School of BioSciences - Research Publications

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Deciphering the Interactions in the Root-Soil Nexus Caused by Urease and Nitrification Inhibitors: A Review

Gupta, S ; Yildirim, S ; Andrikopoulos, B ; Wille, U ; Roessner, U (MDPI, 2023-06)

Optimizing nitrogen (N) availability to plants is crucial for achieving maximum crop yield and quality. However, ensuring the appropriate supply of N to crops is challenging due to the various pathways through which N can be lost, such as ammonia (NH3) volatilization, nitrous oxide emissions, denitrification, nitrate (NO3−) leaching, and runoff. Additionally, N can become immobilized by soil minerals when ammonium (NH4+) gets trapped in the interlayers of clay minerals. Although synchronizing N availability with plant uptake could potentially reduce N loss, this approach is hindered by the fact that N loss from crop fields is typically influenced by a combination of management practices (which can be controlled) and weather dynamics, particularly precipitation, temperature fluctuations, and wind (which are beyond our control). In recent years, the use of urease and nitrification inhibitors has emerged as a strategy to temporarily delay the microbiological transformations of N-based fertilizers, thereby synchronizing N availability with plant uptake and mitigating N loss. Urease inhibitors slow down the hydrolysis of urea to NH4+ and reduce nitrogen loss through NH3 volatilization. Nitrification inhibitors temporarily inhibit soil bacteria (Nitrosomonas spp.) that convert NH4+ to nitrite (NO2−), thereby slowing down the first and rate-determining step of the nitrification process and reducing nitrogen loss as NO3− or through denitrification. This review aims to provide a comprehensive understanding of urease and nitrification inhibitor technologies and their profound implications for plants and root nitrogen uptake. It underscores the critical need to develop design principles for inhibitors with enhanced efficiency, highlighting their potential to revolutionize agricultural practices. Furthermore, this review offers valuable insights into future directions for inhibitor usage and emphasizes the essential traits that superior inhibitors should possess, thereby paving the way for innovative advancements in optimizing nitrogen management and ensuring sustainable crop production.
Genomic exploration of coral-associated bacteria: identifying probiotic candidates to increase coral bleaching resilience in Galaxea fascicularis

Doering, T ; Tandon, K ; Topa, SHH ; Pidot, SJJ ; Blackall, LLL ; van Oppen, MJH (BMC, 2023-08-19)

BACKGROUND: Reef-building corals are acutely threatened by ocean warming, calling for active interventions to reduce coral bleaching and mortality. Corals associate with a wide diversity of bacteria which can influence coral health, but knowledge of specific functions that may be beneficial for corals under thermal stress is scant. Under the oxidative stress theory of coral bleaching, bacteria that scavenge reactive oxygen (ROS) or nitrogen species (RNS) are expected to enhance coral thermal resilience. Further, bacterial carbon export might substitute the carbon supply from algal photosymbionts, enhance thermal resilience and facilitate bleaching recovery. To identify probiotic bacterial candidates, we sequenced the genomes of 82 pure-cultured bacteria that were isolated from the emerging coral model Galaxea fascicularis. RESULTS: Genomic analyses showed bacterial isolates were affiliated with 37 genera. Isolates such as Ruegeria, Muricauda and Roseovarius were found to encode genes for the synthesis of the antioxidants mannitol, glutathione, dimethylsulfide, dimethylsulfoniopropionate, zeaxanthin and/or β-carotene. Genes involved in RNS-scavenging were found in many G. fascicularis-associated bacteria, which represents a novel finding for several genera (including Pseudophaeobacter). Transporters that are suggested to export carbon (semiSWEET) were detected in seven isolates, including Pseudovibrio and Roseibium. Further, a range of bacterial strains, including strains of Roseibium and Roseovarius, revealed genomic features that may enhance colonisation and association of bacteria with the coral host, such as secretion systems and eukaryote-like repeat proteins. CONCLUSIONS: Our work provides an in-depth genomic analysis of the functional potential of G. fascicularis-associated bacteria and identifies novel combinations of traits that may enhance the coral's ability to withstand coral bleaching. Identifying and characterising bacteria that are beneficial for corals is critical for the development of effective probiotics that boost coral climate resilience. Video Abstract.
Modelling structural colour from helicoidal multi-layer thin films with natural disorder

