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Intragenomic variants of a putative effector drive early-stage infection in a broad host-range rust fungus
No full textRust fungi are pathogens that impact plants of environmental, agricultural, cultural, and economic importance. Their mechanisms of pathogenicity are not well-understood but are likely governed by effectors, secreted proteins that manipulate host cellular processes to facilitate infection and suppress immune responses. We sought to understand how three effector candidates (EFC1, EFC2, and EFC3) expressed in the first stages of Austropuccinia psidii (myrtle rust) infection influence pathogenicity. We experimentally tested gene function through application of double-stranded RNA (dsRNA) and characterised the genomic landscape of putative effectors expressed during infection to assess whether putative effectors are needed for infection, and whether they are under selection pressure. One of the three screened candidates, EFC1, met our criteria of an effector in that it was predicted to be secreted, and was needed to cause but not maintain infection. We identified that this effector belongs to a gene family of intragenomic variants in tandem repeats flanked by transposable elements. Single nucleotide polymorphisms among these variants have signatures of non-neutral selection. This effector has predicted structural homology to a glycosaminoglycan-binding domain and may have a role in pectin or chitin-binding. We hypothesise that intragenomic variability in this family of effector genes facilitates host-range versatility in the A. psidii-Myrtaceae pathosystem.Competing Interest StatementThe authors have declared no competing interest
Detection and Characterisation of Colistin-Resistant Escherichia coli in Broiler Meats
No full textThe irrational use of antimicrobials has led to the emergence of resistance, impacting not only pathogenic bacteria but also commensal bacteria. Resistance against colistin, a last-resort antibiotic, mediated by globally disseminated plasmid-borne mobile colistin resistance (mcr) genes, has raised significant global concerns. This cross-sectional study aimed to investigate the antimicrobial resistance patterns of colistin-resistant Escherichia coli (E. coli) and mobilised colistin resistance (mcr 1–5) genes from broiler meat. A total of 570 broiler samples (285 liver and 285 muscle) were collected from 7 supermarkets and 11 live bird markets (LBMs) in Chattogram metropolitan areas of Bangladesh. The isolation and identification of E. coli were carried out using standard bacteriological and molecular techniques. Antimicrobial susceptibility testing (AST) was performed using the Kirby–Bauer disc diffusion method, and colistin’s minimum inhibitory concentration (MIC) was determined by the broth microdilution (BMD) method. Colistin-resistant isolates were further tested for the presence of mcr (1–5) genes using polymerase chain reaction (PCR). Out of the 570 samples, 311 (54.56%; 95% confidence interval: 50.46–58.60) were positive for E. coli. AST results showed the highest resistance to sulphamethoxazole–trimethoprim (89.39%), while the highest susceptibility was observed for cefalexin (62.70%). A total of 296 isolates (95.18%) were found to be multidrug-resistant (MDR), with the multiple antibiotic resistance (MAR) index ranging from 0.38 to 1. Additionally, 41 isolates (13.18%) exhibited resistance to five antimicrobial classes, with resistance patterns of CIP + SXT + AMP + DO + TE + CT. A total of 233 isolates (74.92%) were resistant to colistin (MIC > 2 mg/L). A strong correlation between colistin resistance and the presence of the mcr-1 gene was observed (r = 1). All phenotypic colistin-resistant E. coli isolates carried the mcr-1 gene, while no isolates were positive for mcr (2–5). The detection of mcr genes in E. coli strains from poultry sources poses a significant risk, as these resistance genes can be transferred to humans through the food chain. The prevalence of multidrug-resistant Escherichia coli and the mcr-1 gene in poultry products in Bangladesh presents a significant public health and food safety concern
Clade divination – phenotypic data facilitates epidemiological inferences from soybean dwarf virus sequence analysis
