Publications

Clerc, EE, Raina, J-B, Peaudecerf, FJ, Seymour, JR & Stocker, R 2022, 'Survival in a Sea of Gradients: Bacterial and Archaeal Foraging in a Heterogeneous Ocean' in The Microbiomes of Humans, Animals, Plants, and the Environment, Springer International Publishing, pp. 47-102.
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Kuzhiumparambil, U, Kumar, M, Nizio, KD, Alonso, D, Gorst-Allman, P, Kelly, C, MacLeod, B, Forbes, S & Ralph, P 2022, 'Metabolomic profiling of anthropogenically threatened Australian seagrass Zostera muelleri using one- and two-dimensional gas chromatography' in Applied Environmental Metabolomics, Elsevier, pp. 135-151.
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The global decline of seagrass meadows due to sustained pressure from anthropogenic activities and the ongoing threat from climate change has weakened their capacity for supporting coastal productivity and fisheries habitats, while also increasing sediment erosion. The ongoing efforts to prevent seagrass decline require novel tools to monitor seagrass health and assess the effects of habitat management. Such monitoring tools require the use of sensitive indicators to assess the intensity of environmental stressors and to monitor the corresponding responses of seagrass. Environmental metabolomics has proven valuable in identifying such phenotypic traits of abiotic and biotic stress in plants. The identification of metabolite changes in seagrass linked to an environmental stress response may lead to the development of a molecular diagnostic tool that could be used to give an early warning of seagrass stress. Therefore, we explore the potential of one- and two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (1D and 2D GC-TOFMS) in Australia’s most threatened seagrass species—Zostera muelleri. Overall, GC×GC-TOFMS outperformed GC-TOFMS and offered a robust, comprehensive, and superior analytical sensitivity and resolution with a total of 156 metabolites compared to 93 identified in GC-TOFMS. Among these metabolites, >  50% were identified exclusively in GC×GC-TOFMS and include secondary metabolites of the phenylpropenoid class, phytohormones, and various sugar and amino acid derivatives. Therefore, GC×GC-TOFMS represents a comprehensive metabolomics platform for both discovery and targeted studies in seagrass that may aid diagnostic tool development for more targeted seagrass management.

Lawson, CA, Camp, E, Davy, SK, Ferrier-Pagès, C, Matthews, J & Suggett, DJ 2022, 'Informing Coral Reef Conservation Through Metabolomic Approaches' in Coral Reefs of the World, Springer International Publishing, pp. 179-202.
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Matthews, JL, Cunning, R, Witson-Williams, R, Oakley, CA, Lutz, A, Roessner, U, Grossman, AR, Weis, VM, Gates, RD & Davy, SK 2022, 'The metabolic significance of symbiont community composition in the coral-algal symbiosis' in Applied Environmental Metabolomics, Elsevier, pp. 211-229.
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McCauley, JI, Ortega, JS, Gentile, C & Ralph, PJ 2022, 'Chapter 7 Microalgal applications in biomedicine and healthcare' in Algae-Based Biomaterials for Sustainable Development, Elsevier, pp. 133-156.
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McCauley, JI, Ortega, JS, Gentile, C & Ralph, PJ 2022, 'Microalgal applications in biomedicine and healthcare' in Algae-Based Biomaterials for Sustainable Development, Elsevier, pp. 133-156.
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The field of research that explores the use of microalgae in biomedicine and health is complex and diverse. Numerous research avenues currently explore the use of microalgae in biomedicine and heath such as: focusing on establishing and boosting nutritional profiles for food applications; identification, characterisation and utilisation of microalgal metabolites with biological activity as functional ingredients and/or drugs; utilisation of recombinant technology to genetically modify the algae for use as production systems for enzymes, antibodies, growth factors, drugs, and vaccines; or the use of microalgae as a source of “biomaterial” for use in applications such as drug carriers or cellular scaffolds for tissue engineering. To illustrate the diversity of microalgae and its potential for utilisation in a wide variety of biomedical and heath care applications, this chapter will present a concise overview of this broad applicability of microalgae in biomedicine and health, while highlighting research that is also occurring into the production and biorefinery of these compounds to facilitate a viable transition from laboratory to commercial production. Thus, this chapter aims to bridge the knowledge gap between both existing and potentially new algae applications, in particular, the use of microalgae as a source of “biomaterials” for biomedicine and health applications.

Mirakhorli, F, Mohseni, SS, Bazaz, SR, Mehrizi, AA, Ralph, PJ & Warkiani, ME 2022, 'Microfluidic Platforms for Cell Sorting' in Sustainable Separation Engineering: Materials, Techniques and Process Development, Wiley, pp. 653-695.
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Microfluidic platforms have evolved in recent years to assist researchers and biologists in performing biological and medical assays for cell separation and sorting. These microfluidic systems are competitive alternatives to conventional methods in terms of cost, sample volume reduction, high sensitivity, portability, fast processing, and elimination of chemical labels required for detection. In this chapter, these techniques have been classified into two major groups, active and passive, based on their energy intake and operating standards. Each separation technique was described briefly, and their operational principles were explained in detail. To specify the applications of each technique, the most recent popular examples have been explained along with common metrics used for the evolution of microfluidic system, including efficiency, accuracy, and throughput. This chapter is designed to be helpful for researchers who aim to develop unique microfluidic separator systems with further innovative designs in microfluidic platforms.

Ngo, HH, Vo, HNP, Guo, W, Lee, D-J & Zhang, S 2022, 'Carbon dioxide fixation and phycoremediation by algae-based technologies for biofuels and biomaterials' in Biomass, Biofuels, Biochemicals, Elsevier, pp. 253-277.
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Nguyen, LN, Vu, MT, Vu, HP, Zdarta, J, Mohammed, JAH, Pathak, N, Ralph, PJ & Nghiem, LD 2022, 'Chapter 4 Seaweed carrageenans: Productions and applications' in Algae-Based Biomaterials for Sustainable Development, pp. 67-80.
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Shahid, M, Khurshid, M, Mehmood, MA, Malik, S, Manzoor, I & Muhammad, S 2022, 'Bacterial Contamination in Food Chain: Sources, Impact and Control' in Climate Change and Ecosystems, CRC Press, pp. 203-216.
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Vo, HNP, Chaiwong, C, Zheng, L, Nguyen, TMH, Koottatep, T & Nguyen, TT 2022, 'Algae-based biomaterials in 3D printing for applications in medical, environmental remediation, and commercial products' in Algae-Based Biomaterials for Sustainable Development, Elsevier, pp. 185-202.
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Alderdice, R, Hume, BCC, Kühl, M, Pernice, M, Suggett, DJ & Voolstra, CR 2022, 'Disparate Inventories of Hypoxia Gene Sets Across Corals Align With Inferred Environmental Resilience', Frontiers in Marine Science, vol. 9, pp. 1-14.
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Aquatic deoxygenation has been flagged as an overlooked but key factor contributing to mass bleaching-induced coral mortality. During deoxygenation events triggered by coastal nutrient pollution and ocean warming, oxygen supplies lower to concentrations that can elicit an aerobic metabolic crisis i.e., hypoxia. Surprisingly little is known of the fundamental hypoxia gene set inventory that corals possess to respond to lowered oxygen (i.e., deoxygenation). For instance, it is unclear whether gene copy number differences exist across species that may affect the efficacy of a measured transcriptomic stress response. Therefore, we conducted an ortholog-based meta-analysis to investigate how hypoxia gene inventories differ amongst coral species to assess putative copy number variations (CNVs). We specifically elucidated CNVs for a compiled list of 32 hypoxia genes across 24 protein sets from species with a sequenced genome spanning corals from the robust and complex clade. We found approximately a third of the investigated genes exhibited copy number differences, and these differences were species-specific rather than attributable to the robust-complex split. Interestingly, we consistently found the highest gene expansion present in Porites lutea, which is considered to exhibit inherently greater stress tolerance than other species. Consequently, our analysis suggests that hypoxia stress gene expansion may coincide with increased stress tolerance. As such, the unevenly expanded (or reduced) hypoxia genes presented here provide key genes of interest to target in examining (or diagnosing) coral stress responses. Important next steps will involve determining to what extent such gene copy differences align with certain coral traits.

Alderdice, R, Perna, G, Cárdenas, A, Hume, BCC, Wolf, M, Kühl, M, Pernice, M, Suggett, DJ & Voolstra, CR 2022, 'Deoxygenation lowers the thermal threshold of coral bleaching', Scientific Reports, vol. 12, no. 1, pp. 1-14.
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AbstractExposure to deoxygenation from climate warming and pollution is emerging as a contributing factor of coral bleaching and mortality. However, the combined effects of heating and deoxygenation on bleaching susceptibility remain unknown. Here, we employed short-term thermal stress assays to show that deoxygenated seawater can lower the thermal limit of an Acropora coral by as much as 1 °C or 0.4 °C based on bleaching index scores or dark-acclimated photosynthetic efficiencies, respectively. Using RNA-Seq, we show similar stress responses to heat with and without deoxygenated seawater, both activating putative key genes of the hypoxia-inducible factor response system indicative of cellular hypoxia. We also detect distinct deoxygenation responses, including a disruption of O2-dependent photo-reception/-protection, redox status, and activation of an immune response prior to the onset of bleaching. Thus, corals are even more vulnerable when faced with heat stress in deoxygenated waters. This highlights the need to integrate dissolved O2 measurements into global monitoring programs of coral reefs.

Alderdice, R, Pernice, M, Cárdenas, A, Hughes, DJ, Harrison, PL, Boulotte, N, Chartrand, K, Kühl, M, Suggett, DJ & Voolstra, CR 2022, 'Hypoxia as a physiological cue and pathological stress for coral larvae', Molecular Ecology, vol. 31, no. 2, pp. 571-587.
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AbstractOcean deoxygenation events are intensifying worldwide and can rapidly drive adult corals into a state of metabolic crisis and bleaching‐induced mortality, but whether coral larvae are subject to similar stress remains untested. We experimentally exposed apo‐symbiotic coral larvae of Acropora selago to deoxygenation stress with subsequent reoxygenation aligned to their night‐day light cycle, and followed their gene expression using RNA‐Seq. After 12 h of deoxygenation stress (~2 mg O2/L), coral planulae demonstrated a low expression of HIF‐targeted hypoxia response genes concomitant with a significantly high expression of PHD2 (a promoter of HIFα proteasomal degradation), similar to corresponding adult corals. Despite exhibiting a consistent swimming phenotype compared to control samples, the differential gene expression observed in planulae exposed to deoxygenation‐reoxygenation suggests a disruption of pathways involved in developmental regulation, mitochondrial activity, lipid metabolism, and O2‐sensitive epigenetic regulators. Importantly, we found that treated larvae exhibited a disruption in the expression of conserved HIF‐targeted developmental regulators, for example, Homeobox (HOX) genes, corroborating how changes in external oxygen levels can affect animal development. We discuss how the observed deoxygenation responses may be indicative of a possible acclimation response or alternatively may imply negative latent impacts for coral larval fitness.

Archer, NS, Bluff, A, Eddy, A, Nikhil, CK, Hazell, N, Frank, D & Johnston, A 2022, 'Odour enhances the sense of presence in a virtual reality environment', PLOS ONE, vol. 17, no. 3, pp. e0265039-e0265039.
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Virtual reality (VR) headsets provide immersive audio-visual experiences for users, but usually neglect to provide olfactory cues that can provide additional information about our environment in the real world. This paper examines whether the introduction of smells into the VR environment enhances users’ experience, including their sense of presence through collection of both psychological and physiological measures. Using precise odour administration with an olfactometer, study participants were exposed to smells while they were immersed in the popular PlayStation VR game “Resident Evil 7”. A within-subject study design was undertaken where participants (n = 22) walked-through the same VR environment twice, with or without the introduction of associated congruent odour stimuli. Directly after each gameplay, participants completed a questionnaire to determine their sense of presence from the overall gameplay and their sense of immersion in each of the virtual scenes. Additionally, physiological measurements (heart rate, body temperature and skin electrodermal activity) were collected from participants (n = 11) for each gameplay. The results showed the addition of odours significantly increased participants’ sense of spatial presence in the VR environment compared to VR with no odour. Participants also rated the realism of VR experience with odour higher compared to no odour, however odour addition did not result in change in emotional state of participants (arousal, pleasure, dominance). Further, the participants’ physiological responses were impacted by the addition of odour. Odour mediated physiological changes were dependent on whether the VR environment was novel, as the effect of odour on physiological response was lost when participants experienced the aroma on the second gameplay. Overall, the results indicate the addition of odours to a VR environment had a significant effect on both the psychological and physiological experience showing...

Barolo, L, Commault, AS, Abbriano, RM, Padula, MP, Kim, M, Kuzhiumparambil, U, Ralph, PJ & Pernice, M 2022, 'Unassembled cell wall proteins form aggregates in the extracellular space of Chlamydomonas reinhardtii strain UVM4', Applied Microbiology and Biotechnology, vol. 106, no. 11, pp. 4145-4156.
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Abstract The green microalga Chlamydomonas reinhardtii is emerging as a promising cell biofactory for secreted recombinant protein (RP) production. In recent years, the generation of the broadly used cell wall–deficient mutant strain UVM4 has allowed for a drastic increase in secreted RP yields. However, purification of secreted RPs from the extracellular space of C. reinhardtii strain UVM4 is challenging. Previous studies suggest that secreted RPs are trapped in a matrix of cell wall protein aggregates populating the secretome of strain UVM4, making it difficult to isolate and purify the RPs. To better understand the nature and behaviour of these extracellular protein aggregates, we analysed and compared the extracellular proteome of the strain UVM4 to its cell-walled ancestor, C. reinhardtii strain 137c. When grown under the same conditions, strain UVM4 produced a unique extracellular proteomic profile, including a higher abundance of secreted cell wall glycoproteins. Further characterization of high molecular weight extracellular protein aggregates in strain UVM4 revealed that they are largely comprised of pherophorins, a specific class of cell wall glycoproteins. Our results offer important new insights into the extracellular space of strain UVM4, including strain-specific secreted cell wall proteins and the composition of the aggregates possibly related to impaired RP purification. The discovery of pherophorins as a major component of extracellular protein aggregates will inform future strategies to remove or prevent aggregate formation, enhance purification of secreted RPs, and improve yields of recombinant biopharmaceuticals in this emerging cell biofactory. Key points •

Brunet, M, Le Duff, N, Barbeyron, T & Thomas, F 2022, 'Consuming fresh macroalgae induces specific catabolic pathways, stress reactions and Type IX secretion in marine flavobacterial pioneer degraders', The ISME Journal, vol. 16, no. 8, pp. 2027-2039.
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Abstract Macroalgae represent huge amounts of biomass worldwide, largely recycled by marine heterotrophic bacteria. We investigated the strategies of bacteria within the flavobacterial genus Zobellia to initiate the degradation of whole algal tissues, which has received little attention compared to the degradation of isolated polysaccharides. Zobellia galactanivorans DsijT has the capacity to use fresh brown macroalgae as a sole carbon source and extensively degrades algal tissues via the secretion of extracellular enzymes, even in the absence of physical contact with the algae. Co-cultures experiments with the non-degrading strain Tenacibaculum aestuarii SMK-4T showed that Z. galactanivorans can act as a pioneer that initiates algal breakdown and shares public goods with other bacteria. A comparison of eight Zobellia strains, and strong transcriptomic shifts in Z. galactanivorans cells using fresh macroalgae vs. isolated polysaccharides, revealed potential overlooked traits of pioneer bacteria. Besides brown algal polysaccharide degradation, they notably include oxidative stress resistance proteins, type IX secretion system proteins and novel uncharacterized polysaccharide utilization loci. Overall, this work highlights the relevance of studying fresh macroalga degradation to fully understand the metabolic and ecological strategies of pioneer microbial degraders, key players in macroalgal biomass remineralization.

Butt, N, Halpern, BS, O'Hara, CC, Allcock, AL, Polidoro, B, Sherman, S, Byrne, M, Birkeland, C, Dwyer, RG, Frazier, M, Woodworth, BK, Arango, CP, Kingsford, MJ, Udyawer, V, Hutchings, P, Scanes, E, McClaren, EJ, Maxwell, SM, Diaz‐Pulido, G, Dugan, E, Simmons, BA, Wenger, AS, Linardich, C & Klein, CJ 2022, 'A trait‐based framework for assessing the vulnerability of marine species to human impacts', Ecosphere, vol. 13, no. 2.
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AbstractMarine species and ecosystems are widely affected by anthropogenic stressors, ranging from pollution and fishing to climate change. Comprehensive assessments of how species and ecosystems are impacted by anthropogenic stressors are critical for guiding conservation and management investments. Previous global risk or vulnerability assessments have focused on marine habitats, or on limited taxa or specific regions. However, information about the susceptibility of marine species across a range of taxa to different stressors everywhere is required to predict how marine biodiversity will respond to human pressures. We present a novel framework that uses life‐history traits to assess species' vulnerability to a stressor, which we compare across more than 44,000 species from 12 taxonomic groups (classes). Using expert elicitation and literature review, we assessed every combination of each of 42 traits and 22 anthropogenic stressors to calculate each species' or representative species group's sensitivity and adaptive capacity to stressors, and then used these assessments to derive their overall relative vulnerability. The stressors with the greatest potential impact were related to biomass removal (e.g., fisheries), pollution, and climate change. The taxa with the highest vulnerabilities across the range of stressors were mollusks, corals, and echinoderms, while elasmobranchs had the highest vulnerability to fishing‐related stressors. Traits likely to confer vulnerability to climate change stressors were related to the presence of calcium carbonate structures, and whether a species exists across the interface of marine, terrestrial, and atmospheric realms. Traits likely to confer vulnerability to pollution stressors were related to planktonic state, organism size, and respiration. Such a replicable, broadly applicable method is useful for informing ocean conservation and management decisions at a range of scales, and th...

