School of Agriculture, Food and Ecosystem Sciences - Research Publications
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ItemCurrent and future adoption of leucaena-grass pastures in northern Australia(CENTRO INT AGRICULTURA TROPICAL-CIAT, 2019-09-01)Keynote paper presented at the International Leucaena Conference, 1‒3 November 2018, Brisbane, Queensland, Australia.The leucaena-grass pastures and target markets for adoption project was commissioned by Meat & Livestock Australia (MLA) to examine the scope for further adoption of leucaena-grass pastures in northern Australia. Drawing upon stakeholder and producer interviews, focus groups, mapping of biophysical factors critical to growing leucaena and a review of existing literature, regional adoption profiles were developed using the ADOPT model. This work outlines the current and future potential for adoption of leucaena in northern Australia and recommends 5 interrelated strategic actions designed to support the ongoing adoption. These actions have been designed to address the complex technical, social and biophysical requirements for successful adoption and will require collaboration between investors, The Leucaena Network, producers, government agencies and the private sector to be effective.
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ItemPhenolic Compounds Profiling and Their Antioxidant Capacity in the Peel, Pulp, and Seed of Australian Grown Avocado(MDPI, 2023-01-01)Avocados (Persea americana M.) are highly valued fruits consumed worldwide, and there are numerous commercially available varieties on the market. However, the high demand for fruit also results in increased food waste. Thus, this study was conducted for comprehensive profiling of polyphenols of Hass, Reed, and Wurtz avocados obtained from the Australian local market. Ripe Hass peel recorded the highest TPC (77.85 mg GAE/g), TTC (148.98 mg CE/g), DPPH (71.03 mg AAE/g), FRAP (3.05 mg AAE/g), RPA (24.45 mg AAE/g), and ABTS (75.77 mg AAE/g) values; unripe Hass peel recorded the highest TFC (3.44 mg QE/g); and Wurtz peel recorded the highest TAC (35.02 mg AAE/g). Correlation analysis revealed that TPC and TTC were significantly correlated with the antioxidant capacity of the extracts. A total of 348 polyphenols were screened in the peel. A total of 134 compounds including 36 phenolic acids, 70 flavonoids, 11 lignans, 2 stilbenes, and another 15 polyphenols, were characterised through LC-ESI-QTOF-MS/MS, where the majority were from peels and seeds of samples extract. Overall, the hierarchical heat map revealed that there were a significant amount of polyphenols in peels and seeds. Epicatechin, kaempferol, and protocatechuic acid showed higher concentrations in Reed pulp. Wurtz peel contains a higher concentration of hydroxybenzoic acid. Our results showed that avocado wastes have a considerable amount of polyphenols, exhibiting antioxidant activities. Each sample has its unique value proposition based on its phenolic profile. This study may increase confidence in utilising by-products and encourage further investigation into avocado by-products as nutraceuticals.
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ItemCost-effective mitigation of nitrogen pollution from global croplands(NATURE PORTFOLIO, 2023-01-05)Cropland is a main source of global nitrogen pollution1,2. Mitigating nitrogen pollution from global croplands is a grand challenge because of the nature of non-point-source pollution from millions of farms and the constraints to implementing pollution-reduction measures, such as lack of financial resources and limited nitrogen-management knowledge of farmers3. Here we synthesize 1,521 field observations worldwide and identify 11 key measures that can reduce nitrogen losses from croplands to air and water by 30-70%, while increasing crop yield and nitrogen use efficiency (NUE) by 10-30% and 10-80%, respectively. Overall, adoption of this package of measures on global croplands would allow the production of 17 ± 3 Tg (1012 g) more crop nitrogen (20% increase) with 22 ± 4 Tg less nitrogen fertilizer used (21% reduction) and 26 ± 5 Tg less nitrogen pollution (32% reduction) to the environment for the considered base year of 2015. These changes could gain a global societal benefit of 476 ± 123 billion US dollars (USD) for food supply, human health, ecosystems and climate, with net mitigation costs of only 19 ± 5 billion USD, of which 15 ± 4 billion USD fertilizer saving offsets 44% of the gross mitigation cost. To mitigate nitrogen pollution from croplands in the future, innovative policies such as a nitrogen credit system (NCS) could be implemented to select, incentivize and, where necessary, subsidize the adoption of these measures.
