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Molecular delimitation of cryptic Australian squid species of the genus Uroteuthis Rehder, 1945 (Cephalopoda: Loliginidae), provides a baseline of diversity to resolve classification challenges throughout the Indo-Pacific
Get PDFThis study provides a comprehensive molecular phylogenetic analysis of Uroteuthis squid from the Indo-Pacific region. The main aim was to increase sample coverage from northern and eastern Australian waters to resolve the identity and distribution of Uroteuthis species taken by local fisheries. Two mitochondrial regions, cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S rRNA), were sequenced from 220 new specimens and analysed with a further 51 sequences from GenBank to create a combined phylogeny for the genus. Three nuclear regions, 18S ribosomal DNA (18S rDNA), 28S ribosomal DNA (28S rDNA) and rhodopsin, were also sequenced from representatives of each species. Based on the mitochondrial phylogeny plus distance and tree-based delimitation models, a COI species barcode gap of 4–5% is proposed for discriminating Uroteuthis species. Applying this gap partitioned many described species into species complexes; for example, U. duvaucelii, U. noctiluca and U. edulis resolved into 10 species. Although more conserved, mitochondrial 16S rRNA sequences differentiated all new species clades, whereas none of the nuclear markers resolved the closest species. Results confirm that neither U. chinensis nor U. edulis occurs in Australian waters. Five undescribed species are identified from northern and eastern Australia, of which four are consistent with earlier allozyme studies (and two align with existing DNA sequences). One is a new southeastern, deeper shelf species differentiated in this study, along with a sixth undescribed species from Indonesian waters. Results of the molecular analysis are now being used to inform complementary morphometric analyses for new species descriptions, and genetic stock structure assessments of these important fisheries resources
The genomes of two Australian isolates of Verticillium dahliae recovered from cotton fields
Get PDFVerticillium wilt is a major disease in a wide variety of crops and is caused by the fungus Verticillium dahliae Kleb. In Australian cotton growing regions two pathotypes of V. dahliae are described, namely non-defoliating and defoliating, classified on their ability to cause defoliation in cotton (Gossypium hirsutum) as well as okra (Abelmoschus esculentus) and olives (Olea europaea). Herein we report the genomes of two isolates of V. dahliae, one predicted to be non-defoliating and the other predicted to be defoliating. Phylogenomic analysis places each isolate into separate clades, but the highly aggressive, predicted defoliating, strain lacks the genomic features reported as important for causing defoliation on cotton in other regions
Marine Aquarium Fish Fishery Species-Specific Vulnerability Assessment
No full textThe purpose of the Marine Aquarium Fish Fishery Vulnerability Assessment (MAFF VA) was to assess the relative vulnerability of marine ornamental fishes by evaluating their resilience to disturbance and their susceptibility to the negative effects of fishing activities. The MAFF VA also identifies avenues where vulnerability can be further understood, managed or mitigated within the Marine Aquarium Fish Fishery (MAFF).
The Productivity and Susceptibility Analysis (PSA) for data-poor fisheries was adapted and utilised for this assessment. The PSA is a semi-quantitative, species-level assessment that provides indicative vulnerability ratings (i.e. low, medium, high) and the key drivers of this vulnerability for 137 marine ornamental fishes harvested in the MAFF. This vulnerability was calculated based on the biological characteristics (productivity) and fishery-impact profile (susceptibility) of each species.
Of the 137 species assessed, one was assigned a high-vulnerability rating, 32 a medium-vulnerability rating and 104 a low-vulnerability rating. The influence of attributes on the final vulnerability ratings and key drivers of vulnerability varied, showing a high degree of species-specificity. The MAFF VA can be built on through subsequent assessments to examine the vulnerability of secondary species and emerging priorities.