Buzova, D, Braghini, MR, Bianco, SD, Lo Re, O, Raffaele, M, Frohlich, J, Kisheva, A, Crudele, A, Mosca, A, Sartorelli, MR, Balsano, C, Cerveny, J, Mazza, T, Alisi, A & Vinciguerra, M 2022, 'Profiling of cell‐free DNA methylation and histone signatures in pediatric NAFLD: A pilot study', Hepatology Communications, vol. 6, no. 12, pp. 3311-3323.
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Abstract Nonalcoholic fatty liver disease (NAFLD) has become the most common chronic liver disease in children and adolescents, increasing the risk of its progression toward nonalcoholic steatohepatitis (NASH), cirrhosis, and cancer. There is an urgent need for noninvasive early diagnostic and prognostic tools such as epigenetic marks (epimarks), which would replace liver biopsy in the future. We used plasma samples from 67 children with biopsy‐proven NAFLD, and as controls we used samples from 20 children negative for steatosis by ultrasound. All patients were genotyped for patatin‐like phospholipase domain containing 3 (PNPLA3), transmembrane 6 superfamily member 2 (TM6SF2), membrane bound O‐acyltransferase domain containing 7 (MBOAT7), and klotho‐β (KLB) gene variants, and data on anthropometric and biochemical parameters were collected. Furthermore, plasma cell‐free DNA (cfDNA) methylation was quantified using a commercially available kit, and ImageStream(X) was used for the detection of free circulating histone complexes and variants. We found a significant enrichment of the levels of histone macroH2A1.2 in the plasma of children with NAFLD compared to controls, and a strong correlation between cfDNA methylation levels and NASH. Receiver operating characteristic curve analysis demonstrated that combination of cfDNA methylation, PNPLA3 rs738409 variant, coupled with either high‐density lipoprotein cholesterol or alanine aminotransferase levels can strongly predict the progression of pediatric NAFLD to NASH with area under the curve >0.87. Conclusion: Our pilot study combined epimarks and genetic and metabolic markers for a robust risk assessment of NAFLD development and progression in children, offering a promising noninvasive tool for the consistent diagnosis and prognosis of pediatric NAFLD. Further studies are necessary to identify their pathogenic origin and fu...

Camp, EF, Kahlke, T, Signal, B, Oakley, CA, Lutz, A, Davy, SK, Suggett, DJ & Leggat, WP 2022, 'Proteome metabolome and transcriptome data for three Symbiodiniaceae under ambient and heat stress conditions', Scientific Data, vol. 9, no. 1, pp. 1-10.
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AbstractThe Symbiodiniaceae are a taxonomically and functionally diverse family of marine dinoflagellates. Their symbiotic relationship with invertebrates such as scleractinian corals has made them the focus of decades of research to resolve the underlying biology regulating their sensitivity to stressors, particularly thermal stress. Research to-date suggests that Symbiodiniaceae stress sensitivity is governed by a complex interplay between phylogenetic dependent and independent traits (diversity of characteristics of a species). Consequently, there is a need for datasets that simultaneously broadly resolve molecular and physiological processes under stressed and non-stressed conditions. Therefore, we provide a dataset simultaneously generating transcriptome, metabolome, and proteome data for three ecologically important Symbiodiniaceae isolates under nutrient replete growth conditions and two temperature treatments (ca. 26 °C and 32 °C). Elevated sea surface temperature is primarily responsible for coral bleaching events that occur when the coral-Symbiodiniaceae relationship has been disrupted. Symbiodiniaceae can strongly influence their host’s response to thermal stress and consequently it is necessary to resolve drivers of Symbiodiniaceae heat stress tolerance. We anticipate these datasets to expand our understanding on the key genotypic and functional properties that influence the sensitivities of Symbiodiniaceae to thermal stress.

Camp, EF, Nitschke, MR, Clases, D, Gonzalez de Vega, R, Reich, HG, Goyen, S & Suggett, DJ 2022, 'Micronutrient content drives elementome variability amongst the Symbiodiniaceae', BMC Plant Biology, vol. 22, no. 1, pp. 1-14.
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AbstractBackgroundElements are the basis of life on Earth, whereby organisms are essentially evolved chemical substances that dynamically interact with each other and their environment. Determining species elemental quotas (their elementome) is a key indicator for their success across environments with different resource availabilities. Elementomes remain undescribed for functionally diverse dinoflagellates within the family Symbiodiniaceae that includes coral endosymbionts. We used dry combustion and ICP-MS to assess whether Symbiodiniaceae (ten isolates spanning five generaBreviolum, Cladocopium, Durusdinium, Effrenium, Symbiodinium) maintained under long-term nutrient replete conditions have unique elementomes (six key macronutrients and nine micronutrients) that would reflect evolutionarily conserved preferential elemental acquisition. For three isolates we assessed how elevated temperature impacted their elementomes. Further, we tested whether Symbiodiniaceae conform to common stoichiometric hypotheses (e.g., the growth rate hypothesis) documented in other marine algae. This study considers whether Symbiodiniaceae isolates possess unique elementomes reflective of their natural ecologies, evolutionary histories, and resistance to environmental change.ResultsSymbiodiniaceae isolates maintained under long-term luxury uptake conditions, all exhibited highly divergent elementomes from one another, driven primarily by differential content of micronutrients. All N:P and C:P ratios were below the Redfield ratio values, whereas C:N was close to the Redfield value. Elevated temperature resulted in a more homogenised elementome across isolates. The Family-level elementome was (C19.8N2.6P1.0S18.8K0.7Ca...

Cao, H-L, Nguyen, HAD, Luu, TH, Vu, HTT, Pham, D, Vu, VTN, Le, HH, Nguyen, DXB, Truong, TT, Nguyen, H-D & Nguyen, C-N 2022, 'Localized automation solutions in response to the first wave of COVID-19: a story from Vietnam', International Journal of Pervasive Computing and Communications, vol. 18, no. 5, pp. 548-562.
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Purpose COVID-19 hits every country’s health-care system and economy. There is a trend toward using automation technology in response to the COVID-19 crisis not only in developed countries but also in those with lower levels of technology development. However, current studies mainly focus on the world level, and only a few ones report deployments at the country level. The purpose of this paper is to investigate the use of automation solutions in Vietnam with locally available materials mainly in the first wave from January to July 2020. Design/methodology/approach The authors collected COVID-related automation solutions during the first wave of COVID-19 in Vietnam from January to July 2020 through a search process. The analysis and insights of a panel consisting of various disciplines (i.e. academia, health care, government, entrepreneur and media) aim at providing a clear picture of how and to what extent these solutions have been deployed. Findings The authors found seven groups of solutions from low to high research and development (R&D) levels deployed across the country with various funding sources. Low R&D solutions were widely spread owing to simplicity and affordability. High R&D solutions were mainly deployed in big cities. Most of the solutions were deployed during the first phases when international supply chains were limited with a significant contribution of the media. Higher R&D solutions have opportunities to be deployed in the reopening phase. However, challenges can be listed as limited interdisciplinary research teams, market demand, the local supporting industry, end-user validation ...

Cárdenas, A, Raina, J-B, Pogoreutz, C, Rädecker, N, Bougoure, J, Guagliardo, P, Pernice, M & Voolstra, CR 2022, 'Greater functional diversity and redundancy of coral endolithic microbiomes align with lower coral bleaching susceptibility', The ISME Journal, vol. 16, no. 10, pp. 2406-2420.
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Abstract The skeleton of reef-building coral harbors diverse microbial communities that could compensate for metabolic deficiencies caused by the loss of algal endosymbionts, i.e., coral bleaching. However, it is unknown to what extent endolith taxonomic diversity and functional potential might contribute to thermal resilience. Here we exposed Goniastrea edwardsi and Porites lutea, two common reef-building corals from the central Red Sea to a 17-day long heat stress. Using hyperspectral imaging, marker gene/metagenomic sequencing, and NanoSIMS, we characterized their endolithic microbiomes together with 15N and 13C assimilation of two skeletal compartments: the endolithic band directly below the coral tissue and the deep skeleton. The bleaching-resistant G. edwardsi was associated with endolithic microbiomes of greater functional diversity and redundancy that exhibited lower N and C assimilation than endoliths in the bleaching-sensitive P. lutea. We propose that the lower endolithic primary productivity in G. edwardsi can be attributed to the dominance of chemolithotrophs. Lower primary production within the skeleton may prevent unbalanced nutrient fluxes to coral tissues under heat stress, thereby preserving nutrient-limiting conditions characteristic of a stable coral-algal symbiosis. Our findings link coral endolithic microbiome structure and function to bleaching susceptibility, providing new avenues for understanding and eventually mitigating reef loss.

Charon, J, Kahlke, T, Larsson, ME, Abbriano, R, Commault, A, Burke, J, Ralph, P & Holmes, EC 2022, 'Diverse RNA Viruses Associated with Diatom, Eustigmatophyte, Dinoflagellate, and Rhodophyte Microalgae Cultures', Journal of Virology, vol. 96, no. 20, p. e0078322.
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Our knowledge of the diversity of RNA viruses infecting microbial algae—the microalgae—is minimal. However, describing the RNA viruses infecting these organisms is of primary importance at both the ecological and economic scales because of the fundamental roles these organisms play in aquatic environments and their growing value across a range of industrial fields.

Dukic, E, Gollan, PJ, Grebe, S, Paakkarinen, V, Herdean, A, Aro, E-M & Spetea, C 2022, 'The Arabidopsis thylakoid chloride channel ClCe regulates ATP availability for light-harvesting complex II protein phosphorylation', Frontiers in Plant Science, vol. 13, no. Women in Plant Physiology: 2022.
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Coping with changes in light intensity is challenging for plants, but well-designed mechanisms allow them to acclimate to most unpredicted situations. The thylakoid K+/H+ antiporter KEA3 and the voltage-dependent Cl− channel VCCN1 play important roles in light acclimation by fine-tuning electron transport and photoprotection. Good evidence exists that the thylakoid Cl− channel ClCe is involved in the regulation of photosynthesis and state transitions in conditions of low light. However, a detailed mechanistic understanding of this effect is lacking. Here we report that the ClCe loss-of-function in Arabidopsis thaliana results in lower levels of phosphorylated light-harvesting complex II (LHCII) proteins as well as lower levels of the photosystem I-LHCII complexes relative to wild type (WT) in low light conditions. The phosphorylation of the photosystem II core D1/D2 proteins was less affected either in low or high light conditions. In low light conditions, the steady-state levels of ATP synthase conductivity and of the total proton flux available for ATP synthesis were lower in ClCe loss-of-function mutants, but comparable to WT at standard and high light intensity. As a long-term acclimation strategy, expression of the ClCe gene was upregulated in WT plants grown in light-limiting conditions, but not in WT plants grown in standard light even when exposed for up to 8 h to low light. Taken together, these results suggest a role of ClCe in the regulation of the ATP synthase activity which under low light conditions impacts LHCII protein phosphorylation and state transitions.

Dylgjeri, E, Kothari, V, Shafi, AA, Semenova, G, Gallagher, PT, Guan, YF, Pang, A, Goodwin, JF, Irani, S, McCann, JJ, Mandigo, AC, Chand, S, McNair, CM, Vasilevskaya, I, Schiewer, MJ, Lallas, CD, McCue, PA, Gomella, LG, Seifert, EL, Carroll, JS, Butler, LM, Holst, J, Kelly, WK & Knudsen, KE 2022, 'A Novel Role for DNA-PK in Metabolism by Regulating Glycolysis in Castration-Resistant Prostate Cancer', Clinical Cancer Research, vol. 28, no. 7, pp. 1446-1459.
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Abstract Purpose: DNA-dependent protein kinase catalytic subunit (DNA-PKcs, herein referred as DNA-PK) is a multifunctional kinase of high cancer relevance. DNA-PK is deregulated in multiple tumor types, including prostate cancer, and is associated with poor outcomes. DNA-PK was previously nominated as a therapeutic target and DNA-PK inhibitors are currently undergoing clinical investigation. Although DNA-PK is well studied in DNA repair and transcriptional regulation, much remains to be understood about the way by which DNA-PK drives aggressive disease phenotypes. Experimental Design: Here, unbiased proteomic and metabolomic approaches in clinically relevant tumor models uncovered a novel role of DNA-PK in metabolic regulation of cancer progression. DNA-PK regulation of metabolism was interrogated using pharmacologic and genetic perturbation using in vitro cell models, in vivo xenografts, and ex vivo in patient-derived explants (PDE). Results: Key findings reveal: (i) the first-in-field DNA-PK protein interactome; (ii) numerous DNA-PK novel partners involved in glycolysis; (iii) DNA-PK interacts with, phosphorylates (in vitro), and increases the enzymatic activity of glycolytic enzymes ALDOA and PKM2; (iv) DNA-PK drives synthesis of glucose-derived pyruvate and lactate; (v) DNA-PK regulates glycolysis in vitro, in vivo, and ex vivo; and (vi) combination of DNA-PK inhibitor with glycolytic inhibitor 2-deoxyglucose leads to additive anti-proliferative effects in aggressive disease. Conclus...

Elbourne, LDH, Sutcliffe, B, Humphreys, W, Focardi, A, Saccò, M, Campbell, MA, Paulsen, IT & Tetu, SG 2022, 'Unravelling Stratified Microbial Assemblages in Australia’s Only Deep Anchialine System, The Bundera Sinkhole', Frontiers in Marine Science, vol. 9.
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Bundera sinkhole, located in north-western Australia, is the only known continental anchialine system in the Southern Hemisphere. Anchialine environments are characterised by stratified water columns with complex physicochemical profiles spanning hypoxic and anoxic regions, often displaying high levels of endemism. Research on these systems has focused on eukaryotic fauna, however interest in the microbial diversity of these environments is growing, enabled by next-generation DNA sequencing. Here we report detailed analyses of the microbial communities across a depth profile within Bundera sinkhole (from 2 to 28 m), involving parallel physicochemical measurements, cell population counts and 16S rRNA amplicon analyses. We observed clear shifts in microbial cell counts, community diversity, structure and membership across the depth profile, reflecting changing levels of light, organic and inorganic energy sources as well as shifts in pH and salinity. While Proteobacteria were the most abundant phylum found, there was a high degree of taxonomic novelty within these microbial communities, with 13,028 unique amplicon sequence variants (ASVs) identified, belonging to 67 identifiable bacterial and archaeal phyla. Of these ~4,600, more than one third of the total, were unclassified below family level. A small number of ASVs were highly abundant at select depths, all of which were part of the set not classified below family level. The 2 m and 6 m samples had in common two highly abundant ASVs, belonging to the Ectothiorhodospiraceae and Thiotrichaceae families, while the 8 m community contained a single predominant ASV belonging to family Thioglobaceae. At lower depths a different Ectothiorhodospiraceae ASV comprised up to 68% relative abundance, peaking at 26 and 28 m. Canonical correspondence analyses indicated that community structure was strongly influenced by differences in key physicochemical parameters, particularly salinity, dissolved organic and...

Feng, S, Ngo, HH, Guo, W, Chang, SW, Nguyen, DD, Liu, Y, Zhang, S, Phong Vo, HN, Bui, XT & Ngoc Hoang, B 2022, 'Volatile fatty acids production from waste streams by anaerobic digestion: A critical review of the roles and application of enzymes', Bioresource Technology, vol. 359, pp. 127420-127420.
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Volatile fatty acids (VFAs) produced from organic-rich wastewater by anaerobic digestion attract attention due to the increasing volatile fatty acids market, sustainability and environmentally friendly characteristics. This review aims to give an overview of the roles and applications of enzymes, a biocatalyst which plays a significant role in anaerobic digestion, to enhance volatile fatty acids production. This paper systematically overviewed: (i) the enzymatic pathways of VFAs formation, competition, and consumption; (ii) the applications of enzymes in VFAs production; and (iii) feasible measures to boost the enzymatic processes. Furthermore, this review presents a critical evaluation on the major obstacles and feasible future research directions for the better applications of enzymatic processes to promote VFAs production from wastewater.

Fernandez, E, Seymour, JR & Petrou, K 2022, 'Phytoplankton Sources and Sinks of Dimethylsulphoniopropionate (DMSP) in Temperate Coastal Waters of Australia', Microorganisms, vol. 10, no. 8, pp. 1539-1539.
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The ecologically important organic sulfur compound, dimethylsulfoniopropionate (DMSP), is ubiquitous in marine environments. Produced by some species of phytoplankton and bacteria, it plays a key role in cellular responses to environmental change. Recently, uptake of DMSP by non-DMSP-producing phytoplankton species has been demonstrated, highlighting knowledge gaps concerning DMSP distribution through the marine microbial food web. In this study, we traced the uptake and distribution of DMSP through a natural marine microbial community collected from off the eastern coastline Australia. We found a diverse phytoplankton community representing six major taxonomic groups and conducted DMSP-enrichment experiments both on the whole community, and the community separated into large (≥8.0 µm), medium (3.0–8.0 µm), and small (0.2–3.0 µm) size fractions. Our results revealed active uptake of DMSP in all three size fractions of the community, with the largest fraction (>8 µm) forming the major DMSP sink, where enrichment resulted in an increase of DMSPp by 144%. We observed evidence for DMSP catabolism in all size fractions with DMSP enrichment, highlighting loss from the system via MeSH or DMS production. Based on taxonomic diversity, we postulate the sources of DMSP were the dinoflagellates, Phaeocystis sp., and Trichodesmium sp., which were present in a relatively high abundance, and the sinks for DMSP were the diatoms and picoeucaryotes in this temperate community. These findings corroborate the role of hitherto disregarded phytoplankton taxa as potentially important players in the cycling of DMSP in coastal waters of Australia and emphasize the need to better understand the fate of accumulated DMSP and its significance in cellular metabolism of non-DMSP producers.

Focardi, A, Moore, LR, Raina, J-B, Seymour, JR, Paulsen, IT & Tetu, SG 2022, 'Plastic leachates impair picophytoplankton and dramatically reshape the marine microbiome', Microbiome, vol. 10, no. 1, p. 179.
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Abstract Background Each year, approximately 9.5 million metric tons of plastic waste enter the ocean with the potential to adversely impact all trophic levels. Until now, our understanding of the impact of plastic pollution on marine microorganisms has been largely restricted to the microbial assemblages that colonize plastic particles. However, plastic debris also leaches considerable amounts of chemical additives into the water, and this has the potential to impact key groups of planktonic marine microbes, not just those organisms attached to plastic surfaces. Results To investigate this, we explored the population and genetic level responses of a marine microbial community following exposure to leachate from a common plastic (polyvinyl chloride) or zinc, a specific plastic additive. Both the full mix of substances leached from polyvinyl chloride (PVC) and zinc alone had profound impacts on the taxonomic and functional diversity of our natural planktonic community. Microbial primary producers, both prokaryotic and eukaryotic, which comprise the base of the marine food web, were strongly impaired by exposure to plastic leachates, showing significant declines in photosynthetic efficiency, diversity, and abundance. Key heterotrophic taxa, such as SAR11, which are the most abundant planktonic organisms in the ocean, also exhibited significant declines in relative abundance when exposed to higher levels of PVC leachate. In contrast, many copiotrophic bacteria, including members of the Alteromonadales, dramatically increased in relative abundance under both exposure treatments. Moreover, functional gene and genome analyses, derived from metagenomes, revealed that PVC leachate exposure selects for fast-adapting, motile organisms, along with enrichmen...