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ItemNo Preview AvailableAridity differentially alters the stability of soil bacterial and fungal networks in coastal and inland areas of Australia(WILEY, 2022-09-16)Despite the importance of soil bacterial and fungal communities for ecosystem services and human welfare, how their ecological networks respond to climatic aridity have yet been evaluated. Here, we collected soil samples from 47 sites across 2500 km in coastal and inland areas of eastern Australia with contrasting status of aridity. We found that the diversity of both bacteria and fungi significantly differed between inland and coastal soils. Despite the significant differences in soil nutrient availability and stoichiometry between the inland and coastal regions, aridity was the most important predictor of bacterial and fungal community compositions. Aridity has altered the potential microbial migration rates and further impacted the microbial assembly processes by increasing the importance of stochasticity in bacterial and fungal communities. More importantly, ecological network analysis indicated that aridity enhanced the complexity and stability of the bacterial network but reduced that of the fungal network, possibly due to the contrasting impacts of aridity on the community-level habitat niche breadth and overlaps. Our work paves the way towards a more comprehensive understanding of how climate changes will alter soil microbial communities, which is integral to predicting their long-term consequences for ecosystem sustainability and resilience to future disturbances.
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ItemGenetic variation in histone modifications and gene expression identifies regulatory variants in the mammary gland of cattle(BMC, 2022-12-08)BACKGROUND: Causal variants for complex traits, such as eQTL are often found in non-coding regions of the genome, where they are hypothesised to influence phenotypes by regulating gene expression. Many regulatory regions are marked by histone modifications, which can be assayed by chromatin immunoprecipitation followed by sequencing (ChIP-seq). Sequence reads from ChIP-seq form peaks at putative regulatory regions, which may reflect the amount of regulatory activity at this region. Therefore, eQTL which are also associated with differences in histone modifications are excellent candidate causal variants. RESULTS: We assayed the histone modifications H3K4Me3, H3K4Me1 and H3K27ac and mRNA in the mammary gland of up to 400 animals. We identified QTL for peak height (histone QTL), exon expression (eeQTL), allele specific expression (aseQTL) and allele specific binding (asbQTL). By intersecting these results, we identify variants which may influence gene expression by altering regulatory regions of the genome, and may be causal variants for other traits. Lastly, we find that these variants are found in putative transcription factor binding sites, identifying a mechanism for the effect of many eQTL. CONCLUSIONS: We find that allele specific and traditional QTL analysis often identify the same genetic variants and provide evidence that many eQTL are regulatory variants which alter activity at regulatory regions of the bovine genome. Our work provides methodological and biological updates on how regulatory mechanisms interplay at multi-omics levels.
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ItemThe global distribution and environmental drivers of the soil antibiotic resistome(BMC, 2022-12-12)BACKGROUND: Little is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earth's largest reservoirs of ARGs, which are integral for soil microbial competition, and have potential implications for plant and human health. Yet, their diversity and global patterns remain poorly described. Here, we analyzed 285 ARGs in soils from 1012 sites across all continents and created the first global atlas with the distributions of topsoil ARGs. RESULTS: We show that ARGs peaked in high latitude cold and boreal forests. Climatic seasonality and mobile genetic elements, associated with the transmission of antibiotic resistance, were also key drivers of their global distribution. Dominant ARGs were mainly related to multidrug resistance genes and efflux pump machineries. We further pinpointed the global hotspots of the diversity and proportions of soil ARGs. CONCLUSIONS: Together, our work provides the foundation for a better understanding of the ecology and global distribution of the environmental soil antibiotic resistome. Video Abstract.
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ItemUsing eDNA metabarcoding to understand the effect of fire on the diet of small mammals in a woodland ecosystem(WILEY, 2022-11-01)Food acquisition is a fundamental process that drives animal distribution and abundance, influencing how species respond to changing environments. Disturbances such as fire create significant shifts in available dietary resources, yet, for many species, we lack basic information about what they eat, let alone how they respond to a changing resource base. In order to create effective management strategies, faunal conservation in flammable landscapes requires a greater understanding of what animals eat and how this change following a fire. What animals eat in postfire environments has received little attention due to the time-consuming methodologies and low-resolution identification of food taxa. Recently, molecular techniques have been developed to identify food DNA in scats, making it possible to identify animal diets with enhanced resolution. The primary aim of this study was to utilize eDNA metabarcoding to obtain an improved understanding of the diet of three native Australian small mammal species: yellow-footed antechinus (Antechinus flavipes), heath mouse (Pseudomys shortridgei), and bush rat (Rattus fuscipes). Specifically, we sought to understand the difference in the overall diet of the three species and how diet changed over time after fire. Yellow-footed antechinus diets mostly consisted of moths, and plants belonging to myrtles and legume families while bush rats consumed legumes, myrtles, rushes, and beetles. Heath mouse diet was dominated by rushes. All three species shifted their diets over time after fire, with most pronounced shifts in the bush rats and least for heath mice. Identifying critical food resources for native animals will allow conservation managers to consider the effect of fire management actions on these resources and help conserve the species that use them.
