School of Agriculture, Food and Ecosystem Sciences - Research Publications

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    Computationally reproducing results from meta-analyses in ecology and evolutionary biology using shared code and data
    Kambouris, S ; Wilkinson, DP ; Smith, ET ; Fidler, F ; Kaiser, E (PUBLIC LIBRARY SCIENCE, 2024-03-13)
    Many journals in ecology and evolutionary biology encourage or require authors to make their data and code available alongside articles. In this study we investigated how often this data and code could be used together, when both were available, to computationally reproduce results published in articles. We surveyed the data and code sharing practices of 177 meta-analyses published in ecology and evolutionary biology journals published between 2015-17: 60% of articles shared data only, 1% shared code only, and 15% shared both data and code. In each of the articles which had shared both (n = 26), we selected a target result and attempted to reproduce it. Using the shared data and code files, we successfully reproduced the targeted results in 27-73% of the 26 articles, depending on the stringency of the criteria applied for a successful reproduction. The results from this sample of meta-analyses in the 2015-17 literature can provide a benchmark for future meta-research studies gauging the computational reproducibility of published research in ecology and evolutionary biology.
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    Back to the future for drought tolerance
    Guadarrama-Escobar, LM ; Hunt, J ; Gurung, A ; Zarco-Tejada, PJ ; Shabala, S ; Camino, C ; Hernandez, P ; Pourkheirandish, M (WILEY, 2024-04)
    Global agriculture faces increasing pressure to produce more food with fewer resources. Drought, exacerbated by climate change, is a major agricultural constraint costing the industry an estimated US$80 billion per year in lost production. Wild relatives of domesticated crops, including wheat (Triticum spp.) and barley (Hordeum vulgare L.), are an underutilized source of drought tolerance genes. However, managing their undesirable characteristics, assessing drought responses, and selecting lines with heritable traits remains a significant challenge. Here, we propose a novel strategy of using multi-trait selection criteria based on high-throughput spectral images to facilitate the assessment and selection challenge. The importance of measuring plant capacity for sustained carbon fixation under drought stress is explored, and an image-based transpiration efficiency (iTE) index obtained via a combination of hyperspectral and thermal imaging, is proposed. Incorporating iTE along with other drought-related variables in selection criteria will allow the identification of accessions with diverse tolerance mechanisms. A comprehensive approach that merges high-throughput phenotyping and de novo domestication is proposed for developing drought-tolerant prebreeding material and providing breeders with access to gene pools containing unexplored drought tolerance mechanisms.
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    National-scale investigation reveals the dominant role of phyllosphere fungal pathogens in sorghum yield loss
    Ren, P ; Sun, A ; Jiao, X ; Chen, Q-L ; Li, F ; He, J-Z ; Hu, H-W (PERGAMON-ELSEVIER SCIENCE LTD, 2024-03)
    Fungal plant pathogens threaten crop production and sustainable agricultural development. However, the environmental factors driving their diversity and nationwide biogeographic model remain elusive, impacting our capacity to predict their changes under future climate scenarios. Here, we analyzed potential fungal plant pathogens from 563 samples collected from 57 agricultural fields across China. Over 28.0% of fungal taxa in the phyllosphere were identified as potential plant pathogens, compared to 22.3% in the rhizosphere. Dominant fungal plant pathogen groups were Cladosporium (in the phyllosphere) and Fusarium (in the rhizosphere), with higher diversity observed in the phyllosphere than in rhizosphere soil. Deterministic processes played an important role in shaping the potential fungal plant pathogen community assembly in both habitats. Mean annual precipitation and temperature were the most important factor influencing phyllosphere fungal plant pathogen richness. Significantly negative relationships were found between fungal pathogen diversity and sorghum yield. Notably, compared to the rhizosphere, the phyllosphere fungal plant pathogen diversity played a more crucial role in sorghum yield. Together, our work provides novel insights into the factors governing the spatial patterns of fungal plant pathogens in the crop microbiome, and highlights the potential significance of aboveground phyllosphere fungal plant pathogens in crop productivity.
