1
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Ochiai KK, Hanawa D, Ogawa HA, Tanaka H, Uesaka K, Edzuka T, Shirae-Kurabayashi M, Toyoda A, Itoh T, Goshima G. Genome sequence and cell biological toolbox of the highly regenerative, coenocytic green feather alga Bryopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38642374 DOI: 10.1111/tpj.16764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 02/10/2024] [Accepted: 03/27/2024] [Indexed: 04/22/2024]
Abstract
Green feather algae (Bryopsidales) undergo a unique life cycle in which a single cell repeatedly executes nuclear division without cytokinesis, resulting in the development of a thallus (>100 mm) with characteristic morphology called coenocyte. Bryopsis is a representative coenocytic alga that has exceptionally high regeneration ability: extruded cytoplasm aggregates rapidly in seawater, leading to the formation of protoplasts. However, the genetic basis of the unique cell biology of Bryopsis remains poorly understood. Here, we present a high-quality assembly and annotation of the nuclear genome of Bryopsis sp. (90.7 Mbp, 27 contigs, N50 = 6.7 Mbp, 14 034 protein-coding genes). Comparative genomic analyses indicate that the genes encoding BPL-1/Bryohealin, the aggregation-promoting lectin, are heavily duplicated in Bryopsis, whereas homologous genes are absent in other ulvophyceans, suggesting the basis of regeneration capability of Bryopsis. Bryopsis sp. possesses >30 kinesins but only a single myosin, which differs from other green algae that have multiple types of myosin genes. Consistent with this biased motor toolkit, we observed that the bidirectional motility of chloroplasts in the cytoplasm was dependent on microtubules but not actin in Bryopsis sp. Most genes required for cytokinesis in plants are present in Bryopsis, including those in the SNARE or kinesin superfamily. Nevertheless, a kinesin crucial for cytokinesis initiation in plants (NACK/Kinesin-7II) is hardly expressed in the coenocytic part of the thallus, possibly underlying the lack of cytokinesis in this portion. The present genome sequence lays the foundation for experimental biology in coenocytic macroalgae.
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Affiliation(s)
- Kanta K Ochiai
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, 517-0004, Japan
| | - Daiki Hanawa
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Harumi A Ogawa
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, 517-0004, Japan
| | - Hiroyuki Tanaka
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Kazuma Uesaka
- Centre for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
| | - Tomoya Edzuka
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, 517-0004, Japan
| | - Maki Shirae-Kurabayashi
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, 517-0004, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Gohta Goshima
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, 517-0004, Japan
- Department of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
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2
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Domozych DS, LoRicco JG. The extracellular matrix of green algae. PLANT PHYSIOLOGY 2023; 194:15-32. [PMID: 37399237 PMCID: PMC10762512 DOI: 10.1093/plphys/kiad384] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 07/05/2023]
Abstract
Green algae display a wide range of extracellular matrix (ECM) components that include various types of cell walls (CW), scales, crystalline glycoprotein coverings, hydrophobic compounds, and complex gels or mucilage. Recently, new information derived from genomic/transcriptomic screening, advanced biochemical analyses, immunocytochemical studies, and ecophysiology has significantly enhanced and refined our understanding of the green algal ECM. In the later diverging charophyte group of green algae, the CW and other ECM components provide insight into the evolution of plants and the ways the ECM modulates during environmental stress. Chlorophytes produce diverse ECM components, many of which have been exploited for various uses in medicine, food, and biofuel production. This review highlights major advances in ECM studies of green algae.
