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Modelling peanuts for nut-in-shell and fodder yield in the northern Australian tropics
No full textPeanuts are a popular crop grown for their nutrient-rich nuts-in-shells. These crops also play a crucial role in enhancing the sustainability of farming systems. In addition to the nuts-in-shell, which the crop starts producing below-ground four to six weeks after sowing, peanuts make a substantial amount of above-ground biomass, mainly nitrogen-rich green foliage, stems, and branches. We hypothesized that some part of the above-ground biomass could be harvested or grazed without affecting the growth of the developing pods, making it valuable fodder for cattle or dry hay, especially in times of scarcity. In various tropical regions of northern Australia, experiments supported by the Cooperative Research Centre for Developing Northern Australia (CRCNA) have explored the dual potential of peanuts - for both nuts-in-shell production and grazing purposes. Leveraging the data from these experiments, we have refined and validated the APSIM model to simulate these dual-purpose capabilities of peanuts. This presentation aims to delve into this model's applications to explore the dual-purpose potential of peanuts in two environments
Multi-omic profiles of Sorghum genotypes with contrasting heat tolerance connect pathways related to thermotolerance
No full textUnderstanding how crop varieties acclimate to elevated temperatures is key to priming them for future climates. Here, we exposed two genotypes of Sorghum bicolor (one sensitive to heat shock (Sen) and one tolerant (Tol)) from multiple growth temperatures to a six-day heat shock (reaching 45°C), carrying out a suite of measurements before and during heat shock. Sen consistently reduced photosynthetic functioning during heat shock, while Tol increased its photosynthetic rate. Higher abundance of heat shock protein transcripts and metabolites related to heat tolerance were noted for Tol when compared to Sen both before and during heat shock, which can be attributed to constitutive and inducible responses to elevated temperatures. In addition, important changes in metabolic pathways were clearly identified for Tol during heat shock (including upregulation of raffinose family oligosaccharides and downregulation of the GABA catalytic pathway), even as the concentration of hexose sugars became depleted. We infer Tol was able to tolerate elevated temperatures due to an upregulation of osmoprotectants, chaperones and reactive oxygen species scavengers and by the suppression of SnRK1 via transcripts and metabolites during heat shock. Our results highlight potential targets for attributes of high temperature tolerance which can be utilised in future breeding trials
East Coast Otter Trawl Fishery Regional Risk Assessments. Species of Conservation Concern
No full textThe East Coast Otter Trawl Fishery (ECOTF) has been the subject of many historical risk assessments. The most recent of these was published in 2023 by Fisheries Queensland and assessed the risk posed by trawling operations at a whole-of-fishery level, focusing on species with ongoing conservation concerns. This current report provides further context to the outputs of this previous study by establishing regional-specific risk profiles for the same 62 species.
To allow for greater flexibility and minimise the potential of risk overestimates occurring, the regional assessments were developed using a Likelihood and Consequence Analysis (LCA). This methodology considers the consequence of a species interacting with the ECOTF and the likelihood of the consequence coming to fruition within the current fishing environment. The LCA is fully-qualitative and assigns each species with an indicative risk rating of negligible, low, low-medium, medium, or high.
A cross-comparison of the species distribution data and prescribed management boundaries produced an assessment list of 43 species for the Northern Trawl Region, 46 species for the Central Trawl Region, 46 species for the Southern Inshore Trawl Region, 49 species for the Southern Offshore Trawl Region and 30 species for the Moreton Bay Trawl Region. Across the entire assessment, only two species were found to be at high risk while the majority were classified as either low or low-medium risk.