Fu, F, Tschitschko, B, Hutchins, DA, Larsson, ME, Baker, KG, McInnes, A, Kahlke, T, Verma, A, Murray, SA & Doblin, MA 2022, 'Temperature variability interacts with mean temperature to influence the predictability of microbial phenotypes', Global Change Biology, vol. 28, no. 19, pp. 5741-5754.
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AbstractDespite their relatively high thermal optima (Topt), tropical taxa may be particularly vulnerable to a rising baseline and increased temperature variation because they live in relatively stable temperatures closer to their Topt. We examined how microbial eukaryotes with differing thermal histories responded to temperature fluctuations of different amplitudes (0 control, ±2, ±4°C) around mean temperatures below or above their Topt. Cosmopolitan dinoflagellates were selected based on their distinct thermal traits and included two species of the same genus (tropical and temperate Coolia spp.), and two strains of the same species maintained at different temperatures for >500 generations (tropical Amphidinium massartii control temperature and high temperature, CT and HT, respectively). There was a universal decline in population growth rate under temperature fluctuations, but strains with narrower thermal niche breadth (temperate Coolia and HT) showed ~10% greater reduction in growth. At suboptimal mean temperatures, cells in the cool phase of the fluctuation stopped dividing, fixed less carbon (C) and had enlarged cell volumes that scaled positively with elemental C, N, and P and C:Chlorophyll‐a. However, at a supra‐optimal mean temperature, fixed C was directed away from cell division and novel trait combinations developed, leading to greater phenotypic diversity. At the molecular level, heat‐shock proteins, and chaperones, in addition to transcripts involving genome rearrangements, were upregulated in CT and HT during the warm phase of the supra‐optimal fluctuation (30 ± 4°C), a stress response indicating protection. In contrast, the tropical Coolia

Gardner, SG, Nitschke, MR, O’Brien, J, Motti, CA, Seymour, JR, Ralph, PJ, Petrou, K & Raina, J-B 2022, 'Increased DMSP availability during thermal stress influences DMSP-degrading bacteria in coral mucus', Frontiers in Marine Science, vol. 9.
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Reef-building corals are among the largest producers of dimethylsulfoniopropionate (DMSP), an essential compound in marine biogeochemical cycles. DMSP can be catabolised in coral mucus by a wide diversity of coral-associated bacteria, where it can either be demethylated, leading to the incorporation of sulfur and carbon into bacterial biomass – or cleaved by lyases, releasing the climatically-active gas dimethyl sulfide (DMS). It has been demonstrated that thermal stress increases DMSP concentrations in many coral species, however the effect of increased DMSP availability on coral-associated bacteria has not been explored. Here we performed thermal stress experiments to examine how changes in DMSP availability impact bacterial degradation pathways in the mucus of Acropora millepora. DMSP concentrations increased with temperature, reaching a maximum of 177.3 μM after 10 days of heat stress, which represents the highest concentration of DMSP recorded in any environment to date. Bacterial communities in coral mucus were significantly different from the surrounding seawater, yet they did not vary significantly between temperature or time. However, during thermal stress, when DMSP concentrations increased, a significant increase in the abundance of both the demethylation gene dmdA and the cleavage gene dddP were recorded. Importantly, our results show that for the highest DMSP concentrations recorded (above 30 μM), the cleavage pathway became more abundant than the demethylation pathway. This suggests that under high DMSP concentrations characteristic of heat stress, a larger fraction of the DMSP pool in the coral mucus is likely catabolised through the DMS-producing cleavage pathway.

Garner, N, Ross, PM, Falkenberg, LJ, Seymour, JR, Siboni, N & Scanes, E 2022, 'Can seagrass modify the effects of ocean acidification on oysters?', Marine Pollution Bulletin, vol. 177, pp. 113438-113438.
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Solutions are being sought to ameliorate the impacts of anthropogenic climate change. Seagrass may be a solution to provide refugia from climate change for marine organisms. This study aimed to determine if the seagrass Zostera muelleri sub spp. capricorni benefits the Sydney rock oyster Saccostrea glomerata, and if these benefits can modify any anticipated negative impacts of ocean acidification. Future and ambient ocean acidification conditions were simulated in 52 L mesocosms at control (381 μatm) and elevated (848 μatm) CO2 with and without Z. muelleri. Oyster growth, physiology and microbiomes of oysters and seagrass were measured. Seagrass was beneficial to oyster growth at ambient pCO2, but did not positively modify the impacts of ocean acidification on oysters at elevated pCO2. Oyster microbiomes were altered by the presence of seagrass but not by elevated pCO2. Our results indicate seagrasses may not be a panacea for the impacts of climate change.

Gill, RL, Collins, S, Argyle, PA, Larsson, ME, Fleck, R & Doblin, MA 2022, 'Predictability of thermal fluctuations influences functional traits of a cosmopolitan marine diatom', Proceedings of the Royal Society B: Biological Sciences, vol. 289, no. 1973, p. 20212581.
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Evolutionary theory predicts that organismal plasticity should evolve in environments that fluctuate regularly. However, in environments that fluctuate less predictably, plasticity may be constrained because environmental cues become less reliable for expressing the optimum phenotype. Here, we examine how the predictability of +5°C temperature fluctuations impacts the phenotype of the marine diatomThalassiosira pseudonana. Thermal regimes were informed by temperatures experienced by microbes in an ocean simulation and featured regular or irregular temporal sequences of fluctuations that induced mild physiological stress. Physiological traits (growth, cell size, complexity and pigmentation) were quantified at the individual cell level using flow cytometry. Changes in cellular complexity emerged as the first impact of predictability after only 8–11 days, followed by deleterious impacts on growth on days 13–16. Specifically, cells with a history of irregular fluctuation exposure exhibited a 50% reduction in growth compared with the stable reference environment, while growth was 3–18 times higher when fluctuations were regular. We observed no evidence of heat hardening (increasingly positive growth) with recurrent fluctuations. This study demonstrates that unpredictable temperature fluctuations impact this cosmopolitan diatom under ecologically relevant time frames, suggesting shifts in environmental stochasticity under a changing climate could have widespread consequences among ocean primary producers.

González-Pech, RA, Hughes, DJ, Strudwick, P, Lewis, BM, Booth, DJ, Figueira, WF, Sommer, B, Suggett, DJ & Matthews, J 2022, 'Physiological factors facilitating the persistence of Pocillopora aliciae and Plesiastrea versipora in temperate reefs of south-eastern Australia under ocean warming', Coral Reefs, vol. 41, no. 4, pp. 1239-1253.
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AbstractHigh-latitude reefs are suboptimal coral habitats, but such habitats are increasingly considered to be potential refugia from climate change for range-shifting coral reef species. Notably, tropical reef fish have been observed along the south-east coast of Australia, but their establishment on temperate rocky reefs is currently limited by winter minimum temperatures and other resource needs, such as structurally complex habitats typical of tropical reefs. Recent expansion of the branching subtropical coral Pocillopora aliciae in rocky reefs near Sydney (34° S) could diversify the architectural structure of temperate marine environments, thereby providing potential shelter for tropical reef taxa in warming seas. Here, we investigated whether future environmental conditions (i.e. temperature increase) can influence the dominance of the subtropical branching coral P. aliciae over the resident encrusting coral Plesiastrea versipora in coastal Sydney by characterising physiological (e.g. metabolic stability) and behavioural (e.g. interspecific competitive hierarchy) traits that contribute to their competitive fitness. Our results suggest that a metabolic response, mediated by sterol and lipid metabolic pathways and provision of antioxidants, allows P. aliciae to reduce cellular stress and withstand exposure to short-term increased temperature. Conversely, P. versipora was more susceptible to heat exposure with no metabolic mediation observed. While P. versipora displayed greater aggressive behaviour when in direct contact with P. aliciae under all temperature conditions, the superior physiological and metabolic flexibility under increased temperatures o...

Grima, AJ, Clases, D, Gonzalez de Vega, R, Nitschke, MR, Goyen, S, Suggett, DJ & Camp, EF 2022, 'Species-specific elementomes for scleractinian coral hosts and their associated Symbiodiniaceae', Coral Reefs, vol. 41, no. 4, pp. 1115-1130.
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AbstractIncreasing anthropogenic pressure on coral reefs is creating an urgent need to understand how and where corals can proliferate both now and under future scenarios. Resolving environmental limits of corals has progressed through the accurate identification of corals’ ‘realised ecological niche’. Here we expand the ecological niche concept to account for corals’ ‘biogeochemical niche’ (BN), defined as the chemical space in which a coral is adapted to survive, and which is identifiable by a unique quantity and proportion of elements (termed “elementome”). BN theory has been commonly applied to other taxa, successfully predicting species distributions and stress responses by their elementomes. Here, we apply the BN theory to corals for the first time, by using dry combustion and inductively coupled plasma–mass spectrometry (ICP-MS) to determine five key macronutrients and thirteen trace elements of four diverse scleractinian coral species from the Great Barrier Reef (GBR): Acropora hyacinthus; Echinopora lamellosa; Pocillopora cf. meandrina; and Pocillopora cf. verrucosa. The elementomes were investigated in both host and Symbiodiniaceae, and the latter had the highest elemental concentrations (except molybdenum). Each coral species associated with distinct members of the genus Cladocopium (determined by ITS2 analysis) with photo-physiological data suggesting specialisation of Cladocopium functional biology. Distinct endosymbiont community structure and functioning between corals with different elementomes confirms that BN theory holds as metabolic compatibility alters across host–symbiont associations. Additional work is needed to understand the plasticity of coral elementomes, and in turn BN, over space and time to aid predictions on coral distribution and survival with environmenta...

Hallstrøm, S, Raina, J-B, Ostrowski, M, Parks, DH, Tyson, GW, Hugenholtz, P, Stocker, R, Seymour, JR & Riemann, L 2022, 'Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean', The ISME Journal, vol. 16, no. 11, pp. 2525-2534.
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Abstract Heterotrophic bacterial diazotrophs (HBDs) are ubiquitous in the pelagic ocean, where they have been predicted to carry out the anaerobic process of nitrogen fixation within low-oxygen microenvironments associated with marine pelagic particles. However, the mechanisms enabling particle colonization by HBDs are unknown. We hypothesized that HBDs use chemotaxis to locate and colonize suitable microenvironments, and showed that a cultivated marine HBD is chemotactic toward amino acids and phytoplankton-derived DOM. Using an in situ chemotaxis assay, we also discovered that diverse HBDs at a coastal site are motile and chemotactic toward DOM from various phytoplankton taxa and, indeed, that the proportion of diazotrophs was up to seven times higher among the motile fraction of the bacterial community compared to the bulk seawater community. Finally, three of four HBD isolates and 16 of 17 HBD metagenome assembled genomes, recovered from major ocean basins and locations along the Australian coast, each encoded >85% of proteins affiliated with the bacterial chemotaxis pathway. These results document the widespread capacity for chemotaxis in diverse and globally relevant marine HBDs. We suggest that HBDs could use chemotaxis to seek out and colonize low-oxygen microenvironments suitable for nitrogen fixation, such as those formed on marine particles. Chemotaxis in HBDs could therefore affect marine nitrogen and carbon biogeochemistry by facilitating nitrogen fixation within otherwise oxic waters, while also altering particle degradation and the efficiency of the biological pump.

Haydon, TD, Suggett, DJ, Siboni, N, Kahlke, T, Camp, EF & Seymour, JR 2022, 'Temporal Variation in the Microbiome of Tropical and Temperate Octocorals', Microbial Ecology, vol. 83, no. 4, pp. 1073-1087.
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Bacterial members of the coral holobiont play an important role in determining coral fitness. However, most knowledge of the coral microbiome has come from reef-building scleractinian corals, with far less known about the nature and importance of the microbiome of octocorals (subclass Octocorallia), which contribute significantly to reef biodiversity and functional complexity. We examined the diversity and structure of the bacterial component of octocoral microbiomes over summer and winter, with a focus on two temperate (Erythropodium hicksoni, Capnella gaboensis; Sydney Harbour) and two tropical (Sinularia sp., Sarcophyton sp.; Heron Island) species common to reefs in eastern Australia. Bacterial communities associated with these octocorals were also compared to common temperate (Plesiastrea versipora) and tropical (Acropora aspera) hard corals from the same reefs. Using 16S rRNA amplicon sequencing, bacterial diversity was found to be heterogeneous among octocorals, but we observed changes in composition between summer and winter for some species (C. gaboensis and Sinularia sp.), but not for others (E. hicksoni and Sarcophyton sp.). Bacterial community structure differed significantly between all octocoral species within both the temperate and tropical environments. However, on a seasonal basis, those differences were less pronounced. The microbiomes of C. gaboensis and Sinularia sp. were dominated by bacteria belonging to the genus Endozoicomonas, which were a key conserved feature of their core microbiomes. In contrast to previous studies, our analysis revealed that Endozoicomonas phylotypes are shared across different octocoral species, inhabiting different environments. Together, our data demonstrates that octocorals harbour a broad diversity of bacterial partners, some of which comprise 'core microbiomes' that potentially impart important functional roles to their hosts.

Herdean, A, Sutherland, DL & Ralph, PJ 2022, 'Phenoplate: An innovative method for assessing interacting effects of temperature and light on non-photochemical quenching in microalgae under chemical stress', New Biotechnology, vol. 66, pp. 89-96.
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Hoque, MM, Noorian, P, Espinoza-Vergara, G, Manuneedhi Cholan, P, Kim, M, Rahman, MH, Labbate, M, Rice, SA, Pernice, M, Oehlers, SH & McDougald, D 2022, 'Adaptation to an amoeba host drives selection of virulence-associated traits in Vibrio cholerae', The ISME Journal, vol. 16, no. 3, pp. 856-867.
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Abstract Predation by heterotrophic protists drives the emergence of adaptive traits in bacteria, and often these traits lead to altered interactions with hosts and persistence in the environment. Here we studied adaptation of the cholera pathogen, Vibrio cholerae during long-term co-incubation with the protist host, Acanthamoeba castellanii. We determined phenotypic and genotypic changes associated with long-term intra-amoebal host adaptation and how this impacts pathogen survival and fitness. We showed that adaptation to the amoeba host leads to temporal changes in multiple phenotypic traits in V. cholerae that facilitate increased survival and competitive fitness in amoeba. Genome sequencing and mutational analysis revealed that these altered lifestyles were linked to non-synonymous mutations in conserved regions of the flagellar transcriptional regulator, flrA. Additionally, the mutations resulted in enhanced colonisation in zebrafish, establishing a link between adaptation of V. cholerae to amoeba predation and enhanced environmental persistence. Our results show that pressure imposed by amoeba on V. cholerae selects for flrA mutations that serves as a key driver for adaptation. Importantly, this study provides evidence that adaptive traits that evolve in pathogens in response to environmental predatory pressure impact the colonisation of eukaryotic organisms by these pathogens.

Hosseinkhani, N, McCauley, JI & Ralph, PJ 2022, 'Key challenges for the commercial expansion of ingredients from algae into human food products', Algal Research, vol. 64, pp. 102696-102696.
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Howlett, L, Camp, EF, Edmondson, J, Edmondson, J, Agius, T, Hosp, R, Coulthard, P, Edmondson, S & Suggett, DJ 2022, 'Adoption of coral propagation and out-planting via the tourism industry to advance site stewardship on the northern Great Barrier Reef', Ocean & Coastal Management, vol. 225, pp. 106199-106199.
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Hughes, DJ, Alexander, J, Cobbs, G, Kühl, M, Cooney, C, Pernice, M, Varkey, D, Voolstra, CR & Suggett, DJ 2022, 'Widespread oxyregulation in tropical corals under hypoxia', Marine Pollution Bulletin, vol. 179, pp. 113722-113722.
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Hughes, DJ, Raina, J-B, Nielsen, DA, Suggett, DJ & Kühl, M 2022, 'Disentangling compartment functions in sessile marine invertebrates', Trends in Ecology & Evolution, vol. 37, no. 9, pp. 740-748.
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Sessile invertebrates are frequently sampled and processed whole for downstream analyses. However, their apparent structural simplicity is deceptive as these organisms often harbour discrete compartments. These compartments have physicochemical conditions that differ markedly from neighbouring tissues, and that have likely evolved to support specific functions. Here, we argue that such compartments should be specifically targeted when characterising sessile invertebrate biology and we use the coral gastrovascular cavity to support our argument. This complex compartment displays steep and dynamic chemical gradients, harbours distinct microorganisms, and presumably plays a key role in coral biology. Disentangling the functions played by (and amongst) compartments will likely provide transformative insight into the biology of sessile invertebrates and their future under environmental change.

Hurtado-McCormick, V, Commault, A, Herdean, A, Price, S, Pernice, M & Ralph, P 2022, 'Generation of Synechocystis sp. PCC 6803 mutant with enhanced laccase-like activity', Bioresource Technology Reports, vol. 20, pp. 101266-101266.
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Cyanobacteria offer a good alternative to fungi for laccase production at industrial scales. Random mutagenesis approaches with ethyl methanesulfonate were used in combination with enzymatic assays screenings to select a mutant of Synechocystis sp., A2, with enhanced extracellular laccase-like activity. Anthraquinone dye decolourisation assay revealed 7 % enhanced decolourisation in A2 relative to wild type after 24 h. Comparison of the microbiome composition, structure and richness of the wild type and A2 strains confirmed that the improved traits were due to the mutation(s) and not the associated bacteria. The newly isolated Synechocystis mutant is the first example of successful random mutagenesis of cyanobacteria for laccase production. Attempts to characterise the biochemical reaction and putative laccase in A2 strain were unsuccessful but will be the subject of further research. This study suggests that random mutagenesis as a powerful approach for generating cyanobacterial strains with enhanced laccase-like activity for prospective commercial applications.

Inomura, K, Masuda, T, Eichner, M, Rabouille, S, Zavřel, T, Červený, J, Vancová, M, Bernát, G, Armin, G, Claquin, P, Kotabová, E, Stephan, S, Suggett, DJ, Deutsch, C & Prášil, O 2022, 'Erratum to “Quantifying Cyanothece growth under DIC limitation” [Comput. Struct. Biotechnol. J. 19 (2021) 6456–6464]', Computational and Structural Biotechnology Journal, vol. 20, pp. 385-385.
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[This corrects the article DOI: 10.1016/j.csbj.2021.11.036.].

Iwasaki, K, Szabó, M, Tamburic, B, Evenhuis, C, Zavafer, A, Kuzhiumparambil, U & Ralph, P 2022, 'Investigating the impact of light quality on macromolecular of', Functional Plant Biology, vol. 49, no. 6, pp. 554-564.
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Diatoms (Bacillariophyceae) are important to primary productivity of aquatic ecosystems. This algal group is also a valuable source of high value compounds that are utilised as aquaculture feed. The productivity of diatoms is strongly driven by light and CO2 availability, and macro- and micronutrient concentrations. The light dependency of biomass productivity and metabolite composition is well researched in diatoms, but information on the impact of light quality, particularly the productivity return on energy invested when using different monochromatic light sources, remains scarce. In this work, the productivity return on energy invested of improving growth rate, photosynthetic activity, and metabolite productivity of the diatom Chaetoceros muelleri under defined wavelengths (blue, red, and green) as well as while light is analysed. By adjusting the different light qualities to equal photosynthetically utilisable radiation, it was found that the growth rate and photosynthetic oxygen evolution was unchanged under white, blue, and green light, but it was lower under red light. Blue light improved the productivity return on energy invested for biomass, total protein, total lipid, total carbohydrate, and in fatty acids production, which would suggest that blue light should be used for aquaculture feed production.