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Affiliation(s)
- David S Domozych
- Department of Biology, Skidmore College, Saratoga Springs, NY 12866, USA
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3
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Pushpakumara BLDU, Tandon K, Willis A, Verbruggen H. The Bacterial Microbiome of the Coral Skeleton Algal Symbiont Ostreobium Shows Preferential Associations and Signatures of Phylosymbiosis. MICROBIAL ECOLOGY 2023; 86:2032-2046. [PMID: 37002423 PMCID: PMC10497448 DOI: 10.1007/s00248-023-02209-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
Ostreobium, the major algal symbiont of the coral skeleton, remains understudied despite extensive research on the coral holobiont. The enclosed nature of the coral skeleton might reduce the dispersal and exposure of residing bacteria to the outside environment, allowing stronger associations with the algae. Here, we describe the bacterial communities associated with cultured strains of 5 Ostreobium clades using 16S rRNA sequencing. We shed light on their likely physical associations by comparative analysis of three datasets generated to capture (1) all algae associated bacteria, (2) enriched tightly attached and potential intracellular bacteria, and (3) bacteria in spent media. Our data showed that while some bacteria may be loosely attached, some tend to be tightly attached or potentially intracellular. Although colonised with diverse bacteria, Ostreobium preferentially associated with 34 bacterial taxa revealing a core microbiome. These bacteria include known nitrogen cyclers, polysaccharide degraders, sulphate reducers, antimicrobial compound producers, methylotrophs, and vitamin B12 producers. By analysing co-occurrence networks of 16S rRNA datasets from Porites lutea and Paragoniastrea australensis skeleton samples, we show that the Ostreobium-bacterial associations present in the cultures are likely to also occur in their natural environment. Finally, our data show significant congruence between the Ostreobium phylogeny and the community composition of its tightly associated microbiome, largely due to the phylosymbiotic signal originating from the core bacterial taxa. This study offers insight into the Ostreobium microbiome and reveals preferential associations that warrant further testing from functional and evolutionary perspectives.
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Affiliation(s)
| | - Kshitij Tandon
- School of Biosciences, University of Melbourne, Victoria, 3010, Australia
| | - Anusuya Willis
- Australian National Algae Culture Collection, CSIRO, Tasmania, 7000, Victoria, Australia
| | - Heroen Verbruggen
- School of Biosciences, University of Melbourne, Victoria, 3010, Australia
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4
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Alesmail M, Becerra Y, Betancourt KJ, Bracy SM, Castro AT, Cea C, Chavez J, Del Angel J, Diaz E, Diaz-Guzman Y, Dominguez J, Estrada JG, Frei LG, Gabrielson PW, Gallardo A, Garcia MR, Gonzalez E, Gonzalez Rocha A, Guzman-Bermudez D, Hebert CR, Hernandez M, Hughey JR, Lee Z, Leyva Romero A, Martinez E, Martinez N, Medina KH, Morales M, Moreno AM, Nava I, Nono AN, Ochoa SA, Perez A, Perez N, Perez Pulido E, Poduska S, Ramirez KN, Reyes D, Richardson K, Rodriguez J, Rodriguez AM, Serrano-Lopez C, Velasquez AG, Villanueva G. Complete Chloroplast Genome of an Endophytic Ostreobium sp. (Ostreobiaceae) from the U.S. Virgin Islands. Microbiol Resour Announc 2023; 12:e0027223. [PMID: 37093049 DOI: 10.1128/mra.00272-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
We present the complete chloroplast genome sequence of an endophytic Ostreobium sp. isolated from a 19th-century coralline red algal specimen from St. Croix, U.S. Virgin Islands. The chloroplast genome is 84,848 bp in length, contains 114 genes, and has a high level of gene synteny to other Ostreobiaceae.
