Improved traceability of Shiga-toxin-producing <Emphasis Type="Italic">Escherichia coli</Emphasis> using CRISPRs for detection and typing

Among strains of Shiga-toxin-producing Escherichia coli (STEC), seven serogroups (O26, O45, O103, O111, O121, O145, and O157) are frequently associated with severe clinical illness in humans. The development of methods for their reliable detection from complex samples such as food has been challenging thus far, and is currently based on the PCR detection of the major virulence genes stx1, stx2, and eae, and O-serogroup-specific genes. However, this approach lacks resolution. Moreover, new STEC serotypes are continuously emerging worldwide. For example, in May 2011, strains belonging to the hitherto rarely detected STEC serotype O104:H4 were identified as causative agents of one of the world’s largest outbreak of disease with a high incidence of hemorrhagic colitis and hemolytic uremic syndrome in the infected patients. Discriminant typing of pathogens is crucial for epidemiological surveillance and investigations of outbreaks, and especially for tracking and tracing in case of accidental and deliberate contamination of food and water samples. Clustered regularly interspaced short palindromic repeats (CRISPRs) are composed of short, highly conserved DNA repeats separated by unique sequences of similar length. This distinctive sequence signature of CRISPRs can be used for strain typing in several bacterial species including STEC. This review discusses how CRISPRs have recently been used for STEC identification and typing.     

Lysimeter Experiments to Investigate the Fate of Chemicals in Soils – Comparison of Five Different Lysimeter Systems

Several lysimeter scenarios and approaches exist to study the fate of agro-chemicals or contaminants from deposition in soil columns. In many systems just transport and leaching of the parent compound is followed, in some systems the leaching and transport of the metabolites is investigated as well. In more sophisticated lysimeter systems the volatilization and also the mineralization of the applied chemicals can be additionally monitored. Depending on the lysimeter system used and on the fact whether the applied chemicals are ¹⁴C-labeled or not, different results and various interpretations of the results might be achieved. Different lysimeter systems are described in this paper and a real dataset of a specific lysimeter experiment was transferred and evaluated in a virtual approach in the different lysimeter systems in order to show the advantages and disadvantages of the various systems.     

Vapour pressures, aqueous solubility, Henry's law constants and air/water partition coefficients of 1,8-dichlorooctane and 1,8-dibromooctane

New data on the vapour pressures and aqueous solubility of 1,8-dichlorooctane and 1,8-dibromooctane are reported as a function of temperature between 20 °C and 80 °C and 1 °C and 40 °C, respectively. For the vapour pressures, a static method was used during the measurements which have an estimated uncertainty between 3% and 5%. The aqueous solubilities were determined using a dynamic saturation column method and the values are accurate to within ±10%. 1,8-Dichlorooctane is more volatile than 1,8-dibromooctane in the temperature range covered (p_sat varies from 3 to 250 Pa and from 0.53 to 62 Pa, respectively) and is also approximately three times more soluble in water (mole fraction solubilities at 25 °C of 5.95 × 10⁻⁷ and 1.92 × 10⁻⁷, respectively). A combination of the two sets of data allowed the calculation of the Henry’s law constants and the air water partition coefficients. A simple group contribution concept was used to rationalize the data obtained.     

Flood-risk management strategies for an uncertain future: living with Rhine River floods in The Netherlands?

Social pressure on alluvial plains and deltas is large, both from an economic point of view and from a nature conservation point of view. Gradually, flood risks increase with economic development, because the expected damage increases, and with higher dikes, because the flooding depth increases. Global change, changing social desires, but also changing views, require a revision of flood-risk management strategies for the long term. These should be based on resilience as opposed to the resistence strategy of heightening dikes. Resilience strategies for flood-risk management imply that the river is allowed to temporarily flood large areas, whereas the flood damage is minimized by adapting land use. Such strategies are thus based on risk management and 'living with floods' instead of on hazard control. For The Netherlands, one of the most densely populated deltas in the world, alternative resilience strategies have been elaborated and assessed for their hydraulic functioning and 'sustainability criteria'.     

Preliminary ecotoxicological characterization of a new energetic substance, CL-20

A new energetic substance hexanitrohexaazaisowurtzitane (or CL-20) was tested for its toxicities to various ecological receptors. CL-20 (epsilon-polymorph) was amended to soil or deionized water to construct concentration gradients. Results of Microtox (15-min contact) and 96-h algae growth inhibition tests indicate that CL-20 showed no adverse effects on the bioluminescence of marine bacteria Vibrio fischeri and the cell density of freshwater green algae Selenastrum capricornutum respectively, up to its water solubility (ca. 3.6 mg l(-1)). CL-20 and its possible biotransformation products did not inhibit seed germination and early seedling (16-19 d) growth of alfalfa (Medicago sativa) and perennial ryegrass (Lolium perenne) up to 10,000 mg kg(-1) in a Sassafras sandy loam soil (SSL). Indigenous soil microorganisms in SSL and a garden soil were exposed to CL-20 for one or two weeks before dehydrogenase activity (DHA) or potential nitrification activity (PNA) were assayed. Results indicate that up to 10,000 mg kg(-1) soil of CL-20 had no statistically significant effects on microbial communities measured as DHA or on the ammonium oxidizing bacteria determined as PNA in both soils. Data indicates that CL-20 was not acutely toxic to the species or microbial communities tested and that further studies are required to address the potential long-term environmental impact of CL-20 and its possible degradation products.     