Johnson, M, Burns, B, Herdean, A, Angeloski, A, Ralph, P, Morris, T, Kindler, G, Wong, H, Kuzhiumparambil, U, Sedger, L & Larkum, A 2022, 'A Cyanobacteria Enriched Layer of Shark Bay Stromatolites Reveals a New Acaryochloris Strain Living in Near Infrared Light', Microorganisms, vol. 10, no. 5, pp. 1035-1035.
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The genus Acaryochloris is unique among phototrophic organisms due to the dominance of chlorophyll d in its photosynthetic reaction centres and light-harvesting proteins. This allows Acaryochloris to capture light energy for photosynthesis over an extended spectrum of up to ~760 nm in the near infra-red (NIR) spectrum. Acaryochloris sp. has been reported in a variety of ecological niches, ranging from polar to tropical shallow aquatic sites. Here, we report a new Acarychloris strain isolated from an NIR-enriched stratified microbial layer 4–6 mm under the surface of stromatolite mats located in the Hamelin Pool of Shark Bay, Western Australia. Pigment analysis by spectrometry/fluorometry, flow cytometry and spectral confocal microscopy identifies unique patterns in pigment content that likely reflect niche adaption. For example, unlike the original A. marina species (type strain MBIC11017), this new strain, Acarychloris LARK001, shows little change in the chlorophyll d/a ratio in response to changes in light wavelength, displays a different Fv/Fm response and lacks detectable levels of phycocyanin. Indeed, 16S rRNA analysis supports the identity of the A. marina LARK001 strain as close to but distinct from from the A. marina HICR111A strain first isolated from Heron Island and previously found on the Great Barrier Reef under coral rubble on the reef flat. Taken together, A. marina LARK001 is a new cyanobacterial strain adapted to the stromatolite mats in Shark Bay.

Khan, AZ, Malik, S, Mehmood, MA, Shahid, A, Shahzad, T, Zhao, X-Q, Bai, F-W & Liu, C-G 2022, 'Two-stage algal cultivation for the biotransformation of urban wastewater’s pollutants into multiple bioproducts in a circular bioeconomy paradigm', Energy Conversion and Management, vol. 273, pp. 116400-116400.
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Resource recovery and recycling of urban wastewater have become essential due to rapidly depleting water resources. Here, a newly isolated cyanobacterium Pseudoscillatoria coralii BERC01 was employed for the biotreatment of urban wastewater (UWW) via a two-stage cultivation system followed by biotransformation of the biomass into multiple bioproducts. During the stage-I, the cyanobacterial strain BERC01 removed 100 % suspended solids (9–27 g/L) from the UWW within 3–7 days via biosorption, and the resultant biomass was used as a soil amender which improved the phosphate availability, microbial carbon biomass, and nitrate-nitrogen of the soil by 2.65–5.86-fold, 2.27–3.65-fold, and 3.20–6.57-fold, respectively. During stage-II, re-culturing the BERC01 in the recycled water improved the productivities of carbohydrates and proteins by 10-fold and 3-fold, respectively, when compared to the control. Cultivation of BERC01 also improved the pH of UWW (9.47 ± 0.2 – 10.93 ± 0.16) to reduce the bacterial and/or fungal contamination. The two-stage cultivation of BERC01 in the UWW lowered the total nitrogen, total phosphorous, chemical oxygen demand, and biological oxygen demand of the UWW by 41.94 %, 95 %, 79 %, and 89.64 %, respectively, bringing the quality of treated water within the WHO's safety limits of agricultural purposes. Cascading processing of the stage-II biomass yielded food-grade pigments (phycocyanin = 148.95 ± 1.81 mg/g, allophycocyanin = 51.92 ± 0.51 mg/g), and 470–490 mg/g of lipids which contained compounds of pharmaceutical interest such as undecanoic acid, pentadecanoic acid, and eicosanoic acid. Finally, the pigment-free and de-oiled residual biomass (PDRB) was completely valorized to mycoprotein and α-amylase through fungal fermentation using 10–50 g/L PDRB as a sole source of nutrition. Resultantly, Aspergillus niger and Aspergillus oryzae produced 98.44 U/mL and 118.56 U/mL of α-amylase in 96 h of incubation, respectively, whereas the protein conten...

Kindler, GS, Wong, HL, Larkum, AWD, Johnson, M, MacLeod, FI & Burns, BP 2022, 'Genome-resolved metagenomics provides insights into the functional complexity of microbial mats in Blue Holes, Shark Bay', FEMS Microbiology Ecology, vol. 98, no. 1, p. fiab158.
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ABSTRACTThe present study describes for the first time the community composition and functional potential of the microbial mats found in the supratidal, gypsum-rich and hypersaline region of Blue Holes, Shark Bay. This was achieved via high-throughput metagenomic sequencing of total mat community DNA and complementary analyses using hyperspectral confocal microscopy. Mat communities were dominated by Proteobacteria (29%), followed by Bacteroidetes/Chlorobi group (11%) and Planctomycetes (10%). These mats were found to also harbour a diverse community of potentially novel microorganisms, including members from the DPANN, Asgard archaea and candidate phyla radiation, with highest diversity found in the lower regions (∼14–20 mm depth) of the mat. In addition to pathways for major metabolic cycles, a range of putative rhodopsins with previously uncharacterized motifs and functions were identified along with heliorhodopsins and putative schizorhodopsins. Critical microbial interactions were also inferred, and from 117 medium- to high-quality metagenome-assembled genomes, viral defence mechanisms (CRISPR, BREX and DISARM), elemental transport, osmoprotection, heavy metal resistance and UV resistance were also detected. These analyses have provided a greater understanding of these distinct mat systems in Shark Bay, including key insights into adaptive responses and proposing that photoheterotrophy may be an important lifestyle in Blue Holes.

King, K, Bramucci, AR, Labbate, M, Raina, J-B & Seymour, JR 2022, 'Heterogeneous Growth Enhancement of Vibrio cholerae in the Presence of Different Phytoplankton Species', Applied and Environmental Microbiology, vol. 88, no. 17, p. e0115822.
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Many environmental strains of V. cholerae do not cause cholera epidemics but remain a public health concern due to their roles in milder gastrointestinal illnesses. With emerging evidence that these infections are increasing due to climate change, determining the ecological drivers that enable outbreaks of V. cholerae in coastal environments is becoming critical.

Klein, SG, Geraldi, NR, Anton, A, Schmidt‐Roach, S, Ziegler, M, Cziesielski, MJ, Martin, C, Rädecker, N, Frölicher, TL, Mumby, PJ, Pandolfi, JM, Suggett, DJ, Voolstra, CR, Aranda, M & Duarte, CM 2022, 'Projecting coral responses to intensifying marine heatwaves under ocean acidification', Global Change Biology, vol. 28, no. 5, pp. 1753-1765.
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AbstractOver this century, coral reefs will run the gauntlet of climate change, as marine heatwaves (MHWs) become more intense and frequent, and ocean acidification (OA) progresses. However, we still lack a quantitative assessment of how, and to what degree, OA will moderate the responses of corals to MHWs as they intensify throughout this century. Here, we first projected future MHW intensities for tropical regions under three future greenhouse gas emissions scenario (representative concentration pathways, RCP2.6, RCP4.5 and RCP8.5) for the near‐term (2021–2040), mid‐century (2041–2060) and late‐century (2081–2100). We then combined these MHW intensity projections with a global data set of 1,788 experiments to assess coral attribute performance and survival under the three emissions scenarios for the near‐term, mid‐century and late‐century in the presence and absence of OA. Although warming and OA had predominately additive impacts on the coral responses, the contribution of OA in affecting most coral attributes was minor relative to the dominant role of intensifying MHWs. However, the addition of OA led to greater decreases in photosynthesis and survival under intermediate and unrestricted emissions scenario for the mid‐ and late‐century than if intensifying MHWs were considered as the only driver. These results show that role of OA in modulating coral responses to intensifying MHWs depended on the focal coral attribute and extremity of the scenario examined. Specifically, intensifying MHWs and OA will cause increasing instances of coral bleaching and substantial declines in coral productivity, calcification and survival within the next two decades under the low and intermediate emissions scenario. These projections suggest that corals must rapidly adapt or acclimatize to projected ocean conditions to persist, which is far more likely under a low emissions scenario and with increasing efforts to manage reefs to enhance...

Kondaveeti, S, Petri, DFS & Jeong, HE 2022, 'Efficiency of air-dried and freeze-dried alginate/xanthan beads in batch, recirculating and column adsorption processes', International Journal of Biological Macromolecules, vol. 204, pp. 345-355.
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Kuzhiumparambil, U, Labeeuw, L, Commault, A, Vu, HP, Nguyen, LN, Ralph, PJ & Nghiem, LD 2022, 'Effects of harvesting on morphological and biochemical characteristics of microalgal biomass harvested by polyacrylamide addition, pH-induced flocculation, and centrifugation', Bioresource Technology, vol. 359, pp. 127433-127433.
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The effects of microalgae harvesting methods on microalgal biomass quality were evaluated using three species namely the freshwater green alga Chlorella vulgaris, marine red alga Porphyridium purpureum and marine diatom Phaeodactylum tricornutum. Harvesting efficiencies of polyacrylamide addition, alkaline addition, and centrifugation ranged from 85 to 95, 59-92 and 100%, respectively, across these species. Morphology of the harvested cells (i.e. compromised cell walls) was significantly impacted by alkaline pH-induced flocculation for all three species. Over 50% of C. vulgaris cells were compromised with alkaline pH compared to < 10% with polyacrylamide and centrifugation. The metabolic profiles varied depending on harvesting methods. Species-specific decrease of certain metabolites was observed. These results suggest that the method of harvest can alter the metabolic profile of the biomass amongst the three harvesting methods, polyacrylamide addition showed higher harvesting efficiency with less compromised cells and higher retention of industry important biochemicals.

LaJeunesse, TC, Wiedenmann, J, Casado-Amezúa, P, D’Ambra, I, Turnham, KE, Nitschke, MR, Oakley, CA, Goffredo, S, Spano, CA, Cubillos, VM, Davy, SK & Suggett, DJ 2022, 'Revival of Philozoon Geddes for host-specialized dinoflagellates, ‘zooxanthellae’, in animals from coastal temperate zones of northern and southern hemispheres', European Journal of Phycology, vol. 57, no. 2, pp. 166-180.
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Larsson, ME, Bramucci, AR, Collins, S, Hallegraeff, G, Kahlke, T, Raina, J-B, Seymour, JR & Doblin, MA 2022, 'Mucospheres produced by a mixotrophic protist impact ocean carbon cycling', Nature Communications, vol. 13, no. 1, p. 1301.
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AbstractMixotrophic protists (unicellular eukaryotes) that engage in both phototrophy (photosynthesis) and phago-heterotrophy (engulfment of particles)—are predicted to contribute substantially to energy fluxes and marine biogeochemical cycles. However, their impact remains largely unquantified. Here we describe the sophisticated foraging strategy of a widespread mixotrophic dinoflagellate, involving the production of carbon-rich ‘mucospheres’ that attract, capture, and immobilise microbial prey facilitating their consumption. We provide a detailed characterisation of this previously undescribed behaviour and reveal that it represents an overlooked, yet quantitatively significant mechanism for oceanic carbon fluxes. Following feeding, the mucospheres laden with surplus prey are discarded and sink, contributing an estimated 0.17–1.24 mg m−2 d−1 of particulate organic carbon, or 0.02–0.15 Gt to the biological pump annually, which represents 0.1–0.7% of the estimated total export from the euphotic zone. These findings demonstrate how the complex foraging behaviour of a single species of mixotrophic protist can disproportionally contribute to the vertical flux of carbon in the ocean.

Le Reun, N, Bramucci, A, O’Brien, J, Ostrowski, M, Brown, MV, Van de Kamp, J, Bodrossy, L, Raina, J-B, Ajani, P & Seymour, J 2022, 'Diatom Biogeography, Temporal Dynamics, and Links to Bacterioplankton across Seven Oceanographic Time-Series Sites Spanning the Australian Continent', Microorganisms, vol. 10, no. 2, pp. 338-338.
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Diatom communities significantly influence ocean primary productivity and carbon cycling, but their spatial and temporal dynamics are highly heterogeneous and are governed by a complex diverse suite of abiotic and biotic factors. We examined the seasonal and biogeographical dynamics of diatom communities in Australian coastal waters using amplicon sequencing data (18S-16S rRNA gene) derived from a network of oceanographic time-series spanning the Australian continent. We demonstrate that diatom community composition in this region displays significant biogeography, with each site harbouring distinct community structures. Temperature and nutrients were identified as the key environmental contributors to differences in diatom communities at all sites, collectively explaining 21% of the variability observed in diatoms assemblages. However, specific groups of bacteria previously implicated in mutualistic ecological interactions with diatoms (Rhodobacteraceae, Flavobacteriaceae and Alteromonadaceae) also explained a further 4% of the spatial dynamics observed in diatom community structure. We also demonstrate that the two most temperate sites (Port Hacking and Maria Island) exhibited strong seasonality in diatom community and that at these sites, winter diatom communities co-occurred with higher proportion of Alteromonadaceae. In addition, we identified significant co-occurrence between specific diatom and bacterial amplicon sequence variants (ASVs), with members of the Roseobacter and Flavobacteria clades strongly correlated with some of the most abundant diatom genera (Skeletonema, Thalassiosira, and Cylindrotheca). We propose that some of these co-occurrences might be indicative of ecologically important interactions between diatoms and bacteria. Our analyses reveal that in addition to physico-chemical conditions (i.e., temperature, nutrients), the relative abundance of specific groups of bacteria appear to play an important role in shaping the sp...

Lee, S-H, Kang, M, Jang, H, Kondaveeti, S, Sun, K, Kim, S, Park, H-H & Jeong, HE 2022, 'Bifunctional Amphiphilic Nanospikes with Antifogging and Antibiofouling Properties', ACS Applied Materials & Interfaces, vol. 14, no. 34, pp. 39478-39488.
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Leggat, W, Heron, SF, Fordyce, A, Suggett, DJ & Ainsworth, TD 2022, 'Experiment Degree Heating Week (eDHW) as a novel metric to reconcile and validate past and future global coral bleaching studies', Journal of Environmental Management, vol. 301, pp. 113919-113919.
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Coral bleaching has increasingly impacted reefs worldwide over the past four decades. Despite almost 40 years of research into the mechanistic, physiological, ecological, biophysical and climatic drivers of coral bleaching, metrics to allow comparison between ecological observations and experimental simulations still do not exist. Here we describe a novel metric - experimental Degree Heating Week (eDHW) - with which to standardise the persistently variable thermal conditions employed across experimental studies of coral bleaching by modify the widely used Degree Heating Week (DHW) metric used in ecological studies to standardise cumulative heat loading.

Lewis, BM, Suggett, DS, Prentis, PJ & Nothdurft, LD 2022, 'Cellular adaptations leading to coral fragment attachment on artificial substrates in Acropora millepora (Am-CAM)', Scientific Reports, vol. 12, no. 1, p. 18431.
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AbstractReproductive propagation by asexual fragmentation in the reef-building coral Acropora millepora depends on (1) successful attachment to the reef substrate through modification of soft tissues and (2) a permanent bond with skeletal encrustation. Despite decades of research examining asexual propagation in corals, the initial response, cellular reorganisation, and development leading to fragment substrate attachment via a newly formed skeleton has not been documented in its entirety. Here, we establish the first 'coral attachment model' for this species ('Am-CAM') by developing novel methods that allow correlation of fluorescence and electron microscopy image data with in vivo microscopic time-lapse imagery. This multi-scale imaging approach identified three distinct phases involved in asexual propagation: (1) the contact response of the coral fragment when contact with the substrate, followed by (2) fragment stabilisation through anchoring by the soft tissue, and (3) formation of a 'lappet-like appendage' structure leading to substrate bonding of the tissue for encrustation through the onset of skeletal calcification. In developing Am-CAM, we provide new biological insights that can enable reef researchers, managers and coral restoration practitioners to begin evaluating attachment effectiveness, which is needed to optimise species-substrate compatibility and achieve effective outplanting.

Lewis, RE, Davy, SK, Gardner, SG, Rongo, T, Suggett, DJ & Nitschke, MR 2022, 'Colony self-shading facilitates Symbiodiniaceae cohabitation in a South Pacific coral community', Coral Reefs, vol. 41, no. 5, pp. 1433-1447.
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AbstractThe ecological success of tropical corals is regulated by symbiotic dinoflagellate algae (Symbiodiniaceae). Corals can associate with multiple Symbiodiniaceae species simultaneously, yet the conditions that permit Symbiodiniaceae cohabitation are not understood. We examined how corals self-shade their own tissues causing within-colony light gradients that drive Symbiodiniaceae photoacclimatory processes and positional genetic disparity. Paired light ‘exposed’ and ‘shaded’ samples from 20 coral species were collected from a shallow coral reef (Rarotonga, Cook Islands). Through active chlorophyll fluorometry, rapid light curves revealed that exposed Symbiodiniaceae exhibited 50% higher values in minimum saturating irradiances and demonstrated a shift towards preferential nonphotochemical quenching [1 – Q], consistent with higher overall light exposure. High-throughput or targeted DNA sequencing of ITS2 and psbAncr markers demonstrated that corals harboured distinct and/or differentially abundant Symbiodiniaceae ITS2 sequences (typically rare in relative abundance) or multiple ITS2 intragenomic variant profiles across shaded vs exposed regions. In Hydnophora cf. microconos, within-colony symbiont genetic disparity was positively correlated with the magnitude of difference in [1 – Q] utilisation. Together, these results suggest that within-colony light gradients produce distinct optical niches that enable symbiont cohabitation via photoadaptation, a phenomenon that is expected to increase the adaptive capacity of corals under future climates.

