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The development of the Canopy Pasture Probe (CAPP), for acquisition of in situ pasture canopy reflectance factor, required a suitable large reflectance standard. Spectralon® has been successfully used worldwide as a reflectance standard, but large panels (greater than 20 cm diameter) suitable for use with the CAPP are very expensive. In this context, a large, durable and low cost reflectance standard has been evaluated for use with an Analytical Spectral Devices FieldSpec® Pro FR spectroradiometer attached to the CAPP. In this study various ceramic tiles, barium sulphate powders, white paint and a Kodak card were tested. The material which best suited the requirements for a reflectance standard was the white ceramic tile sourced from Argentina. This tile produced around 80% total reflectance with reasonable uniformity over the spectral range analysed (400-2400 nm); and the vegetation spectra acquired using this tile as reference sample were very similar in shape to the vegetation spectra acquired using spectralon® as a white reference. [ABSTRACT FROM AUTHOR]

In order to assess the speed and accuracy of a real-time PCR assay targeting the lukS-PV gene of Panton–Valentine leukocidin (PVL)-positive Staphylococcus aureus, 700 S. aureus strains were tested and the results were compared to those achieved with block cycler PCR. Cross-reactivity was tested with 166 other bacterial species. Using this homogeneous real-time PCR assay format, the presence or absence of genetic information for PVL, which is also found in community-associated methicillin-resistant S. aureus, was correctly identified from pure culture and directly in various types of clinical specimens. [ABSTRACT FROM AUTHOR]

The nutritive value of pasture is an important determinant of the performance of grazing livestock. Proximal sensing of in situ pasture is a potential technique for rapid prediction of nutritive value. In this study, multispectral radiometry was used to obtain pasture spectral reflectance during different seasons (autumn, spring and summer) in 2009-2010 from commercial farms throughout New Zealand. The analytical data set ( n = 420) was analysed to develop season-specific and combined models for predicting pasture nutritive-value parameters. The predicted parameters included crude protein ( CP), acid detergent fibre ( ADF), neutral detergent fibre ( NDF), ash, lignin, lipid, metabolizable energy ( ME) and organic matter digestibility ( OMD) using a partial least squares regression analysis. The calibration models were tested by internal and external validation. The results suggested that the global models can predict the pasture nutritive value parameters ( CP, ADF, NDF, lignin, ME and OMD) with moderate accuracy (0·64 ≤ r2 ≤ 0·70) while ash and lipid are poorly predicted (0·33 ≤ r2 ≤ 0·40). However, the season-specific models improved the prediction accuracy, in autumn (0·73 ≤ r2 ≤ 0·83) for CP, ADF, NDF and lignin; in spring (0·61 ≤ r2 ≤ 0·78) for CP and ash; in summer (0·77 ≤ r2 ≤ 0·80) for CP and ash, indicating a seasonal impact on spectral response. [ABSTRACT FROM AUTHOR]

A study was conducted to explore the potential use of a hand-held (proximal) hyperspectral sensor equipped with a canopy pasture probe to assess a number of pasture quality parameters: crude protein (CP), acid detergent fibre (ADF), neutral detergent fibre (NDF), ash, dietary cation-anion difference (DCAD), lignin, lipid, metabolisable energy (ME) and organic matter digestibility (OMD) during the autumn season 2009. Partial least squares regression was used to develop a relationship between each of these pasture quality parameters and spectral reflectance acquired in the 500-2 400 nm range. Overall, satisfactory results were produced with high coefficients of determination ( R), Nash-Sutcliffe efficiency (NSE) and ratio prediction to deviation (RPD). High accuracy (low root mean square error-RMSE values) for pasture quality parameters such as CP, ADF, NDF, ash, DCAD, lignin, ME and OMD was achieved; although lipid was poorly predicted. These results suggest that in situ canopy reflectance can be used to predict the pasture quality in a timely fashion so as to assist farmers in their decision making. [ABSTRACT FROM AUTHOR]

Decision support tools for precise irrigation scheduling are required to improve the efficiency of irrigation water use globally. This article presents a method for mapping soil variability and relating it to soil hydraulic properties so that soil management zones for variable-rate irrigation can be defined. A soil-water balance is used to schedule hypothetical irrigation events based on one blanket application of water to eliminate plant stress (uniform rate irrigation, or URI) and compares this to variable-rate irrigation (VRI), where irrigation is tailored to specific soil zone available water-holding capacity (TA WC) values. The key performance indicators, i.e., irrigation water use, drainage water loss, nitrogen leaching, energy use, irrigation water use efficiency (IWUE), and virtual water content, are used to compare URI and VRI at three contrasting sites using four years of climate data for a dairy pasture and maize crop and two years of climate data for a potato crop. Our research found that VRI saved 9% to 19% irrigation water, with accompanying energy saving. Loss of water by drainage, during the period of irrigation, was also reduced by 25% to 45% using VRI, which reduced the risk of nitrogen leaching. Virtual water content of these three primary products further illustrates potential benefits of VRI and shows that virtual water content of potato production used the least water per unit of dry matter production. [ABSTRACT FROM AUTHOR]