These regional assessments may be built on through subsequent assessments examining the risk posed to additional species and/or emerging priorities. With additional information, some species scores may be further refined. Alternatively, where necessary improved evidence may facilitate the removal of species from subsequent regional assessments
The aquastatin biosynthetic gene cluster encodes a versatile polyketide synthase capable of synthesising heteromeric depsides with diverse alkyl side chains
No full textDepsides have garnered substantial interest due to the diverse biological activities exhibited by members of this class. Among these are the antibacterial aquastatins, glycosylated heteromeric depsides formed through the condensation of orsellinic acid with corticiolic acid. In this work, we isolated aquastatins and the recently described geministatins, along with several novel aquastatin-related depsides with different alkyl side chains from the fungus Austroacremonium gemini MST-FP2131. The structures were determined through comprehensive spectroscopic analysis and chemical degradation. Genome mining and heterologous expression in Aspergillus nidulans and Saccharomyces cerevisiae revealed that aquastatin biosynthesis requires only two genes: a non-reducing polyketide synthase (SAT-KS-AT-PT-ACP-TE) and a glycosyltransferase. We demonstrated that the single polyketide synthase can synthesise an acetyl-primed orsellinic acid and alkylresorcylate with various chain lengths (C14, C16, or C18) by incorporating different long-chain acyl-CoAs as starter units, and then join these as heteromeric depsides. Using chemical degradation, we generated a series of analogues and showed that several aglycone depsides exhibit antibacterial activity against Staphylococcus aureus and methicillin-resistant S. aureus (MRSA), as well as antifungal and cytotoxic activities. Interestingly, heterologous expression of the aquastatin gene cluster in A. nidulans produced higher levels of geministatins with Δ15,16 and Δ18,19 double bonds, which have superior bioactivities compared to the aquastatins but are only present as minor compounds in the native fungus A. gemini
Geographical origin discrimination of lemon myrtle (Backhousia citriodora) leaf powder using near-infrared hyperspectral imaging
Get PDFLemon myrtle (LM), Backhousia citriodora, is a popular flavouring agent and herbal tea from Australia. To ensure traceability and consumer trust in global food supply chain, rapid and non-destructive tools are crucial. In this study, hyperspectral images were acquired from 91 L M samples sourced from three different origins (Malaysia, Queensland, and New South Wales (Australia)), within 950–2500 nm range. Classification models were developed using linear partial least squares-discriminant analysis (PLS-DA) with two approaches, pixel-based (trained by all spectral data points) and sample-based (trained by average spectrum). All models achieved classification accuracies above 96%. The sample-based PLS-DA model, trained by mean-centring transformed data, demonstrated the highest discriminatory performance. Both approaches show potential for LM origin classification, but the sample-based model is more suitable for automated and rapid industry applications due to its shorter calculation time. However, additional spectral data acquisition is necessary to improve the model and fully explore its capabilities and limitations
Knowledge and values drive acceptability of lethal control of kangaroos among the Australian public
Get PDFWildlife management actions are increasingly contingent on acceptance by the broader public. Consequently, understanding factors that influence acceptability of different management options is important. In Australia, kangaroos (native large herbivores, Macropus spp., Osphranter spp.) are managed using lethal control for a range of context-specific reasons. We surveyed 1293 members of the Australian public to test whether acceptability of lethal control of kangaroos depends on the reason for the control, values towards wildlife (assessed using the Wildlife Values Orientation questionnaire), and knowledge about kangaroos. We also tested whether acceptability could be shifted by providing relevant information. Lethal control of kangaroos for biocentric reasons (i.e., agricultural protection, biodiversity conservation, animal welfare) was more acceptable than lethal control of kangaroos for anthropocentric reasons (i.e., human consumption, human safety). Acceptability was greater among survey respondents high on the domination orientation (i.e., valuing wildlife for human benefits), and lower among those high on the mutualism orientation (i.e., valuing wildlife for its own intrinsic value). Acceptability was also positively associated with knowledge of kangaroo ecology and management. Provision of information did not impact acceptability of lethal control for any reason except for human use, which, while not significant, showed promise that acceptability of lethal control for this reason could be influential to the public. Additionally, while the acceptability of lethal control varied widely among the Australian population, there was little evidence of polarisation, suggesting that large sectors of the public may be amenable to different perspectives
In Situ Sucrose Injection for Alteration of Carbohydrate Reserve Dynamics in Grapevine
Get PDFInconsistent yield of subtropical table grape across seasons is often associated with low carbohydrate reserves during flowering. In an attempt to increase TNC and thus yield, sucrose was injected into treated trunks during periods of high carbohydrate demand (i.e., between budburst and flowering). Total non-structural carbohydrate (TNC) concentration dynamics were assessed in the grapevine root and trunk tissues of both control and treated vines. In the control (untreated) vines, the TNC concentration in root and trunk tissues was 13.5% and 7.5% w/dw at leaf fall and 7.2% and 3.7% w/dw at flowering, respectively. This decrease in carbohydrate reserve was estimated at ~500 g/vine and is associated with the re-establishment of the plant canopy in early spring. Carbohydrate reserves remained stable or rose slightly between flowering and harvest and recovered between crop harvest and leaf fall. In treated vines, a constantly pressurised low-pressure in situ trunk injection system (69 kPa) with 5% w/v sucrose solution over 45 days from budburst (to flowering), in each of the two seasons, delivered a widely variable amount of sucrose into each vine with variation ascribed to the amount of internal dead wood in the trunk. In the best circumstances, an average of 150 g sucrose/vine/season was injected, and sucrose-injected vines had higher trunk TNC reserve (4.1% compared to 3.6% w/dw in the control) at flowering. A δ13C (‰) analysis confirmed the presence of injected sucrose in the shoot at flowering. However, the correlation between the amount of loaded sucrose and δ13C in young shoot tissue was poor, indicative of variable partitioning patterns. Inflorescence number per vine and berry yield were markedly higher in sucrose-injected vines, but differences were not significant given the high variation between vines. The addition of KCl to the sucrose solution and use of the healthy vines are recommended to increase sucrose loading using the injection method to address inconsistent yielding of subtropical table grape