The MAFF VA identified several limitations within the current management regime and the harvest strategy framework. Key recommendations include updating the Marine Aquarium Fish Fishery Harvest Strategy 2021–2026, minimising potential long-term risks to Tier 1 and Tier 2 species and the continued implementation of the Queensland Marine Aquarium Fish Fishery Data Improvement Plan
Agronomic adaptations to heat stress: Sowing summer crops earlier
Get PDFContext Summer crops are exposed to heat and drought stresses at critical stages during and after flowering, and their intensity and frequency are likely to increase with climate change. Agronomic stress avoidance offers the opportunity to temporally separate critical crop stages from heat and drought events. However, it might require sowing cold-sensitive summer crops earlier into colder than recommended soil temperatures. There is a need to understand how cold is too cold to sow summer crops early in late winter as well as what are the yield benefits and risks. Objective Here, we quantify the likely benefits and trade-offs of sowing sorghum, a summer cereal, earlier to adapt to the increased frequency and intensity of heat and water stresses during flowering and grain filling. Methods Two years of multi-environment (n=32) genotype by management trials were conducted across the main sorghum growing regions of Australia. Environments (E) consisted of the combination of years, sites, three times of sowing (early, spring, and summer), and the use of supplementary irrigation. At each E a factorial combination of four plant populations (M) and eight commercial sorghum hybrids (G) were sown with three replications. Crop growth and yield components were measured, and the APSIM model was used to simulate all trials and treatments to quantify risks and derive insights into functional relationships between simulated and measured environmental covariates, and measured crop traits. Results The tested hybrids showed small differences in cold tolerance during crop establishment. Across the tested environments, the G×M combinations produced up to 60 % variation in treatment yields across environment yields, which varied between <0.5 to about 10 t ha−1; this translated into a ∼5.5-fold variation in water use efficiency. Significant G×E and M×E interactions were observed for grain yield components. No G×M or G×E×M interactions were observed on yield or yield components. Early sowing was associated with a reduced risk of heat stress and water use transfer from vegetative to reproductive stages. Early sowing in late winter or early spring resulted in no significant yield gain or loss when all sites and years were included in the analysis. However, early sowing yielded between 1 and 2 t ha−1 more when the hottest sites and years were considered separately. This resulted from both the avoidance of heat stresses and milder or no terminal drought stresses. Conclusions Early sowing of sorghum can reduce the likelihood of heat stresses around flowering as well as the likelihood of terminal drought stresses. Advantages include reduced yield losses in the hottest years and a transfer of water use to grain filling stages, resulting in increased grain yield and improved grain quality parameters. Implications Early sowing, an agronomic adaptation, offers the opportunity to quickly adapt to the increase in the frequency and intensity of extreme hot events during critical crop stages. However, for the practice to be de-risked, there is a need to increase cold and chilling tolerance in sorghum and/or identify interventions that enhance seed germination and seedling vigour when the crop is sown early into cold soils
The genomes of Australian wild limes
Get PDFAustralian wild limes occur in highly diverse range of environments and are a unique genetic resource within the genus Citrus. Here we compare the haplotype-resolved genome assemblies of six Australian native limes, including four new assemblies generated using PacBio HiFi and Hi-C sequencing data. The size of the genomes was between 315 and 391 Mb with contig N50s from 29.5 to 35 Mb. Gene completeness of the assemblies was estimated to be from 98.4 to 99.3% and the annotations from 97.7 to 98.9% based upon BUSCO, confirming the high contiguity and completeness of the assembled genomes. High collinearity was observed among the genomes and the two haplotype assemblies for each species. Gene duplication and evolutionary analysis demonstrated that the Australian citrus have undergone only one ancient whole-genome triplication event during evolution. The highest number of species-specific and expanded gene families were found in C. glauca and they were primarily enriched in purine, thiamine metabolism, amino acids and aromatic amino acids metabolism which might help C. glauca to mitigate drought, salinity, and pathogen attacks in the drier environments in which this species is found. Unique genes related to terpene biosynthesis, glutathione metabolism, and toll-like receptors in C. australasica, and starch and sucrose metabolism genes in both C. australis and C. australasica might be important candidate genes for HLB tolerance in these species. Expanded gene families were not lineage specific, however, a greater number of genes related to plant-pathogen interactions, predominantly disease resistant protein, was found in C. australasica and C. australis
Effect of gum Arabic on antifungal photodynamic activity of curcumin against Botrytis cinerea spores
No full textThis study investigated the effect of gum Arabic on curcumin's phototoxicity against Botrytis cinerea, a significant cause of postharvest losses in horticultural produce. Curcumin-loaded nanoparticle suspensions and emulsions stabilized with gum Arabic were prepared and their absorbance, fluorescence emission, physicochemical properties, antimicrobial photodynamic activity (using response surface methodology (RSM)), and reactive oxygen species (ROS) generation (via electron paramagnetic resonance (EPR) spectroscopy) were evaluated. Fluorescence emission exhibited a blue shift (510–550 nm) in both formulations, with emulsions showing higher intensities due to a more hydrophobic environment. Gum Arabic concentration significantly influenced the physicochemical properties of both suspensions, with nanoparticle size decreasing from 572.80 nm to 202.80 nm as gum Arabic concentration increased from 0.5 % to 2.5 % (at 65 μM curcumin). Nanoparticle suspensions demonstrated higher antimicrobial efficacy, reducing B. cinerea spores by 0.39–3.40 log10(CFU.ml−1), compared to 0.00–0.46 log10(CFU.ml−1) in emulsions. The phototoxic effect was dependent on curcumin concentration and light irradiance, as demonstrated by RSM. EPR confirmed the generation of superoxide anion and hydroxyl radicals in both formulations, which indicated a Type I photodynamic mechanism, with nanoparticle suspensions having a sustained ROS generation. Overall, gum Arabic did not impair curcumin's antifungal photodynamic activity, making it as a promising stabiliser for curcumin-based treatments
