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.     

Obstacles to climate change adaptation decisions: a case study of sea-level rise and coastal protection measures in Kiribati

International aid is increasingly focused on adaptation to climate change. At recent meetings of the parties to the United Nations Framework Convention on Climate Change, the developed world agreed to rapidly increase international assistance to help the developing world respond to the impacts of climate change. In this paper, we examine the decision-making challenges facing internationally supported climate change adaptation projects, using the example of efforts to implement coastal protection measures (e.g. sea walls, mangrove planting) in Kiribati. The central equatorial Pacific country is home to the Kiribati Adaptation Project, the first national-level climate change adaptation project supported by the World Bank. Drawing on interview and document research conducted over an 8-year period, we trace the forces influencing decisions about coastal protection measures, starting from the variability and uncertainty in climate change projections, through the trade-offs between different measures, to the social, political, and economic context in which decisions are finally made. We then discuss how sub-optimal adaptation measures may be implemented despite years of planning, consultation, and technical studies. This qualitative analysis of the real-world process of climate change adaptation reveals that embracing a culturally appropriate and short-term (~20 years) planning horizon, while not ignoring the longer-term future, may reduce the influence of scientific uncertainty on decisions and provide opportunities to learn from mistakes, reassess the science, and adjust suboptimal investments. The limiting element in this approach to adaptation is likely to be the availability of consistent, long-term financing.     

Evaluation of genotoxicity and coumarin production in conventional and organic cultivation systems of Mikania glomerata Spreng

Abstract

Mikania glomerata Sprengel, popularly known as “guaco,” is used in Brazilian folk medicine for several inflammatory and allergic conditions. Besides, the popular use “guaco” is indicated by the Brazilian Ministry of Health as a safe and effective herbal medicine. The biological activity of M. glomerata extracts is due to the presence of the coumarins, a large family of phenolic substances found in plants and is made of fused benzene and α-pyrone rings. Considering that there are few data on the biological effects of the extracts of M. glomerata, mainly in genetic level, this work aims to evaluate, in vitro, the genotoxicity and coumarin production in M. glomerata in conventional and organic growing. The data showed that the organic culture system showed double the concentration of coumarin being significantly more productive than the conventional system. Besides, the results of comet assay suggest that extracts of M. glomerata cultivated in a conventional system was genotoxic, increased DNA damage levels while the organic extracts seem to have antigenotoxic effect possibly due to the concentration of coumarins. Additional biochemical investigations are necessary to elucidate the mechanisms of action of M. glomerata extracts, which were found to have a role in protection against DNA damage.     

Molecular probes and microarrays for the detection of toxic algae in the genera Dinophysis and Phalacroma (Dinophyta)

Dinophysis and Phalacroma species containing diarrheic shellfish toxins and pectenotoxins occur in coastal temperate waters all year round and prevent the harvesting of mussels during several months each year in regions in Europe, Chile, Japan, and New Zealand. Toxicity varies among morphologically similar species, and a precise identification is needed for early warning systems. Molecular techniques using ribosomal DNA sequences offer a means to identify and detect precisely the potentially toxic species. We designed molecular probes targeting the 18S rDNA at the family and genus levels for Dinophysis and Phalacroma and at the species level for Dinophysis acuminata, Dinophysis acuta, and Dinophysis norvegica, the most commonly occurring, potentially toxic species of these genera in Western European waters. Dot blot hybridizations with polymerase chain reaction (PCR)-amplified rDNA from 17 microalgae were used to demonstrate probe specificity. The probes were modified along with other published fluorescence in situ hybridization and PCR probes and tested for a microarray platform within the MIDTAL project (http://www.midtal.com). The microarray was applied to field samples from Norway and Spain and compared to microscopic cell counts. These probes may be useful for early warning systems and monitoring and can also be used in population dynamic studies to distinguish species and life cycle stages, such as cysts, and their distribution in time and space.     