Li, J, Ahmed, W, Metcalfe, S, Smith, WJM, Tscharke, B, Lynch, P, Sherman, P, Vo, PHN, Kaserzon, SL, Simpson, SL, McCarthy, DT, Thomas, KV, Mueller, JF & Thai, P 2022, 'Monitoring of SARS-CoV-2 in sewersheds with low COVID-19 cases using a passive sampling technique', Water Research, vol. 218, pp. 118481-118481.
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Monitoring SARS-CoV-2 RNA in sewer systems, upstream of a wastewater treatment plant, is an effective approach for understanding potential COVID-19 transmission in communities with higher spatial resolutions. Passive sampling devices provide a practical solution for frequent sampling within sewer networks where the use of autosamplers is not feasible. Currently, the design of upstream sampling is impeded by limited understanding of the fate of SARS-CoV-2 RNA in sewers and the sensitivity of passive samplers for the number of infected individuals in a catchment. In this study, passive samplers containing electronegative membranes were applied for at least 24-h continuous sampling in sewer systems. When monitoring SARS-CoV-2 along a trunk sewer pipe, we found RNA signals decreased proportionally to increasing dilutions, with non-detects occurring at the end of pipe. The passive sampling membranes were able to detect SARS-CoV-2 shed by >2 COVID-19 infection cases in 10,000 people. Moreover, upstream monitoring in multiple sewersheds using passive samplers identified the emergence of SARS-CoV-2 in wastewater one week ahead of clinical reporting and reflected the spatiotemporal spread of a COVID-19 cluster within a city. This study provides important information to guide the development of wastewater surveillance strategies at catchment and subcatchment levels using different sampling techniques.

Malik, S, Ashraf, MUF, Shahid, A, Javed, MR, Khan, AZ, Usman, M, Manivannan, A, Mehmood, MA & Ashraf, GA 2022, 'Characterization of a newly isolated self-flocculating microalga Bracteacoccus pseudominor BERC09 and its evaluation as a candidate for a multiproduct algal biorefinery', Chemosphere, vol. 304, pp. 135346-135346.
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Microalgae have the highest capability to fix the atmospheric carbon and wastewater-derived nutrients to produce high-value bioproducts including lipids and carotenoids. However, their lower titers and single-product-oriented biomass processing have made the overall process expensive. Hence, increased metabolite titer and processing of the biomass for more than one product are required to ensure the commercial robustness of the algal biorefinery. In this study, a newly isolated algal strain was identified as Bracteacoccus pseudominor BERC09 through phylogenetic analysis based on the 18S rRNA gene sequence. Basic characterization of the strain revealed its promising potential to produce carotenoids and lipids. The lipids and carotenoid biosynthesis pathways of BERC09 were further triggered by manipulating the abiotic factors including nitrogen sources (NaNO3, KNO3, NH4Cl, Urea), nitrogen concentrations (0.06-0.36 gL-1), light intensity (150 μmolm-2s-1 to 300 μmolm-2s-1), and light quality (white and blue). Resultantly, 300 μmolm-2s-1 of blue light yielded 0.768 gL-1 of biomass, 8.4 mgg-1 of carotenoids, and 390 mgg-1 of lipids, and supplementation of 0.36 gL-1 of KNO3 further improved metabolism and yielded 0.814 gL-1 of biomass, 11.86 mgg-1 of carotenoids, and 424 mgg-1 of lipids. Overall, the optimal combination of light and nitrogen concurrently improved biomass, carotenoids, and lipids by 3.5-fold, 6-fold, and 4-fold than control, respectively. Besides, the excellent glycoproteins-based self-flocculation ability of the strain rendered an easier harvesting via gravity sedimentation. Hence, this biomass can be processed in a cascading fashion to use this strain as a candidate for a multiproduct biorefinery to achieve commercial robustness and environmental sustainability.

Malik, S, Shahid, A, Betenbaugh, MJ, Liu, C-G & Mehmood, MA 2022, 'A novel wastewater-derived cascading algal biorefinery route for complete valorization of the biomass to biodiesel and value-added bioproducts', Energy Conversion and Management, vol. 256, pp. 115360-115360.
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Integration of multiproduct algal biorefineries with wastewater treatment systems could offer a sustainable approach to produce green products in a circular bioeconomy paradigm while keeping the water-energy-environment nexus sustainable. The present study demonstrated a novel biorefinery route employing a newly isolated self-flocculating microalga Chlamydomonas sp. BERC07. Here, the urban wastewater served as a low-cost growth media and improved biomass production (1.24 g/L) by 2-fold with concomitant removal of 100% total nitrogen, 94% total phosphorus, 56% COD, and 41% BOD. To lower the harvesting cost, an inducible sedimentation-based harvesting system was developed by employing the lowest dose of a commercial-grade flocculant, potash alum (0.27 kg/1000L culture) which improved the sedimentation rate of algal flocs by 240-fold with a biomass recovery efficiency of 96–98%. Later, the wastewater-derived biomass was subjected to downstream processing in a cascading fashion for its complete valorization. The biomass yielded 1.83 mg/g of carotenoids and 480 mg/g of lipids. The lipids were transesterified to produce biodiesel which completely met the preset European and American biodiesel quality standards. After carotenoids and lipids extraction, the residual biomass was fermented using Aspergillus niger and Aspergillus oryzae for the very first time. Interestingly, the A. oryzae outcompeted the A. niger and produced 131.6 U/mL of α-amylase along with 375–384 mg/g of mycoproteins utilizing 75–100 g/L of the residual algal biomass as a sole feedstock. All solvents involved in the product recovery were recycled to the primary wastewater, leaving no waste at the end of the processing pipeline. Overall, the data demonstrated a novel and sustainable biorefinery route with the most efficient harvesting and the complete valorization of the biomass, in a zero-waste approach. However, further upscaling, life cycle assessment, and technoeconomic analyses will be required to...

Malik, S, Shahid, A, Haider, MN, Amin, M, Betenbaugh, MJ, Mehmood, MA, Haq, MAU, Syafiuddin, A & Boopathy, R 2022, 'Prospects of Multiproduct Algal Biorefineries Involving Cascading Processing of the Biomass Employing a Zero-Waste Approach', Current Pollution Reports, vol. 8, no. 2, pp. 147-158.
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Purpose of Review: Increasing environmental problems demand mitigation solutions to fulfill sustainability development goals. Microalgae offer possibility of valorizing the CO2 and wastewater-derived nutrients to produce numerous industrial bioproducts. However, developing self-sustained systems for the complete valorization of algal biomass into valuable biobased products is challenging. Currently, sustainable algal processing faces several challenges including costly cultivation, difficult harvesting, and incomplete biomass valorization. This review assessed the prospects of emerging technologies focusing on the integrated approaches for sustainable algal biorefinery development ensuring the sustainability of environment-water-energy nexus. Recent Findings: Evaluation of various upstream, midstream, and downstream processing technologies provided insights into the processing issues. In upstream processing, high-rate algal ponds and integrated carbon capture and transformation technologies offer waste valorization into eco-friendly algal production. A brief comparison of harvesting technologies mainly focusing on chemical and biological flocculation has shown that integrating physical and biological harvesting methods are more reliable and efficient. Overview of downstream processing has indicated that biomass processing in a cascading manner offers the complete biomass valorization in a zero-waste paradigm. Summary: Assessment of cultivation-to-production technologies highlighted that “zero-waste” algal biorefinery has the potential to become reality by integrating the industry 4.0 and phenomics approaches with eco-friendly cultivation, harvesting, and processing technologies. Hybrid methods based on integrated cascading processing offer complete biomass valorization in a circular bioeconomy paradigm. Graphical Abstract: [Figure not available: see fulltext.]

McLeod, IM, Hein, MY, Babcock, R, Bay, L, Bourne, DG, Cook, N, Doropoulos, C, Gibbs, M, Harrison, P, Lockie, S, van Oppen, MJH, Mattocks, N, Page, CA, Randall, CJ, Smith, A, Smith, HA, Suggett, DJ, Taylor, B, Vella, KJ, Wachenfeld, D & Boström-Einarsson, L 2022, 'Coral restoration and adaptation in Australia: The first five years', PLOS ONE, vol. 17, no. 11, pp. e0273325-e0273325.
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While coral reefs in Australia have historically been a showcase of conventional management informed by research, recent declines in coral cover have triggered efforts to innovate and integrate intervention and restoration actions into management frameworks. Here we outline the multi-faceted intervention approaches that have developed in Australia since 2017, from newly implemented in-water programs, research to enhance coral resilience and investigations into socio-economic perspectives on restoration goals. We describe in-water projects using coral gardening, substrate stabilisation, coral repositioning, macro-algae removal, and larval-based restoration techniques. Three areas of research focus are also presented to illustrate the breadth of Australian research on coral restoration, (1) the transdisciplinary Reef Restoration and Adaptation Program (RRAP), one of the world’s largest research and development programs focused on coral reefs, (2) interventions to enhance coral performance under climate change, and (3) research into socio-cultural perspectives. Together, these projects and the recent research focus reflect an increasing urgency for action to confront the coral reef crisis, develop new and additional tools to manage coral reefs, and the consequent increase in funding opportunities and management appetite for implementation. The rapid progress in trialling and deploying coral restoration in Australia builds on decades of overseas experience, and advances in research and development are showing positive signs that coral restoration can be a valuable tool to improve resilience at local scales (i.e., high early survival rates across a variety of methods and coral species, strong community engagement with local stakeholders). RRAP is focused on creating interventions to help coral reefs at multiple scales, from micro scales (i.e., interventions targeting small areas within a specific reef site) to large scales (i.e., interventions target...

Nguyen, LN, Aditya, L, Vu, HP, Johir, AH, Bennar, L, Ralph, P, Hoang, NB, Zdarta, J & Nghiem, LD 2022, 'Nutrient Removal by Algae-Based Wastewater Treatment', Current Pollution Reports, vol. 8, no. 4, pp. 369-383.
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AbstractAlgae cultivation complements wastewater treatment (WWT) principles as the process uptakes nutrients while assimilates CO2 into biomass. Thus, the application of algae-based WWT is on the upward trajectory as more attention for recovery nutrients and CO2 capture while reducing its economic challenge in the circular economy concept. However, the complexity of wastewater and algal ecological characteristics induces techno-economic challenges for industry implementation. Algae-based WWT relies totally on the ability of algae to uptake and store nutrients in the biomass. Therefore, the removal efficiency is proportional to biomass productivity. This removal mechanism limits algae applications to low nutrient concentration wastewater. The hydraulic retention time (HRT) of algae-based WWT is significantly long (i.e. > 10 days), compared to a few hours in bacteria-based process. Phototrophic algae are the most used process in algae-based WWT studies as well as in pilot-scale trials. Application of phototrophic algae in wastewater faces challenges to supply CO2 and illumination. Collectively, significant landscape is required for illumination. Algae-based WWT has limited organic removals, which require pretreatment of wastewaters before flowing into the algal process. Algae-based WWT can be used in connection with the bacteria-based WWT to remove partial nutrients while capturing CO2. Future research should strive to achieve fast and high growth rate, strong environmental tolerance species, and simple downstream processing and high-value biomass. There is also a clear and urgent need for more systematic analysis of biomass for both carbon credit assessment and economic values to facilitate identification and prioritisation of barriers to lower the cost algae-based WWT. Graphical abstract

Nguyen, LN, Vu, HP, Fu, Q, Abu Hasan Johir, M, Ibrahim, I, Mofijur, M, Labeeuw, L, Pernice, M, Ralph, PJ & Nghiem, LD 2022, 'Synthesis and evaluation of cationic polyacrylamide and polyacrylate flocculants for harvesting freshwater and marine microalgae', Chemical Engineering Journal, vol. 433, pp. 133623-133623.
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This study addresses the challenge of microalgae harvesting through the development of flocculants. Two positively charged cationic polymers including poly[2 (acryloyloxy)ethyl]trimethylammonium chloride (PAETAC) and poly(3 acrylamidopropyl)trimethylammonium chloride (PAmPTAC) were synthesized using the UV-induced radical polymerization, for harvesting both freshwater and marine microalgae. The results show that the synthesized polymers have excellent flocculation performance for both freshwater green microalgae (Chlorella vulgaris) and marine red microalgae (Porphyridium purpureum). PAETAC outperformed PAmPTAC for both Chlorella vulgaris and Porphyridium purpureum microalgae. The optimal PAETAC doses for Chlorella vulgaris and Porphyridium purpureum microalgae were 50 and 4.8 mg/g of dry biomass while the optimal PAmPTAC doses were 252 and 35 mg/g of dry biomass respectively. Additionally, the floc formation with the PAETAC was more stable than PAmPTAC, which supported the dewatering step via sieving. The superior performance can be attributed to the higher molecular weight of the PAETAC polymer when compared to the PAmPTAC polymer. In comparison to commercially available polydiallyldimethylammonium chloride (PolyDADMAC), the newly synthesised PAETAC and PAmPTAC polymers demonstrated superior flocculation efficiency at a lower dose. The findings of this study established a platform technology for designing and synthesising cationic flocculants for use in microalgae harvesting.

Nguyen, TMH, Bräunig, J, Kookana, RS, Kaserzon, SL, Knight, ER, Vo, HNP, Kabiri, S, Navarro, DA, Grimison, C, Riddell, N, Higgins, CP, McLaughlin, MJ & Mueller, JF 2022, 'Assessment of Mobilization Potential of Per- and Polyfluoroalkyl Substances for Soil Remediation', Environmental Science & Technology, vol. 56, no. 14, pp. 10030-10041.
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This study investigated the mobilization of a wide range of per- and polyfluoroalkyl substances (PFASs) present in aqueous film-forming foams (AFFFs) in water-saturated soils through one-dimensional (1-D) column experiments with a view to assessing the feasibility of their remediation by soil desorption and washing. Results indicated that sorption/desorption of most of the shorter-carbon-chain PFASs (C ≤ 6) in soil reached greater than 99% rapidly─after approximately two pore volumes (PVs) and were well predicted by an equilibrium transport model, indicating that they will be readily removed by soil washing technologies. In contrast, the equilibrium model failed to predict the mobilization of longer-chain PFASs (C ≥ 7), indicating the presence of nonequilibrium sorption/desorption (confirmed by a flow interruption experiment). The actual time taken to attain 99% sorption/desorption was up to 5 times longer than predicted by the equilibrium model (e.g., ∼62 PVs versus ∼12 PVs predicted for perfluorooctane sulfonate (PFOS) in loamy sand). The increasing contribution of hydrophobic interactions over the electrostatic interactions is suggested as the main driving factor of the nonequilibrium processes. The inverse linear relationship (R2 = 0.6, p < 0.0001) between the nonequilibrium mass transfer rate coefficient and the Freundlich sorption coefficient could potentially be a useful means for preliminary evaluation of potential nonequilibrium sorption/desorption of PFASs in soils.

Nielsen, JJV, Matthews, G, Frith, KR, Harrison, HB, Marzonie, MR, Slaughter, KL, Suggett, DJ & Bay, LK 2022, 'Experimental considerations of acute heat stress assays to quantify coral thermal tolerance', Scientific Reports, vol. 12, no. 1, pp. 1-13.
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AbstractUnderstanding the distribution and abundance of heat tolerant corals across seascapes is imperative for predicting responses to climate change and to support novel management actions. Thermal tolerance is variable in corals and intrinsic and extrinsic drivers of tolerance are not well understood. Traditional experimental evaluations of coral heat and bleaching tolerance typically involve ramp-and-hold experiments run across days to weeks within aquarium facilities with limits to colony replication. Field-based acute heat stress assays have emerged as an alternative experimental approach to rapidly quantify heat tolerance in many samples yet the role of key methodological considerations on the stress response measured remains unresolved. Here, we quantify the effects of coral fragment size, sampling time point, and physiological measures on the acute heat stress response in adult corals. The effect of fragment size differed between species (Acropora tenuis and Pocillopora damicornis). Most physiological parameters measured here declined over time (tissue colour, chlorophyll-a and protein content) from the onset of heating, with the exception of maximum photosynthetic efficiency (Fv/Fm) which was surprisingly stable over this time scale. Based on our experiments, we identified photosynthetic efficiency, tissue colour change, and host-specific assays such as catalase activity as key physiological measures for rapid quantification of thermal tolerance. We recommend that future applications of acute heat stress assays include larger fragments (> 9 cm2) where possible and sample between 10 and 24 h after the end of heat stress. A validated high-throughput experimental ...

Nitschke, MR, Rosset, SL, Oakley, CA, Gardner, SG, Camp, EF, Suggett, DJ & Davy, SK 2022, 'The diversity and ecology of Symbiodiniaceae: A traits-based review', Advances in Marine Biology, vol. 92, pp. 55-127.
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Among the most successful microeukaryotes to form mutualisms with animals are dinoflagellates in the family Symbiodiniaceae. These photosynthetic symbioses drive significant primary production and are responsible for the formation of coral reef ecosystems but are particularly sensitive when environmental conditions become extreme. Annual episodes of widespread coral bleaching (disassociation of the mutualistic partnership) and mortality are forecasted from the year 2060 under current trends of ocean warming. However, host cnidarians and dinoflagellate symbionts display exceptional genetic and functional diversity, and meaningful predictions of the future that embrace this biological complexity are difficult to make. A recent move to trait-based biology (and an understanding of how traits are shaped by the environment) has been adopted to move past this problem. The aim of this review is to: (1) provide an overview of the major cnidarian lineages that are symbiotic with Symbiodiniaceae; (2) summarise the symbiodiniacean genera associated with cnidarians with reference to recent changes in taxonomy and systematics; (3) examine the knowledge gaps in Symbiodiniaceae life history from a trait-based perspective; (4) review Symbiodiniaceae trait variation along three abiotic gradients (light, nutrients, and temperature); and (5) provide recommendations for future research of Symbiodiniaceae traits. We anticipate that a detailed understanding of traits will further reveal basic knowledge of the evolution and functional diversity of these mutualisms, as well as enhance future efforts to model stability and change in ecosystems dependent on cnidarian-dinoflagellate organisms.

O’Brien, J, McParland, EL, Bramucci, AR, Ostrowski, M, Siboni, N, Ingleton, T, Brown, MV, Levine, NM, Laverock, B, Petrou, K & Seymour, J 2022, 'The Microbiological Drivers of Temporally Dynamic Dimethylsulfoniopropionate Cycling Processes in Australian Coastal Shelf Waters', Frontiers in Microbiology, vol. 13, pp. 1-19.
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The organic sulfur compounds dimethylsulfoniopropionate (DMSP) and dimethyl sulfoxide (DMSO) play major roles in the marine microbial food web and have substantial climatic importance as sources and sinks of dimethyl sulfide (DMS). Seasonal shifts in the abundance and diversity of the phytoplankton and bacteria that cycle DMSP are likely to impact marine DMS (O) (P) concentrations, but the dynamic nature of these microbial interactions is still poorly resolved. Here, we examined the relationships between microbial community dynamics with DMS (O) (P) concentrations during a 2-year oceanographic time series conducted on the east Australian coast. Heterogenous temporal patterns were apparent in chlorophyll a (chl a) and DMSP concentrations, but the relationship between these parameters varied over time, suggesting the phytoplankton and bacterial community composition were affecting the net DMSP concentrations through differential DMSP production and degradation. Significant increases in DMSP were regularly measured in spring blooms dominated by predicted high DMSP-producing lineages of phytoplankton (Heterocapsa, Prorocentrum, Alexandrium, and Micromonas), while spring blooms that were dominated by predicted low DMSP-producing phytoplankton (Thalassiosira) demonstrated negligible increases in DMSP concentrations. During elevated DMSP concentrations, a significant increase in the relative abundance of the key copiotrophic bacterial lineage Rhodobacterales was accompanied by a three-fold increase in the gene, encoding the first step of DMSP demethylation (dmdA). Significant temporal shifts in DMS concentrations were measured and were significantly correlated with both fractions (0.2–2 μm and &gt;2 μm) of microbial DMSP lyase activity....

