Ahmad, N, Mehmood, MA & Malik, S 2020, 'Recombinant Protein Production in Microalgae: Emerging Trends', Protein & Peptide Letters, vol. 27, no. 2, pp. 105-110.
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:In recent years, microalgae have emerged as an alternative platform for large-scaleproduction of recombinant proteins for different commercial applications. As a productionplatform, it has several advantages, including rapid growth, easily scale up and ability to grow withor without the external carbon source. Genetic transformation of several species has beenestablished. Of these, Chlamydomonas reinhardtii has become significantly attractive for itspotential to express foreign proteins inexpensively. All its three genomes – nuclear, mitochondrialand chloroplastic – have been sequenced. As a result, a wealth of information about its geneticmachinery, protein expression mechanism (transcription, translation and post-translationalmodifications) is available. Over the years, various molecular tools have been developed for themanipulation of all these genomes. Various studies show that the transformation of the chloroplastgenome has several advantages over nuclear transformation from the biopharming point of view.According to a recent survey, over 100 recombinant proteins have been expressed in algalchloroplasts. However, the expression levels achieved in the algal chloroplast genome are generallylower compared to the chloroplasts of higher plants. Work is therefore needed to make the algalchloroplast transformation commercially competitive. In this review, we discuss some examplesfrom the algal research, which could play their role in making algal chloroplast commerciallysuccessful.
Ajani, PA, Larsson, ME, Woodcock, S, Rubio, A, Farrell, H, Brett, S & Murray, SA 2020, 'Fifteen years of Pseudo-nitzschia in an Australian estuary, including the first potentially toxic P. delicatissima bloom in the southern hemisphere', Estuarine, Coastal and Shelf Science, vol. 236, pp. 106651-106651.
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© 2020 Elsevier Ltd In March 2018, an unprecedented bloom of a species of Pseudo-nitzschia occurred in Berowra Creek, a major tributary of the Hawkesbury River estuary, New South Wales, Australia (max cell abundance 5.7 × 106 cells L−1). Morphological and phylogenetic analysis showed the bloom was dominated by the species P. delicatissima, with toxin characterization by LC-MS confirming one of the seven strains isolated produced domoic acid (DA), at a concentration of 0.34 pg DA per cell. In response to this unprecedented bloom, we used a fifteen year series of phytoplankton and physico-chemical data to relate environmental factors to spatial and temporal variability of Pseudo-nitzschia species throughout the estuary. Species in the Pseudo-nitzschia delicatissima group consistently dominated all locations monitored throughout the estuary, with peak cell densities observed in the austral autumn (lowest in winter). Overall, Generalised Additive Models (GAMs) suggested that high cell concentrations of Pseudo-nitzschia were linked to an increase in soluble reactive phosphorus and a decrease in total nitrogen at all sites, with up to 55% of the deviance explained. Twenty species of Pseudo-nitzschia have now been reported in Australian coastal waters, four of which are confirmed DA producers. We hypothesise that increased urbanization, nutrient input and warmer waters could combine to increase Pseudo-nitzschia blooms in south-eastern Australia.
Ajani, PA, Lim, HC, Verma, A, Lassudrie, M, McBean, K, Doblin, MA & Murray, SA 2020, 'First report of the potentially toxic marine diatom Pseudo‐nitzschia simulans (Bacillariophyceae) from the East Australian Current', Phycological Research, vol. 68, no. 3, pp. 254-259.
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SUMMARYCertain species of the marine diatom genus Pseudo‐nitzschia are responsible for the production of the domoic acid (DA), a neurotoxin that can bioaccumulate in the food chain and cause amnesic shellfish poisoning (ASP) in animals and humans. This study extends our knowledge by reporting on the first observation of the potentially toxic species Pseudo‐nitzschia simulans from this region. One clonal strain of P. simulans was isolated from the East Australian Current and characterized using light and transmission electron microscopy, and phylogenetic analyses based on regions of the internal transcribed spacer (ITS) and the D1–D3 region of the large subunit (LSU) of the nuclear‐encoded ribosomal deoxyribonucleic acid (rDNA), as well as examined for DA production as measured by liquid chromatography–mass spectrometry. Although this strain was non‐toxic under the defined growth conditions, the results unambiguously confirmed that this isolate is the potentially toxic species P. simulans – the first report of this species from the Southern Hemisphere.
Antonaru, LA, Cardona, T, Larkum, AWD & Nürnberg, DJ 2020, 'Global distribution of a chlorophyll f cyanobacterial marker', The ISME Journal, vol. 14, no. 9, pp. 2275-2287.
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Abstract Some cyanobacteria use light outside the visible spectrum for oxygenic photosynthesis. The far-red light (FRL) region is made accessible through a complex acclimation process that involves the formation of new phycobilisomes and photosystems containing chlorophyll f. Diverse cyanobacteria ranging from unicellular to branched-filamentous forms show this response. These organisms have been isolated from shaded environments such as microbial mats, soil, rock, and stromatolites. However, the full spread of chlorophyll f-containing species in nature is still unknown. Currently, discovering new chlorophyll f cyanobacteria involves lengthy incubation times under selective far-red light. We have used a marker gene to detect chlorophyll f organisms in environmental samples and metagenomic data. This marker, apcE2, encodes a phycobilisome linker associated with FRL-photosynthesis. By focusing on a far-red motif within the sequence, degenerate PCR and BLAST searches can effectively discriminate against the normal chlorophyll a-associated apcE. Even short recovered sequences carry enough information for phylogenetic placement. Markers of chlorophyll f photosynthesis were found in metagenomic datasets from diverse environments around the globe, including cyanobacterial symbionts, hypersaline lakes, corals, and the Arctic/Antarctic regions. This additional information enabled higher phylogenetic resolution supporting the hypothesis that vertical descent, as opposed to horizontal gene transfer, is largely responsible for this phenotype’s distribution.
Babayan, A, Neumann, MHD, Herdean, A, Shaffer, JM, Janning, M, Kobus, F, Loges, S, Di Pasquale, F, Kubista, M, Schlumpberger, M, Lampignano, R, Krahn, T, Schlange, T, Sprenger-Haussels, M, Pantel, K & Kloten, V 2020, 'Multicenter Evaluation of Independent High-Throughput and RT-qPCR Technologies for the Development of Analytical Workflows for Circulating miRNA Analysis', Cancers, vol. 12, no. 5, pp. 1166-1166.
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Background: Among emerging circulating biomarkers, miRNA has the potential to detect lung cancer and follow the course of the disease. However, miRNA analysis deserves further standardization before implementation into clinical trials or practice. Here, we performed international ring experiments to explore (pre)-analytical factors relevant to the outcome of miRNA blood tests in the context of the EU network CANCER-ID. Methods: Cell-free (cfmiRNA) and extracellular vesicle-derived miRNA (EVmiRNA) were extracted using the miRNeasy Serum/Plasma Advanced, and the ExoRNeasy Maxi kit, respectively, in a plasma cohort of 27 NSCLC patients and 20 healthy individuals. Extracted miRNA was investigated using small RNA sequencing and hybridization platforms. Validation of the identified miRNA candidates was performed using quantitative PCR. Results: We demonstrate the highest read counts in healthy individuals and NSCLC patients using QIAseq. Moreover, QIAseq showed 15.9% and 162.9% more cfmiRNA and EVmiRNA miRNA counts, respectively, in NSCLC patients compared to healthy control samples. However, a systematic comparison of selected miRNAs revealed little agreement between high-throughput platforms, thus some miRNAs are detected with one technology, but not with the other. Adding to this, 35% (9 of 26) of selected miRNAs in the cfmiRNA and 42% (11 of 26) in the EVmiRNA fraction were differentially expressed by at least one qPCR platform; about half of the miRNAs (54%) were concordant for both platforms. Conclusions: Changing of (pre)-analytical methods of miRNA analysis has a significant impact on blood test results and is therefore a major confounding factor. In addition, to confirm miRNA biomarker candidates screening studies should be followed by targeted validation using an independent platform or technology.
Baird, ME, Wild-Allen, KA, Parslow, J, Mongin, M, Robson, B, Skerratt, J, Rizwi, F, Soja-Woźniak, M, Jones, E, Herzfeld, M, Margvelashvili, N, Andrewartha, J, Langlais, C, Adams, MP, Cherukuru, N, Gustafsson, M, Hadley, S, Ralph, PJ, Rosebrock, U, Schroeder, T, Laiolo, L, Harrison, D & Steven, ADL 2020, 'CSIRO Environmental Modelling Suite (EMS): scientific description of the optical and biogeochemical models (vB3p0)', Geoscientific Model Development, vol. 13, no. 9, pp. 4503-4553.
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Abstract. Since the mid-1990s, Australia's Commonwealth Science Industry and Research Organisation (CSIRO) has been developing a biogeochemical (BGC) model for coupling with a hydrodynamic and sediment model for application in estuaries, coastal waters and shelf seas. The suite of coupled models is referred to as the CSIRO Environmental Modelling Suite (EMS) and has been applied at tens of locations around the Australian continent. At a mature point in the BGC model's development, this paper presents a full mathematical description, as well as links to the freely available code and user guide. The mathematical description is structured into processes so that the details of new parameterisations can be easily identified, along with their derivation. In EMS, the underwater light field is simulated by a spectrally resolved optical model that calculates vertical light attenuation from the scattering and absorption of 20+ optically active constituents. The BGC model itself cycles carbon, nitrogen, phosphorous and oxygen through multiple phytoplankton, zooplankton, detritus and dissolved organic and inorganic forms in multiple water column and sediment layers. The water column is dynamically coupled to the sediment to resolve deposition, resuspension and benthic–pelagic biogeochemical fluxes. With a focus on shallow waters, the model also includes detailed representations of benthic plants such as seagrass, macroalgae and coral polyps. A second focus has been on, where possible, the use of geometric derivations of physical limits to constrain ecological rates. This geometric approach generally requires population-based rates to be derived from initially considering the size and shape of individuals. For example, zooplankton grazing considers encounter rates of one predator on a prey field based on summing relative motion of the predator with the prey individuals and the search area; chlorophyll synthesis includes a geometrically derived self-shading t...
Bao, T, Damtie, MM, Hosseinzadeh, A, Wei, W, Jin, J, Phong Vo, HN, Ye, JS, Liu, Y, Wang, XF, Yu, ZM, Chen, ZJ, Wu, K, Frost, RL & Ni, B-J 2020, 'Bentonite-supported nano zero-valent iron composite as a green catalyst for bisphenol A degradation: Preparation, performance, and mechanism of action', Journal of Environmental Management, vol. 260, pp. 110105-110105.
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Bisphenol A (BPA) is a toxic environmental pollutant commonly found in wastewater. Using non-toxic materials and eco-friendly technology to remove this pollutant from wastewater presents multiple advantages. Treatment of wastewater with clay minerals has received growing interest because of the environment friendliness of these materials. Bentonite is a 2:1 layered phyllosilicate clay mineral that can support nano-metal catalysts. It can prevent the agglomeration of nano-metal catalysts and improve their activity. In this article, a green catalytic nano zero-valent iron/bentonite composite material (NZVI@bentonite) was synthesized via liquid-phase reduction. The average size of NZVI was approximately 40-50 nm. Good dispersion and low aggregation were observed when NZVI was loaded on the surface or embedded into the nanosheets of bentonite. Degradation of BPA, a harmful contaminant widely found in wastewater at relatively high levels, by NZVI@bentonite was then investigated and compared with that by pristine NZVI through batch Fenton-like reaction experiments. Compared with pristine NZVI and bentonite alone, the NZVI@bentonite showed a higher BPA degradation ratio and offered highly effective BPA degradation up to 450 mg/g in wastewater under optimum operating conditions. Adsorption coupled with the Fenton-like reaction was responsible for BPA degradation by NZVI@bentonite. This work extends the application of NZVI@bentonite as an effective green catalyst for BPA degradation in aqueous environments.
Barolo, L, Abbriano, RM, Commault, AS, George, J, Kahlke, T, Fabris, M, Padula, MP, Lopez, A, Ralph, PJ & Pernice, M 2020, 'Perspectives for Glyco-Engineering of Recombinant Biopharmaceuticals from Microalgae', Cells, vol. 9, no. 3, pp. 633-633.
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Microalgae exhibit great potential for recombinant therapeutic protein production, due to lower production costs, immunity to human pathogens, and advanced genetic toolkits. However, a fundamental aspect to consider for recombinant biopharmaceutical production is the presence of correct post-translational modifications. Multiple recent studies focusing on glycosylation in microalgae have revealed unique species-specific patterns absent in humans. Glycosylation is particularly important for protein function and is directly responsible for recombinant biopharmaceutical immunogenicity. Therefore, it is necessary to fully characterise this key feature in microalgae before these organisms can be established as industrially relevant microbial biofactories. Here, we review the work done to date on production of recombinant biopharmaceuticals in microalgae, experimental and computational evidence for N- and O-glycosylation in diverse microalgal groups, established approaches for glyco-engineering, and perspectives for their application in microalgal systems. The insights from this review may be applied to future glyco-engineering attempts to humanize recombinant therapeutic proteins and to potentially obtain cheaper, fully functional biopharmaceuticals from microalgae.
Bates, H, Zavafer, A, Szabó, M & Ralph, PJ 2020, 'The Phenobottle, an open-source photobioreactor platform for environmental simulation', Algal Research, vol. 52, pp. 102105-102105.
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© 2020 Elsevier B.V. Microalgal biotechnologies have great potential for biofuels, bioremediation, food technologies and more recently the production of pharmaceuticals. However, a major obstacle to use microalgae industrially is the optimisation of environmental parameters to the microalgal species of interest (light, CO2 availability, nutrients, etc.). If one aims to optimise productivity, the use of photobioreactors (PBRs) is essential. However, the restrictive design of the few commercial bioreactors and their elevated costs (> $10,000 USD ea.) prevents their use as a mainstream tool. To propel microalgal research we present the Phenobottle, a fully customizable open-source PBR platform (consisting of hardware and software). As the optimisation of photosynthesis is a central process to increasing the productivity of microalgae, the Phenobottle is equipped with a chlorophyll a fluorometer and growth sensors to probe metabolic performance in near-real time. An introductory guide is provided and the Phenobottle's sensors are benchmarked against commercial instruments using the model green alga Chlorella vulgaris.
Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2020, 'Catalytic Valorization of Native Biomass in a Deep Eutectic Solvent: A Systematic Approach toward High-Yielding Reactions of Polysaccharides', ACS Sustainable Chemistry & Engineering, vol. 8, no. 1, pp. 678-685.
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Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2020, 'Towards furfural from the reaction of cellulosic biomass in zinc chloride hydrate solvents', Industrial Crops and Products, vol. 146, pp. 112179-112179.
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Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2020, 'Understanding the role of the substrate and the metal triflate acidic catalyst in sugar platform biorefineries: A comprehensive systematic approach to catalytic transformations of (poly)carbohydrates in ethanol', Chemical Engineering Journal, vol. 399, pp. 125816-125816.
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© 2020 Elsevier B.V. We systematically explore a range of model conversions of mono- and disaccharides, and of linear and branched polysaccharides under the catalytic action of metal trifluoromethanesulfonates (metal triflates) in ethanol. This highlights the preferred reactivity of specific (poly)carbohydrates, and the interplay between selectivities of the reactions and the dominating catalyst activity (Brønsted or Lewis). It unambiguously delineates that selectivities of acid-catalysed transformations of (poly)carbohydrates into value added platform chemicals rely on the origin of the substrate, any (pre)treatment, the acidic catalyst, and the reaction conditions. The optimised catalytic systems enable very efficient conversion of cellulosic carbohydrates into significantly value added ethyl glucosides (yields up to 63%), ethyl xylosides (yields up to 69%), ethyl levulinate (yields up to 75%), ethyl lactate (yields up to 98%), ethoxyacetaldehyde diethylacetal (yields up to 33%), and furfural diethylacetal (yields up to 44%), depending on the substrate and reaction conditions.
Bodachivskyi, I, Page, CJ, Kuzhiumparambil, U, Hinkley, SFR, Sims, IM & Williams, DBG 2020, 'Dissolution of Cellulose: Are Ionic Liquids Innocent or Noninnocent Solvents?', ACS Sustainable Chemistry & Engineering, vol. 8, no. 27, pp. 10142-10150.
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© 2020 American Chemical Society. Cellulose is a naturally abundant and readily accessible substrate for large scale biorefinery technologies. There has been a significant focus on ionic liquids as alternative solvents for the valorization of cellulosic substances. Ionic liquids dissolve cellulose in varying degrees, facilitating ready chemical transformations. However, there is no self-contained set of knowledge and information on the influence (or not) of the simple dissolution process on the cellulose molecule. Herein, we detail the dissolution, recovery, and characterization of cellulose in various classes of ionic solvents in a systematic study. This provides a view of the stability of cellulose in each solvent. We consider the major classes of ionic liquids commonly employed for cellulose chemistry, the dissolution in zinc chloride hydrate systems, quaternary ammonium salts, and deep eutectic solvents under varied processing conditions. We regenerate cellulosic material from the solvent and characterize the polymer employing gravimetric analysis, IR spectroscopy, and size exclusion chromatography. Surprisingly, most ionic liquids employed caused reduction in the MW of the cellulose.
Boström-Einarsson, L, Babcock, RC, Bayraktarov, E, Ceccarelli, D, Cook, N, Ferse, SCA, Hancock, B, Harrison, P, Hein, M, Shaver, E, Smith, A, Suggett, D, Stewart-Sinclair, PJ, Vardi, T & McLeod, IM 2020, 'Coral restoration – A systematic review of current methods, successes, failures and future directions', PLOS ONE, vol. 15, no. 1, pp. e0226631-e0226631.
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Coral reef ecosystems have suffered an unprecedented loss of habitat-forming hard corals in recent decades. While marine conservation has historically focused on passive habitat protection, demand for and interest in active restoration has been growing in recent decades. However, a disconnect between coral restoration practitioners, coral reef managers and scientists has resulted in a disjointed field where it is difficult to gain an overview of existing knowledge. To address this, we aimed to synthesise the available knowledge in a comprehensive global review of coral restoration methods, incorporating data from the peer-reviewed scientific literature, complemented with grey literature and through a survey of coral restoration practitioners. We found that coral restoration case studies are dominated by short-term projects, with 60% of all projects reporting less than 18 months of monitoring of the restored sites. Similarly, most projects are relatively small in spatial scale, with a median size of restored area of 100 m2. A diverse range of species are represented in the dataset, with 229 different species from 72 coral genera. Overall, coral restoration projects focused primarily on fast-growing branching corals (59% of studies), and report survival between 60 and 70%. To date, the relatively young field of coral restoration has been plagued by similar 'growing pains' as ecological restoration in other ecosystems. These include 1) a lack of clear and achievable objectives, 2) a lack of appropriate and standardised monitoring and reporting and, 3) poorly designed projects in relation to stated objectives. Mitigating these will be crucial to successfully scale up projects, and to retain public trust in restoration as a tool for resilience based management. Finally, while it is clear that practitioners have developed effective methods to successfully grow corals at small scales, it is critical not to view restoration as a replacement for meaningful actio...