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Affiliation(s)
- Mustafa Alesmail
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Yulissa Becerra
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Kimberly J Betancourt
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Shelly M Bracy
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Anevay T Castro
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Cynthia Cea
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Justin Chavez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Janet Del Angel
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Edgar Diaz
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Yael Diaz-Guzman
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jonathan Dominguez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jocelynnicole G Estrada
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Lashabelle G Frei
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Paul W Gabrielson
- Biology Department and Herbarium, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Andrea Gallardo
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Miriam R Garcia
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Eva Gonzalez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Anthony Gonzalez Rocha
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Diego Guzman-Bermudez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Cassidy R Hebert
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Marlene Hernandez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jeffery R Hughey
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Zachary Lee
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Alexandra Leyva Romero
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Eric Martinez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Nathaniel Martinez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Kazimiera H Medina
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Miguel Morales
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Alexis M Moreno
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Isabella Nava
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Alyssa N Nono
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Samuel A Ochoa
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Amy Perez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Natasha Perez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Edwin Perez Pulido
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Sophie Poduska
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Kimberly N Ramirez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Denise Reyes
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Kelsey Richardson
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Juanaisa Rodriguez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Alondra M Rodriguez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Clarisa Serrano-Lopez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Andrea G Velasquez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Gezelle Villanueva
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
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5
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Reich HG, Camp EF, Roger LM, Putnam HM. The trace metal economy of the coral holobiont: supplies, demands and exchanges. Biol Rev Camb Philos Soc 2023; 98:623-642. [PMID: 36897260 DOI: 10.1111/brv.12922] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022]
Abstract
The juxtaposition of highly productive coral reef ecosystems in oligotrophic waters has spurred substantial interest and progress in our understanding of macronutrient uptake, exchange, and recycling among coral holobiont partners (host coral, dinoflagellate endosymbiont, endolithic algae, fungi, viruses, bacterial communities). By contrast, the contribution of trace metals to the physiological performance of the coral holobiont and, in turn, the functional ecology of reef-building corals remains unclear. The coral holobiont's trace metal economy is a network of supply, demand, and exchanges upheld by cross-kingdom symbiotic partnerships. Each partner has unique trace metal requirements that are central to their biochemical functions and the metabolic stability of the holobiont. Organismal homeostasis and the exchanges among partners determine the ability of the coral holobiont to adjust to fluctuating trace metal supplies in heterogeneous reef environments. This review details the requirements for trace metals in core biological processes and describes how metal exchanges among holobiont partners are key to sustaining complex nutritional symbioses in oligotrophic environments. Specifically, we discuss how trace metals contribute to partner compatibility, ability to cope with stress, and thereby to organismal fitness and distribution. Beyond holobiont trace metal cycling, we outline how the dynamic nature of the availability of environmental trace metal supplies can be influenced by a variability of abiotic factors (e.g. temperature, light, pH, etc.). Climate change will have profound consequences on the availability of trace metals and further intensify the myriad stressors that influence coral survival. Lastly, we suggest future research directions necessary for understanding the impacts of trace metals on the coral holobiont symbioses spanning subcellular to organismal levels, which will inform nutrient cycling in coral ecosystems more broadly. Collectively, this cross-scale elucidation of the role of trace metals for the coral holobiont will allow us to improve forecasts of future coral reef function.
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Affiliation(s)
- Hannah G Reich
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI, 02881, USA
| | - Emma F Camp
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Liza M Roger
- Chemical & Life Science Engineering, Virginia Commonwealth University, 601 W. Main Street, Richmond, VA, 23284, USA
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI, 02881, USA
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6
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Mohamed AR, Ochsenkühn MA, Kazlak AM, Moustafa A, Amin SA. The coral microbiome: towards an understanding of the molecular mechanisms of coral-microbiota interactions. FEMS Microbiol Rev 2023; 47:fuad005. [PMID: 36882224 PMCID: PMC10045912 DOI: 10.1093/femsre/fuad005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships within corals. Here, we provide an overview of the complexity of the coral microbiome focusing on taxonomic diversity and functions of well-studied and cryptic microbes. Mining the coral literature indicate that while corals collectively harbour a third of all marine bacterial phyla, known bacterial symbionts and antagonists of corals represent a minute fraction of this diversity and that these taxa cluster into select genera, suggesting selective evolutionary mechanisms enabled these bacteria to gain a niche within the holobiont. Recent advances in coral microbiome research aimed at leveraging microbiome manipulation to increase coral's fitness to help mitigate heat stress-related mortality are discussed. Then, insights into the potential mechanisms through which microbiota can communicate with and modify host responses are examined by describing known recognition patterns, potential microbially derived coral epigenome effector proteins and coral gene regulation. Finally, the power of omics tools used to study corals are highlighted with emphasis on an integrated host-microbiota multiomics framework to understand the underlying mechanisms during symbiosis and climate change-driven dysbiosis.