Raptors and Red Grouse: Conservation Conflicts and Management Solutions

Abstract: Recovering predator populations may present problems for conservationists if their prey are of economic or conservation value. We address this issue by examining the conflict between raptor conservation and management of Red Grouse (   Lagopus l. scoticus ) in Britain. Heather moorland is a distinctive habitat that supports an important assemblage of breeding birds. Large areas of moorland are managed by private landowners for shooting grouse. Although grouse shooting benefits conservation by retaining heather moorland, it is currently unclear whether grouse management directly benefits other upland birds. Human persecution has greatly restricted the range and abundance of most raptor species in Britain. Following the introduction of bird protection laws, the decline in gamekeeping, and the restriction of organochlorine pesticides, raptor populations have started to recover. Persecution of raptors on grouse moors is widespread and limits the range and abundance of Hen Harriers (  Circus cyaneus ), Peregrine Falcons (   Falco peregrinus ), and Golden Eagles ( Aquila chrysaetos ). In some circumstances, raptor predation can reduce both the breeding density and productivity of Red Grouse. Limitation of grouse populations through raptor predation is most likely to occur where raptors are at high density because of the abundance of alternative prey, and grouse are at low density either because of poor management or the cyclic nature of some grouse populations. In the long term, habitat management may reduce densities of alternative prey, leading to reductions in raptor densities and their predation on grouse. More active intervention may be required, however, if grouse moors are to remain viable in the short-term. Current research is focused on manipulating harrier diet through diversionary feeding. Complementary research is needed to investigate methods to reduce raptor numbers locally while ensuring their national status.     

Documentation of bioaerosol concentrations in an indoor composting facility in France

Bioaerosol concentrations were investigated in a totally indoor composting facility processing fermentable household and green wastes to assess their variability. Stationary samples were collected by filtration close to specific composting operations and then were analysed for cultivable mesophilic bacteria, thermophilic bacteria, mesophilic fungi, thermophilic fungi, endotoxins and total airborne bacteria (DAPI-staining). Indoor concentrations exceeded the background levels, between 500 and 5400 EU m(-3) for endotoxins, 10(4) and 10(6) CFU m(-3) for cultivable bacteria and generally below 10(5) CFU m(-3) for airborne cultivable fungi. No significant (p > 0.05) differences were observed between the indoor composting operations. Successive 30 minute bioaerosol samples were collected to investigate the variation of cultivable mesophilic microorganisms over the work shift. Concentrations of mesophilic bacteria and fungi varied up to 1 log unit depending on the time at which they were collected in the day. Total airborne particles, counted using an optical particle counter, were present at up to 10(8) particles m(-3) and several concentration peaks were noted. Values for total airborne bacteria were roughly 70-fold higher than cultivable bacteria. These results raise the question of the sampling strategy (duration of sampling; number of samples to be collected) used in similar studies. They provide new bioaerosol concentration data in a composting facility and suggest that the filtration sampling method might be a useful tool for exposure measurements in that occupational environment.     

Urban stormwater harvesting and reuse: a probe into the chemical, toxicology and microbiological contaminants in water quality

Stormwater is one of the last major untapped urban water resources that can be exploited as an alternative water source in Australia. The information in the current Australian Guidelines for Water Recycling relating to stormwater harvesting and reuse only emphasises on a limited number of stormwater quality parameters. In order to supply stormwater as a source for higher value end-uses, a more comprehensive assessment on the potential public health risks has to be undertaken. Owing to the stochastic variations in rainfall, catchment hydrology and also the types of non-point pollution sources that can provide contaminants relating to different anthropogenic activities and catchment land uses, the characterisation of public health risks in stormwater is complex, tedious and not always possible through the conventional detection and analytical methods. In this study, a holistic approach was undertaken to assess the potential public health risks in urban stormwater samples from a medium-density residential catchment. A combined chemical–toxicological assessment was used to characterise the potential health risks arising from chemical contaminants, while a combination of standard culture methods and quantitative polymerase chain reaction (qPCR) methods was used for detection and quantification of faecal indicator bacteria (FIB) and pathogens in urban stormwater. Results showed that the concentration of chemical contaminants and associated toxicity were relatively low when benchmarked against other alternative water sources such as recycled wastewater. However, the concentrations of heavy metals particularly cadmium and lead have exceeded the Australian guideline values, indicating potential public health risks. Also, high numbers of FIB were detected in urban stormwater samples obtained from wet weather events. In addition, qPCR detection of human-related pathogens suggested there are frequent sewage ingressions into the urban stormwater runoff during wet weather events. Further water quality monitoring study will be conducted at different contrasting urban catchments in order to undertake a more comprehensive public health risk assessment for urban stormwater.