Genetic diversity, aggressiveness and metalaxyl sensitivity of Pythium aphanidermatum populations infecting cucumber in Oman

Seventy three isolates of Pythium aphanidermatum obtained from cucumber from four different regions of Oman and 16 isolates of muskmelon from the Batinah region in Oman were characterized for aggressiveness, sensitivity to metalaxyl and genetic diversity using AFLP fingerprinting. Twenty isolates of P. aphanidermatum from diverse hosts from different countries were also included in the study. Most isolates from Oman were found to be aggressive on cucumber seedlings and all were highly sensitive to metalaxyl (EC50 < 0•80 µg mL−1). Isolates from cucumber and muskmelon were as aggressive as each other on both hosts (P > 0.05), which implies a lack of host specialization in P. aphanidermatum on these two hosts in Oman. AFLP analysis of all isolates using four primer-pair combinations resolved 152 bands, of which 61 (~40%) were polymorphic. Isolates of P. aphanidermatum from Oman and other countries exhibited high genetic similarity (mean = 94.1%) and produced 59 different AFLP profiles. Analysis of molecular variance indicated that most AFLP variation among populations of P. aphanidermatum in Oman was associated with geographical regions (FST = 0.118; P < 0.0001), not hosts (FST = -0.004; P = 0.4323). These data were supported by the high rate of recovery (24%) of identical phenotypes between cucumber and muskmelon fields in the same region as compared to the low recovery (10%) across regions in Oman, which suggests more frequent movement of Pythium inoculum among muskmelon and cucumber fields in the same region compared to movement across geographically separated regions. However, recovering clones among regions and different countries may imply circulation of Pythium inoculum via common sources in Oman and also intercontinental spread of isolates.

Genetic diversity, aggressiveness and metalaxyl sensitivity of Pythium spinosum infecting cucumber in Oman

A total of 24 isolates of Pythium spinosum from cucumber obtained from five regions in Oman were characterized for genetic diversity using amplified fragment length polymorphism (AFLP) fingerprinting and three isolates from the Netherlands, South Africa and Japan were included for comparison. Isolates from Oman were also characterized for aggressiveness on cucumber seedlings and sensitivity to metalaxyl. Identity of all isolates was confirmed using sequences of the internal transcribed spacer (ITS) region of the ribosomal DNA (rDNA), which showed more than 99% nucleotide similarity among all isolates. Using six primer-pair combinations, AFLP fingerprinting resolved 295 AFLP markers of which 193 were polymorphic among isolates from other countries and only six were polymorphic among isolates of P. spinosum from Oman. Seven different AFLP phenotypes of P. spinosum were recovered in Oman; two of them were found to contain over 79% of isolates and one was recovered from all regions in Oman. Phenotypes from Oman showed very high (?99%) levels of genetic similarity to each other compared to moderate (mean =53%) levels of genetic similarity with phenotypes from other countries. In addition, all isolates from Oman were found to be highly sensitive to metalaxyl and all were aggressive on cucumber seedlings at 25°C. The high genetic similarity among phenotypes of P. spinosum in Oman as well as recovering two major clones across regions may suggest that P. spinosum has been recently introduced in Oman via a common source.

The sensitivity of updated NIR PLS models for fruit sorting to initial parameter settings

Partial least squares regression models on NIR spectra are often optimised (for wavelength range, mathematical pretreatment and outlier elimination) in terms of calibration terms of validation performance with reference to totally independent populations.

Molecular characterisation, pathogenesis and fungicide sensitivity of Pythium spp. from table beet (Beta vulgaris var. vulgaris) grown in the Lockyer Valley, Queensland

