Kirsty Bayliss

Plant pests significantly reduce crop yield, which impacts access, availability and food utilisation. Rice is a staple crop for almost half of the world's population. Asia (including the Indo-Pacific Region, IPR) contributes 90% and consumes 86% of global rice production, but is among the most food-insecure regions in the world, with an increase of 16 million (to 113 million) moderately/severely food-insecure people in the region in the last 5 years. Outbreaks of the rice blast pathogen Pyricularia oryzae in the IPR could significantly affect global food security. Modelling indicates that an extreme case of 80% loss of rice crops across the IPR could increase global rice prices by 50-95%, increasing food insecurity for net exporter countries while creating price shocks in importing countries. This study used the four pillars of food security as a framework to evaluate the impact of rice blast on food availability, access, utilisation, and stability. The objective was to determine if biosecurity measures might be easily implemented to reduce the risk of the disease and increase food security in the region. Biosecurity was claimed as essential for managing rice blast across the pre-border/border/post-border continuum to reduce the risk to food security. Australia and New Zealand may be able to assist with the implementation of biosecurity measures as they are the most significant leaders in this field in the IPR. Regional agencies such as the Asia and Pacific Plant Protection Commission might assist the IPR in identifying threats through intelligence gathering and pathway modelling for pre-border activities. To be effective, the biosecurity system needs all stakeholders to work together.

The variability of the rhizosphere microbial community has not been well-studied in avocado plantations at the field-scale. This research aimed to determine if the bacterial and fungal communities in the rhizosphere and/or the soil physicochemical properties from two commercial avocado orchards varied with different sampling designs (grid-based, longitudinal transect, and zigzag transect), and in turn if this changed the soil physicochemical properties driving the composition of the microbial communities. There were no differences in alpha diversity of bacteria or fungi based on sampling design in either orchard, and bacterial and fungal alpha diversity showed no evidence of spatial autocorrelation. Bacterial community composition in Orchard 1 varied with sampling design, whereas no differences were observed for bacterial community composition in Orchard 2 or for fungal community composition in either orchard. In each orchard, at least 50 % of the most abundant bacterial taxa were common between the sampling designs, however, less than 40 % the most abundant fungal taxa were common between the sampling designs. Canonical correspondence analysis indicated that the edaphic drivers of bacterial and fungal communities in Orchard 1 differed based on the sampling design. These results highlight the importance of field-scale sampling design for accurately characterising avocado rhizosphere bacterial and fungal communities particularly when such data will inform orchard management decisions. Soil sampling using a random, grid-based design is recommended as a simple and reliable method for monoculture fruit tree orchards.

Cold plasma is a promising non-thermal method for managing postharvest pathogens that cause mould and fruit decay. This study evaluated cold plasma (CP) and plasma-activated water (PAW) to control the postharvest fungal pathogens associated with strawberries. Fresh ‘Fronteras’ strawberries were treated with CP, PAW, or PAW applied as a mist (PAWM), and quality parameters, including spoilage, firmness, colour, and weight were measured on days 0 and 6. Propidium monoazide (PMA), a dye that selectively binds to the DNA of non-viable cells and prevents PCR amplification, was used to differentiate between viable and non-viable fungi following treatment. Strawberries treated with CP or immersed in PAW for 60 s had significantly reduced visible decay at day 6 without affecting fruit quality, but PAWM was ineffective at reducing spoilage. All treatments significantly reduced fungal diversity when measured using PMA-based metabarcoding after storing for 6 d at 4 °C, compared to the untreated control, with significantly lower abundance of viable fungi. Viable Cladosporium (strawberry pathogen) and Rhodotorula (biocontrol for berry fruit) accounted for 98 % of fungal communities in all treatments after 6 d. Differential abundance analysis showed that all treatments inhibited Filobasidium and Cystofilobasidium while reducing Botrytis abundance. These results demonstrate the potential of CP and PAW treatments to reduce fungal communities, including pathogens, and thus spoilage of postharvest strawberries.

