Cytorhabdovirus phosphoprotein shows RNA silencing suppressor activity in plants, but not in insect cells

RNA silencing in plants and insects provides an antiviral defense and as a countermeasure most viruses encode RNA silencing suppressors (RSS). For the family Rhabdoviridae, no detailed functional RSS studies have been reported in plant hosts and insect vectors. In agroinfiltrated Nicotiana benthamiana leaves we show for the first time for a cytorhabdovirus, lettuce necrotic yellows virus (LNYV), that one of the nucleocapsid core proteins, phosphoprotein (P) has relatively weak local RSS activity and delays systemic silencing of a GFP reporter. Analysis of GFP small RNAs indicated that the P protein did not prevent siRNA accumulation. To explore RSS activity in insects, we used a Flock House virus replicon system in Drosophila S2 cells. In contrast to the plant host, LNYV P protein did not exhibit RSS activity in the insect cells. Taken together our results suggest that P protein may target plant-specific components of RNA silencing post siRNA biogenesis.

First complete genome sequence of a capsicum chlorosis tospovirus isolate from Australia with an unusually large S RNA intergenic region

The first complete genome sequence of capsicum chlorosis virus (CaCV) from Australia was determined using a combination of Illumina HiSeq RNA and Sanger sequencing technologies. Australian CaCV had a tripartite genome structure like other CaCV isolates. The large (L) RNA was 8913 nucleotides (nt) in length and contained a single open reading frame (ORF) of 8634 nt encoding a predicted RNA-dependent RNA polymerase (RdRp) in the viral-complementary (vc) sense. The medium (M) and small (S) RNA segments were 4846 and 3944 nt in length, respectively, each containing two non-overlapping ORFs in ambisense orientation, separated by intergenic regions (IGR). The M segment contained ORFs encoding the predicted non-structural movement protein (NSm; 927 nt) and precursor of glycoproteins (GP; 3366 nt) in the viral sense (v) and vc strand, respectively, separated by a 449-nt IGR. The S segment coded for the predicted nucleocapsid (N) protein (828 nt) and non-structural suppressor of silencing protein (NSs; 1320 nt) in the vc and v strand, respectively. The S RNA contained an IGR of 1663 nt, being the largest IGR of all CaCV isolates sequenced so far. Comparison of the Australian CaCV genome with complete CaCV genome sequences from other geographic regions showed highest sequence identity with a Taiwanese isolate. Genome sequence comparisons and phylogeny of all available CaCV isolates provided evidence for at least two highly diverged groups of CaCV isolates that may warrant re-classification of AIT-Thailand and CP-China isolates as unique tospoviruses, separate from CaCV.

First report of Phoma multirostrata in Australia

Dark grey leaf lesions were observed on coriander (Coriandrum sativum) commercially grown at Wanneroo, Western Australia during November 2013. A species of Phoma was consistently isolated from leaf lesions. The pathogen was identified as Phoma multirostrata using morphological characteristics, DNA sequencing comparisons and pathogenicity testing. This is the first report of Phoma multirostrata causing leaf spot on coriander in Australia.

Do Human Extraintestinal Escherichia coli Infections Resistant to Expanded-Spectrum Cephalosporins Originate From Food-Producing Animals? A Systematic Review

To find out whether food-producing animals (FPAs) are a source of extraintestinal expanded-spectrum cephalosporin-resistant Escherichia coli (ESCR-EC) infections in humans, Medline, Embase, and the Cochrane Database of Systematic Reviews were systematically reviewed. Thirty-four original, peer-reviewed publications were identified for inclusion. Six molecular epidemiology studies supported the transfer of resistance via whole bacterium transmission (WBT), which was best characterized among poultry in the Netherlands. Thirteen molecular epidemiology studies supported transmission of resistance via mobile genetic elements, which demonstrated greater diversity of geography and host FPA. Seventeen molecular epidemiology studies did not support WBT and two did not support mobile genetic element-mediated transmission. Four observational epidemiology studies were consistent with zoonotic transmission. Overall, there is evidence that a proportion of human extraintestinal ESCR-EC infections originate from FPAs. Poultry, in particular, is probably a source, but the quantitative and geographical extent of the problem is unclear and requires further investigation.