Davis, TJ ; Ospina-Rozo, L ; Stuart-Fox, D ; Roberts, A (Optica Publishing Group, 2023-10-23)

A coupled mode theory based on Takagi-Taupin equations describing electromagnetic scattering from distorted periodic arrays is applied to the problem of light scattering from beetles. We extend the method to include perturbations in the permittivity tensor to helicoidal arrays seen in many species of scarab beetle and optically anisotropic layered materials more generally. This extension permits analysis of typical dislocations arising from the biological assembly process and the presence of other structures in the elytra. We show that by extracting structural information from transmission electron microscopy data, including characteristic disorder parameters, good agreement with spectral specular and non-specular reflectance measurements is obtained.
Her6 and Prox1a are novel regulators of photoreceptor regeneration in the zebrafish retina.

Veen, K ; Krylov, A ; Yu, S ; He, J ; Boyd, P ; Hyde, DR ; Mantamadiotis, T ; Cheng, LY ; Jusuf, PR ; Barsh, GS (Public Library of Science (PLoS), 2023-11)

Damage to light-sensing photoreceptors (PRs) occurs in highly prevalent retinal diseases. As humans cannot regenerate new PRs, these diseases often lead to irreversible blindness. Intriguingly, animals, such as the zebrafish, can regenerate PRs efficiently and restore functional vision. Upon injury, mature Müller glia (MG) undergo reprogramming to adopt a stem cell-like state. This process is similar to cellular dedifferentiation, and results in the generation of progenitor cells, which, in turn, proliferate and differentiate to replace lost retinal neurons. In this study, we tested whether factors involved in dedifferentiation of Drosophila CNS are implicated in the regenerative response in the zebrafish retina. We found that hairy-related 6 (her6) negatively regulates of PR production by regulating the rate of cell divisions in the MG-derived progenitors. prospero homeobox 1a (prox1a) is expressed in differentiated PRs and may promote PR differentiation through phase separation. Interestingly, upon Her6 downregulation, Prox1a is precociously upregulated in the PRs, to promote PR differentiation; conversely, loss of Prox1a also induces a downregulation of Her6. Together, we identified two novel candidates of PR regeneration that cross regulate each other; these may be exploited to promote human retinal regeneration and vision recovery.
Chemical mutagenesis and thermal selection of coral photosymbionts induce adaptation to heat stress with trait trade-offs

Scharfenstein, HJ ; Alvarez-Roa, C ; Peplow, LM ; Buerger, P ; Chan, WY ; van Oppen, MJH (WILEY, 2023-09)

Despite the relevance of heat-evolved microalgal endosymbionts to coral reef restoration, to date, few Symbiodiniaceae strains have been thermally enhanced via experimental evolution. Here, we investigated whether the thermal tolerance of Symbiodiniaceae can be increased through chemical mutagenesis followed by thermal selection. Strains of Durusdinium trenchii, Fugacium kawagutii and Symbiodinium pilosum were exposed to ethyl methanesulfonate to induce random mutagenesis, and then underwent thermal selection at high temperature (31/33°C). After 4.6-5 years of experimental evolution, the in vitro thermal tolerance of these strains was assessed via reciprocal transplant experiments to ambient (27°C) and elevated (31/35°C) temperatures. Growth, photosynthetic efficiency, oxidative stress and nutrient use were measured to compare thermal tolerance between strains. Heat-evolved D. trenchii, F. kawagutii and S. pilosum strains all exhibited increased photosynthetic efficiency under thermal stress. However, trade-offs in growth rates were observed for the heat-evolved D. trenchii lineage at both ambient and elevated temperatures. Reduced phosphate and nitrate uptake rates in F. kawagutii and S. pilosum heat-evolved lineages, respectively, suggest alterations in nutrition resource usage and allocation processes may have occurred. Increased phosphate uptake rates of the heat-evolved D. trenchii strain indicate that experimental evolution resulted in further trade-offs in this species. These findings deepen our understanding of the physiological responses of Symbiodiniaceae cultures to thermal selection and their capacity to adapt to elevated temperatures. The new heat-evolved Symbiodiniaceae developed here may be beneficial for coral reef restoration efforts if their enhanced thermal tolerance can be conferred in hospite.
Heat-evolved algal symbionts enhance bleaching tolerance of adult corals without trade-off against growth

