School of Agriculture, Food and Ecosystem Sciences - Research Publications
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ItemOpportunities to improve nitrogen use efficiency in an intensive vegetable system without compromising yield(WILEY, 2021-05)Intensive vegetable cropping systems rely heavily on nitrogen (N) inputs from multiple synthetic and organic fertilizer applications. The majority of applied N is lost to the environment through numerous pathways, including as nitrous oxide (N2 O). A field trial was conducted to examine the opportunities to reduce N input in an intensive vegetable system without compromising yield. Treatments applied were control (no N), manure (M, 408 kg N ha-1 from chicken manure), grower practice (GP, 408 kg N ha-1 from chicken manure + 195 kg N ha-1 from fertilizer), and 2/3 GP (two-thirds of the total N input in GP), all with and without 3,4-dimethylpyrazole phosphate (DMPP). Nitrogen recovery in the GP treatment was determined using 15 N-labeled fertilizer. Using only manure significantly lowered celery (Apium graveolens L.) yield and apparent N use efficiency (ANUE) compared with GP. Reducing N input by one-third did not affect yield or ANUE. Use of DMPP increased ANUE despite no yield improvement. More than 50% of the applied N in the GP treatment was lost to the environment, with almost 10 kg N ha-1 emitted as N2 O over the season, which was 67 times more than from the control. Reducing the N input by one-third or using manure only reduced N2 O emissions by more than 70% relative to GP. This study shows that there is a clear opportunity to reduce N input and N2 O emissions in high-fertilizer-input vegetable systems without compromising vegetable yield.
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ItemAn empirical analysis of the use of agricultural mobile applications among smallholder farmers in Myanmar(WILEY, 2021-03)Abstract Mobile phone applications (apps) designed to assist smallholder farmers improve decision‐making have been revolutionizing the agriculture sector. These apps offer solutions to farmer information needs by providing weather information, crop market trends, pest and disease damage identification, and advice on pesticide and fertilizer use. They also facilitate interaction with fellow farmers, extension workers and other stakeholders in the value chain who are interested in information exchange. Much previous research has investigated the contribution of mobile apps to agricultural production. This study explored the agricultural mobile apps available in Myanmar, analyzed factors affecting their use and assessed the potential for farm‐based decision support. Our findings indicate that when introducing mobile‐based tools, focus should be given to younger, more educated farmers growing more specialized crops. The main constraints to adopt agricultural apps are lack of access to smartphone and/or internet (63%) and lack of digital knowledge (20%). However, smallholder farmers in Myanmar were optimistic and positive toward agricultural apps for effective utilization. We also found that majority of the surveyed farmers were familiar with information received through Facebook groups. Incorporating useful information and functions from an agricultural mobile app to a Facebook Page could have a more useful and sustainable impact.
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ItemThe potential and practice of arboreal camera trapping(WILEY, 2021-10)Abstract Arboreal camera trapping is a burgeoning method providing a novel and effective technique to answer research questions across a variety of ecosystems, and it has the capacity to improve our understanding of a wide range of taxa. However, while terrestrial camera trapping has received much attention, there is little guidance for dealing with the unique challenges of working in the arboreal realm. Our review draws on the expertise of researchers from six continents and the broader literature to investigate the advantages and disadvantages of arboreal camera trapping, and challenges to consider when using this technology. We also include mini‐guides with detailed information on the current arboreal camera trap literature, mounts used to install arboreal cameras, tree climbing pointers and safety tips, methods for deploying cameras without climbing, and tips for managing interference with camera function. We find that arboreal camera traps have been most commonly used in the study of mammals in forests; however, there is potential for this method to be applied to a broad range of habitats including urban areas, and taxa such as birds, amphibians, invertebrates, and plants. Methods in arboreal camera trapping could be improved by developing a greater understanding of the factors affecting detection of species. The most common challenges of arboreal camera trapping are camera placement and camera site access. These can be overcome by understanding correct camera orientation, managing potential sources of interference in front of cameras, utilizing appropriate cameras mounts and training researchers properly. Given the benefits and opportunities presented by arboreal camera trapping, it is likely to become an ever‐more popular method of studying arboreal species and systems. The information synthesized in this review provides guidance for future studies to help direct more reliable and robust ecological inferences from arboreal camera trapping.