No full textSoybean dwarf virus (SbDV; family Tombusviridae, genus Luteovirus, species Luteovirus glycinis), transmitted solely by aphids in a persistent manner, can cause significant losses in cultivated Fabaceae. SbDV isolates are categorised into four strains; YP, YS, DP and DS. Yellowing (Y) and dwarfing (D) strains differ in their symptom expression and host range. P strains are transmitted by Acyrthosiphon pisum (pea aphid), and S strains are transmitted by Aulacorthum solani (foxglove aphid). Genetically, Y and D strains separate into two clades at every genomic region except for the N-terminal region of the read through domain (N-RTD) in which P and S strains separate. SbDV diversity in Australia has yet to be significantly investigated and so complete genome sequences were obtained from 41 isolates infecting cultivated Fabaceae in two regions of Australia (‘northeast’ and ‘southwest’). Phylogenetic analyses were conducted on the whole genome and the N-RTD of these sequences together with 50 sequences available on GenBank. At the whole genome level, isolates separated into D and Y clades. At the N-RTD level, with two exceptions, isolates separated into P and S clades. All south-west isolates were in the Y clade, whilst north-east isolates were in both the Y and D clades. All isolates sequenced were in the P group suggesting Ac. pisum is the primary vector of SbDV in these regions. Although biological evidence suggests S strain isolates are common in the southeast of Australia, just one previously sequenced Tasmanian isolate was available and was in the Y and S clades. Relevant biological data available for each isolate supported inferences made from phylogenetic clade. This study suggests that at least three of the four SbDV strains are present in Australia and is an example of the importance of continued collection of phenotypic data to provide more power to genetic analyses
Preparing for the transition of banana quarantine and diagnostics to Mickleham
No full textBanana (Musa sp.) tissue cultures are currently imported and grown through post-entry quarantine (PEQ) in dedicated Queensland Department of Agriculture and Fisheries (QDAF) class 6.7 Approved Arrangement facilities, with a process management system approved by the Federal Department of Agriculture Fisheries and Forestry (DAFF). Importation of banana germplasm was recently resourced by two Hort Innovation projects, BA10020 and BA16001, which together imported thirty-three banana cultivars and met all facility, husbandry and testing costs. Now that these projects are completed, the costs of facility maintenance and accreditation fall to the banana industry. Due to the high on-going costs of maintaining accreditation of pathway-specific glasshouse and tissue culture facilities, alternative arrangements are being sought to transition the importation of banana germplasm through DAFF’s national PEQ facility at Mickleham. As a first step, growth trials of domestic Musa material at PEQ Mickleham were successfully completed, proving that the multi-commodity glasshouses there are fit for growing bananas. As a second step, DAFF PEQ staff travelled to QDAF laboratories at the Ecosciences Precinct in Brisbane, Queensland to develop their skills in banana pathogen detection during PEQ screening of imported banana germplasm. Dr Kathy Crew led the training covering the biology of banana viral and phytoplasma pathogens as well as practical training in the laboratory demonstrating specialist laboratory techniques such as virus purification, immunosorbent electron microscopy and multiplex immunocapture molecular assays for known banana viruses. Further steps in transitioning banana diagnostics to Mickleham PEQ will include a reciprocal visit by Dr Crew to PEQ Mickleham for further training and troubleshooting, as well as side-by-side evaluation of current diagnostic methods and high throughput sequencing (HTS) of sRNA, for banana germplasm diagnostics
Exploring Phages as Promising Biocontrol Agents for managing Bacterial Diseases in Plants
No full textBacteriophages (phages) are beneficial viruses that infect and replicate within bacteria, presenting a promising agent for combating bacterial diseases in diverse ecosystems including agriculture. In recent years, there has been a growing interest in harnessing the potential of bacteriophages to control plant bacterial pathogens due to their specificity, efficacy, and environmentally friendly nature. In this study, we tried to recover lytic phages from local environmental samples; soil, irrigation water, rotted fruits, and organic manure with the aim to evaluate their presence and efficacy against soft rot pathogens. In total, eight lytic phages were isolated from ten environmental sources. Phages infecting Pseudomonas spp. were commonly recovered from a diverse range of environmental samples in comparison to Pectobacterium brasiliense, Klebsiealle oxytoca and Dickeya fangzhongdai. Enriched organic manures and rotted potato tuber assays were found to be effective (in vitro) and inhibited the growth of soft rot causing pathogens of potato soft rot, banana corm rot, bacterial soft rot of lettuce and leaf spot of parsley. Morphological characterization using electron microscopy (TEM) revealed that a P. brasiliense phage belongs to family Podoviridae and Pseudomonas sp. phages to Siphoviridae and Myoviridae. In conclusion, bacteriophages hold immense potential as sustainable and ecofriendly alternative for managing bacterial diseases in plants. 