Roots of tomato plants (Solanum lycopersicum) are vulnerable to soil-borne pathogenic fungi, bacteria and nematodes. Current control methods for these biotic stressors have limitations, necessitating the need for new eco-friendly alternatives. The rhizosphere microbiome is an effective natural barrier to invasion by soil-borne pathogens, and there is scope to harness this inherent capacity to improve the management of pathogens. This review examined molecular analyses of the taxonomic composition, abundance and function of the rhizosphere microbiome in healthy and diseased field-grown tomato plants for evidence of the role of the microbiome in disease suppression. The role of biological products in manipulating the rhizosphere microbiome to suppress soil-borne pathogens in field-grown tomato crops was also analysed. We discuss likely mechanisms underpinning microbiome-mediated tolerance to biotic stress in tomato crops and highlight research gaps to be considered in future investigations. Identifying functionally beneficial rhizosphere microbiota in healthy tomato crops may provide new insights into understanding plant–pathogen interactions and allow new strategies for exploring disease control.

The increasing prevalence of Fusarium graminearum, a major causative pathogen of Fusarium head blight in cereal crops, leads to contamination of grain with mycotoxins, which necessitates the development of effective management strategies. This study investigated whether postharvest Blown-Arc plasma treatment could reduce F. graminearum and associated mycotoxins in field-infested grain. Postharvest Blown-Arc plasma treatment for 60 or 180 s was trialled to reduce Fusarium graminearum and deoxynivalenol (DON) mycotoxins in field-infested wheat grain. Changes in fungal components of the grain microbiome following the treatment were assessed using metabarcoding analysis of the nuclear ribosomal internal transcribed spacer gene region, and liquid chromatography mass spectrophotometry was used to measure changes in concentrations of the mycotoxins deoxynivalenol (DON), DON-3-glucoside (DON3-G) and 3-acetyl-DON (3-ADON). Fusarium spp. were the most common taxa in the grain over two seasons, with the relative abundance being higher in 2020 (72%) compared to 2021 (45%). Postharvest plasma treatment of field-infested grain for 60 or 180 s did not significantly lower Fusarium abundance. Alpha and beta diversity of the natural mycobiota in the grain were also unaffected. The concentrations of mycotoxins were not significantly different after the treatments, except that in the 2021 trial, the 180 s treatment caused a significant increase in DON concentration. We concluded that the postharvest plasma treatment used in this study did not reduce Fusarium contamination or the concentration of mycotoxins, DON, DON3-G and 3-ADON in field-infested grain. The results highlight the importance of using field-infested grain in experiments, as opposed to grain inoculated under laboratory conditions, which provides only superficial infection. This approach is crucial for accurately understanding the dynamics of treatment efficacy.
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Spirulina (Arthrospira platensis) is a blue-green alga valued for its protein, phycocyanin, and other bioactive compounds. However, its commercial outdoor cultivation makes it susceptible to microbial contamination, affecting both biomass productivity and quality. Additionally, most commercial Spirulina is sold in dried forms such as powder, flakes, and tablets, which can degrade these bioactive components. To address these issues, non-thermal techniques, such as cold plasma, offer a promising solution by effectively reducing microbial contamination while preserving product quality without the need for drying. This study investigated the potential of bubbling cold plasma-activated (BCPA) air through freshly grown Spirulina to reduce microbial contamination and maintain quality during storage. Spirulina grown in an outdoor paddle-wheel driven pond was harvested in paste form, resuspended in deionized water, treated with plasma-activated air and stored at 4 °C for 28 days. The treatment significantly reduced microbial contamination and maintained Spirulina biomass and pigment contents compared to untreated control. The cellular structure remained intact, and colour changes were minimal in the treated samples when compared to the controls. Moreover, the Spirulina suspension pH became acidic (pH = 4), and oxidation-reduction potential was significantly higher (>150 mV) in treated samples compared to controls throughout the storage period. The results demonstrate the potential for BCPA air to maintain the quality of fresh Spirulina. This finding may have significant applications in the Spirulina industry for offering customers fresh products rather than dried Spirulina.