Brandimarti, ME, Gray, R, Coulson, G, Cripps, JK, Wilson, ME, Death, C, Snape, M, Wimpenny, C, Silva, FRO, Miller, EJ, Scanes, E, Spielman, D, Thomas, G & Herbert, CA 2020, 'Reference intervals for parameters of health of eastern grey kangaroos Macropus giganteus and management implications across their geographic range', Wildlife Biology, vol. 2020, no. 3, pp. 1-20.
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Reference intervals (RIs) describe baseline parameters of healthy animals, providing a powerful tool for wildlife managers to monitor health, identify disease and assess animal welfare. This paper reports haematological, glucose and serum protein RIs for one of Australia's most iconic and managed mammals, the eastern grey kangaroo Macropus giganteus. Blood samples (n = 514) were collected from 11 populations of eastern grey kangaroos, across much of their geographic range. A species‐level RI was initially established based on samples collected from four sites (n = 245) and was further partitioned based on significant differences associated with sexual maturity and season. Unique population means were established from a further seven sites to investigate the importance of biotic (sex and sexual maturity) and abiotic (season, site, rainfall, temperature and laboratory) factors on kangaroo health parameters. Random forest analysis of health parameters revealed that abiotic factors (site, rainfall, temperature and season) were largely responsible for differences in haematological, glucose and serum protein values. Sex was found to have no influence, while sexual maturity and laboratory of analysis had moderate effects. Based on these findings, interpretation of individual and population haematological and serum protein values requires careful consideration of the timing of sample collection, environmental conditions and sexual maturity. When assessing kangaroo health, the relevant sexual maturity RI must be considered initially. For populations with similarities to those described (for example high density or captive populations) users should also consider site specific mean haematological and serum protein values. The RIs reported are valuable when establishing the health status of kangaroo populations. Furthermore, understanding the influence of biotic and abiotic factors will improve the utility of these RIs to assess h...
Buzova, D, Maugeri, A, Liguori, A, Napodano, C, Lo Re, O, Oben, J, Alisi, A, Gasbarrini, A, Grieco, A, Cerveny, J, Miele, L & Vinciguerra, M 2020, 'Circulating histone signature of human lean metabolic-associated fatty liver disease (MAFLD)', Clinical Epigenetics, vol. 12, no. 1, p. 126.
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AbstractBackgroundAlthough metabolic associate fatty liver disease (MAFLD) is associated with obesity, it can also occur in lean patients. MAFLD is more aggressive in lean patients compared to obese patients, with a higher risk of mortality. Specific biomarkers to diagnose differentially lean or overweight MAFLD are missing. Histones and nucleosomes are released in the bloodstream upon cell death. Here, we propose a new, fast, imaging and epigenetics based approach to investigate the severity of steatosis in lean MAFLD patients.ResultsA total of 53 non-obese patients with histologically confirmed diagnosis of MAFLD were recruited. Twenty patients displayed steatosis grade 1 (0–33%), 24 patients with steatosis grade 2 (34–66%) and 9 patients with steatosis grade 3 (67–100%). The levels of circulating nucleosomes were assayed using enzyme-linked immunosorbent assay, while individual histones or histone dimers were assayed in serum samples by means of a new advanced flow cytometry ImageStream(X)-adapted method. Circulating nucleosome levels associated poorly with MAFLD in the absence of obesity. We implemented successfully a multi-channel flow methodology on ImageStream(X), to image single histone staining (H2A, H2B, H3, H4, macroH2A1.1 and macroH2A1.2). We report here a significant depletion of the levels of histone variants macroH2A1.1 and macroH2A1.2 in the serum of lean MAFLD patients, either individually or in complex with H2B.ConclusionsIn summary, we identified a new circulating histone signature able to discriminate the severity of steatosis in individuals with lean MAFLD, using a rapid and non-invasive ImageStream(X)-based imaging technology.
Camp, EF, Kahlke, T, Nitschke, MR, Varkey, D, Fisher, NL, Fujise, L, Goyen, S, Hughes, DJ, Lawson, CA, Ros, M, Woodcock, S, Xiao, K, Leggat, W & Suggett, DJ 2020, 'Revealing changes in the microbiome of Symbiodiniaceae under thermal stress', Environmental Microbiology, vol. 22, no. 4, pp. 1294-1309.
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SummarySymbiodiniaceae are a diverse family of marine dinoflagellates, well known as coral endosymbionts. Isolation and in vitro culture of Symbiodiniaceae strains for physiological studies is a widely adopted tool, especially in the context of understanding how environmental stress perturbs Symbiodiniaceae cell functioning. While the bacterial microbiomes of corals often correlate with coral health, the bacterial communities co‐cultured with Symbiodiniaceae isolates have been largely overlooked, despite the potential of bacteria to significantly influence the emergent physiological properties of Symbiodiniaceae cultures. We examined the physiological response to heat stress by Symbiodiniaceae isolates (spanning three genera) with well‐described thermal tolerances, and combined these observations with matched changes in bacterial composition and abundance through 16S rRNA metabarcoding. Under thermal stress, there were Symbiodiniaceae strain‐specific changes in maximum quantum yield of photosystem II (proxy for health) and growth rates that were accompanied by changes in the relative abundance of multiple Symbiodiniaceae‐specific bacteria. However, there were no Symbiodiniaceae‐independent signatures of bacterial community reorganisation under heat stress. Notably, the thermally tolerant Durusdinium trenchii (ITS2 major profile D1a) had the most stable bacterial community under heat stress. Ultimately, this study highlights the complexity of Symbiodiniaceae‐bacteria interactions and provides a first step towards uncoupling their relative contributions towards Symbiodiniaceae physiological functioning.
Camp, EF, Suggett, DJ, Pogoreutz, C, Nitschke, MR, Houlbreque, F, Hume, BCC, Gardner, SG, Zampighi, M, Rodolfo-Metalpa, R & Voolstra, CR 2020, 'Corals exhibit distinct patterns of microbial reorganisation to thrive in an extreme inshore environment', Coral Reefs, vol. 39, no. 3, pp. 701-716.
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© 2020, Springer-Verlag GmbH Germany, part of Springer Nature. Climate change threatens the survival of scleractinian coral from exposure to concurrent ocean warming, acidification and deoxygenation; how corals can potentially adapt to this trio of stressors is currently unknown. This study investigates three coral species (Acropora muricata, Acropora pulchra and Porites lutea) dominant in an extreme mangrove lagoon (Bouraké, New Caledonia) where abiotic conditions exceed those predicted for many reef sites over the next 100 years under climate change and compared them to conspecifics from an environmentally more benign reef habitat. We studied holobiont physiology as well as plasticity in coral-associated microorganisms (Symbiodiniaceae and bacteria) through ITS2 and 16S rRNA sequencing, respectively. We hypothesised that differences in coral-associated microorganisms (Symbiodiniaceae and bacteria) between the lagoonal and adjacent reef habitats may support coral host productivity and ultimately the ability of corals to live in extreme environments. In the lagoon, all coral species exhibited a metabolic adjustment of reduced photosynthesis-to-respiration ratios (P/R), but this was accompanied by highly divergent coral host-specific microbial associations. This was substantiated by the absence of shared ITS2-type profiles (proxies for Symbiodiniaceae genotypes). We observed that ITS2 profiles originating from Durusdinium taxa made up < 3% and a novel Symbiodinium ITS2 profile A1-A1v associated with A. pulchra. Bacterial community profiles were also highly divergent in corals from the lagoonal environment, whereas corals from the reef site were consistently dominated by Hahellaceae, Endozoicomonas. As such, differences in host–microorganism associations aligned with different physiologies and habitats. Our results argue that a multitude of host–microorganism associations are required to fulfill the changing nutritional demands of corals persisting into e...
Carney, RL, Brown, MV, Siboni, N, Raina, J-B, Kahlke, T, Mitrovic, SM & Seymour, JR 2020, 'Highly heterogeneous temporal dynamics in the abundance and diversity of the emerging pathogens Arcobacter at an urban beach', Water Research, vol. 171, pp. 115405-115405.
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While the significance of Arcobacter in clinical settings grows, the ecological dynamics of potentially pathogenic Arcobacter in coastal marine environments remains unclear. In this study, we monitored the temporal dynamics of Arcobacter at an urban beach subject to significant stormwater input and wet weather sewer overflows (WWSO). Weekly monitoring of bacterial communities over 24 months using 16S rRNA amplicon sequencing revealed large, intermittent peaks in the relative abundance of Arcobacter. Quantitative PCR was subsequently employed to track absolute abundance of Arcobacter 23S rRNA gene copies, revealing peaks in abundance reaching up to 108 gene copies L-1, with these increases statistically correlated with stormwater and WWSO intrusion. Notably, peaks in Arcobacter abundance were poorly correlated with enterococci plate counts, and remained elevated for one week following heavy rainfall. Using oligotyping we discriminated single nucleotide variants (SNVs) within the Arcobacter population, revealing 10 distinct clusters of SNVs that we defined as Arcobacter 'ecotypes', with each displaying distinct temporal dynamics. The most abundant ecotype during stormwater and modelled WWSO events displayed 16S rRNA sequence similarity to A. cryaerophilius, a species previously implicated in human illness. Our findings highlight the diverse environmental drivers of Arcobacter abundance within coastal settings and point to a potentially important, yet overlooked exposure risk of these potential pathogens to humans.
Ceccarelli, DM, McLeod, IM, Boström-Einarsson, L, Bryan, SE, Chartrand, KM, Emslie, MJ, Gibbs, MT, Gonzalez Rivero, M, Hein, MY, Heyward, A, Kenyon, TM, Lewis, BM, Mattocks, N, Newlands, M, Schläppy, M-L, Suggett, DJ & Bay, LK 2020, 'Substrate stabilisation and small structures in coral restoration: State of knowledge, and considerations for management and implementation', PLOS ONE, vol. 15, no. 10, pp. e0240846-e0240846.
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Coral reef ecosystems are under increasing pressure from local and regional stressors and a changing climate. Current management focuses on reducing stressors to allow for natural recovery, but in many areas where coral reefs are damaged, natural recovery can be restricted, delayed or interrupted because of unstable, unconsolidated coral fragments, or rubble. Rubble fields are a natural component of coral reefs, but repeated or high-magnitude disturbances can prevent natural cementation and consolidation processes, so that coral recruits fail to survive. A suite of interventions have been used to target this issue globally, such as using mesh to stabilise rubble, removing the rubble to reveal hard substrate and deploying rocks or other hard substrates over the rubble to facilitate recruit survival. Small, modular structures can be used at multiple scales, with or without attached coral fragments, to create structural complexity and settlement surfaces. However, these can introduce foreign materials to the reef, and a limited understanding of natural recovery processes exists for the potential of this type of active intervention to successfully restore local coral reef structure. This review synthesises available knowledge about the ecological role of coral rubble, natural coral recolonisation and recovery rates and the potential benefits and risks associated with active interventions in this rapidly evolving field. Fundamental knowledge gaps include baseline levels of rubble, the structural complexity of reef habitats in space and time, natural rubble consolidation processes and the risks associated with each intervention method. Any restoration intervention needs to be underpinned by risk assessment, and the decision to repair rubble fields must arise from an understanding of when and where unconsolidated substrate and lack of structure impair natural reef recovery and ecological function. Monitoring is necessary to ascertain the success or failure of ...
Clark, JS, Poore, AGB, Coleman, MA & Doblin, MA 2020, 'Local Scale Thermal Environment and Limited Gene Flow Indicates Vulnerability of Warm Edge Populations in a Habitat Forming Macroalga', Frontiers in Marine Science, vol. 7.
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© Copyright © 2020 Clark, Poore, Coleman and Doblin. Species inhabiting warm-edge populations of their distribution are suggested to be at the forefront of global warming due to reduced fitness, limited gene flow and living close to their physiological thermal limits. Determining the scale that governs thermal niche and the functional responses of habitat-forming species to environmental stressors is critical for successful conservation efforts, particularly as coastal ecosystems are impacted by global change. Here, we examine the susceptibility of warm-edge populations to warming, in the habitat-forming macroalga, Hormosira banksii, from south-eastern Australia. We use a quantitative breeding design to quantify intraspecific variation in thermal performance (growth, ontogenic development and photosynthetic efficiency) of different genotypes sourced from sites at the equatorward distributional edge (warm-edge) and those toward the center of its distribution (non-edge). The genetic diversity and structure of H. banksii was also examined using microsatellite markers amongst the same sites. Our results found variable responses in thermal performance for growth and development. Warm-edge germlings grew optimally in lower temperatures tested and had narrower thermal breadth compared to non-edge germlings which grew in higher and more broader temperatures. Warm-edge germlings however, showed greater plasticity to tolerate high light indicated by a greater proportion of energy being dissipated as regulated non-photochemical quenching [Y(NPQ)] than non-regulated non-photochemical quenching [Y(NO)]. Overall genetic diversity was lower at the warm-edge location with evidence of increased structuring and reduced gene flow in comparison to the non-edge location. Evidence of genetic structuring was not found locally between high and low shore within sites. Together, these data suggest that non-edge populations may be “thermally buffered” from increased temperatures associated...
Clerc, EE, Raina, J-B, Lambert, BS, Seymour, J & Stocker, R 2020, 'In Situ Chemotaxis Assay to Examine Microbial Behavior in Aquatic Ecosystems', Journal of Visualized Experiments, vol. 2020, no. 159.
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Microbial behaviors, such as motility and chemotaxis (the ability of a cell to alter its movement in response to a chemical gradient), are widespread across the bacterial and archaeal domains. Chemotaxis can result in substantial resource acquisition advantages in heterogeneous environments. It also plays a crucial role in symbiotic interactions, disease, and global processes, such as biogeochemical cycling. However, current techniques restrict chemotaxis research to the laboratory and are not easily applicable in the field. Presented here is a step-by-step protocol for the deployment of the in situ chemotaxis assay (ISCA), a device that enables robust interrogation of microbial chemotaxis directly in the natural environment. The ISCA is a microfluidic device consisting of a 20 well array, in which chemicals of interest can be loaded. Once deployed in aqueous environments, chemicals diffuse out of the wells, creating concentration gradients that microbes sense and respond to by swimming into the wells via chemotaxis. The well contents can then be sampled and used to (1) quantify strength of the chemotactic responses to specific compounds through flow cytometry, (2) isolate and culture responsive microorganisms, and (3) characterize the identity and genomic potential of the responding populations through molecular techniques. The ISCA is a flexible platform that can be deployed in any system with an aqueous phase, including marine, freshwater, and soil environments.
Collins, S, Boyd, PW & Doblin, MA 2020, 'Evolution, Microbes, and Changing Ocean Conditions', Annual Review of Marine Science, vol. 12, no. 1, pp. 181-208.
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Experimental evolution and the associated theory are underutilized in marine microbial studies; the two fields have developed largely in isolation. Here, we review evolutionary tools for addressing four key areas of ocean global change biology: linking plastic and evolutionary trait changes, the contribution of environmental variability to determining trait values, the role of multiple environmental drivers in trait change, and the fate of populations near their tolerance limits. Wherever possible, we highlight which data from marine studies could use evolutionary approaches and where marine model systems can advance our understanding of evolution. Finally, we discuss the emerging field of marine microbial experimental evolution. We propose a framework linking changes in environmental quality (defined as the cumulative effect on population growth rate) with population traits affecting evolutionary potential, in order to understand which evolutionary processes are likely to be most important across a range of locations for different types of marine microbes.
Commault, AS, Kaur Walia, N, Fabris, M, Barolo, L, Siboni, N, Adriaans, J, Ralph, PJ & Pernice, M 2020, 'Effect of biphasic temperature regime on therapeutic recombinant protein production in the green alga Chlamydomonas reinhardtii', Algal Research, vol. 50, pp. 101997-101997.
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© 2020 Elsevier B.V. Microalgae are increasingly being considered for recombinant protein production because of low cultivation costs, absence of endotoxins and insusceptibility to human infectious agents. Despite these advantages, the yield of recombinant protein produced in microalgae is still low compared to more established expression systems and optimization at the genetic and cultivation levels is required for this new system to be economically viable. This study investigates the effect of biphasic temperature regimes on the yield of recombinant human interferon alpha 2a (IFN-α2a), a therapeutic protein known for its anti-cancer and anti-viral properties, produced by the model green alga Chlamydomonas reinhardtii (Cr.IFN-α2a). Biphasic growth is commonly employed to increase recombinant protein production in mammalian cell lines used for commercial production of therapeutic proteins, with a lowering of the temperature resulting in higher yields. In this study, lowering the temperature from 25 °C to 15 °C in mid-exponential growth phase increased the accumulation of Cr.IFN-α2a by 3.3-fold while it slowed down the growth of the three C. reinhardtii transgenic lines tested. In contrast, a rise of temperature from 25 °C to 35 °C accelerated cell growth, while negatively impacting the production of Cr.IFN-α2a. After a two-step chromatography purification, the Cr.IFN-α2a produced was estimated to be 53% pure with a yield of 90 μg/L of culture. The amino acid sequence of Cr.IFN-α2a was confirmed by mass spectrometry. However, the anti-viral activity of Cr.IFN-α2a was found to be 10 times lower than the human IFN-α2a standard produced using E. coli when challenged in a cytopathic effect (CPE) assay, likely due to the formation of aggregates. While the molecular mechanisms driving the accumulation of Cr.IFN-α2a at lower temperature remains unclear, our results support that reducing the temperature at the peak of expression is a valid strategy to increase the yield o...
Drápela, S, Khirsariya, P, van Weerden, WM, Fedr, R, Suchánková, T, Búzová, D, Červený, J, Hampl, A, Puhr, M, Watson, WR, Culig, Z, Krejčí, L, Paruch, K & Souček, K 2020, 'The CHK1 inhibitor MU380 significantly increases the sensitivity of human docetaxel‐resistant prostate cancer cells to gemcitabine through the induction of mitotic catastrophe', Molecular Oncology, vol. 14, no. 10, pp. 2487-2503.
