1
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Ruggiero MV, Buffoli M, Wolf KKE, D'Alelio D, Di Tuccio V, Lombardi E, Manfellotto F, Vitale L, Margiotta F, Sarno D, John U, Ferrante MI, Montresor M. Multiannual patterns of genetic structure and mating type ratios highlight the complex bloom dynamics of a marine planktonic diatom. Sci Rep 2024; 14:6028. [PMID: 38472358 DOI: 10.1038/s41598-024-56292-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/05/2024] [Indexed: 03/14/2024] Open
Abstract
Understanding the genetic structure of populations and the processes responsible for its spatial and temporal dynamics is vital for assessing species' adaptability and survival in changing environments. We investigate the genetic fingerprinting of blooming populations of the marine diatom Pseudo-nitzschia multistriata in the Gulf of Naples (Mediterranean Sea) from 2008 to 2020. Strains were genotyped using microsatellite fingerprinting and natural samples were also analysed with Microsatellite Pool-seq Barcoding based on Illumina sequencing of microsatellite loci. Both approaches revealed a clonal expansion event in 2013 and a more stable genetic structure during 2017-2020 compared to previous years. The identification of a mating type (MT) determination gene allowed to assign MT to strains isolated over the years. MTs were generally at equilibrium with two notable exceptions, including the clonal bloom of 2013. The populations exhibited linkage equilibrium in most blooms, indicating that sexual reproduction leads to genetic homogenization. Our findings show that P. multistriata blooms exhibit a dynamic genetic and demographic composition over time, most probably determined by deeper-layer cell inocula. Occasional clonal expansions and MT imbalances can potentially affect the persistence and ecological success of planktonic diatoms.
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Affiliation(s)
| | - Marina Buffoli
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Klara K E Wolf
- Institut für Marine Ökosystem- und Fischereiwissenschaften, Universität Hamburg, Hamburg, Germany
- Limnological Institute, Environmental Genomics, University of Konstanz, Konstanz, Germany
| | - Domenico D'Alelio
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Viviana Di Tuccio
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Ernestina Lombardi
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Francesco Manfellotto
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Laura Vitale
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Francesca Margiotta
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Diana Sarno
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Uwe John
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Maria Immacolata Ferrante
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- Oceanography Section, National Institute of Oceanography and Applied Geophysics, Trieste, Italy
| | - Marina Montresor
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy.
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2
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Filatov DA, Kirkpatrick M. How does evolution work in superabundant microbes? Trends Microbiol 2024:S0966-842X(24)00024-6. [PMID: 38360431 DOI: 10.1016/j.tim.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/17/2024]
Abstract
Marine phytoplankton play crucial roles in the Earth's ecological, chemical, and geological processes. They are responsible for about half of global primary production and drive the ocean biological carbon pump. Understanding how plankton species may adapt to the Earth's rapidly changing environments is evidently an urgent priority. This problem requires evolutionary genetic approaches as evolution occurs at the level of allele frequency change within populations driven by genetic drift and natural selection (microevolution). Plankters such as the coccolithophore Gephyrocapsa huxleyi and the cyanobacterium Prochlorococcus 'marinus' are among Earth's most abundant organisms. In this opinion paper we discuss how evolution in astronomically large populations of superabundant microbes (SAMs) may act fundamentally differently than it does in the populations of more modest size found in well-studied organisms. This offers exciting opportunities to study evolution in the conditions that have yet to be explored and also leads to unique challenges. Exploring these opportunities and challenges is the goal of this article.