O’Brien, J, McParland, EL, Bramucci, AR, Siboni, N, Ostrowski, M, Kahlke, T, Levine, NM, Brown, MV, van de Kamp, J, Bodrossy, L, Messer, LF, Petrou, K & Seymour, JR 2022, 'Biogeographical and seasonal dynamics of the marine Roseobacter community and ecological links to DMSP-producing phytoplankton', ISME Communications, vol. 2, no. 1, p. 16.
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Abstract Ecological interactions between marine bacteria and phytoplankton play a pivotal role in governing the ocean’s major biogeochemical cycles. Among these, members of the marine Roseobacter Group (MRG) can establish mutualistic relationships with phytoplankton that are, in part, maintained by exchanges of the organosulfur compound, dimethylsulfoniopropionate (DMSP). Yet most of what is known about these interactions has been derived from culture-based laboratory studies. To investigate temporal and spatial co-occurrence patterns between members of the MRG and DMSP-producing phytoplankton we analysed 16S and 18S rRNA gene amplicon sequence variants (ASVs) derived from 5 years of monthly samples from seven environmentally distinct Australian oceanographic time-series. The MRG and DMSP-producer communities often displayed contemporaneous seasonality, which was greater in subtropical and temperate environments compared to tropical environments. The relative abundance of both groups varied latitudinally, displaying a poleward increase, peaking (MRG at 33% of total bacteria, DMSP producers at 42% of eukaryotic phototrophs) during recurrent spring-summer phytoplankton blooms in the most temperate site (Maria Island, Tasmania). Network analysis identified 20,140 significant positive correlations between MRG ASVs and DMSP producers and revealed that MRGs exhibit significantly stronger correlations to high DMSP producers relative to other DMSP-degrading bacteria (Pelagibacter, SAR86 and Actinobacteria). By utilising the power of a continental network of oceanographic time-series, this study provides in situ confirmation of interactions found in laboratory studies and demonstrates that the ecological dynamics of an important group of marine bacteria are shaped by the production of an abundant and biogeochemically significant organosulfur compound.

O'Brien, J, Focardi, A, Deschaseaux, ESM, Petrou, K, Ostrowski, M, Beckley, LE & Seymour, JR 2022, 'Microbial dimethylsulfoniopropionate (DMSP) cycling in the ultraoligotrophic eastern Indian Ocean', Deep Sea Research Part II: Topical Studies in Oceanography, vol. 206, pp. 105195-105195.
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Dimethylsulfoniopropionate (DMSP) is an important source of dissolved organic matter for the marine food web and its cycling is a key step in ocean-atmosphere fluxes involved in the global sulfur cycle. To date, the abundance and biogeography of the genes encoding bacterial DMSP cycling in the eastern Indian Ocean (EIO) is virtually unknown. Moreover, DMSP measurements from the IO are sparse compared to other major oceans. In May–June 2019, we characterized dissolved DMSP (DMSPd) concentrations and the abundance of representative bacterial DMSP cycling genes along the 110 °E transect line as part of a voyage that contributed to Australia's involvement in the second International Indian Ocean Expedition. During the multidisciplinary voyage, surface water samples were collected from 19 stations spanning temperate to tropical waters of the EIO (39.5 °S to 11.5 °S, 110 °E). Somewhat surprisingly, a trend of greater DMSPd was measured in ultraoligotrophic (<0.02 μmol L−1 of nitrate/nitrite), low latitude waters compared to relatively nutrient-rich high latitudes, which contradicts global DMSPd patterns of high concentrations at high latitudes. Additionally, the average DMSPd concentration in EIO samples (17.2 ± 18.64 nM) was an order of magnitude greater than concentrations previously reported at similar latitudes in the Pacific and Atlantic Oceans, which suggests DMSPd is a readily available food source for microbes in a region that is often considered an ocean desert. The abundances of the bacterial DMSP production gene (dsyB), the DMSP lyase gene (dddP) and phylogenetically diverse DMSP demethylation genes (dmdA subclade A/1, D/all and E/2) were reported for the first time in the EIO region, demonstrating significant shifts in all genes with latitude. The SAR11 dmdA (D/all) gene was the dominant DMSP degradation gene across the transect (3.4 ± 0.94% of bacteria) and was notably positively correlated to DMSPd, demonstrating a tight coupling between the var...

Pettersen, AK, Coleman, MA, Latombe, G, Gonzalez, SV, Williams, NLR, Seymour, JR, Campbell, AH, Thomas, T, Ferrari, R, Stuart‐Smith, RD, Edgar, GJ, Steinberg, PD & Marzinelli, EM 2022, 'Spatial compositional turnover varies with trophic level and body size in marine assemblages of micro‐ and macroorganisms', Global Ecology and Biogeography, vol. 31, no. 8, pp. 1556-1570.
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AbstractAimSpatial compositional turnover varies considerably among co‐occurring assemblages of organisms, presumably shaped by common processes related to species traits. We investigated patterns of spatial turnover in a diverse set of marine assemblages using zeta diversity, which extends traditional pairwise measures of turnover to capture the roles of both rare and common species in shaping assemblage turnover. We tested the generality of hypothesized patterns related to ecological traits and provide insights into mechanisms of biodiversity change.LocationTemperate pelagic and benthic marine assemblages of micro‐ and macroorganisms along south‐eastern Australia (30–36° S latitude).Time period2008–2021.Major taxa studiedBacteria, phytoplankton, zooplankton, fish, and macrobenthic groups.MethodsSix marine datasets spanning bacteria to fishes were collated for measures of “species” occurrence, with a 1° latitude grain. For each assemblage, ecological traits of body size, habitat and trophic level were analysed for the form and rate of decline in zeta diversity and for the species retention rate.ResultsSpecies at higher trophic levels showed two to three times the rate of zeta diversity decline compared with lower trophic levels, indicating an increase in turnover from phytoplankton to carnivorous fishes. Body size showed the hypothesized unimodal relationship with rates of turnover for macroorganisms. Patterns of bacterial turnover contrasted with those found for macroorganisms, with the highest levels of turnover in pelagic habitats compared with benthic (kelp‐associated) hab...

Poddar, N, Scofield, J, Shi, S, Prime, EL, Kentish, SE, Qiao, GG & Martin, GJO 2022, 'Evaporation reduction and salinity control in microalgae production ponds using chemical monolayers', Algal Research, vol. 66, pp. 102783-102783.
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Price, S, Kuzhiumparambil, U, Pernice, M & Ralph, P 2022, 'Techno-economic analysis of cyanobacterial PHB bioplastic production', Journal of Environmental Chemical Engineering, vol. 10, no. 3, pp. 107502-107502.
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Quek, L-E, van Geldermalsen, M, Guan, YF, Wahi, K, Mayoh, C, Balaban, S, Pang, A, Wang, Q, Cowley, MJ, Brown, KK, Turner, N, Hoy, AJ & Holst, J 2022, 'Glutamine addiction promotes glucose oxidation in triple-negative breast cancer', Oncogene, vol. 41, no. 34, pp. 4066-4078.
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AbstractGlutamine is a conditionally essential nutrient for many cancer cells, but it remains unclear how consuming glutamine in excess of growth requirements confers greater fitness to glutamine-addicted cancers. By contrasting two breast cancer subtypes with distinct glutamine dependencies, we show that glutamine-indispensable triple-negative breast cancer (TNBC) cells rely on a non-canonical glutamine-to-glutamate overflow, with glutamine carbon routed once through the TCA cycle. Importantly, this single-pass glutaminolysis increases TCA cycle fluxes and replenishes TCA cycle intermediates in TNBC cells, a process that achieves net oxidation of glucose but not glutamine. The coupling of glucose and glutamine catabolism appears hard-wired via a distinct TNBC gene expression profile biased to strip and then sequester glutamine nitrogen, but hampers the ability of TNBC cells to oxidise glucose when glutamine is limiting. Our results provide a new understanding of how metabolically rigid TNBC cells are sensitive to glutamine deprivation and a way to select vulnerable TNBC subtypes that may be responsive to metabolic-targeted therapies.

Quigley, KM, Hein, M & Suggett, DJ 2022, 'Translating the 10 golden rules of reforestation for coral reef restoration', Conservation Biology, vol. 36, no. 4, pp. 1-8.
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AbstractEfforts are accelerating to protect and restore ecosystems globally. With trillions of dollars in ecosystem services at stake, no clear framework exists for developing or prioritizing approaches to restore coral reefs even as efforts and investment opportunities to do so grow worldwide. Restoration may buy time for climate change mitigation, but it lacks rigorous guidance to meet objectives of scalability and effectiveness. Lessons from restoration of terrestrial ecosystems can and should be rapidly adopted for coral reef restoration. We propose how the 10 golden rules of effective forest restoration can be translated to accelerate efforts to restore coral reefs based on established principles of resilience, management, and local stewardship. We summarize steps to undertake reef restoration as a management strategy in the context of the diverse ecosystem service values that coral reefs provide. Outlining a clear blueprint is timely as more stakeholders seek to undertake restoration as the UN Decade on Ecosystem Restoration begins.

Rädecker, N, Pogoreutz, C, Gegner, HM, Cárdenas, A, Perna, G, Geißler, L, Roth, F, Bougoure, J, Guagliardo, P, Struck, U, Wild, C, Pernice, M, Raina, J-B, Meibom, A & Voolstra, CR 2022, 'Heat stress reduces the contribution of diazotrophs to coral holobiont nitrogen cycling', The ISME Journal, vol. 16, no. 4, pp. 1110-1118.
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Abstract Efficient nutrient cycling in the coral-algal symbiosis requires constant but limited nitrogen availability. Coral-associated diazotrophs, i.e., prokaryotes capable of fixing dinitrogen, may thus support productivity in a stable coral-algal symbiosis but could contribute to its breakdown when overstimulated. However, the effects of environmental conditions on diazotroph communities and their interaction with other members of the coral holobiont remain poorly understood. Here we assessed the effects of heat stress on diazotroph diversity and their contribution to holobiont nutrient cycling in the reef-building coral Stylophora pistillata from the central Red Sea. In a stable symbiotic state, we found that nitrogen fixation by coral-associated diazotrophs constitutes a source of nitrogen to the algal symbionts. Heat stress caused an increase in nitrogen fixation concomitant with a change in diazotroph communities. Yet, this additional fixed nitrogen was not assimilated by the coral tissue or the algal symbionts. We conclude that although diazotrophs may support coral holobiont functioning under low nitrogen availability, altered nutrient cycling during heat stress abates the dependence of the coral host and its algal symbionts on diazotroph-derived nitrogen. Consequently, the role of nitrogen fixation in the coral holobiont is strongly dependent on its nutritional status and varies dynamically with environmental conditions.

Raes, EJ, Hörstmann, C, Landry, MR, Beckley, LE, Marin, M, Thompson, P, Antoine, D, Focardi, A, O'Brien, J, Ostrowski, M & Waite, AM 2022, 'Dynamic change in an ocean desert: Microbial diversity and trophic transfer along the 110 °E meridional in the Indian Ocean', Deep Sea Research Part II: Topical Studies in Oceanography, vol. 201, pp. 105097-105097.
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The eastern Indian Ocean is among the most oligotrophic regions in the world and has been described as an ocean desert. Limited information exists on microbial community profiles from marker gene data, and an open question in this system is how energy is transported from the base of the food web to higher trophic levels. Here we show that, along a 3300 km long transect in the ultra-oligotrophic eastern Indian Ocean, both alpha and beta diversity metrics for prokaryotic and eukaryotic trophic groups revealed remarkably strong latitudinal trends. The latitudinal Shannon diversity pattern for autotrophic eukaryotes furthermore aligned with the isotopic δ13C ratios of particulate organic carbon, fractionated zooplankton and hand-picked fish larvae, suggesting a close trophic linkage between autotrophic eukaryotes and higher trophic levels. Our data also showed an increasing contribution of eukaryotic mixotrophs and a high contribution of heterotrophic eukaryotes towards warmer waters. These findings highlight that not only the recycling of organic matter via bacterial regeneration is important in this system but that mixo- and heterotrophic eukaryotes play a major role in redistributing energy within the marine food web of these oligotrophic waters. Our data provide a baseline to understand how environmental changes such as warming surface waters might impact the open-ocean food web in this oligotrophic basin.

Raina, J-B, Lambert, BS, Parks, DH, Rinke, C, Siboni, N, Bramucci, A, Ostrowski, M, Signal, B, Lutz, A, Mendis, H, Rubino, F, Fernandez, VI, Stocker, R, Hugenholtz, P, Tyson, GW & Seymour, JR 2022, 'Chemotaxis shapes the microscale organization of the ocean’s microbiome', Nature, vol. 605, no. 7908, pp. 132-138.
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The capacity of planktonic marine microorganisms to actively seek out and exploit microscale chemical hotspots has been widely theorized to affect ocean-basin scale biogeochemistry1-3, but has never been examined comprehensively in situ among natural microbial communities. Here, using a field-based microfluidic platform to quantify the behavioural responses of marine bacteria and archaea, we observed significant levels of chemotaxis towards microscale hotspots of phytoplankton-derived dissolved organic matter (DOM) at a coastal field site across multiple deployments, spanning several months. Microscale metagenomics revealed that a wide diversity of marine prokaryotes, spanning 27 bacterial and 2 archaeal phyla, displayed chemotaxis towards microscale patches of DOM derived from ten globally distributed phytoplankton species. The distinct DOM composition of each phytoplankton species attracted phylogenetically and functionally discrete populations of bacteria and archaea, with 54% of chemotactic prokaryotes displaying highly specific responses to the DOM derived from only one or two phytoplankton species. Prokaryotes exhibiting chemotaxis towards phytoplankton-derived compounds were significantly enriched in the capacity to transport and metabolize specific phytoplankton-derived chemicals, and displayed enrichment in functions conducive to symbiotic relationships, including genes involved in the production of siderophores, B vitamins and growth-promoting hormones. Our findings demonstrate that the swimming behaviour of natural prokaryotic assemblages is governed by specific chemical cues, which dictate important biogeochemical transformation processes and the establishment of ecological interactions that structure the base of the marine food web.

Ratnasari, A, Syafiuddin, A, Boopathy, R, Malik, S, Aamer Mehmood, M, Amalia, R, Dwi Prastyo, D & Syamimi Zaidi, N 2022, 'Advances in pretreatment technology for handling the palm oil mill effluent: Challenges and prospects', Bioresource Technology, vol. 344, no. Pt B, pp. 126239-126239.
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The palm oil mill effluent (POME) from palm milling oil activities is discharged into various water bodies which poses several environmental problems including turbidity, increases COD and BOD, adds oil and grease, increases total nitrogen, and other pollutants. Therefore, it requires effective treatment to remove the pollutants before disposal. The objective was to critically discuss the performance of POME pretreatments along with their limitations. To offer a coverage on the present less efficient technologies, the opportunities and challenges of advanced pretreatments that combine magnetic materials and natural composites as adsorbents are comprehensively reviewed here. Moreover, potential of various magnetic materials for POME pretreatment has been described. Several existing pretreatment methods such as physical pretreatments, chemical pretreatments, coagulation-flocculation, and adsorption can remove pollutant content from POME with certain limitations and the use of magnetic composite adsorbents can enhance the treatment efficiency.

Razavi Bazaz, S, Mihandust, A, Salomon, R, Joushani, HAN, Li, W, A. Amiri, H, Mirakhorli, F, Zhand, S, Shrestha, J, Miansari, M, Thierry, B, Jin, D & Ebrahimi Warkiani, M 2022, 'Zigzag microchannel for rigid inertial separation and enrichment (Z-RISE) of cells and particles', Lab on a Chip, vol. 22, no. 21, pp. 4093-4109.
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Overview of the zigzag microchannel for rigid inertial separation and enrichment (Z-RISE). The proposed device has superior performance for particle focusing and separation.

Rintoul, MS, Courtney, TA, Dohner, JL, Giddings, SN, Kekuewa, SAH, Mitarai, S, Monismith, SG, Pezner, AK & Andersson, AJ 2022, 'The Effects of Light Intensity and Flow Speed on Biogeochemical Variability Within a Fringing Coral Reef in Onna‐Son, Okinawa, Japan', Journal of Geophysical Research: Oceans, vol. 127, no. 12.
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AbstractGlobal warming and ocean acidification are driving declines in seawater dissolved oxygen (DO) concentrations and pH. Predicting how these changes will affect shallow, near‐shore environments such as coral reefs is challenging due to their high natural biogeochemical variability present over both spatial (m to km) and temporal (diel to seasonal) scales. To make predictions, we must understand the drivers of this variability. The impact of metabolic processes on coral reef biogeochemical variability has been the subject of significant research effort, however, physical factors, including flow speed and light intensity, have received less attention. Here, we measured seawater flow, photosynthetically active radiation (PAR), pH, and DO at three reef habitats (reef flat, lagoon, and outflow channel) in a fringing coral reef system in Okinawa, Japan for 3 weeks in October 2019. During the study, pH ranged from 7.86 to 8.37 units while DO varied from 127 to 369 μmol/kg. Circulation was primarily wave‐driven with mean flow speeds ranging from 14 to 26 cm/s. Flow direction became increasingly consistent at higher flow speeds and traced benthic striations visible in satellite imagery. Multiple linear regression models of daytime changes in pH and DO versus daily mean flow speed and PAR described 25%–74% of the observed variability across all sites while at night, flow speed alone accounted for 7%–75% of the observed variability. These results demonstrate PAR, water flow speed, and the path water takes play important roles in controlling biogeochemical variability within coral reefs and must be considered when assessing their vulnerability to both local and global environmental change.