Table beet production in the Lockyer Valley of south-eastern Queensland is known to be adversely affected by soilborne root disease from infection by Pythium spp. However, little is known regarding the species or genotypes that are the causal agents of both pre- and post-emergence damping off. Based on RFLP analysis with HhaI, HinfI and MboI of the PCR amplified ITS region DNA from soil and diseased plant samples, the majority of 130 Pythium isolates could be grouped into three genotypes, designated LVP A, LVP B and LVP C. These groups comprised 43, 41 and 7% of all isolates, respectively. Deoxyribonucleic acid sequence analysis of the ITS region indicated that LVP A was a strain of Pythium aphanidermatum, with greater than 99% similarity to the corresponding P. aphanidermatum sequences from the publicly accessible databases. The DNA sequences from LVP B and LVP C were most closely related to P. ultimum and P. dissotocum, respectively. Lower frequencies of other distinct isolates with unique RFLP patterns were also obtained with high levels of similarity (>97%) to P. heterothallicum, P. periplocum and genotypes of P. ultimum other than LVP B. Inoculation trials of 1- and 4-week-old beet seedlings indicated that compared with isolates of the LVP B genotype, a higher frequency of LVP A isolates caused disease. Isolates with the LVP A, LVP B and LVP C genotypes were highly sensitive to the fungicide Ridomil MZ, which suppressed radial growth on V8 agar between approximately four and thirty fold at 5 μg/mL metalaxyl and 40 μg/mL mancozeb, a concentration far lower than the recommended field application rate.

Parameter estimation and sensitivity analysis of fat deposition models in beef steers using acslXtreme.

The Davis Growth Model (a dynamic steer growth model encompassing 4 fat deposition models) is currently being used by the phenotypic prediction program of the Cooperative Research Centre (CRC) for Beef Genetic Technologies to predict P8 fat (mm) in beef cattle to assist beef producers meet market specifications. The concepts of cellular hyperplasia and hypertrophy are integral components of the Davis Growth Model. The net synthesis of total body fat (kg) is calculated from the net energy available after accounting tor energy needs for maintenance and protein synthesis. Total body fat (kg) is then partitioned into 4 fat depots (intermuscular, intramuscular, subcutaneous, and visceral). This paper reports on the parameter estimation and sensitivity analysis of the DNA (deoxyribonucleic acid) logistic growth equations and the fat deposition first-order differential equations in the Davis Growth Model using acslXtreme (Hunstville, AL, USA, Xcellon). The DNA and fat deposition parameter coefficients were found to be important determinants of model function; the DNA parameter coefficients with days on feed >100 days and the fat deposition parameter coefficients for all days on feed. The generalized NL2SOL optimization algorithm had the fastest processing time and the minimum number of objective function evaluations when estimating the 4 fat deposition parameter coefficients with 2 observed values (initial and final fat). The subcutaneous fat parameter coefficient did indicate a metabolic difference for frame sizes. The results look promising and the prototype Davis Growth Model has the potential to assist the beef industry meet market specifications.

Do elasmobranch reactions to magnetic fields in water show promise for bycatch mitigation?

Elasmobranchs are under increasing pressure from targeted fisheries worldwide, but unregulated bycatch is perhaps their greatest threat. This study tested five elasmobranch bycatch species (Sphyrna lewini, Carcharhinus tilstoni, Carcharhinus amblyrhynchos, Rhizoprionodon acutus, Glyphis glyphis) and one targeted teleost species (Lates calcarifer) to determine whether magnetic fields caused a reaction response and/or change in spatial use of an experimental arena. All elasmobranch species reacted to magnets at distances between 0.26 and 0.58 m at magnetic strengths between 25 and 234 gauss and avoided the area around the magnets. Contrastingly, the teleosts showed no reaction response and congregated around the magnets. The different reactions of the teleosts and elasmobranchs are presumably driven by the presence of ampullae of Lorenzini in the elasmobranchs; different reaction distances between elasmobranch species appeared to correlate with their feeding ecology. Elasmobranchs with a higher reliance on the electroreceptive sense to locate prey reacted to the magnets at the greatest distance, except G. glyphis. Notably, this is the only elasmobranch species tested with a fresh- and saltwater phase in their ecology, which may account for the decreased magnetic sensitivity. The application of magnets worldwide to mitigate the bycatch of elasmobranchs appears promising based on these results.

Net radiation dynamics: performance of 20 daily net radiation models as related to model structure and intricacy in two climates.