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Affiliation(s)
- Dmitry A Filatov
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
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3
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Chaumier T, Yang F, Manirakiza E, Ait-Mohamed O, Wu Y, Chandola U, Jesus B, Piganeau G, Groisillier A, Tirichine L. Genome-wide assessment of genetic diversity and transcript variations in 17 accessions of the model diatom Phaeodactylum tricornutum. ISME COMMUNICATIONS 2024; 4:ycad008. [PMID: 38304080 PMCID: PMC10833087 DOI: 10.1093/ismeco/ycad008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/01/2023] [Accepted: 12/13/2023] [Indexed: 02/03/2024]
Abstract
Diatoms, a prominent group of phytoplankton, have a significant impact on both the oceanic food chain and carbon sequestration, thereby playing a crucial role in regulating the climate. These highly diverse organisms show a wide geographic distribution across various latitudes. In addition to their ecological significance, diatoms represent a vital source of bioactive compounds that are widely used in biotechnology applications. In the present study, we investigated the genetic and transcriptomic diversity of 17 accessions of the model diatom Phaeodactylum tricornutum including those sampled a century ago as well as more recently collected accessions. The analysis of the data reveals a higher genetic diversity and the emergence of novel clades, indicating an increasing diversity within the P. tricornutum population structure, compared to the previous study and a persistent long-term balancing selection of genes in old and newly sampled accessions. However, the study did not establish a clear link between the year of sampling and genetic diversity, thereby, rejecting the hypothesis of loss of heterozygoty in cultured strains. Transcript analysis identified novel transcript including noncoding RNA and other categories of small RNA such as PiwiRNAs. Additionally, transcripts analysis using differential expression as well as Weighted Gene Correlation Network Analysis has provided evidence that the suppression or downregulation of genes cannot be solely attributed to loss-of-function mutations. This implies that other contributing factors, such as epigenetic modifications, may play a crucial role in regulating gene expression. Our study provides novel genetic resources, which are now accessible through the platform PhaeoEpiview (https://PhaeoEpiView.univ-nantes.fr), that offer both ease of use and advanced tools to further investigate microalgae biology and ecology, consequently enriching our current understanding of these organisms.
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Affiliation(s)
| | - Feng Yang
- Nantes Université, CNRS, US2B, UMR 6286, Nantes F-44000, France
| | - Eric Manirakiza
- Nantes Université, CNRS, US2B, UMR 6286, Nantes F-44000, France
| | - Ouardia Ait-Mohamed
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, Paris 75005, France
| | - Yue Wu
- Nantes Université, CNRS, US2B, UMR 6286, Nantes F-44000, France
| | - Udita Chandola
- Nantes Université, CNRS, US2B, UMR 6286, Nantes F-44000, France
| | - Bruno Jesus
- Institut des Substances et Organismes de la Mer, ISOMer, Nantes Université, UR 2160, Nantes F-44000, France
| | - Gwenael Piganeau
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, F-66650 Banyuls-sur-Mer, France
| | | | - Leila Tirichine
- Nantes Université, CNRS, US2B, UMR 6286, Nantes F-44000, France
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4
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Al Zouabi L, Stefanutti M, Roumeliotis S, Le Meur G, Boumard B, Riddiford N, Rubanova N, Bohec M, Gervais L, Servant N, Bardin AJ. Molecular underpinnings and environmental drivers of loss of heterozygosity in Drosophila intestinal stem cells. Cell Rep 2023; 42:113485. [PMID: 38032794 DOI: 10.1016/j.celrep.2023.113485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/29/2023] [Accepted: 11/08/2023] [Indexed: 12/02/2023] Open
Abstract
During development and aging, genome mutation leading to loss of heterozygosity (LOH) can uncover recessive phenotypes within tissue compartments. This phenomenon occurs in normal human tissues and is prevalent in pathological genetic conditions and cancers. While studies in yeast have defined DNA repair mechanisms that can promote LOH, the predominant pathways and environmental triggers in somatic tissues of multicellular organisms are not well understood. Here, we investigate mechanisms underlying LOH in intestinal stem cells in Drosophila. Infection with the pathogenic bacteria, Erwinia carotovora carotovora 15, but not Pseudomonas entomophila, increases LOH frequency. Using whole genome sequencing of somatic LOH events, we demonstrate that they arise primarily via mitotic recombination. Molecular features and genetic evidence argue against a break-induced replication mechanism and instead support cross-over via double Holliday junction-based repair. This study provides a mechanistic understanding of mitotic recombination, an important mediator of LOH, and its effects on stem cells in vivo.