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Affiliation(s)
- Amin R Mohamed
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Michael A Ochsenkühn
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Ahmed M Kazlak
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
| | - Ahmed Moustafa
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
- Department of Biology, American University in Cairo, New Cairo 11835, Egypt
| | - Shady A Amin
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
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7
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Bowles AMC, Williamson CJ, Williams TA, Lenton TM, Donoghue PCJ. The origin and early evolution of plants. TRENDS IN PLANT SCIENCE 2023; 28:312-329. [PMID: 36328872 DOI: 10.1016/j.tplants.2022.09.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/23/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Plant (archaeplastid) evolution has transformed the biosphere, but we are only now beginning to learn how this took place through comparative genomics, phylogenetics, and the fossil record. This has illuminated the phylogeny of Archaeplastida, Viridiplantae, and Streptophyta, and has resolved the evolution of key characters, genes, and genomes - revealing that many key innovations evolved long before the clades with which they have been casually associated. Molecular clock analyses estimate that Streptophyta and Viridiplantae emerged in the late Mesoproterozoic to late Neoproterozoic, whereas Archaeplastida emerged in the late-mid Palaeoproterozoic. Together, these insights inform on the coevolution of plants and the Earth system that transformed ecology and global biogeochemical cycles, increased weathering, and precipitated snowball Earth events, during which they would have been key to oxygen production and net primary productivity (NPP).
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Affiliation(s)
- Alexander M C Bowles
- School of Geographical Sciences, University of Bristol, University Road, Bristol BS8 1SS, UK; Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
| | | | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Timothy M Lenton
- Global Systems Institute, University of Exeter, Laver Building, North Park Road, Exeter EX4 4QE, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
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8
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Every refuge has its price: Ostreobium as a model for understanding how algae can live in rock and stay in business. Semin Cell Dev Biol 2023; 134:27-36. [PMID: 35341677 DOI: 10.1016/j.semcdb.2022.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/20/2022] [Accepted: 03/08/2022] [Indexed: 11/23/2022]
Abstract
Ostreobium is a siphonous green alga in the Bryopsidales (Chlorophyta) that burrows into calcium carbonate (CaCO3) substrates. In this habitat, it lives under environmental conditions unusual for an alga (i.e., low light and low oxygen) and it is a major agent of carbonate reef bioerosion. In coral skeletons, Ostreobium can form conspicuous green bands recognizable by the naked eye and it is thought to contribute to the coral's nutritional needs. With coral reefs in global decline, there is a renewed focus on understanding Ostreobium biology and its roles in the coral holobiont. This review summarizes knowledge on Ostreobium's morphological structure, biodiversity and evolution, photosynthesis, mechanism of bioerosion and its role as a member of the coral holobiont. We discuss the resources available to study Ostreobium biology, lay out some of the uncharted territories in Ostreobium biology and offer perspectives for future research.