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As treatment options for patients with incurable metastatic castration‐resistant prostate cancer (mCRPC) are considerably limited, novel effective therapeutic options are needed. Checkpoint kinase 1 (CHK1) is a highly conserved protein kinase implicated in the DNA damage response (DDR) pathway that prevents the accumulation of DNA damage and controls regular genome duplication. CHK1 has been associated with prostate cancer (PCa) induction, progression, and lethality; hence, CHK1 inhibitors SCH900776 (also known as MK‐8776) and the more effective SCH900776 analog MU380 may have clinical applications in the therapy of PCa. Synergistic induction of DNA damage with CHK1 inhibition represents a promising therapeutic approach that has been tested in many types of malignancies, but not in chemoresistant mCRPC. Here, we report that such therapeutic approach may be exploited using the synergistic action of the antimetabolite gemcitabine (GEM) and CHK1 inhibitors SCH900776 and MU380 in docetaxel‐resistant (DR) mCRPC. Given the results, both CHK1 inhibitors significantly potentiated the sensitivity to GEM in a panel of chemo‐naïve and matched DR PCa cell lines under 2D conditions. MU380 exhibited a stronger synergistic effect with GEM than clinical candidate SCH900776. MU380 alone or in combination with GEM significantly reduced spheroid size and increased apoptosis in all patient‐derived xenograft 3D cultures, with a higher impact in DR models. Combined treatment induced premature mitosis from G1 phase resulting in the mitotic catastrophe as a prestage of apoptosis. Finally, treatment by MU380 alone, or in combination with GEM, significantly inhibited tumor growth of both PC339‐DOC and PC346C‐DOC xenograft models in mice. Taken together, our data suggest that metabolically robust and selective CHK1 inhibitor MU380 can bypass docetaxel resistance and improve the effectiveness of GEM in DR mCRPC models. This approach might allow for dose reduction of GEM an...
Fabris, M, Abbriano, RM, Pernice, M, Sutherland, DL, Commault, AS, Hall, CC, Labeeuw, L, McCauley, JI, Kuzhiuparambil, U, Ray, P, Kahlke, T & Ralph, PJ 2020, 'Emerging Technologies in Algal Biotechnology: Toward the Establishment of a Sustainable, Algae-Based Bioeconomy', Frontiers in Plant Science, vol. 11.
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Mankind has recognized the value of land plants as renewable sources of food, medicine, and materials for millennia. Throughout human history, agricultural methods were continuously modified and improved to meet the changing needs of civilization. Today, our rapidly growing population requires further innovation to address the practical limitations and serious environmental concerns associated with current industrial and agricultural practices. Microalgae are a diverse group of unicellular photosynthetic organisms that are emerging as next-generation resources with the potential to address urgent industrial and agricultural demands. The extensive biological diversity of algae can be leveraged to produce a wealth of valuable bioproducts, either naturally or via genetic manipulation. Microalgae additionally possess a set of intrinsic advantages, such as low production costs, no requirement for arable land, and the capacity to grow rapidly in both large-scale outdoor systems and scalable, fully contained photobioreactors. Here, we review technical advancements, novel fields of application, and products in the field of algal biotechnology to illustrate how algae could present high-tech, low-cost, and environmentally friendly solutions to many current and future needs of our society. We discuss how emerging technologies such as synthetic biology, high-throughput phenomics, and the application of internet of things (IoT) automation to algal manufacturing technology can advance the understanding of algal biology and, ultimately, drive the establishment of an algal-based bioeconomy.
Fabris, M, George, J, Kuzhiumparambil, U, Lawson, CA, Jaramillo-Madrid, AC, Abbriano, RM, Vickers, CE & Ralph, P 2020, 'Extrachromosomal Genetic Engineering of the Marine Diatom Phaeodactylum tricornutum Enables the Heterologous Production of Monoterpenoids', ACS Synthetic Biology, vol. 9, no. 3, pp. 598-612.
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Geraniol is a commercially relevant plant-derived monoterpenoid that is a main component of rose essential oil and used as insect repellent. Geraniol is also a key intermediate compound in the biosynthesis of the monoterpenoid indole alkaloids (MIAs), a group of over 2000 compounds that include high-value pharmaceuticals. As plants naturally produce extremely small amounts of these molecules and their chemical synthesis is complex, industrially sourcing these compounds is costly and inefficient. Hence, microbial hosts suitable to produce MIA precursors through synthetic biology and metabolic engineering are currently being sought. Here, we evaluated the suitability of a eukaryotic microalga, the marine diatom Phaeodactylum tricornutum, for the heterologous production of monoterpenoids. Profiling of endogenous metabolism revealed that P. tricornutum, unlike other microbes employed for industrial production of terpenoids, accumulates free pools of the precursor geranyl diphosphate. To evaluate the potential for larger synthetic biology applications, we engineered P. tricornutum through extrachromosomal, episome-based expression, for the heterologous biosynthesis of the MIA intermediate geraniol. By profiling the production of geraniol resulting from various genetic and cultivation arrangements, P. tricornutum reached the maximum geraniol titer of 0.309 mg/L in phototrophic conditions. This work provides (i) a detailed analysis of P. tricornutum endogenous terpenoid metabolism, (ii) a successful demonstration of extrachromosomal expression for metabolic pathway engineering with potential gene-stacking applications, and (iii) a convincing proof-of-concept of the suitability of P. tricornutum as a novel production platform for heterologous monoterpenoids, with potential for complex pathway engineering aimed at the heterologous production of MIAs.
Fisher, NL, Campbell, DA, Hughes, DJ, Kuzhiumparambil, U, Halsey, KH, Ralph, PJ & Suggett, DJ 2020, 'Divergence of photosynthetic strategies amongst marine diatoms', PLOS ONE, vol. 15, no. 12, pp. e0244252-e0244252.
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Marine phytoplankton, and in particular diatoms, are responsible for almost half of all primary production on Earth. Diatom species thrive from polar to tropical waters and across light environments that are highly complex to relatively benign, and so have evolved highly divergent strategies for regulating light capture and utilization. It is increasingly well established that diatoms have achieved such successful ecosystem dominance by regulating excitation energy available for generating photosynthetic energy via highly flexible light harvesting strategies. However, how different light harvesting strategies and downstream pathways for oxygen production and consumption interact to balance excitation pressure remains unknown. We therefore examined the responses of three diatom taxa adapted to inherently different light climates (estuarine Thalassioisira weissflogii, coastal Thalassiosira pseudonana and oceanic Thalassiosira oceanica) during transient shifts from a moderate to high growth irradiance (85 to 1200 μmol photons m-2 s-1). Transient high light exposure caused T. weissflogii to rapidly downregulate PSII with substantial nonphotochemical quenching, protecting PSII from inactivation or damage, and obviating the need for induction of O2 consuming (light-dependent respiration, LDR) pathways. In contrast, T. oceanica retained high excitation pressure on PSII, but with little change in RCII photochemical turnover, thereby requiring moderate repair activity and greater reliance on LDR. T. pseudonana exhibited an intermediate response compared to the other two diatom species, exhibiting some downregulation and inactivation of PSII, but high rep...
Fleck, R, Gill, RL, Pettit, T, Irga, PJ, Williams, NLR, Seymour, JR & Torpy, FR 2020, 'Characterisation of fungal and bacterial dynamics in an active green wall used for indoor air pollutant removal', Building and Environment, vol. 179, pp. 106987-106987.
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© 2020 Elsevier Ltd Indoor air quality (IAQ) is of growing public health concern which has prompted the use of plants to phytoremediate air pollution in interior spaces. Active green walls are emerging as a means of reducing indoor contaminants and have demonstrated efficacy comparable to conventional air filtering technologies. However, the use of active airflow through organic substrates has the potential to emit bioaerosols into the surrounding environment, where the potential risk to human health is largely unknown. In this study, we demonstrate that two indoor green walls (with and without active airflow) contribute significantly to the ambient fungal load, however concentrations remained well below WHO safety guidelines. Bacterial dynamics within the rhizosphere/substrate of the operational botanical biofilters displayed variability across plant species. Phyla-wide distribution generally aligned with previous literature; however, differences from those previously reported were observed at the genus level, possibly due to geographic location, substrate composition, or plant species selection. Targeted assessment of Legionella aerosol contamination, an under-addressed potential pathogen for these active systems, yielded no positive identification during the sampling period. We conclude that active green walls host a unique bacterial profile and do not emit harmful levels of fungal propagules or pose significant risk of aerosolised Legionella species, provided systems are well monitored and maintained.
Focardi, A, Ostrowski, M, Goossen, K, Brown, MV & Paulsen, I 2020, 'Investigating the Diversity of Marine Bacteriophage in Contrasting Water Masses Associated with the East Australian Current (EAC) System', Viruses, vol. 12, no. 3, pp. 317-317.
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Virus- and bacteriophage-induced mortality can have a significant impact on marine productivity and alter the flux of nutrients in marine microbial food-webs. Viral mediated horizontal gene transfer can also influence host fitness and community composition. However, there are very few studies of marine viral diversity in the Southern Hemisphere, which hampers our ability to fully understand the complex interplay of biotic and abiotic factors that shape microbial communities. We carried out the first genetic study of bacteriophage communities within a dynamic western boundary current (WBC) system, the east Australian current (EAC). Virus DNA sequences were extracted from 63 assembled metagenomes and six metaviromes obtained from various depths at 24 different locations. More than 1700 bacteriophage genomic fragments (>9 kbps) were recovered from the assembled sequences. Bacteriophage diversity displayed distinct depth and regional patterns. There were clear differences in the bacteriophage populations associated with the EAC and Tasman Sea euphotic zones, at both the taxonomic and functional level. In contrast, bathypelagic phages were similar across the two oceanic regions. These data provide the first characterisation of viral diversity across a dynamic western boundary current, which is an emerging model for studying the response of microbial communities to climate change.
Gao, C, Fernandez, VI, Lee, KS, Fenizia, S, Pohnert, G, Seymour, JR, Raina, J-B & Stocker, R 2020, 'Single-cell bacterial transcription measurements reveal the importance of dimethylsulfoniopropionate (DMSP) hotspots in ocean sulfur cycling', Nature Communications, vol. 11, no. 1, p. 1942.
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AbstractDimethylsulfoniopropionate (DMSP) is a pivotal compound in marine biogeochemical cycles and a key chemical currency in microbial interactions. Marine bacteria transform DMSP via two competing pathways with considerably different biogeochemical implications: demethylation channels sulfur into the microbial food web, whereas cleavage releases sulfur into the atmosphere. Here, we present single-cell measurements of the expression of these two pathways using engineered fluorescent reporter strains of Ruegeria pomeroyi DSS-3, and find that external DMSP concentration dictates the relative expression of the two pathways. DMSP induces an upregulation of both pathways, but only at high concentrations (>1 μM for demethylation; >35 nM for cleavage), characteristic of microscale hotspots such as the vicinity of phytoplankton cells. Co-incubations between DMSP-producing microalgae and bacteria revealed an increase in cleavage pathway expression close to the microalgae’s surface. These results indicate that bacterial utilization of microscale DMSP hotspots is an important determinant of the fate of sulfur in the ocean.
George, J, Kahlke, T, Abbriano, RM, Kuzhiumparambil, U, Ralph, PJ & Fabris, M 2020, 'Metabolic Engineering Strategies in Diatoms Reveal Unique Phenotypes and Genetic Configurations With Implications for Algal Genetics and Synthetic Biology', Frontiers in Bioengineering and Biotechnology, vol. 8.
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Gibbs, M, Scanes, E, Parker, L, Byrne, M, O’Connor, W, Virtue, P & Ross, P 2020, 'Larval energetics of the Sydney rock oyster Saccostrea glomerata and Pacific oyster Magallana gigas', Marine Ecology Progress Series, vol. 656, pp. 51-64.
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Larvae are a critical dispersal stage of marine invertebrates, and their survival depends on nutrition and energetics. This study compared the size, survival, metabolic rate and egg and larval lipid class profiles of larvae of the endemic Sydney rock oyster Saccostrea glomerata and the invasive Pacific oyster Magallana gigas through a period of starvation for 5 and 9 d after fertilisation. Starved larvae grew without food until 5 d of age, at which point they stopped developing, but resumed growth when fed. Egg lipids profiles comprised 78.1 and 74.5% triacylglycerol for M. gigas and S. glomerata respectively. When fed, larvae of M. gigas were significantly larger in size and had faster growth and similar survival compared to S. glomerata. When starved, larvae of M. gigas and S. glomerata grew at similar rates, and there was a trend for lower survival of M. gigas. Larval endogenous lipid reserves were deleted in the first 24 h. Larvae of M. gigas had more total lipids and comparatively more diacylglycerols, monoacylglycerols, phospholipids and cholesterol, whereas S. glomerata had more diacylglycerols and produced sterol esters. Starvation altered the patterns of lipid assimilation, and metabolic rates of larvae of M. gigas and S. glomerata differed over time. When starved, S. glomerata larvae had greater capacity to cope with starvation compared to M. gigas, perhaps due to an evolutionary history in oligotrophic estuaries. As the climate rapidly changes in this global climate-change hotspot, S. glomerata is likely to be ...
Hughes, DJ, Alderdice, R, Cooney, C, Kühl, M, Pernice, M, Voolstra, CR & Suggett, DJ 2020, 'Coral reef survival under accelerating ocean deoxygenation', Nature Climate Change, vol. 10, no. 4, pp. 296-307.
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Hurtado-McCormick, V, Kahlke, T, Krix, D, Larkum, A, Ralph, PJ & Seymour, JR 2020, 'Seagrass leaf reddening alters the microbiome of Zostera muelleri', Marine Ecology Progress Series, vol. 646, pp. 29-44.
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Seagrasses host an extremely diverse microbiome that plays fundamental roles in seagrass health and productivity but may be sensitive to shifts in host physiology. Here, we observed a leaf reddening phenomenon in Zostera muelleri and characterized bacterial assemblages associated with green and reddened leaves to determine whether this change in leaf pigmentation stimulates shifts in the seagrass microbiome. Using 16S rRNA gene amplicon sequencing, we observed that the microbiome associated with 4 different leaf pigmentation categories (i.e. green, white, purple and black) differed significantly, with substantial changes in microbiome composition when the tissue is whitened (non-pigmented). Actinobacteria, Rhodobacteraceae, Erythrobacter, Sulfitobacter and Granulosicoccus were enriched in black and/or purple tissues and discriminated these microbiomes from those associated with green leaves. Contrastingly, all ‘discriminatory’ zero-radius operational taxonomic units (zOTUs) were depleted within the communities associated with white samples. While 40% of the abundant zOTUs identified were exclusively associated with a single pigmentation category, only 3% were shared across all categories, indicating partitioning of the phyllosphere microbiome. However, a significant proportion of the ‘normal’ (green) leaf core microbiome was also retained in the core communities associated with black (70%) and purple (70%) tissues. Contrastingly, no core zOTUs were maintained in the white tissues. These results indicate that environmentally driven physiological shifts in seagrasses, such as leaf reddening expressed in response to high irradiance, can impact the seagrass leaf microbiome, resulting in significant shifts in the microbiome of reddened leaves with the most extreme expression (in white tissue...
Jaramillo-Madrid, AC, Abbriano, R, Ashworth, J, Fabris, M & Ralph, PJ 2020, 'Overexpression of key sterol pathway enzymes in two model marine diatoms alters sterol profiles inPhaeodactylum tricornutum', Pharmaceuticals, vol. 13, no. 12, p. 2020.07.30.228171.
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AbstractSterols are a class of triterpenoid molecules with diverse functional roles in eukaryotic cells, including intracellular signaling and regulation of cell membrane fluidity. Diatoms are a dominant eukaryotic phytoplankton group that produce a wide diversity of sterol compounds. The enzymes 3-hydroxy-3-methyl glutaryl CoA reductase (HMGR) and squalene epoxidase (SQE) have been reported to be rate-limiting steps in sterol biosynthesis in other model eukaryotes; however, the extent to which these enzymes regulate triterpenoid production in diatoms is not known. To probe the role of these two metabolic nodes in the regulation of sterol metabolic flux in diatoms, we independently over-expressed two versions of the nativeHMGRand a conventional, heterologous SQE gene in the diatomsThalassiosira pseudonanaandPhaeodactylum tricornutum. Overexpression of these key enzymes resulted in significant differential accumulation of downstream sterol pathway intermediates inP. tricornutum. HMGR-mVenus overexpression resulted in the accumulation of squalene, cycloartenol, and obtusifoliol, while cycloartenol and obtusifoliol accumulated in response to heterologous NoSQE-mVenus overexpression. In addition, accumulation of the end-point sterol 24-methylenecholesta-5,24(24’)-dien-3β-ol was observed in allP. tricornutumoverexpression lines, and campesterol increased 3-fold inP. tricornutumlines expressing NoSQE-mVenus. Minor differences in end-point sterol composition were also found inT. pseudonana, but no accumulation of sterol pathway intermediates was observed. Despite the successful manipulation of pathway intermediates and individual sterols inP. tricornutum, total sterol levels did not change...
Jaramillo-Madrid, AC, Abbriano, R, Ashworth, J, Fabris, M, Pernice, M & Ralph, PJ 2020, 'Overexpression of Key Sterol Pathway Enzymes in Two Model Marine Diatoms Alters Sterol Profiles in Phaeodactylum tricornutum', Pharmaceuticals, vol. 13, no. 12, pp. 481-481.
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Sterols are a class of triterpenoid molecules with diverse functional roles in eukaryotic cells, including intracellular signaling and regulation of cell membrane fluidity. Diatoms are a dominant eukaryotic phytoplankton group that produce a wide diversity of sterol compounds. The enzymes 3-hydroxy-3-methyl glutaryl CoA reductase (HMGR) and squalene epoxidase (SQE) have been reported to be rate-limiting steps in sterol biosynthesis in other model eukaryotes; however, the extent to which these enzymes regulate triterpenoid production in diatoms is not known. To probe the role of these two metabolic nodes in the regulation of sterol metabolic flux in diatoms, we independently over-expressed two versions of the native HMGR and a conventional, heterologous SQE gene in the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum. Overexpression of these key enzymes resulted in significant differential accumulation of downstream sterol pathway intermediates in P. tricornutum. HMGR-mVenus overexpression resulted in the accumulation of squalene, cycloartenol, and obtusifoliol, while cycloartenol and obtusifoliol accumulated in response to heterologous NoSQE-mVenus overexpression. In addition, accumulation of the end-point sterol 24-methylenecholesta-5,24(24’)-dien-3β-ol was observed in all P. tricornutum overexpression lines, and campesterol increased three-fold in P. tricornutum lines expressing NoSQE-mVenus. Minor differences in end-point sterol composition were also found in T. pseudonana, but no accumulation of sterol pathway intermediates was observed. Despite the successful manipulation of pathway intermediates and individual sterols in P. tricornutum, total sterol levels did not change significantly in transformed lines, suggesting the existence of tight pathway regulation to maintain total sterol content.
