A study on identification of bacteria in environmental samples using single-cell Raman spectroscopy: feasibility and reference libraries

We report on our recent efforts towards identifying bacteria in environmental samples by means of Raman spectroscopy. We established a database of Raman spectra from bacteria submitted to various environmental conditions. This dataset was used to verify that Raman typing is possible from measurements performed in non-ideal conditions. Starting from the same dataset, we then varied the phenotype and matrix diversity content included in the reference library used to train the statistical model. The results show that it is possible to obtain models with an extended coverage of spectral variabilities, compared to environment-specific models trained on spectra from a restricted set of conditions. Broad coverage models are desirable for environmental samples since the exact conditions of the bacteria cannot be controlled.     

Impact of vegetated filter strips on sorbed herbicide concentrations and sorption equilibrium in agricultural plots

The objective was to investigate the impact of vegetated filter strips on exported atrazine and deethylatrazine concentrations [dissolved and sorbed to eroded sediments (>1.5?μm)], the deethylatrazine to atrazine ratio in water and sediments, the ratio of sorbed to dissolved herbicides in runoff and subsurface infiltration as well as field equilibrium state under natural climate during two seasons. We hypothesize that sorption equilibrium was not achieved in 2004 because of the short delay (<24?h) between herbicide application and the first rain event. In 2005, observations suggest that possible changing sorption equilibrium conditions were reached (20?days after atrazine application), especially for eroded sediments submitted to changing environmental conditions in subsurface. If confirmed by other experiments, this will raise the question of the representativeness of laboratory-determined soil sorption coefficients to predict the fate of pesticides.     

BRC4Env,a network of Biological Resource Centres for research in environmental and agricultural sciences

The Biological Resource Centre for the Environment BRC4Env is a network of Biological Resource Centres (BRCs) and collections whose leading objectives are to improve the visibility of genetic and biological resources maintained by its BRCs and collections and to facilitate their use by a large research community, from agriculture research to life sciences and environmental sciences. Its added value relies on sharing skills, harmonizing practices, triggering projects in comparative biology, and ultimately proposing a single-entry portal to facilitate access to documented samples, taking into account the partnership policies of research institutions as well as the legal frame which varies with the biological nature of resources. BRC4Env currently includes three BRCs: the Centre for Soil Genetic Resources of the platform GenoSol, in partnership with the European Conservatory of Soil Samples; the Egg Parasitoids Collection (EP-Coll); and the collection of ichthyological samples, Colisa. BRC4Env is also associated to several biological collections: microbial consortia (entomopathogenic bacteria, freshwater microalgae…), terrestrial arthropods, nematodes (plant parasitic, entomopathogenic, animal parasitic...), and small mammals. The BRCs and collections of BRC4Env are involved in partnership with academic scientists, as well as private companies, in the fields of medicinal mining, biocontrol, sustainable agriculture, and additional sectors. Moreover, the staff of the BRCs is involved in many training courses for students from French licence degree to Ph.D, engineers, as well as ongoing training.     

Pollution sources and occurrences of selected persistent organic pollutants (POPs) in sediments of the Mekong River delta, South Vietnam

The Mekong River delta is one of the largest agricultural land in the Southeast Asia. It plays a very important role for agriculture and fisheries in South Vietnam. However, comprehensive studies on the environmental pollution of persistent organic pollutants (POPs) in Mekong River delta have not been carried out in recent years. In this study, we collected sediment samples from the Mekong River to evaluate the contamination and ecological risks caused by several POPs. The contamination pattern of POPs was DDT>PCBs>CHLs>HCHs>HCB. DDTs are the most abundant pollutants, their concentration ranging from 0.01 to 110 ng/g dry wt, followed by PCBs (0.039-9.2 ng/g dry wt). DDTs and PCBs concentrations were higher in sediment from adjacent to urban areas than those from rural and agricultural sites, suggesting urban areas as important point sources of DDTs and PCBs to the river. Ratio of p,p'-DDT/p,p'-DDE was lower compared to those previously reported. However, some samples still had the ratio higher than 0.5, indicating recent input of DDT into the aquatic environments. This result shows that although the magnitude of contamination decreased over time, recent inputs of DDTs to the river still occur. Some sediment samples had concentrations of DDT compounds higher than the standards from the Canadian Environmental Quality Guideline, suggesting continuous monitoring for POPs contamination in the Mekong River is necessary.     

Influence of hydropower dams on the composition of the suspended and riverbank sediments in the Danube

Large hydropower dams have major impacts on flow regime, sediment transport and the characteristics of water and sediment in downstream rivers. The Gabcikovo and Iron Gate dams divide the studied Danube transect (rkm 1895-795) into three parts. In the Gabcikovo Reservoir (length of 40km) only a part of the incoming suspended sediments were deposited. Contrary to this, in the much larger Iron Gate backwater zone and reservoir (length of 310km) all riverine suspended sediments were deposited within the reservoir. Subsequently, suspended sediments were transported by tributaries into the Iron Gate backwater zone. Here they were modified by fractional sedimentation before they transgressed downstream via the dams. Compared with undammed Danube sections, Iron Gate reservoir sediment and suspended matter showed higher clay contents and different K/Ga and Metal/Ga ratios. These findings emphasize the importance of reservoir-river sediment-fractionation.     

Mission assurance policy and risk management in cybersecurity

Mission assurance policy and risk management are essential in enabling decision makers to ensure successful completion of missions by addressing the security status of cyber assets. This paper presents a novel mission assurance policy that adapts to the dynamic security status of all mission assets to quickly and automatically determine mission assurance level and to decide what changes are needed accordingly. The novelty of this mission assurance policy stems from using a time Petri net model for determining the security status of cyber assets, and then employing binary or multi-valued logic decision diagrams to assess the mission assurance level. The ability of a mission assurance policy to successfully complete its objectives depends mainly on whether a risk management scheme is provided to reduce risk to an acceptable level. To that end, this paper also describes a risk management scheme to systematically deal with the main factors of risk management such as the temporal interdependencies of cyber assets, impact of attacks, and risk mitigation. Given that the status of cyber assets changes due to the dynamic cybersecurity environment of asset vulnerabilities, threats, and recovery, the proposed mission assurance policy and risk management scheme enable decision makers to cope with the real-time assessment of mission assurance level.     

Can non-breeding be a cost of breeding dispersal?

Breeding habitat selection and dispersal are crucial processes that affect many components of fitness. Breeding dispersal entails costs, one of which has been neglected: dispersing animals may miss breeding opportunities because breeding dispersal requires finding a new nesting site and mate, two time- and energy-consuming activities. Dispersers are expected to be prone to non-breeding. We used the kittiwake (Rissa tridactyla) to test whether breeding dispersal influences breeding probability. Breeding probability was associated with dispersal, in that both were negatively influenced by private information (previous individual reproductive success) and public information (average reproductive success of conspecifics) about patch quality. Furthermore, the probability of skipping breeding was 1.7 times higher in birds that settled in a new patch relative to those that remained on the same patch. Finally, non-breeders that resumed breeding were 4.4 times more likely to disperse than birds that bred in successive years. Although private information may influence breeding probability directly, the link between breeding probability and public information may be indirect, through the influence of public information on breeding dispersal, non-breeding thus being a cost of dispersal. These results support the hypothesis that dispersal may result in not being able to breed. More generally, non-breeding (which can be interpreted as an extreme form of breeding failure) may reveal costs of various previous activities. Because monitoring the non-breeding portion of a population is difficult, non-breeders have been neglected in many studies of reproduction trade-offs.