Horizontal gene transfer of atrazine-degrading genes (atz) from Agrobacterium tumefaciens St96-4 pADP1::Tn5 to bacteria of maize-cultivated soil

The plasmid pADP1::Tn5 derived from pADP1[Atr+] carrying a Tn5 transposon conferring kanamycin and streptomycin resistances was constructed and introduced in Agrobacterium tumefaciens St96-4. This genetically modified strain was inoculated (approximately 10(8) cfu g(-1)) in potted soils planted with maize and treated or not with atrazine (1.5 mg kg(-1)). Bulk and maize rhizosphere soils were sampled 39 days after planting to look for soil indigenous bacteria that had acquired pADP1::Tn5. Four transconjugants were isolated from four different soil samples. The estimated transfer frequency of pADP1::Tn5 was 10(-4) per donor. Maize rhizosphere and atrazine treatment had no obvious effect on pADP1::Tn5 transfer frequency. The sequencing of the 16S rDNA sequences of the transconjugants revealed that they were almost identical and highly similar to that of Variovorax spp (97%). In addition, their characterization suggested that the atzA and atzB genes had been transferred from pADP1::Tn5 to the bacterial chromosome in two of the four transconjugants. These data suggest that the atz degrading genes are horizontally transferred in soil and possibly subjected to gene rearrangement.     

Degradation of simazine by microorganisms isolated from soils of Spanish olive fields

The capability of the microbial flora isolated from an olive field soil from Andalusia to mineralize simazine has been analyzed. From this soil, a group of bacteria capable of degrading 60 mg simazine litre(-1) in less than a week has been isolated. These microorganisms showed a low capacity for degrading this herbicide to carbon dioxide. When total DNA was isolated from this group of bacteria, we were able to detect by PCR the presence of only the atzC and the trzN genes. Some components of this bacterial population have been identified by sequencing of specific fragments from bacterial 16S rDNA, including Variovorax sp, Pseudoxanthomonas mexicana Thierry et al, Acidovorax sp and Methylopila capsulata Doronina et al. These data suggest that this consortium of bacteria performs an incomplete degradation of the simazine     

Impact of maize mucilage on atrazine mineralization and atzC abundance

Soil was amended with maize mucilage, a major rhizodeposit, to study its role on the number of culturable soil micro-organisms, the structure of the bacterial community, atrazine mineralization and atzC abundance. The maximal percentage of atrazine mineralization was lower for mucilage-amended than for water-amended soil. Total culturable soil bacteria and 16S rDNA copy number, measured by RT-PCR, presented similar values and were not significantly (P < 0.05) different among treatments. Mucilage applied at a rate of 70 microg C g(-1) dry soil day(-1) over two weeks did not modify the abundance of the total soil microflora. Global structure of soil bacterial communities revealed by RISA analysis was not modified by maize mucilage amendment. Abundance of atzC sequence was only augmented by mucilage addition at the beginning of the experiment. However, this increase was not sustainable in time, as atzC copy number increased in water-amended soil which, in turn, corresponded with the higher percentage of atrazine mineralization observed in this soil. Maize mucilage amendment alone contributed only to minor changes in the atrazine-degrading community in the studied soil.     

The ‘habitat backbone’ as strategy to conserve pioneer species in dynamic port habitats: lessons from the natterjack toad (Bufo calamita) in the Port of Antwerp (Belgium)

Biodiversity conservation in economic areas like ports has recently become more important in the European Union due to a stricter interpretation of nature protection laws. In this study we develop a planning and design strategy—the ‘habitat backbone’—with which to support the long-term survival of pioneer species that occur in ports and have low dispersal abilities. For those species, long-term survival in port areas is uncertain because supply of their habitats (on vacant lots) is capricious and depends on land use dynamics. By gaining knowledge about spatial and temporal characteristics of these dynamics we were able to develop a solution to conserve such species. Our solution is based on the creation of permanent habitat—defined as a ‘backbone’—on (semi-) public land with an overall carrying capacity sufficient to support persistent populations. This best ensures long-term survival, and the backbone may also act as refugium. Satellite populations that emerge on adjacent vacant lots will thereby add to the persistence of the overall metapopulation. Management of permanent habitat is focused on retaining early-successional stages of vegetation. Implementing this strategy in the case of the natterjack toad in the Port of Antwerp taught us that realization of a habitat backbone is possible only if landowners, local governments and environmental NGOs cooperate. In the case at hand, such cooperation resulted in a plan that should ensure a coherent and persistent habitat network in which a chorus of some 1,400 natterjack toads could be accommodated—more than the number of toads currently observed. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Congenital lacrimal fistula in two prim'Holstein calves

Two 4‐ and 8‐month‐old prim'Holstein calves were presented for chronic epiphora. Examination of the affected eyes revealed an abnormal duct opening inferonasal to the medial canthus. A diagnosis of congenital lacrimal fistula was made based on conventional and computed tomographic‐dacryocystography findings. These revealed an ectopic channel connecting the nasolacrimal duct to the skin opening near the medial canthus. Both of the calves were surgically treated with resection and closure of the ectopic duct and placement of a nasolacrimal stent.     

