Publications

Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2021, 'Biomass Processing via Acid Catalysis', Wiley, pp. 23-55.
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Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2021, 'Biomass Processing via Acid Catalysis' in Biomass Valorization Sustainable Methods for the Production of Chemicals, pp. 25-55.
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This chapter aims to define efficient methods for the acid-catalyzed conversion of biomass into targeted value-added products. Acid catalysts can be classified as Lewis acids or Brønsted acids and may be further classified as heterogeneous or homogeneous. Polysaccharides, such as glucans and xylans, can be depolymerized into monomer sugars in the presence of Brønsted acid catalysts; such monosaccharides have many applications from organic synthesis to energy sources for fermentation. ionic liquids are a class of green solvents that consist solely of ions and, under certain conditions, are able to fully dissolve cellulosic polysaccharides. The chapter discusses the chemistry accompanying catalytic transformations of carbohydrates and lignin into specific products, defining the overall role of the acidic catalyst, solvent, and processing parameters. In numerous bench-scale processes, acid catalysis has been shown to be a universal tool to source value-added products from reactions of low value or waste cellulosic materials.

Aamer Mehmood, M, Shahid, A, Malik, S, Wang, N, Rizwan Javed, M, Nabeel Haider, M, Verma, P, Umer Farooq Ashraf, M, Habib, N, Syafiuddin, A & Boopathy, R 2021, 'Advances in developing metabolically engineered microbial platforms to produce fourth-generation biofuels and high-value biochemicals', Bioresource Technology, vol. 337, pp. 125510-125510.
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Producing bio-based chemicals is imperative to establish an eco-friendly circular bioeconomy. However, the compromised titer of these biochemicals hampers their commercial implementation. Advances in genetic engineering tools have enabled researchers to develop robust strains producing desired titers of the next-generation biofuels and biochemicals. The native and non-native pathways have been extensively engineered in various host strains via pathway reconstruction and metabolic flux redirection of lipid metabolism and central carbon metabolism to produce myriad biomolecules including alcohols, isoprenoids, hydrocarbons, fatty-acids, and their derivatives. This review has briefly covered the research efforts made during the previous decade to produce advanced biofuels and biochemicals through engineered microbial platforms along with the engineering approaches employed. The efficiency of the various techniques along with their shortcomings is also covered to provide a comprehensive overview of the progress and future directions to achieve higher titer of fourth-generation biofuels and biochemicals while keeping environmental sustainability intact.

Ajani, PA, Petrou, K, Larsson, ME, Nielsen, DA, Burke, J & Murray, SA 2021, 'Phenotypic trait variability as an indication of adaptive capacity in a cosmopolitan marine diatom', Environmental Microbiology, vol. 23, no. 1, pp. 207-223.
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SummaryDetermining the adaptive capacity of marine phytoplankton is important in predicting changes in phytoplankton responses to ocean warming. Phytoplankton may consist of high levels of standing phenotypic and genetic variability, the basis of rapid evolution; however, few studies have quantified trait variability within and amongst closely related diatom species. Using 35 clonal cultures of the ubiquitous marine diatom Leptocylindrus isolated from six locations, spanning 2000 km of the south‐eastern Australian coastline, we found evidence of significant intraspecific morphological and metabolic trait variability, which for 8 of 9 traits (growth rate, biovolume, C:N, silica deposition, silica incorporation rate, chl‐a, and photosynthetic efficiency under dark adapted, growth irradiance, and high‐light adaptation) were greater within a species than between species. Moreover, only two traits revealed a latitudinal trend with strains isolated from lower latitudes showing significantly higher silicification rates and protein:lipid content compared to their higher latitude counterparts. These data mirror recent studies on diatom intraspecific genetic diversity, which has found comparable levels of genetic diversity at a single site to those thousands of kilometres apart, and provide evidence of a functional role of diatom diversity that will allow for rapid adaptation via ecological selection on standing variation in response to changing conditions.

Alderdice, R, Suggett, DJ, Cárdenas, A, Hughes, DJ, Kühl, M, Pernice, M & Voolstra, CR 2021, 'Divergent expression of hypoxia response systems under deoxygenation in reef‐forming corals aligns with bleaching susceptibility', Global Change Biology, vol. 27, no. 2, pp. 312-326.
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AbstractExposure of marine life to low oxygen is accelerating worldwide via climate change and localized pollution. Mass coral bleaching and mortality have recently occurred where reefs have experienced chronic low oxygen events. However, the mechanistic basis of tolerance to oxygen levels inadequate to sustain normal functioning (i.e. hypoxia) and whether it contributes to bleaching susceptibility, remain unknown. We therefore experimentally exposed colonies of the environmentally resilient Acropora tenuis, a common reef‐building coral from the Great Barrier Reef, to deoxygenation–reoxygenation stress that was aligned to their natural night–day light cycle. Specifically, the treatment involved removing the ‘night‐time O2 buffer’ to challenge the inherent hypoxia thresholds. RNA‐Seq analysis revealed that coral possess a complete and active hypoxia‐inducible factor (HIF)‐mediated hypoxia response system (HRS) homologous to other metazoans. As expected, A. tenuis exhibited bleaching resistance and showed a strong inducibility of HIF target genes in response to deoxygenation stress. We applied this same approach in parallel to a colony of Acropora selago, known to be environmnetally susceptible, which conversely exhibited a bleaching phenotype response. This phenotypic divergence of A. selago was accompanied by contrasting gene expression profiles indicative of varied effectiveness of their HIF‐HRS. Based on our RNA‐Seq analysis, we propose (a) that the HIF‐HRS is central for corals to manage deoxygenation stress and (b) that key genes of this system (and the wider gene network) may contribute to variation in coral bleaching susceptibility. Our analysis suggests that heat shock protein (hsp) 70 and 90 are important for low oxygen stress tolerance and further highlights how hsp90 expression might ...

Alshamrani, R, Arshad, MH, Gull, M, Nawaz, MZ & Malik, S 2021, 'Identification of non-coding RNAs in the hyper thermophilic bacteriumThermotoga maritima MSB8 through comparative genomics and in-silicoanalyses', Asian Journal of Agriculture and Biology, vol. 2022, no. Online First, pp. 1-9.
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Thermotoga maritima is a hyperthermophile with the potential to produce thermostable commercial enzymes which can be used for saccharification of plant biomass for subsequent fermentation to bioproducts. The molecular mechanism involved in the hyper thermostability in this bacterium is still not well-understood. It is known that small noncoding RNAs (ncRNAs) regulate and modulate the gene expression of various biological processes at transcriptional and post-transcriptional levels, hence coordinate the adaptation processes in response to environmental stimuli in both prokaryotes and eukaryotes. To understand the role of small ncRNAs in the hyper thermostability of T. maritima, an in silico-based approach was employed involving the identification of the ncRNAs in this bacterium on a genome-wide scale. A novel pipeline was constructed which involved a combination of various bioinformatics algorithms. In total, 20804 orthologous groups were predicted on the genome of T. maritima and 20 other bacteria (reference genomes) by the OrthoMCL tool. By using the “Perl” and “Bash” languages 258 orthologous IGR datasets were created. Among these datasets, small ncRNAs were identified by employing RNAz and RNA Infernal tools. Total 28 ncRNA candidates were predicted by the RNAz tool and 9 candidates were confirmed as novel cis-regulatory small ncRNAs in T. maritima MSB8 by Infernal tool and were named as Tmn (T. maritima ncRNAs). This work provides novel insights into the role of ncRNAs in the stress adaptability of MSB8 and can give a much better understanding of the lifestyle of this bacterium after validation of the data through wet-lab approaches. Having a clear understanding of the thermo-tolerance mechanism, the MSB8 can be exploited in the future for the commercial production of thermostable compounds and biohydrogen.

Argyle, PA, Walworth, NG, Hinners, J, Collins, S, Levine, NM & Doblin, MA 2021, 'Multivariate trait analysis reveals diatom plasticity constrained to a reduced set of biological axes', ISME Communications, vol. 1, no. 1, p. 59.
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Abstract Trait-based approaches to phytoplankton ecology have gained traction in recent decades as phenotypic traits are incorporated into ecological and biogeochemical models. Here, we use high-throughput phenotyping to explore both intra- and interspecific constraints on trait combinations that are expressed in the cosmopolitan marine diatom genus Thalassiosira. We demonstrate that within Thalassiosira, phenotypic diversity cannot be predicted from genotypic diversity, and moreover, plasticity can create highly divergent phenotypes that are incongruent with taxonomic grouping. Significantly, multivariate phenotypes can be represented in reduced dimensional space using principal component analysis with 77.7% of the variance captured by two orthogonal axes, here termed a ‘trait-scape’. Furthermore, this trait-scape can be recovered with a reduced set of traits. Plastic responses to the new environments expanded phenotypic trait values and the trait-scape, however, the overall pattern of response to the new environments was similar between strains and many trait correlations remained constant. These findings demonstrate that trait-scapes can be used to reveal common constraints on multi-trait plasticity in phytoplankton with divergent underlying phenotypes. Understanding how to integrate trait correlational constraints and trade-offs into theoretical frameworks like biogeochemical models will be critical to predict how microbial responses to environmental change will impact elemental cycling now and into the future.

Bao, T, Damtie, MM, Wei, W, Phong Vo, HN, Nguyen, KH, Hosseinzadeh, A, Cho, K, Yu, ZM, Jin, J, Wei, XL, Wu, K, Frost, RL & Ni, B-J 2021, 'Simultaneous adsorption and degradation of bisphenol A on magnetic illite clay composite: Eco-friendly preparation, characterizations, and catalytic mechanism', Journal of Cleaner Production, vol. 287, pp. 125068-125068.
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Excess bisphenol A (BPA) is a pollutant of concern in different water sources. In this work, magnetic illite clay-composite material (Fe3O4@illite) was synthesized via the coprecipitation method by loading Fe3O4 nanoparticles (nano-Fe3O4) onto the surfaces of illite clay. Results from different characterizations showed that nano-Fe3O4 was embedded into illite clay nanosheets and existed on the surfaces of illite clay, thereby reducing the degree of agglomeration and improving dispersibility. The catalytic BPA degradation of Fe3O4@illite and nano-Fe3O4 confirmed the superior performance of Fe3O4@illite compared with that of nano-Fe3O4. The optimum operating parameters for degradation were 0.3 mL of H2O2 at pH of 3 in the presence of Fe3O4@illite, which provided a maximum degradation capacity up to 816, 364, 113, and 68 mg/g for epoxy BPA concentration of resin wastewater (266 mg/L), synthetic wastewater (80 mg/L), Hefei City swan lake (25 mg/L), and Hefei University lake wastewater (14.94 mg/L), respectively, in 180 min reaction time. The degradation data conformed to the pseudo-first-order kinetic model. The degradation pathways and mineralization study revealed that the adsorption-Fenton-like reaction was the principal mechanism that demonstrated 100% degradation efficiency of Fe3O4@illite even after nine successive runs. The regeneration and reusability tendency analysis ensured that Fe3O4@illite can be easily separated by using magnets. Therefore, Fe3O4@illite composite with H2O2 Fenton-like technology was a promising method for BPA degradation.

Beltrán, VH, Puill-Stephan, E, Howells, E, Flores-Moya, A, Doblin, M, Núñez-Lara, E, Escamilla, V, López, T & van Oppen, MJH 2021, 'Physiological diversity among sympatric, conspecific endosymbionts of coral (Cladocopium C1acro) from the Great Barrier Reef', Coral Reefs, vol. 40, no. 4, pp. 985-997.
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Birrer, SC, Wemheuer, F, Dafforn, KA, Gribben, PE, Steinberg, PD, Simpson, SL, Potts, J, Scanes, P, Doblin, MA & Johnston, EL 2021, 'Legacy Metal Contaminants and Excess Nutrients in Low Flow Estuarine Embayments Alter Composition and Function of Benthic Bacterial Communities', Frontiers in Microbiology, vol. 12, p. 661177.
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Coastal systems such as estuaries are threatened by multiple anthropogenic stressors worldwide. However, how these stressors and estuarine hydrology shape benthic bacterial communities and their functions remains poorly known. Here, we surveyed sediment bacterial communities in poorly flushed embayments and well flushed channels in Sydney Harbour, Australia, using 16S rRNA gene sequencing. Sediment samples were collected monthly during the Austral summer-autumn 2014 at increasing distance from a large storm drain in each channel and embayment. Bacterial communities differed significantly between sites that varied in proximity to storm drains, with a gradient of change apparent for sites within embayments. We explored this pattern for embayment sites with analysis of RNA-Seq gene expression patterns and found higher expression of multiple genes involved in bacterial stress response far from storm drains, suggesting that bacterial communities close to storm drains may be more tolerant of localised anthropogenic stressors. Several bacterial groups also differed close to and far from storm drains, suggesting their potential utility as bioindicators to monitor contaminants in estuarine sediments. Overall, our study provides useful insights into changes in the composition and functioning of benthic bacterial communities as a result of multiple anthropogenic stressors in differing hydrological conditions.

Bramucci, AR, Focardi, A, Rinke, C, Hugenholtz, P, Tyson, GW, Seymour, JR & Raina, J-B 2021, 'Microvolume DNA extraction methods for microscale amplicon and metagenomic studies', ISME Communications, vol. 1, no. 1, pp. 1-5.
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Abstract Investigating the composition and metabolic capacity of aquatic microbial assemblages usually requires the filtration of multi-litre samples, which are up to 1 million-fold larger than the microenvironments within which microbes are predicted to be spatially organised. To determine if community profiles can be reliably generated from microlitre volumes, we sampled seawater at a coastal and an oceanic site, filtered and homogenised them, and extracted DNA from bulk samples (2 L) and microvolumes (100, 10 and 1 μL) using two new approaches. These microvolume DNA extraction methods involve either physical or chemical lysis (through pH/thermal shock and lytic enzymes/surfactants, respectively), directly followed by the capture of DNA on magnetic beads. Downstream analysis of extracted DNA using both amplicon sequencing and metagenomics, revealed strong correlation with standard large volume approaches, demonstrating the fidelity of taxonomic and functional profiles of microbial communities in as little as 1 μL of seawater. This volume is six orders of magnitude smaller than most standard operating procedures for marine metagenomics, which will allow precise sampling of the heterogenous landscape that microbes inhabit.

Brunet, M, de Bettignies, F, Le Duff, N, Tanguy, G, Davoult, D, Leblanc, C, Gobet, A & Thomas, F 2021, 'Accumulation of detached kelp biomass in a subtidal temperate coastal ecosystem induces succession of epiphytic and sediment bacterial communities', Environmental Microbiology, vol. 23, no. 3, pp. 1638-1655.
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SummaryKelps are dominant primary producers in temperate coastal ecosystems. Large amounts of kelp biomass can be exported to the seafloor during the algal growth cycle or following storms, creating new ecological niches for the associated microbiota. Here, we investigated the bacterial community associated with the kelp Laminaria hyperborea during its accumulation and degradation on the seafloor. Kelp tissue, seawater and sediment were sampled during a 6‐month in situ experiment simulating kelp detritus accumulation. Evaluation of the epiphytic bacterial community abundance, structure, taxonomic composition and predicted functional profiles evidenced a biphasic succession. Initially, dominant genera (Hellea, Litorimonas, Granulosicoccus) showed a rapid and drastic decrease in sequence abundance, probably outcompeted by algal polysaccharide‐degraders such as Bacteroidia members which responded within 4 weeks. Acidimicrobiia, especially members of the Sva0996 marine group, colonized the degrading kelp biomass after 11 weeks. These secondary colonizers could act as opportunistic scavenger bacteria assimilating substrates exposed by early degraders. In parallel, kelp accumulation modified bacterial communities in the underlying sediment, notably favouring anaerobic taxa potentially involved in the sulfur and nitrogen cycles. Overall, this study provides insights into the bacterial degradation of algal biomass in situ, an important link in coastal trophic chains.

Brunet, M, Le Duff, N, Fuchs, BM, Amann, R, Barbeyron, T & Thomas, F 2021, 'Specific detection and quantification of the marine flavobacterial genus Zobellia on macroalgae using novel qPCR and CARD-FISH assays', Systematic and Applied Microbiology, vol. 44, no. 6, pp. 126269-126269.
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The flavobacterial genus Zobellia is considered as a model to study macroalgal polysaccharide degradation. The lack of data regarding its prevalence and abundance in coastal habitats constitutes a bottleneck to assess its ecological strategies. To overcome this issue, real-time quantitative PCR (qPCR) and fluorescence in situ hybridization (FISH) methods targeting the 16S rRNA gene were optimized to specifically detect and quantify Zobellia on the surface of diverse macroalgae. The newly designed qPCR primers and FISH probes targeted 98 and 100% of the Zobellia strains in silico and their specificity was confirmed using pure bacterial cultures. The dynamic range of the qPCR assay spanned 8 orders of magnitude from 10 to 108 16S rRNA gene copies and the detection limit was 0.01% relative abundance of Zobellia in environmental samples. Zobellia-16S rRNA gene copies were detected on all surveyed brown, green and red macroalgae, in proportion varying between 0.1 and 0.9% of the total bacterial copies. The absolute and relative abundance of Zobellia varied with tissue aging on the kelp Laminaria digitata. Zobellia cells were successfully visualized in Ulva lactuca and stranded Palmaria palmata surface biofilm using CARD-FISH, representing in the latter 105Zobellia cells·cm-2 and 0.43% of total bacterial cells. Overall, qPCR and CARD-FISH assays enabled robust detection, quantification and localization of Zobellia representatives in complex samples, underlining their ecological relevance as primary biomass degraders potentially cross-feeding other microorganisms.