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9
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Kato S, Misumi O, Maruyama S, Nozaki H, Tsujimoto-Inui Y, Takusagawa M, Suzuki S, Kuwata K, Noda S, Ito N, Okabe Y, Sakamoto T, Yagisawa F, Matsunaga TM, Matsubayashi Y, Yamaguchi H, Kawachi M, Kuroiwa H, Kuroiwa T, Matsunaga S. Genomic analysis of an ultrasmall freshwater green alga, Medakamo hakoo. Commun Biol 2023; 6:89. [PMID: 36690657 PMCID: PMC9871001 DOI: 10.1038/s42003-022-04367-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/12/2022] [Indexed: 01/24/2023] Open
Abstract
Ultrasmall algae have attracted the attention of biologists investigating the basic mechanisms underlying living systems. Their potential as effective organisms for producing useful substances is also of interest in bioindustry. Although genomic information is indispensable for elucidating metabolism and promoting molecular breeding, many ultrasmall algae remain genetically uncharacterized. Here, we present the nuclear genome sequence of an ultrasmall green alga of freshwater habitats, Medakamo hakoo. Evolutionary analyses suggest that this species belongs to a new genus within the class Trebouxiophyceae. Sequencing analyses revealed that its genome, comprising 15.8 Mbp and 7629 genes, is among the smallest known genomes in the Viridiplantae. Its genome has relatively few genes associated with genetic information processing, basal transcription factors, and RNA transport. Comparative analyses revealed that 1263 orthogroups were shared among 15 ultrasmall algae from distinct phylogenetic lineages. The shared gene sets will enable identification of genes essential for algal metabolism and cellular functions.
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Affiliation(s)
- Shoichi Kato
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, 278-8510, Japan
| | - Osami Misumi
- Department of Biological Science and Chemistry, Faculty of Science, Graduate School of Medicine, Yamaguchi University, Yoshida, Yamaguchi, 753-8512, Japan
| | - Shinichiro Maruyama
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Aobaku, Sendai, 980-8578, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, 112-8610, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Tokyo, 113-0033, Japan
- Biodiversity Division, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Yayoi Tsujimoto-Inui
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Mari Takusagawa
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Shigekatsu Suzuki
- Biodiversity Division, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Saki Noda
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Nanami Ito
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Yoji Okabe
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, 278-8510, Japan
| | - Fumi Yagisawa
- Center for Research Advancement and Collaboration, University of the Ryukyus, Okinawa, 903-0213, Japan
- Graduate School of Engineering and Science, University of the Ryukyus, Okinawa, 903-0213, Japan
| | - Tomoko M Matsunaga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Yoshikatsu Matsubayashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Haruyo Yamaguchi
- Biodiversity Division, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Masanobu Kawachi
- Biodiversity Division, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Haruko Kuroiwa
- Department of Chemical and Biological Science, Faculty of Science, Japan Women's University, Tokyo, 112-8681, Japan
| | - Tsuneyoshi Kuroiwa
- Department of Chemical and Biological Science, Faculty of Science, Japan Women's University, Tokyo, 112-8681, Japan.
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, 278-8510, Japan.
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.
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10
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Ricci F, Leggat W, Page CE, Ainsworth TD. Coral growth anomalies, neoplasms, and tumors in the Anthropocene. Trends Microbiol 2022; 30:1160-1173. [PMID: 35718641 DOI: 10.1016/j.tim.2022.05.013] [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: 02/18/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 01/13/2023]
Abstract
One of the most widespread coral diseases linked to anthropogenic activities and recorded on reefs worldwide is characterized by anomalous growth formations in stony corals, referred to as coral growth anomalies (GAs). The biological functions of GA tissue include limited reproduction, reduced access to resources, and weakened ability to defend against predators. Transcriptomic analyses have revealed that, in some cases, disease progression can involve host genes related to oncogenesis, suggesting that the GA tissues may be malignant neoplasms such as those developed by vertebrates. The number of studies reporting the presence of GAs in common reef-forming species highlights the urgency of a thorough understanding of the pathology and causative factors of this disease and its parallels to higher organism malignant tissue growth. Here, we review the current state of knowledge on the etiology and holobiont features of GAs in reef-building corals.