A focus on the European hamster to illustrate how to monitor endangered species

Agriculture intensification, marked by the generalization of crop monoculture, by the increase in plot size and by the reduction of plant diversity, has led to huge decline in wildlife in European farmlands. In such habitat, research has long been biased towards birds and invertebrates, while very few studies have investigated the effect on small mammals. Considering the European hamster, Cricetus cricetus, we therefore review the different techniques that can be used to investigate the impact of environmental changes and conservation measures in small and endangered wild mammals. We suggest that only a multidisciplinary approach will allow exploration of these effects, combining experimental laboratory work on captive‐bred animals with the monitoring of wild individuals. In particular, individual energy balance has to be investigated and measured as accurately as possible, through either biochemical or bio‐logging techniques. It is, indeed, the most affected physiological trait in a changing environment, as it determines both the reproductive output and the survival of the individual. We also discuss the inconvenience of capture–release approaches for such an endangered species and emphasize the disturbance that experimental protocols could impose on the hamster.     

Does moder development along a pure beech (Fagus sylvatica L.) chronosequence result from changes in litter production or in decomposition rates?

The development of temperate deciduous and conifers forests stands usually results in accumulation of forest floor organic matter and a shift from mull to moder humus forms. It has been suggested that an increase in nutrient uptake by trees during their rapid growth phase leads to topsoil acidification, decrease in earthworm density and thereby a decrease in litter turnover. The focus of this paper was to examine if the mull-moder shift with forest ageing results from higher leaf litter production and/or lower litter decay rates. The objectives of this research were to determine (1) changes in macro-morphological properties of humus forms, leaf litter production, litter decay rates, soil nutrients content and pH along a 130-year pure beech (Fagus sylvatica L.) chronosequence in Normandy (Northwest France), (2) if humus form varied from mull to moder with increasing stand age, and (3) if a shift from mull to moder resulted from increased litter production, decreased litter decay rates, or both. Annual litter production did not change significantly along the chronosequence (mean 2.41 t ha⁻¹). In contrast, litter decay rates decreased significantly during the rapid growth phase of trees. In consequence, the litter turnover time (1/k) was lower in the youngest stands (20 months) compared to the oldest ones (31 months). Even in the absence of a significant pattern of variation, litter production was positively correlated with the thickness of the OF (Oi) horizon. In contrast, litter decay was strongly negatively correlated with maximum thickness of the OH (Oa) horizon, suggesting that the appearance of the humification layer was mainly due to a decrease in litter decay rate. We did not find significant changes in the main properties of the organo-mineral horizon, suggesting that soil nutrient availability may not directly affect litter dynamics. We concluded that moder development along the chronosequence resulted in decreasing litter decay rates during the aggradation phase while litter production was stable. Further studies are required to identify the ecological factors responsible for moder development along forest ageing.     

Niche partitioning based on soil type and climate at the landscape scale in a community of plant-feeding nematodes

Understanding how environmental factors structure communities is important in conservation biology and ecosystem management. The aim of this study was to test the hypothesis that a plant-feeding nematode community composed of six species is structured by soil type and climate at the landscape scale, and that niche partitioning via these factors is consistent with the coexistence of the species. Martinique has an impressive diversity of abiotic factors (climate and soil type) over a relatively small land area, which facilitates the study of how soil type and climate affect the nematode community.We conducted this study by building an extensive data set containing the abundance of each nematode species on banana (3708 samples and 5,673,705 nematodes) in a wide range of sites in Martinique. The data set also contained environmental data (soil, climate) and plantation age. We analyzed the response of each nematode species to climate and soil type with a generalized linear model in order to understand whether niche partitioning of factors could contribute to the coexistence of the nematode species.Temperature, rainfall, soil type, and plantation age significantly affected the abundance of the six nematode species. While some pairs of species shared the same environmental niches, other showed clear niche partitioning along climatic axes. The two dominant species, Radopholus similis and Helicotylenchus multicinctus, have similar convergent ecological niches regarding climate, soil type, plantation age, and host range. These two species, which often co-occur, probably have different resources at the root scale. Soil type and climate structure plant-feeding nematode species community at the island scale. Further studies need to evaluate coexistence at the root scale among dominant species.     

Polybrominated Diphenyl Ether Dynamics in Ambient Air and Atmospheric Bulk/Wet Deposition in Downtown Paris (France)

This study reports on the polybrominated diphenyl ether (PBDE) atmospheric dynamics in the dense urban environment of downtown Paris (France). Eight PBDE congeners (BDE-28, BDE-47, BDE-100, BDE-99, BDE-154, BDE-153, BDE-183 and BDE-209) were simultaneously analysed in bulk and wet atmospheric deposition, as well as in ambient air (gaseous/particulate phases), twice a month over a 12-month period (May 2008–May 2009). The total air concentration of Σ 8PBDEs ranged between 12 and 185 pg m⁻³, and the seasonal variations of PBDE levels were controlled by air temperature (except for BDE-209). Regarding bulk deposition, Σ 8PBDE flux was in the range 5–94 ng m⁻² day⁻¹, and it was positively correlated with atmospheric particulate phase PBDE concentrations. Meanwhile, the measured wet deposition flux of Σ 8PBDE ranged between 2 and 24 ng m⁻² day⁻¹, and its median contribution to bulk deposition was 39% only, which highlights the importance of dry deposition.