Celis-Plá, PSM, Rearte, TA, Neori, A, Masojídek, J, Bonomi-Barufi, J, Álvarez-Gómez, F, Ranglová, K, Carmo da Silva, J, Abdala, R, Gómez, C, Caporgno, M, Torzillo, G, Silva Benavides, AM, Ralph, PJ, Fávero Massocato, T, Atzmüller, R, Vega, J, Chávez, P & Figueroa, FL 2021, 'A new approach for cultivating the cyanobacterium Nostoc calcicola (MACC-612) to produce biomass and bioactive compounds using a thin-layer raceway pond', Algal Research, vol. 59, pp. 102421-102421.
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Chow, WS, Larkum, AWD, Pfündel, E, Ritchie, RJ, Scheer, H & Strid, Å 2021, 'A tribute to Robert John Porra (august 7, 1931–may 16, 2019)', Photosynthesis Research, vol. 147, no. 2, pp. 125-130.
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Clifton, J, Osman, EO, Suggett, DJ & Smith, DJ 2021, 'Resolving conservation and development tensions in a small island state: A governance analysis of Curieuse Marine National Park, Seychelles', Marine Policy, vol. 127, pp. 103617-103617.
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© 2019 Elsevier Ltd The management and conservation of marine resources in Seychelles, a small island developing state (SIDS) in the western Indian Ocean, is fundamental to maintaining the flow of international visitors which forms the mainstay of the nation's economy. There is an increasing trend towards empowering non-governmental organisations and parastatal entities with protected area management responsibilities, which partly reflects the chronic underfunding of the state protected area management institution. This paper explores these and related issues through a governance analysis of Curieuse Marine National Park, which is the most popular state-owned marine national park in terms of recorded visitor numbers. This demonstrates that the inability to implement economic incentives through not fully capitalising on the use and non-use values of the park has deleterious consequences for managing the combined impacts of tourism and fisheries on the ecological assets of the park. Furthermore, the capacity of the state management institution is being eroded through a focus on the development of an extensive network of new marine protected areas under the direction of an international non-governmental organisation. Suggestions are made that could strengthen economic, participative and interpretative incentives to provide a more sustainable basis for marine national park management.

Cole, VJ, Parker, LM, Scanes, E, Wright, J, Barnett, L & Ross, PM 2021, 'Climate change alters shellfish reef communities: A temperate mesocosm experiment', Marine Pollution Bulletin, vol. 173, pp. 113113-113113.
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Commault, AS, Kuzhiumparambil, U, Herdean, A, Fabris, M, Jaramillo-Madrid, AC, Abbriano, RM, Ralph, PJ & Pernice, M 2021, 'Methyl Jasmonate and Methyl-β-Cyclodextrin Individually Boost Triterpenoid Biosynthesis in Chlamydomonas Reinhardtii UVM4', Pharmaceuticals, vol. 14, no. 2, pp. 125-125.
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The commercialisation of valuable plant triterpenoids faces major challenges, including low abundance in natural hosts and costly downstream purification procedures. Endeavours to produce these compounds at industrial scale using microbial systems are gaining attention. Here, we report on a strategy to enrich the biomass of the biotechnologically-relevant Chlamydomonas reinhardtii strain UVM4 with valuable triterpenes, such as squalene and (S)-2,3-epoxysqualene. C. reinhardtii UVM4 was subjected to the elicitor compounds methyl jasmonate (MeJA) and methyl-β-cyclodextrine (MβCD) to increase triterpene yields. MeJA treatment triggered oxidative stress, arrested growth, and altered the photosynthetic activity of the cells, while increasing squalene, (S)-2,3-epoxysqualene, and cycloartenol contents. Applying MβCD to cultures of C. reinhardtii lead to the sequestration of the two main sterols (ergosterol and 7-dehydroporiferasterol) into the growth medium and the intracellular accumulation of the intermediate cycloartenol, without compromising cell growth. When MβCD was applied in combination with MeJA, it counteracted the negative effects of MeJA on cell growth and physiology, but no synergistic effect on triterpene yield was observed. Together, our findings provide strategies for the triterpene enrichment of microalgal biomass and medium.

Cziesielski, MJ, Duarte, CM, Aalismail, N, Al-Hafedh, Y, Anton, A, Baalkhuyur, F, Baker, AC, Balke, T, Baums, IB, Berumen, M, Chalastani, VI, Cornwell, B, Daffonchio, D, Diele, K, Farooq, E, Gattuso, J-P, He, S, Lovelock, CE, Mcleod, E, Macreadie, PI, Marba, N, Martin, C, Muniz-Barreto, M, Kadinijappali, KP, Prihartato, P, Rabaoui, L, Saderne, V, Schmidt-Roach, S, Suggett, DJ, Sweet, M, Statton, J, Teicher, S, Trevathan-Tackett, SM, Joydas, TV, Yahya, R & Aranda, M 2021, 'Investing in Blue Natural Capital to Secure a Future for the Red Sea Ecosystems', Frontiers in Marine Science, vol. 7, p. 603722.
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For millennia, coastal and marine ecosystems have adapted and flourished in the Red Sea’s unique environment. Surrounded by deserts on all sides, the Red Sea is subjected to high dust inputs and receives very little freshwater input, and so harbors a high salinity. Coral reefs, seagrass meadows, and mangroves flourish in this environment and provide socio-economic and environmental benefits to the bordering coastlines and countries. Interestingly, while coral reef ecosystems are currently experiencing rapid decline on a global scale, those in the Red Sea appear to be in relatively better shape. That said, they are certainly not immune to the stressors that cause degradation, such as increasing ocean temperature, acidification and pollution. In many regions, ecosystems are already severely deteriorating and are further threatened by increasing population pressure and large coastal development projects. Degradation of these marine habitats will lead to environmental costs, as well as significant economic losses. Therefore, it will result in a missed opportunity for the bordering countries to develop a sustainable blue economy and integrate innovative nature-based solutions. Recognizing that securing the Red Sea ecosystems’ future must occur in synergy with continued social and economic growth, we developed an action plan for the conservation, restoration, and growth of marine environments of the Red Sea. We then investigated the level of resources for financial and economic investment that may incentivize these activities. This study presents a set of commercially viable financial investment strategies, ecological innovations, and sustainable development opportunities, which can, if implemented strategically, help ensure long-term economic benefits while promoting environmental conservation. We make a case for investing in blue natural capital and propose a strategic development model that relies on maintaining the health of natural ecosystems to ...

Falkenberg, LJ, Scanes, E, Ducker, J & Ross, PM 2021, 'Biotic habitats as refugia under ocean acidification', Conservation Physiology, vol. 9, no. 1, p. coab077.
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Abstract Habitat-forming organisms have an important role in ameliorating stressful conditions and may be of particular relevance under a changing climate. Increasing CO2 emissions are driving a range of environmental changes, and one of the key concerns is the rapid acceleration of ocean acidification and associated reduction in pH. Such changes in seawater chemistry are anticipated to have direct negative effects on calcifying organisms, which could, in turn, have negative ecological, economic and human health impacts. However, these calcifying organisms do not exist in isolation, but rather are part of complex ecosystems. Here, we use a qualitative narrative synthesis framework to explore (i) how habitat-forming organisms can act to restrict environmental stress, both now and in the future; (ii) the ways their capacity to do so is modified by local context; and (iii) their potential to buffer the effects of future change through physiological processes and how this can be influenced by management adopted. Specifically, we highlight examples that consider the ability of macroalgae and seagrasses to alter water carbonate chemistry, influence resident organisms under current conditions and their capacity to do so under future conditions, while also recognizing the potential role of other habitats such as adjacent mangroves and saltmarshes. Importantly, we note that the outcome of interactions between these functional groups will be context dependent, influenced by the local abiotic and biotic characteristics. This dependence provides local managers with opportunities to create conditions that enhance the likelihood of successful amelioration. Where individuals and populations are managed effectively, habitat formers could provide local refugia for resident organisms of ecological and economic importance under an acidifying ocean.

Fernandez, E, Ostrowski, M, Siboni, N, Seymour, JR & Petrou, K 2021, 'Uptake of Dimethylsulfoniopropionate (DMSP) by Natural Microbial Communities of the Great Barrier Reef (GBR), Australia', Microorganisms, vol. 9, no. 9, pp. 1891-1891.
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Dimethylsulfoniopropionate (DMSP) is a key organic sulfur compound that is produced by many phytoplankton and macrophytes and is ubiquitous in marine environments. Following its release into the water column, DMSP is primarily metabolised by heterotrophic bacterioplankton, but recent evidence indicates that non-DMSP producing phytoplankton can also assimilate DMSP from the surrounding environment. In this study, we examined the uptake of DMSP by communities of bacteria and phytoplankton within the waters of the Great Barrier Reef (GBR), Australia. We incubated natural GBR seawater with DMSP and quantified the uptake of DMSP by different fractions of the microbial community (>8 µm, 3–8 µm, <3 µm). We also evaluated how microbial community composition and the abundances of DMSP degrading genes are influenced by elevated dissolved DMSP levels. Our results showed uptake and accumulation of DMSP in all size fractions of the microbial community, with the largest fraction (>8 µm) forming the dominant sink, increasing in particulate DMSP by 44–115% upon DMSP enrichment. Longer-term incubations showed however, that DMSP retention was short lived (<24 h) and microbial responses to DMSP enrichment differed depending on the community carbon and sulfur demand. The response of the microbial communities from inside the reef indicated a preference towards cleaving DMSP into the climatically active aerosol dimethyl sulfide (DMS), whereas communities from the outer reef were sulfur and carbon limited, resulting in more DMSP being utilised by the cells. Our results show that DMSP uptake is shared across members of the microbial community, highlighting larger phytoplankton taxa as potentially relevant DMSP reservoirs and provide new information on sulfur cycling as a function of community metabolism in deeper, oligotrophic GBR waters.

Fujise, L, Suggett, DJ, Stat, M, Kahlke, T, Bunce, M, Gardner, SG, Goyen, S, Woodcock, S, Ralph, PJ, Seymour, JR, Siboni, N & Nitschke, MR 2021, 'Unlocking the phylogenetic diversity, primary habitats, and abundances of free‐living Symbiodiniaceae on a coral reef', Molecular Ecology, vol. 30, no. 1, pp. 343-360.
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AbstractDinoflagellates of the family Symbiodiniaceae form mutualistic symbioses with marine invertebrates such as reef‐building corals, but also inhabit reef environments as free‐living cells. Most coral species acquire Symbiodiniaceae horizontally from the surrounding environment during the larval and/or recruitment phase, however the phylogenetic diversity and ecology of free‐living Symbiodiniaceae on coral reefs is largely unknown. We coupled environmental DNA sequencing and genus‐specific qPCR to resolve the community structure and cell abundances of free‐living Symbiodiniaceae in the water column, sediment, and macroalgae and compared these to coral symbionts. Sampling was conducted at two time points, one of which coincided with the annual coral spawning event when recombination between hosts and free‐living Symbiodiniaceae is assumed to be critical. Amplicons of the internal transcribed spacer (ITS2) region were assigned to 12 of the 15 Symbiodiniaceae genera or genera‐equivalent lineages. Community compositions were separated by habitat, with water samples containing a high proportion of sequences corresponding to coral symbionts of the genus Cladocopium, potentially as a result of cell expulsion from in hospite populations. Sediment‐associated Symbiodiniaceae communities were distinct, potentially due to the presence of exclusively free‐living species. Intriguingly, macroalgal surfaces displayed the highest cell abundances of Symbiodiniaceae, suggesting a key role for macroalgae in ensuring the ecological success of corals through maintenance of a continuum between environmental and symbiotic populations of Symbiodiniaceae.

Gao, C, Garren, M, Penn, K, Fernandez, VI, Seymour, JR, Thompson, JR, Raina, J-B & Stocker, R 2021, 'Coral mucus rapidly induces chemokinesis and genome-wide transcriptional shifts toward early pathogenesis in a bacterial coral pathogen', The ISME Journal, vol. 15, no. 12, pp. 3668-3682.
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Abstract Elevated seawater temperatures have contributed to the rise of coral disease mediated by bacterial pathogens, such as the globally distributed Vibrio coralliilyticus, which utilizes coral mucus as a chemical cue to locate stressed corals. However, the physiological events in the pathogens that follow their entry into the coral host environment remain unknown. Here, we present simultaneous measurements of the behavioral and transcriptional responses of V. coralliilyticus BAA-450 incubated in coral mucus. Video microscopy revealed a strong and rapid chemokinetic behavioral response by the pathogen, characterized by a two-fold increase in average swimming speed within 6 min of coral mucus exposure. RNA sequencing showed that this bacterial behavior was accompanied by an equally rapid differential expression of 53% of the genes in the V. coralliilyticus genome. Specifically, transcript abundance 10 min after mucus exposure showed upregulation of genes involved in quorum sensing, biofilm formation, and nutrient metabolism, and downregulation of flagella synthesis and chemotaxis genes. After 60 min, we observed upregulation of genes associated with virulence, including zinc metalloproteases responsible for causing coral tissue damage and algal symbiont photoinactivation, and secretion systems that may export toxins. Together, our results suggest that V. coralliilyticus employs a suite of behavioral and transcriptional responses to rapidly shift into a distinct infection mode within minutes of exposure to the coral microenvironment.

Gibbs, MC, Parker, LM, Scanes, E, Byrne, M, O’Connor, WA & Ross, PM 2021, 'Adult exposure to ocean acidification and warming leads to limited beneficial responses for oyster larvae', ICES Journal of Marine Science, vol. 78, no. 6, pp. 2017-2030.
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AbstractThere is a need to understand the responses of marine molluscs in this era of rapid climate change. Transgenerational plasticity that results in resilient offspring provides a mechanism for rapid acclimation of marine organisms to climate change. This study tested the hypothesis that adult parental exposure to elevated pCO2 and warming will have transgenerational benefits for offspring in the oysters Saccostrea glomerata and Crassostrea gigas. Adult S. glomerata and C. gigas were exposed to orthogonal treatments of ambient and elevated pCO2, and ambient and elevated temperature for 8 weeks. Gametes were collected and fertilized, larvae were then reared for 9 days under ambient and elevated pCO2. Egg lipidome and larval morphology and lipidome were measured. Parental exposure to warming and elevated pCO2 led to limited beneficial transgenerational responses for eggs and larvae of S. glomerata and C. gigas. Overall, larvae of S. glomerata were more sensitive than C. gigas, and both species had some capacity for transgenerational plasticity. This study supports the idea that transgenerational plasticity acts as an acclimatory mechanism for marine organisms to cope with the stress of climate change, but there are limitations, and it may not be a panacea or act equally in different species.

Gibbs, MC, Parker, LM, Scanes, E, Byrne, M, O’Connor, WA & Ross, PM 2021, 'Adult exposure to ocean acidification and warming remains beneficial for oyster larvae following starvation', ICES Journal of Marine Science, vol. 78, no. 5, pp. 1587-1598.
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Abstract Climate change is expected to warm and acidify oceans and alter the phenology of phytoplankton, creating a mismatch between larvae and their food. Transgenerational plasticity (TGP) may allow marine species to acclimate to climate change; however, it is expected that this may come with elevated energetic demands. This study used the oysters, Saccostrea glomerata and Crassostrea gigas, to test the effects of adult parental exposure to elevated pCO2 and temperature on larvae during starvation and recovery. It was anticipated that beneficial effects of TGP will be limited when larvae oyster are starved. Transgenerational responses and lipid reserves of larvae were measured for 2 weeks. Larvae of C. gigas and S. glomerata from parents exposed to elevated pCO2 had greater survival when exposed to elevated CO2, but this differed between species and temperature. For S. glomerata, survival of larvae was greatest when the conditions experienced by larvae matched the condition of their parents. For C. gigas, survival of larvae was greater when parents and larvae were exposed to elevated pCO2. Larvae of both species used lipids when starved. The total lipid content was dependent on parental exposure and temperature. Against expectations, the beneficial TGP responses of larvae remained, despite starvation.