Untangling multi-species fisheries data with species distribution models
Get PDFLong-term trends in fisheries catch are useful to monitor effects of fishing on wild populations. However, fisheries catch data are often aggregated in multi-species complexes, complicating assessments of individual species. Non-target species are often grouped together in this way, but this becomes problematic when increasingly common shifts toward targeting incidental species demand closer management focus at the species level. Species distribution models (SDMs) offer an under-utilised tool to allocate aggregated catch data among species for individual assessments. Here, we present a case study of two shovel-nosed lobsters (Thenus spp.), previously caught incidentally and recorded together in logbook records, to illustrate the design and use of catch allocation SDMs to untangle multi-species data for stock assessments of individual species. We demonstrate how catch allocation SDMs reveal previously masked species-specific catch trends from aggregated data and can identify shifts in fishing behaviour, e.g., changes in target species. Finally, we review key assumptions and limitations of this approach that may arise when applied across a broad geographic or taxonomic scope. Our aim is to provide a template to assist researchers and managers seeking to assess stocks of individual species using aggregated multi-species data
AgAsk: an agent to help answer farmer’s questions from scientific documents
Get PDFDecisions in agriculture are increasingly data-driven. However, valuable agricultural knowledge is often locked away in free-text reports, manuals and journal articles. Specialised search systems are needed that can mine agricultural information to provide relevant answers to users’ questions. This paper presents AgAsk—an agent able to answer natural language agriculture questions by mining scientific documents. We carefully survey and analyse farmers’ information needs. On the basis of these needs, we release an information retrieval test collection comprising real questions, a large collection of scientific documents split in passages, and ground truth relevance assessments indicating which passages are relevant to each question. We implement and evaluate a number of information retrieval models to answer farmers questions, including two state-of-the-art neural ranking models. We show that neural rankers are highly effective at matching passages to questions in this context. Finally, we propose a deployment architecture for AgAsk that includes a client based on the Telegram messaging platform and retrieval model deployed on commodity hardware. The test collection we provide is intended to stimulate more research in methods to match natural language to answers in scientific documents. While the retrieval models were evaluated in the agriculture domain, they are generalisable and of interest to others working on similar problems. The test collection is available at: https://github.com/ielab/agvaluate
Whole-genome comparison using complete genomes from Campylobacter fetus strains revealed single nucleotide polymorphisms on non-genomic islands for subspecies differentiation
Get PDFIntroduction
Bovine Genital Campylobacteriosis (BGC), caused by Campylobacter fetus subsp. venerealis, is a sexually transmitted bacterium that significantly impacts cattle reproductive performance. However, current detection methods lack consistency and reliability due to the close genetic similarity between C. fetus subsp. venerealis and C. fetus subsp. fetus. Therefore, this study aimed to utilize complete genome analysis to distinguish genetic features between C. fetus subsp. venerealis and other subspecies, thereby enhancing BGC detection for routine screening and epidemiological studies.
Methods and results
This study reported the complete genomes of four C. fetus subsp. fetus and five C. fetus subsp. venerealis, sequenced using long-read sequencing technologies. Comparative whole-genome analyses (n = 25) were conducted, incorporating an additional 16 complete C. fetus genomes from the NCBI database, to investigate the genomic differences between these two closely related C. fetus subspecies. Pan-genomic analyses revealed a core genome consisting of 1,561 genes and an accessory pangenome of 1,064 genes between the two C. fetus subspecies. However, no unique predicted genes were identified in either subspecies. Nonetheless, whole-genome single nucleotide polymorphisms (SNPs) analysis identified 289 SNPs unique to one or the C. fetus subspecies. After the removal of SNPs located on putative genomic islands, recombination sites, and those causing synonymous amino acid changes, the remaining 184 SNPs were functionally annotated. Candidate SNPs that were annotated with the KEGG “Peptidoglycan Biosynthesis” pathway were recruited for further analysis due to their potential association with the glycine intolerance characteristic of C. fetus subsp. venerealis and its biovar variant. Verification with 58 annotated C. fetus genomes, both complete and incomplete, from RefSeq, successfully classified these seven SNPs into two groups, aligning with their phenotypic identification as CFF ( Campylobacter fetus subsp. fetus) or CFV/CFVi ( Campylobacter fetus subsp. venerealis and its biovar variant). Furthermore, we demonstrated the application of mraY SNPs for detecting C. fetus subspecies using a quantitative PCR assay.
Discussion
Our results highlighted the high genetic stability of C. fetus subspecies. Nevertheless, Campylobacter fetus subsp. venerealis and its biovar variants encoded common SNPs in genes related to glycine intolerance, which differentiates them from C. fetus subsp. fetus. This discovery highlights the potential of employing a multiple-SNP assay for the precise differentiation of C. fetus subspecies