Chan, WY ; Meyers, L ; Rudd, D ; Topa, SH ; van Oppen, MJH (WILEY, 2023-12)

Ocean warming has caused coral mass bleaching and mortality worldwide and the persistence of symbiotic reef-building corals requires rapid acclimation or adaptation. Experimental evolution of the coral's microalgal symbionts followed by their introduction into coral is one potential method to enhance coral thermotolerance. Heat-evolved microalgal symbionts of the generalist species, Cladocopium proliferum (strain SS8), were exposed to elevated temperature (31°C) for ~10 years, and were introduced into four genotypes of chemically bleached adult fragments of the scleractinian coral, Galaxea fascicularis. Two of the four coral genotypes acquired SS8. The new symbionts persisted for the 5 months of the experiment and enhanced adult coral thermotolerance, compared with corals that were inoculated with the wild-type C. proliferum strain. Thermotolerance of SS8-corals was similar to that of coral fragments from the same colony hosting the homologous symbiont, Durusdinium sp., which is naturally heat tolerant. However, SS8-coral fragments exhibited faster growth and recovered cell density and photochemical efficiency more quickly following chemical bleaching and inoculation under ambient temperature relative to Durusdinium-corals. Mass spectrometry imaging suggests that algal pigments involved in photobiology and oxidative stress were the greatest contributors to the thermotolerance differences between coral hosting heat-evolved versus wild-type C. proliferum. These pigments may have increased photoprotection in the heat-evolved symbionts. This is the first laboratory study to show that thermotolerance of adult corals (G. fascicularis) can be enhanced via the uptake of exogenously supplied, heat-evolved symbionts, without a trade-off against growth under ambient temperature. Importantly, heat-evolved C. proliferum remained in the corals in moderate abundance 2 years after first inoculation, suggesting long-term stability of this novel symbiosis and potential long-term benefits to coral thermotolerance.
Assessing the contribution of bacteria to the heat tolerance of experimentally evolved coral photosymbionts

Maire, J ; Deore, P ; Jameson, VJ ; Sakkas, M ; Perez-Gonzalez, A ; Blackall, LL ; van Oppen, MJH (WILEY, 2023-10-17)

Coral reefs are extremely vulnerable to ocean warming, which triggers coral bleaching-the loss of endosymbiotic microalgae (Symbiodiniaceae) from coral tissues, often leading to death. To enhance coral climate resilience, the symbiont, Cladocopium proliferum was experimentally evolved for >10 years under elevated temperatures resulting in increased heat tolerance. Bacterial 16S rRNA gene metabarcoding showed the composition of intra- and extracellular bacterial communities of heat-evolved strains was significantly different from that of wild-type strains, suggesting bacteria responded to elevated temperatures, and may even play a role in C. proliferum thermal tolerance. To assess whether microbiome transplantation could enhance heat tolerance of the sensitive wild-type C. proliferum, we transplanted bacterial communities from heat-evolved to the wild-type strain and subjected it to acute heat stress. Microbiome transplantation resulted in the incorporation of only 30 low-abundance strains into the microbiome of wild-type cultures, while the relative abundance of 14 pre-existing strains doubled in inoculated versus uninoculated samples. Inoculation with either wild-type or heat-evolved bacterial communities boosted C. proliferum growth, although no difference in heat tolerance was observed between the two inoculation treatments. This study provides evidence that Symbiodiniaceae-associated bacterial communities respond to heat selection and may contribute to coral adaptation to climate change.
Selecting coral species for reef restoration

Madin, JS ; McWilliam, M ; Quigley, K ; Bay, LK ; Bellwood, D ; Doropoulos, C ; Fernandes, L ; Harrison, P ; Hoey, AS ; Mumby, PJ ; Ortiz, JC ; Richards, ZT ; Riginos, C ; Schiettekatte, NMD ; Suggett, DJ ; van Oppen, MJH (WILEY, 2023-08-01)