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ItemRats and the city: Implications of urbanization on zoonotic disease risk in Southeast Asia(NATL ACAD SCIENCES, 2022-09-27)Urbanization is rapidly transforming much of Southeast Asia, altering the structure and function of the landscape, as well as the frequency and intensity of the interactions between people, animals, and the environment. In this study, we explored the impact of urbanization on zoonotic disease risk by simultaneously characterizing changes in the ecology of animal reservoirs (rodents), ectoparasite vectors (ticks), and pathogens across a gradient of urbanization in Kuching, a city in Malaysian Borneo. We sampled 863 rodents across rural, developing, and urban locations and found that rodent species diversity decreased with increasing urbanization-from 10 species in the rural location to 4 in the rural location. Notably, two species appeared to thrive in urban areas, as follows: the invasive urban exploiter Rattus rattus (n = 375) and the native urban adapter Sundamys muelleri (n = 331). R. rattus was strongly associated with built infrastructure across the gradient and carried a high diversity of pathogens, including multihost zoonoses capable of environmental transmission (e.g., Leptospira spp.). In contrast, S. muelleri was restricted to green patches where it was found at high densities and was strongly associated with the presence of ticks, including the medically important genera Amblyomma, Haemaphysalis, and Ixodes. Our analyses reveal that zoonotic disease risk is elevated and heterogeneously distributed in urban environments and highlight the potential for targeted risk reduction through pest management and public health messaging.
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ItemComparative enteric-methane emissions of dairy farms in northern Victoria, Australia(CSIRO Publishing, 2023)Context: Enteric methane (CH4) is a source of greenhouse gas (GHG) in agriculture, which needs to be reduced. A variety of feeding systems for dairy production is being used in south-eastern Australia, but there are few studies that compare CH4 emissions and emission intensity (EI) of milk production across these systems. Aims: The objective was to estimate the lactating cows’ enteric-CH4 emissions, EI and their seasonal changes, across different feeding systems in northern Victoria, Australia. Methods: A Tier 2 inventory methodology was used to estimate the enteric-CH4 emissions and EI. Four case-study farms were selected to represent a range of feeding systems, Farms A, B, C and D were categorised as System 4–5 (hybrid–total mixed ration system), System 4 (hybrid system), System 2 (moderate–high bail system) and System 2 respectively. Monthly feed, animal and production data were sourced from June 2019 to May 2020. Key results: Average enteric-CH4 emissions of Farms A and B (13.1 and 12.9 kg CO2e/head.day respectively) were greater than those of Farms C and D (11.7 and 11.6 kg CO2e/head.day respectively). Furthermore, CH4 EI was greater in Farms C and D (0.49 and 0.48 CO2-e kg/kg fat- and protein-corrected milk (FPCM) respectively) and it was lower in both Farms A and B (0.46 CO2-e kg/kg FPCM). Overall, Farms A and B using Feeding-system 4–5 with greater-producing cows produced more CH4 but with less CH4 EI than did the Farms C and D, which are mainly pasture-based. Conclusions: These findings suggest that to reduce CH4 EI requires a move towards Feeding-system 4–5. However, on the basis of the results of the current study, pasture-based systems have an advantage over hybrid/total mixed ration feeding systems, as these farms have lower absolute CH4 emissions, which helps address climate change. Implications: Estimation of CH4 emissions, EI and seasonal changes in them gives farmers the opportunity to identify the mitigation strategies and plan specific strategies that fit the particular feeding system and season. However, more research needs to be conducted to check the feasibility of doing this.
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ItemAlginate-inulin-chitosan based microspheres alter metabolic fate of encapsulated quercetin, promote short chain fatty acid production, and modulate pig gut microbiota(ELSEVIER SCI LTD, 2023-08-30)Quercetin loaded alginate microspheres, fabricated with the inclusion of inulin as a prebiotic source and chitosan as protective coating (ALINCH-Q), were subjected to in vitro colonic fermentation using pig fecal microbiota, with empty microspheres ALINCH-E, unencapsulated quercetin UQ and media only Blank as parallel studies. ALINCH-Q altered quercetin biotransformation towards higher production of 3-hydroxyphenylpropionic acid and 3-hydroxyphenylacetic acid, and further metabolism of 3,4-dihydroxyphenylacetic acid and 4-hydroxyphenylacetic acid compared to UQ. In addition, ALINCH-Q but not ALINCH-E or UQ significantly promoted SCFAs production compared to Blank. Furthermore, the ALINCH-Q microspheres altered the microbial compositions, increased the relative abundance of Lactobacillus, Turicibacter, Eubacterium, and Clostridium, while decreased that of the potentially pathogenic Enterococcus. The results suggest an interplay between the dietary fiber matrix and quercetin in producing these effects, and that ALINCH-Q could serve as a potential targeted delivery vehicle for quercetin to exert beneficial biological effects in the colon.