We compared daily net radiation (Rn) estimates from 19 methods with the ASCE-EWRI Rn estimates in two climates: Clay Center, Nebraska (sub-humid) and Davis, California (semi-arid) for the calendar year. The performances of all 20 methods, including the ASCE-EWRI Rn method, were then evaluated against Rn data measured over a non-stressed maize canopy during two growing seasons in 2005 and 2006 at Clay Center. Methods differ in terms of inputs, structure, and equation intricacy. Most methods differ in estimating the cloudiness factor, emissivity (e), and calculating net longwave radiation (Rnl). All methods use albedo (a) of 0.23 for a reference grass/alfalfa surface. When comparing the performance of all 20 Rn methods with measured Rn, we hypothesized that the a values for grass/alfalfa and non-stressed maize canopy were similar enough to only cause minor differences in Rn and grass- and alfalfa-reference evapotranspiration (ETo and ETr) estimates. The measured seasonal average a for the maize canopy was 0.19 in both years. Using a = 0.19 instead of a = 0.23 resulted in 6% overestimation of Rn. Using a = 0.19 instead of a = 0.23 for ETo and ETr estimations, the 6% difference in Rn translated to only 4% and 3% differences in ETo and ETr, respectively, supporting the validity of our hypothesis. Most methods had good correlations with the ASCE-EWRI Rn (r2 > 0.95). The root mean square difference (RMSD) was less than 2 MJ m-2 d-1 between 12 methods and the ASCE-EWRI Rn at Clay Center and between 14 methods and the ASCE-EWRI Rn at Davis. The performance of some methods showed variations between the two climates. In general, r2 values were higher for the semi-arid climate than for the sub-humid climate. Methods that use dynamic e as a function of mean air temperature performed better in both climates than those that calculate e using actual vapor pressure. The ASCE-EWRI-estimated Rn values had one of the best agreements with the measured Rn (r2 = 0.93, RMSD = 1.44 MJ m-2 d-1), and estimates were within 7% of the measured Rn. The Rn estimates from six methods, including the ASCE-EWRI, were not significantly different from measured Rn. Most methods underestimated measured Rn by 6% to 23%. Some of the differences between measured and estimated Rn were attributed to the poor estimation of Rnl. We conducted sensitivity analyses to evaluate the effect of Rnl on Rn, ETo, and ETr. The Rnl effect on Rn was linear and strong, but its effect on ETo and ETr was subsidiary. Results suggest that the Rn data measured over green vegetation (e.g., irrigated maize canopy) can be an alternative Rn data source for ET estimations when measured Rn data over the reference surface are not available. In the absence of measured Rn, another alternative would be using one of the Rn models that we analyzed when all the input variables are not available to solve the ASCE-EWRI Rn equation. Our results can be used to provide practical information on which method to select based on data availability for reliable estimates of daily Rn in climates similar to Clay Center and Davis.

Antibiotic Sensitivity Testing

Respiratory bacterial pathogens in pigs are currently treated with antibiotics. Intervet - Schering Plough markets an antibiotic called Nurflor (Florfenicol) targeting respiratory pathogens. This project tests the effectiveness of this antibiotic against a series of respiratory pathogens. 6 isolates will be tested per serovar/strain and the isolates will be from 4 different farms using MIC testing. The sensitivity of Florfenicol will be compared to sensitivity of the organisms to Tilmicosin and Amoxicillin. Development of resistance to certain antibiotics have been reported, so it is important to have alternative antibiotics available to treat the respiratory pathogens on farms.

Soil carbon stock in the tropical rangelands of Australia: Effects of soil type and grazing pressure, and determination of sampling requirement.