As the global population continues to grow, the demand for sustainable food sources is rising. Plant-based diets, renowned for their potential to address this demand while promoting public health, food security and environmental sustainability, have gained recognition. Within the realm of sustainable dietary choices, Spirulina (Arthrospira platensis), a microalga, has emerged as a promising source of sustainable protein and nutrition. With its exceptional nutritional value and versatile applications in food, feed, and nutraceuticals, Spirulina stands out as a valuable resource. However, large-scale Spirulina cultivation faces a significant challenge in the form of contamination. Mass cultivation in open pond systems makes it susceptible to various contaminants, jeopardizing product quality and production efficiency. This issue has driven the industry to primarily offer dried Spirulina products, raising questions about the feasibility of delivering fresh Spirulina to the market. To overcome this challenge, effective decontamination techniques are crucial to ensure product safety without compromising nutritional value and sensory attributes. In this review, we assess various decontamination methods for Spirulina products, with a special focus on the application of cold plasma. Cold plasma, a non-thermal ionized gas, has demonstrated its efficacy in sterilizing a variety of food products while preserving their quality. Although research on the use of cold plasma in algal-based products is currently limited, this review seeks to bridge knowledge gaps, assess the challenges, and explore potential solutions for integrating cold plasma into Spirulina production. This review aims to provide valuable insights into innovative processes for combating contaminants in fresh Spirulina, paving the way for improved product safety and quality while retaining its nutritional excellence.

Spoilage of postharvest strawberries by fungal pathogens is a major global concern. This study employed culture-dependent and culture-independent methods to identify postharvest fungal communities of strawberries in Western Australia (WA). Ripe strawberries from eight varieties were sampled twice, early and late in the growing season, from 20 farms in two growing regions. At the first sampling time, traditional isolation and identification demonstrated a high abundance of Botrytis and Cladosporium in Region 1. Mucor was abundant at the second sampling time in Region 1 and both times in Region 2. Metabarcoding confirmed variety-specific fungal communities in WA strawberries. Botrytis and Cladosporium were predominant in Region 1 and Region 2 samples with more than 50% read abundance except on variety Suncoast. No Mucor sequences were detected using metabarcoding, although they were isolated from all samples using culture-based methods. Sisquoc, a hydroponic variety, had a significantly higher fungal diversity than the soil-grown varieties. Varieties Suncoast and Albion exhibited the lowest fungal diversity compared to others. This study demonstrated the value of using culture-dependent and culture-independent methods to investigate the complexity of fungal microbiomes of postharvest strawberries.

Plant-microbe interaction research has had a transformative trajectory, from individual microbial isolate studies to comprehensive analyses of plant microbiomes within the broader phytobiome framework. Acknowledging the indispensable role of plant microbiomes in shaping plant health, agriculture, and ecosystem resilience, we underscore the urgent need for sustainable crop production strategies in the face of contemporary challenges. We discuss how the synergies between advancements in 'omics technologies and artificial intelligence can help advance the profound potential of plant microbiomes. Furthermore, we propose a multifaceted approach encompassing translational considerations, transdisciplinary research initiatives, public-private partnerships, regulatory policy development, and pragmatic expectations for the practical application of plant microbiome knowledge across diverse agricultural landscapes. We advocate for strategic collaboration and intentional transdisciplinary efforts to unlock the benefits offered by plant microbiomes and address pressing global issues in food security. By emphasizing a nuanced understanding of plant microbiome complexities and fostering realistic expectations, we encourage the scientific community to navigate the transformative journey from discoveries in the laboratory to field applications. As companies specializing in agricultural microbes and microbiomes undergo shifts, we highlight the necessity of understanding how to approach sustainable agriculture with site-specific management solutions. While cautioning against over-promising, we underscore the excitement of exploring the many impacts of microbiome-plant interactions. We emphasize the importance of collaborative endeavors with societal partners to accelerate our collective capacity to harness the diverse and yet-to-be-discovered beneficial activities of plant microbiomes.

Enzymatic browning is a biological process that can have significant consequences for fresh produce, such as quality reduction in fruit and vegetables. It is primarily initiated by polyphenol oxidase (PPO) (EC 1.14.18.1 and EC 1.10.3.1) which catalyses the oxidation of phenolic compounds. It is thought that subsequent non-enzymatic reactions result in these compounds polymerising into dark pigments called melanins. Most work to date has investigated the kinetics of PPO with anti-browning techniques focussed on inhibition of the enzyme. However, there is substantially less knowledge on how the subsequent non-enzymatic reactions contribute to enzymatic browning. This review considers the current knowledge and recent advances in non-enzymatic reactions occurring after phenolic oxidation, in particular the role of non-PPO substrates. Enzymatic browning reaction models are compared, and a generalised redox cycling mechanism is proposed. The review identifies future areas for mechanistic research which may inform the development of new anti-browning processes.
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