Gibbs, MC, Parker, LM, Scanes, E, Byrne, M, O'Connor, WA & Ross, PM 2021, 'Energetic lipid responses of larval oysters to ocean acidification', Marine Pollution Bulletin, vol. 168, pp. 112441-112441.
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Climate change will increase energetic demands on marine invertebrate larvae and make planktonic food more unpredictable. This study determined the impact of ocean acidification on larval energetics of the oysters Saccostrea glomerata and Crassostrea gigas. Larvae of both oysters were reared until the 9-day-old, umbonate stage under orthogonal combinations of ambient and elevated p CO 2 (340 and 856 μatm) and food was limited. Elevated p CO 2 reduced the survival, size and larval energetics, larvae of C. gigas being more resilient than S. glomerata. When larvae were fed, elevated p CO 2 reduced lipid levels across all lipid classes. When larvae were unfed elevated p CO 2 resulted in increased lipid levels and mortality. Ocean acidification and food will interact to limit larval energetics. Larvae of S. glomerata will be more impacted than C. gigas and this is of concern given their aquacultural status and ecological function.

Grottoli, AG, Toonen, RJ, van Woesik, R, Vega Thurber, R, Warner, ME, McLachlan, RH, Price, JT, Bahr, KD, Baums, IB, Castillo, KD, Coffroth, MA, Cunning, R, Dobson, KL, Donahue, MJ, Hench, JL, Iglesias‐Prieto, R, Kemp, DW, Kenkel, CD, Kline, DI, Kuffner, IB, Matthews, JL, Mayfield, AB, Padilla‐Gamiño, JL, Palumbi, S, Voolstra, CR, Weis, VM & Wu, HC 2021, 'Increasing comparability among coral bleaching experiments', Ecological Applications, vol. 31, no. 4.
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AbstractCoral bleaching is the single largest global threat to coral reefs worldwide. Integrating the diverse body of work on coral bleaching is critical to understanding and combating this global problem. Yet investigating the drivers, patterns, and processes of coral bleaching poses a major challenge. A recent review of published experiments revealed a wide range of experimental variables used across studies. Such a wide range of approaches enhances discovery, but without full transparency in the experimental and analytical methods used, can also make comparisons among studies challenging. To increase comparability but not stifle innovation, we propose a common framework for coral bleaching experiments that includes consideration of coral provenance, experimental conditions, and husbandry. For example, reporting the number of genets used, collection site conditions, the experimental temperature offset(s) from the maximum monthly mean (MMM) of the collection site, experimental light conditions, flow, and the feeding regime will greatly facilitate comparability across studies. Similarly, quantifying common response variables of endosymbiont (Symbiodiniaceae) and holobiont phenotypes (i.e., color, chlorophyll, endosymbiont cell density, mortality, and skeletal growth) could further facilitate cross‐study comparisons. While no single bleaching experiment can provide the data necessary to determine global coral responses of all corals to current and future ocean warming, linking studies through a common framework as outlined here, would help increase comparability among experiments, facilitate synthetic insights into the causes and underlying mechanisms of coral bleaching, and reveal unique bleaching responses among genets, species, and regions. Such a collaborative framework that fosters transparency in methods used would strengthen comparisons among studies that can help inform coral reef management and facilitate conserv...

Haydon, TD, Seymour, JR, Raina, J-B, Edmondson, J, Siboni, N, Matthews, JL, Camp, EF & Suggett, DJ 2021, 'Rapid Shifts in Bacterial Communities and Homogeneity of Symbiodiniaceae in Colonies of Pocillopora acuta Transplanted Between Reef and Mangrove Environments', Frontiers in Microbiology, vol. 12, p. 756091.
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It has been proposed that an effective approach for predicting whether and how reef-forming corals persist under future climate change is to examine populations thriving in present day extreme environments, such as mangrove lagoons, where water temperatures can exceed those of reef environments by more than 3°C, pH levels are more acidic (pH &lt; 7.9, often below 7.6) and O2 concentrations are regularly considered hypoxic (&lt;2 mg/L). Defining the physiological features of these “extreme” corals, as well as their relationships with the, often symbiotic, organisms within their microbiome, could increase our understanding of how corals will persist into the future. To better understand coral-microbe relationships that potentially underpin coral persistence within extreme mangrove environments, we therefore conducted a 9-month reciprocal transplant experiment, whereby specimens of the coral Pocillopora acuta were transplanted between adjacent mangrove and reef sites on the northern Great Barrier Reef. Bacterial communities associated with P. acuta specimens native to the reef environment were dominated by Endozoicomonas, while Symbiodiniaceae communities were dominated by members of the Cladocopium genus. In contrast, P. acuta colonies native to the mangrove site exhibited highly diverse bacterial communities with no dominating members, and Symbiodiniaceae communities dominated by Durusdinium. All corals survived for 9 months after being transplanted from reef-to-mangrove, mangrove-to-reef environments (as well as control within environment transplants), and during this time there were significant changes in the bacterial communities, but not in the Symbiodiniaceae communities or their photo-physiological functioning. In reef-to-mangrove transplanted corals, t...

Herdean, A, Hall, CC, Pham, LL, Macdonald Miller, S, Pernice, M & Ralph, PJ 2021, 'Action Spectra and Excitation Emission Matrices reveal the broad range of usable photosynthetic active radiation for Phaeodactylum tricornutum', Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol. 1862, no. 9, pp. 148461-148461.
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Holland, MM, Everett, JD, Cox, MJ, Doblin, MA & Suthers, IM 2021, 'Pelagic forage fish distribution in a dynamic shelf ecosystem – Thermal demands and zooplankton prey distribution', Estuarine, Coastal and Shelf Science, vol. 249, pp. 107074-107074.
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Howlett, L, Camp, EF, Edmondson, J, Henderson, N & Suggett, DJ 2021, 'Coral growth, survivorship and return-on-effort within nurseries at high-value sites on the Great Barrier Reef', PLOS ONE, vol. 16, no. 1, pp. e0244961-e0244961.
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Coral reefs are deteriorating worldwide prompting reef managers and stakeholders to increasingly explore new management tools. Following back-to-back bleaching in 2016/2017, multi-taxa coral nurseries were established in 2018 for the first time on the Great Barrier Reef (GBR) to aid reef maintenance and restoration at a “high-value” location–Opal Reef–frequented by the tourism industry. Various coral species (n = 11) were propagated within shallow water (ca. 4-7m) platforms installed across two sites characterised by differing environmental exposure–one adjacent to a deep-water channel (Blue Lagoon) and one that was relatively sheltered (RayBan). Growth rates of coral fragments placed onto nurseries were highly variable across taxa but generally higher at Blue Lagoon (2.1–10.8 cm2 month-1 over 12 months) compared to RayBan (0.6–6.6 cm2 month-1 over 9 months). Growth at Blue Lagoon was largely independent of season, except for Acropora tenuis and Acropora hyacinthus, where growth rates were 15–20% higher for December 2018-July 2019 (“warm season”) compared to August-December 2018 (“cool season”). Survivorship across all 2,536 nursery fragments was ca. 80–100%, with some species exhibiting higher survivorship at Blue Lagoon (Acropora loripes, Porites cylindrica) and others at RayBan (A. hyacinthus, Montipora hispida). Parallel measurements of growth and survivorship were used to determine relative return-on-effort (RRE) scores as an integrated metric of “success” accounting for life history trade-offs, complementing the mutually exclusive assessment of growth or survivorship. RRE scores within sites (across species) were largely driven by growth, whereas RRE scores between sites ...

Hudspith, M, Rix, L, Achlatis, M, Bougoure, J, Guagliardo, P, Clode, PL, Webster, NS, Muyzer, G, Pernice, M & de Goeij, JM 2021, 'Subcellular view of host–microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan–microbe symbiosis', Microbiome, vol. 9, no. 1.
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Abstract Background Sponges are increasingly recognised as key ecosystem engineers in many aquatic habitats. They play an important role in nutrient cycling due to their unrivalled capacity for processing both dissolved and particulate organic matter (DOM and POM) and the exceptional metabolic repertoire of their diverse and abundant microbial communities. Functional studies determining the role of host and microbiome in organic nutrient uptake and exchange, however, are limited. Therefore, we coupled pulse-chase isotopic tracer techniques with nanoscale secondary ion mass spectrometry (NanoSIMS) to visualise the uptake and translocation of 13C- and 15N-labelled dissolved and particulate organic food at subcellular level in the high microbial abundance sponge Plakortis angulospiculatus and the low microbial abundance sponge Halisarca caerulea. Results The two sponge species showed significant enrichment of DOM- and POM-derived 13C and 15N into their tissue over time. Microbial symbionts were actively involved in the assimilation of DOM, but host filtering cells (choanocytes) appeared to be the primary site of DOM and POM uptake in both sponge species overall, via pinocytosis and phagocytosis, respectively. Translocation of carbon and nitrogen from choanocytes to microbial symbionts occurred over time, irrespective of microbial abundance, reflecting recycling of host waste products by the microbiome. Conclusions Here, we provide empirical evidence indicating that the prokaryotic communities of a high and ...

Hughes, DJ, Giannini, FC, Ciotti, AM, Doblin, MA, Ralph, PJ, Varkey, D, Verma, A & Suggett, DJ 2021, 'Taxonomic Variability in the Electron Requirement for Carbon Fixation Across Marine Phytoplankton', Journal of Phycology, vol. 57, no. 1, pp. 111-127.
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Fast Repetition Rate fluorometry (FRRf) has been increasingly used to measure marine primary productivity by oceanographers to understand how carbon (C) uptake patterns vary over space and time in the global ocean. As FRRf measures electron transport rates through photosystem II (ETRPSII), a critical, but difficult to predict conversion factor termed the “electron requirement for carbon fixation” (Φe,C) is needed to scale ETRPSII to C‐fixation rates. Recent studies have generally focused on understanding environmental regulation of Φe,C, while taxonomic control has been explored by only a handful of laboratory studies encompassing a limited diversity of phytoplankton species. We therefore assessed Φe,C for a wide range of marine phytoplankton (n = 17 strains) spanning multiple taxonomic and size classes. Data mined from previous studies were further considered to determine whether Φe,C variability could be explained by taxonomy versus other phenotypic traits influencing growth and physiological performance (e.g., cell size). We found that Φe,C exhibited considerable variability (~4–10 mol e‐ · [mol C]−1) and was negatively correlated with growth rate (R2 = 0.7, P < 0.01). Diatoms exhibited a lower Φe,C compared to chlorophytes during steady‐state, nutrient‐replete growth. Inclusion of meta‐analysis data did not find significant relationships between Φe,C and class, or growth rate, although confounding factors inherent to methodological inconsistencies between studies likely contributed to this. Knowledge of empirical relationships between Φe,C and growth rate coupled with recent improvements in ...

Hurtado-McCormick, V, Kahlke, T, Petrou, K, Jeffries, T, Ralph, PJ & Seymour, JR 2021, 'Corrigendum: Regional and Microenvironmental Scale Characterization of the Zostera muelleri Seagrass Microbiome', Frontiers in Microbiology, vol. 12, p. 642964.
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[This corrects the article DOI: 10.3389/fmicb.2019.01011.].

Hurtado-McCormick, V, Krix, D, Tschitschko, B, Siboni, N, Ralph, PJ & Seymour, JR 2021, 'Shifts in the seagrass leaf microbiome associated with wasting disease in', Marine and Freshwater Research, vol. 72, no. 9, pp. 1303-1320.
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Seagrass wasting disease (SWD), an infection believed to be caused by Labyrinthula zosterae, has been linked to seagrass declines in several places around the world. However, there is uncertainty about the mechanisms of disease and the potential involvement of opportunistic colonising microorganisms. Using 16S rRNA gene amplicon sequencing, we compared the microbiome of SWD lesions in leaves of Zostera muelleri with communities in adjacent asymptomatic tissues and healthy leaves. The microbiome of healthy leaf tissues was dominated by Pseudomonas and Burkholderia, whereas the most predominant taxa within adjacent tissues were Pseudomonas and Rubidimonas. Members of the Saprospiraceae, potential macroalgal pathogens, were over-represented within SWD lesions. These pronounced changes in microbiome structure were also apparent when we examined the core microbiome of different tissue types. Although the core microbiome associated with healthy leaves included three operational taxonomic units (OTUs) classified as Burkholderia, Cryomorphaceae and the SAR11 clade, a single core OTU from the Arenicella was found within adjacent tissues. Burkholderia are diazotrophic microorganisms and may play an important role in seagrass nitrogen acquisition. In contrast, some members of the Arenicella have been implicated in necrotic disease in other benthic animals. Moreover, microbiome structure was maintained across sites within healthy tissues, but not within SWD lesions or the tissues immediately adjacent to lesions. Predicted functional profiles revealed increased photoautotrophic functions in SWD tissues relative to healthy leaves, but no increase in pathogenicity or virulence. Notably, we demonstrated the presence of L. zosterae in SWD lesions by polymerase chain reaction, but only in one of the two sampled locations, which indicates that other microbiological factors may be involved in the initiation or development of SWD-like symptoms. This study suggests t...

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 2021, 'Quantifying Cyanothece growth under DIC limitation', Computational and Structural Biotechnology Journal, vol. 19, pp. 6456-6464.
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The photoautotrophic, unicellular N2-fixer, Cyanothece, is a model organism that has been widely used to study photosynthesis regulation, the structure of photosystems, and the temporal segregation of carbon (C) and nitrogen (N) fixation in light and dark phases of the diel cycle. Here, we present a simple quantitative model and experimental data that together, suggest external dissolved inorganic carbon (DIC) concentration as a major limiting factor for Cyanothece growth, due to its high C-storage requirement. Using experimental data from a parallel laboratory study as a basis, we show that after the onset of the light period, DIC was rapidly consumed by photosynthesis, leading to a sharp drop in the rate of photosynthesis and C accumulation. In N2-fixing cultures, high rates of photosynthesis in the morning enabled rapid conversion of DIC to intracellular C storage, hastening DIC consumption to levels that limited further uptake. The N2-fixing condition allows only a small fraction of fixed C for cellular growth since a large fraction was reserved in storage to fuel night-time N2 fixation. Our model provides a framework for resolving DIC limitation in aquatic ecosystem simulations, where DIC as a growth-limiting factor has rarely been considered, and importantly emphasizes the effect of intracellular C allocation on growth rate that varies depending on the growth environment.

Iwasaki, K, Evenhuis, C, Tamburic, B, Kuzhiumparambil, U, O'Connor, W, Ralph, P & Szabó, M 2021, 'Improving light and CO2 availability to enhance the growth rate of the diatom, Chaetoceros muelleri', Algal Research, vol. 55, pp. 102234-102234.
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Diatoms (Bacillariophyceae) are an important source of feed for juvenile animals in aquaculture hatcheries. Increasing the yield of feed cultures by optimizing illumination and inorganic carbon supply could significantly reduce operational costs for hatcheries. In this study, the growth dynamics and photosynthetic efficiency of the aquaculture-relevant diatom Chaetoceros muelleri were monitored and modelled under four different light and CO2 conditions. By increasing the availability of both light and CO2, a growth rate of 1.59 ± 0.12 (day−1) was achieved for C. muelleri, an increase of approximately 89% compared to 0.84 ± 0.08 (day−1) which was recorded in cultures under light limitation with no CO2 addition. The real-time monitoring and modelling of growth dynamics and photosynthesis rates in different light and CO2 conditions have demonstrated that light availability can be improved by minimizing the path length of light through the culture, and the importance of on-demand CO2 supply. The techniques and results outlined in this study could be used to potentially improve biomass production in hatcheries.

King, WL, Kaestli, M, Siboni, N, Padovan, A, Christian, K, Mills, D, Seymour, J & Gibb, K 2021, 'Pearl Oyster Bacterial Community Structure Is Governed by Location and Tissue-Type, but Vibrio Species Are Shared Among Oyster Tissues', Frontiers in Microbiology, vol. 12, pp. 1-11.
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Diseases of bivalves of aquacultural importance, including the valuable Australian silver-lipped pearl oyster (Pinctada maxima), have been increasing in frequency and severity. The bivalve microbiome is linked to health and disease dynamics, particularly in oysters, with putative pathogens within the Vibrio genus commonly implicated in oyster diseases. Previous studies have been biased toward the Pacific oyster because of its global dominance in oyster aquaculture, while much less is known about the microbiome of P. maxima. We sought to address this knowledge gap by characterizing the P. maxima bacterial community, and we hypothesized that bacterial community composition, and specifically the occurrence of Vibrio, will vary according to the sampled microenvironment. We also predicted that the inside shell swab bacterial composition could represent a source of microbial spillover biofilm into the solid pearl oyster tissues, thus providing a useful predictive sampling environment. We found that there was significant heterogeneity in bacterial composition between different pearl oyster tissues, which is consistent with patterns reported in other bivalve species and supports the hypothesis that each tissue type represents a unique microenvironment for bacterial colonization. We suggest that, based on the strong effect of tissue-type on the pearl oyster bacterial community, future studies should apply caution when attempting to compare microbial patterns from different locations, and when searching for disease agents. The lack of association with water at each farm also supported the unique nature of the microbial communities in oyster tissues. In contrast to the whole bacterial community, there was no significant difference in the Vibrio community among tissue types nor location. These resu...