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Affiliation(s)
- Lara Al Zouabi
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France
| | - Marine Stefanutti
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France
| | - Spyridon Roumeliotis
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France
| | - Gwenn Le Meur
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France
| | - Benjamin Boumard
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France
| | - Nick Riddiford
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France
| | - Natalia Rubanova
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France; Bioinformatics, Biostatistics, Epidemiology and Computational Systems Unit, Institut Curie, PSL Research University, INSERM U900, 75005 Paris, France
| | - Mylène Bohec
- ICGex Next-Generation Sequencing Platform, Institut Curie, PSL Research University, 75005 Paris, France
| | - Louis Gervais
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France
| | - Nicolas Servant
- Bioinformatics, Biostatistics, Epidemiology and Computational Systems Unit, Institut Curie, PSL Research University, INSERM U900, 75005 Paris, France
| | - Allison J Bardin
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France.
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5
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Macdonald Miller S, Abbriano RM, Herdean A, Banati R, Ralph PJ, Pernice M. Random mutagenesis of Phaeodactylum tricornutum using ultraviolet, chemical, and X-radiation demonstrates the need for temporal analysis of phenotype stability. Sci Rep 2023; 13:22385. [PMID: 38104215 PMCID: PMC10725415 DOI: 10.1038/s41598-023-45899-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 10/25/2023] [Indexed: 12/19/2023] Open
Abstract
We investigated two non-ionising mutagens in the form of ultraviolet radiation (UV) and ethyl methanosulfonate (EMS) and an ionising mutagen (X-ray) as methods to increase fucoxanthin content in the model diatom Phaeodactylum tricornutum. We implemented an ultra-high throughput method using fluorescence-activated cell sorting (FACS) and live culture spectral deconvolution for isolation and screening of potential pigment mutants, and assessed phenotype stability by measuring pigment content over 6 months using high-performance liquid chromatography (HPLC) to investigate the viability of long-term mutants. Both UV and EMS resulted in significantly higher fucoxanthin within the 6 month period after treatment, likely as a result of phenotype instability. A maximum fucoxanthin content of 135 ± 10% wild-type found in the EMS strain, a 35% increase. We found mutants generated using all methods underwent reversion to the wild-type phenotype within a 6 month time period. X-ray treatments produced a consistently unstable phenotype even at the maximum treatment of 1000 Grays, while a UV mutant and an EMS mutant reverted to wild-type after 4 months and 6 months, respectively, despite showing previously higher fucoxanthin than wild-type. This work provides new insights into key areas of microalgal biotechnology, by (i) demonstrating the use of an ionising mutagen (X-ray) on a biotechnologically relevant microalga, and by (ii) introducing temporal analysis of mutants which has substantial implications for strain creation and utility for industrial applications.
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Affiliation(s)
- Sean Macdonald Miller
- Faculty of Science, Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, 2007, Australia.
| | - Raffaela M Abbriano
- Faculty of Science, Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Andrei Herdean
- Faculty of Science, Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Richard Banati
- Australian Nuclear Science and Technology Organisation (ANSTO), Kirrawee DC, NSW, 2232, Australia
- Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Peter J Ralph
- Faculty of Science, Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Mathieu Pernice
- Faculty of Science, Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, 2007, Australia
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6
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Russo MT, Rogato A, Jaubert M, Karas BJ, Falciatore A. Phaeodactylum tricornutum: An established model species for diatom molecular research and an emerging chassis for algal synthetic biology. JOURNAL OF PHYCOLOGY 2023; 59:1114-1122. [PMID: 37975560 DOI: 10.1111/jpy.13400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/05/2023] [Indexed: 11/19/2023]
Abstract
Diatoms are prominent and highly diverse microalgae in aquatic environments. Compared with other diatom species, Phaeodactylum tricornutum is an "atypical diatom" displaying three different morphotypes and lacking the usual silica shell. Despite being of limited ecological relevance, its ease of growth in the laboratory and well-known physiology, alongside the steady increase in genome-enabled information coupled with effective tools for manipulating gene expression, have meant it has gained increased recognition as a powerful experimental model for molecular research on diatoms. We here present a brief overview of how over the last 25 years P. tricornutum has contributed to the unveiling of fundamental aspects of diatom biology, while also emerging as a new tool for algal process engineering and synthetic biology.