Phylodynamic evidence of the migration of turnip mosaic potyvirus from Europe to Australia and New Zealand

Turnip mosaic virus (TuMV) is a potyvirus that is transmitted by aphids and infects a wide range of plant species. We investigated the evolution of this pathogen by collecting 32 isolates of TuMV, mostly from Brassicaceae plants, in Australia and New Zealand. We performed a variety of sequence-based phylogenetic and population genetic analyses of the complete genomic sequences and of three non-recombinogenic regions of those sequences. The substitution rates, divergence times and phylogeographical patterns of the virus populations were estimated. Six inter- and seven intralineage recombination-type patterns were found in the genomes of the Australian and New Zealand isolates, and all were novel. Only one recombination-type pattern has been found in both countries. The Australian and New Zealand populations were genetically different, and were different from the European and Asian populations. Our Bayesian coalescent analyses, based on a combination of novel and published sequence data from three nonrecombinogenic protein-encoding regions, showed that TuMV probably started to migrate from Europe to Australia and New Zealand more than 80 years ago, and that distinct populations arose as a result of evolutionary drivers such as recombination. The basal-B2 subpopulation in Australia and New Zealand seems to be older than those of the world-B2 and -B3 populations. To our knowledge, our study presents the first population genetic analysis of TuMV in Australia and New Zealand. We have shown that the time of migration of TuMV correlates well with the establishment of agriculture and migration of Europeans to these countries.

Modified Atmosphere Packaging (MAP) for Control of Black Spot Formation in Chilled Prawns

The marketing of organically labeled prawns is predominately in a cooked or raw frozen form to avoid the development of melanosis (black spot). Certification for organic status prohibits the use of any added chemicals. The application of 60% CO2/40%N2 modified atmosphere to chilled (raw) prawns using two species of prawn was investigated for the ability to control black spot formation. Sensory assessment and microbiological counts were used to determine the end of product shelf life. Modified atmosphere packaged (MAP) prawns exhibited no melanosis for up to 16 days. The high quality life was retained for 12 days; shelf life of 16 days, according to standard microbiological criteria, was achieved, which is more than twice previously reported for non-MAP prawns. Results suggest MAP may be an effective method for the marketing of organically grown prawns as well as those produced by conventional prawn aquaculture without application of the normal chemicals used to prevent black spot. Copyright © 2014 Crown Copyright.

Astaxanthin profiles and corresponding colour properties in Australian farmed black tiger prawn (Penaeus monodon) during frozen storage

The colour of commercial cooked black tiger prawns (Penaeus monodon) is a key quality requirement to ensure product is not rejected in wholesale markets. The colour, due to the carotenoid astaxanthin, can be impacted by frozen storage, but changes in colour or astaxanthin profile, during frozen storage, have not been studied in detail. Subsequently in this study, the aims were to define the astaxanthin (as cis, trans, mono-ester and di-ester forms) content, together with the colour properties, in both pleopods (legs) and abdominal segments. Changes in astaxanthin content and colour properties were further determined during frozen storage (−20°C). Total astaxanthin content was seen to decrease in all samples over time, with the rate of degradation being significantly greater (P < 0.05) in pleopods than abdomen. In both pleopods and abdomen, rate of degradation of esterified forms was significantly greater (P < 0.05) than non-esterified forms. Hue angle (increase), a* value (decrease) and L value (increase) were all seen to significantly change (P < 0.05) during storage, with changes being more prevalent in the pleopods. The pleopods are the key indicator of astaxanthin and colour loss in cooked black tiger prawns and preservation strategies are required to preserve astaxanthin and colour during frozen storage.