Labeeuw, L, Commault, AS, Kuzhiumparambil, U, Emmerton, B, Nguyen, LN, Nghiem, LD & Ralph, PJ 2021, 'A comprehensive analysis of an effective flocculation method for high quality microalgal biomass harvesting', Science of The Total Environment, vol. 752, pp. 141708-141708.
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Laiolo, L, Matear, R, Soja-Woźniak, M, Suggett, DJ, Hughes, DJ, Baird, ME & Doblin, MA 2021, 'Modelling the impact of phytoplankton cell size and abundance on inherent optical properties (IOPs) and a remotely sensed chlorophyll-a product', Journal of Marine Systems, vol. 213, pp. 103460-103460.
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© 2020 Elsevier B.V. Ocean colour data are commonly used to quantify primary production, study phytoplankton dynamics and calibrate marine models, thus understanding the origin of errors in the retrieved chlorophyll-a (Chl-a) product is critical. One source of uncertainty in retrieved Chl-a products can be related to large photosynthetic cells, characterised by lower mass-specific absorption coefficients due to increased packaging effect. Here, we explore the relationship between phytoplankton size structure and an ocean colour product using optical simulations and in situ observations. Specifically, we use an optical model to explore how phytoplankton cell size and abundance influence phytoplankton absorption and backscattering coefficients and the implication this has for water leaving radiance and the estimated Chl-a derived from satellite ocean colour. The optical model simulations show phytoplankton cell size has a significant impact on the remote-sensing reflectance, with Chl-a packaged in 5 to 10 μm cells resulting in about 54 to 76% the simulated ocean colour Chl-a compared to 1 μm cells, as determined by an algorithm that converts reflectances to Chl-a. To support optical simulations, size-fractionated Chl-a samples were collected from several water masses to investigate the phytoplankton size contribution (i.e., < 2 μm, 2–10 μm and > 10 μm) to the total Chl-a. We focused on the offshore eastern Australian ocean region, largely characterised by oligotrophic waters in which phytoplankton dominate the optical properties of the water column. Of the 22 stations sampled, a total of ten in situ size fractionated Chl-a measurements were matched-up with the corresponding clear-sky satellite Chl-a product. The matched-up points revealed a systematic underestimation of in situ Chl-a. With the low amount of data, it was not possible to statistically relate the satellite underestimation to a specific phytoplankton size class, but the observations showed th...

Lawson, CA, Raina, J, Deschaseaux, E, Hrebien, V, Possell, M, Seymour, JR & Suggett, DJ 2021, 'Heat stress decreases the diversity, abundance and functional potential of coral gas emissions', Global Change Biology, vol. 27, no. 4, pp. 879-891.
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AbstractTerrestrial ecosystems emit large quantities of biogenic volatile organic compounds (BVOCs), many of which play important roles in abiotic stress responses, pathogen and grazing defences, inter‐ and intra‐species communications, and climate regulation. Conversely, comparatively little is known about the diversity and functional potential of BVOCs produced in the marine environment, especially in highly productive coral reefs. Here we describe the first ‘volatilomes’ of two common reef‐building corals, Acropora intermedia and Pocillopora damicornis, and how the functional potential of their gaseous emissions is altered by heat stress events that are driving rapid deterioration of coral reef ecosystems worldwide. A total of 87 BVOCs were detected from the two species and the chemical richness of both coral volatilomes—particularly the chemical classes of alkanes and carboxylic acids—decreased during heat stress by 41% and 62% in A. intermedia and P. damicornis, respectively. Across both coral species, the abundance of individual compounds changed significantly during heat stress, with the majority (>86%) significantly decreasing compared to control conditions. Additionally, almost 60% of the coral volatilome (or 52 BVOCs) could be assigned to four key functional groups based on their activities in other species or systems, including stress response, chemical signalling, climate regulation and antimicrobial activity. The total number of compounds assigned to these functions decreased significantly under heat stress for both A. intermedia (by 35%) and P. damicornis (by 64%), with most dramatic losses found for climatically active BVOCs in P. damicornis and antimicrobial BVOCs in A. intermedia. Together...

Leal, E, de Beyer, L, O'Connor, W, Dove, M, Ralph, PJ & Pernice, M 2021, 'Production optimisation of Tisochrysis lutea as a live feed for juvenile Sydney rock oysters, Saccostrea glomerata, using large-scale photobioreactors', Aquaculture, vol. 533, pp. 736077-736077.
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© 2020 Elsevier B.V. The aquaculture industry uses microalgae as a live feed for juvenile oysters in hatcheries to meet their nutritional requirements, including their need for several essential Poly Unsaturated Fatty Acids (PUFAs) such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). The mass culture of microalgae is not only a major bottleneck for the production of juvenile oysters, but also a significant cost, accounting for 20–50% of hatchery operating costs. Currently, low biomass concentrations, high production costs and poor cultivation systems limit the quantity and quality of microalgae feed. This study focused on Tisochrysis lutea, a microalgae species commonly used in aquaculture, and we assessed the potential of photobioreactors with an improved light source and CO2 input to increase biomass production and improve biochemical composition of algal feed. Two photobioreactor systems were compared: the current industry set up (DPI) comprising fluorescent lighting and minimal CO2 input versus an optimized system utilising LEDs and increased CO2. Cultures of T. lutea were monitored over a 12-day growth period and harvested on day 14 for biochemical analysis. Final cell density was significantly higher in the optimized system relative to the conventional culture systems (6.2 × 106 cells / mL versus 3.7 × 106 cells / mL, respectively). The biochemical profile of T. lutea was not significantly different between the two photobioreactors systems. The algal biomass produced during this comparative experiment was used in a feeding trial on oyster spat, Saccostrea glomerata. Spat fed with algae produced in optimized vs conventional photobioreactors showed no significant difference in growth, but oyster spat fed with T. lutea grown in optimized photobioreactors did show a significant increase in their EPA content. Overall, our results contribute to our understanding of how altered culture conditions affect microalgal production and biochemical composit...

Leong, HS, Watanabe, S, Kuzhiumparambil, U, Fong, CY, Moy, HY, Yao, YJ, Witting, PK & Fu, S 2021, 'Monitoring metabolism of synthetic cannabinoid 4F-MDMB-BINACA via high-resolution mass spectrometry assessed in cultured hepatoma cell line, fungus, liver microsomes and confirmed using urine samples', Forensic Toxicology, vol. 39, no. 1, pp. 198-212.
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Abstract Purpose A tert-leucinate derivative synthetic cannabinoid, methyl (2S)-2-([1-(4-fluorobutyl)-1H-indazole-3-carbonyl]amino)-3,3-dimethylbutanoate (4F-MDMB-BINACA, 4F-MDMB-BUTINACA or 4F-ADB) is known to adversely impact health. This study aimed to evaluate the suitability of three different modes of monitoring metabolism: HepG2 liver cells, fungus Cunninghamella elegans (C. elegans) and pooled human liver microsomes (HLM) for comparison with human in-vivo metabolism in identifying suitable urinary marker(s) for 4F-MDMB-BINACA intake. Methods Tentative structure elucidation of in-vitro metabolites was performed on HepG2, C. elegans and HLM using liquid chromatography–tandem mass spectrometry and high-resolution mass spectrometry analysis. In-vivo metabolites obtained from twenty authentic human urine samples were analysed using liquid chromatography–Orbitrap mass spectrometry. Results Incubation with HepG2, C. elegans and HLM yielded nine, twenty-three and seventeen metabolites of 4F-MDMB-BINACA, respectively, formed via ester hydrolysis, hydroxylation, carboxylation, dehydrogenation, oxidative defluorination, carbonylation or reaction combinations. Phase II metabolites of glucosidation and sulfation were also exclusively identified using C. elegans model. Eight in-vivo metabolites tentatively identified were mainly products of ester hydrolysis with or without additional dehydrogenation,

Maire, J, Girvan, SK, Barkla, SE, Perez-Gonzalez, A, Suggett, DJ, Blackall, LL & van Oppen, MJH 2021, 'Correction to: Intracellular bacteria are common and taxonomically diverse in cultured and in hospite algal endosymbionts of coral reefs', The ISME Journal, vol. 15, no. 7, pp. 2168-2170.
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Abstract A Correction to this paper has been published: https://doi.org/10.1038/s41396-021-00970-6

Maire, J, Girvan, SK, Barkla, SE, Perez-Gonzalez, A, Suggett, DJ, Blackall, LL & van Oppen, MJH 2021, 'Intracellular bacteria are common and taxonomically diverse in cultured and in hospite algal endosymbionts of coral reefs', The ISME Journal, vol. 15, no. 7, pp. 2028-2042.
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Abstract Corals house a variety of microorganisms which they depend on for their survival, including endosymbiotic dinoflagellates (Symbiodiniaceae) and bacteria. While cnidarian–microorganism interactions are widely studied, Symbiodiniaceae–bacteria interactions are only just beginning to receive attention. Here, we describe the localization and composition of the bacterial communities associated with cultures of 11 Symbiodiniaceae strains from nine species and six genera. Three-dimensional confocal laser scanning and electron microscopy revealed bacteria are present inside the Symbiodiniaceae cells as well as closely associated with their external cell surface. Bacterial pure cultures and 16S rRNA gene metabarcoding from Symbiodiniaceae cultures highlighted distinct and highly diverse bacterial communities occur intracellularly, closely associated with the Symbiodiniaceae outer cell surface and loosely associated (i.e., in the surrounding culture media). The intracellular bacteria are highly conserved across Symbiodiniaceae species, suggesting they may be involved in Symbiodiniaceae physiology. Our findings provide unique new insights into the biology of Symbiodiniaceae.

Malik, S, Shahid, A, Liu, C-G, Zafar Khan, A, Nawaz, MZ, Zhu, H & Mehmood, MA 2021, 'Developing fourth-generation biofuels secreting microbial cell factories for enhanced productivity and efficient product recovery; a review', Fuel, vol. 298, pp. 120858-120858.
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Fourth generation (4G) biofuels have been found compatible with engines, storage systems, and transport facilities. Due to advances in synthetic biology and genetic engineering tools, considerable progress has been made in producing 4G biofuels including high-carbon alcohols, long-chain hydrocarbons, terpenoids-based, and/or fatty-acid derived biofuels using Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris, Yarrowia lypolytica, and Zymomonas mobilis as microbial cellular factories. However, these microbial platforms face various challenges including low product titers, low product yields, difficult product recovery incurring intensive energy consumption, and discharge of large amounts of wastewater. All these issues make the production and recovery of these biofuels expensive and commercially non-competitive. However, various genetic manipulation approaches including overexpression of heat-shock proteins, enhanced production of precursor molecules, regulating redox-balance, and membrane engineering have been employed to cope with these challenges. This review discusses the progress made in the molecular approaches for the enhanced biosynthesis and easier recovery of these biofuels through employing the secreting microbial cell factories. Besides, based on the data published on membrane transporters in previous fifteen years, selected fungal and bacterial membrane efflux pumps are studied to evaluate their biofuel secretion potential as future targets to be employed in the biofuel secreting microbial cell factories to achieve commercial robustness in the future.

Mandigo, AC, Yuan, W, Xu, K, Gallagher, P, Pang, A, Guan, YF, Shafi, AA, Thangavel, C, Sheehan, B, Bogdan, D, Paschalis, A, McCann, JJ, Laufer, TS, Gordon, N, Vasilevskaya, IA, Dylgjeri, E, Chand, SN, Schiewer, MJ, Domingo-Domenech, J, Den, RB, Holst, J, McCue, PA, de Bono, JS, McNair, C & Knudsen, KE 2021, 'RB/E2F1 as a Master Regulator of Cancer Cell Metabolism in Advanced Disease', Cancer Discovery, vol. 11, no. 9, pp. 2334-2353.
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Abstract Loss of the retinoblastoma (RB) tumor suppressor protein is a critical step in reprogramming biological networks that drive cancer progression, although mechanistic insight has been largely limited to the impact of RB loss on cell-cycle regulation. Here, isogenic modeling of RB loss identified disease stage–specific rewiring of E2F1 function, providing the first-in-field mapping of the E2F1 cistrome and transcriptome after RB loss across disease progression. Biochemical and functional assessment using both in vitro and in vivo models identified an unexpected, prominent role for E2F1 in regulation of redox metabolism after RB loss, driving an increase in the synthesis of the antioxidant glutathione, specific to advanced disease. These E2F1-dependent events resulted in protection from reactive oxygen species in response to therapeutic intervention. On balance, these findings reveal novel pathways through which RB loss promotes cancer progression and highlight potentially new nodes of intervention for treating RB-deficient cancers. Significance: This study identifies stage-specific consequences of RB loss across cancer progression that have a direct impact on tumor response to clinically utilized therapeutics. The study herein is the first to investigate the effect of RB loss on global metabolic regulation and link RB/E2F1 to redox control in multiple advanced diseases. This article is highlighted in the In This Issue feature, p. 2113

Messer, LF, Brown, MV, Van Ruth, PD, Doubell, M & Seymour, JR 2021, 'Temperate southern Australian coastal waters are characterised by surprisingly high rates of nitrogen fixation and diversity of diazotrophs', PeerJ, vol. 9, pp. e10809-e10809.
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Biological dinitrogen (N2) fixation is one mechanism by which specific microorganisms (diazotrophs) can ameliorate nitrogen (N) limitation. Historically, rates of N2 fixation were believed to be limited outside of the low nutrient tropical and subtropical open ocean; however, emerging evidence suggests that N2 fixation is also a significant process within temperate coastal waters. Using a combination of amplicon sequencing, targeting the nitrogenase reductase gene (nifH), quantitative nifH PCR, and 15N2 stable isotope tracer experiments, we investigated spatial patterns of diazotroph assemblage structure and N2 fixation rates within the temperate coastal waters of southern Australia during Austral autumn and summer. Relative to previous studies in open ocean environments, including tropical northern Australia, and tropical and temperate estuaries, our results indicate that high rates of N2 fixation (10–64 nmol L−1 d−1) can occur within the large inverse estuary Spencer Gulf, while comparatively low rates of N2 fixation (2 nmol L−1 d−1) were observed in the adjacent continental shelf waters. Across the dataset, low concentrations of NO3/NO2 were significantly correlated with the highest N2 fixation rates, suggesting that N2 fixation could be an important source of new N in the region as dissolved inorganic N concentrations are typically limiting. Overall, the underlying diazotrophic community was dominated by nifH sequences from Cluster 1 unicellular cyanobacteria of the UCYN-A clade, as well as non-cyanobacterial diazotrophs related to ...

Metia, S, Nguyen, HAD & Ha, QP 2021, 'IoT-Enabled Wireless Sensor Networks for Air Pollution Monitoring with Extended Fractional-Order Kalman Filtering', Sensors, vol. 21, no. 16, pp. 5313-5313.
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This paper presents the development of high-performance wireless sensor networks for local monitoring of air pollution. The proposed system, enabled by the Internet of Things (IoT), is based on low-cost sensors collocated in a redundant configuration for collecting and transferring air quality data. Reliability and accuracy of the monitoring system are enhanced by using extended fractional-order Kalman filtering (EFKF) for data assimilation and recovery of the missing information. Its effectiveness is verified through monitoring particulate matters at a suburban site during the wildfire season 2019–2020 and the Coronavirus disease 2019 (COVID-19) lockdown period. The proposed approach is of interest to achieve microclimate responsiveness in a local area.

