other hand, it shows high values attributable to anthropogenic contamination. Finally, axis 4 is driven by anthropogenic copper contamination. At the French territory scale, we show that the main factors controlling trace elements distribution in the topsoil are soil texture, variations in parent material geology and weathering, and various anthropogenic sources.

Within/between population crosses reveal genetic basis for siring success in Silene latifolia (Caryophyllaceae).

Divergence at reproductive traits can generate barriers among populations, and may result from several mechanisms, including drift, local selection and co-adaptation between the sexes. Intersexual co-adaptation can arise through sexually antagonistic co-evolution, a timely hypothesis addressed in animals but, to our knowledge, not yet in flowering plants. We investigated whether male and female population of origin affected pollen competition success, offspring fitness and sex ratio in crosses within/between six genetically differentiated populations of the white campion, Silene latifolia. Each female was crossed with pollen from one focus male from the same population, and pollen from two focus males from two distinct populations, both as single-donor and two-donor crosses against a fixed tester male with a 2-h interpollination interval (n = 288 crosses). We analysed paternity with microsatellite DNA. Male populations of origin significantly differed for siring success and in vitro pollen germination rates. In vitro pollen germination rate was heritable. Siring success also depended on sex ratio in the female family of origin, but only in between-population crosses. In some female populations, two-donor crosses produced less female-biased sex ratios compared with single-donor crosses, yet in other female populations the reverse was true. Offspring sex ratio varied with donor number, depending on the female population. Within/between population crosses did not differ significantly in seed set or offspring fitness, nor were siring success and offspring fitness significantly correlated. Altogether this suggests reproductive divergence for traits affecting pollen competition in S. latifolia.

Geostatistical assessment of Pb in soil around Paris, France.

This paper presents a survey on soil Pb contamination around Paris (France) using the French soil monitoring network. The first aim of this study is to estimate the total amount of anthropogenic Pb inputs in soils and to distinguish Pb due to diffuse pollution from geochemical background Pb. Secondly, this study tries to find the main controlling factors of the spatial distribution of anthropogenic Pb. We used the technique of relative topsoil enhancement to evaluate the anthropogenic stock of Pb and we performed lognormal kriging to map Pb regional distribution. The results show a strong gradient of anthropogenic stock of Pb around the urban Paris area. We estimate a total amount of anthropogenic stock of Pb close to 143,000 metric tons, which corresponds to an average accumulation of 5.9 t km(-2). Our study suggests that a grid-based survey can help to quantify diffuse Pb contamination by using robust techniques of calculation and that it might also be used to validate predictions of deposition models.

Tumour necrosis factor, IL-1 and IL-6 in bronchoalveolar washings and their in vitro production during Nippostrongylus brasiliensis infection.

Bronchoalveolar washings (BAW) were obtained from rats primarily infected with N. brasiliensis during the early infection stage that coincides with the lung passage of the parasite and the recruitment of inflammatory cells. BAW were tested for IL-1, IL-6 and tumour necrosis factor (TNF) activities. We found that IL-1 production occurred only on day 1 post infection and ceased thereafter. IL-6 activity was present as from day 1 with a maximum on day 3 post infection and then returned to its normal levels on day 5 post infection. TNF activity was not recovered in BAW at any time of the early infection. Results obtained from the in vitro culture of BAW-adherent cells demonstrated that on day 1 post infection IL-1, but also large amounts of TNF were produced spontaneously, whereas IL-6 was continuously released. Bacterial lipopolysaccharide (LPS) stimulation of the cell culture resulted in an amplification of the cytokine production. Our results suggest that pulmonary cytokines detected in BAW were at least in part produced by alveolar macrophages. Furthermore, the kinetics of IL-1, TNF and IL-6 production show that these monokines are induced at different times during the course of infection, suggesting that cytokine production may follow different regulation patterns during the early phase of N. brasiliensis infection.