Development and Evaluation of a Multiplexed Real-Time TaqMan RT-PCR Assay with a Sample Process Control for Detection of F-specific RNA Coliphage Genogroups I and IV

There are increasing concerns of zoonotic transmission of some animal enteric viruses, such as calicivirus, hepatitis E virus, and rotavirus, which are closely related to human pathogenic strains. Most enteric viruses are detected by molecular techniques because they cannot be cultured. Surrogates such as F-RNA coliphages are cultivable but few molecular methods exist. Individual real-time TaqMan RT-PCR assays for the replicase gene of F-RNA coliphage genogroups I and IV were developed and multiplexed with a real-time TaqMan RT-PCR assay for feline calicivirus as a sample process control for the simultaneous detection and enumeration of genogroup I and IV F-RNA coliphages. Genogroup IV were successfully detected with the multiplexed assay in 80% of fecal samples that contained F-RNA coliphage levels ≥3.2 log plaque forming units (pfu). F-RNA coliphage were at or below the limit of detection in most fecal samples when levels were ≤4 log pfu/g.     

Cover crop effects on nitrous oxide emission from a manure-treated Mollisol

Agriculture contributes 40–60% of the total annual N₂O emissions to the atmosphere. Development of management practices to reduce these emissions would have a significant impact on greenhouse gas levels. Non-leguminous cover crops are efficient scavengers of residual soil NO₃, thereby reducing leaching losses. However, the effect of a grass cover crop on N₂O emissions from soil receiving liquid swine manure has not been evaluated. This study investigated: (i) the temporal patterns of N₂O emissions following addition of swine manure slurry in a laboratory setting under fluctuating soil moisture regimes; (ii) assessed the potential of a rye (Secale cereale L.) cover crop to decrease N₂O emissions under these conditions; and (iii) quantified field N₂O emissions in response to either spring applied urea ammonium nitrate (UAN) or different rates of fall-applied liquid swine manure, in the presence or absence of a rye/oat winter cover crop. Laboratory experiments investigating cover crop effects N₂O emissions were performed in a controlled environment chamber programmed for a 14 h light period, 18 °C day temperature, and 15 °C night temperature. Treatments with or without a living rye cover crop were treated with either: (i) no manure; (ii) a phosphorus-based manure application rate (low manure): or (iii) a nitrogen-based manure application rate (high manure). We observed a significant reduction in N₂O emissions in the presence of the rye cover crop. Field experiments were performed on a fine-loamy soil in Central Iowa from October 12, 2005 to October 2, 2006. We observed no significant effect of the cover crop on cumulative N₂O emissions in the field. The primary factor influencing N₂O emission was N application rate, regardless of form or timing. The response of N₂O emission to N additions was non-linear, with progressively more N₂O emitted with increasing N application. These results indicate that while cover crops have the potential to reduce N₂O emissions, N application rate may be the overriding factor.     

The floristics and conservation status of sand-dune communities in Wales

An inventory of the vascular plants, bryophytes, fungi and terricolous lichens recorded within the different sand-dune communities in Wales has been compiled and a summary of the importance of these different taxonomic groups to the ecology and conservation of sand dunes is provided. The total floristic assemblage amounted to 945 species, with vascular plants representing 439 of these. Fungi unexpectedly formed the next most important group with ca. 289 species, followed by bryophytes (171 species) and terricolous lichens (66 species). However, very few of these species are confined to sand dunes. Of the vascular plants only ca. 7 % (32 species) could be classed as either wholly dependent or strongly associated with sand dunes, whereas up to 13% (22 species) of the bryophytes fell within this category. Of the fungi only 4% (10 species) appear to be restricted to sand dunes, but none of the lichen species could be classed as being either limited to, or strongly associated with, this habitat. Over 9% (91 species) of the total flora are considered to be rare, scarce or endangered within the UK or Europe, and ca. 8% of the vascular plant species are considered to be endemic or near-endemic to Europe. The inventory therefore not only provides an insight in the overall plant diversity of dune systems in Wales, it also gives an indication of the proportion of species that are under threat, and the numbers of species that are more-or-less totally dependent on sand dunes. In the discussion various relevant sand-dune management issues are addressed.     

POTENTIAL EFFECTS OF CLIMATE CHANGE ON AGRICULTURAL WATER USE IN THE SOUTHEAST U.S.1

ABSTRACT: Climate change has the potential to have dramatic effects on the agricultural sector nationally and internationally as documented in many research papers. This paper reports on research that was focused on a specific crop growing area to demonstrate how farm managers might respond to climate-induced yield changes and the implications of these responses for agricultural water use. The Hadley model was used to generate climate scenarios for important agricultural areas of Georgia in 2030 and 2090. Linked crop response models indicated generally positive yield changes, as increased temperatures were associated with increased precipitation and CO2. Using a farm management model, differences in climate-induced yield impacts among crops led to changes in crop mix and associated water use; non-irrigated cropland received greater benefit since irrigated land was already receiving adequate moisture. Model results suggest that farm managers will increase cropping intensity by decreasing fallowing and increasing double cropping; corn acreage decreased dramatically, peanuts decreased moderately and cotton and winter wheat increased. Water use on currently irrigated cropland fell. The potential for increased water use through conversion of agriculturally important, but currently non-irrigated, growing areas is substantial.     