Abstract Humans have long sought to restore species but little attention has been directed at how to best select a subset of foundation species for maintaining rich assemblages that support ecosystems, like coral reefs and rainforests, which are increasingly threatened by environmental change. We propose a two‐part hedging approach that selects optimized sets of species for restoration. The first part acknowledges that biodiversity supports ecosystem functions and services, and so it ensures precaution against loss by allocating an even spread of phenotypic traits. The second part maximizes species and ecosystem persistence by weighting species based on characteristics that are known to improve ecological persistence—for example abundance, species range and tolerance to environmental change. Using existing phenotypic‐trait and ecological data for reef building corals, we identified sets of ecologically persistent species by examining marginal returns in occupancy of phenotypic trait space. We compared optimal sets of species with those from the world's southern‐most coral reef, which naturally harbours low coral diversity, to show these occupy much of the trait space. Comparison with an existing coral restoration program indicated that current corals used for restoration only cover part of the desired trait space and programs may be improved by including species with different traits. Synthesis and applications. While there are many possible criteria for selecting species for restoration, the approach proposed here addresses the need to insure against unpredictable losses of ecosystem services by focusing on a wide range of phenotypic traits and ecological characteristics. Furthermore, the flexibility of the approach enables the functional goals of restoration to vary depending on environmental context, stakeholder values, and the spatial and temporal scales at which meaningful impacts can be achieved.
Long-term exposure to experimental light affects the ground-dwelling invertebrate community, independent of light spectra

Spoelstra, K ; Teurlincx, S ; Courbois, M ; Hopkins, ZM ; Visser, ME ; Jones, TM ; Hopkins, GR (ROYAL SOC, 2023-12-18)

Our planet endures a progressive increase in artificial light at night (ALAN), which affects virtually all species, and thereby biodiversity. Mitigation strategies include reducing its intensity and duration, and the adjustment of light spectrum using modern light emitting diode (LED) light sources. Here, we studied ground-dwelling invertebrate (predominantly insects, arachnids, molluscs, millipedes, woodlice and worms) diversity and community composition after 3 or 4 years of continued nightly exposure (every night from sunset to sunrise) to experimental ALAN with three different spectra (white-, and green- and red-dominated light), as well as for a dark control, in natural forest-edge habitat. Diversity of pitfall-trapped ground-dwelling invertebrates, and the local contribution to beta diversity, did not differ between the dark control and illuminated sites, or between the different spectra. The invertebrate community composition, however, was significantly affected by the presence of light. Keeping lights off during single nights did show an immediate effect on the composition of trapped invertebrates compared to illuminated nights. These effects of light on species composition may impact ecosystems by cascading effects across the food web. This article is part of the theme issue 'Light pollution in complex ecological systems'.
COVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting.

Conway, E ; Walker, CR ; Baker, C ; Lydeamore, MJ ; Ryan, GE ; Campbell, T ; Miller, JC ; Rebuli, N ; Yeung, M ; Kabashima, G ; Geard, N ; Wood, J ; McCaw, JM ; McVernon, J ; Golding, N ; Price, DJ ; Shearer, FM (The Royal Society, 2023-08-30)

Since the emergence of SARS-CoV-2 in 2019 through to mid-2021, much of the Australian population lived in a COVID-19-free environment. This followed the broadly successful implementation of a strong suppression strategy, including international border closures. With the availability of COVID-19 vaccines in early 2021, the national government sought to transition from a state of minimal incidence and strong suppression activities to one of high vaccine coverage and reduced restrictions but with still-manageable transmission. This transition is articulated in the national 're-opening' plan released in July 2021. Here, we report on the dynamic modelling study that directly informed policies within the national re-opening plan including the identification of priority age groups for vaccination, target vaccine coverage thresholds and the anticipated requirements for continued public health measures-assuming circulation of the Delta SARS-CoV-2 variant. Our findings demonstrated that adult vaccine coverage needed to be at least 60% to minimize public health and clinical impacts following the establishment of community transmission. They also supported the need for continued application of test-trace-isolate-quarantine and social measures during the vaccine roll-out phase and beyond.

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