Mote, S, Gupta, V, De, K, Nanajkar, M, Damare, SR & Ingole, B 2021, 'Bacterial diversity associated with a newly described bioeroding sponge, Cliona thomasi, from the coral reefs on the West Coast of India', Folia Microbiologica, vol. 66, no. 2, pp. 203-211.
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Nguyen, HD, Azzi, M, White, S, Salter, D, Trieu, T, Morgan, G, Rahman, M, Watt, S, Riley, M, Chang, LT-C, Barthelemy, X, Fuchs, D, Lieschke, K & Nguyen, H 2021, 'The Summer 2019–2020 Wildfires in East Coast Australia and Their Impacts on Air Quality and Health in New South Wales, Australia', International Journal of Environmental Research and Public Health, vol. 18, no. 7, pp. 3538-3538.
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The 2019–2020 summer wildfire event on the east coast of Australia was a series of major wildfires occurring from November 2019 to end of January 2020 across the states of Queensland, New South Wales (NSW), Victoria and South Australia. The wildfires were unprecedent in scope and the extensive character of the wildfires caused smoke pollutants to be transported not only to New Zealand, but also across the Pacific Ocean to South America. At the peak of the wildfires, smoke plumes were injected into the stratosphere at a height of up to 25 km and hence transported across the globe. The meteorological and air quality Weather Research and Forecasting with Chemistry (WRF-Chem) model is used together with the air quality monitoring data collected during the bushfire period and remote sensing data from the Moderate Resolution Imaging Spectroradiometer (MODIS) and Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) satellites to determine the extent of the wildfires, the pollutant transport and their impacts on air quality and health of the exposed population in NSW. The results showed that the WRF-Chem model using Fire Emission Inventory (FINN) from National Center for Atmospheric Research (NCAR) to simulate the dispersion and transport of pollutants from wildfires predicted the daily concentration of PM2.5 having the correlation (R2) and index of agreement (IOA) from 0.6 to 0.75 and 0.61 to 0.86, respectively, when compared with the ground-based data. The impact on health endpoints such as mortality and respiratory and cardiovascular diseases hospitalizations across the modelling domain was then estimated. The estimated health impact on each of the Australian Bureau of Statistics (ABS) census districts (SA4) of New South Wales was calculated based on epidemiological assumptions of the impact function and incidence rate data from the 2016 ABS and NSW Department of Health statistical health records. Summing up all SA4 census dist...

Nguyen, HM, Bulleri, F, Marín-Guirao, L, Pernice, M & Procaccini, G 2021, 'Photo-physiology and morphology reveal divergent warming responses in northern and southern hemisphere seagrasses', Marine Biology, vol. 168, no. 8.
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Nguyen, HM, Ralph, PJ, Marín‐Guirao, L, Pernice, M & Procaccini, G 2021, 'Seagrasses in an era of ocean warming: a review', Biological Reviews, vol. 96, no. 5, pp. 2009-2030.
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ABSTRACTSeagrasses are valuable sources of food and habitat for marine life and are one of Earth's most efficient carbon sinks. However, they are facing a global decline due to ocean warming and eutrophication. In the last decade, with the advent of new technology and molecular advances, there has been a dramatic increase in the number of studies focusing on the effects of ocean warming on seagrasses. Here, we provide a comprehensive review of the future of seagrasses in an era of ocean warming. We have gathered information from published studies to identify potential commonalities in the effects of warming and the responses of seagrasses across four distinct levels: molecular, biochemical/physiological, morphological/population, and ecosystem/planetary. To date, we know that although warming strongly affects seagrasses at all four levels, seagrass responses diverge amongst species, populations, and over depths. Furthermore, warming alters seagrass distribution causing massive die‐offs in some seagrass populations, whilst also causing tropicalization and migration of temperate species. In this review, we evaluate the combined effects of ocean warming with other environmental stressors and emphasize the need for multiple‐stressor studies to provide a deeper understanding of seagrass resilience. We conclude by discussing the most significant knowledge gaps and future directions for seagrass research.

Nguyen, LN, Vu, MT, Abu Hasan Johir, M, Pernice, M, Ngo, HH, Zdarta, J, Jesionowski, T & Nghiem, LD 2021, 'Promotion of direct interspecies electron transfer and potential impact of conductive materials in anaerobic digestion and its downstream processing - a critical review', Bioresource Technology, vol. 341, pp. 125847-125847.
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Nguyen, VK, King, WL, Siboni, N, Mahbub, KR, Rahman, MH, Jenkins, C, Dove, M, O'Connor, W, Seymour, JR & Labbate, M 2021, 'Dynamics of the Sydney rock oyster microbiota before and during a QX disease event', Aquaculture, vol. 541, pp. 736821-736821.
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The Sydney rock oyster (SRO; Saccostrea glomerata) is the most intensively farmed oyster species in Australia however, Queensland unknown (QX) disease has resulted in substantial losses and impeded productivity. QX disease is caused by infection with the parasite Marteilia sydneyi, and like other diseases, outbreaks are driven by a series of complex environmental and host factors such as seasonality, seawater salinity and oyster genetics. A potential but understudied factor in QX disease is the SRO microbiota, which we sought to examine before and during a QX disease outbreak. Using 16S rRNA (V1 – V3 region) amplicon sequencing, we examined the microbiota of SROs deployed in an estuary where QX disease occurs, with sampling conducted fortnightly over 22 weeks. Marteilia sydneyi was detected in the SROs by PCR (QX-positive), 16 weeks after the first sampling event and sporonts were observed in the digestive gland two weeks later on. There were no apparent patterns observed between the microbiota of QX-positive SROs with and without digestive gland sporonts however, the microbiota of QX-positive SROs was significantly different from those sampled prior to detection of M. sydneyi and from those negative for M. sydneyi post detection. As a result, shifts in microbiota structure occurred before sporulation in the digestive gland and either before or shortly after pathogen colonisation. The microbiota shifts associated with QX-positive oysters were principally driven by a relative abundance increase of operational taxonomic units (OTUs) assigned to unclassified species of the Borrelia and Candidatus Hepatoplasma genera and a relative abundance decrease in an OTU assigned to an unclassified species of the Mycoplasma genus. Since Mycoplasma species are common microbiota features of SROs and other oysters, we propose that there may be an important ecological link between Mycoplasma species and the health state of SROs.

Olander, A, Lawson, CA, Possell, M, Raina, J-B, Ueland, M & Suggett, DJ 2021, 'Comparative volatilomics of coral endosymbionts from one- and comprehensive two-dimensional gas chromatography approaches', Marine Biology, vol. 168, no. 5, p. 76.
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Volatilomics, the examination of all biogenic volatile organic compounds (BVOCs) emitted by an organism or system, holds potential as a novel screening tool for taxonomy, fitness, and ecological functioning. Volatilomics has been largely applied to terrestrial environments, but highly productive coastal marine systems, which are major sources of specific BVOCs, such as dimethyl sulfide, have been largely neglected. Volatilomic measurements are highly method-dependent, with different instrumentation impacting the diversity of identified BVOCs—therefore, understanding these biases is critical to reconcile studies. Here, we investigated BVOCs emitted by two species of coral endosymbiotic microalgae (Symbiodinium tridacnidorum and Durusdinium trenchii) using gas chromatography–mass spectrometry (GC–MS) and comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry (GC × GC–TOFMS). Seven chemical classes were detected by both instruments, the most common being aromatic hydrocarbons. However, GC × GC resolved seven times more BVOCs than GC–MS (290 vs. 40), with a higher proportion of compounds tentatively identified (173 vs. 14). Notably, nine chemical classes were exclusively identified by GC × GC, including alkane, alkene, aldehyde, ester, and nitrile BVOCs—each potentially fulfilling undescribed functions in marine organisms. The microalgal species investigated shared a large proportion of BVOCs, and this result was consistent across instruments (97 and 98% shared compounds via GC × GC and GC–MS, respectively), suggesting consistent retrieval of general patterns between instruments. This method comparison is the first of its kind in marine systems and confirms the greater analytical power of GC × GC, required to help resolve complex BVOC emissions and the identification of their roles in marine systems.

Padovan, A, Siboni, N, Kaestli, M, King, WL, Seymour, JR & Gibb, K 2021, 'Occurrence and dynamics of potentially pathogenic vibrios in the wet-dry tropics of northern Australia', Marine Environmental Research, vol. 169, pp. 105405-105405.
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Bacteria from the Vibrio genus are a ubiquitous component of coastal and estuarine ecosystems with several pathogenic Vibrio species displaying preferences for warm tropical waters. We studied the spatial and temporal abundance of three key human potential pathogens V. parahaemolyticus, V. cholerae and V. vulnificus in northern tropical Australia, over the wet and dry seasons, to identify environmental parameters influencing their abundance. Quantitative PCR (qPCR) analysis revealed that V. parahaemolyticus occurred more frequently and in higher abundance than V. cholerae and V. vulnificus across all locations examined. All three species were more abundant during the wet season, with V. parahaemolyticus abundance correlated to temperature and conductivity, whereas nutrient concentrations and turbidity best explained V. vulnificus abundance. In addition to these targeted qPCR analyses, we assessed the composition and dynamics of the entire Vibrio community using hsp60 amplicon sequencing. Using this approach, 42 Vibrio species were identified, including a number of other pathogenic species such as V. alginolyticus, V. mimicus and V. fluvialis. The Vibrio community was more diverse in the wet season, with temperature and dissolved oxygen as the key factors governing community composition. Seasonal differences were primarily driven by a greater abundance of V. parahaemolyticus and V. vulnificus during the wet season, while spatial differences were driven by different abundances of V. harveyi, V. campbellii, V. cholerae and V. navarrensis. When we related the abundance of Vibrio to other bacterial taxa, defined using 16S rRNA gene amplicon sequencing, V. parahaemolyticus was negatively correlated to several taxa, including members of the Rickettsiales and Saccharimonadales, while V. vulnificus was negatively correlated to Rhobacteriaceae and Cyanobiaceae. In contrast, V. alginolyticus, V. harveyi and V. mediterranei were all positively correlated to Cyanoba...

Parker, LM, Scanes, E, O'Connor, WA & Ross, PM 2021, 'Transgenerational plasticity responses of oysters to ocean acidification differ with habitat', Journal of Experimental Biology, vol. 224, no. 12, p. jeb.239269.
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ABSTRACT Transgenerational plasticity (TGP) has been identified as a critical mechanism of acclimation that may buffer marine organisms against climate change, yet whether the TGP response of marine organisms is altered depending on their habitat is unknown. Many marine organisms are found in intertidal zones where they experience episodes of emersion (air exposure) daily as the tide rises and recedes. During episodes of emersion, the accumulation of metabolic carbon dioxide (CO2) leads to hypercapnia for many species. How this metabolic hypercapnia impacts the TGP response of marine organisms to climate change is unknown as all previous transgenerational studies have been done under subtidal conditions, where parents are constantly immersed. Here, we assess the capacity of the ecologically and economically important oyster, Saccostrea glomerata, to acclimate to elevated CO2 dependent on habitat, across its vertical distribution, from the subtidal to intertidal zone. Tidal habitat altered both the existing tolerance and transgenerational response of S. glomerata to elevated CO2. Overall, larvae from parents conditioned in an intertidal habitat had a greater existing tolerance to elevated CO2 than larvae from parents conditioned in a subtidal habitat, but had a lower capacity for beneficial TGP following parental exposure to elevated CO2. Our results suggest that the TGP responses of marine species will not be uniform across their distribution and highlights the need to consider the habitat of a species when assessing TGP responses to climate change stressors.

Polerecky, L, Masuda, T, Eichner, M, Rabouille, S, Vancová, M, Kienhuis, MVM, Bernát, G, Bonomi-Barufi, J, Campbell, DA, Claquin, P, Červený, J, Giordano, M, Kotabová, E, Kromkamp, J, Lombardi, AT, Lukeš, M, Prášil, O, Stephan, S, Suggett, D, Zavřel, T & Halsey, KH 2021, 'Temporal Patterns and Intra- and Inter-Cellular Variability in Carbon and Nitrogen Assimilation by the Unicellular Cyanobacterium Cyanothece sp. ATCC 51142', Frontiers in Microbiology, vol. 12, p. 620915.
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Unicellular nitrogen fixing cyanobacteria (UCYN) are abundant members of phytoplankton communities in a wide range of marine environments, including those with rapidly changing nitrogen (N) concentrations. We hypothesized that differences in N availability (N2 vs. combined N) would cause UCYN to shift strategies of intracellular N and C allocation. We used transmission electron microscopy and nanoscale secondary ion mass spectrometry imaging to track assimilation and intracellular allocation of 13C-labeled CO2 and 15N-labeled N2 or NO3 at different periods across a diel cycle in Cyanothece sp. ATCC 51142. We present new ideas on interpreting these imaging data, including the influences of pre-incubation cellular C and N contents and turnover rates of inclusion bodies. Within cultures growing diazotrophically, distinct subpopulations were detected that fixed N2 at night or in the morning. Additional significant within-population heterogeneity was likely caused by differences in the relative amounts of N assimilated into cyanophycin from sources external and internal to the cells. Whether growing on N2 or NO3, cells prioritized cyanophycin synthesis when N assimilation rates were highest. N assimilation in cells growing on NO3 switched from cyanophycin synthesis to protein synthesis, suggesting that once a cyanophycin quota is met, it is bypassed in favor of protein synthesis. Growth on NO3 also revealed that at night, there is a very low level of CO2 assimilation into polysaccharides simultaneous with their catabolism for protein synthesis. This study revealed multiple, detailed mechanisms underlying C and N management in Cyanothece that facilita...

Rabouille, S, Campbell, DA, Masuda, T, Zavřel, T, Bernát, G, Polerecky, L, Halsey, K, Eichner, M, Kotabová, E, Stephan, S, Lukeš, M, Claquin, P, Bonomi-Barufi, J, Lombardi, AT, Červený, J, Suggett, DJ, Giordano, M, Kromkamp, JC & Prášil, O 2021, 'Electron & Biomass Dynamics of Cyanothece Under Interacting Nitrogen & Carbon Limitations', Frontiers in Microbiology, vol. 12, pp. 1-21.
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Marine diazotrophs are a diverse group with key roles in biogeochemical fluxes linked to primary productivity. The unicellular, diazotrophic cyanobacterium Cyanothece is widely found in coastal, subtropical oceans. We analyze the consequences of diazotrophy on growth efficiency, compared to NO3–-supported growth in Cyanothece, to understand how cells cope with N2-fixation when they also have to face carbon limitation, which may transiently affect populations in coastal environments or during blooms of phytoplankton communities. When grown in obligate diazotrophy, cells face the double burden of a more ATP-demanding N-acquisition mode and additional metabolic losses imposed by the transient storage of reducing potential as carbohydrate, compared to a hypothetical N2 assimilation directly driven by photosynthetic electron transport. Further, this energetic burden imposed by N2-fixation could not be alleviated, despite the high irradiance level within the cultures, because photosynthesis was limited by the availability of dissolved inorganic carbon (DIC), and possibly by a constrained capacity for carbon storage. DIC limitation exacerbates the costs on growth imposed by nitrogen fixation. Therefore, the competitive efficiency of diazotrophs could be hindered in areas with insufficient renewal of dissolved gases and/or with intense phytoplankton biomass that both decrease available light energy and draw the DIC level down.

Rädecker, N, Pogoreutz, C, Gegner, HM, Cárdenas, A, Roth, F, Bougoure, J, Guagliardo, P, Wild, C, Pernice, M, Raina, J-B, Meibom, A & Voolstra, CR 2021, 'Heat stress destabilizes symbiotic nutrient cycling in corals', Proceedings of the National Academy of Sciences, vol. 118, no. 5, pp. e2022653118-e2022653118.
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Significance Ocean warming is causing repeated mass coral bleaching, leading to catastrophic losses of coral reefs worldwide. Our ability to slow or revert this decline is hampered by an incomplete understanding of the processes underlying the breakdown of the coral–algal symbiosis. Here, we show that heat stress destabilizes the nutrient cycling between corals and their endosymbiotic algae long before bleaching becomes apparent. Notably, increased metabolic energy demands shift the coral–algal symbiosis from a nitrogen- to a carbon-limited state, reducing translocation and recycling of photosynthetic carbon. This effectively undermines the ecological advantage of harboring algal symbionts and directly contributes to the breakdown of the coral–algal symbiosis during heat stress.

Radfar, P, Bazaz, SR, Mirakhorli, F & Warkiani, ME 2021, 'The Role of 3D Printing in the Fight Against Covid-19 Outbreak', Journal of 3D Printing in Medicine, vol. 5, no. 1, pp. 51-60.
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Along with the COVID-19 pandemic, urgent needs for medical and specialized products, especially personal protective equipment, has been overwhelming. The conventional production line of medical devices has been challenged by excessive global demand, and the need for an easy, low-cost and rapid fabrication method is felt more than ever. In a scramble to address this shortfall, manufacturers referred to additive manufacturing or 3D printing to fill the gap and increase the production line of medical devices. Various previously/conventionally fabricated designs have been modified and redesigned to suit the 3D printing requirement to fight against COVID-19. In this perspective, various designs accommodated for the current worldwide outbreak of COVID-19 are discussed and how 3D printing could help the global community against the current and future conditions has been explored.

Raes, EJ, Karsh, K, Sow, SLS, Ostrowski, M, Brown, MV, van de Kamp, J, Franco-Santos, RM, Bodrossy, L & Waite, AM 2021, 'Metabolic pathways inferred from a bacterial marker gene illuminate ecological changes across South Pacific frontal boundaries', Nature Communications, vol. 12, no. 1, pp. 11-12.
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AbstractGlobal oceanographic monitoring initiatives originally measured abiotic essential ocean variables but are currently incorporating biological and metagenomic sampling programs. There is, however, a large knowledge gap on how to infer bacterial functions, the information sought by biogeochemists, ecologists, and modelers, from the bacterial taxonomic information (produced by bacterial marker gene surveys). Here, we provide a correlative understanding of how a bacterial marker gene (16S rRNA) can be used to infer latitudinal trends for metabolic pathways in global monitoring campaigns. From a transect spanning 7000 km in the South Pacific Ocean we infer ten metabolic pathways from 16S rRNA gene sequences and 11 corresponding metagenome samples, which relate to metabolic processes of primary productivity, temperature-regulated thermodynamic effects, coping strategies for nutrient limitation, energy metabolism, and organic matter degradation. This study demonstrates that low-cost, high-throughput bacterial marker gene data, can be used to infer shifts in the metabolic strategies at the community scale.