Simple molecular method to distinguish the identity of Calanus species (Copepoda: Calanoida) at any developmental stage

Diagnostic morphological characteristics of copepods of the genus Calanus are restricted largely to minor variations in secondary sex characteristics. This presents a persistent problem in the identification of individuals to species level, especially for immature stages. We have developed a simple molecular technique to distinguish between the North Atlantic Calanus species (C. helgolandicus, C. finmarchicus, C. glacialis and C. hyperboreus) at any life stage. Using the polymerase chain-reaction (PCR), the mitochodrial large subunit (16S) ribosomal RNA (rRNA) gene was amplified from individual copepods preserved in ethanol. Subsequent digestion of the amplified products with the restriction enzymes DdeI and VspI, followed by electrophoretic separation in 2% agarose (Metaphor, FMC Ltd), produced a characteristic pattern for each species. The versatility of the method is demonstrated by the unambiguous identification to species of any life stage, from egg to adult, and of individual body parts. Received: 11 May 1998 / Accepted: 5 August 1998     

Identifying socioeconomic and biophysical factors driving forest loss in protected areas

Protected areas (PAs) are a commonly used strategy to confront forest conversion and biodiversity loss. Although determining drivers of forest loss is central to conservation success, understanding of them is limited by conventional modeling assumptions. We used random forest regression to evaluate potential drivers of deforestation in PAs in Mexico, while accounting for nonlinear relationships and higher order interactions underlying deforestation processes. Socioeconomic drivers (e.g., road density, human population density) and underlying biophysical conditions (e.g., precipitation, distance to water, elevation, slope) were stronger predictors of forest loss than PA characteristics, such as age, type, and management effectiveness. Within PA characteristics, variables reflecting collaborative and equitable management and PA size were the strongest predictors of forest loss, albeit with less explanatory power than socioeconomic and biophysical variables. In contrast to previously used methods, which typically have been based on the assumption of linear relationships, we found that the associations between most predictors and forest loss are nonlinear. Our results can inform decisions on the allocation of PA resources by strengthening management in PAs with the highest risk of deforestation and help preemptively protect key biodiversity areas that may be vulnerable to deforestation in the future.     

Early warning: Integrating eco‐efficiency aspects into the product development process

Improving the eco‐efficiency of products is gaining increasing attention within industry. Through eco‐efficiency, companies aim to reduce the environmental impact of their products throughout the entire life cycle, while at the same time creating promising market opportunities or reducing costs. This article describes how companies can integrate eco‐efficiency aspects into the product development process. © 2000 John Wiley & Sons, Inc.     

Collaborative Watershed Planning in Washington State: Implementing the Watershed Planning Act

In 1998 the Washington State Legislature enacted the Watershed Planning Act, which encourages local governments to develop watershed plans using collaborative processes. Objectives of the statute are to address water resource and water quality issues, salmon habitat needs and to establish instream flows. This exploratory study sought to examine two aspects of how local governments are implementing the Act: challenges and benefits associated with collaborative watershed planning and the capacity of local governments to conduct collaborative watershed planning. Using documents and interview data from four cases, it was found that all planning groups experience similar challenges, although newer planning groups experienced more challenges than groups with previous planning experience. Challenges include issues surrounding the collaborative process, interagency co-ordination and trust. Local governments struggle with building capacity to plan, particularly in the areas of funding, technical expertise, incentives for participation, adequate time to conduct planning and questions regarding appropriate scale and scope of their planning efforts. Despite the challenges, collaborative watershed planning is well underway, with more than 37 planning units conducting planning under the Act.     

Inexpensive substrate sampler for macroinvertebrates

Assessment of aquatic macroinvertebrates is a critical component of many watershed monitoring programs and passive samplers are often used to collect long-term site data, especially in environments where active sampling is not possible. However, standard passive samplers can be expensive and lost in extreme conditions. We developed a sampler using plastic soda bottles (PSB) filled with river rock and compared its effectiveness with standard Hester-Dendy samplers in both lotic and lentic environments. Abundance, taxa richness, and macroinvertebrate composition showed no significant differences between sampler types in either habitat type. PSB samplers, which can be constructed for less than one dollar each, collected the same number of organisms and represented the same diversity as Hester-Dendy devices that cost around $38 each. In studies where funds are limited, PSB samplers appear to be suitable for passive monitoring.