44 However, challenges still exist in scaling up of phage production, field application and molecular characterization of isolated phages. Continued research efforts are in progress to address knowledge gaps, optimize phage-based interventions, and integrating phage-based strategies into existing agricultural practices
Epidemiological Risk Factors and Modelling Approaches for Risk Assessment of Lumpy Skin Disease Virus Introduction and Spread: Methodological Review and Implications for Risk-Based Surveillance in Australia
Get PDFLumpy skin disease (LSD) is a vector-borne infection caused by the poxvirus lumpy skin disease virus (LSDV) and is a serious disease of cattle, water buffalo, and banteng. While the disease has never occurred in Australia, it is regarded as a growing threat to the Australian cattle industry as there is on-going spread of the disease throughout Asia. The development of geospatial decision support tools, such as spatial epidemiological modelling, may assist in assessing areas at greater risk of this threat. To guide the design of disease modelling approaches to support future risk-based surveillance, existing LSDV epidemiological models need to be evaluated. In this study, we performed a literature review to evaluate existing LSDV epidemiological models, identify key risk factors for introduction and spread of LSDV, and consider previously adopted control strategies. The PRISMA guidelines were used to establish the processes for article selection and information extraction, and the PICO process was used to formulate search terms. From studies that met our inclusion criteria, we extracted information on LSDV epidemiological model structure and parameterisation, risk factors for LSDV transmission and spread, and biosecurity control strategies. The literature search retrieved a total of 402 articles from four databases, of which 68 were identified for inclusion in this review following screening. Of the 68 articles reviewed, 47 explored risk factors associated with LSDV transmission and spread, four explored risk factors of LSDV introduction, four explored existing surveillance strategies in LSD-free countries, and 14 presented epidemiological models. Our findings indicate that there are various risk factors for LSDV transmission in LSD endemic countries, including long-distance airborne movement of infected vectors such as stable flies and cattle movement between countries over land borders. Key risk factors for LSDV spread in LSD endemic countries include physical environmental characteristics, weather conditions, and population distributions of livestock and vectors. Our results indicate that while a variety of modelling studies have been conducted, the majority of studies experimentally explored LSD transmission mechanisms in vectors and cattle. Spatial and spatio-temporal models have primarily been developed for LSD endemic countries and focus on the spread of the disease in terms of environmental factors in relation to previous LSD events. There were very few studies on LSD-free countries, and these only focussed on risk of LSD introduction through specific entry pathways. This review did not identify any literature exploring the risk of spread of LSDV following introduction in LSD-free countries or geospatial modelling of the suitability of LSD-free countries for LSDV incursions. In conjunction with the risk parameters and models described in the identified literature, there is need to consider a wide range of risk factors specific to Australia to inform the design of risk-based surveillance for LSD in Australia
Identification of environment similarities using a crop model to assist the cultivation and breeding of a new crop in a new region
Get PDFContext
Rainfed crop-growing environments are known for their high yield variability, especially in the subtropics and tropics. Improving the resilience of crops to such environments could be enhanced with breeding and agronomy research focusing on groups of similar environments.
Aim
This study presents a framework for developing these groups using the Agricultural Production Systems Simulator (APSIM, ver. 7.10) model.