Ros, M, Suggett, DJ, Edmondson, J, Haydon, T, Hughes, DJ, Kim, M, Guagliardo, P, Bougoure, J, Pernice, M, Raina, J-B & Camp, EF 2021, 'Symbiont shuffling across environmental gradients aligns with changes in carbon uptake and translocation in the reef-building coral Pocillopora acuta', Coral Reefs, vol. 40, no. 2, pp. 595-607.
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Rosset, SL, Oakley, CA, Ferrier-Pagès, C, Suggett, DJ, Weis, VM & Davy, SK 2021, 'The Molecular Language of the Cnidarian–Dinoflagellate Symbiosis', Trends in Microbiology, vol. 29, no. 4, pp. 320-333.
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The cnidarian-dinoflagellate symbiosis is of huge importance as it underpins the success of coral reefs, yet we know very little about how the host cnidarian and its dinoflagellate endosymbionts communicate with each other to form a functionally integrated unit. Here, we review the current knowledge of interpartner molecular signaling in this symbiosis, with an emphasis on lipids, glycans, reactive species, biogenic volatiles, and noncoding RNA. We draw upon evidence of these compounds from recent omics-based studies of cnidarian-dinoflagellate symbiosis and discuss the signaling roles that they play in other, better-studied symbioses. We then consider how improved knowledge of interpartner signaling might be used to develop solutions to the coral reef crisis by, for example, engineering more thermally resistant corals.

Rouhi, O, Razavi Bazaz, S, Niazmand, H, Mirakhorli, F, Mas-hafi, S, A. Amiri, H, Miansari, M & Ebrahimi Warkiani, M 2021, 'Numerical and Experimental Study of Cross-Sectional Effects on the Mixing Performance of the Spiral Microfluidics', Micromachines, vol. 12, no. 12, pp. 1470-1470.
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Mixing at the microscale is of great importance for various applications ranging from biological and chemical synthesis to drug delivery. Among the numerous types of micromixers that have been developed, planar passive spiral micromixers have gained considerable interest due to their ease of fabrication and integration into complex miniaturized systems. However, less attention has been paid to non-planar spiral micromixers with various cross-sections and the effects of these cross-sections on the total performance of the micromixer. Here, mixing performance in a spiral micromixer with different channel cross-sections is evaluated experimentally and numerically in the Re range of 0.001 to 50. The accuracy of the 3D-finite element model was first verified at different flow rates by tracking the mixing index across the loops, which were directly proportional to the spiral radius and were hence also proportional to the Dean flow. It is shown that higher flow rates induce stronger vortices compared to lower flow rates; thus, fewer loops are required for efficient mixing. The numerical study revealed that a large-angle outward trapezoidal cross-section provides the highest mixing performance, reaching efficiencies of up to 95%. Moreover, the velocity/vorticity along the channel length was analyzed and discussed to evaluate channel mixing performance. A relatively low pressure drop (<130 kPa) makes these passive spiral micromixers ideal candidates for various lab-on-chip applications.

Rouzé, H, Galand, PE, Medina, M, Bongaerts, P, Pichon, M, Pérez-Rosales, G, Torda, G, Moya, A, Bardout, G, Périé-Bardout, E, Marivint, E, Lagarrigue, G, Leblond, J, Gazzola, F, Pujolle, S, Mollon, N, Mittau, A, Fauchet, J, Paulme, N, Pete, R, Peyrusse, K, Ferucci, A, Magnan, A, Horlaville, M, Breton, C, Gouin, M, Markocic, T, Jubert, I, Herrmann, P, Raina, J-B & Hédouin, L 2021, 'Symbiotic associations of the deepest recorded photosynthetic scleractinian coral (172 m depth)', The ISME Journal, vol. 15, no. 5, pp. 1564-1568.
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Abstract The symbiosis between scleractinian corals and photosynthetic algae from the family Symbiodiniaceae underpins the health and productivity of tropical coral reef ecosystems. While this photosymbiotic association has been extensively studied in shallow waters (&lt;30 m depth), we do not know how deeper corals, inhabiting large and vastly underexplored mesophotic coral ecosystems, modulate their symbiotic associations to grow in environments that receive less than 1% of surface irradiance. Here we report on the deepest photosymbiotic scleractinian corals collected to date (172 m depth), and use amplicon sequencing to identify the associated symbiotic communities. The corals, identified as Leptoseris hawaiiensis, were confirmed to host Symbiodiniaceae, predominantly of the genus Cladocopium, a single species of endolithic algae from the genus Ostreobium, and diverse communities of prokaryotes. Our results expand the reported depth range of photosynthetic scleractinian corals (0–172 m depth), and provide new insights on their symbiotic associations at the lower depth extremes of tropical coral reefs.

Scanes, E, Parker, LM, Seymour, JR, Siboni, N, Dove, MC, O’Connor, WA & Ross, PM 2021, 'Microbiomes of an oyster are shaped by metabolism and environment', Scientific Reports, vol. 11, no. 1.
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AbstractMicrobiomes can both influence and be influenced by metabolism, but this relationship remains unexplored for invertebrates. We examined the relationship between microbiome and metabolism in response to climate change using oysters as a model marine invertebrate. Oysters form economies and ecosystems across the globe, yet are vulnerable to climate change. Nine genetic lineages of the oyster Saccostrea glomerata were exposed to ambient and elevated temperature and PCO2 treatments. The metabolic rate (MR) and metabolic by-products of extracellular pH and CO2 were measured. The oyster-associated bacterial community in haemolymph was characterised using 16 s rRNA gene sequencing. We found a significant negative relationship between MR and bacterial richness. Bacterial community composition was also significantly influenced by MR, extracellular CO2 and extracellular pH. The effects of extracellular CO2 depended on genotype, and the effects of extracellular pH depended on CO2 and temperature treatments. Changes in MR aligned with a shift in the relative abundance of 152 Amplicon Sequencing Variants (ASVs), with 113 negatively correlated with MR. Some spirochaete ASVs showed positive relationships with MR. We have identified a clear relationship between host metabolism and the microbiome in oysters. Altering this relationship will likely have consequences for the 12 billion USD oyster economy.

Scanes, E, Parker, LM, Seymour, JR, Siboni, N, King, WL, Danckert, NP, Wegner, KM, Dove, MC, O'Connor, WA & Ross, PM 2021, 'Climate change alters the haemolymph microbiome of oysters', Marine Pollution Bulletin, vol. 164, pp. 111991-111991.
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The wellbeing of marine organisms is connected to their microbiome. Oysters are a vital food source and provide ecological services, yet little is known about how climate change such as ocean acidification and warming will affect their microbiome. We exposed the Sydney rock oyster, Saccostrea glomerata, to orthogonal combinations of temperature (24, 28 °C) and pCO₂ (400 and 1000 μatm) for eight weeks and used amplicon sequencing of the 16S rRNA (V3-V4) gene to characterise the bacterial community in haemolymph. Overall, elevated pCO₂ and temperature interacted to alter the microbiome of oysters, with a clear partitioning of treatments in CAP ordinations. Elevated pCO₂ was the strongest driver of species diversity and richness and elevated temperature also increased species richness. Climate change, both ocean acidification and warming, will alter the microbiome of S. glomerata which may increase the susceptibility of oysters to disease.

Scanes, E, Parker, LM, Seymour, JR, Siboni, N, King, WL, Wegner, KM, Dove, MC, O'Connor, WA & Ross, PM 2021, 'Microbiome response differs among selected lines of Sydney rock oysters to ocean warming and acidification', FEMS Microbiology Ecology, vol. 97, no. 8, pp. 1-13.
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ABSTRACTOyster microbiomes are integral to healthy function and can be altered by climate change conditions. Genetic variation among oysters is known to influence the response of oysters to climate change and may ameliorate any adverse effects on oyster microbiome; however, this remains unstudied. Nine full-sibling selected breeding lines of the Sydney rock oyster (Saccostrea glomerata) were exposed to predicted warming (ambient = 24°C, elevated = 28°C) and ocean acidification (ambient pCO2 = 400, elevated pCO2 = 1000 µatm) for 4 weeks. The haemolymph bacterial microbiome was characterized using 16S rRNA (V3–V4) gene sequencing and varied among oyster lines in the control (ambient pCO2, 24°C) treatment. Microbiomes were also altered by climate change dependent on oyster lines. Bacterial α-diversity increased in response to elevated pCO2 in two selected lines, while bacterial β-diversity was significantly altered by combinations of elevated pCO2 and temperature in four selected lines. Climate change treatments caused shifts in the abundance of multiple amplicon sequence variants driving change in the microbiome of some selected lines. We show that oyster genetic background may influence the Sydney rock oyster haemolymph microbiome under climate change and that future assisted evolution breeding programs to enhance resilience should consider the oyster microbiome.

Schuback, N, Tortell, PD, Berman-Frank, I, Campbell, DA, Ciotti, A, Courtecuisse, E, Erickson, ZK, Fujiki, T, Halsey, K, Hickman, AE, Huot, Y, Gorbunov, MY, Hughes, DJ, Kolber, ZS, Moore, CM, Oxborough, K, Prášil, O, Robinson, CM, Ryan-Keogh, TJ, Silsbe, G, Simis, S, Suggett, DJ, Thomalla, S & Varkey, DR 2021, 'Single-Turnover Variable Chlorophyll Fluorescence as a Tool for Assessing Phytoplankton Photosynthesis and Primary Productivity: Opportunities, Caveats and Recommendations', Frontiers in Marine Science, vol. 8, pp. 1-24.
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Phytoplankton photosynthetic physiology can be investigated through single-turnover variable chlorophyll fluorescence (ST-ChlF) approaches, which carry unique potential to autonomously collect data at high spatial and temporal resolution. Over the past decades, significant progress has been made in the development and application of ST-ChlF methods in aquatic ecosystems, and in the interpretation of the resulting observations. At the same time, however, an increasing number of sensor types, sampling protocols, and data processing algorithms have created confusion and uncertainty among potential users, with a growing divergence of practice among different research groups. In this review, we assist the existing and upcoming user community by providing an overview of current approaches and consensus recommendations for the use of ST-ChlF measurements to examine in-situ phytoplankton productivity and photo-physiology. We argue that a consistency of practice and adherence to basic operational and quality control standards is critical to ensuring data inter-comparability. Large datasets of inter-comparable and globally coherent ST-ChlF observations hold the potential to reveal large-scale patterns and trends in phytoplankton photo-physiology, photosynthetic rates and bottom-up controls on primary productivity. As such, they hold great potential to provide invaluable physiological observations on the scales relevant for the development and validation of ecosystem models and remote sensing algorithms.

Sezginer, Y, Suggett, DJ, Izett, RW & Tortell, PD 2021, 'Irradiance and nutrient-dependent effects on photosynthetic electron transport in Arctic phytoplankton: A comparison of two chlorophyll fluorescence-based approaches to derive primary photochemistry', PLOS ONE, vol. 16, no. 12, pp. e0256410-e0256410.
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We employed Fast Repetition Rate fluorometry for high-resolution mapping of marine phytoplankton photophysiology and primary photochemistry in the Lancaster Sound and Barrow Strait regions of the Canadian Arctic Archipelago in the summer of 2019. Continuous ship-board analysis of chlorophyll a variable fluorescence demonstrated relatively low photochemical efficiency over most of the cruise-track, with the exception of localized regions within Barrow Strait, where there was increased vertical mixing and proximity to land-based nutrient sources. Along the full transect, we observed strong non-photochemical quenching of chlorophyll fluorescence, with relaxation times longer than the 5-minute period used for dark acclimation. Such long-term quenching effects complicate continuous underway acquisition of fluorescence amplitude-based estimates of photosynthetic electron transport rates, which rely on dark acclimation of samples. As an alternative, we employed a new algorithm to derive electron transport rates based on analysis of fluorescence relaxation kinetics, which does not require dark acclimation. Direct comparison of kinetics- and amplitude-based electron transport rate measurements demonstrated that kinetic-based estimates were, on average, 2-fold higher than amplitude-based values. The magnitude of decoupling between the two electron transport rate estimates increased in association with photophysiological diagnostics of nutrient stress. Discrepancies between electron transport rate estimates likely resulted from the use of different photophysiological parameters to derive the kinetics- and amplitude-based algorithms, and choice of numerical model used to fit variable fluorescence curves and analyze fluorescence kinetics under actinic light. Our results highlight environmental and methodological influences on fluorescence-based photochemistry estimates, and prompt discussion of best-practices for future underway fl...

Shahid, A, Khan, AZ, Malik, S, Liu, C-G, Mehmood, MA, Syafiuddin, A, Wang, N, Zhu, H & Boopathy, R 2021, 'Advances in Green Technologies for the Removal of Effluent Organic Matter from the Urban Wastewater', Current Pollution Reports, vol. 7, no. 4, pp. 463-475.
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Purpose of Review: Effluent organic matter (EfOM) is a blend of organic matter, microbial constituents, biological metabolites, and synthetic chemicals which is originated mainly due to anthropogenic activities and is a matter of emerging environmental concern. The presence of EfOM poses a major challenge in the wastewater treatment processes. This review is aimed to assess the recent progress in developing innovative green approaches for the biotransformation of EfOM into ecofriendly products which is vital to attain the “zero-waste” paradigm to achieve wastewater reclamation and environmental sustainability under the umbrella of circular bioeconomy. Recent Findings: Characteristics of EfOM and its impact on wastewater treatment processes have been evaluated. The potential and shortcomings of the traditional, advanced, and biological approaches for the EfOM removal have been described. Recent strategies which are based on the combination of two or more of these technologies (hybrid systems) have been discussed to address the challenges/shortcomings of the standalone technologies and to improve the process efficiency. Microalgae and cyanobacteria-based removal of EfOM along with its subsequent utilization as a soil amender is proposed as a novel trend in the future. Summary: Assessment of the previously employed technologies provided an insight into their working mechanisms which have suggested several improvements in the processes. Besides, hybrid systems could be an ecofriendly removal of EfOM via biosorption.

Shahid, A, Malik, S, Liu, C-G, Musharraf, SG, Siddiqui, AJ, Khan, F, Tarbiah, NI, Gull, M, Rashid, U & Mehmood, MA 2021, 'Characterization of a newly isolated cyanobacterium Plectonema terebrans for biotransformation of the wastewater-derived nutrients to biofuel and high-value bioproducts', Journal of Water Process Engineering, vol. 39, pp. 101702-101702.
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Cultivating photosynthetic microbes in city wastewater may help to achieve environmental sustainability owing to concomitant pollutant removal, biological transformation of the nutrients into bioproducts, and atmospheric carbon fixation. Cyanobacteria are the most efficient photosynthetic fixers of atmospheric carbon along with the microalgae. The present study was focused on optimizing the growth conditions for a newly isolated filamentous cyanobacterium Plectonema terebrans BERC10 to achieve enhanced biomass and metabolite productivity for a multiproduct biorefinery using various compositions of synthetic wastewaters. Higher biomass productivity of 140 mg L−1 d−1 (dried mass) with CO2 sequestration rate of 250 mg L−1 day−1 was achieved by mimicking the summer (32 ± 2 °C) cultivation conditions, which was further favored by the wastewater-derived alkalinity (pH 10.0–11.0). The biomass produced was rich in carbohydrates and lipids, having 58.68 mgg−1d−1 and 39.25 mgg−1d−1 of carbohydrate and lipid productivities, respectively. While winter cultivation conditions (22 ± 2 °C) favored higher protein productivity (34.49 mgg−1d−1) when compared to summer conditions. Additionally, in response to excessive nutrients and alkalinity (pH 10.0), it produced 180-198 mgg-1 of phycobilins. Considering the multiproduct concept, the phycobilins were extracted and lipids from the residual biomass were converted to biodiesel and analyzed by gas chromatography-mass spectrometry (GC–MS). Intrestingly, phycobilin extraction had no negative impact on the quality and content of the biodiesel in the residual biomass. These features make the Plectonema terebrans BERC10 a promising candidate for the biological transformation of wastewater derived nutrients to biofuels and bioproducts.