Jaramillo-Madrid, AC, Ashworth, J & Ralph, PJ 2020, 'Levels of Diatom Minor Sterols Respond to Changes in Temperature and Salinity', Journal of Marine Science and Engineering, vol. 8, no. 2, pp. 85-85.
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Diatoms are a broadly distributed and evolutionarily diversified group of microalgae that produce a diverse range of sterol compounds. Sterols are triterpenoids that play essential roles in membrane-related processes in eukaryotic cells. Some sterol compounds possess bioactivities that promote human health and are currently used as nutraceuticals. The relationship between sterol diversity in diatoms and their acclimation to different environments is not well understood. In this study, we investigated the occurrence of different sterol types across twelve diatom species, as well as the effect of temperature reduction and changes in salinity on the sterol contents of three model diatom species. In the diatoms Thalassiosira pseudonana, Phaeodactylum tricornutum and Chaetoceros muelleri, we found that changes in the relative contents of minor sterols accompanied shifts in temperature and salinity. This may be indicative of acquired adaptive traits in diatom metabolism.
Jaramillo-Madrid, AC, Ashworth, J, Fabris, M & Ralph, PJ 2020, 'The unique sterol biosynthesis pathway of three model diatoms consists of a conserved core and diversified endpoints', Algal Research, vol. 48, pp. 101902-101902.
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© 2020 Diatoms produce a wide diversity of sterols among different species, the biosynthesis and conservation of which is not yet fully understood. To investigate the conservation and divergence of sterol biosynthesis pathways among diatoms, we performed comparative metabolic profiling and transcriptomics for a centric diatom (Thalassiosira pseudonana), a pennate diatom (Phaeodactylum tricornutum) and a chaetocerid (Chaetoceros muelleri) in response to inhibitors of enzymes involved in sterol biosynthesis. These three model diatoms, which are representative of distinct clades, share a unique core phytosterol biosynthesis pathway that relies on a terbinafine-insensitive alternative squalene epoxidase and the cyclization of 2,3-epoxysqualene into cycloartenol by a conserved oxidosqualene cyclase. Lineage-specific divergence in the synthesis of sterol precursors was found in the species analyzed. Cholesterol synthesis in diatoms seems to occur via cycloartenol rather than lanosterol. The diversification of natural sterols produced by each species appears to occur downstream of all experimentally targeted enzymes, suggesting adaptive specialization in terminal synthesis pathways.
Keating, SM, Waltemath, D, König, M, Zhang, F, Dräger, A, Chaouiya, C, Bergmann, FT, Finney, A, Gillespie, CS, Helikar, T, Hoops, S, Malik‐Sheriff, RS, Moodie, SL, Moraru, II, Myers, CJ, Naldi, A, Olivier, BG, Sahle, S, Schaff, JC, Smith, LP, Swat, MJ, Thieffry, D, Watanabe, L, Wilkinson, DJ, Blinov, ML, Begley, K, Faeder, JR, Gómez, HF, Hamm, TM, Inagaki, Y, Liebermeister, W, Lister, AL, Lucio, D, Mjolsness, E, Proctor, CJ, Raman, K, Rodriguez, N, Shaffer, CA, Shapiro, BE, Stelling, J, Swainston, N, Tanimura, N, Wagner, J, Meier‐Schellersheim, M, Sauro, HM, Palsson, B, Bolouri, H, Kitano, H, Funahashi, A, Hermjakob, H, Doyle, JC, Hucka, M, Adams, RR, Allen, NA, Angermann, BR, Antoniotti, M, Bader, GD, Červený, J, Courtot, M, Cox, CD, Dalle Pezze, P, Demir, E, Denney, WS, Dharuri, H, Dorier, J, Drasdo, D, Ebrahim, A, Eichner, J, Elf, J, Endler, L, Evelo, CT, Flamm, C, Fleming, RMT, Fröhlich, M, Glont, M, Gonçalves, E, Golebiewski, M, Grabski, H, Gutteridge, A, Hachmeister, D, Harris, LA, Heavner, BD, Henkel, R, Hlavacek, WS, Hu, B, Hyduke, DR, de Jong, H, Juty, N, Karp, PD, Karr, JR, Kell, DB, Keller, R, Kiselev, I, Klamt, S, Klipp, E, Knüpfer, C, Kolpakov, F, Krause, F, Kutmon, M, Laibe, C, Lawless, C, Li, L, Loew, LM, Machne, R, Matsuoka, Y, Mendes, P, Mi, H, Mittag, F, Monteiro, PT, Natarajan, KN, Nielsen, PMF, Nguyen, T, Palmisano, A, Pettit, J, Pfau, T, Phair, RD, Radivoyevitch, T, Rohwer, JM, Ruebenacker, OA, Saez‐Rodriguez, J, Scharm, M, Schmidt, H, Schreiber, F, Schubert, M, Schulte, R, Sealfon, SC, Smallbone, K, Soliman, S, Stefan, MI, Sullivan, DP, Takahashi, K, Teusink, B, Tolnay, D, Vazirabad, I, von Kamp, A, Wittig, U, Wrzodek, C, Wrzodek, F, Xenarios, I, Zhukova, A & Zucker, J 2020, 'SBMLLevel 3: an extensible format for the exchange and reuse of biological models', Molecular Systems Biology, vol. 16, no. 8.
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King, WL, Siboni, N, Kahlke, T, Dove, M, O'Connor, W, Mahbub, KR, Jenkins, C, Seymour, JR & Labbate, M 2020, 'Regional and oyster microenvironmental scale heterogeneity in the Pacific oyster bacterial community', FEMS Microbiology Ecology, vol. 96, no. 5.
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ABSTRACTDifferent organs of a host represent distinct microenvironments resulting in the establishment of multiple discrete bacterial communities within a host. These discrete bacterial communities can also vary according to geographical location. For the Pacific oyster, Crassostrea gigas, the factors governing bacterial diversity and abundance of different oyster microenvironments are poorly understood. In this study, the factors shaping bacterial abundance, diversity and composition associated with the C. gigas mantle, gill, adductor muscle and digestive gland were characterised using 16S (V3-V4) rRNA amplicon sequencing across six discrete estuaries. Both location and tissue-type, with tissue-type being the stronger determinant, were factors driving bacterial community composition. Bacterial communities from wave-dominated estuaries had similar compositions and higher bacterial abundance despite being geographically distant from one another, possibly indicating that functional estuarine morphology characteristics are a factor shaping the oyster bacterial community. Despite the bacterial community heterogeneity, examinations of the core bacterial community identified Spirochaetaceae bacteria as conserved across all sites and samples. Whereas members of the Vulcaniibacterium, Spirochaetaceae and Margulisbacteria, and Polynucleobacter were regionally conserved members of the digestive gland, gill and mantle bacterial communities, respectively. This indicates that baseline bacterial community profiles for specific locations are necessary when investigating bacterial communities in oyster health.
Kühl, M, Trampe, E, Mosshammer, M, Johnson, M, Larkum, AWD, Frigaard, N-U & Koren, K 2020, 'Substantial near-infrared radiation-driven photosynthesis of chlorophyll f-containing cyanobacteria in a natural habitat', eLife, vol. 9.
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Far-red absorbing chlorophylls are constitutively present as chlorophyll (Chl) d in the cyanobacterium Acaryochloris marina, or dynamically expressed by synthesis of Chl f, red-shifted phycobiliproteins and minor amounts of Chl d via far-red light photoacclimation in a range of cyanobacteria, which enables them to use near-infrared-radiation (NIR) for oxygenic photosynthesis. While the biochemistry and molecular physiology of Chl f-containing cyanobacteria has been unraveled in culture studies, their ecological significance remains unexplored and no data on their in situ activity exist. With a novel combination of hyperspectral imaging, confocal laser scanning microscopy, and nanoparticle-based O2 imaging, we demonstrate substantial NIR-driven oxygenic photosynthesis by endolithic, Chl f-containing cyanobacteria within natural beachrock biofilms that are widespread on (sub)tropical coastlines. This indicates an important role of NIR-driven oxygenic photosynthesis in primary production of endolithic and other shaded habitats.
Kulk, G, Platt, T, Dingle, J, Jackson, T, Jönsson, B, Bouman, H, Babin, M, Brewin, R, Doblin, M, Estrada, M, Figueiras, F, Furuya, K, González-Benítez, N, Gudfinnsson, H, Gudmundsson, K, Huang, B, Isada, T, Kovač, Ž, Lutz, V, Marañón, E, Raman, M, Richardson, K, Rozema, P, Poll, W, Segura, V, Tilstone, G, Uitz, J, Dongen-Vogels, V, Yoshikawa, T & Sathyendranath, S 2020, 'Primary Production, an Index of Climate Change in the Ocean: Satellite-Based Estimates over Two Decades', Remote Sensing, vol. 12, no. 5, pp. 826-826.
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Primary production by marine phytoplankton is one of the largest fluxes of carbon on our planet. In the past few decades, considerable progress has been made in estimating global primary production at high spatial and temporal scales by combining in situ measurements of primary production with remote-sensing observations of phytoplankton biomass. One of the major challenges in this approach lies in the assignment of the appropriate model parameters that define the photosynthetic response of phytoplankton to the light field. In the present study, a global database of in situ measurements of photosynthesis versus irradiance (P-I) parameters and a 20-year record of climate quality satellite observations were used to assess global primary production and its variability with seasons and locations as well as between years. In addition, the sensitivity of the computed primary production to potential changes in the photosynthetic response of phytoplankton cells under changing environmental conditions was investigated. Global annual primary production varied from 38.8 to 42.1 Gt C yr − 1 over the period of 1998–2018. Inter-annual changes in global primary production did not follow a linear trend, and regional differences in the magnitude and direction of change in primary production were observed. Trends in primary production followed directly from changes in chlorophyll-a and were related to changes in the physico-chemical conditions of the water column due to inter-annual and multidecadal climate oscillations. Moreover, the sensitivity analysis in which P-I parameters were adjusted by ±1 standard deviation showed the importance of accurately assigning photosynthetic parameters in global and regional calculations of primary production. The assimilation number of the P-I curve showed strong relationships with environmental variables such as temperature and had a practically one-to-one relationship with the magnitude of change in primary product...
Lampignano, R, Neumann, MHD, Weber, S, Kloten, V, Herdean, A, Voss, T, Groelz, D, Babayan, A, Tibbesma, M, Schlumpberger, M, Chemi, F, Rothwell, DG, Wikman, H, Galizzi, J-P, Riise Bergheim, I, Russnes, H, Mussolin, B, Bonin, S, Voigt, C, Musa, H, Pinzani, P, Lianidou, E, Brady, G, Speicher, MR, Pantel, K, Betsou, F, Schuuring, E, Kubista, M, Ammerlaan, W, Sprenger-Haussels, M, Schlange, T & Heitzer, E 2020, 'Multicenter Evaluation of Circulating Cell-Free DNA Extraction and Downstream Analyses for the Development of Standardized (Pre)analytical Work Flows', Clinical Chemistry, vol. 66, no. 1, pp. 149-160.
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AbstractBACKGROUNDIn cancer patients, circulating cell-free DNA (ccfDNA) can contain tumor-derived DNA (ctDNA), which enables noninvasive diagnosis, real-time monitoring, and treatment susceptibility testing. However, ctDNA fractions are highly variable, which challenges downstream applications. Therefore, established preanalytical work flows in combination with cost-efficient and reproducible reference materials for ccfDNA analyses are crucial for analytical validity and subsequently for clinical decision-making.METHODSWe describe the efforts of the Innovative Medicines Initiative consortium CANCER-ID (http://www.cancer-id.eu) for comparing different technologies for ccfDNA purification, quantification, and characterization in a multicenter setting. To this end, in-house generated mononucleosomal DNA (mnDNA) from lung cancer cell lines carrying known TP53 mutations was spiked in pools of plasma from healthy donors generated from 2 different blood collection tubes (BCTs). ccfDNA extraction was performed at 15 partner sites according to their respective routine practice. Downstream analysis of ccfDNA with respect to recovery, integrity, and mutation analysis was performed centralized at 4 different sites.RESULTSWe demonstrate suitability of mnDNA as a surrogate for ccfDNA as a process quality control from nucleic acid extraction to mutation detection. Although automated extraction protocols and quantitative PCR-based quantification methods yielded the most consistent and precise results, some kits preferentially recovered spiked mnDNA over endogenous ccfDNA. Mutated TP53 fragments derived from mnDNA were consistently detected using both next-generation sequencing-based deep sequencing and droplet digital PCR independently of BCT.
Lawson, CA, Seymour, JR, Possell, M, Suggett, DJ & Raina, J-B 2020, 'The Volatilomes of Symbiodiniaceae-Associated Bacteria Are Influenced by Chemicals Derived From Their Algal Partner', Frontiers in Marine Science, vol. 7.
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© Copyright © 2020 Lawson, Seymour, Possell, Suggett and Raina. Biogenic volatile organic compounds (BVOCs) are a large group of molecules involved in trophic interactions, stress response and atmospheric chemistry. Although they have been extensively studied in terrestrial ecosystems, their identity and prevalence in the marine environment remains largely unexplored. Here we characterized the volatilome of two abundant marine bacteria that were previously identified as members of the core microbiome of Symbiodiniaceae (phylum: Dinoflagellata), the photosynthetic endosymbionts of reef building corals. To determine the influence of Symbiodiniaceae exudate on their associated bacteria, we incubated isolates of Marinobacter adhaerens HP15 and Labrenzia sp. 21p with Symbiodiniaceae culture filtrate or culture medium (control) and investigated their volatilomes using GC–MS. The volatilome of Labrenzia sp. incubated in Symbiodiniaceae filtrate was significantly different and more diverse relative to the control. In contrast, the overall composition of the M. adhaerens volatilomes were consistent between treatment and control. Among the 35 compounds detected in both bacterial species, the dominant chemical functional groups were halogenated hydrocarbons, aromatic hydrocarbons and organosulfurs, some of which are known to play roles in inter-organism signaling, to act as antioxidants and as antimicrobials. This study provides new insights into the potential sources and diversity of marine BVOCs, uncovering a wide range of molecules that may play important physiological and ecological roles for these organisms, while also revealing the role of Symbiodiniaceae-associated bacteria in the emission of important atmospheric gases.
Liu, P-C, Peacock, WJ, Wang, L, Furbank, R, Larkum, A & Dennis, ES 2020, 'Leaf growth in early development is key to biomass heterosis in Arabidopsis', Journal of Experimental Botany, vol. 71, no. 8, pp. 2439-2450.
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AbstractArabidopsis thaliana hybrids have similar properties to hybrid crops, with greater biomass relative to the parents. We asked whether the greater biomass was due to increased photosynthetic efficiency per unit leaf area or to overall increased leaf area and increased total photosynthate per plant. We found that photosynthetic parameters (electron transport rate, CO2 assimilation rate, chlorophyll content, and chloroplast number) were unchanged on a leaf unit area and unit fresh weight basis between parents and hybrids, indicating that heterosis is not a result of increased photosynthetic efficiency. To investigate the possibility of increased leaf area producing more photosynthate per plant, we studied C24×Landsberg erecta (Ler) hybrids in detail. These hybrids have earlier germination and leaf growth than the parents, leading to a larger leaf area at any point in development of the plant. The developing leaves of the hybrids are significantly larger than those of the parents, with consequent greater production of photosynthate and an increased contribution to heterosis. The set of leaves contributing to heterosis changes as the plant develops; the four most recently emerged leaves make the greatest contribution. As a leaf matures, its contribution to heterosis attenuates. While photosynthesis per unit leaf area is unchanged at any stage of development in the hybrid, leaf area is greater and the amount of photosynthate per plant is increased.
Mahbub, KR, King, WL, Siboni, N, Nguyen, VK, Rahman, MM, Megharaj, M, Seymour, JR, Franks, AE & Labbate, M 2020, 'Long-lasting effect of mercury contamination on the soil microbiota and its co-selection of antibiotic resistance', Environmental Pollution, vol. 265, no. Pt B, pp. 115057-115057.
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Antibiotic resistance genes (ARGs) in the environment are an exposure risk to humans and animals and is emerging as a global public health concern. In this study, mercury (Hg) driven co-selection of ARGs was investigated under controlled conditions in two Australian non-agricultural soils with differing pH. Soils were spiked with increasing concentrations of inorganic Hg and left to age for 5 years. Both soils contained ARGs conferring resistance to tetracycline (tetA, tetB), sulphonamides (sul1), trimethoprim (dfrA1) and the ARG indicator class 1 integron-integrase gene, intI1, as measured by qPCR. The last resort antibiotic vancomycin resistance gene, vanB and quinolone resistance gene, qnrS were not detected. Hg driven co-selection of several ARGs namely intI1, tetA and tetB were observed in the alkaline soil within the tested Hg concentrations. No co-selection of the experimental ARGs was observed in the neutral pH soil. 16S rRNA sequencing revealed proliferation of Proteobacteria and Bacteriodetes in Hg contaminated neutral and alkaline soils respectively. Multivariate analyses revealed a strong effect of Hg, soil pH and organic carbon content on the co-selection of ARGs in the experimental soils. Additionally, although aging caused a significant reduction in Hg content, agriculturally important bacterial phyla such as Nitrospirae did not regrow in the contaminated soils. The results suggest that mercury can drive co-selection of ARGs in contaminated non-agricultural soils over five years of aging which is linked to soil microbiota shift and metal chemistry in the soil.
Malik, S, Khan, F, Atta, Z, Habib, N, Haider, MN, Wang, N, Alam, A, Jambi, EJ, Gull, M, Mehmood, MA & Zhu, H 2020, 'Microalgal flocculation: Global research progress and prospects for algal biorefinery', Biotechnology and Applied Biochemistry, vol. 67, no. 1, pp. 52-60.