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ItemEfficient effort allocation in line-transect distance sampling of high-density species: When to walk further, measure less-often and gain precision(WILEY, 2021-06)Abstract Line‐transect distance sampling is widely used to estimate population densities using distances of observed targets from transect lines to model detectability. When the target taxa are high density, the frequent measuring of distances may make the method seem impractical. We present a method that improves the efficiency of distance sampling when the target species occurs at high density. Only a proportion of targets are measured to model the detection function, and the time saved on the survey is then used to cover a longer total length of transect and accrue a larger ‘count only’ sample. This approach can improve the precision of the population density estimate when the cost of measuring the distance to a detected target is more than half the cost of walking to the next target. We find the optimal proportion of distances to measure that minimises the variance of the density estimate for a fixed survey budget. We quantify how much this optimised strategy increases the precision of the density estimate compared with conventional line‐transect distance sampling. We then use simulated distance sampling data to test our expressions, and illustrate circumstances under which the optimised approach would be beneficial using distance sampling data on high‐density plants. The simulations indicate that the optimised method delivers benefits in precision, but the magnitude of the benefit is lower than predicted from our expressions, which are based on an asymptotic approximation of the variance. We apply an adjustment to the predicted benefit equation to account for this difference, and show that, in all three plant case studies, the optimised approach could improve the precision gained from a distance sampling survey between 20% and 50%. This new approach could broaden the ecological contexts in which distance sampling is applied, to include estimation of densities of abundant taxa where plots are conventionally used. The method may have interesting applications for other survey types, including multispecies surveys or those using cues or signs that occur at high density.
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ItemDefining and evaluating predictions of joint species distribution models(WILEY, 2021-03)Abstract Joint species distribution models (JSDMs) simultaneously model the distributions of multiple species, while accounting for residual co‐occurrence patterns. Despite increasing adoption of JSDMs in the literature, the question of how to define and evaluate JSDM predictions has only begun to be explored. We define four different JSDM prediction types that correspond to different aspects of species distribution and community assemblage processes. Marginal predictions are environment‐only predictions akin to predictions from single‐species models; joint predictions simultaneously predict entire community assemblages; and conditional marginal and conditional joint predictions are made at the species or assemblage level, conditional on the known occurrence state of one or more species at a site. We define five different classes of metrics that can be used to evaluate these types of predictions: threshold‐dependent, threshold‐independent, community dissimilarity, species richness and likelihood metrics. We illustrate different prediction types and evaluation metrics using a case study in which we fit a JSDM to a frog occurrence dataset collected in Melbourne, Australia. Joint species distribution models present opportunities to investigate the facets of species distribution and community assemblage processes that are not possible to explore with single‐species models. We show that there are a variety of different metrics available to evaluate JSDM predictions, and that choice of prediction type and evaluation metric should closely match the questions being investigated.
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ItemWine phenolic profile altered by yeast: Mechanisms and influences(WILEY, 2021-07)Grape phenolic compounds undergo various types of transformations during winemaking under the influences of yeasts, which further impacts the sensory attributes, thus the quality of wine. Understanding the roles of yeasts in phenolics transformation is important for controlling wine quality through fermentation culture selection. This literature review discusses the mechanisms of how yeasts alter the phenolic compounds during winemaking, summarizes the effects of Saccharomyces cerevisiae and non-Saccharomyces yeasts on the content and composition of phenolics in wine, and highlights the influences of mixed cultural fermentation on the phenolic profile of wine. Collectively, this paper aims to provide a deeper understanding on yeast-phenolics interactions and to identify the current literature gaps for future research.