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    Developing biomass allometric equations for small trees in mixed-species forests of tropical rainforest ecozone
    Adinugroho, WC ; Krisnawati, H ; Imanuddin, R ; Siregar, CA ; Weston, CJ ; Volkova, L (ELSEVIER, 2023-09)
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    Attribution of extreme events to climate change in the Australian region - A review
    Lane, TP ; King, AD ; Perkins-Kirkpatrick, SE ; Pitman, AJ ; Alexander, LV ; Arblaster, JM ; Bindoff, NL ; Bishop, CH ; Black, MT ; Bradstock, RA ; Clarke, HG ; Gallant, AJE ; Grose, MR ; Holbrook, NJ ; Holland, GJ ; Hope, PK ; Karoly, DJ ; Raupach, TH ; Ukkola, AM (ELSEVIER, 2023-12)
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    LC-ESI-QTOF-MS/MS characterization of phenolic compounds in Australian native passion fruits and their potential antioxidant activities
    Liu, H ; Agar, OT ; Imran, A ; Barrow, CJ ; Dunshea, FR ; Suleria, HAR (WILEY, 2024-04)
    Passion fruits, renowned globally for their polyphenolic content and associated health benefits, have enjoyed growing attention from consumers and producers alike. While global cultivar development progresses, Australia has pioneered several native cultivars tailored for its distinct planting conditions. Despite their cultivation, comprehensive studies on the phenolic profiles and antioxidant capacities of these Australian-native passion fruits are notably lacking. This study aims to investigate and compare the polyphenolic content present in the by-products, which are peel (L), and consumable portions, which are the pulp and seeds (P), of four indigenous cultivars: 'Misty Gem' (MG), 'Flamengo' (FG), 'Sweetheart' (SW), and 'Panama' (SH). Employing LC-ESI-QTOF-MS/MS for profiling, a comprehensive list of polyphenols was curated. Additionally, various antioxidant assays-DPPH, FRAP, ABTS, RPA, FICA, and •OH-RSA-were performed to evaluate their antioxidant potential. A total of 61 polyphenols were identified, categorized into phenolic acid (19), flavonoids (33), and other phenolic substances (9). In the antioxidant assays, the SHP sample exhibited the highest •OH--RSA activity at 98.64 ± 1.45 mg AAE/g, while the FGL sample demonstrated prominent DPPH, FRAP, and ABTS activities with values of 32.47 ± 1.92 mg TE/g, 62.50 ± 3.70 mg TE/g, and 57.84 ± 1.22 mg AAE/g, respectively. Additionally, TPC and several antioxidant assays had a significant positive correlation, including DPPH, FRAP, and ABTS. The Australian-native passion fruits revealed distinct polyphenolic profiles and diverse antioxidant capacities, establishing a foundation for deeper health benefit analyses. This study accentuates the significance of understanding region-specific cultivars and their potential nutraceutical applications.
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    Fox control and fire influence the occurrence of invasive predators and threatened native prey
    Rees, MW ; Wintle, BA ; Robley, A ; Pascoe, JH ; Le Pla, M ; Birnbaum, EK ; Hradsky, BA (SPRINGER, 2024-03)
    Abstract It can be challenging to distinguish management impacts from other population drivers, including ‘natural’ processes and co-occurring threats. However, disentangling processes is important, particularly when management may have unintended consequences, such as mesopredator release. We explored the effects of long-term, broadscale poison-baiting programs on the distribution of red foxes Vulpes vulpes (targeted invasive predator), feral cats Felis catus (unmanaged invasive competitor) and two of their threatened native prey in two fire-affected regions of south-eastern Australia. We synthesised data from 3667 camera-trap deployments at 1232 sites (172,052 trap-nights), combining experimental manipulation of foxes and fire with space-for-time approaches. Fox control effectiveness—in terms of decreased probability of fox occurrence and increased probability of prey occurrence—depended on the duration and intensity of the poison-baiting program. The effects of fox control on prey occurrence also varied between the two native prey species: fox control was strongly beneficial to the long-nosed potoroo Potorous tridactylus but had no measurable effect on southern brown bandicoot Isoodon obesulus occurrence. Feral cat occupancy tended to be higher in landscapes with long-term fox control, although we found no effect of fox-bait density on fine-scale cat occurrence. Time since fire (0–80 years) was associated with the occurrence of each study species, but its association with invasive predators also differed among vegetation types. Invasive predators and altered fire regimes are key, often overlapping, biodiversity threats. Our work highlights the importance of fine-scale monitoring and consideration of multiple drivers in distribution models to develop effective, tailored conservation strategies.
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    The role of nitrogen management in achieving global sustainable development goals
    Zhang, C ; Gu, B ; Liang, X ; Lam, SK ; Zhou, Y ; Chen, D (ELSEVIER, 2024-02)
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    The influence of spatial arrangement and site conditions on the fate of infiltrated stormwater
    Poozan, A ; Fletcher, TD ; Arora, M ; William Western, A ; James Burns, M (Elsevier BV, 2024-02-01)
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    Assessment of changes in sensory perception, biometrics and emotional response for space exploration by simulating microgravity positions
    Viejo, CG ; Harris, N ; Fuentes, S (ELSEVIER, 2024-01)
    Long-term space exploration endeavors, encompassing journeys from the Earth to the Moon by 2030 and subsequent voyages from the Moon to Mars by 2040, necessitate the utilization of plant-based materials not solely for sustenance and refreshments but also the production of pharmaceuticals and repair compounds, such as plastics, among others. Nevertheless, the vital aspects of research in this domain pertain to the nutritional value and sensory perception associated with plant-based food. Prior investigations have shown altered sensory perception in space, manifested as diminished olfactory sensations and heightened taste perception (saltiness and sweetness). Nonetheless, studies concerning changes in aroma, basic tastes, and mouthfeel have been limited due to the logistical challenges associated with conducting experiments in the unique environment of space. To address this limitation, the present study employed sensory trials and biometrics from video using simulated microgravity chairs to simulate alterations in sensory perception akin to those encountered in space conditions. The findings of this study align with previous reports of changes in aroma and taste perception and contribute to the understanding of changes in the mouthfeel, heart rate, blood pressure, and emotional response that could be experienced in space environments. These experimental endeavors are critical to facilitate the advancement and development of novel plants and food materials tailored to the requirements of long-term space exploration.