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AbstractMicroalgal research has made significant progress due to versatile and high‐value industrial applications of microalgal biomass or its derivatives. However, to explore their full potential and to achieve commercial robustness, microalgal biorefinery needs cost‐effective technologies to produce, harvest, and process the microalgal biomass on large scale as higher production and harvesting cost is one of the key hindrances in the commercialization of algae‐based products. Among several other algal biomass harvesting technologies, self‐flocculation seems to be an attractive, low‐cost, and eco‐friendly harvesting technology. This review covers various flocculation‐based methods that have been employed to harvest microalgal biomass with a special emphasis on self‐flocculation in microalgae. Moreover, genetic engineering approaches to induce self‐flocculation in non‐flocculating microalgae along with the factors affecting self‐flocculation and recent research trends have also been discussed. It is concluded that self‐flocculation is the most desired approach for the energy‐ and environment‐efficient harvesting of microalgal biomass. However, its poorly understood genetic basis needs to be deciphered through detailed studies to harness its potential for the algal biorefinery.
Mantri, VA, Kazi, MA, Balar, NB, Gupta, V & Gajaria, T 2020, 'Concise review of green algal genus Ulva Linnaeus', Journal of Applied Phycology, vol. 32, no. 5, pp. 2725-2741.
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Matthews, JL, Cunning, R, Ritson-Williams, R, Oakley, CA, Lutz, A, Roessner, U, Grossman, AR, Weis, VM, Gates, RD & Davy, SK 2020, 'Metabolite pools of the reef building coral Montipora capitata are unaffected by Symbiodiniaceae community composition', Coral Reefs, vol. 39, no. 6, pp. 1727-1737.
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© 2020, Springer-Verlag GmbH Germany, part of Springer Nature. Some reef corals form stable, dominant or codominant associations with multiple endosymbiotic dinoflagellate species (family Symbiodiniaceae). Given the immense genetic and physiological diversity within this family, Symbiodiniaceae community composition has the potential to impact the nutritional physiology and fitness of the cnidarian host and all associated symbionts. Here we assessed the impact of the symbiont community composition on the metabolome of the coral Montipora capitata in Kāne‘ohe Bay, Hawai‘i, where different colonies can be dominated by stress-tolerant Durusdinium glynnii or stress-sensitive Cladocopium spp. Based on our existing knowledge of these symbiont taxa, we hypothesised that the metabolite profile of D. glynnii-dominated corals would be consistent with poorer nutritional support of the host relative to those corals dominated by Cladocopium spp. However, comparative metabolite profiling revealed that the metabolite pools of the host and symbiont were unaffected by differences in the abundance of the two symbionts within the community. The abundance of the individual metabolites was the same in the host and in the endosymbiont regardless of whether the host was populated with D. glynnii or Cladocopium spp. These results suggest that coral-dinoflagellate symbioses have the potential to undergo physiological adjustments over time to accommodate differences in their resident symbionts. Such mechanisms may involve host heterotrophic compensation (increasing the level of nutrition generated by feeding relative to delivery from the algae), dynamic regulation of metabolic pathways when exchange of metabolites between the organisms differs, and/or modification of both the type and quantity of metabolites that are exchanged. We discuss these adjustments and the implications for the physiology and survival of reef corals under changing environmental regimes.
Matthews, JL, Raina, J, Kahlke, T, Seymour, JR, van Oppen, MJH & Suggett, DJ 2020, 'Symbiodiniaceae‐bacteria interactions: rethinking metabolite exchange in reef‐building corals as multi‐partner metabolic networks', Environmental Microbiology, vol. 22, no. 5, pp. 1675-1687.
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SummaryThe intimate relationship between scleractinian corals and their associated microorganisms is fundamental to healthy coral reef ecosystems. Coral‐associated microbes (Symbiodiniaceae and other protists, bacteria, archaea, fungi and viruses) support coral health and resilience through metabolite transfer, inter‐partner signalling, and genetic exchange. However, much of our understanding of the coral holobiont relationship has come from studies that have investigated either coral‐Symbiodiniaceae or coral‐bacteria interactions in isolation, while relatively little research has focused on other ecological and metabolic interactions potentially occurring within the coral multi‐partner symbiotic network. Recent evidences of intimate coupling between phytoplankton and bacteria have demonstrated that obligate resource exchange between partners fundamentally drives their ecological success. Here, we posit that similar associations with bacterial consortia regulate Symbiodiniaceae productivity and are in turn central to the health of corals. Indeed, we propose that this bacteria‐Symbiodiniaceae‐coral relationship underpins the coral holobiont's nutrition, stress tolerance and potentially influences the future survival of coral reef ecosystems under changing environmental conditions. Resolving Symbiodiniaceae‐bacteria associations is therefore a logical next step towards understanding the complex multi‐partner interactions occurring in the coral holobiont.
McCauley, JI, Labeeuw, L, Jaramillo-Madrid, AC, Nguyen, LN, Nghiem, LD, Chaves, AV & Ralph, PJ 2020, 'Management of Enteric Methanogenesis in Ruminants by Algal-Derived Feed Additives', Current Pollution Reports, vol. 6, no. 3, pp. 188-205.
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© 2020, Springer Nature Switzerland AG. Purpose of Review: In this paper, we critically review the current state of nutritional management strategies to reduce methane emissions resulting from enteric fermentation in livestock production. In this context, it highlights the novel strategy regarding the use of macroalgal- and microalgal-derived feed additives. Recent Findings: Several feed management strategies for ruminants focus on the inclusion of nutritional supplements, increasing proportion of starch, or supplementation with high-energy lipids. These strategies aim to improve animal productivity, whilst at the same time reduce methane emissions. Algae supplements are currently investigated as novel ingredients for decreasing methanogenesis, with the potential production of algal biomass also contributing to reducing greenhouse gas emissions. Thus, utilisation of algal biomass as a feed concentrate in dietary supplementation presents a sustainable and environmentally friendly strategy. Summary: This review summarises the current stage of research on dietary strategies and their influences on the metabolic processes during enteric fermentation. This information is essential for developing strategies to mitigate methane emissions in the livestock industry. We specifically present the opportunities that algae could offer as a feed additive for methanogenic reduction in cattle. The data compiled from the peer-reviewed literature revealed synergistic effects of algal biomass on methane reduction and animal productivity. However, the challenges regarding the mass cultivation of macro- and microalgae were noticed. Considering the diversity of algal species, future research should increase screening efforts to include more species and dosage evaluation, along with efforts to see if such effects are sustained over time.
Messer, LF, Ostrowski, M, Doblin, MA, Petrou, K, Baird, ME, Ingleton, T, Bissett, A, Van de Kamp, J, Nelson, T, Paulsen, I, Bodrossy, L, Fuhrman, JA, Seymour, JR & Brown, MV 2020, 'Microbial tropicalization driven by a strengthening western ocean boundary current', Global Change Biology, vol. 26, no. 10, pp. 5613-5629.
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AbstractWestern boundary currents (WBCs) redistribute heat and oligotrophic seawater from the tropics to temperate latitudes, with several displaying substantial climate change‐driven intensification over the last century. Strengthening WBCs have been implicated in the poleward range expansion of marine macroflora and fauna, however, the impacts on the structure and function of temperate microbial communities are largely unknown. Here we show that the major subtropical WBC of the South Pacific Ocean, the East Australian Current (EAC), transports microbial assemblages that maintain tropical and oligotrophic (k‐strategist) signatures, to seasonally displace more copiotrophic (r‐strategist) temperate microbial populations within temperate latitudes of the Tasman Sea. We identified specific characteristics of EAC microbial assemblages compared with non‐EAC assemblages, including strain transitions within the SAR11 clade, enrichment of Prochlorococcus, predicted smaller genome sizes and shifts in the importance of several functional genes, including those associated with cyanobacterial photosynthesis, secondary metabolism and fatty acid and lipid transport. At a temperate time‐series site in the Tasman Sea, we observed significant reductions in standing stocks of total carbon and chlorophyll a, and a shift towards smaller phytoplankton and carnivorous copepods, associated with the seasonal impact of the EAC microbial assemblage. In light of the substantial shifts in microbial assemblage structure and function associated with the EAC, we conclude that climate‐driven expansions of WBCs will expand the range of tropical oligotrophic microbes, and potentially profoundly impact the trophic status of temperate waters.
Miller, AD, Coleman, MA, Clark, J, Cook, R, Naga, Z, Doblin, MA, Hoffmann, AA, Sherman, CDH & Bellgrove, A 2020, 'Local thermal adaptation and limited gene flow constrain future climate responses of a marine ecosystem engineer', Evolutionary Applications, vol. 13, no. 5, pp. 918-934.
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AbstractRising ocean temperatures and extreme temperature events have precipitated declines and local extinctions in many marine species globally, but patterns of loss are often uneven across species ranges for reasons that are poorly understood. Knowledge of the extent of local adaptation and gene flow may explain such patterns and help predict future trajectories under scenarios of climate change. We test the extent to which local differentiation in thermal tolerance is influenced by gene flow and local adaptation using a widely distributed intertidal seaweed (Hormosira banksii) from temperate Australia. Population surveys across ~2,000 km of the species range revealed strong genetic structuring at regional and local scales (global FST = 0.243) reflecting extremely limited gene flow, while common garden experiments (14‐day exposures to 15, 18, 21°C) revealed strong site differences in early development and mortality in response to elevated temperature. Embryos from many sites spanning a longitudinal thermal gradient showed suppressed development and increased mortality to elevated water temperatures, but populations originating from warmer and more variable thermal environments tended to be less susceptible to warming. Notably, there was significant local‐scale variation in the thermal responses of embryos within regions which was corroborated by the finding of small‐scale genetic differences. We expect the observed genetic and phenotypic differentiation to lead to uneven responses to warming sea surface temperatures in this important marine foundation species. The study highlights the challenges of predicting species responses to thermal stress and the importance of management strategies that incorporate evolutionary potential for “climate‐proofing” marine ecosystems.
Murray, JS, Nishimura, T, Finch, SC, Rhodes, LL, Puddick, J, Harwood, DT, Larsson, ME, Doblin, MA, Leung, P, Yan, M, Rise, F, Wilkins, AL & Prinsep, MR 2020, 'The role of 44-methylgambierone in ciguatera fish poisoning: Acute toxicity, production by marine microalgae and its potential as a biomarker for Gambierdiscus spp.', Harmful Algae, vol. 97, pp. 101853-101853.
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Ciguatera fish poisoning (CFP) is prevalent around the tropical and sub-tropical latitudes of the world and impacts many Pacific island communities intrinsically linked to the reef system for sustenance and trade. While the genus Gambierdiscus has been linked with CFP, it is commonly found on tropical reef systems in microalgal assemblages with other genera of toxin-producing, epiphytic and/or benthic dinoflagellates - Amphidinium, Coolia, Fukuyoa, Ostreopsis and Prorocentrum. Identifying a biomarker compound that can be used for the early detection of Gambierdiscus blooms, specifically in a mixed microalgal community, is paramount in enabling the development of management and mitigation strategies. Following on from the recent structural elucidation of 44-methylgambierone, its potential to contribute to CFP intoxication events and applicability as a biomarker compound for Gambierdiscus spp. was investigated. The acute toxicity of this secondary metabolite was determined by intraperitoneal injection using mice, which showed it to be of low toxicity, with an LD50 between 20 and 38 mg kg-1. The production of 44-methylgambierone by 252 marine microalgal isolates consisting of 90 species from 32 genera across seven classes, was assessed by liquid chromatography-tandem mass spectrometry. It was discovered that the production of this secondary metabolite was ubiquitous to the eight Gambierdiscus species tested, however not all isolates of G. carpenteri, and some species/isolates of Coolia and Fukuyoa.
Najafpour, MM, Zaharieva, I, Zand, Z, Maedeh Hosseini, S, Kouzmanova, M, Hołyńska, M, Tranca, I, Larkum, AW, Shen, J-R & Allakhverdiev, SI 2020, 'Water-oxidizing complex in Photosystem II: Its structure and relation to manganese-oxide based catalysts', Coordination Chemistry Reviews, vol. 409, pp. 213183-213183.
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© 2020 Elsevier B.V. Cyanobacteria, green algae, and higher plants provide the major part of molecular O2 of Earth atmosphere via water oxidation of oxygenic photosynthesis. The water-oxidizing complex is a manganese-calcium oxide-based cluster embedded in Photosystem II that oxidizes water with high turnover frequency. The atomic structure and analysis of the Mn-Ca cluster are important in understanding the mechanism of water oxidation and for the design of efficient artificial water-oxidizing catalysts. With this short review, we aim to introduce the basic features of the biological water oxidation to the new-comers in the field. Taking into account the recent structural studies, including a high-resolution, radiation-damage-free structure of the water-oxidizing complex, and structures of intermediate S-states revealed by femtosecond X-ray free electron lasers, we discuss the structure and functions of the biologically active site and its implications for the development of inorganic catalysts for solar fuels production.
Nguyen, HM, Kim, M, Ralph, PJ, Marín-Guirao, L, Pernice, M & Procaccini, G 2020, 'Stress Memory in Seagrasses: First Insight Into the Effects of Thermal Priming and the Role of Epigenetic Modifications', Frontiers in Plant Science, vol. 11, p. 494.
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While thermal priming and the relative role of epigenetic modifications have been widely studied in terrestrial plants, their roles remain unexplored in seagrasses so far. Here, we experimentally compared the ability of two different functional types of seagrass species, dominant in the Southern hemisphere, climax species Posidonia australis and pioneer species Zostera muelleri, to acquire thermal-stress memory to better survive successive stressful thermal events. To this end, a two-heatwave experimental design was conducted in a mesocosm setup. Findings across levels of biological organization including the molecular (gene expression), physiological (photosynthetic performances and pigments content) and organismal (growth) levels provided the first evidence of thermal priming in seagrasses. Non-preheated plants suffered a significant reduction in photosynthetic capacity, leaf growth and chlorophyll a content, while preheated plants were able to cope better with the recurrent stressful event. Gene expression results demonstrated significant regulation of methylation-related genes in response to thermal stress, suggesting that epigenetic modifications could play a central role in seagrass thermal stress memory. In addition, we revealed some interspecific differences in thermal responses between the two different functional types of seagrass species. These results provide the first insights into thermal priming and relative epigenetic modifications in seagrasses paving the way for more comprehensive forecasting and management of thermal stress in these marine foundation species in an era of rapid environmental change.
Nguyen, LN, Commault, AS, Kahlke, T, Ralph, PJ, Semblante, GU, Johir, MAH & Nghiem, LD 2020, 'Genome sequencing as a new window into the microbial community of membrane bioreactors – A critical review', Science of The Total Environment, vol. 704, pp. 135279-135279.
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Recent developed sequencing techniques have resulted in a new and unprecedented way to study biological wastewater treatment, in which most organisms are uncultivable. This review provides (i) an insight on state-of-the-art sequencing techniques and their limitations; (ii) a critical assessment of the microbial community in biological reactor and biofouling layer in a membrane bioreactor (MBR). The data from high-throughput sequencing has been used to infer microbial growth conditions and metabolisms of microorganisms present in MBRs at the time of sampling. These data shed new insight to two fundamental questions about a microbial community in the MBR process namely the microbial composition (who are they?) and the functions of each specific microbial assemblage (what are their function?). The results to date also highlight the complexity of the microbial community growing on MBRs. Environmental conditions are dynamic and diverse, and can influence the diversity and structural dynamics of any given microbial community for wastewater treatment. The benefits of understanding the structure of microbial communities on three major aspects of the MBR process (i.e. nutrient removal, biofouling control, and micropollutant removal) were symmetrically delineated. This review also indicates that the deployment of microbial community analysis for a practical engineering context, in terms of process design and system optimization, can be further realized.
Nguyen, LN, Truong, MV, Nguyen, AQ, Johir, MAH, Commault, AS, Ralph, PJ, Semblante, GU & Nghiem, LD 2020, 'A sequential membrane bioreactor followed by a membrane microalgal reactor for nutrient removal and algal biomass production', Environmental Science: Water Research & Technology, vol. 6, no. 1, pp. 189-196.
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A hybrid process combining a single compartment aerobic membrane bioreactor (MBR) and a membrane microalgal reactor (MMR) was evaluated for nutrient removal and microalgal biomass production.
Nguyen, T-T-D, Nguyen, T-T, An Binh, Q, Bui, X-T, Ngo, HH, Vo, HNP, Andrew Lin, K-Y, Vo, T-D-H, Guo, W, Lin, C & Breider, F 2020, 'Co-culture of microalgae-activated sludge for wastewater treatment and biomass production: Exploring their role under different inoculation ratios', Bioresource Technology, vol. 314, pp. 123754-123754.
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In this study, mixed culture (microalgae:activated sludge) of a photobioreactor (PBR) were investigated at different inoculation ratios (1:0, 9:1, 3:1, 1:1, 0:1 wt/wt). This work was not only to determine the optimal ratio for pollutant remediation and biomass production but also to explore the role of microorganisms in the co-culture system. The results showed high total biomass concentrations were obtained from 1:0 and 3:1 ratio being values of 1.06, 1.12 g L-1, respectively. Microalgae played a dominant role in nitrogen removal via biological assimilation while activated sludge was responsible for improving COD removal. Compared with the single culture of microalgae, the symbiosis between microalgae and bacteria occurred at 3:1 and 1:1 ratio facilitated a higher COD removal by 37.5-45.7 %. In general, combined assessment based on treatment performance and biomass productivity facilitated to select an optimal ratio of 3:1 for the operation of the co-culture PBR.
Nguyen, VK, King, WL, Siboni, N, Mahbub, KR, Dove, M, O'Connor, W, Seymour, JR & Labbate, M 2020, 'The Sydney rock oyster microbiota is influenced by location, season and genetics', Aquaculture, vol. 527, pp. 735472-735472.