Roper, CD, Camp, EF, Edmondson, J & Suggett, DJ 2022, 'Combined impacts of natural recruitment and active propagation for coral population recovery on the Great Barrier Reef', Marine Ecology Progress Series, vol. 700, pp. 95-109.
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Coral populations on the Great Barrier Reef (GBR) are experiencing long-term shifts in size structure, including steep declines in small colonies, driving major concerns for recovery through the supply of new recruits. Whilst coral restoration began on the GBR in 2018, the combined influence of natural recruitment and outplanting for coral population recovery has not been evaluated. Here, we assessed 2 sites (Rayban and Mojo) at Opal Reef that were subject to intensive outplant efforts over a 3 yr period (2018-2021). Coral cover did not change significantly, with a baseline of 15% in 2018 and a cover of 28 and 25% in Rayban outplant and control areas, respectively, in 2021, while Mojo exhibited a coral cover of 38% in 2018 and 52% (outplant area) and 29% (control area) in 2021. Natural recruitment in 2021 did not vary by site and was characterised by a settlement rate of 5.5 and 3.7 recruits tile-1 at Rayban and Mojo, respectively. Juvenile coral abundance and diversity were similar for control and outplant areas at each site. Over the 3 yr period, coral cover as a metric did not identify differences between control and outplant areas; however, size-frequency distributions of key coral taxa revealed a higher frequency of small to mid-sized colonies in outplant communities compared to controls. Given that no differences were observed in recruitment rates or juvenile abundances, variations in population structure appear to be driven by planting efforts rather than natural recovery. Our results demonstrate the need for combined monitoring of natural versus intervention-based rehabilitation to understand the impact of coral propagation efforts for local site recovery.

Ross, PM, Scanes, E, Poronnik, P, Coates, H & Locke, W 2022, 'Understanding STEM academics’ responses and resilience to educational reform of academic roles in higher education', International Journal of STEM Education, vol. 9, no. 1.
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AbstractBackgroundAcross the globe, there have been significant reforms to improve STEM education at all levels. A significant part of this has been teacher reform. While the responses and resilience of STEM teachers to educational reforms in secondary education have received significant attention, the responses and resilience of STEM teachers in higher education remains understudied. In higher education, educational reforms of academic roles have seen increasing numbers of STEM academics focussed on education. Responses of STEM academics to education reform of the academic role have some parallels with teacher resilience, but there are also potential misalignments within a culture which values and prioritises science disciplinary research. This study examined the responses of STEM academics in higher education to educational reform of the academic role using the theoretical construct of resilience and Bronfenbrenner’s socio-ecological model. This was a 2-year case study of 32 academics and senior educational leaders in higher education in STEM. Data collection included semi-structured interviews which were theme coded and inductively analysed.ResultsThe responses and resilience of STEM academics focussed on education appeared to be dependent on interactions between individual disposition in the microsystem and influences of the exosystem and the external macrosystem. Five major themes emerged about the value and quality, scholarship and expertise, progress and mobility, status and identity and community and culture of STEM academics focussed on education. The exosystem was a significant unidirectional influence on STEM academics where judgements were made concerning academic performance, awards, and promotion. Responses of senior leaders in the exosystem were influenced by the macrosystem and culture of science. Academics f...

Shahid, A, Siddiqui, AJ, Musharraf, SG, Liu, C-G, Malik, S, Syafiuddin, A, Boopathy, R, Tarbiah, NI, Gull, M & Mehmood, MA 2022, 'Untargeted metabolomics of the alkaliphilic cyanobacterium Plectonema terebrans elucidated novel stress-responsive metabolic modulations', Journal of Proteomics, vol. 252, pp. 104447-104447.
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Alkaliphilic cyanobacteria are suitable candidates to study the effect of alkaline wastewater cultivation on molecular metabolic responses. In the present study, the impact of wastewater, alkalinity, and alkaline wastewater cultivation was studied on the biomass production, biochemical composition, and the alkalinity responsive molecular mechanism through metabolomics. The results suggested a 1.29 to 1.44-fold higher biomass production along with improved lipid, carbohydrate, and pigment production under alkaline wastewater cultivation. The metabolomics analysis showed 1.2-fold and 5.54-fold increase in the indole-acetic acid and phytoene biosynthesis which contributed to overall enhanced cell differentiation and photo-protectiveness. Furthermore, lower levels of Ribulose-1,5-bisphosphate (RuBP), and higher levels of 2-phosphoglycerate and 3-phosphoglycerate suggested the efficient fixation of CO2 into biomass, and storage compounds including polysaccharides, lipids, and sterols. Interestingly, except L-histidine and L-phenylalanine, all the metabolites related to protein biosynthesis were downregulated in response to wastewater and alkaline wastewater cultivation. The cells protected themselves from alkalinity and nutrient stress by improving the biosynthesis of sterols, non-toxic antioxidants, and osmo-protectants. Alkaline wastewater cultivation regulated the activation of carbon concentration mechanism (CCM), glycolysis, fatty-acid biosynthesis, and shikimate pathway. The data revealed the importance of alkaline wastewater cultivation for improved CO2 fixation, wastewater treatment, and producing valuable bioproducts including phytoene, Lyso PC 18:0, and sterols. These metabolic pathways could be future targets of metabolic engineering for improving biomass and metabolite production. SIGNIFICANCE: Alkalinity is an imperative factor, responsible for the contamination control and biochemical regulation in cyanobactera, especially during the wastewater cultivati...

Smith, P, Beaumont, L, Bernacchi, CJ, Byrne, M, Cheung, W, Conant, RT, Cotrufo, F, Feng, X, Janssens, I, Jones, H, Kirschbaum, MUF, Kobayashi, K, LaRoche, J, Luo, Y, McKechnie, A, Penuelas, J, Piao, S, Robinson, S, Sage, RF, Sugget, DJ, Thackeray, SJ, Way, D & Long, SP 2022, 'Essential outcomes for COP26', Global Change Biology, vol. 28, no. 1, pp. 1-3.
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Sow, SLS, Brown, MV, Clarke, LJ, Bissett, A, van de Kamp, J, Trull, TW, Raes, EJ, Seymour, JR, Bramucci, AR, Ostrowski, M, Boyd, PW, Deagle, BE, Pardo, PC, Sloyan, BM & Bodrossy, L 2022, 'Biogeography of Southern Ocean prokaryotes: a comparison of the Indian and Pacific sectors', Environmental Microbiology, vol. 24, no. 5, pp. 2449-2466.
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SummaryWe investigated the Southern Ocean (SO) prokaryote community structure via zero‐radius operational taxonomic unit (zOTU) libraries generated from 16S rRNA gene sequencing of 223 full water column profiles. Samples reveal the prokaryote diversity trend between discrete water masses across multiple depths and latitudes in Indian (71–99°E, summer) and Pacific (170–174°W, autumn‐winter) sectors of the SO. At higher taxonomic levels (phylum‐family) we observed water masses to harbour distinct communities across both sectors, but observed sectorial variations at lower taxonomic levels (genus‐zOTU) and relative abundance shifts for key taxa such as Flavobacteria, SAR324/Marinimicrobia, Nitrosopumilus and Nitrosopelagicus at both epi‐ and bathy‐abyssopelagic water masses. Common surface bacteria were abundant in several deep‐water masses and vice‐versa suggesting connectivity between surface and deep‐water microbial assemblages. Bacteria from same‐sector Antarctic Bottom Water samples showed patchy, high beta‐diversity which did not correlate well with measured environmental parameters or geographical distance. Unconventional depth distribution patterns were observed for key archaeal groups: Crenarchaeota was found across all depths in the water column and persistent high relative abundances of common epipelagic archaeon Nitrosopelagicus was observed in deep‐water masses. Our findings reveal substantial regional variability of SO prokaryote assemblages that we argue should be considered in wide‐scale SO ecosystem microbial modelling.

Strudwick, P, Seymour, J, Camp, EF, Edmondson, J, Haydon, T, Howlett, L, Le Reun, N, Siboni, N & Suggett, DJ 2022, 'Correction to: Impacts of nursery-based propagation and out-planting on coral-associated bacterial communities', Coral Reefs, vol. 41, no. 2, pp. 473-473.
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Strudwick, P, Seymour, J, Camp, EF, Edmondson, J, Haydon, T, Howlett, L, Le Reun, N, Siboni, N & Suggett, DJ 2022, 'Impacts of nursery-based propagation and out-planting on coral-associated bacterial communities', Coral Reefs, vol. 41, no. 1, pp. 95-112.
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Efforts to manage coral reef declines are increasingly turning towards in situ propagation of corals to aid reef recovery. Understanding the factors that influence ‘success’ throughout the propagation process is therefore critical to ensure efforts are viable and cost-effective, yet the extent to which propagation practices potentially impact the underlying coral biology remains unknown. Given growing evidence for the importance of the coral microbiome, we examined the influence of nursery-based propagation and out-planting on the bacterial communities of two coral species–Acropora millepora and Pocillopora verrucosa–increasingly propagated on the northern Great Barrier Reef (Opal Reef). Bacterial communities of coral fragments were characterised over four months of nursery propagation (sampling points: zero, seven and 125 days) and one month of subsequent out-planting (sampling points: zero, one and 30 days). Bacterial community structure differed between A. millepora and P. verrucosa throughout the experiment and species-specific temporal dynamics were observed during the transplantation of corals into nurseries and subsequent out-planting back to the reef. P. verrucosa bacterial community structure remained stable over time in the natural reef environment and within the nursery. In contrast, A. millepora bacterial communities within the nursery significantly changed over time, whereas those associated with source colonies within the natural reef environment remained unchanged. However, after one month of out-planting, the composition, richness and diversity of A. millepora bacterial communities were not statistically different to those associated with the source colonies. We interpret the transient shift of A. millepora bacterial communities within the nursery as an impact of distinctive environmental conditions in nurseries compared to natural reef settings, and the greater responsiveness of A. millepora bacterial communities to environmental change...

Suggett, DJ & van Oppen, MJH 2022, 'Horizon scan of rapidly advancing coral restoration approaches for 21st century reef management', Emerging Topics in Life Sciences, vol. 6, no. 1, pp. 125-136.
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Coral reef restoration activity is accelerating worldwide in efforts to offset the rate of reef health declines. Many advances have already been made in restoration practices centred on coral biology (coral restoration), and particularly those that look to employ the high adaptive state and capacity of corals in order to ensure that efforts rebuilding coral biomass also equip reefs with enhanced resilience to future stress. We horizon scan the state-of-play for the many coral restoration innovations already underway across the complex life cycle for corals that spans both asexual and sexual reproduction — assisted evolution (manipulations targeted to the coral host and host-associated microbes), biobanking, as well as scalable coral propagation and planting — and how these innovations are in different stages of maturity to support new 21st century reef management frameworks. Realising the potential for coral restoration tools as management aids undoubtedly rests on validating different approaches as their application continues to scale. Whilst the ecosystem service responses to increased scaling still largely remain to be seen, coral restoration has already delivered immense new understanding of coral and coral-associated microbial biology that has long lagged behind advances in other reef sciences.

Suzzi, AL, Stat, M, MacFarlane, GR, Seymour, JR, Williams, NLR, Gaston, TF, Alam, MR & Huggett, MJ 2022, 'Legacy metal contamination is reflected in the fish gut microbiome in an urbanised estuary', Environmental Pollution, vol. 314, pp. 120222-120222.
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Unzueta-Martínez, A, Scanes, E, Parker, LM, Ross, PM, O’Connor, W & Bowen, JL 2022, 'Microbiomes of the Sydney Rock Oyster are acquired through both vertical and horizontal transmission', Animal Microbiome, vol. 4, no. 1.
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AbstractBackgroundThe term holobiont is widely accepted to describe animal hosts and their associated microorganisms. The genomes of all that the holobiont encompasses, are termed the hologenome and it has been proposed as a unit of selection in evolution. To demonstrate that natural selection acts on the hologenome, a significant portion of the associated microbial genomes should be transferred between generations. Using the Sydney Rock Oyster (Saccostrea glomerata) as a model, we tested if the microbes of this broadcast spawning species could be passed down to the next generation by conducting single parent crosses and tracking the microbiome from parent to offspring and throughout early larval stages using 16S rRNA gene amplicon sequencing. From each cross, we sampled adult tissues (mantle, gill, stomach, gonad, eggs or sperm), larvae (D-veliger, umbo, eyed pediveliger, and spat), and the surrounding environment (water and algae feed) for microbial community analysis.ResultsWe found that each larval stage has a distinct microbiome that is partially influenced by their parental microbiome, particularly the maternal egg microbiome. We also demonstrate the presence of core microbes that are consistent across all families, persist throughout early life stages (from eggs to spat), and are not detected in the microbiomes of the surrounding environment. In addition to the core microbiomes that span all life cycle stages, there is also evidence of environmentally acquired microbial communities, with earlier larval stages (D-veliger and umbo), more influenced by seawater microbiomes, and later larval stages (eyed pediveliger and spat) dominated by microbial members that are specific to oysters and not detected in the surrounding environment.Conclusion

Vega Thurber, R, Schmeltzer, ER, Grottoli, AG, van Woesik, R, Toonen, RJ, Warner, M, Dobson, KL, McLachlan, RH, Barott, K, Barshis, DJ, Baumann, J, Chapron, L, Combosch, DJ, Correa, AMS, DeCarlo, TM, Hagedorn, M, Hédouin, L, Hoadley, K, Felis, T, Ferrier-Pagès, C, Kenkel, C, Kuffner, IB, Matthews, J, Medina, M, Meyer, C, Oster, C, Price, J, Putnam, HM & Sawall, Y 2022, 'Unified methods in collecting, preserving, and archiving coral bleaching and restoration specimens to increase sample utility and interdisciplinary collaboration', PeerJ, vol. 10, pp. e14176-e14176.
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Coral reefs are declining worldwide primarily because of bleaching and subsequent mortality resulting from thermal stress. Currently, extensive efforts to engage in more holistic research and restoration endeavors have considerably expanded the techniques applied to examine coral samples. Despite such advances, coral bleaching and restoration studies are often conducted within a specific disciplinary focus, where specimens are collected, preserved, and archived in ways that are not always conducive to further downstream analyses by specialists in other disciplines. This approach may prevent the full utilization of unexpended specimens, leading to siloed research, duplicative efforts, unnecessary loss of additional corals to research endeavors, and overall increased costs. A recent US National Science Foundation-sponsored workshop set out to consolidate our collective knowledge across the disciplines of Omics, Physiology, and Microscopy and Imaging regarding the methods used for coral sample collection, preservation, and archiving. Here, we highlight knowledge gaps and propose some simple steps for collecting, preserving, and archiving coral-bleaching specimens that can increase the impact of individual coral bleaching and restoration studies, as well as foster additional analyses and future discoveries through collaboration. Rapid freezing of samples in liquid nitrogen or placing at −80 °C to −20 °C is optimal for most Omics and Physiology studies with a few exceptions; however, freezing samples removes the potential for many Microscopy and Imaging-based analyses due to the alteration of tissue integrity during freezing. For Microscopy and Imaging, samples are best stored in aldehydes. The use of sterile gloves and receptacles during collection supports the downstream analysis of host-associated bacterial and viral communities which are particularly germane to disease and restoration efforts. Across all disciplines, the use of aseptic techniques...

Vo, HNP, Nguyen, TMH, Ngo, HH, Guo, W & Shukla, P 2022, 'Biochar sorption of perfluoroalkyl substances (PFASs) in aqueous film-forming foams-impacted groundwater: Effects of PFASs properties and groundwater chemistry', Chemosphere, vol. 286, no. Pt 1, pp. 131622-131622.
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The widespread use of per- and polyfluoroalkyl substances (PFASs)-related products such as aqueous film-forming foams (AFFF) has led to increasing contamination of groundwater systems. The concentration of PFASs in AFFF-impacted groundwater can be several orders of magnitude higher than the drinking water standard. There is a need for a sustainable and effective sorbent to remove PFASs from groundwater. This work aims to investigate the sorption of PFASs in groundwater by biochar column. The specific objectives are to understand the influences of PFASs properties and groundwater chemistry to PFASs sorption by biochar. The PFASs-spiked Milli-Q water (including 19 PFASs) and four aqueous film-forming foams (AFFF)-impacted groundwater were used. The partitioning coefficients (log Kd) of long chain PFASs ranged from 0.77 to 4.63 while for short chain PFASs they remained below 0.68. For long chain PFASs (C ≥ 7), log Kd increased by 0.5 and 0.8 for each CF2 moiety of PFCAs and PFSAs, respectively. Dissolved organic matter (DOM) was the most influential factor in PFASs sorption over pH, salinity, and specific ultraviolet absorbance (SUVA). DOM contained hydrophobic compounds and metal ions which can form DOM-PFASs complexes to provide more sorption sites for PFASs. The finding is useful for executing PFASs remediation by biochar filtration column, especially legacy long chain PFASs, for groundwater remediation.

Wangpraseurt, D, Sun, Y, You, S, Chua, S, Noel, SK, Willard, HF, Berry, DB, Clifford, AM, Plummer, S, Xiang, Y, Hwang, HH, Kaandorp, J, Diaz, JM, La Jeunesse, TC, Pernice, M, Vignolini, S, Tresguerres, M & Chen, S 2022, 'Bioprinted Living Coral Microenvironments Mimicking Coral‐Algal Symbiosis', Advanced Functional Materials, vol. 32, no. 35, pp. 1-11.
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AbstractThe coral‐algal symbiosis is the biological engine that drives one of the most spectacular structures on Earth: the coral reef. Here, living coral microhabitats are engineered using 3D bioprinting, as biomimetic model system of the coral‐algal symbiosis. Various bioinks for the encapsulation of coral photosymbiotic microalgae (Breviolum psygmophilum) are developed and coral mass transfer phenomena are mimicked by 3D bioprinting coral tissue and skeleton microscale features. At the tissue–seawater interface, the biomimetic coral polyp and connective tissue structures successfully replicate the natural build‐up of the O2 diffusive boundary layer. Inside the bioprinted construct, coral‐like microscale gastric cavities are engineered using a multi‐material bioprinting process. Underneath the tissue, the constructs mimic the porous architecture of the coral aragonite skeleton at the micrometer scale, which can be manipulated to assess the effects of skeletal architecture on stress‐related hydrogen peroxide (H2O2) production. The bioprinted living coral microhabitats replicate the diffusion‐related phenomena that underlie the functioning and breakdown of the coral‐algal symbiosis and can be exploited for the additive manufacturing of synthetic designer corals.