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Affiliation(s)
- Monia T Russo
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Alessandra Rogato
- Institute of Biosciences and Bioresources, National Research Council, IBBR-CNR, Naples, Italy
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Marianne Jaubert
- UMR7141 Laboratoire de Biologie du chloroplaste et perception de la lumière chez les micro-algues, Institut de Biologie Physico-Chimique, Paris, France
| | - Bogumil J Karas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario, Canada
| | - Angela Falciatore
- UMR7141 Laboratoire de Biologie du chloroplaste et perception de la lumière chez les micro-algues, Institut de Biologie Physico-Chimique, Paris, France
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7
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Jiang Y, Cao T, Yang Y, Zhang H, Zhang J, Li X. A chlorophyll c synthase widely co-opted by phytoplankton. Science 2023; 382:92-98. [PMID: 37797009 DOI: 10.1126/science.adg7921] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 08/30/2023] [Indexed: 10/07/2023]
Abstract
Marine and terrestrial photosynthesis exhibit a schism in the accessory chlorophyll (Chl) that complements the function of Chl a: Chl b for green plants versus Chl c for most eukaryotic phytoplankton. The enzymes that mediate Chl c biosynthesis have long remained elusive. In this work, we identified the CHLC dioxygenase (Phatr3_J43737) from the marine diatom Phaeodactylum tricornutum as the Chl c synthase. The chlc mutants lacked Chl c, instead accumulating its precursors, and exhibited growth defects. In vitro, recombinant CHLC protein converted these precursors into Chl c, thereby confirming its identity. Phylogenetic evidence demonstrates conserved use of CHLC across phyla but also the existence of distinct Chl c synthases in different algal groups. Our study addresses a long-outstanding question with implications for both contemporary and ancient marine photosynthesis.
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Affiliation(s)
- Yanyou Jiang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Tianjun Cao
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yuqing Yang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Huan Zhang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Jingyu Zhang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Xiaobo Li
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
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8
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Abbriano RM, George J, Kahlke T, Commault AS, Fabris M. Mobilization of a diatom mutator-like element (MULE) transposon inactivates the uridine monophosphate synthase (UMPS) locus in Phaeodactylum tricornutum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:926-936. [PMID: 37147901 DOI: 10.1111/tpj.16271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/18/2023] [Accepted: 04/29/2023] [Indexed: 05/07/2023]
Abstract
Diatoms are photosynthetic unicellular microalgae that drive global ecological phenomena in the biosphere and are emerging as sustainable feedstock for an increasing number of industrial applications. Diatoms exhibit enormous taxonomic and genetic diversity, which often results in peculiar biochemical and biological traits. Transposable elements (TEs) represent a substantial portion of diatom genomes and have been hypothesized to exert a relevant role in enriching genetic diversity and making a core contribution to genome evolution. Here, through long-read whole-genome sequencing, we identified a mutator-like element (MULE) in the model diatom Phaeodactylum tricornutum, and we report the direct observation of its mobilization within the course of a single laboratory experiment. Under selective conditions, this TE inactivated the uridine monophosphate synthase (UMPS) gene of P. tricornutum, one of the few endogenous genetic loci currently targeted for selectable auxotrophy for functional genetics and genome-editing applications. We report the observation of a recently mobilized transposon in diatoms with unique features. These include the combined presence of a MULE transposase with zinc-finger SWIM-type domains and a diatom-specific E3 ubiquitin ligase of the zinc-finger UBR type, which are suggestive of a mobilization mechanism. Our findings provide new elements for the understanding of the role of TEs in diatom genome evolution and in the enrichment of intraspecific genetic variability.