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© 2020 Elsevier B.V. Queensland unknown (QX) disease is a significant cause of economic loss for the Sydney rock oyster (SRO) aquaculture industry. Evidence is emerging that QX disease is multi-factorial in nature, with a number of environmental and host factors contributing to disease dynamics. Efforts to mitigate the impacts of QX disease are primarily focused on breeding for disease resistance however, the mechanisms that drive disease resistance are poorly understood. One potential factor influencing disease resistance is the microbiota. To determine the influence of location, season and disease resistance on the SRO microbiota, we used 16S rRNA (V1 – V3 region) amplicon sequencing. The microbiota of six SRO families with two categorised as QX-resistant and four as QX-susceptible, deployed to two different locations (Port Stephens and Wallis Lake, NSW, Australia) and over two seasons (Austral summer and winter), were characterised. As expected, the SRO microbiota was distinct to the microbial community found in seawater. Further, the SRO microbiota was significantly influenced by location and season, with operational taxonomic units (OTUs) assigned to the Candidatus Hepatoplasma and Endozoicomonas genera identified as significant drivers of microbiota dissimilarity between locations and seasons. Disease resistance also significantly influenced the SRO microbiota but only at the winter time point which is before the typical QX disease period. Overall, OTUs assigned to the Mycoplasma, Borrelia and Endozoicomonas genera were over-represented in QX-resistant SRO microbiota, whereas members of the Pseudoalteromonas, Vibrio, and Candidatus Hepatoplasma genera were over-represented in QX-sensitive microbiota. These findings confirm the influencing role of location and season on the microbiota structure as evidenced in other molluscan species, but also provide preliminary evidence that the microbiota assemblage before the QX disease period may be important ...
Oliver, T, Sánchez-Baracaldo, P, Larkum, AW, Rutherford, AW & Cardona, T 2020, 'Time-resolved comparative molecular evolution of oxygenic photosynthesis', Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol. 1862, no. 6, p. 2020.02.28.969766.
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AbstractOxygenic photosynthesis starts with the oxidation of water to O2, a light-driven reaction catalysed by photosystem II. Cyanobacteria are the only prokaryotes capable of water oxidation and therefore, it is assumed that relative to the origin of life and bioenergetics, the origin of oxygenic photosynthesis is a late innovation. However, when exactly water oxidation originated remains an unanswered question. Here we use relaxed molecular clocks to compare one of the two ancestral core duplications that are unique to water-oxidizing photosystem II, that leading to CP43 and CP47, with some of the oldest well-described events in the history of life. Namely, the duplication leading to the Alpha and Beta subunits of the catalytic head of ATP synthase, and the divergence of archaeal and bacterial RNA polymerases and ribosomes. We also compare it with more recent events such as the duplication of cyanobacteria-specific FtsH metalloprotease subunits, of CP43 variants used in a variety of photoacclimation responses, and the speciation events leading to Margulisbacteria, Sericytochromatia, Vampirovibrionia, and other clades containing anoxygenic phototrophs. We demonstrate that the ancestral core duplication of photosystem II exhibits patterns in the rates of protein evolution through geological time that are nearly identical to those of the ATP synthase, RNA polymerase, or the ribosome. Furthermore, we use ancestral sequence reconstruction in combination with comparative structural biology of photosystem subunits, to provide additional evidence supporting the premise that water oxidation had originated before the ancestral core duplications. Our work suggests that photosynthetic water oxidation originated closer to the origin of life and bioenergetics than can be documented based on species trees alone.
Osman, EO, Suggett, DJ, Voolstra, CR, Pettay, DT, Clark, DR, Pogoreutz, C, Sampayo, EM, Warner, ME & Smith, DJ 2020, 'Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities', Microbiome, vol. 8, no. 1.
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Abstract Background The capacity of reef-building corals to tolerate (or adapt to) heat stress is a key factor determining their resilience to future climate change. Changes in coral microbiome composition (particularly for microalgal endosymbionts and bacteria) is a potential mechanism that may assist corals to thrive in warm waters. The northern Red Sea experiences extreme temperatures anomalies, yet corals in this area rarely bleach suggesting possible refugia to climate change. However, the coral microbiome composition, and how it relates to the capacity to thrive in warm waters in this region, is entirely unknown. Results We investigated microbiomes for six coral species (Porites nodifera, Favia favus, Pocillopora damicornis, Seriatopora hystrix, Xenia umbellata, and Sarcophyton trocheliophorum) from five sites in the northern Red Sea spanning 4° of latitude and summer mean temperature ranges from 26.6 °C to 29.3 °C. A total of 19 distinct dinoflagellate endosymbionts were identified as belonging to three genera in the family Symbiodiniaceae (Symbiodinium, Cladocopium, and Durusdinium). Of these, 86% belonged to the genus Cladocopium, with notably five novel types (19%). The endosymbiont community showed a high degree of host-specificity despite the latitudinal gradient. In contrast, the diversity and composition of bacterial communities of the surface mucus layer (SML)—a compartment particularly sensitive to environmental change—varied significantly between sites, however for any given coral was species...
Pereira, RRC, Scanes, E, Gibbs, M, Byrne, M & Ross, PM 2020, 'Can prior exposure to stress enhance resilience to ocean warming in two oyster species?', PLOS ONE, vol. 15, no. 4, pp. e0228527-e0228527.
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Securing economically and ecologically significant molluscs, as our oceans warm due to climate change, is a global priority. South eastern Australia receives warm water in a strengthening East Australia Current and so resident species are vulnerable to elevated temperature and marine heat waves. This study tested whether prior exposure to elevated temperature can enhance resilience of oysters to ocean warming. Two Australian species, the flat oyster, Ostrea angasi, and the Sydney rock oyster, Saccostrea glomerata, were obtained as adults and 'heat shocked' by exposure to a dose of warm water in the laboratory. Oysters were then transferred to elevated seawater temperature conditions where the thermal outfall from power generation was used as a proxy to investigate the impacts of ocean warming. Shell growth, condition index, lipid content and survival of flat oysters and condition of Sydney rock oysters were all significantly reduced by elevated seawater temperature in the field. Flat oysters grew faster than Sydney rock oysters at ambient temperature, but their growth and survival was more sensitive to elevated temperature. 'Stress inoculation' by heat shock did little to ameliorate the negative effects of increased temperature, although the survival of heat-shocked flat oysters was greater than non-heat shocked oysters. Further investigations are required to determine if early exposure to heat stress can enhance resilience of oysters to ocean warming.
Pernice, M, Raina, J-B, Rädecker, N, Cárdenas, A, Pogoreutz, C & Voolstra, CR 2020, 'Down to the bone: the role of overlooked endolithic microbiomes in reef coral health', The ISME Journal, vol. 14, no. 2, pp. 325-334.
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Abstract Reef-building corals harbour an astonishing diversity of microorganisms, including endosymbiotic microalgae, bacteria, archaea, and fungi. The metabolic interactions within this symbiotic consortium are fundamental to the ecological success of corals and the unique productivity of coral reef ecosystems. Over the last two decades, scientific efforts have been primarily channelled into dissecting the symbioses occurring in coral tissues. Although easily accessible, this compartment is only 2–3 mm thick, whereas the underlying calcium carbonate skeleton occupies the vast internal volume of corals. Far from being devoid of life, the skeleton harbours a wide array of algae, endolithic fungi, heterotrophic bacteria, and other boring eukaryotes, often forming distinct bands visible to the bare eye. Some of the critical functions of these endolithic microorganisms in coral health, such as nutrient cycling and metabolite transfer, which could enable the survival of corals during thermal stress, have long been demonstrated. In addition, some of these microorganisms can dissolve calcium carbonate, weakening the coral skeleton and therefore may play a major role in reef erosion. Yet, experimental data are wanting due to methodological limitations. Recent technological and conceptual advances now allow us to tease apart the complex physical, ecological, and chemical interactions at the heart of coral endolithic microbial communities. These new capabilities have resulted in an excellent body of research and provide an exciting outlook to further address the functional microbial ecology of the “overlooked” coral skeleton.
Pezner, AK, Pivovaroff, AL, Sun, W, Sharifi, MR, Rundel, PW & Seibt, U 2020, 'Plant Functional Traits Predict the Drought Response of Native California Plant Species', International Journal of Plant Sciences, vol. 181, no. 2, pp. 256-265.
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Phong Vo, HN, Ngo, HH, Guo, W, Hong Nguyen, TM, Li, J, Liang, H, Deng, L, Chen, Z & Hang Nguyen, TA 2020, 'Poly‐and perfluoroalkyl substances in water and wastewater: A comprehensive review from sources to remediation', Journal of Water Process Engineering, vol. 36, pp. 101393-101393.
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© 2020 Elsevier Ltd Per- and polyfluoroalkyl substances (PFAS) are pollutants have attracted major concern due to their high persistence and bioaccumulation. They are causing increasingly serious epidemiological problems in many communities globally due to consuming PFAS-contaminated water sources. Necessarily, the behavior of PFAS in water and wastewater needs to be understood better. This study attempts to comprehensively review, analyze and discuss PFAS based on the following key aspects: (i) sources, (ii) occurrence in water and wastewater, (iii) transformation, fate and migration, and (iv) remediation technologies. Studies indicated that modern water and wastewater treatment plants cannot deal completely with PFAS and in some cases, the removal efficiency is minus -3500-fold. The main reasons are the high hydrophobicity of PFAS and presence of PFAS precursors. Precursors can account for 33–63% of total PFAS concentration in water and wastewater. Detection and identification of precursors are challenging due to the requirement of advanced analytical instrument and standard chemicals. Several technologies have been developed for PFAS remediation involving two main mechanisms: separation-concentration and destruction. The most widespread in-use technology is adsorption because it is reasonably affordable. Anion exchange resin and synthesized materials are the most effective sorbents having a sorption capacity of 100–2000 mg PFAS/g sorbent, effective within a few hours. The destruction technology such as plasma can also be a promising one for degrading PFAS to below health-based standard in 1 min. However, plasma is costly and not yet ready for full scale application.
Poddar, N, Elahee Doomun, SN, Callahan, DL, Kowalski, GM & Martin, GJO 2020, 'The assimilation of glycerol into lipid acyl chains and associated carbon backbones of Nannochloropsis salina varies under nitrogen replete and deplete conditions', Biotechnology and Bioengineering, vol. 117, no. 11, pp. 3299-3309.
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AbstractMixotrophic cultivation can increase microalgae productivity, yet the associated lipid metabolism remains mostly unknown. Stable isotope labeling was used to track assimilation of glycerol into the triacylglyceride (TAG) and membrane lipids of Nannochloropsis salina. In N‐replete media, glycerol uptake and 13C incorporation into acyl chains were, respectively, 6‐fold and 12‐fold higher than in N‐deplete conditions. In N‐replete cultures, 42% of the carbon in the consumed glycerol was assimilated into lipid acyl chains, mostly in membrane lipids rather than TAG. In N‐deplete cultures, only 11% of the limited amount of consumed glycerol was fixed into lipid acyl chains. Labeled lipid‐associated glycerol backbones were predominantly 13C3 labeled, suggesting that intact glycerol molecules were directly esterified with fatty acids/polar head groups. However, the presence of singly and doubly labeled lipid‐bound glycerol species suggested that some glycerol also went through the central carbon metabolism before forming glycerol‐3‐phosphate destined for lipid esterification. 13C incorporation was higher in the saturated and monounsaturated than the polyunsaturated acyl chains of TAG, indicating the flux of carbon from glycerol went first to de novo fatty acid synthesis before acyl editing reactions. The results demonstrate that nitrogen availability influences both glycerol consumption and utilization for lipid synthesis in Nannochloropsis, providing novel insights for developing mixotrophic cultivation strategies.
Poddar, N, Sen, R & Martin, GJO 2020, 'Bacterial abundance and diversity in Microchloropsis salina (formerly Nannochloropsis salina) cultures in response to the presence of ammonium, nitrate and glycerol', Journal of Applied Phycology, vol. 32, no. 2, pp. 839-850.
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Price, S, Kuzhiumparambil, U, Pernice, M & Ralph, PJ 2020, 'Cyanobacterial polyhydroxybutyrate for sustainable bioplastic production: Critical review and perspectives', Journal of Environmental Chemical Engineering, vol. 8, no. 4, pp. 104007-104007.
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© 2020 Elsevier Ltd. PHB is a promising bioplastic material that naturally accumulates in many strains of cyanobacteria. This comprehensive review covers recent advances in several topics including PHB metabolism, material properties, relevant extraction methods and protocols, industrial cultivation strategy, current economic assessment and much more. Ultimately, the profitability of cyanobacterial PHB production is controlled by low PHB productivity as well as expensive cultivation and harvesting equipment. Several research areas for improving viability of cyanobacterial PHB production have also been summarised and perspectives on future efforts suggested including; screening, genetic modification, wastewater cultivation and using chemical modulators among others.
Raven, JA, Suggett, DJ & Giordano, M 2020, 'Inorganic carbon concentrating mechanisms in free‐living and symbiotic dinoflagellates and chromerids', Journal of Phycology, vol. 56, no. 6, pp. 1377-1397.
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Photosynthetic dinoflagellates are ecologically and biogeochemically important in marine and freshwater environments. However, surprisingly little is known of how this group acquires inorganic carbon or how these diverse processes evolved. Consequently, how CO2 availability ultimately influences the success of dinoflagellates over space and time remains poorly resolved compared to other microalgal groups. Here we review the evidence. Photosynthetic core dinoflagellates have a Form II RuBisCO (replaced by Form IB or Form ID in derived dinoflagellates). The in vitro kinetics of the Form II RuBisCO from dinoflagellates are largely unknown, but dinoflagellates with Form II (and other) RuBisCOs have inorganic carbon concentrating mechanisms (CCMs), as indicated by in vivo internal inorganic C accumulation and affinity for external inorganic C. However, the location of the membrane(s) at which the essential active transport component(s) of the CCM occur(s) is (are) unresolved; isolation and characterization of functionally competent chloroplasts would help in this respect. Endosymbiotic Symbiodiniaceae (in Foraminifera, Acantharia, Radiolaria, Ciliata, Porifera, Acoela, Cnidaria, and Mollusca) obtain inorganic C by transport from seawater through host tissue. In corals this transport apparently provides an inorganic C concentration around the photobiont that obviates the need for photobiont CCM. This is not the case for tridacnid bivalves, medusae, or, possibly, Foraminifera. Overcoming these long‐standing knowledge gaps relies on technical advances (e.g., the in vitro kinetics of Form II RuBisCO) that can functionally track the fate of inorganic C forms.
Rinke, C, Rubino, F, Messer, LF, Youssef, N, Parks, DH, Chuvochina, M, Brown, M, Jeffries, T, Tyson, GW, Seymour, JR & Hugenholtz, P 2020, 'Correction: A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.)', The ISME Journal, vol. 14, no. 3, pp. 878-878.
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Abstract An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Ros, M, Camp, EF, Hughes, DJ, Crosswell, JR, Warner, ME, Leggat, WP & Suggett, DJ 2020, 'Unlocking the black‐box of inorganic carbon‐uptake and utilization strategies among coral endosymbionts (Symbiodiniaceae)', Limnology and Oceanography, vol. 65, no. 8, pp. 1747-1763.
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AbstractDinoflagellates within the family Symbiodiniaceae are widespread and fuel metabolism of reef‐forming corals through photosynthesis. Adaptation in capacity to harvest and utilize light, and “safely” process photosynthetically generated energy is a key factor regulating their broad ecological success. However, whether such adaptive capacity similarly extends to how Symbiodiniaceae species and genotypes assimilate inorganic carbon (Ci) remains unexplored. We build on recent approaches exploring functional diversity of fitness traits to identify whether Ci uptake and incorporation could be reconciled with evolutionary adaptation among Symbiodiniaceae. We examined phylogenetically diverse Symbiodiniaceae cultures (23 isolates, 6 genera) to track how carbon was invested into cellular uptake, excretion, and growth (cell size, division, storage). Gross carbon uptake rates (GPC) over 1 h varied among isolates grown at 26°C (0.63–3.08 pg C [cell h]−1) with no evident pattern with algal phylogeny. Intriguingly, net carbon uptake rates (24 h) were often higher (1.01–5.54 pg C [cell h]−1) than corresponding values of GPC—we discuss how such GPC measurements may reflect highly conserved biological characteristics for cultured cells linked to high metabolic dependency on photorespiration and heterotrophy. Three isolates from different genera (Cladocopium goreaui, Durusdinium trenchii, and Effrenium voratum) were additionally grown at 20°C and 30°C. Here, Ci uptake consistently decreased with temperature‐driven declines in growth rate, suggesting environmental regulation outweighs phylogenetic organization of carbon assimilation capacity among Symbiodiniaceae. Together, these data demonstrate environmental regulation and ecological success among Symbiodiniaceae likely rests on plasticity of upstream photosyn...
Scanes, E, Parker, LM, O'Connor, WA, Dove, MC & Ross, PM 2020, 'Heatwaves alter survival of the Sydney rock oyster, Saccostrea glomerata', Marine Pollution Bulletin, vol. 158, pp. 111389-111389.
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Heatwaves are an increasing threat to organisms across the globe. Marine and atmospheric heatwaves are predicted to impact sessile intertidal marine organisms, especially when exposed at low tide and unable to seek refuge. The study aimed to determine whether a simulated atmospheric heatwave will alter the survival of selectively bred families of Sydney rock oysters (Saccostrea glomerata), and whether survival is dependent on morphological and physiological traits. The survival of S. glomerata families to a simulated atmospheric heatwave varied from 25 to 60% and was not correlated with morphology or physiology. Survival may depend on the presence of genotypes that translate into molecular defenses such as heat-shock proteins and inhibitor of apoptosis proteins that provide oysters with resilience. Understanding the responses among families of oysters to heatwaves is critical if we are to restore the ecological services of oyster reefs and sustain oyster aquaculture.
Scanes, E, Scanes, PR & Ross, PM 2020, 'Climate change rapidly warms and acidifies Australian estuaries', Nature Communications, vol. 11, no. 1, p. 1803.
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AbstractClimate change is impacting ecosystems worldwide. Estuaries are diverse and important aquatic ecosystems; and yet until now we have lacked information on the response of estuaries to climate change. Here we present data from a twelve-year monitoring program, involving 6200 observations of 166 estuaries along >1100 kilometres of the Australian coastline encompassing all estuary morphologies. Estuary temperatures increased by 2.16 °C on average over 12 years, at a rate of 0.2 °C year−1, with waters acidifying at a rate of 0.09 pH units and freshening at 0.086 PSU year−1. The response of estuaries to climate change is dependent on their morphology. Lagoons and rivers are warming and acidifying at the fastest rate because of shallow average depths and limited oceanic exchange. The changes measured are an order of magnitude faster than predicted by global ocean and atmospheric models, indicating that existing global models may not be useful to predict change in estuaries.