Methods
As a case study, the framework was applied for pigeonpea (Cajanus cajan L. Millsp.) as a potential new pulse crop for the Australian northern grains region. The model was first validated and then used to simulate yield, compute heat and drought stress events and analyse their frequencies for 45 locations over 62 seasons from 1960 to 2021.
Key results
The model performed satisfactorily compared to field trial data for several sowing dates and locations. The simulated yield varied greatly across locations and seasons, with heat-stress events (maximum temperature ≥35°C) and rainfall showing highly significant associations with this variability. The study identified seven groups of locations after converting the simulated yield into percentiles, followed by clustering. Drought-and-heat stress patterns varied across these groups but less so within each group. Yield percentiles significantly declined over the seasons in three of the seven groups, likely due to changing climate.
Conclusions
The framework helped identify pigeonpea’s key production agroecological regions and the drought and heat constraints within each region.
Implications
The framework can be applied to other crops and regions to determine environmental similarity
Seasonal dynamics of fallow and cropping lands in the broadacre cropping region of Australia
No full textFallowing is an important strategy for enhancing soil health, water harvesting and crop yields, thus improving sustainability and reducing production risks in dryland farming systems in Australia. However, accurate data regarding the location, frequency, extent, and duration of fallow land is not readily available at high spatio-temporal resolutions before and during a cropping season. As a result, continental maps depicting seasonal dynamics of fallow and cropping lands and their responses to climate change and human activities remain missing. This study set out to develop an automated approach to discriminate fallow areas from cropping areas within Australian broadacre cropping region. This was done by applying a mathematical algorithm of turning point detection technique to a curve fitted vegetation index time series from 2016 to 2022, derived from high spatial (10 m) and temporal (5-days) resolution Sentinel-2 data. Specifically, we aimed to derive: (i) 5-day revisit fallow/cropping map layers; (ii) key attributes of the fallow and cropping periods (e.g., start, end, duration); (iii) cropping intensity and area. The proposed approach yielded a high and significant overall accuracy, surpassing 92% with substantial balanced accuracy (>0.9) against >3000 fields for individual winter and summer seasons across Australia. In addition, this study's temporal and geographical outputs, encompassing seasonal attributes, cropping intensity and cropping areas, robustly enhanced the understanding of seasonal cropping dynamics and historical shifts in dryland farming practices. Findings derived from this analysis aligned well with extreme climatic events and changes in crop activities adopted in response to such events. Future research will aim to extract key seasonal dynamics attributes influenced by cropping practices, enhancing the conversion of high-resolution earth observation data into actionable industry knowledge
Enhancing strategic deployment of baiting transects for invasive species control – a case study for feral pig baiting in north-eastern Australia
Get PDFBaits are used to deliver lethal or other substances in wildlife management programs across the globe. Successful baiting campaigns are contingent upon the availability of baits to target animals. Bait density is often increased in an attempt to improve bait encounter probabilities. However, this comes with a concomitant increase in cost and may result in significant bait wastage if deployed in areas of low target species activity.
The aim of this study was to assess the effectiveness, efficiency and cost of different bait transect methods in intersecting home and core ranges of feral pigs as a case study to determine optimal spacing and placement of baiting transects
Agrivoltaic grazing systems in Queensland The potential, challenges, and opportunities for the coexistence of grazing and solar power plants in Queensland
Get PDFThis report provides a review of the potential, challenges, and opportunities for the co-existence of grazing systems and utility-scale solar energy production in Queensland. This preliminary review and analysis indicates that solar power plants and livestock grazing need not be mutually exclusive. There has been a lack of uptake of cattle co-grazing in Australia (and internationally) and further work is required to identify the particular impediments that apply and whether these can be overcome. Flocks of meat sheep are relatively rare in the regions of eastern Queensland where the majority of solar power plants are proposed for development. Further work is required to identify whether flocks of meat sheep can be established and expanded in these regions to undertake the amount of grazing likely to become available on solar power plants (i.e. ca. 100,000 ha)