Continuous combined microwave and hot air treatment of apples for fruit fly (Bactrocera tryoni and B. jarvisi) disinfestation

Apples at 24 ± 2 °C were heated in a pilot scale hot air assisted (40 °C) continuous pentagonal microwave system, to evaluate the effectiveness of this treatment on insect mortality (variety Mutsu) and fruit quality (variety Granny Smith). An average temperature of 53.4 ± 1.3 °C at core, bottom and flesh of the apple was recorded at the end of the treatment. One hundred percent mortality of the most tolerant stage of Queensland fruit fly (Bactrocera tryoni, Froggatt) and Jarvis's fruit fly (Bactrocera jarvisi, Tryon), were observed when the Mortality value (M52, equivalent time of isothermal treatment at 52 °C) at the slowest heating point applicable for each experiment was ≥ 50 min and ≥ 37 min, respectively. Results showed that microwave heat treatment is effective for insect disinfestation without any adverse impact on total soluble solids, flesh or peel firmness of the treated apples. The treated apples recorded a significantly higher pH and lower ion leakage than the untreated apples after 3 or 4 weeks. Therefore, the microwave heat treatment has the potential to be developed as an alternative chemical free quarantine treatment against economically significant insect pests. Industrial relevance Hot air assisted microwave heating of fruits and vegetables, is more cost effective compared to vapour heat treatment and ionising radiation for disinfestation of insects. Microwave treatment is environmentally friendly compared to fumigation and chemical treatments. Hot air assisted microwave disinfestation can be performed at farms or centralised pack houses since the capital cost would be comparatively lower than vapour heat or ionising radiation treatments.

Reconfiguring agriculture through the relocation of production systems for water, environment and food security under climate change

The prospect of climate change has revived both fears of food insecurity and its corollary, market opportunities for agricultural production. In Australia, with its long history of state-sponsored agricultural development, there is renewed interest in the agricultural development of tropical and sub-tropical northern regions. Climate projections suggest that there will be less water available to the main irrigation systems of the eastern central and southern regions of Australia, while net rainfall could be sustained or even increase in the northern areas. Hence, there could be more intensive use of northern agricultural areas, with the relocation of some production of economically important commodities such as vegetables, rice and cotton. The problem is that the expansion of cropping in northern Australia has been constrained by agronomic and economic considerations. The present paper examines the economics, at both farm and regional level, of relocating some cotton production from the east-central irrigation areas to the north where there is an existing irrigation scheme together with some industry and individual interest in such relocation. Integrated modelling and expert knowledge are used to examine this example of prospective climate change adaptation. Farm-level simulations show that without adaptation, overall gross margins will decrease under a combination of climate change and reduction in water availability. A dynamic regional Computable General Equilibrium model is used to explore two scenarios of relocating cotton production from south east Queensland, to sugar-dominated areas in northern Queensland. Overall, an increase in real economic output and real income was realized when some cotton production was relocated to sugar cane fallow land/new land. There were, however, large negative effects on regional economies where cotton production displaced sugar cane. It is concluded that even excluding the agronomic uncertainties, which are not examined here, there is unlikely to be significant market-driven relocation of cotton production.

Fate of pathogen indicators in a domestic blend of food waste and wastewater through a two-stage anaerobic digestion system

Anaerobic digestion is a viable on-site treatment technology for rich organic waste streams such as food waste and blackwater. In contrast to large-scale municipal wastewater treatment plants which are typically located away from the community, the effluent from any type of on-site system is a potential pathogenic hazard because of the intimacy of the system to the community. The native concentrations of the pathogen indicators Escherichia coli, Clostridium perfringens and somatic coliphage were tracked for 30 days under stable operation (organic loading rate (OLR) = 1.8 kgCOD m(-3) day(-1), methane yield = 52% on a chemical oxygen demand (COD) basis) of a two-stage laboratory-scale digester treating a mixture of food waste and blackwater. E. coli numbers were reduced by a factor of 10(6.4) in the thermophilic stage, from 10(7.5+/-0.3) to 10(1.1+/-0.1) cfu 100 mL(-1), but regenerated by a factor of 10(4) in the mesophilic stage. Neither the thermophilic nor mesophilic stages had any significant impact on C. perfringens concentrations. Coliphage concentrations were reduced by a factor of 10(1.4) across the two stages. The study shows that anaerobic digestion only reduces pathogen counts marginally but that counts in effluent samples could be readily reduced to below detection limits by filtration through a 0.22 microm membrane, to investigate membrane filtration as a possible sanitation technique.