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Affiliation(s)
- Raffaela M Abbriano
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW, 2007, Australia
| | - Jestin George
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW, 2007, Australia
| | - Tim Kahlke
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW, 2007, Australia
| | - Audrey S Commault
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW, 2007, Australia
| | - Michele Fabris
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW, 2007, Australia
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD, 4001, Australia
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9
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Otte A, Winder JC, Deng L, Schmutz J, Jenkins J, Grigoriev IV, Hopes A, Mock T. The diatom Fragilariopsis cylindrus: A model alga to understand cold-adapted life. JOURNAL OF PHYCOLOGY 2023; 59:301-306. [PMID: 36856453 DOI: 10.1111/jpy.13325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 02/24/2023] [Accepted: 02/24/2023] [Indexed: 05/28/2023]
Abstract
Diatoms are significant primary producers especially in cold, turbulent, and nutrient-rich surface oceans. Hence, they are abundant in polar oceans, but also underpin most of the polar food webs and related biogeochemical cycles. The cold-adapted pennate diatom Fragilariopsis cylindrus is considered a keystone species in polar oceans and sea ice because it can thrive under different environmental conditions if temperatures are low. In this perspective paper, we provide insights into the latest molecular work that has been done on F. cylindrus and discuss its role as a model alga to understand cold-adapted life.
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Affiliation(s)
- Antonia Otte
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Johanna C Winder
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Longji Deng
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Igor V Grigoriev
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich, UK
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10
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Sant’Anna FH, Finger Andreis T, Salvato RS, Muterle Varela AP, Comerlato J, Gregianini TS, Barcellos RB, de Souza Godinho FM, Resende PC, da Luz Wallau G, y Castro TR, Casarin BC, de Almeida Vieira A, Schwarzbold AV, de Arruda Trindade P, Tumioto Giannini GL, Freese L, Bristot G, Brasil CS, de Oliveira Rocha B, Martins PB, de Oliveira FH, van Oosterhout C, Wendland E. Incipient Parallel Evolution of SARS-CoV-2 Deltacron Variant in South Brazil. Vaccines (Basel) 2023; 11:vaccines11020212. [PMID: 36851091 PMCID: PMC9961971 DOI: 10.3390/vaccines11020212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
With the coexistence of multiple lineages and increased international travel, recombination and gene flow are likely to become increasingly important in the adaptive evolution of SARS-CoV-2. These processes could result in genetic introgression and the incipient parallel evolution of multiple recombinant lineages. However, identifying recombinant lineages is challenging, and the true extent of recombinant evolution in SARS-CoV-2 may be underestimated. This study describes the first SARS-CoV-2 Deltacron recombinant case identified in Brazil. We demonstrate that the recombination breakpoint is at the beginning of the Spike gene. The 5' genome portion (circa 22 kb) resembles the AY.101 (Delta), and the 3' genome portion (circa 8 kb nucleotides) is most similar to the BA.1.1 (Omicron). Furthermore, evolutionary genomic analyses indicate that the new strain emerged after a single recombination event between lineages of diverse geographical locations in December 2021 in South Brazil. This Deltacron, AYBA-RS, is one of the dozens of recombinants described in 2022. The submission of only four sequences in the GISAID database suggests that this lineage had a minor epidemiological impact. However, the recent emergence of this and other Deltacron recombinant lineages (XD, XF, and XS) suggests that gene flow and recombination may play an increasingly important role in the COVID-19 pandemic. We explain the evolutionary and population genetic theory that supports this assertion, concluding that this stresses the need for continued genomic surveillance. This monitoring is vital for countries where multiple variants are present, as well as for countries that receive significant inbound international travel.