Shahid, A, Malik, S, Zhu, H, Xu, J, Nawaz, MZ, Nawaz, S, Asraful Alam, M & Mehmood, MA 2020, 'Cultivating microalgae in wastewater for biomass production, pollutant removal, and atmospheric carbon mitigation; a review', Science of The Total Environment, vol. 704, pp. 135303-135303.
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Water shortage is one of the leading global problems along with the depletion of energy resources and environmental deterioration. Recent industrialization, global mobility, and increasing population have adversely affected the freshwater resources. The wastewater sources are categorized as domestic, agricultural and industrial effluents and their disposal into water bodies poses a harmful impact on human and animal health due to the presence of higher amounts of nitrogen, phosphorus, sulfur, heavy metals and other organic/inorganic pollutants. Several conventional treatment methods have been employed, but none of those can be termed as a universal method due to their high cost, less efficiency, and non-environment friendly nature. Alternatively, wastewater treatment using microalgae (phycoremediation) offers several advantages over chemical-based treatment methods. Microalgae cultivation using wastewater offers the highest atmospheric carbon fixation rate (1.83 kg CO2/kg of biomass) and fastest biomass productivity (40-50% higher than terrestrial crops) among all terrestrial bio-remediators with concomitant pollutant removal (80-100%). Moreover, the algal biomass may contain high-value metabolites including omega-3-fatty acids, pigments, amino acids, and high sugar content. Hence, after extraction of high-value compounds, residual biomass can be either directly converted to energy through thermochemical transformation or can be used to produce biofuels through biological fermentation or transesterification. This review highlights the recent advances in microalgal biotechnology to establish a biorefinery approach to treat wastewater. The articulation of wastewater treatment facilities with microalgal biorefinery, the use of microalgal consortia, the possible merits, and demerits of phycoremediation are also discussed. The impact of wastewater-derived nutrient stress and its exploitation to modify the algal metabolite content in view of future concerns of cost-ben...
Siboni, N, Abrego, D, Puill-Stephan, E, King, WL, Bourne, DG, Raina, J-B, Seymour, JR & Harder, T 2020, 'Crustose coralline algae that promote coral larval settlement harbor distinct surface bacterial communities', Coral Reefs, vol. 39, no. 6, pp. 1703-1713.
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© 2020, Springer-Verlag GmbH Germany, part of Springer Nature. Most benthic invertebrates, including ecosystem engineers such as corals, sponges and bivalves, have a motile planktonic larval phase and rely on specific chemical cues to identify a suitable substrate to settle. Crustose coralline algae (CCA) can induce settlement and metamorphosis responses in many invertebrates including corals. We tested the respective coral settlement capacity of multiple CCA species in a choice experiment and investigated the composition of their microbiomes. Our findings revealed that coral larval settlement was drastically influenced by CCA genera and also suggest that bacterial communities on the CCA surface can potentially serve as a driver of coral larval settlement. The composition of the bacterial communities on the surface of the least attractive CCA genus, Neogoniolithon fosliei, was markedly different from the other genera, Porolithon gardineri and Titanoderma prototypum and was significantly enriched in Vibrio and Flammeovirgaceae. The activity of CCA-associated bacterial communities may contribute to some of the variability observed in settlement responses between CCA species. Specific bacterial ASVs assigned to the Neptuniibacter, Methylotrophic Group 3 and Cellvibrionaceae were positively correlated with coral settlement. Conversely, ASVs assigned as Vibrio and Flammeovirga were negatively correlated with coral settlement. This study identifies putative bacterial taxa involved in coral settlement, which is an essential step to understand the chemical cues involved in this process and to predict the ability of corals to recolonize damaged reefs following disturbances.
Soja-Woźniak, M, Laiolo, L, Baird, ME, Matear, R, Clementson, L, Schroeder, T, Doblin, MA & Suthers, IM 2020, 'Effect of phytoplankton community size structure on remote-sensing reflectance and chlorophyll a products', Journal of Marine Systems, vol. 211, pp. 103400-103400.
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© 2020 Elsevier B.V. Remotely-sensed ocean colour is the main tool for estimating chlorophyll a (Chl-a) concentration and primary productivity on the global scale. In order to investigate the source of errors in remotely-sensed Chl-a concentration we obtained in situ bio-optical properties, in situ reflectances, satellite-derived reflectances and the Chl-a concentration satellite products of the Ocean and Land Colour Instrument (OLCI) Instrument on board Sentinel-3 A in waters off eastern Australia. The mesoscale eddies of these oligotrophic waters provide contrasting phytoplankton communities that allowed us to focus on the effect of phytoplankton size as a source of errors. In these waters, cold-core cyclonic eddies (CE) are dominated by large phytoplankton cells, while small cells dominate warm-core anticyclonic eddies (ACE). The chlorophyll-specific absorption and backscattering from contrasting sites show significant difference due to the differing package effect of phytoplankton size distributions. After normalising the absorption and backscattering spectra to Chl-a associated with just small phytoplankton, the spectra of optical properties become much more similar, showing that small-sized phytoplankton dominate IOPs even when large cells contain the greater fraction of Chl-a concentration of the phytoplankton community. Measured in situ reflectances agreed with reflectances calculated using a simple optical model based on measured IOPs. Furthermore, the in situ measured reflectances agreed well with the OLCI reflectance (mean normalised bias (MNB) of 7% for wavelengths <600 nm). However, a systematic underestimation of Chl-a concentrations by the OLCI algorithms was found in the region of cyclonic eddies characterised by increased Chl-a concentration and dominance of large-sized phytoplankton. A similar underprediction was found in Chl-a concentration calculated with the band-ratio OC4Me algorithm using in situ and IOP-calculated reflectance. Excluding Ch...
Suggett, DJ & Smith, DJ 2020, 'Coral bleaching patterns are the outcome of complex biological and environmental networking', Global Change Biology, vol. 26, no. 1, pp. 68-79.
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AbstractContinued declines in coral reef health over the past three decades have been punctuated by severe mass coral bleaching‐induced mortality events that have grown in intensity and frequency under climate change. Intensive global research efforts have therefore persistently focused on bleaching phenomena to understand where corals bleach, when and why—resulting in a large—yet still somewhat patchy—knowledge base. Particularly catastrophic bleaching‐induced coral mortality events in the past 5 years have catalyzed calls for a more diverse set of reef management tools, extending far beyond climate mitigation and reef protection, to also include more aggressive interventions. However, the effectiveness of these various tools now rests on rapidly assimilating our knowledge base of coral bleaching into more integrated frameworks. Here, we consider how the past three decades of intensive coral bleaching research has established the basis for complex biological and environmental networks, which together regulate outcomes of bleaching severity. We discuss how we now have enough scaffold for conceptual biological and environmental frameworks underpinning bleaching susceptibility, but that new tools are urgently required to translate this to an operational system informing—and testing—bleaching outcomes. Specifically, adopting network models that can fully describe and predict metabolic functioning of coral holobionts, and how this functioning is regulated by complex doses and interactions among environmental factors. Identifying knowledge gaps limiting operation of such models is the logical step to immediately guide and prioritize future experiments and observations. We are at a time‐critical point where we can implement new capacity to resolve how coral bleaching patterns emerge from complex biological–environmental networks, and so more effectively inform rapidly evolving ecological management and social adaptation framew...
Suggett, DJ, Edmondson, J, Howlett, L & Camp, EF 2020, 'Coralclip®: a low‐cost solution for rapid and targeted out‐planting of coral at scale', Restoration Ecology, vol. 28, no. 2, pp. 289-296.
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Re‐attaching or out‐planting coral as fragments, colonies, and on larval settlement devices to substrates is a major bottleneck limiting scalabilty and viability of reef restoration practices. Many attachment approaches are in use, but none that are low‐cost, opportunistic, rapid but effective, for integration into existing tour operations on the Great Barrier Reef (GBR) where staff and boat time is a major cost and chemical fixatives cannot be easily used. We describe a novel attachment device—Coralclip®—developed to meet this need and so aid maintenance and restoration of GBR tourism sites. Coralclip® is a stainless steel springclip attached by a nail integrated through the spring coil, and can be deployed with a coral fragment in as fast as 15 seconds. Initial laboratory tests demonstrated that Coralclip® secured coral fragments or larval settlement tiles under dynamic flow regimes characteristic of exposed reefs. Coral out‐planting from fragments of opportunity and from nurseries (n = 4,580; 0.3–1.9 coral/minute; US$0.6–3.0/coral deployed) or larval settlement tiles (n = 400; 2.5 tiles/minute; US$0.5 tile deployed−1) when deployed by divers from routine boat operations at Opal Reef confirmed highly effective attachment, with ≤15% failure of clips found after 3–7 months. We discuss how Coralclip® is a cost‐effective means to support reef maintenance and restoration practices.
Sukačová, K, Búzová, D & Červený, J 2020, 'Biphasic optimization approach for maximization of lipid production by the microalga Chlorella pyrenoidosa', Folia Microbiologica, vol. 65, no. 5, pp. 901-908.
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Sutherland, DL & Ralph, PJ 2020, '15 years of research on wastewater treatment high rate algal ponds in New Zealand: discoveries and future directions', New Zealand Journal of Botany, vol. 58, no. 4, pp. 334-357.
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© 2020, © 2020 The Royal Society of New Zealand. Over the last 15 years, New Zealand led research on wastewater treatment high rate algal ponds (HRAP) has focused on ways to optimise pond performance, particularly with respect to nutrient removal and resource recovery (microalgal biomass production). The primary motivation for most of this research has been the need to cost-effectively improve wastewater treatment, particularly in small towns and rural communities, where wastewater treatment would otherwise be unaffordable. The ability to recover resources (water and nutrients) helps enable a circular bio-economy, through the reuse of these recovered resources in future products. New Zealand HRAP research has focused on 10 broad categories, including improving pond performance (nutrient removal and biomass yield), environmental impacts of HRAPs, pond design and operation, microalgal and zooplankton community composition and control, algal-based products, enhancing phosphorus removal, biomass harvesting and emerging contaminants. Research has been carried out at a range of scales, including mesocosm, pilot-scale and full-scale. Simple modification to how HRAPs are operated, such as culture depth, operating ponds in series, biomass recycling and night-time CO2 addition, have been shown to improve pond performance, particularly nutrient removal, biomass productivity, species dominance maintenance or zooplankton graze control. However, despite our improved understandings over the last 15 years, there are still a number of priorities for increasing HRAP performance, including effective CO2 addition at full-scale, improving phosphorus removal and reducing potential environmental impacts of HRAPs. Uptake of HRAP technology by local government bodies and industries is low and the reasons for this are not fully clear. Cost-effective and sustainable harvesting of the microalgal/bacterial biomass, to ensure effluent discharge meets total nutrient and total suspended solids ...
Sutherland, DL, Burke, J & Ralph, PJ 2020, 'Flow-way water depth affects algal productivity and nutrient uptake in a filamentous algae nutrient scrubber', Journal of Applied Phycology, vol. 32, no. 6, pp. 4321-4332.
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© 2020, Springer Nature B.V. Filamentous algae treatment systems can provide cost-effective treatment of a range of wastewater types. In the current study, filamentous algae nutrient scrubbers (FANS), treating anaerobically digested food-waste centrate, were used to investigate the role of flow-way water depth (5, 10 and 15 mm) on productivity and nutrient removal. The study found that the proportion of light reaching the surface of the filamentous algae mat (Emat) increased with decreasing water depth, with 5-mm depth significantly higher than 10 mm (p < 0.05) and 15 mm (p < 0.01). On all sampling occasions, both the total solids and ash-free dry mass biomass productivities, as well as the chlorophyll a biomass, were all significantly higher (p < 0.01) on the FANS operated at 5 mm depth compared with 15 mm. Both the percentage carbon (C) and percentage phosphorus (P) were significantly higher in the biomass from 15 mm compared with 5 and 10 mm deep. Percentage nitrogen (N) content did not differ significantly between treatments but biological nitrogen removal rates (particulate N removed m−2 day−1) were significantly higher on the 5-mm-deep FANS compared with the 10 mm deep (p < 0.05) and the 15 mm deep (p < 0.01). The C:N ratio of algal biomass varied but not with depth whereas the C:P ratio significantly decreased (p < 0.01) with increasing water depth. These results indicate the important roles that light and water depth play on the performance of FANS.
Sutherland, DL, Burke, J & Ralph, PJ 2020, 'Increased harvest frequency improves biomass yields and nutrient removal on a filamentous algae nutrient scrubber', Algal Research, vol. 51, pp. 102073-102073.
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Sutherland, DL, Burke, J, Leal, E & Ralph, PJ 2020, 'Effects of nutrient load on microalgal productivity and community composition grown in anaerobically digested food-waste centrate', Algal Research, vol. 51, pp. 102037-102037.
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© 2020 Elsevier B.V. Anaerobic digestion of food waste has many environmental benefits over traditional landfilling and is a promising technology to convert food waste to energy. However, the centrate, a liquid by-product of anaerobic digestion, is high in total ammonia, with concentrations ~20,000 g m−3, which requires treatment being discharged to the environment. Microalgae offer a promising and cost-effective treatment solution for this centrate but some dilution is required to prevent free-ammonia inhibition. In this study, we investigate the performance of microalgae, grown outdoors in high rate algal mesocosms, under three different total ammonia loads i) 20 g m−3 (20N), ii) 60 g m−3 (60 N) and iii) 100 g m−3 (100N). Both total suspended solids (TSS) and volatile suspended solids (VSS) increased with increasing nutrient load, with 100 N significantly higher (p < .01) than 60 N and 20 N biomass. The percentage nitrogen uptake was significantly higher in 20 N compared to 60 N (p < .05) and 100 N (p < .01). In contrast, the percentage biological uptake of phosphorus (P) did not differ significantly between treatments. Total microalgal biovolume increased with increasing nutrient load with nine species of chlorophytes (green algae) observed across all treatments throughout the experiment. Bray–Curtis percentage similarities between the microalgal community relative abundance, showed that the community in the 100 N treatment was at least 50% dissimilar to 20 N and 60 N, which were at least 75% similar to each other throughout the course of the experiment. These results indicate the capability of microalgae to bioremediate centrate from anaerobically digested food waste with high ammonia loading. Coupled centrate treatment and resource recovery could help support the circular bioeconomy.
Sutherland, DL, Howard-Williams, C, Ralph, P & Hawes, I 2020, 'Environmental drivers that influence microalgal species in meltwater pools on the McMurdo Ice Shelf, Antarctica', Polar Biology, vol. 43, no. 5, pp. 467-482.
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© 2020, Springer-Verlag GmbH Germany, part of Springer Nature. Rich in both microbial mat biomass and species diversity, the meltwater ponds of the McMurdo Ice Shelf (MIS) form important biodiversity and productivity elements in an otherwise barren landscape. These ponds are thought to be sensitive indicators of climate change-driven fluxes in pond water balance but our ability to predict such effects is confounded by our poor understanding of the inherent variability of these communities in response to the physico-chemical environment. Understanding how microbial communities are shaped across broad physico-chemical gradients may allow better predictions of the effects of climate change on the MIS wetlands. Our study found that distinct clustering of community types against environmental variables was apparent for both the diatom and cyanobacterial communities. For diatoms, conductivity was correlated with the separation of five significantly distinct communities. Significant differences in NH4–N concentrations were correlated to the three distinct cyanobacterial communities but many of the cyanobacteria morphotypes were recorded across a wide ecological range. More distinct community types suggested that diatoms were more sensitive to environmental change in these ponds than the cyanobacteria, despite the latter’s overall dominance. Distinct community clusters for diatoms, and to a lesser extent cyanobacteria, suggest that changes at a functional group level may be more important than at the level of individual species. Further understanding of diatom functional groups would provide us with the opportunity to hindcast past climates and water budgets within the Antarctic region. However, the disconnect between biomass and community composition currently prevents hindcasting past productivities in relation to environmental changes.
Sutherland, DL, Park, J, Heubeck, S, Ralph, PJ & Craggs, RJ 2020, 'Size matters – Microalgae production and nutrient removal in wastewater treatment high rate algal ponds of three different sizes', Algal Research, vol. 45, pp. 101734-101734.
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© 2019 Elsevier B.V. High rate algal ponds for coupled wastewater treatment and resource recovery have been the focus of much international research over the last 15 years. Microalgal biomass productivity reported in full-scale studies (1-ha or greater) have often been substantially lower than that reported from smaller scale ponds in similar climates, regardless of the season or the dominant microalgal species used. The disconnect between smaller-scale and full-scale productivity is unclear and uncertainty remains regarding the applicability of smaller scale studies to full-scale systems. In order to better understand the differences in reported productivity, the performance of three different size wastewater treatment high rate algal ponds (5 m2, 330 m2 and 1-ha) were assessed with respect to nutrient removal and microalgal productivity over three seasons. Both daily areal nutrient removal and biomass production were affected by the size of the pond. NH4-N removal via nitrification/denitrification decreased with increasing pond size, with the highest removal rate in the 5 m2 pond and the lowest in the 1-ha. Microalgal areal productivity was maximal in the 330 m2 pond, suggesting that a combination of mixing frequency and higher photosynthetic potential under low light conditions were the main drivers of enhanced productivity in this pond compared to the 5 m2 (mesocosm) and 1-ha (full-scale) ponds. The lowest daily nutrient removal and biomass production occurred in the 1-ha (full-scale) pond. Our results suggest that, based on the current design and operation of high rate algal ponds, the optimum size for maximum productivity is considerably smaller than the current full-scale systems. This has implications for commercial scale systems, with respect to capital and operational costs.
Sutherland, DL, Park, J, Ralph, PJ & Craggs, RJ 2020, 'Improved microalgal productivity and nutrient removal through operating wastewater high rate algal ponds in series', Algal Research, vol. 47, pp. 101850-101850.