On-going, high-profile public debate about climate change has focussed attention on how to monitor the soil organic carbon stock (C(s)) of rangelands (savannas). Unfortunately, optimal sampling of the rangelands for baseline C(s) - the critical first step towards efficient monitoring - has received relatively little attention to date. Moreover, in the rangelands of tropical Australia relatively little is known about how C(s) is influenced by the practice of cattle grazing. To address these issues we used linear mixed models to: (i) unravel how grazing pressure (over a 12-year period) and soil type have affected C(s) and the stable carbon isotope ratio of soil organic carbon (delta(13)C) (a measure of the relative contributions of C(3) and C(4) vegetation to C(s)); (ii) examine the spatial covariation of C(s) and delta(13)C; and, (iii) explore the amount of soil sampling required to adequately determine baseline C(s). Modelling was done in the context of the material coordinate system for the soil profile, therefore the depths reported, while conventional, are only nominal. Linear mixed models revealed that soil type and grazing pressure interacted to influence C(s) to a depth of 0.3 m in the profile. At a depth of 0.5 m there was no effect of grazing on C(s), but the soil type effect on C(s) was significant. Soil type influenced delta(13)C to a soil depth of 0.5 m but there was no effect of grazing at any depth examined. The linear mixed model also revealed the strong negative correlation of C(s) with delta(13)C, particularly to a depth of 0.1 m in the soil profile. This suggested that increased C(s) at the study site was associated with increased input of C from C(3) trees and shrubs relative to the C(4) perennial grasses; as the latter form the bulk of the cattle diet, we contend that C sequestration may be negatively correlated with forage production. Our baseline C(s) sampling recommendation for cattle-grazing properties of the tropical rangelands of Australia is to: (i) divide the property into units of apparently uniform soil type and grazing management; (ii) use stratified simple random sampling to spread at least 25 soil sampling locations about each unit, with at least two samples collected per stratum. This will be adequate to accurately estimate baseline mean C(s) to within 20% of the true mean, to a nominal depth of 0.3 m in the profile.

Comparative effects of thermal and high pressure processing on phenolic phytochemicals in different strawberry cultivars

Abstract It is widely considered that high pressure processing (HPP) results in better retention of micronutrients and phytochemicals compared to thermal pasteurization (TP), although some studies indicate that this may not be true in all cases. The aims of this study were (1) to objectively compare the effects of HPP under commercial processing conditions with thermal pasteurization (TP) on the stability of phenolic antioxidants in strawberries following processing and during storage and (2) to evaluate the influence of varietal differences and hence differences in biochemical composition of strawberries on the stability of phenolic antioxidants. Strawberry puree samples from cultivars Camarosa, Rubygem, and Festival were subjected to HPP (600 MPa/20 °C/5 min) and TP (88 °C/2 min). The activities of oxidative enzymes were evaluated before and after processing. Furthermore, the antioxidant capacity (total phenolic content (TPC), oxygen radical absorbance capacity (ORAC), and ferric reducing antioxidant power (FRAP)) and individual anthocyanins (by HPLC) were determined prior to and following processing and after three months of refrigerated storage (4 °C). Depending on the cultivar, HPP caused 15–38% and 20–33% inactivation of polyphenol oxidase and peroxidase, respectively, compared to almost complete inactivation of these enzymes by TP. Significant decreases (p < 0.05) in ORAC, FRAP, TPC and anthocyanin contents were observed during processing and storage of both HPP and TP samples. Anthocyanins were the most affected with only 19–25% retention after three months of refrigerated storage (4 °C). Slightly higher (p < 0.05) loss of TPC and antioxidant capacity were observed during storage of HPP samples compared to TP. Industrial Relevance: The results of the study demonstrated that both high pressure processing and thermal pasteurization result in high retention of phenolic phytochemicals in strawberry products. Under the conditions investigated, high pressure processing did not result in a better retention of phenolic phytochemicals compared to thermal pasteurization. In fact, a slightly higher loss of total polyphenol content and antioxidant capacity were observed during refrigerated storage of HPP processed samples. Our results showed that, high pressure processing may not always be a better alternative to thermal processing for strawberry puree processing if the main objective is better retention of phenolic antioxidants. However, it should be noted that other quality attributes such as sensory properties, where distinct advantages of HPP are expected, were outside the scope of this study.