Aims: The DNA-intercalating dye ethidium bromide monoazide (EMA) has recently been used as a DNA binding agent to differentiate viable and dead bacterial cells by selectively penetrating through the damaged membrane of dead cells and blocking the DNA amplification during the polymerase chain reaction (PCR). We optimized and tested the assay in vitro using Staphylococcus aureus and Staphylococcus epidermidis cultures to distinguish viable from dead bacteria, with the goal of reducing false positive PCR results. Methods and Results: Viable and heat-inactivated bacteria were treated with EMA or left untreated before DNA extraction. A real-time PCR assay for the detection of the tuf gene in each DNA extract was used. Our results indicated that EMA influenced viable bacteria as well as dead bacteria, and the effect of EMA depended on the EMA concentration and bacterial number. Conclusions: EMA is not a suitable indicator of bacterial viability, at least with respect to Staphylococcus species. Significance and Impact of the Study: Determining the viability of pathogens has a major impact on interpreting the results of molecular tests for bacteria and subsequent clinical management of patients. To this end, several methods are being evaluated. One of these methods – intercalating DNA of dead bacteria by EMA – looked very promising, but our study found it unsatisfactory for S. aureus and coagulase-negative Staphylococci. [ABSTRACT FROM AUTHOR]

Multi-spectral remote sensing of green vegetation provides an opportunity for assessing biophysical and biochemical properties. This technique could play a crucial role in pasture management by providing the means to evaluate pasture quality in situ. In this study, the potential of a 16-channel multi-spectral radiometer (MSR) for predicting pasture quality, crude protein (CP), acid detergent fibre (ADF), neutral detergent fibre (NDF), ash, dietary cation-anion difference (DCAD), lignin, lipid, metabolisable energy (ME) and organic matter digestibility (OMD) was evaluated. In situ canopy spectral reflectance was acquired from mixed pastures, under commercial farm conditions in New Zealand. The multi-spectral data were evaluated by single wavelength, linear and non-linear renormalized difference vegetation index (RDVI), and stepwise multiple linear regression (SMLR) models. The selected non-linear, exponential fit, RDVI index models described (0.65 ≤ r ≤ 0.85) of the variation of pasture quality components (CP, DCAD, ME and OMD), while CP, ash, DCAD, lipid, ME and OMD were estimated with moderate accuracy (0.60 ≤ r ≤ 0.80) by the SMLR model. The remaining pasture quality components ADF, NDF and lignin were poorly explained (0.40 ≤ r ≤ 0.58) by the models. This experiment concluded that the MSR has potential to rapidly estimate pasture quality in the field using non-destructive sampling. [ABSTRACT FROM AUTHOR]

This paper reports the development and evaluation of a field technique for in situ measurement of root density using a portable spectroradiometer. The technique was evaluated at two sites in permanent pasture on contrasting soils (an Allophanic and a Fluvial Recent soil) in the Manawatu region, New Zealand. Using a modified soil probe, reflectance spectra (350–2500 nm) were acquired from horizontal surfaces at three depths (15, 30 and 60 mm) of an 80-mm diameter soil core, totalling 108 samples for both soils. After scanning, 3-mm soil slices were taken at each depth for root density measurement and soil carbon (C) and nitrogen (N) analysis. The two soils exhibited a wide range of root densities from 1.53 to 37.03 mg dry root g−1 soil. The average root density in the Fluvial soil (13.21 mg g−1) was twice that in the Allophanic soil (6.88 mg g−1). Calibration models, developed using partial least squares regression (PLSR) of the first derivative spectra and reference data, were able to predict root density on unknown samples using a leave-one-out cross-validation procedure. The root density predictions were more accurate when the samples from the two soil types were separated (rather than grouped) to give sub-populations ( n = 54) of spectral data with more similar attributes. A better prediction of root density was achieved in the Allophanic soil ( r2 = 0.83, ratio prediction to deviation (RPD ) = 2.44, root mean square error of cross-validation (RMSECV ) = 1.96 mg g −1) than in the Fluvial soil ( r2 = 0.75, RPD = 1.98, RMSECV = 5.11 mg g −1). It is concluded that pasture root density can be predicted from soil reflectance spectra acquired from field soil cores. Improved PLSR models for predicting field root density can be produced by selecting calibration data from field data sources with similar spectral attributes to the validation set. Root density and soil C content can be predicted independently, which could be particularly useful in studies examining potential rates of soil organic matter change. [ABSTRACT FROM AUTHOR]