Shahid, A, Usman, M, Atta, Z, Musharraf, SG, Malik, S, Elkamel, A, Shahid, M, Abdulhamid Alkhattabi, N, Gull, M & Mehmood, MA 2021, 'Impact of wastewater cultivation on pollutant removal, biomass production, metabolite biosynthesis, and carbon dioxide fixation of newly isolated cyanobacteria in a multiproduct biorefinery paradigm', Bioresource Technology, vol. 333, pp. 125194-125194.
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The impact of wastewater cultivation was studied on pollutant removal, biomass production, and biosynthesis of high-value metabolites by newly isolated cyanobacteria namely Acaryochloris marina BERC03, Oscillatoria sp. BERC04, and Pleurocapsa sp. BERC06. During cultivation in urabn wastewater, its pH used to adjust from pH 8.0 to 11, offering contamination-free cultivation, and flotation-based easy harvesting. Besides, wastewater cultivation improved biomass production by 1.3-fold when compared to control along with 3.54-4.2 gL-1 of CO2 fixation, concomitantly removing suspended organic matter, total nitrogen, and phosphorus by 100%, 53%, and 88%, respectively. Biomass accumulated 26-36% carbohydrates, 15-28% proteins, 38-43% lipids, and 6.3-9.5% phycobilins, where phycobilin yield was improved by 1.6-fold when compared to control. Lipids extracted from the pigment-free biomass were trans-esterified to biodiesel where pigment extraction showed no negative impact on quality of the biodiesel. These strains demonstrated the potential to become feedstock of an integrated biorefinery using urban wastewater as low-cost growth media.

Songsomboon, K, Brenton, Z, Heuser, J, Kresovich, S, Shakoor, N, Mockler, T & Cooper, EA 2021, 'Genomic patterns of structural variation among diverse genotypes of Sorghum bicolor and a potential role for deletions in local adaptation', G3 Genes|Genomes|Genetics, vol. 11, no. 7.
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Abstract Genomic structural mutations, especially deletions, are an important source of variation in many species and can play key roles in phenotypic diversification and evolution. Previous work in many plant species has identified multiple instances of structural variations (SVs) occurring in or near genes related to stress response and disease resistance, suggesting a possible role for SVs in local adaptation. Sorghum [Sorghum bicolor (L.) Moench] is one of the most widely grown cereal crops in the world. It has been adapted to an array of different climates as well as bred for multiple purposes, resulting in a striking phenotypic diversity. In this study, we identified genome-wide SVs in the Biomass Association Panel, a collection of 347 diverse sorghum genotypes collected from multiple countries and continents. Using Illumina-based, short-read whole-genome resequencing data from every genotype, we found a total of 24,648 SVs, including 22,359 deletions. The global site frequency spectrum of deletions and other types of SVs fit a model of neutral evolution, suggesting that the majority of these mutations were not under any types of selection. Clustering results based on single nucleotide polymorphisms separated the genotypes into eight clusters which largely corresponded with geographic origins, with many of the large deletions we uncovered being unique to a single cluster. Even though most deletions appeared to be neutral, a handful of cluster-specific deletions were found in genes related to biotic and abiotic stress responses, supporting the possibility that at least some of these deletions contribute to local adaptation in sorghum.

Supasri, K, Kumar, M, Mathew, M, Signal, B, Padula, M, Suggett, D & Ralph, P 2021, 'Evaluation of Filter, Paramagnetic, and STAGETips Aided Workflows for Proteome Profiling of Symbiodiniaceae Dinoflagellate', Processes, vol. 9, no. 6, pp. 983-983.
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The integrity of coral reef ecosystems worldwide rests on a fine-tuned symbiotic interaction between an invertebrate and a dinoflagellate microalga from the family Symbiodiniaceae. Recent advances in bottom-up shotgun proteomic approaches and the availability of vast amounts of genetic information about Symbiodiniaceae have provided a unique opportunity to better understand the molecular mechanisms underpinning the interactions of coral-Symbiodiniaceae. However, the resilience of this dinoflagellate cell wall, as well as the presence of polyanionic and phenolics cell wall components, requires the optimization of sample preparation techniques for successful implementation of bottom-up proteomics. Therefore, in this study we compare three different workflows—filter-aided sample preparation (FASP), single-pot solid-phase-enhanced sample preparation (SP3), and stop-and-go-extraction tips (STAGETips, ST)—to develop a high-throughput proteotyping protocol for Symbiodiniaceae algal research. We used the model isolate Symbiodinium tridacnidorum. We show that SP3 outperformed ST and FASP with regard to robustness, digestion efficiency, and contaminant removal, which led to the highest number of total (3799) and unique proteins detected from 23,593 peptides. Most of these proteins were detected with ≥2 unique peptides (73%), zero missed tryptic peptide cleavages (91%), and hydrophilic peptides (>70%). To demonstrate the functionality of this optimized SP3 sample preparation workflow, we examined the proteome of S. tridacnidorum to better understand the molecular mechanism of peridinin-chlorophyll-protein complex (PCP, light harvesting protein) accumulation under low light (LL, 30 μmol photon m−2 s−1). Cells exposed to LL for 7 days upregulated various light harvesting complex (LHCs) proteins through the mevalonate-independent pathway; proteins of this pathway were at 2- to 6-fold higher levels than the control of 120 μmol photon m−2 s−1. Potentially, L...

Supasri, KM, Kumar, M, Segečová, A, McCauley, JI, Herdean, A, Padula, MP, O’Meara, T & Ralph, PJ 2021, 'Characterisation and Bioactivity Analysis of Peridinin-Chlorophyll a-Protein (PCP) Isolated from Symbiodinium tridacnidorum CS-73', Journal of Marine Science and Engineering, vol. 9, no. 12, pp. 1387-1387.
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Peridinin-Chlorophyll a-Proteins (PCP) are the major light harvesting proteins in photosynthetic dinoflagellates. PCP shows great variation in protein length, pigment ratio, sequence, and spectroscopic properties. PCP conjugates (PerCP) are widely used as fluorescent probes for cellular and tissue analysis in the biomedical field. PCP consists of a peridinin carotenoid; thereby, it can potentially be used as a bioactive compound in pharmaceutical applications. However, the biological activities of PCP are yet to be explored. In this study, we extracted, purified, and partially characterised the PCP from Symbiodinium tridacnidorum (CS-73) and explored its antioxidant, anti-cancer and anti-inflammation bioactivities. The PCP was purified using an ÄKTA™ PURE system and predicted to be of 17.3 kDa molecular weight (confirmed as a single band on SDS-PAGE) with an isoelectric point (pI) 5.6. LC-MS/MS and bioinformatic analysis of purified PCP digested with trypsin indicated it was 164 amino acids long with >90% sequence similarity to PCP of SymA3.s6014_g3 (belonging to clade A of Symbiodinium sp.) confirmed with 59 peptide combinations matched across its protein sequence. The spectroscopic properties of purified PCP showed a slight shift in absorption and emission spectra to previously documented analysis in Symbiodinium species possibly due to variation in amino acid sequences that interact with chl a and peridinin. Purified PCP consisted of a 19-amino-acid-long signal peptide at its N terminal and nine helixes in its secondary structure, with several protein binding sites and no DNA/RNA binding site. Furthermore, purified PCP exhibited antioxidant and in vitro anti-inflammation bioactivities, and anti-cancer activities against human metastatic breast adenocarcinoma (MDA-MB-231) and human colorectal (HTC-15) cancer cell lines. Together, all these findings present PCP as a promising candidate for continued investigations for pharmaceutical applicat...

Sutherland, DL & Ralph, PJ 2021, 'Differing growth responses in four related microalgal genera grown under autotrophic, mixotrophic and heterotrophic conditions', Journal of Applied Phycology, vol. 33, no. 6, pp. 3539-3553.
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Sutherland, DL & Ralph, PJ 2021, 'Productivity and community response along an ammonia gradient in cultured wild marine microalgae, using wastewater-derived nutrients for cost-effective feedstock production', Journal of Applied Phycology, vol. 33, no. 5, pp. 2933-2945.
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Sutherland, DL & Ralph, PJ 2021, 'Shortening hydraulic retention time through effluent recycling: impacts on wastewater treatment and biomass production in microalgal treatment systems', Journal of Applied Phycology, vol. 33, no. 6, pp. 3873-3884.
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Sutherland, DL, Burke, J & Ralph, PJ 2021, 'High-throughput screening for heterotrophic growth in microalgae using the Biolog Plate assay', New Biotechnology, vol. 65, pp. 61-68.
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Sutherland, DL, Burke, J & Ralph, PJ 2021, 'Trade-offs between effluent quality and ammonia volatilisation with CO2 augmented microalgal treatment of anaerobically digested food-waste centrate', Journal of Environmental Management, vol. 277, pp. 111398-111398.
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Diversion of food waste from landfill disposal to waste-to-energy facilities has become both an environmentally and economically viable option to support the circular bioeconomy. However, the liquid centrate produced during anaerobic digestion is high in total ammonia, with concentrations ~2000 g m-3, and can release gaseous emissions, including ammonia, methane, CO2 and nitrous oxide, to the atmosphere. Further treatment is required before discharge to sewer, or to the environment. Microalgal wastewater treatment systems augmented with CO2 offer a promising and cost-effective treatment solution for reducing both total ammonia concentrations and ammonia volatilisation. In this study, we investigate the effects of augmenting CO2 on nutrient removal and specifically nitrogen losses, as well as biomass productivity under two difference hydraulic retention times (HRT). Both CO2 addition and HRT affect nitrogen losses, with the percentage removal of total ammonia significantly lower (p < 0.01) when CO2 was added to the treatments, while increased HRT significantly increased (p < 0.05) total ammonia percentage removal. Total nitrogen budgets showed significantly lower (p < 0.01) abiotic nitrogen losses from the system when CO2 was added to the culture but at the expense of effluent quality. Both total suspended solids and volatile suspended solids significantly increased (p < 0.01) under longer HRT (8 days), with CO2 addition, while chlorophyll-a biomass significantly increased (p < 0.01) on longer HRT, regardless of CO2 addition. These results demonstrate that, while CO2 augmentation helped to mitigate ammonia losses to atmosphere, the trade-off was poorer effluent quality. Coupling CO2 augmentation with longer HRT increased biomass production and nutrient removal efficiency. This study provides an insight into how simple operational changes can alleviate some of the trade-offs between atmospheric losses and effluent quality. However, in order to manage the trade-off ...

Sutherland, DL, McCauley, J, Labeeuw, L, Ray, P, Kuzhiumparambil, U, Hall, C, Doblin, M, Nguyen, LN & Ralph, PJ 2021, 'How microalgal biotechnology can assist with the UN Sustainable Development Goals for natural resource management', Current Research in Environmental Sustainability, vol. 3, pp. 100050-100050.
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Sutherland, DL, Park, J, Ralph, PJ & Craggs, R 2021, 'Ammonia, pH and dissolved inorganic carbon supply drive whole pond metabolism in full-scale wastewater high rate algal ponds', Algal Research, vol. 58, pp. 102405-102405.
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Vardi, T, Hoot, WC, Levy, J, Shaver, E, Winters, RS, Banaszak, AT, Baums, IB, Chamberland, VF, Cook, N, Gulko, D, Hein, MY, Kaufman, L, Loewe, M, Lundgren, P, Lustic, C, MacGowan, P, Matz, MV, McGonigle, M, McLeod, I, Moore, J, Moore, T, Pivard, S, Pollock, FJ, Rinkevich, B, Suggett, DJ, Suleiman, S, Viehman, TS, Villalobos, T, Weis, VM, Wolke, C & Montoya‐Maya, PH 2021, 'Six priorities to advance the science and practice of coral reef restoration worldwide', Restoration Ecology, vol. 29, no. 8.
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Coral reef restoration is a rapidly growing movement galvanized by the accelerating degradation of the world's tropical coral reefs. The need for concerted and collaborative action focused on the recovery of coral reef ecosystems coalesced in the creation of the Coral Restoration Consortium (CRC) in 2017. In March 2020, the CRC leadership team met for a biennial review of international coral reef restoration efforts and a discussion of perceived knowledge and implementation bottlenecks that may impair scalability and efficacy. Herein we present six priorities wherein the CRC will foster scientific advancement and collaboration to: (1) increase restoration efficiency, focusing on scale and cost‐effectiveness of deployment; (2) scale up larval‐based coral restoration efforts, emphasizing recruit health, growth, and survival; (3) ensure restoration of threatened coral species proceeds within a population‐genetics management context; (4) support a holistic approach to coral reef ecosystem restoration; (5) develop and promote the use of standardized terms and metrics for coral reef restoration; and (6) support coral reef restoration practitioners working in diverse geographic locations. These priorities are not exhaustive nor do we imply that accomplishing these tasks alone will be sufficient to restore coral reefs globally; rather these are topics where we feel the CRC community of practice can make timely and significant contributions to facilitate the growth of coral reef restoration as a practical conservation strategy. The goal for these collective actions is to provide tangible, local‐scale advancements in reef condition that offset declines resulting from local and global stressors including climate change.

Vo, HNP, Ngo, HH, Guo, W, Nguyen, KH, Chang, SW, Nguyen, DD, Cheng, D, Bui, XT, Liu, Y & Zhang, X 2021, 'Effect of calcium peroxide pretreatment on the remediation of sulfonamide antibiotics (SMs) by Chlorella sp.', Science of The Total Environment, vol. 793, pp. 148598-148598.
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This study investigated the effect of CaO₂ pretreatment on sulfonamide antibiotics (SMs) remediation by Chlorella sp. Results showed that a CaO₂ dose ranging from 0.05 to 0.1 g/g biomass was the best and led to higher SMs removal efficacy 5-10% higher than the control. The contributions made by cometabolism and CaO₂ in SMs remediation were very similar. Bioassimilation could remove 24% of sulfadiazine (SDZ) and sulfamethazine (SMZ), and accounted for 38% of sulfamethoxazole (SMX) remediation. Pretreatment by CaO₂ wielded a positive effect on microalgae. The extracellular polymeric substances (EPS) level of the CaO₂ pretreatment microalgae was three times higher when subjected to non-pretreatment. For the long-term, pretreatment microalgae removed SMs 10-20% more than the non-pretreatment microalgae. Protein fractions of EPS in continuous operation produced up to 90 mg/L for cometabolism. For bioassimilation, SMX intensity of the pretreatment samples was 160-fold less than the non-treatment one. It indicated the CaO₂ pretreatment has enhanced the biochemical function of the intracellular environment of microalgae. Peroxidase enzyme involved positively in the cometabolism and degradation of SMs to several metabolites including ring cleavage, hydroxylation and pterin-related conjugation.

Voolstra, CR, Quigley, KM, Davies, SW, Parkinson, JE, Peixoto, RS, Aranda, M, Baker, AC, Barno, AR, Barshis, DJ, Benzoni, F, Bonito, V, Bourne, DG, Buitrago-López, C, Bridge, TCL, Chan, CX, Combosch, DJ, Craggs, J, Frommlet, JC, Herrera, S, Quattrini, AM, Röthig, T, Reimer, JD, Rubio-Portillo, E, Suggett, DJ, Villela, H, Ziegler, M & Sweet, M 2021, 'Consensus Guidelines for Advancing Coral Holobiont Genome and Specimen Voucher Deposition', Frontiers in Marine Science, vol. 8, pp. 1-12.
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Coral research is being ushered into the genomic era. To fully capitalize on the potential discoveries from this genomic revolution, the rapidly increasing number of high-quality genomes requires effective pairing with rigorous taxonomic characterizations of specimens and the contextualization of their ecological relevance. However, to date there is no formal framework that genomicists, taxonomists, and coral scientists can collectively use to systematically acquire and link these data. Spurred by the recently announced “Coral symbiosis sensitivity to environmental change hub” under the “Aquatic Symbiosis Genomics Project” - a collaboration between the Wellcome Sanger Institute and the Gordon and Betty Moore Foundation to generate gold-standard genome sequences for coral animal hosts and their associated Symbiodiniaceae microalgae (among the sequencing of many other symbiotic aquatic species) - we outline consensus guidelines to reconcile different types of data. The metaorganism nature of the coral holobiont provides a particular challenge in this context and is a key factor to consider for developing a framework to consolidate genomic, taxonomic, and ecological (meta)data. Ideally, genomic data should be accompanied by taxonomic references, i.e., skeletal vouchers as formal morphological references for corals and strain specimens in the case of microalgal and bacterial symbionts (cultured isolates). However, exhaustive taxonomic characterization of all coral holobiont member species is currently not feasible simply because we do not have a comprehensive understanding of all the organisms that constitute the coral holobiont. Nevertheless, guidelines on minimal, recommended, and ideal-case descriptions for the major coral holobiont constituents (coral animal, Symbiodiniaceae microalgae, and prokaryotes) will undoubtedly help in future referencing and will facilitate comparative studies. We hope that the guidelines outlined here, which we will ad...

