Detection and genetic diversity of porcine rotavirus A,B and C in eastern Australian piggeries

Rotaviruses (RV) have a high prevalence in piggeries worldwide and are one of the major pathogens causing severe diarrhoea in young pigs. RV species A, B, and C have been linked to piglet diarrhoea in Australian pig herds, but their genetic diversity has not been studied in detail. Based on sequencing of the structural viral protein 7 (VP7) RVA G genotypes G3, G4 and G5, and RVC types G1, G3, G5, and G6 have been identified in Australian piggeries in previous studies. Although occurrence of RVB was reported in Australia in 1988, no further genetic analysis has been conducted. To improve health management decisions in Australian pig herds, more information on RV prevalence and genetic diversity is needed. Here, 243 enteric samples collected from 20 pig farms within Eastern Australia were analysed for the presence of RV in different age groups using a novel PCR-based multiplex assay (Pork MultiPath™ enteric panel). RVA, RVB, and RVC were detected in 10, 14, and 14 farms, respectively. Further sequencing of VP7 in selected RV-positive samples revealed G genotypes G2, G5, G9 (RVA), G6, G8, G14, G16, G20 (RVB), and G1, G3, G5, G6 (RVC) present. RVA was only detected in young (<10 weeks old) pigs whereas RVB and RVC were also detected in older animals (>11 weeks old). Interestingly, RVB and RVC G-type occurrence differed between age groups. In conclusion, this study provides new insights on the prevalence and diversity of different RV species in pig herds of Eastern Australia whilst demonstrating the ability of the Pork MultiPath™ technology to accurately differentiate between these RV species.     

Flow alteration and thermal pollution depress modelled growth rates of an iconic riverine fish,the Murray cod Maccullochella peelii

The serial discontinuity concept (SDC) proposes that hypolimnetic‐releasing impoundments cause major disruptions to the naturally occurring physical, chemical and biological gradients of rivers but that this impact diminishes with distance downstream. Such a gradient in discharge, flow velocity and temperature regime occurs below a large hypolimnetic‐releasing impoundment, the Hume Dam, on the River Murray in south‐eastern Australia. To examine the effects of this disturbance gradient on a warm‐water large‐bodied freshwater fish, the Murray cod (Maccullochella peelii), a bioenergetics model was developed and calibrated to explore energy expended under differing water velocities and temperature regimes. Model simulations predicted negative growth of juveniles directly downstream of the impoundment, due largely to the energetic costs associated with active and, to a lesser extent, standard metabolism outweighing the achievable energetic gains through food consumption. As flow velocity and temperature regimes became more favourable downstream, so did the simulated growth of the species. It was not until +239 km downstream of the impoundment that the model predicted that flow velocity and temperature regimes were suitable for greater weight gains. The modelled growth responses of juvenile Murray cod are consistent with the predictions of the SDC, emphasising that changes in the bioenergetics of individuals are likely to be reflected in reduced growth rates under the changed flow velocity and temperature regimes imposed by disturbance gradients. This research represents a valuable step in the biological understanding of Murray cod within variable riverine environments and emphasises the urgency required to mitigate impacts associated with hypolimnetic impoundments.     

Ace and ace-like genes of invasive redlegged earth mite: copy number variation,target-site mutations,and their associations with organophosphate insensitivity

Background

Invasive Australian populations of redlegged earth mite, Halotydeus destructor (Tucker), are evolving increasing organophosphate resistance. In addition to the canonical ace gene, the target gene of organophosphates, the H. destructor genome contains many radiated ace-like genes that vary in copy number and amino acid sequence. In this work, we characterise copy number and target-site mutation variation at the canonical ace and ace-like genes and test for potential associations with organophosphate insensitivity. This was achieved through comparisons of whole-genome pool-seq data from alive and dead mites following organophosphate exposure.