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Affiliation(s)
| | | | - Richard Steiner Salvato
- Centro de Desenvolvimento Científico e Tecnológico, Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CDCT/CEVS/SES-RS), Porto Alegre 90450-190, RS, Brazil
| | | | | | - Tatiana Schäffer Gregianini
- Laboratório Central de Saúde Pública, Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (LACEN/CEVS/SES-RS), Porto Alegre 90450-190, RS, Brazil
| | - Regina Bones Barcellos
- Centro de Desenvolvimento Científico e Tecnológico, Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CDCT/CEVS/SES-RS), Porto Alegre 90450-190, RS, Brazil
| | - Fernanda Marques de Souza Godinho
- Centro de Desenvolvimento Científico e Tecnológico, Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CDCT/CEVS/SES-RS), Porto Alegre 90450-190, RS, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
| | - Gabriel da Luz Wallau
- Departamento de Entomologia e Núcleo de Bioinformática, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz Pernambuco (FIOCRUZ-PE), Recife 50740-465, PE, Brazil
| | - Thaís Regina y Castro
- Departamento de Análises Clínicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil
| | - Bruna Campestrini Casarin
- Departamento de Análises Clínicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil
| | - Andressa de Almeida Vieira
- Departamento de Análises Clínicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil
| | | | | | | | - Luana Freese
- Hospital Moinhos de Vento, Porto Alegre 90035-000, RS, Brazil
| | - Giovana Bristot
- Hospital Moinhos de Vento, Porto Alegre 90035-000, RS, Brazil
| | | | | | | | | | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- Correspondence:
| | - Eliana Wendland
- Hospital Moinhos de Vento, Porto Alegre 90035-000, RS, Brazil
- Graduate Program in Biosciences, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil
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11
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Nef C, Madoui MA, Pelletier É, Bowler C. Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros. PLoS Biol 2022; 20:e3001893. [PMID: 36441816 PMCID: PMC9731442 DOI: 10.1371/journal.pbio.3001893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 12/08/2022] [Accepted: 10/27/2022] [Indexed: 11/30/2022] Open
Abstract
Diatoms form a diverse and abundant group of photosynthetic protists that are essential players in marine ecosystems. However, the microevolutionary structure of their populations remains poorly understood, particularly in polar regions. Exploring how closely related diatoms adapt to different environments is essential given their short generation times, which may allow rapid adaptations, and their prevalence in marine regions dramatically impacted by climate change, such as the Arctic and Southern Oceans. Here, we address genetic diversity patterns in Chaetoceros, the most abundant diatom genus and one of the most diverse, using 11 metagenome-assembled genomes (MAGs) reconstructed from Tara Oceans metagenomes. Genome-resolved metagenomics on these MAGs confirmed a prevalent distribution of Chaetoceros in the Arctic Ocean with lower dispersal in the Pacific and Southern Oceans as well as in the Mediterranean Sea. Single-nucleotide variants identified within the different MAG populations allowed us to draw a landscape of Chaetoceros genetic diversity and revealed an elevated genetic structure in some Arctic Ocean populations. Gene flow patterns of closely related Chaetoceros populations seemed to correlate with distinct abiotic factors rather than with geographic distance. We found clear positive selection of genes involved in nutrient availability responses, in particular for iron (e.g., ISIP2a, flavodoxin), silicate, and phosphate (e.g., polyamine synthase), that were further supported by analysis of Chaetoceros transcriptomes. Altogether, these results highlight the importance of environmental selection in shaping diatom diversity patterns and provide new insights into their metapopulation genomics through the integration of metagenomic and environmental data.
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Affiliation(s)
- Charlotte Nef
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
| | - Mohammed-Amin Madoui
- Service d’Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, Dijon, 21000, France
| | - Éric Pelletier
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Metabolic Genomics, Genoscope, Institut de Biologie François-Jacob, CEA, CNRS, Université Evry, Université Paris Saclay, Evry, France
| | - Chris Bowler
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- * E-mail:
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12
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Giguere DJ, Bahcheli AT, Slattery SS, Patel RR, Browne TS, Flatley M, Karas BJ, Edgell DR, Gloor GB. Telomere-to-telomere genome assembly of Phaeodactylum tricornutum. PeerJ 2022; 10:e13607. [PMID: 35811822 PMCID: PMC9266582 DOI: 10.7717/peerj.13607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 05/27/2022] [Indexed: 01/17/2023] Open
Abstract
Phaeodactylum tricornutum is a marine diatom with a growing genetic toolbox available and is being used in many synthetic biology applications. While most of the genome has been assembled, the currently available genome assembly is not a completed telomere-to-telomere assembly. Here, we used Oxford Nanopore long reads to build a telomere-to-telomere genome for Phaeodactylum tricornutum. We developed a graph-based approach to extract all unique telomeres, and used this information to manually correct assembly errors. In total, we found 25 nuclear chromosomes that comprise all previously assembled fragments, in addition to the chloroplast and mitochondrial genomes. We found that chromosome 19 has filtered long-read coverage and a quality estimate that suggests significantly less haplotype sequence variation than the other chromosomes. This work improves upon the previous genome assembly and provides new opportunities for genetic engineering of this species, including creating designer synthetic chromosomes.