Soil organic matter accumulation and concomitant fertility changes in soils recently converted from plantation forest to pastoral agriculture in the Taupo-Rotorua Volcanic Zone have been observed, with a probable soil C sequestration rate of 6.1 t ha-1 year-1, and a soil N sequestration rate of 0.45 t ha-1 year-1, to 150 mm soil depth, for the first 5 years after conversion at two of three selected farms. Rapid increases in Olsen P were observed, with soils reaching their optimum agronomic range within 3-5 years after conversion, at two of three farms. A decreasing C:N ratio with time since conversion reflects improved fertility status, and implies that in initial years of pasture establishment, N losses are reduced due to its immobilisation into soil organic matter. These research findings suggest that land-use change from plantation forest to pastoral farm, with inputs of N, P, K and S to soils, allows significant soil C and N sequestration for at least 5 years after conversion. This rate of C sequestration could be used as an offset for forest C sink loss in future emissions trading systems. Further research is required to at least 0.3 m depth to confirm this preliminary study. [ABSTRACT FROM AUTHOR]

The objective of this study was to examine the feasibility of using a two-step, fully biological and sustainable strategy for the treatment of carbohydrate rich wastes. The primary step in this strategy involves the application of thermostable enzymes produced by the thermophilic, aerobic fungus, Talaromyces emersonii, to carbohydrate wastes producing a liquid hydrolysate discharged at elevated temperatures. To assess the potential of thermophilic treatment of this hydrolysate, a comparative study of thermophilic and mesophilic digestion of four sugar rich thermozyme hydrolysate waste streams was conducted by operating two high rate upflow anaerobic hybrid reactors (UAHR) at 37°C (R1) and 55°C (R2). The operational performance of both reactors was monitored from start-up by assessing COD removal efficiencies, volatile fatty acid (VFA) discharge and % methane of the biogas produced. Rapid start-up of both R1 and R2 was achieved on an influent composed of the typical sugar components of the organic fraction of municipal solid waste (OFMSW). Both reactors were subsequently challenged in terms of volumetric loading rate (VLR) and it was found that a VLR of 9gCODl¿1 d¿1 at a hydraulic retention time (HRT) of 1 day severely affected the thermophilic reactor with instability characterised by a build up of volatile fatty acid (VFA) intermediates in the effluent. The influent to both reactors was changed to a simple glucose and sucrose-based influent supplied at a VLR of 4.5gCODl¿1 d¿1 and HRT of 2 days prior to the introduction of thermozyme hydrolysates. Four unique thermozyme hydrolysates were subsequently supplied to the reactors, each for a period of 10 HRTs. The applied hydrolysates were derived from apple pulp, bread, carob powder and cardboard, all of which were successfully and comparably converted by both reactors. The % total carbohydrate removal by both reactors was monitored during the application of the sugar rich thermozyme hydrolysates. This approach offers a sustainable technology for the treatment of carbohydrate rich wastes and highlights the potential of these wastes as substrates for the generation of second-generation biofuels. [Copyright &y& Elsevier]

This paper reports the use of visible/near-infrared reflectance spectroscopy (Vis-NIRS) to predict pasture root density. A population of varying grass root densities was created by growing Moata ryegrass ( Lolium multiflorum Lam.) for 72 days in pots of Ramiha silt loam (Allophanic) and Manawatu fine sandy loam (Recent Fluvial) (60 pots for each soil) differentially fertilized with nitrogen (N) and phosphorus (P) in a glass house experiment. At harvest, the reflectance spectra (350–2500 nm) from flat sectioned horizontal soil slices (1.3 cm depth), taken from 57 selected pots, were recorded using a portable spectroradiometer (ASD FieldSpec Pro, Boulder, CO). Root densities within each of the soil slices were measured using a wet sieving technique. A large variation in root densities (0.46–5.02 mg dry root cm−3) was obtained from the glass house experiment as plant growth responded to the different soils and rates of N and P fertilizer treatment. Pots of the Manawatu soil contained greater ryegrass root densities (1.76–5.02 mg dry root cm−3) than pots of the Ramiha soil (0.46–3.84 mg dry root cm−3). Each soil had visually distinct reflectance spectra in the range 470–2440 nm, but different root masses produced relatively small differences in reflectance spectra. The first two principal components (PC1 and PC2) of a principal component analysis of the first derivative of the spectral reflectance accounted for 71.3% of the spectral variance and clearly separated the Ramiha and Manawatu soils. PC1, which accounted for 58.4% of the spectral variance, was also well correlated to root density. Partial least squares regression (PLSR) of the first derivative of the 10 nm spaced spectral data against measured root densities produced calibration models that allowed quantitative estimates of root densities (without removing outlier, r2 cross-validation = 0.78, ratio of prediction to deviation (RPD) = 2.14, root mean squares error of cross-validation (RMSECV) = 0.60 mg cm−3; with removing outliers, r2 cross-validation = 0.85, RPD = 2.63, RMSECV = 0.47 mg cm−3). The study indicated that spectral reflectance measurement has the potential to quantify root density in soils. [ABSTRACT FROM AUTHOR]