The critical role of extreme heat for maize production in the United States

Statistical studies of rainfed maize yields in the United States(1) and elsewhere(2) have indicated two clear features: a strong negative yield response to accumulation of temperatures above 30 degrees C (or extreme degree days (EDD)), and a relatively weak response to seasonal rainfall. Here we show that the process-based Agricultural Production Systems Simulator (APSIM) is able to reproduce both of these relationships in the Midwestern United States and provide insight into underlying mechanisms. The predominant effects of EDD in APSIM are associated with increased vapour pressure deficit, which contributes to water stress in two ways: by increasing demand for soil water to sustain a given rate of carbon assimilation, and by reducing future supply of soil water by raising transpiration rates. APSIM computes daily water stress as the ratio of water supply to demand, and during the critical month of July this ratio is three times more responsive to 2 degrees C warming than to a 20% precipitation reduction. The results suggest a relatively minor role for direct heat stress on reproductive organs at present temperatures in this region. Effects of elevated CO2 on transpiration efficiency should reduce yield sensitivity to EDD in the coming decades, but at most by 25%.

Interacting effects of vegetation, soils and management on the sensitivity of Australian savanna rangelands to climate change

There is an increasing need to understand what makes vegetation at some locations more sensitive to climate change than others. For savanna rangelands, this requires building knowledge of how forage production in different land types will respond to climate change, and identifying how location-specific land type characteristics, climate and land management control the magnitude and direction of its responses to change. Here, a simulation analysis is used to explore how forage production in 14 land types of the north-eastern Australian rangelands responds to three climate change scenarios of +3A degrees C, +17% rainfall; +2A degrees C, -7% rainfall; and +3A degrees C, -46% rainfall. Our results demonstrate that the controls on forage production responses are complex, with functional characteristics of land types interacting to determine the magnitude and direction of change. Forage production may increase by up to 60% or decrease by up to 90% in response to the extreme scenarios of change. The magnitude of these responses is dependent on whether forage production is water or nitrogen (N) limited, and how climate changes influence these limiting conditions. Forage production responds most to changes in temperature and moisture availability in land types that are water-limited, and shows the least amount of change when growth is restricted by N availability. The fertilisation effects of doubled atmospheric CO2 were found to offset declines in forage production under 2A degrees C warming and a 7% reduction in rainfall. However, rising tree densities and declining land condition are shown to reduce potential opportunities from increases in forage production and raise the sensitivity of pastures to climate-induced water stress. Knowledge of these interactions can be applied in engaging with stakeholders to identify adaptation options.

Strategies to limit the impact of nematode pressure on sugarcane productivity in the Isis

Two trials were done in this project. One was a continuation of work started under a previous GRDC/SRDC-funded activity, 'Strategies to improve the integration of legumes into cane based farming systems'. This trial aimed to assess the impact of trash and tillage management options and nematicide application on nematodes and crop performance. Methods and results are contained in the following publication: Halpin NV, Stirling GR, Rehbein WE, Quinn B, Jakins A, Ginns SP. The impact of trash and tillage management options and nematicide application on crop performance and plant-parasitic nematode populations in a sugarcane/peanut farming system. Proc. Aust. Soc. Sugar Cane Technol. 37, 192-203. Nematicide application in the plant crop significantly reduced total numbers of plant parasitic nematodes (PPN) but there was no impact on yield. Application of nematicide to the ratoon crop significantly reduced sugar yield. The study confirmed other work demonstrating that implementation of strategies like reduced tillage reduced populations of total PPN, suggesting that the soil was more suppressive to PPN in those treatments. The second trial, a variety trial, demonstrated the limited value of nematicide application in sugarcane farming systems. This study has highlighted that growers shouldn’t view nematicides as a ‘cure all’ for paddocks that have historically had high PPN numbers. Nematicides have high mammalian toxicity, have the potential to contaminate ground water (Kookana et al. 1995) and are costly. The cost of nematicide used in R1 was approx. $320 - $350/ha, adding $3.50/t of cane in a 100 t/ha crop. Also, our study demonstrated that a single nematicide treatment at the application rate registered for sugarcane is not very effective in reducing populations of nematode pests. There appears to be some levels of resistance to nematodes within the current suite of varieties available to the southern canelands. For example the soil in plots that were growing Q183 had 560% more root knot nematodes / 200mL soil compared to plots that grew Q245. The authors see great value in investment into a nematode screening program that could rate varieties into groups of susceptibility to both major sugarcane nematode pests. Such a rating could then be built into a decision support ‘tree’ or tool to better enable producers to select varieties on a paddock by paddock basis.