Evaluation of concentration efficiency of the Pseudomonas aeruginosa phage PP7 in various water matrixes by different methods

Enteric viruses monitoring in surface waters requires the concentration of viruses before detection assays. The aim of this study was to evaluate different methods in terms of recovery efficiencies of bacteriophage PP7 of Pseudomonas aeruginosa, measured by real-time PCR, using it as a viral control process in water analysis. Different nucleic acid extraction methods (silica–guanidinium thiocyanate, a commercial kit (Qiagen Viral RNA Kit) and phenol–chloroform with alcohol precipitation) exhibited very low recovery efficiencies (0.08–4.18 %), being the most efficient the commercial kit used for subsequent experiments. To evaluate the efficiency of three concentration methods, PBS (as model for clean water) and water samples from rivers were seeded to reach high (HC, 10⁶ pfu ml^?1) and low concentrations (LC, 10⁴ pfu ml^?1) of PP7. Tangential ultrafiltration proved to be more efficient (50.36?±?12.91, 17.21?±?9.22 and 12.58?±?2.35 % for HC in PBS and two river samples, respectively) than adsorption–elution with negatively charged membranes (1.00?±?1.34, 2.79?±?2.62 and 0.05?±?0.08 % for HC in PBS and two river samples, respectively) and polyethylene glycol precipitation (15.95?±?7.43, 4.01?±?1.12 and 3.91?±?0.54 %, for HC in PBS and two river samples, respectively), being 3.2–50.4 times more efficient than the others for PBS and 2.7–252 times for river samples. Efficiencies also depended on the initial virus concentration and aqueous matrixes composition. In consequence, the incorporation of an internal standard like PP7 along the process is useful as a control of the water concentration procedure, the nucleic acid extraction, the presence of inhibitors and the variability of the recovery among replicas, and for the calculation of the sample limit of detection. Thus, the use of a process control, as presented here, is crucial for the accurate quantification of viral contamination.     

Regional status assessment of stony corals in the US Virgin Islands

States may protect coral reefs using biological water quality standards outlined by the Clean Water Act. This requires biological assessments with indicators sensitive to human disturbance and regional, probability-based survey designs. Stony coral condition was characterized on a regional scale for the first time in the nearshore waters of the US Virgin Islands (USVI). Coral composition, abundance, size, and health were assessed at 66 stations in the St. Croix region in fall 2007 and at 63 stations in the St. Thomas and St. John region in winter 2009. Indicators were chosen for their sensitivity to human disturbance. Both surveys were probability-based (random) designs with station locations preselected from areas covered by hardbottom and coral reef substrate. Taxa richness was as high as 21 species but more than half the area of both regions exhibited taxa richness of <10 species in the 25 m² transect area. Coral density was as high as 5 colonies m^?2 but more than half the area of both regions had <2 colonies m^?2. Both regions showed similar dominant species based on frequency of occurrence and relative abundance. Because of large colony sizes, Montastrea annularis provided more total surface area and live surface area than more abundant species. The surveys establish baseline regional conditions and provide a foundation for long-term regional monitoring envisioned by the USVI Department of Planning and Natural Resources. The probabilistic sampling design assures the data can be used in Clean Water Act reporting.     

Community metabolism in a deep (stratified) tropical reservoir during a period of high water-level fluctuations

As long as lakes and reservoirs are an important component of the global carbon cycle, monitoring of their metabolism is required, especially in the tropics. In particular, the response of deep reservoirs to water-level fluctuations (WLF) is an understudied field. Here, we study community metabolism through oxygen dynamics in a deep monomictic reservoir where high WLF (~10 m) have recently occurred. Simultaneous monitoring of environmental variables and zooplankton dynamics was used to assess the effects of WLF on the metabolism of the eutrophic Valle de Bravo (VB) reservoir, where cyanobacteria blooms are frequent. Mean gross primary production (P _g) was high (2.2 g C m^?2 day^?1), but temporal variation of P _g was low except for a drastic reduction during circulation attributed to zooplankton grazing. The trophogenic layer showed net autotrophy on an annual basis, but turned to net heterotrophy during mixing, and furthermore when the whole water-column oxygen balance was calculated, considering the aphotic respiration (R _aphotic). The high total respiration resulting (3.1 g C m^?2 day^?1) is considered to be partly due to mixing enhanced by WLF. Net ecosystem production was equivalent to a net export of 3.4 mg CO₂?m^?2 day^?1 to the atmosphere. Low water levels are posed to intensify boundary-mixing events driven by the wind during the stratification in VB. Long-term monitoring showed changes in the planktonic community and a strong silicon decrease that matched with low water-level periods. The effects of low water-level on metabolism and planktonic community in VB suggest that water-level manipulation could be a useful management tool to promote phytoplankton groups other than cyanobacteria.     

Human impacts on fire occurrence: a case study of hundred years of forest fires in a dry alpine valley in Switzerland

Forest fire regimes are sensitive to alterations of climate, fuel load, and ignition sources. We investigated the impact of human activities and climate on fire occurrence in a dry continental valley of the Swiss Alps (Valais) by relating fire occurrence to population and road density, biomass removal by livestock grazing and wood harvest, temperature and precipitation in two distinct periods (1904–1955 and 1956–2006) using generalized additive modeling. This study provides evidence for the role played by humans and temperature in shaping fire occurrence. The existence of ignition sources promotes fire occurrence to a certain extent only; for example, high road density tends to be related to fewer fires. Changes in forest uses within the study region seem to be particularly important. Fire occurrence appears to have been negatively associated with livestock pasturing in the forest and wood harvesting, in particular during the period 1904–1955. This study illustrates consistently how fire occurrence has been influenced by land use and socioeconomic conditions. It also suggests that there is no straightforward linear relationship between human factors and fire occurrence.     