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Affiliation(s)
- Daniel J. Giguere
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Alexander T. Bahcheli
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Samuel S. Slattery
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Rushali R. Patel
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Tyler S. Browne
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | | | - Bogumil J. Karas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - David R. Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Gregory B. Gloor
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
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13
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Pinseel E, Nakov T, Van den Berge K, Downey KM, Judy KJ, Kourtchenko O, Kremp A, Ruck EC, Sjöqvist C, Töpel M, Godhe A, Alverson AJ. Strain-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline. THE ISME JOURNAL 2022; 16:1776-1787. [PMID: 35383290 PMCID: PMC9213524 DOI: 10.1038/s41396-022-01230-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 05/01/2023]
Abstract
The salinity gradient separating marine and freshwater environments represents a major ecological divide for microbiota, yet the mechanisms by which marine microbes have adapted to and ultimately diversified in freshwater environments are poorly understood. Here, we take advantage of a natural evolutionary experiment: the colonization of the brackish Baltic Sea by the ancestrally marine diatom Skeletonema marinoi. To understand how diatoms respond to low salinity, we characterized transcriptomic responses of acclimated S. marinoi grown in a common garden. Our experiment included eight strains from source populations spanning the Baltic Sea salinity cline. Gene expression analysis revealed that low salinities induced changes in the cellular metabolism of S. marinoi, including upregulation of photosynthesis and storage compound biosynthesis, increased nutrient demand, and a complex response to oxidative stress. However, the strain effect overshadowed the salinity effect, as strains differed significantly in their response, both regarding the strength and the strategy (direction of gene expression) of their response. The high degree of intraspecific variation in gene expression observed here highlights an important but often overlooked source of biological variation associated with how diatoms respond to environmental change.
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Affiliation(s)
- Eveline Pinseel
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA.
| | - Teofil Nakov
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Koen Van den Berge
- Department of Statistics, University of California, Berkeley, CA, USA
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Kala M Downey
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Kathryn J Judy
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Olga Kourtchenko
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Anke Kremp
- Leibniz-Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Elizabeth C Ruck
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Conny Sjöqvist
- Environmental and Marine Biology, Åbo Akademi University, Åbo, Finland
| | - Mats Töpel
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Anna Godhe
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Andrew J Alverson
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA.
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14
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Potential for Biomass Production and Remediation by Cultivation of the Marine Model Diatom Phaeodactylum tricornutum in Oil Field Produced Wastewater Media. WATER 2021. [DOI: 10.3390/w13192700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
While oilfield produced water (PW) is one of the largest, unclaimed wastewater streams of the oil industry, it could potentially be used as a cultivation medium for microalgae. Microalgae could help with the remediation of this water while also delivering biomass that can be transformed into valuable byproducts such as biofuels. The coupling of these two purposes is expected to cut production costs of biofuels while aiding environmental protection. In this study, we compared the cultivation capacity of the marine model diatom Phaeodactylum tricornutum in media at varying salinities and in media composed of PW from two oilfields in the Central Valley of California that differed drastically in the concentration of inorganic and organic constituents. Specifically, we measured the carrying capacity of these media, the maximum growth rates of P. tricornutum, its cellular lipid accumulation capacity, and its capacity to remediate the most polluted PW source. Our study shows that P. tricornutum can successfully adjust to the tested cultivation media through processes of short-term acclimation and long-term adaptation. Furthermore, the cultivation of P. tricornutum in the most heavily polluted PW source led to significant increases in cell yield and improved photosynthetic capacity during the stationary phase, which could be attributed chiefly to the higher levels of nitrate present in this PW source. Chemical water analyses also demonstrated the capability of P. tricornutum to remediate major nutrient content and potentially harmful elements like fluorine and copper. Because P. tricornutum is amenable to advanced genetic engineering, which could be taken advantage of to improve its cultivation resilience and productivity in an economic setting, we propose this study as a step towards essential follow-up studies that will identify the genetic regulation behind its growth in oilfield PW media and its remediation of the PW constituents.