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© 2020 Elsevier B.V. High rate algal ponds are recognised as a cost effective and efficient upgrade to conventional wastewater ponds for the treatment of a wide range of wastewaters. Their design allows microalgae to proliferate, which, in turn, results in high levels of nutrient removal, via algal assimilation. Furthermore, these ponds offer the opportunity to recover resources, in the form of algal biomass, for beneficial re-use, thus creating a circular bio-economy using wastewater. However, both increased microalgal biomass and nutrient removal is required to make coupled full-scale systems commercially viable. The performance of high rate algal ponds operated in series, on short hydraulic retention time of 4 days, versus in parallel, on a longer retention time of 8 days, was assessed with respect to nutrient removal and microalgal production. For microalgal productivity, the combined total volatile suspended solids (organic matter) and chlorophyll-a biomass were significantly higher (p < 0.01) under Series (191 ± 41 kg per day for volatile suspended solids) than Parallel (127 ± 18 kg per day) operation. The combined total dissolved inorganic nitrogen removed per day was significantly higher (p < 0.01) under Series (23 ± 4 kg of nitrogen per day) than Parallel (17 ± 4 kg) operation. The total amount of phosphorus removed per day was unaffected by mode of operation. Higher biomass production under short retention times came at the expense of nitrogen removal but treatment of the harvested effluent through a second pond in series, resulted in overall higher daily nitrogen removal and biomass production than ponds in parallel, for the same volume of wastewater treated. This study has demonstrated that with simple modifications to pond operation higher microalgal yields and improved effluent water quality without increased capital or operational costs.
Syed, MS, Mirakhorli, F, Marquis, C, Taylor, RA & Warkiani, ME 2020, 'Particle movement and fluid behavior visualization using an optically transparent 3D-printed micro-hydrocyclone', Biomicrofluidics, vol. 14, no. 6, pp. 064106-064106.
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A hydrocyclone is a macroscale separation device employed in various industries, with many advantages, including high-throughput and low operational costs. Translating these advantages to microscale has been a challenge due to the microscale fabrication limitations that can be surmounted using 3D printing technology. Additionally, it is difficult to simulate the performance of real 3D-printed micro-hydrocyclones because of turbulent eddies and the deviations from the design due to printing resolution. To address these issues, we propose a new experimental method for the direct observation of particle motion in 3D printed micro-hydrocyclones. To do so, wax 3D printing and soft lithography were used in combination to construct a transparent micro-hydrocyclone in a single block of polydimethylsiloxane. A high-speed camera and fluorescent particles were employed to obtain clear in situ images and to confirm the presence of the vortex core. To showcase the use of this method, we demonstrate that a well-designed device can achieve a 95% separation efficiency for a sample containing a mixture of (desired) stem cells and (undesired) microcarriers. Overall, we hope that the proposed method for the direct visualization of particle trajectories in micro-hydrocyclones will serve as a tool, which can be leveraged to accelerate the development of micro-hydrocyclones for biomedical applications.
Thackeray, SJ, Robinson, SA, Smith, P, Bruno, R, Kirschbaum, MUF, Bernacchi, C, Byrne, M, Cheung, W, Cotrufo, MF, Gienapp, P, Hartley, S, Janssens, I, Hefin Jones, T, Kobayashi, K, Luo, Y, Penuelas, J, Sage, R, Suggett, DJ, Way, D & Long, S 2020, 'Civil disobedience movements such as School Strike for the Climate are raising public awareness of the climate change emergency', Global Change Biology, vol. 26, no. 3, pp. 1042-1044.
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The IPCC (Intergovernmental Panel on Climate Change) “Special Report on Global Warming of 1.5°C” presented the ambitious target of needing to achieve zero net emissions by 2050 in order to meet the goals of the Paris Agreement (IPCC, 2018). This report led some governments and jurisdictions to declare a climate emergency (Climate Emergency Declaration, 2019) and prompted the rise of movements of activism and civil disobedience such as the School Strike for the Climate and Extinction Rebellion. The reach of these civil actions extends beyond those directly involved, potentially increasing wider public awareness of climate change. Here, we examine trends in indicators of this wider public awareness and engagement and compare these with major global movements of civil disobedience focussed on climate, the release of substantive climate reports, and global governmental gatherings on climate change. We show that these global movements may be increasing public awareness of, and stimulating public engagement with, issues of climate change.
It is not easy to accurately measure public awareness and engagement with the issue of climate change at a global scale. We use two sources of information as indicators of that engagement. First, we used data on the scaled relative frequency of pertinent terms in Google searches ("global warming," "climate change," "climate action," "climate emergency," "climate crisis," downloaded from Google Trends on October 31, 2019, https://www.google.com/trends). Second, we used data on mentions of the terms "climate change" and "global warming" by the global media, assembled by the Media and Climate Change Observatory, MeCCO (Boykoff et al., 2019, downloaded on December 4, 2019). These sources provide monthly data on the attention paid to climate change by anyone searching the internet (from the Google data), and by the newspapers, radio, and television (from the MeCCO data).
Thomas, F, Dittami, SM, Brunet, M, Le Duff, N, Tanguy, G, Leblanc, C & Gobet, A 2020, 'Evaluation of a new primer combination to minimize plastid contamination in 16S rDNA metabarcoding analyses of alga‐associated bacterial communities', Environmental Microbiology Reports, vol. 12, no. 1, pp. 30-37.
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SummaryPlant‐ and alga‐associated bacterial communities are generally described via 16S rDNA metabarcoding using universal primers. As plastid genomes encode 16S rDNA related to cyanobacteria, these data sets frequently contain >90% plastidial sequences, and the bacterial diversity may be under‐sampled. To overcome this limitation we evaluated in silico the taxonomic coverage for four primer combinations targeting the 16S rDNA V3‐V4 region. They included a forward primer universal to Bacteria (S‐D‐Bact‐0341‐b‐S‐17) and four reverse primers designed to avoid plastid DNA amplification. The best primer combination (NOCHL) was compared to the universal primer set in the wet lab using a synthetic community and samples from three macroalgal species. The proportion of plastid sequences was reduced by 99%–100% with the NOCHL primers compared to the universal primers, irrespective of algal hosts, sample collection and extraction protocols. Additionally, the NOCHL primers yielded a higher richness while maintaining the community structure. As Planctomycetes, Verrucomicrobia and Cyanobacteria were underrepresented (70%–90%) compared to universal primers, combining the NOCHL set with taxon‐specific primers may be useful for a complete description of the alga‐associated bacterial diversity. The NOCHL primers represent an innovation to study algal holobionts without amplifying host plastid sequences and may further be applied to other photosynthetic hosts.
Tran, N-AT, Tamburic, B, Evenhuis, CR & Seymour, JR 2020, 'Bacteria-mediated aggregation of the marine phytoplankton Thalassiosira weissflogii and Nannochloropsis oceanica', Journal of Applied Phycology, vol. 32, no. 6, pp. 3735-3748.
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AbstractThe ecological relationships between heterotrophic bacteria and marine phytoplankton are complex and multifaceted, and in some instances include the bacteria-mediated aggregation of phytoplankton cells. It is not known to what extent bacteria stimulate aggregation of marine phytoplankton, the variability in aggregation capacity across different bacterial taxa or the potential role of algogenic exopolymers in this process. Here we screened twenty bacterial isolates, spanning nine orders, for their capacity to stimulate aggregation of two marine phytoplankters, Thalassiosira weissflogii and Nannochloropsis oceanica. In addition to phytoplankton aggregation efficiency, the production of exopolymers was measured using Alcian Blue. Bacterial isolates from the Rhodobacterales, Flavobacteriales and Sphingomonadales orders stimulated the highest levels of cell aggregation in phytoplankton cultures. When co-cultured with bacteria, exopolymer concentration accounted for 34.1% of the aggregation observed in T. weissflogii and 27.7% of the aggregation observed in N. oceanica. Bacteria-mediated aggregation of phytoplankton has potentially important implications for mediating vertical carbon flux in the ocean and in extracting phytoplankton cells from suspension for biotechnological applications.
Trevathan-Tackett, SM, Jeffries, TC, Macreadie, PI, Manojlovic, B & Ralph, P 2020, 'Long-term decomposition captures key steps in microbial breakdown of seagrass litter', Science of The Total Environment, vol. 705, pp. 135806-135806.
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Seagrass biomass represents an important source of organic carbon that can contribute to long-term sediment carbon stocks in coastal ecosystems. There is little empirical data on the long-term microbial decomposition of seagrass detritus, despite this process being one of the key drivers of carbon-cycling in coastal ecosystems, that is, it influences the amount and quality of carbon available for sequestration. Here, our goal was to investigate how litter quality (leaf vs. rhizome/root) and the microbial communities involved in organic matter remineralisation shift over a 2-year field decomposition study north of Sydney, Australia using the temperate seagrass Zostera muelleri. The sites varied in bulk sediment characteristics and the sediment-associated microbial communities, but these variables overall had little influence on long-term seagrass decomposition rates or seagrass-associated microbiomes. The results showed a clear succession of bacterial and archaeal communities for both tissues types from r-strategists such as α- and γ-proteobacteria to K-strategies, including δ-proteobacteria, Bacteroidia and Spirochaetes. We used a new mathematical model to capture how decay rates varied over time and found that two decomposition events occurred for some seagrass leaf samples, possibly due to exudate input from living seagrass roots growing into the litter bag. The new model also indicated that conventional single exponential models overestimate long-term decay rates, and we detected for the first time the refractory, or stable, phase of decomposition for rhizome/root biomass. The stable phase began at approximately 20% mass remaining and after 600 days, and the persistence of rhizome/root biomass was attributed to the anoxic conditions and the preservation of refractory organic matter. While we predict that rhizome/root biomass will contribute more to the long-term sediment carbon stocks, the preservation of leaf carbon may be enhanced at locations were...
Troják, M, Šafránek, D, Brim, L, Šalagovič, J & Červený, J 2020, 'Executable Biochemical Space for Specification and Analysis of Biochemical Systems', Electronic Notes in Theoretical Computer Science, vol. 350, pp. 91-116.
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Trujillo Uruena, M, York, R, Philp, M, Kuzhiumparambil, U, Wei, Z, Yun, K & Fu, S 2020, 'Identification of Unique 4-Methylmethcathinone (4-MMC) Degradation Markers in Putrefied Matrices†', Journal of Analytical Toxicology, vol. 44, no. 8, pp. 803-810.
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Abstract Drug degradation as a consequence of putrefactive bacterial activity is a well-known factor that affects the identification and quantitation of certain substances of forensic interest. Current knowledge on putrefaction-mediated degradation of drugs is, however, significantly lacking. This study aimed to investigate the degradation of 4-methylmethcathinone (4-MMC or mephedrone) and to detect its degradation products in putrefied biological matrices containing 4-MMC. The bacteria species Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae and Proteus vulgaris were grown in brain-heart infusion broth, spiked with 4-MMC and incubated at 37°C for 24 h. Postmortem human blood and fresh porcine liver macerate were also left to putrefy in sample tubes at room temperature for 1 week. Structural elucidation was based on modern spectroscopic analyses including the use of high-resolution mass spectrometry and nuclear magnetic resonance spectroscopy. All four putrefactive bacteria were capable of degrading 4-MMC extensively under the experimental conditions explored. Of particular interest was the discovery of a novel degradation product common to all four bacterial species, which was assigned as 2-hydroxy-1-(4-methylphenyl)propan-1-one (HMP) based on the spectroscopic data. This degradation product was detectable in both postmortem human blood and porcine liver samples. The stability of the identified degradation products, especially HMP, should be further investigated to assess their validity of serving as marker analytes for monitoring 4-MMC in postmortem toxicology.
Verma, A, Hughes, DJ, Harwood, DT, Suggett, DJ, Ralph, PJ & Murray, SA 2020, 'Functional significance of phylogeographic structure in a toxic benthic marine microbial eukaryote over a latitudinal gradient along the East Australian Current', Ecology and Evolution, vol. 10, no. 13, pp. 6257-6273.
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AbstractGenetic diversity in marine microbial eukaryotic populations (protists) drives their ecological success by enabling diverse phenotypes to respond rapidly to changing environmental conditions. Despite enormous population sizes and lack of barriers to gene flow, genetic differentiation that is associated with geographic distance, currents, and environmental gradients has been reported from planktonic protists. However, for benthic protists, which have reduced dispersal opportunities, phylogeography and its phenotypic significance are little known. In recent years, the East Australian Current (EAC) has intensified its southward flow, associated with the tropicalization of temperate waters. Benthic harmful algal species have been increasingly found in south‐eastern Australia. Yet little is known about the potential of these species to adapt or extend their range in relation to changing conditions. Here, we examine genetic diversity and functional niche divergence in a toxic benthic dinoflagellate, Ostreopsis cf. siamensis, along a 1,500 km north–south gradient in southeastern Australia. Sixty‐eight strains were established from eight sampling sites. The study revealed long‐standing genetic diversity among strains established from the northern‐most sites, along with large phenotypic variation in observed physiological traits such as growth rates, cell volume, production of palytoxin‐like compounds, and photophysiological parameters. Strains from the southern populations were more uniform in both genetic and functional traits, and have possibly colonized their habitats more recently. Our study reports significant genetic and functional trait variability in a benthic harmful algal species, indicative of high adaptability, and a possible climate‐driven range extension. The observed high trait variation may facilitate development of harmful algal blooms under dynamic c...
Vo, HNP, Le, G-K, Nguyen, TMH, Nguyen, T-T, Nguyen, T-B, Tra, V-T & Bui, X-T 2020, 'Influence of N/COD ratios and nitrogen forms on aerobic granulation in sequencing batch airlift reactor', Desalination and Water Treatment, vol. 174, pp. 90-97.
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Vo, HNP, Ngo, HH, Guo, W, Chang, SW, Nguyen, DD, Chen, Z, Wang, XC, Chen, R & Zhang, X 2020, 'Microalgae for saline wastewater treatment: a critical review', Critical Reviews in Environmental Science and Technology, vol. 50, no. 12, pp. 1224-1265.
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© 2019, © 2019 Taylor & Francis Group, LLC. Saline wastewater contains numerous pollutants such as nutrients, heavy metals, micropollutants, and organic pollutants. This kind of wastewater needs to be treated prior to discharging. Compared to other technologies for saline wastewater treatment, the microalgae process is considered to be ‘green’ or environmentally friendly as it generates no secondary pollutants and creates profit. To elucidate the issue, this review investigated the following: (1) the nature of saline wastewater; (2) adaptation of microalgae in saline wastewater; (3) pollutants’ remediation by microalgae in saline wastewater; (4) comparisons with other technologies; and (5) future perspectives. Most importantly, during microalgae process, the saline wastewater is transformed from a waste into a source for biofuel and pigment production. This trend implies to heal the environment, cut remediation expenses and raise revenue.
Vo, HNP, Ngo, HH, Guo, W, Liu, Y, Woong Chang, S, Nguyen, DD, Zhang, X, Liang, H & Xue, S 2020, 'Selective carbon sources and salinities enhance enzymes and extracellular polymeric substances extrusion of Chlorella sp. for potential co-metabolism', Bioresource Technology, vol. 303, pp. 122877-122877.
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This study investigated the extracellular polymeric substance (EPS) and enzyme extrusion of Chlorella sp. using seven carbon sources and two salinities for potential pollutant co-metabolism. Results indicated that the levels of biomass, EPS and enzymes of microalgae cultured with glucose and saccharose outcompeted other carbon sources. For pigment production, glycine received the highest chlorophyll and carotene, up to 10 mg/L. The EPS reached 30 mg/L, having doubled the amount of protein than carbohydrate. For superoxide dismutase and peroxidase enzymes, the highest concentrations were beyond 60 U/ml and 6 nmol/d.ml, respectively. This amount could be potentially used for degrading 40% ciprofloxacin of concentration 2000 µg/L. When increasing salinity from 0.1% to 3.5%, the concentrations of pigment, EPS and enzymes rose 3 to 30 times. These results highlighted that certain carbon sources and salinities could induce Chlorella sp. to produce EPS and enzymes for pollutant co-metabolism and also for revenue-raising potential.
Vo, HNP, Ngo, HH, Guo, W, Nguyen, KH, Chang, SW, Nguyen, DD, Liu, Y, Liu, Y, Ding, A & Bui, XT 2020, 'Micropollutants cometabolism of microalgae for wastewater remediation: Effect of carbon sources to cometabolism and degradation products', Water Research, vol. 183, pp. 115974-115974.
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This study investigated the impacts of selective sole carbon source-induced micropollutants (MPs) cometabolism of Chlorella sp. by: (i) extracellular polymeric substances (EPS), superoxide dismutase and peroxidase enzyme production; (ii) MPs removal efficiency and cometabolism rate; (iii) MPs' potential degradation products identification; and (iv) degradation pathways and validation using the Eawag database to differentiate the cometabolism of Chlorella sp. with other microbes. Adding the sole carbon sources in the presence of MPs increased EPS and enzyme concentrations from 2 to 100-fold in comparison with only sole carbon sources. This confirmed that MPs cometabolism had occurred. The removal efficiencies of tetracycline, sulfamethoxazole, and bisphenol A ranged from 16-99%, 32-92%, and 58-99%, respectively. By increasing EPS and enzyme activity, the MPs concentrations accumulated in microalgae cells also fell 400-fold. The cometabolism process resulted in several degradation products of MPs. This study drew an insightful understanding of cometabolism for MPs remediation in wastewater. Based on the results, proper carbon sources for microalgae can be selected for practical applications to remediate MPs in wastewater while simultaneously recovering biomass for several industries and gaining revenue.
Wilkinson, S, Biloria, N & Ralph, P 2020, 'The technical issues associated with algae building technology', International Journal of Building Pathology and Adaptation, vol. 38, no. 5, pp. 673-688.
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PurposeAs the impacts of climate change become more evident, the need to adopt new ways of constructing buildings becomes more urgent. The Earth has experienced hotter climates globally for the last 70 years (NASA, 2019), and this has resulted in unprecedented levels of bushfire in Australia, flooding in the UK and drought in Africa in early 2020 (World Resources Institute, 2019). The predictions are for increased temperatures globally and increasing carbon emissions from fossil fuel consumption. There is a critical need to reduce the reliance on fossil fuels as a building energy source (WCED, 1987). Existing renewables focus on solar, wind and wave power, where technological improvements have increased efficiencies (Hinnells, 2008). Uptake of the technologies is variable depending on location and willingness to adopt renewables. As well as further uptake of existing renewable energy sources, we need to look wider and across traditional discipline groups, at new technologies such as biotechnologies. One potential energy source is biofuels. Biofuels are produced from biomass, which is algae. In 2016, the BIQ, a four-storey apartment building, was constructed in Hamburg, Germany. The BIQ features glazed façade panels filled with algae to produce biomass and solar thermal energy. Could algae building technology (ABT), in the form of façade panels, offer a new renewable energy source?Design/methodology/approachWhat are the technical issues associated with Algae building technology? This qualitative research sought to identify what technical issues likely to arise in terms of algae building construction, operation and maintenance. Semi-structured interviews with 24 experienced built environment professionals in Australia were undertaken in 2016 to assess the most likely issues that cou...