Voolstra, CR, Suggett, DJ, Peixoto, RS, Parkinson, JE, Quigley, KM, Silveira, CB, Sweet, M, Muller, EM, Barshis, DJ, Bourne, DG & Aranda, M 2021, 'Extending the natural adaptive capacity of coral holobionts', Nature Reviews Earth & Environment, vol. 2, no. 11, pp. 747-762.
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Anthropogenic climate change and environmental degradation destroy coral reefs, the ecosystem services they provide, and the livelihoods of close to a billion people who depend on these services. Restoration approaches to increase the resilience of corals are therefore necessary to counter environmental pressures relevant to climate change projections. In this Review, we examine the natural processes that can increase the adaptive capacity of coral holobionts, with the aim of preserving ecosystem functioning under future ocean conditions. Current approaches that centre around restoring reef cover can be integrated with emerging approaches to enhance coral stress resilience and, thereby, allow reefs to regrow under a new set of environmental conditions. Emerging approaches such as standardized acute thermal stress assays, selective sexual propagation, coral probiotics, and environmental hardening could be feasible and scalable in the real world. However, they must follow decision-making criteria that consider the different reef, environmental, and ecological conditions. The implementation of adaptive interventions tailored around nature-based solutions will require standardized frameworks, appropriate ecological risk–benefit assessments, and analytical routines for consistent and effective utilization and global coordination.

Vu, HP, Nguyen, LN, Emmerton, B, Wang, Q, Ralph, PJ & Nghiem, LD 2021, 'Factors governing microalgae harvesting efficiency by flocculation using cationic polymers', Bioresource Technology, vol. 340, pp. 125669-125669.
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This study aims to elucidate the mechanisms governing the harvesting efficiency of Chlorella vulgaris by flocculation using a cationic polymer. Flocculation efficiency increased as microalgae culture matured (i.e. 35-45, 75, and > 97% efficiency at early, late exponential, and stationary phase, respectively. Unlike the negative impact of phosphate on flocculation in traditional wastewater treatment; here, phosphorous residue did not influence the flocculation efficiency of C. vulgaris. The observed dependency of flocculation efficiency on growth phase was driven by changes in microalgal cell properties. Microalgal extracellular polymeric substances (EPS) in both bound and free forms at stationary phase were two and three times higher than those at late and early exponential phase, respectively. Microalgae cells also became more negatively charged as they matured. Negatively charged and high EPS content together with the addition of high molecular weight and positively charged polymer could facilitate effective flocculation via charge neutralisation and bridging.

Vu, HP, Nguyen, LN, Vu, MT, Labeeuw, L, Emmerton, B, Commault, AS, Ralph, PJ, Mahlia, TMI & Nghiem, LD 2021, 'Harvesting Porphyridium purpureum using polyacrylamide polymers and alkaline bases and their impact on biomass quality', Science of The Total Environment, vol. 755, no. Pt 1, pp. 142412-142412.
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This study aims to examine the flocculation efficiency of Porphyridium purpureum (i.e. a red marine microalga with high content of pigments and fatty acids) grown in seawater medium using polyacrylamide polymers and alkaline flocculation. Polymers Flopam™ and FO3801 achieved the highest flocculation efficiency of over 99% at the optimal dose of 21 mg per g of dry biomass through charge neutralisation and bridging mechanism. The addition of sodium hydroxide, potassium hydroxide, and sodium carbonate also achieved flocculation efficiency of 98 and 91%, respectively, but high doses were required (i.e. > 500 mg per g of dry biomass). Calcium hydroxide was not as effective and could only achieve 75% flocculation efficiency. Precipitation of magnesium hydroxide was identified as the major cause of hydroxide-induced flocculation. On the other hand, sodium carbonate addition induced flocculation via both magnesium and calcium carbonate co-precipitation. The large mass of precipitates caused a sweeping effect and enmeshed the microalgal cells to trigger sedimentation. Cell membrane integrity analysis of flocculated P. purpureum indicated that polyacrylamide polymers led to significant compromised cells (i.e. 96%), compared to the alkaline bases (70-96% compromised cells). These results appear to be the first to demonstrate the high efficiency of polyacrylamide polymer and alkaline flocculation of P. purpureum but at the expense of the biomass quality.

Walworth, NG, Hinners, J, Argyle, PA, Leles, SG, Doblin, MA, Collins, S & Levine, NM 2021, 'The evolution of trait correlations constrains phenotypic adaptation to high CO₂in a eukaryotic alga', Proceedings of the Royal Society B: Biological Sciences, vol. 288, no. 1953, pp. 1-9.
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Microbes form the base of food webs and drive biogeochemical cycling. Predicting the effects of microbial evolution on global elemental cycles remains a significant challenge due to the sheer number of interacting environmental and trait combinations. Here, we present an approach for integrating multivariate trait data into a predictive model of trait evolution. We investigated the outcome of thousands of possible adaptive walks parameterized using empirical evolution data from the algaChlamydomonasexposed to high CO2. We found that the direction of historical bias (existing trait correlations) influenced both the rate of adaptation and the evolved phenotypes (trait combinations). Critically, we use fitness landscapes derived directly from empirical trait values to capture known evolutionary phenomena. This work demonstrates that ecological models need to represent both changes in traits and changes in the correlation between traits in order to accurately capture phytoplankton evolution and predict future shifts in elemental cycling.

Wang, Q, Guan, YF, Hancock, SE, Wahi, K, van Geldermalsen, M, Zhang, BK, Pang, A, Nagarajah, R, Mak, B, Freidman, N, Horvath, LG, Turner, N & Holst, J 2021, 'Inhibition of guanosine monophosphate synthetase (GMPS) blocks glutamine metabolism and prostate cancer growth', The Journal of Pathology, vol. 254, no. 2, pp. 135-146.
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AbstractGlutamine is a critical nutrient in cancer; however, its contribution to purine metabolism in prostate cancer has not previously been determined. Guanosine monophosphate synthetase (GMPS) acts in the de novo purine biosynthesis pathway, utilizing a glutamine amide to synthesize the guanine nucleotide. This study demonstrates that GMPS mRNA expression correlates with Gleason score in prostate cancer samples, while high GMPS expression was associated with decreased rates of overall and disease/progression‐free survival. Pharmacological inhibition or knockdown of GMPS significantly decreased cell growth in both LNCaP and PC‐3 prostate cancer cells. We utilized [15N‐(amide)]glutamine and [U‐13C5]glutamine metabolomics to dissect the pathways involved and despite similar growth inhibition by GMPS knockdown, we show unique metabolic effects across each cell line. Using a PC‐3 xenograft mouse model, tumor growth was also significantly decreased after GMPS knockdown, highlighting the importance of glutamine metabolism and providing support for GMPS as a therapeutic target in prostate cancer. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Windhagauer, M, Abbriano, RM, Ashworth, J, Barolo, L, Jaramillo-Madrid, AC, Pernice, M & Doblin, MA 2021, 'Characterisation of novel regulatory sequences compatible with modular assembly in the diatom Phaeodactylum tricornutum', Algal Research, vol. 53, pp. 102159-102159.
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Yan, J, Kuzhiumparambil, U, Bandodkar, A, Bandodkar, S, Dale, RC & Fu, S 2021, 'Cerebrospinal fluid metabolites in tryptophan‐kynurenine and nitric oxide pathways: biomarkers for acute neuroinflammation', Developmental Medicine & Child Neurology, vol. 63, no. 5, pp. 552-559.
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AimTo explore the cerebrospinal fluid (CSF) metabolite features in acute neuroinflammatory diseases and identify potential biomarkers to diagnose and monitor neuroinflammation.MethodA cohort of 14 patients (five females, nine males; mean [median] age 7y 9mo [9y], range 6mo–13y) with acute encephalitis (acute disseminated encephalomyelitis n=6, unknown suspected viral encephalitis n=3, enteroviral encephalitis n=2, seronegative autoimmune encephalitis n=2, herpes simplex encephalitis n=1) and age‐matched non‐inflammatory neurological disease controls (n=14) were investigated using an untargeted metabolomics approach. CSF metabolites were analyzed with liquid chromatography coupled to high resolution mass spectrometry, followed by subsequent multivariate and univariate statistical methods.ResultsA total of 35 metabolites could be discriminated statistically between the groups using supervised orthogonal partial least squares discriminant analysis and analysis of variance. The tryptophan‐kynurenine pathway contributed nine key metabolites. There was a statistical increase of kynurenine, quinolinic acid, and anthranilic acid in patients with encephalitis, whereas tryptophan, 3‐hydroxyanthrnailic acid, and kynurenic acid were decreased. The nitric oxide pathway contributed four metabolites, with elevated asymmetric dimethylarginine and argininosuccinic acid, and decreased arginine and citrulline in patients with encephalitis. An increase in the CSF kynurenine/tryptophan ratio (p<0.001), anthranilic acid/3‐hydroxyanthranilic acid ratio (p<0.001), asymmetric dimethylarginine/a...

Yan, J, Kuzhiumparambil, U, Bandodkar, S, Dale, RC & Fu, S 2021, 'Cerebrospinal fluid metabolomics: detection of neuroinflammation in human central nervous system disease', Clinical & Translational Immunology, vol. 10, no. 8.
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AbstractThe high morbidity and mortality of neuroinflammatory diseases drives significant interest in understanding the underlying mechanisms involved in the innate and adaptive immune response of the central nervous system (CNS). Diagnostic biomarkers are important to define treatable neuroinflammation. Metabolomics is a rapidly evolving research area offering novel insights into metabolic pathways, and elucidation of reliable metabolites as biomarkers for diseases. This review focuses on the emerging literature regarding the detection of neuroinflammation using cerebrospinal fluid (CSF) metabolomics in human cohort studies. Studies of classic neuroinflammatory disorders such as encephalitis, CNS infection and multiple sclerosis confirm the utility of CSF metabolomics. Additionally, studies in neurodegeneration and neuropsychiatry support the emerging potential of CSF metabolomics to detect neuroinflammation in common CNS diseases such as Alzheimer's disease and depression. We demonstrate metabolites in the tryptophan–kynurenine pathway, nitric oxide pathway, neopterin and major lipid species show moderately consistent ability to differentiate patients with neuroinflammation from controls. Integration of CSF metabolomics into clinical practice is warranted to improve recognition and treatment of neuroinflammation.

Ying, L, Sinutok, S, Pramneechote, P, Aiyarak, P, Ralph, PJ & Chotikarn, P 2021, 'Physiological Responses of Pocillopora acuta and Porites lutea Under Plastic and Fishing Net Stress', Frontiers in Marine Science, vol. 8, pp. 1-13.
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Marine debris has become a global problem affecting coral health around the globe. However, the photophysiological responses of corals to marine debris stress remain unclear. Therefore, this study firstly investigated transparent and opaque plastic bag shading and fishing nets directly contacting the coral. Photosynthetic performance, pigment content, symbiont density, and calcification rate of a branching coral Pocillopora acuta and a massive coral Porites lutea were investigated after 4 weeks of exposure to marine debris. The results show that the maximum quantum yield of PSII significantly decreased in P. lutea with all treatments, while P. acuta showed no effect on the maximum quantum yield of PSII from any treatments. Transparent plastic bag shading does not affect P. acuta, but significantly affected the maximum photochemical efficiency of P. lutea. Photoacclimation of cellular pigment content was also observed under opaque plastic bag shading for both species at week 2. Fishing nets had the strongest effect and resulted in P. acuta bleaching and P. lutea partial mortality as well as a decline in zooxanthellae density. Calcification rate of P. acuta significantly decreased with treatments using opaque plastic bag and fishing net, but for P. lutea only the treatment with fishing net gave any observable effects. This study suggests that the sensitivities of corals to marine debris differ strongly by species and morphology of the coral.

Zavafer, A, Bates, H, Labeeuw, L, Kofler, JR & Ralph, PJ 2021, 'Normalized chlorophyll fluorescence imaging: A method to determine irradiance and photosynthetically active radiation in phytoplankton cultures', Algal Research, vol. 56, pp. 102309-102309.
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Zavřel, T, Schoffman, H, Lukeš, M, Fedorko, J, Keren, N & Červený, J 2021, 'Monitoring fitness and productivity in cyanobacteria batch cultures', Algal Research, vol. 56, pp. 102328-102328.
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Ziegler, M, Anton, A, Klein, SG, Rädecker, N, Geraldi, NR, Schmidt‐Roach, S, Saderne, V, Mumby, PJ, Cziesielski, MJ, Martin, C, Frölicher, TL, Pandolfi, JM, Suggett, DJ, Aranda, M, Duarte, CM & Voolstra, CR 2021, 'Integrating environmental variability to broaden the research on coral responses to future ocean conditions', Global Change Biology, vol. 27, no. 21, pp. 5532-5546.
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AbstractOur understanding of the response of reef‐building corals to changes in their physical environment is largely based on laboratory experiments, analysis of long‐term field data, and model projections. Experimental data provide unique insights into how organisms respond to variation of environmental drivers. However, an assessment of how well experimental conditions cover the breadth of environmental conditions and variability where corals live successfully is missing. Here, we compiled and analyzed a globally distributed dataset of in‐situ seasonal and diurnal variability of key environmental drivers (temperature, pCO2, and O2) critical for the growth and livelihood of reef‐building corals. Using a meta‐analysis approach, we compared the variability of environmental conditions assayed in coral experimental studies to current and projected conditions in their natural habitats. We found that annual temperature profiles projected for the end of the 21st century were characterized by distributional shifts in temperatures with warmer winters and longer warm periods in the summer, not just peak temperatures. Furthermore, short‐term hourly fluctuations of temperature and pCO2 may regularly expose corals to conditions beyond the projected average increases for the end of the 21st century. Coral reef sites varied in the degree of coupling between temperature, pCO2, and dissolved O2, which warrants site‐specific, differentiated experimental approaches depending on the local hydrography and influence of biological processes on the carbonate system and O2 availability. Our analysis highlights that a large portion of the natural environmental variability at short and long timescales is underexplored in experimental designs,...

Seymour, J, Williams, N & Siboni, N Department of Planning, Industry and Environment 2021, Microbial source tracking to assess water quality in Central coast Lagoons, NSW.

Ajani, P, Burke, J, Davies, C, Eriksen, R, Larsson, M, Neilsen, D, Petrou, K, Richardson, A & Murray, S 2021, 'TRENDS WITH BENEFITS? PHYTOPLANKTON DYNAMICS UNDER CLIMATE CHANGE AT A LONG TERM PACIFIC OCEAN STATION', TAYLOR & FRANCIS LTD, pp. 103-103.

Brunet, M, Duff, NL, Barbeyron, T & Thomas, F 2021, 'Metabolic strategies of sharing pioneer bacteria mediating fresh macroalgae breakdown', Cold Spring Harbor Laboratory.
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Herdean, A 2021, 'Action Spectra protocol for Opentrons OT-1 liquid handling robot v1', Springer Science and Business Media LLC.
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Hughes, DJ, Crosswell, JR, Doblin, MA, Oxborough, K, Ralph, PJ, Varkey, D & Suggett, DJ 2021, 'Dynamic variability of the phytoplankton electron requirement for carbon fixation in eastern Australian waters'.

Lewis, B, Suggett, D, Prentis, P & Nothdurft, L 2021, 'Revealing the Systematic Nature of Coral Attachment to Reef Substrates', Research Square Platform LLC.
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Madin, JS, McWilliam, M, Quigley, K, Bay, LK, Bellwood, D, Doropoulos, C, Fernandes, L, Harrison, P, Hoey, AS, Mumby, PJ, Ortiz, JC, Richards, ZT, Riginos, C, Schiettekatte, N, Suggett, DJ & van Oppen, MJH 2021, 'Selecting coral species for reef restoration', Cold Spring Harbor Laboratory.
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McKerral, JC, Seymour, JR, Lavery, TJ, Rogers, PJ, Jeffries, TC, Paterson, JS, Roudnew, B, Huveneers, C, Newton, K, van Dongen-Vogels, V, Cribb, NP, Winn, KM, Smith, RJ, Beckmann, CL, Prime, E, Charlton, CM, Kleshnina, M, Grigson, SR, Takeuchi, M, Seuront, L & Mitchell, JG 2021, 'Synergetic impacts of turbulence and fishing reduce ocean biomass', Cold Spring Harbor Laboratory.
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Nguyen, HD, Azzi, M, White, S, Salter, D, Trieu, T, Morgan, G, Rahman, M, Watt, S, Riley, M, Tzu-Chi Cnang, L, Barthelemy, X, Fuchs, D, Lieschke, K & Nguyen, H 2021, 'The Summer 2019-2020 Wildfires in East Coast Australia and Their Impacts on Air Quality and Health in New South Wales, Australia', MDPI AG.
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Sezginer, Y, Suggett, DJ, Izett, RW & Tortell, PD 2021, 'Chlorophyll fluorescence-based estimates of photosynthetic electron transport in Arctic phytoplankton assemblages', Cold Spring Harbor Laboratory.
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