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ItemActivity and bioavailability of food protein-derived angiotensin-I-converting enzyme-inhibitory peptides(WILEY, 2021-03)Angiotensin-I-converting enzyme (ACE) inhibitory peptides are able to inhibit the activity of ACE, which is the key enzymatic factor mediating systemic hypertension. ACE-inhibitory peptides can be obtained from edible proteins and have the function of antihypertension. The amino acid sequences and the secondary structures of ACE-inhibitory peptides determine the inhibitory activities and stability. The resistance of ACE-inhibitory peptides to digestive enzymes and peptidase affect their antihypertensive bioactivity in vivo. In this paper, the mechanism of ACE-inhibition, sources of the inhibitory peptides, structure-activity relationships, stability during digestion, absorption and transportation of ACE-inhibitory peptides, and consumption of ACE-inhibitory peptides are reviewed, which provide guidance to the development of new functional foods and production of antihypertensive nutraceuticals and pharmaceuticals.
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ItemOpportunities for plant-derived enhancers for iron, zinc, and calcium bioavailability: A review(Wiley, 2021-01-14)Understanding of the mechanism of interactions between dietary elements, their salts, and complexing/binding ligands is vital to manage both deficiency and toxicity associated with essential element bioavailability. Numerous mineral ligands are found in both animal and plant foods and are known to exert bioactivity via element chelation resulting in modulation of antioxidant capacity or micobiome metabolism among other physiological outcomes. However, little is explored in the context of dietary mineral ligands and element bioavailability enhancement, particularly with respect to ligands from plant-derived food sources. This review highlights a novel perspective to consider various plant macro/micronutrients as prospective bioavailability enhancing ligands of three essential elements (Fe, Zn, and Ca). We also delineate the molecular mechanisms of the ligand-binding interactions underlying mineral bioaccessibility at the luminal level. We conclude that despite current understandings of some of the structure–activity relationships associated with strong mineral–ligand binding, the physiological links between ligands as element carriers and uptake at targeted sites throughout the gastrointestinal (GI) tract still require more research. The binding behavior of potential ligands in the human diet should be further elucidated and validated using pharmacokinetic approaches and GI models.
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ItemComplete Genome Sequence of Community-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 1, SCCmec IV[2B], Isolated in the 1990s from Northern Western Australia(AMER SOC MICROBIOLOGY, 2021-09)Sequence type 1 (ST1) methicillin-resistant Staphylococcus aureus (MRSA) SCCmec IV[2B] has become one of the most common community-associated MRSA clones in Australia. We report the complete genome sequence of one of the earliest isolated Australian S. aureus ST1-MRSA-IV strains, WBG8287, isolated from an Indigenous Australian patient living in the remote Kimberley region of Western Australia.
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ItemComparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium(MICROBIOLOGY SOC, 2021-10)Members of the Mesorhizobium genus are soil bacteria that often form nitrogen-fixing symbioses with legumes. Most characterised Mesorhizobium spp. genomes are ~8 Mb in size and harbour extensive pangenomes including large integrative and conjugative elements (ICEs) carrying genes required for symbiosis (ICESyms). Here, we document and compare the conjugative mobilome of 41 complete Mesorhizobium genomes. We delineated 56 ICEs and 24 integrative and mobilizable elements (IMEs) collectively occupying 16 distinct integration sites, along with 24 plasmids. We also demonstrated horizontal transfer of the largest (853,775 bp) documented ICE, the tripartite ICEMspSymAA22. The conjugation systems of all identified ICEs and several plasmids were related to those of the paradigm ICESym ICEMlSymR7A, with each carrying conserved genes for conjugative pilus formation (trb), excision (rdfS), DNA transfer (rlxS) and regulation (fseA). ICESyms have likely evolved from a common ancestor, despite occupying a variety of distinct integration sites and specifying symbiosis with diverse legumes. We found extensive evidence for recombination between ICEs and particularly ICESyms, which all uniquely lack the conjugation entry-exclusion factor gene trbK. Frequent duplication, replacement and pseudogenization of genes for quorum-sensing-mediated activation and antiactivation of ICE transfer suggests ICE transfer regulation is constantly evolving. Pangenome-wide association analysis of the ICE identified genes potentially involved in symbiosis, rhizosphere colonisation and/or adaptation to distinct legume hosts. In summary, the Mesorhizobium genus has accumulated a large and dynamic pangenome that evolves through ongoing horizontal gene transfer of large conjugative elements related to ICEMlSymR7A.