Python and MATLAB script used for analysing (regression and classification) the data extracted from hyperspectral images of wheat grain samples infected by Fusarium graminearum
No full textPython and MATLAB scripts were utilised to analyse hyperspectral imaging data from wheat grain samples, which were extracted and organised into Excel spreadsheets. The Python script was employed for classifying wheat grains using Support Vector Machine (SVC) for differentiating between levels of DON concentrations, whilst the MATLAB script was used for regression modelling with Artificial Neural Networks (ANN) for quantifying DON concentrations
Efficacy of pre-emergent herbicides on sicklepod (Senna obtusifolia) in the Dry Tropics of Cape York
No full textThis study determined the efficacy of multiple herbicide treatments applied at a pre-emergent stage on field populations of sicklepod (Senna obtusifolia (L.) Irwin and Barneby) in the dry tropics of far north Queensland. The aim was to identify herbicide treatments that can be applied towards the end of the dry season and activated with the first substantial rains of the Wet Season, to produce more consistent control outcomes, particularly in situations where infestations are inaccessible due to the annual northern wet season. Field sites were established in dense sicklepod at three locations on Cape York: Morehead River, West Normanby River and Oaky Creek. The trial was established just prior to the Wet season in 2019 (October) and monitored at approximately three-monthly intervals for three years. After the initial treatment, several of the herbicides showed high efficacy, with the most efficacious herbicides reapplied after 12 and 24 months to evaluate annual re-treatment effects on seedling regeneration numbers in the following wet seasons. High efficacy was achieved with Conqueror®, Grazon Extra®, Stuka flexi® and Tordon75-D® all of which contained the active ingredient picloram. The complete absence of sicklepod after three years and replacement with grasses or other herbaceous species was observed in some plots. Pre-emergent herbicides have significant potential for future use, particularly for the strategic management of access to infrastructure such as rest stops, property access, and stock watering points
The effectiveness of herbicides and their combinations for controlling Cyperus aromaticus (Navua sedge) in Queensland
No full textSustainable cultivation of crops plays a crucial role in the agricultural sector, directly influencing both the quantity and quality of the end products. This has a direct impact on the overall profitability of farmers. Weed management is a continual challenge, influencing production costs and practices in agriculture. One such weed is Cyperus aromaticus commonly known as Navua sedge which poses a significant threat to Queensland's agriculture and exhibits a remarkable reproductive ability through its rhizome system and prolific seed production. Traditional herbicides, including Glyphosate, halosulfuron, Hexazinone, Imazapic, Imazapyr, and Monosodium methane arsenate (MSMA), show limited efficacy and often require application above recommended rates when controlling established C. aromaticus population, escalating production costs and posing environmental concerns. The objective of the study was to evaluate the efficacy of six herbicides (Sempra, Glyphosate, Paraquat, Imazamox, Imazapyr and MCPA), at a range of application rates (45, 75, 375, 540, or 1500 g a.i./ha), different adjuvants (Banjo, Pulse or Hasten), sequential applications (one, two or three sequential sprays), combinations of herbicides (Halosulfuron-methyl, Glyphosate, and Paraquat), and different growth stages (pre-flowering, flowering, and mowed stages with established rhizomes) of Navua sedge. The results indicate sequential spraying of Sempra and Imazapyr has a significant effect on controlling the established rhizomatic population of C. aromaticus. These findings enrich the existing knowledge for controlling C. aromaticus in areas of North-eastern Queensland and for the weed populations with similar environmental conditions
Characterisation of reproductive tract microbiome and immune biomarkers for bovine genital campylobacteriosis in vaccinated and unvaccinated heifers
No full textBackground: Bovine genital campylobacteriosis (BGC) is a globally important venereal disease of cattle caused by Campylobacter fetus subspecies venerealis. Diagnosis of BGC is highly challenging due to the lack of accurate diagnostic tests.
Methods: To characterise the biomarkers for C. fetus venerealis infection, a total of twelve cycling heifers were selected and categorised as vaccinated (n = 6) with Vibrovax® (Zoetis™) and unvaccinated (n = 6). All heifers were oestrous synchronised with a double dose of prostaglandin (PGF2α) 11 days apart and when in oestrous intravaginally challenged with 2.7 x 109 CFU live C. fetus venerealis. DNA extracted from vaginal mucus samples was screened using a C. fetus qPCR and 16S rRNA was characterised using Illumina sequencing (V5-V8 region). Relative abundances of serum proteins were calculated using sequential window acquisition of all theoretical fragment ion spectra coupled to tandem mass spectrometry (SWATH-MS) for all heifers at three timepoints: pre-challenge, post-challenge and post-recovery.
Results: In 16S rRNA sequencing of vaginal mucus, Campylobacter spp. appeared two days following challenge in unvaccinated compared to 14 days in vaccinated animals, consistent with the qPCR results. Increased relative abundances of Firmicutes and Campylobacterota were identified after C. fetus venerealis challenge and were associated with C. fetus venerealis in vaccinated and unvaccinated heifers. Greater relative abundance of Streptococcus spp. was observed during oestrous rather than dioestrous. In both vaccinated and unvaccinated heifers, Acinetobacter spp. increased after challenge with higher abundance of Corynebacterium spp. in the vaccinated group. A total of 130 unique proteins were identified in SWATH analysis of the serum samples, and the number of differentially abundant proteins found was higher in the vaccinated group after recovery from infection compared to pre-and post-challenge (adjusted P 0.2).
Conclusion: Coglutinin, clusterin, HP homologs, vitamin D binding protein and fetuin B were identified as potential biomarkers for C. fetus venerealis infection and need further study to validate their efficiency as immune biomarkers for BGC