Watanabe, S, Iwai, T, Matsushita, R, Nakanishi, T, Kuzhiumparambil, U, Fu, S & Seto, Y 2022, 'Comparison between human liver microsomes and the fungus Cunninghamella elegans for biotransformation of the synthetic cannabinoid JWH-424 having a bromo-naphthyl moiety analysed by high-resolution mass spectrometry', Forensic Toxicology, vol. 40, no. 2, pp. 278-288.
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Williams, NLR, Siboni, N, King, WL, Balaraju, V, Bramucci, A & Seymour, JR 2022, 'Latitudinal Dynamics of Vibrio along the Eastern Coastline of Australia', Water, vol. 14, no. 16, pp. 2510-2510.
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The marine genus of bacteria, Vibrio, includes several significant human and animal pathogens, highlighting the importance of defining the factors that govern their occurrence in the environment. To determine what controls large-scale spatial patterns among this genus, we examined the abundance and diversity of Vibrio communities along a 4000 km latitudinal gradient spanning the Australian coast. We used a Vibrio-specific amplicon sequencing assay to define Vibrio community diversity, as well as quantitative PCR and digital droplet PCR to identify patterns in the abundances of the human pathogens V. cholera, V. parahaemolyticus and V. vulnificus. The hsp60 amplicon sequencing analysis revealed significant differences in the composition of tropical and temperate Vibrio communities. Over 50% of Vibrio species detected, including the human pathogens V. parahaemolyticus and V. vulnificus, displayed significant correlations with either temperature, salinity, or both, as well as different species of phytoplankton. High levels of V. parahaemolyticus and V. vulnificus were detected in the tropical site at Darwin and the subtropical Gold Coast site, along with high levels of V. parahaemolyticus at the subtropical Sydney site. This study has revealed the key ecological determinants and latitudinal patterns in the abundance and diversity of coastal Vibrio communities, including insights into the distribution of human pathogens, within a region experiencing significant ecological shifts due to climate change.

Williams, NLR, Siboni, N, McLellan, SL, Potts, J, Scanes, P, Johnson, C, James, M, McCann, V & Seymour, JR 2022, 'Rainfall leads to elevated levels of antibiotic resistance genes within seawater at an Australian beach', Environmental Pollution, vol. 307, pp. 119456-119456.
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Anthropogenic waste streams can be major sources of antibiotic resistant microbes within the environment, creating a potential risk to public health. We examined patterns in the occurrence of a suite of antibiotic resistance genes (ARGs) and their links to enteric bacteria at a popular swimming beach in Australia that experiences intermittent contamination by sewage, with potential points of input including stormwater drains and a coastal lagoon. Samples were collected throughout a significant rainfall event (40.8 mm over 3 days) and analysed using both qPCR and 16S rRNA amplicon sequencing. Before the rainfall event, low levels of faecal indicator bacteria and a microbial source tracking human faeces (sewage) marker (Lachno3) were observed. These levels increased over 10x following rainfall. Within lagoon, drain and seawater samples, levels of the ARGs sulI, dfrA1 and qnrS increased by between 1 and 2 orders of magnitude after 20.4 mm of rain, while levels of tetA increased by an order of magnitude after a total of 40.8 mm. After 40.8 mm of rain sulI, tetA and qnrS could be detected 300 m offshore with levels remaining high five days after the rain event. Highest levels of sewage markers and ARGs were observed adjacent to the lagoon (when opened) and in-front of the stormwater drains, pinpointing these as the points of ARG input. Significant positive correlations were observed between all ARGs, and a suite of Amplicon Sequence Variants that were identified as stormwater drain indicator taxa using 16S rRNA amplicon sequencing data. Of note, some stormwater drain indicator taxa, which exhibited correlations to ARG abundance, included the human pathogens Arcobacter butzleri and Bacteroides fragilis. Given that previous research has linked high levels of ARGs in recreationally used environments to antimicrobial resistant pathogen infections, the observed patterns indicate a potentially elevated human health risk at a popular swimming beach following signif...

Williams, NLR, Siboni, N, Potts, J, Campey, M, Johnson, C, Rao, S, Bramucci, A, Scanes, P & Seymour, JR 2022, 'Molecular microbiological approaches reduce ambiguity about the sources of faecal pollution and identify microbial hazards within an urbanised coastal environment', Water Research, vol. 218, pp. 118534-118534.
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Urbanised beaches are regularly impacted by faecal pollution, but management actions to resolve the causes of contamination are often obfuscated by the inability of standard Faecal Indicator Bacteria (FIB) analyses to discriminate sources of faecal material or detect other microbial hazards, including antibiotic resistance genes (ARGs). We aimed to determine the causes, spatial extent, and point sources of faecal contamination within Rose Bay, a highly urbanised beach within Sydney, Australia's largest city, using molecular microbiological approaches. Sampling was performed across a network of transects originating at 9 stormwater drains located on Rose Bay beach over the course of a significant (67.5 mm) rainfall event, whereby samples were taken 6 days prior to any rain, on the day of initial rainfall (3.8 mm), three days later after 43 mm of rain and then four days after any rain. Quantitative PCR (qPCR) was used to target marker genes from bacteria (i.e., Lachnospiraceae and Bacteroides) that have been demonstrated to be specific to human faeces (sewage), along with gene sequences from Heliobacter and Bacteriodes that are specific to bird and dog faeces respectively, and ARGs (sulI, tetA, qnrS, dfrA1 and vanB). 16S rRNA gene amplicon sequencing was also used to discriminate microbial signatures of faecal contamination. Prior to the rain event, low FIB levels (mean: 2.4 CFU/100 ml) were accompanied by generally low levels of the human and animal faecal markers, with the exception of one transect, potentially indicative of a dry weather sewage leak. Following 43 mm of rain, levels of both human faecal markers increased significantly in stormwater drain and seawater samples, with highest levels of these markers pinpointing several stormwater drains as sources of sewage contamination. During this time, sewage contamination was observed up to 1000 m from shore and was significantly and positively correlated with often highly elevated levels of the ARGs d...

Windhagauer, M, Abbriano, RM, Pittrich, DA & Doblin, MA 2022, 'Phosphate-inducible poly-hydroxy butyrate production dynamics in CO2 supplemented upscaled cultivation of engineered Phaeodactylum tricornutum', Journal of Applied Phycology, vol. 34, no. 5, pp. 2259-2270.
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AbstractDiatoms such as Phaeodactylum tricornutum are emerging as sustainable alternatives to traditional eukaryotic microbial cell factories. In order to facilitate a viable process for production of heterologous metabolites, a rational genetic design specifically tailored to metabolic requirements as well as optimised culture conditions are required. In this study we investigated the effect of constitutive and inducible expression of the heterologous poly-3-hydroxybutyrate (PHB) pathway in P. tricornutum using non-integrative episomes in 3 different configurations. Constitutive expression led to downregulation of at least one individual gene out of three (phaA, phaB and phaC) and was outperformed by inducible expression. To further asses and optimise the dynamics of PHB accumulation driven by the inducible alkaline phosphatase 1 promoter, we upscaled the production to lab-scale bioreactors and tested the effect of supplemented CO2 on biomass and PHB accumulation. While ambient CO2 cultivation resulted in a maximum PHB yield of 2.3% cell dry weight (CDW) on day 11, under elevated CO2 concentrations PHB yield peaked at 1.7% CDW on day 8, coincident with PHB titres at 27.9 mg L−1 that were approximately threefold higher than ambient CO2. With other more valuable bio-products in mind, these results highlight the importance of the genetic design as well as substrate availability to supply additional reduction equivalents to boost biomass accumulation and relieve potential enzymatic bottlenecks for improved product accumulation.

Worden, PJ, Bogema, DR, Micallef, ML, Go, J, Deutscher, AT, Labbate, M, Green, TJ, King, WL, Liu, M, Seymour, JR & Jenkins, C 2022, 'Phylogenomic diversity of Vibrio species and other Gammaproteobacteria isolated from Pacific oysters (Crassostrea gigas) during a summer mortality outbreak', Microbial Genomics, vol. 8, no. 12.
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The Pacific oyster (PO), Crassostrea gigas, is an important commercial marine species but periodically experiences large stock losses due to disease events known as summer mortality. Summer mortality has been linked to environmental perturbations and numerous viral and bacterial agents, indicating this disease is multifactorial in nature. In 2013 and 2014, several summer mortality events occurred within the Port Stephens estuary (NSW, Australia). Extensive culture and molecular-based investigations were undertaken and several potentially pathogenic Vibrio species were identified. To improve species identification and genomically characterise isolates obtained from this outbreak, whole-genome sequencing (WGS) and subsequent genomic analyses were performed on 48 bacterial isolates, as well as a further nine isolates from other summer mortality studies using the same batch of juveniles. Average nucleotide identity (ANI) identified most isolates to the species level and included members of the Photobacterium , Pseudoalteromonas<...

Wright, AS, Doblin, MA & Scanes, PR 2022, 'Improper Maintenance Activities Alter Benefits of Urban Stormwater Treatment in a Temperate Constructed Wetland in NSW, Australia', Frontiers in Environmental Chemistry, vol. 3, pp. 1-14.
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Constructed wetlands (CWs) are an effective means to treat nutrient and sediment pollution in urban stormwater runoff to minimise impact on receiving waterways. Maintenance of devices is recognised as a major contributing factor to performance. There is a lack of evidence-based guidance on maintenance activities to optimise treatment, due to a paucity of data from long-term field studies into CW performance before and after maintenance. In this study, the nutrient and sediment removal efficiency (% RE) of a CW was evaluated by calculating removal efficiencies of nitrogen (N), phosphorus (P) and total suspended sediment (TSS) following a long-term sampling program under baseflow and event flow conditions. Sampling was carried out before, during and after maintenance. Maintenance involved removing all aquatic vegetation and 200–300 mm of sediments over a 3-week period, aiming to improve the wetland’s performance. Assessment of dissolved and particulate nutrient fractions allowed a comprehensive investigation into drivers of nutrient removal efficiency. Under baseflow conditions differences in inflow and outflow pollutant concentrations were used to calculate removal efficiency and pollutant loads were used during event flow conditions. Before maintenance, during baseflow conditions the wetland was removing total N (36% RE) but exporting total P (-52% RE) and total sediment (-94% RE). During event-flow conditions all target pollutants were being removed (total N 63% RE, total P 25% RE and TSS 69% RE). phosphorusDuring maintenance, the device continued to remove total N (18% RE) but the physical disturbance of the maintenance resulted in mass export of total P (-120% RE) and total sediment (−2,000% RE) over a short time period, effectively undoing previous treatment. After maintenance, during baseflow conditions, the wetlands’ ability to treat total N decreased (28% RE), improved for total P (1% RE), and became a chronic source of suspended sediment...

Wuerz, M, Lawson, CA, Ueland, M, Oakley, CA, Grossman, AR, Weis, VM, Suggett, DJ & Davy, SK 2022, 'Symbiosis induces unique volatile profiles in the model cnidarian Aiptasia', Journal of Experimental Biology, vol. 225, no. 19, p. jeb244600.
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ABSTRACT The establishment and maintenance of the symbiosis between a cnidarian host and its dinoflagellate symbionts is central to the success of coral reefs. To explore the metabolite production underlying this symbiosis, we focused on a group of low molecular weight secondary metabolites, biogenic volatile organic compounds (BVOCs). BVOCs are released from an organism or environment, and can be collected in the gas phase, allowing non-invasive analysis of an organism's metabolism (i.e. ‘volatilomics’). We characterised volatile profiles of the sea anemone Aiptasia (Exaiptasia diaphana), a model system for cnidarian–dinoflagellate symbiosis, using comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry. We compared volatile profiles between: (1) symbiotic anemones containing their native symbiont, Breviolum minutum; (2) aposymbiotic anemones; and (3) cultured isolates of B. minutum. Overall, 152 BVOCs were detected, and classified into 14 groups based on their chemical structure, the most numerous groups being alkanes and aromatic compounds. A total of 53 BVOCs were differentially abundant between aposymbiotic anemones and B. minutum cultures; 13 between aposymbiotic and symbiotic anemones; and 60 between symbiotic anemones and cultures of B. minutum. More BVOCs were differentially abundant between cultured and symbiotic dinoflagellates than between aposymbiotic and symbiotic anemones, suggesting that symbiosis may modify symbiont physiology more than host physiology. This is the first volatilome analysis of the Aiptasia model system and provides a foundation from which to explore how BVOC production is perturbed under environmental stress, and ultimately the role they play in this important symbiosis.

Zhou, T, Li, X, Zhang, Q, Dong, S, Liu, H, Liu, Y, Chaves, AV, Ralph, PJ, Ruan, R & Wang, Q 2022, 'Ecotoxicological response of Spirulina platensis to coexisted copper and zinc in anaerobic digestion effluent', Science of The Total Environment, vol. 837, pp. 155874-155874.
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Copper ion (Cu2+) and zinc ion (Zn2+) are widely co-existent in anaerobic digestion effluent as typical contaminants. This work aims to explore how Cu2+-Zn2+ association affects physiological properties of S. platensis using Schlösser medium (SM) and sterilized anaerobic digestion effluent (SADE). Microalgae cells viability, biochemical properties, uptake of Cu2+ and Zn2+, and risk assessment associated with the biomass reuse as additives to pigs were comprehensively assessed. Biomass production ranged from 0.03 to 0.28 g/L in SM and 0.63 to 0.79 g/L in SADE due to the presence of Cu2+ and Zn2+. Peak value of chlorophyll-a and carotenoid content during the experiment decreased by 70-100% and 40-100% in SM, and by 70-77% and 30-55% in SADE. Crude protein level reduced by 4-41% in SM and by 65-75% in SADE. The reduction ratio of these compounds was positively related to the Cu2+ and Zn2+ concentrations. Maximum value of saturated and unsaturated fatty acids was both obtained at 0.3 Cu + 2.0 Zn (50.8% and 22.8%, respectively) and 25% SADE reactors (33.8% and 27.7%, respectively). Uptake of Cu in biomass was facilitated by Zn2+ concentration (> 4.0 mg/L). Risk of S. platensis biomass associated with Cu2+ was higher than Zn2+. S. platensis from SM (Cu2+ ≤ 0.3 mg/L and Zn2+ ≤ 4.0 mg/L) and diluted SADE (25% and 50% SADE) reactors could be used as feed additives without any risk (hazard index <1), which provides sufficient protein and fatty acids for pig consumption. These results revealed the promising application of using S. platensis for bioremediation of Cu2+ and Zn2+ in anaerobic digestion effluent and harvesting biomass for animal feed additives.

Berry, F, Retamal, M, Kuzhiumparambil, U & Ralph, P University of Technology Sydney 2022, Market and sustainability potential for algal bioplastics in Australia, Sydney NSW.
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This paper has been developed by the Institute for Sustainable Futures and the Climate Change Cluster (C3) at the University of Technology Sydney. UTS's Climate Change Cluster (C3) are developing flexible bioplastics from algae which have a range of potential applications, in particular to replace petroleum-based plastics and potentially offer a more sustainable alternative. This report aims to provide: • a brief primer on the potential market for algal bioplastics • identification of key hotspots for sustainability considerations in product design • a discussion of the current policy context and how this will influence bioplastic development, and • recommendations for product developers. This paper has been written for investors, government, researchers and the general public, to provide information on the sustainability opportunities and constraints of algal bioplastics in a circular economy.

Trestrail, C, Tondl, E, Fischer, A, Potts, J, Scanes, P, Seymour, J & Doblin, M University of Technology Sydney 2022, Research needs for the assessment and monitoring of nutrients, chemicals & antimicrobials in the marine environment: scoping study., no. Report 1.16, Sydney.

Charon, J, Kahlke, T, Larsson, ME, Abbriano, R, Commault, A, Burke, J, Ralph, P & Holmes, EC 2022, 'Diverse RNA viruses associated with diatom, eustigmatophyte, dinoflagellate and rhodophyte microalgae cultures', Cold Spring Harbor Laboratory.
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Cui, G, Konciute, MK, Ling, L, Esau, L, Raina, J-B, Han, B, Salazar, OR, Presnell, JS, Rädecker, N, Zhong, H, Menzies, J, Cleves, PA, Liew, YJ, Krediet, CJ, Sawiccy, V, Cziesielski, MJ, Guagliardo, P, Bougoure, J, Pernice, M, Hirt, H, Voolstra, CR, Weis, VM, Pringle, JR & Aranda, M 2022, 'Molecular insights into the Darwin paradox of coral reefs from the sea anemone Aiptasia', Cold Spring Harbor Laboratory.
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Doane, MP, Ostrowski, M, Brown, M, Bramucci, A, Bodrossy, L, van de Kamp, J, Bissett, A, Steinberg, P, Doblin, MA & Seymour, J 2022, 'Defining marine bacterioplankton community assembly rules by contrasting the importance of environmental determinants and biotic interactions', Cold Spring Harbor Laboratory.
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Dougan, KE, Bellantuono, AJ, Kahlke, T, Abbriano, RM, Chen, Y, Shah, S, Granados-Cifuentes, C, van Oppen, MJH, Bhattacharya, D, Suggett, DJ, Rodriguez-Lanetty, M & Chan, CX 2022, 'Whole-genome duplication in an algal symbiont bolsters coral heat tolerance', Cold Spring Harbor Laboratory.
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Hinners, J, Argyle, PA, Walworth, NG, Doblin, MA, Levine, NM & Collins, S 2022, 'Multitrait diversification in marine diatoms in constant and warmed environments', Cold Spring Harbor Laboratory.
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Jinni, Y, Unnikrishnan, K, Sushil, B, Russell, D, Nadia, S & Shanlin, F 2022, 'Investigation of metabolic biomarkers: A metabolomics approach', Elsevier BV, pp. S57-S57.
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Johnson, MS, Burns, BP, Herdean, A, Angeloski, A, Ralph, P, Morris, T, Kindler, G, Wong, HL, Kuzhiumparambil, U, Sedger, L & Larkum, AWD 2022, 'A Cyanobacteria Enriched Layer of Shark Bay Stromatolites Reveals a New <em>Acaryochloris</em> strain Living in near Infrared Light', MDPI AG.
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Krishnan, S, DeMaere, MZ, Beck, D, Ostrowski, M, Seymour, JR & Darling, AE 2022, 'Rhometa: Population recombination rate estimation from metagenomic read datasets', Cold Spring Harbor Laboratory.
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Nielsen, JJV, Matthews, G, Frith, KR, Harrison, HB, Marzonie, Slaughter, KL, Suggett, DJ & Bay, LK 2022, 'Experimental considerations of acute heat stress assays to quantify coral thermal tolerance', Research Square Platform LLC.
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Seymour, JR 2022, 'Forecasting ocean microbiome shifts', Springer Science and Business Media LLC, pp. 747-748.
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Shibl, AA, Ochsenkühn, MA, Mohamed, AR, Isaac, A, Coe, LSY, Yun, Y, Skrzypek, G, Raina, J-B, Seymour, JR, Afzal, AJ & Amin, SA 2022, 'Molecular mechanisms of microbiome modulation by the eukaryotic secondary metabolite azelaic acid', Cold Spring Harbor Laboratory.
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Voelker, WG, Krishnan, K, Chougule, K, Alexander, LC, Lu, Z, Olson, A, Ware, D, Songsomboon, K, Ponce, C, Brenton, ZW, Boatwright, JL & Cooper, EA 2022, 'Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes', Cold Spring Harbor Laboratory.
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Walworth, NG, Espinoza, JL, Argyle, PA, Hinners, J, Levine, NM, Doblin, MA, Dupont, CL & Collins, S 2022, 'Rapid reductions in population size drive evolutionary divergence in diatoms', Cold Spring Harbor Laboratory.
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