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15
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Ajani PA, Verma A, Kim JH, Woodcock S, Nishimura T, Farrell H, Zammit A, Brett S, Murray SA. Using qPCR and high-resolution sensor data to model a multi-species Pseudo-nitzschia (Bacillariophyceae) bloom in southeastern Australia. HARMFUL ALGAE 2021; 108:102095. [PMID: 34588117 DOI: 10.1016/j.hal.2021.102095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Harmful algal blooms, including those caused by the toxic diatom Pseudo-nitzschia, can have significant impacts on human health, ecosystem functioning and ultimately food security. In the current study we characterized a bloom of species of Pseudo-nitzschia that occurred in a south-eastern Australian oyster-growing estuary in 2019. Using light microscopy, combined with molecular (ITS/5.8S and LSU D1-D3 rDNA regions) and toxicological evidence, we observed the bloom to consist of multiple species of Pseudo-nitzschia including P. cf. cuspidata, P. hasleana, P. fraudulenta and P. multiseries, with P. cf. cuspidata being the only species that produced domoic acid (3.1 pg DA per cell). As several species of Pseudo-nitzschia co-occurred, only one of which produced DA, we developed a rapid, sensitive and efficient quantitative real-time polymerase chain reaction (qPCR) assay to detect only species belonging to the P. pseudodelicatissima complex Clade I, to which P. cf. cuspidata belongs, and this indicated that P. cuspidata or closely related strains may have dominated the Pseudo-nitzschia community at this time. Finally, using high resolution water temperature and salinity sensor data, we modeled the relationship between light microscopy determined abundance of P. delicatissima group and environmental variables (temperature, salinity, rainfall) at two sites within the estuary. A total of eight General Linear Models (GLMs) explaining between 9 and 54% of the deviance suggested that the temperature (increasing) and/or salinity (decreasing) data were generally more predictive of high cell concentrations than the rainfall data at both sites, and that overall, cell concentrations were more predictive at the more oceanic site than the more upstream site, using this method. We conclude that the combination of rapid molecular methods such as qPCR and real-time sensor data modeling, can provide a more rapid and effective early warning of harmful algal blooms of species of Pseudo-nitzschia, resulting in more beneficial regulatory and management outcomes.
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Affiliation(s)
- Penelope A Ajani
- University of Technology Sydney, School of Life Sciences, Sydney, PO Box 123, Broadway, NSW 2007, Australia; Food Agility CRC Ltd, 81 Broadway, Ulitmo, NSW 2007, Australia.
| | - Arjun Verma
- University of Technology Sydney, School of Life Sciences, Sydney, PO Box 123, Broadway, NSW 2007, Australia; Food Agility CRC Ltd, 81 Broadway, Ulitmo, NSW 2007, Australia
| | - Jin Ho Kim
- Department of Earth and Marine Science, College of Ocean Sciences, Jeju National University, Jeju 63243, Korea
| | - Stephen Woodcock
- University of Technology Sydney, School of Life Sciences, Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | | | - Hazel Farrell
- NSW Food Authority, NSW Department of Primary Industries, PO Box 232, Taree 2430, Australia
| | - Anthony Zammit
- NSW Food Authority, NSW Department of Primary Industries, PO Box 232, Taree 2430, Australia
| | - Steve Brett
- Microalgal Services, 308 Tucker Rd, Ormond 3204, Australia
| | - Shauna A Murray
- University of Technology Sydney, School of Life Sciences, Sydney, PO Box 123, Broadway, NSW 2007, Australia; Food Agility CRC Ltd, 81 Broadway, Ulitmo, NSW 2007, Australia
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