Results

A combination of increased copy number and target-site mutations at the canonical ace was associated with organophosphate insensitivity in H. destructor. Resistant populations were segregating for G119S, A201S, F331Y at the canonical ace. A subset of populations also had copy numbers of canonical ace > 2, which potentially helps overexpress proteins carrying these target-site mutations. Haplotypes possessing different copy numbers and target-site mutations of the canonical ace gene may be under selection across H. destructor populations. We also detected some evidence that increases in copy number of radiated ace-like genes are associated with organophosphate insensitivity, which might suggest potential roles in sequestration or breakdown of organophosphates.

Conclusion

Different combinations of target-site mutations and (or) copy number variation in the canonical ace and ace-like genes may provide non-convergent ways for H. destructor to respond to organophosphate selection. However, these changes may only play a partial role in organophosphate insensitivity, which appears to have a polygenic architecture. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.     

Evaluating a multi-level subsurface drainage system for improved drainage water quality

This paper describes a multi-level drainage system, designed to improve drainage water quality. Results are presented from a field scale land reclamation experiment implemented in the Murrumbidgee Irrigation Area of New South Wales, Australia. A traditional single level drainage system and a multi-level drainage system were compared in the experiment in an irrigated field setting. The single level drainage system consisted of 1.8 m deep drains at 20 m spacing. This configuration is typical of subsurface drainage system design used in the area. The multi-level drainage system consisted of shallow closely spaced drains (3.3 m spacing at 0.75 m depth) underlain by deeper widely spaced drains (20 m spacing at 1.8 m depth). Data on drainage flows and salinity, water table regime and soil salinity were collected over a 2-year period.     

Performance of CERES-Rice and CERES-Wheat models in rice–wheat systems: A review

Rice–wheat (RW) systems are critical to food security and livelihoods of rural and urban poor in south Asia and China, and to regional economies in southeast Australia. The sustainability of RW systems in south Asia is, however, threatened by yield stagnation or decline, and declining partial factor productivity, soil organic C and water availability. Crop models potentially offer a means to readily explore management options to increase yield, and to determine trade-off between yield, resource-use efficiency and environmental outcomes. This paper reviews the performance of CERES-Rice and CERES-Wheat in Asia and Australia in relation to their potential application towards increasing resource use efficiency and yield of RW systems.

The performance of the models was evaluated using simulated and observed data on anthesis and maturity dates, in-season LAI and growth, final grain yield and its components, and soil water and N balances from published studies across Asia and Australia, and then by computing the statistical parameters for the major characters. Over the four data sets examined for anthesis and six for maturity dates, CERES-Rice predicted those dates fairly well (normalised RMSE = 4–5%; D-index = 0.94–0.95), but over the 11 sets for grain and 4 for biomass yield, the predictions were more variable (normalised RMSE = 23% for both; D-index 0.90 and 0.76, for grain and biomass, respectively). Model performance was poorer under conditions of low N, water deficit, and low temperatures during the reproductive stages. Over the three data sets examined, CERES-Wheat predicted the anthesis and maturity dates quite well (normalised RMSE = 4–5%; D-index = 0.94–0.99), and over eight sets for grain and two sets for biomass yield the model predicted them also reasonably well (RMSE = 13–16%; D-index = 0.86–0.97). Only one study evaluated the DSSAT RW sequence model with fairly satisfactory predictions of rice and wheat yields over 20 years with adequate N, but not the long-term change in soil organic C and N. Predictions of in-season LAI and crop growth, and soil and water processes were quite limited to investigate the robustness of model processes.

Application of models to evaluate options to increase water and N use efficiency requires the ability to perform well at the margin where deficit stress begins. While both models generally perform satisfactorily under water and N non-limiting conditions, the little evidence available suggests that they do not perform well under resource-limiting situations. We recommend that the models’ key processes under the water and N limiting conditions be further evaluated urgently. The DSSAT sequence model also needs to be further evaluated against observations for a range of locations and management using data from long-term experiments in RW systems.