Land-cover change in upper Barataria Basin estuary,Louisiana, 1972-1992: increases in Wetland area

The Barataria Basin, Louisiana, USA, is an extensive wetland and coastal estuary system of great economic and intrinsic value. Although high rates of wetland loss along the coastal margin of the Barataria Basin have been well documented, little information exists on whether freshwater wetlands in the upper basin have changed. Our objectives were to quantify land-cover change in the upper basin over 20 years from 1972–1992 and to determine land-cover transition rates among land-cover types. Using 80-m resolution Landsat MSS data from the North American Landscape Characterization (NALC) data archive, we classified images from three time steps (1972, 1985, 1992) into six land-cover types: agriculture, urban, bottomland hardwood forest, swamp forest, freshwater marsh, and open water. Significant changes in land cover occurred within the upper Barataria Basin over the study period. Urban land increased from 8% to 17% of the total upper basin area, primarily due to conversions from agricultural land, and to a lesser degree, bottomland forest. Swamp forest increased from 30% to 41%, associated with conversions from bottomland hardwood forest and freshwater marsh. Overall, bottomland forest decreased 38% and total wetland area increased 21%. Within the upper Barataria, increases in total wetland area may be due to land subsidence. Based on our results, if present trends in the reduction of bottomland forest land cover were to continue, the upper Barataria Basin may have no bottomland hardwood forests left by the year 2025, as it is subjected to multiple stressors both in the higher elevations (from urbanization) and lower elevations (most likely from land subsidence). These results suggest that changes in the upper freshwater portions of coastal estuaries can be large and quite different from patterns observed in the more saline coastal margins.     

Using Science to Assess Environmental Vulnerabilities

Beginning in 1995, the U.S. Environmental Protection Agency (U.S. EPA), Office of Research and Development has focused much of its ecological research in the Mid-Atlantic as part of the Mid-Atlantic Integrated Assessment (MAIA). The goal of MAIA is to improve the assessability of scientific information in environmental decision-making. Following the Environmental Monitoring and Assessment Program (EMAP) whose goal is to guide monitoring that effectively reflects current ecosystem condition and trends, MAIA's second, current, phase of research under the Regional Vulnerability Assessment (ReVA) program is designed to target risk management activities using available data and models. The papers presented here are from a conference held in May 2003 that presented results of research in this second phase of MAIA. The conference was organized into the following topics: 1. Assessing Current Impacts and Vulnerabilities 2. Forecasting Environmental Condition and Vulnerabilities 3. Developing Management Strategies to Optimize the Future, and 4. Assessing and Responding to Environmental Vulnerability.     

Reproductive health in Afghanistan: results of a knowledge, attitudes and practices survey among Afghan women in Kabul

A reproductive-health knowledge, attitudes and practices (KAP) survey was carried out among 468 Afghan women of reproductive age. A convenience sample of women was selected from attendees in the outpatient departments of four health facilities in Kabul. Seventy-nine per cent of respondents had attended at least one antenatal consultation during their last pregnancy. Two-thirds (67 per cent) delivered their first child between 13 and 19 years. The Caesarean-section rate was low (1.6 per cent). Two-thirds (67 per cent) of deliveries occurred in the home. The contraceptive prevalence rate was 23 per cent (16 per cent modern and 7 per cent natural methods). Twenty-four per cent had knowledge of any STIs, although most of these women did not know correctly how to prevent them. Most of the women (93 per cent) needed authorization from their husband or a male relative before seeking professional health-care. In multivariate analysis, women's schooling was significantly associated with antenatal-care attendance (AOR 4.78), institutional delivery (AOR 2.29), skilled attendance at birth (AOR 2.07) and use of family planning (AOR 4.59). Reproductive-health indicators were noted to be poor even among these women living in Kabul, a group often considered to be the most privileged. To meet the reproductive-health needs of Afghan women, the socio-cultural aspects of their situation--especially their decision-making abilities -- will need to be addressed. A long-standing commitment from agencies and donors is required, in which the education of women should be placed as a cornerstone of the reconstruction process of Afghanistan.     

Rough Set Rule Induction for Suitability Assessment

The data that characterize an environmental system are a fundamental part of an environmental decision-support system. However, obtaining complete and consistent data sets for regional studies can be difficult. Data sets are often available only for small study areas within the region, whereas the data themselves contain uncertainty because of system complexity, differences in methodology, or data collection errors. This paper presents rough-set rule induction as one way to deal with data uncertainty while creating predictive if–then rules that generalize data values to the entire region. The approach is illustrated by determining the crop suitability of 14 crops for the agricultural soils of the Willamette River Basin, Oregon, USA. To implement this method, environmental and crop yield data were spatially related to individual soil units, forming the examples needed for the rule induction process. Next, four learning algorithms were defined by using different subsets of environmental attributes. ROSETTA, a software system for rough set analysis, was then used to generate rules using each algorithm. Cross-validation analysis showed that all crops had at least one algorithm with an accuracy rate greater than 68%. After selecting a preferred algorithm, the induced classifier was used to predict the crop suitability of each crop for the unclassified soils. The results suggest that rough set rule induction is a useful method for data generalization and suitability analysis.