Male fighting and “territoriality” within colonies of the ant Cardiocondyla venustula

The ant genus Cardiocondyla is characterized by a bizarre male polymorphism with wingless fighter males and winged disperser males. Winged males have been lost convergently in several clades, and in at least one of them, wingless males have evolved mutual tolerance. To better understand the evolutionary pathways of reproductive tactics, we investigated Cardiocondyla venustula, a species, which in a phylogenetic analysis clusters with species with fighting and species with mutually tolerant, wingless males. Wingless males of C. venustula use their strong mandibles to kill freshly eclosed rival males and also engage in short fights with other adult males, but in addition show a novel behavior hitherto not reported from social insect males: they spread out in the natal nest and defend “territories” against other males. Ant males therefore show a much larger variety of reproductive tactics than previously assumed.     

Spatial distributions and eco-partitioning of soil biogeochemical properties in the Everglades National Park

Large-scale ecosystem restoration efforts, such as those in the Florida Everglades, can be long-term and resource intensive. To gauge success, restoration efforts must have a means to evaluate positive or negative results of instituted activities. Edaphic properties across the Everglades landscape have been determined to be a valuable metric for such evaluation, and as such, a baseline condition from which to make future comparisons and track ecosystem response is necessary. The objectives of this work were to document this baseline condition in the southern most hydrologic unit of the Everglades, Everglades National Park (ENP), and to determine if significant eco-partitioning of soil attributes exists that would suggest the need to focus monitoring efforts in particular eco-types within the ENP landscape. A total of 342 sites were sampled via soil coring and parameters such as total phosphorus (TP), total nitrogen (TN), total carbon (TC), total calcium, total magnesium, and bulk density were measured at three depth increments in the soil profile (floc, 0-10 cm, and 10-20 cm). Geostatistical analysis and GIS applications were employed to interpolate site-specific biogeochemical properties of soils across the entire extent of the ENP. Spatial patterns and eco-type comparisons suggest TC and TN to be highest in Shark River Slough (SRS) and the mangrove interface (MI), following trends of greatest organic soil accumulation. However, TP patterns suggest greatest storages in MI, SRS, and western marl and wet prairies. Eco-partitioning of soil constituents suggest local drivers of geology and hydrology are significant in determining potential areas to focus monitoring for future change detection.     

Application of microbial hot spots enhances pesticide degradation in soils

Through transfer of an active, isoproturon degrading microbial community, pesticide mineralization could be successfully enhanced in various soils under laboratory and outdoor conditions. The microbes, extracted from a soil having high native ability to mineralize this chemical, were established on expanded clay particles and distributed to various soils in the form of microbial "hot spots". Both, diffusion controlled isoproturon mass flow towards these "hot spots" (6microg d(-1)) as well as microbial ability to mineralize the herbicide (approximately 5microg d(-1)) were identified as the main processes enabling a multiple augmentation of the native isoproturon mineralization even in soils with heavy metal contamination. Soil pH-value appears to exert an important effect on the sustainability of this process.     

Isolation and characterization of 1,2,4-trichlorobenzene mineralizing Bordetella sp. and its bioremediation potential in soil

A soil which has been polluted with chlorinated benzenes for more than 25 years was used for isolation of adapted microorganisms able to mineralize 1,2,4-trichlorobenzene (1,2,4-TCB). A microbial community was enriched from this soil and acclimated in liquid culture under aerobic conditions using 1,2,4-TCB as a sole available carbon source. From this community, two strains were isolated and identified by comparative sequence analysis of their 16S-rRNA coding genes as members of the genus Bordetella with Bordetella sp. QJ2-5 as the highest homological strain and with Bordetella petrii as the closest related described species. The 16S-rDNA of the two isolated strains showed a similarity of 100%. These strains were able to mineralize 1,2,4-TCB within two weeks to approximately 50% in liquid culture experiments. One of these strains was reinoculated to an agricultural soil with low native 1,2,4-TCB degradation capacity to investigate its bioremediation potential. The reinoculated strain kept its biodegradation capability: (14)C-labeled 1,2,4-TCB applied to this inoculated soil was mineralized to about 40% within one month of incubation. This indicates a possible application of the isolated Bordetella sp. for bioremediation of 1,2,4-TCB contaminated sites.     

Sustainability, substance flow management and time. Part I Temporal analysis of substance flows

Flows of chemical substances need to be managed in a sustainable way. Sustainable development as a whole and the sustainable management of substance flows in particular are both time issues. These include the importance of the dynamics of substance flows and the way these interconnect with the use of resources, the avoidance of environmental pollution, and their effects on health and food production. Another prerequisite for the proper management of substance flows is justice within and between generations. This requires a systematic approach and a systematic analysis of the issues as well as of the actions to be taken. One tool for such a systematic approach is temporal analysis. It brings the temporal aspects of the substances themselves and of their intended use, as well as factors affecting the stakeholders, such as decision makers, producers and consumers, into focus. In the past, timing factors were rarely taken into account. Knowledge of the temporal dynamics of substance flows and their resultant outcomes, as well as of their interaction with ecological, economic and social systems, is a basic requirement for successful substance flow management. The need to include temporal aspects into substance flow management and how to do so is outlined here. Included are not only politicians but also practitioners and scientists who must explicitly take into account adequate time scales, points in time, breaks and other forms of time in planning and acting.