Fate of key food-borne pathogens associated with intensive pig and poultry farming environments

Intensive pig and poultry farming in Australia can be a source of pathogens with implications for food-safety and/or human illness. Seven studies were undertaken with the following objectives: · Assess the types of zoonotic pathogens in waste · Assess the transfer of pathogens during re-use both within the shed and externally in the environment · The potential for movement of pathogens via aerosols In the first and second studies the extent of zoonotic pathogens was evaluated in both piggery effluent and chicken litter and Salmonella and Campylobacter were detected in both wastes. In the third study the dynamics of Salmonella during litter re-use was examined and results showed a trend for lower Salmonella levels and serovar diversity in re-used litter compared to new litter. Thus, re-use within the poultry farming system posed no increased risk. The fourth study addressed the direct risks of pathogens to farm workers due to reuse of piggery effluent within the pig shed. Based on air-borne Escherichia coli (E. coli) levels, re-using effluent did not pose a risk. In the fifth study high levels of Arcobacter spp. were detected in effluent ponds and freshly irrigated soils with potential food-safety risks during the irrigation of food-crops and pasture. The sixth and seventh studies addressed the risks from aerosols from mechanically ventilated sheds. Staphylococci were shown to have potential as markers, with airborne levels gradually dropping and reaching background levels at 400 m distance. Salmonella was detected (at low levels) both inside and outside the shed (at 10 m). Campylobacter was detected only once inside the shed during the 3-year period (at low levels). Results showed there was minimal risk to humans living adjacent to poultry farms This is the first comprehensive analysis studying key food-safety pathogens and potential public health risks associated with intensively farmed pigs and poultry in Australia.

Re-use of chicken litter across broiler cycles – managing the food-borne pathogen risk

Thus the objectives of this study can be broadly categorised as follows:-  Evaluate current practices adopted (e.g. litter pile-up) prior to re-use of litter for subsequent chicken cycles  To establish pathogen die-off that occurs during currently adopted methods of in-shed treatment of litter  To establish simple physical parameters to monitor this pathogen reduction and create an understanding of such reduction strategies to aid in-shed management of re-use litter  To carry out studies to assess the potential of the re-used litter (once spread) to support pathogens during a typical chicken production cycle.  To provide background data for the development of a simple code of practice for an in-shed litter pile-up process

Managing resistance to chemical treatments in stored products pests

This review focuses on key trends in resistance to chemical treatments in stored product pests, and advances in resistance management, with an emphasis on resistance to the fumigant phosphine. Findings: Phosphine resistance continues to be a major concern. In particular, phosphine resistance in Cryptolestes ferrugineus has emerged as a serious issue, with some populations exhibiting the strongest level detected so far for this fumigant. In response, a 'quick knock down test' has been established to deliver industry and scientists 'same day' advice on the resistance status of field samples; sulfuryl fluoride is being developed as a 'resistance breaker' and phosphine dosages are being revised to manage this problem. There has been major progress in identifying the genes responsible for phosphine resistance and the development of molecular resistance diagnostics for key pests. Several studies on Rhyzopertha dominica have demonstrated that molecular screening can be used to determine the frequency of resistance alleles in samples collected from farm storages. Despite on-going research in several pests, there is no definitive answer to the question of whether there is a fitness cost associated phosphine resistance, with some studies showing a clear cost and others none. Evidence continues to emerge of resistance to grain protectants, including the juvenile hormone analogue methoprene. The development and adoption of spinosad, as a next generation 'green' treatment, and the use of protectant combinations provides opportunities to counter the problem of protectant resistance.Directions for future research: A uniform set of protocols should be developed for phosphine resistance detection for all major species. It should combine 'quick tests' and molecular diagnostics to be adopted internationally. Research is required on the establishment of a decision making system that integrates newly developed grain protectants and fumigants, other alternative control methods, as well as an accurate and rapid resistance detection system for early warning of the emergence of new resistances.