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Affiliation(s)
- Francesco Ricci
- University of New South Wales, School of Biological, Earth and Environmental Sciences, Kensington 2033, NSW, Australia.
| | - William Leggat
- University of Newcastle, School of Environmental and Life Sciences, Callaghan 2309, NSW, Australia
| | - Charlotte E Page
- University of New South Wales, School of Biological, Earth and Environmental Sciences, Kensington 2033, NSW, Australia
| | - Tracy D Ainsworth
- University of New South Wales, School of Biological, Earth and Environmental Sciences, Kensington 2033, NSW, Australia
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11
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Bringloe TT, Fort A, Inaba M, Sulpice R, Ghriofa CN, Mols‐Mortensen A, Filbee‐Dexter K, Vieira C, Kawai H, Hanyuda T, Krause‐Jensen D, Olesen B, Starko S, Verbruggen H. Whole genome population structure of North Atlantic kelp confirms high-latitude glacial refugia. Mol Ecol 2022; 31:6473-6488. [PMID: 36200326 PMCID: PMC10091776 DOI: 10.1111/mec.16714] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 09/21/2022] [Indexed: 01/13/2023]
Abstract
Coastal refugia during the Last Glacial Maximum (~21,000 years ago) have been hypothesized at high latitudes in the North Atlantic, suggesting marine populations persisted through cycles of glaciation and are potentially adapted to local environments. Here, whole-genome sequencing was used to test whether North Atlantic marine coastal populations of the kelp Alaria esculenta survived in the area of southwestern Greenland during the Last Glacial Maximum. We present the first annotated genome for A. esculenta and call variant positions in 54 individuals from populations in Atlantic Canada, Greenland, Faroe Islands, Norway and Ireland. Differentiation across populations was reflected in ~1.9 million single nucleotide polymorphisms, which further revealed mixed ancestry in the Faroe Islands individuals between putative Greenlandic and European lineages. Time-calibrated organellar phylogenies suggested Greenlandic populations were established during the last interglacial period more than 100,000 years ago, and that the Faroe Islands population was probably established following the Last Glacial Maximum. Patterns in population statistics, including nucleotide diversity, minor allele frequencies, heterozygosity and linkage disequilibrium decay, nonetheless suggested glaciation reduced Canadian Atlantic and Greenlandic populations to small effective sizes during the most recent glaciation. Functional differentiation was further reflected in exon read coverage, which revealed expansions unique to Greenland in 337 exons representing 162 genes, and a modest degree of exon loss (103 exons from 56 genes). Altogether, our genomic results provide strong evidence that A. esculenta populations were resilient to past climatic fluctuations related to glaciations and that high-latitude populations are potentially already adapted to local conditions as a result.
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Affiliation(s)
| | - Antoine Fort
- Plant Systems Biology Lab, Ryan Institute, SFI MaREI Centre for Climate, Energy and Marine, School of Natural SciencesNational University of Ireland GalwayGalwayIreland
- Present address:
Department of Life and Physical SciencesAthlone Institute of TechnologyAthloneIreland
| | - Masami Inaba
- Plant Systems Biology Lab, Ryan Institute, SFI MaREI Centre for Climate, Energy and Marine, School of Natural SciencesNational University of Ireland GalwayGalwayIreland
| | - Ronan Sulpice
- Plant Systems Biology Lab, Ryan Institute, SFI MaREI Centre for Climate, Energy and Marine, School of Natural SciencesNational University of Ireland GalwayGalwayIreland
| | - Cliodhna Ní Ghriofa
- Business Development ManagerMarine Innovation Development Centre Páirc Na MaraGalwayIreland
| | | | - Karen Filbee‐Dexter
- School of Biological Sciences and UWA Oceans InstituteUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Christophe Vieira
- Kobe University Research Center for Inland SeasKobe UniversityKobeJapan
| | - Hiroshi Kawai
- Kobe University Research Center for Inland SeasKobe UniversityKobeJapan
| | - Takeaki Hanyuda
- School of Marine BiosciencesKitasato UniversitySagamiharaJapan
| | - Dorte Krause‐Jensen
- Department of EcoscienceAarhus UniversityAarhusDenmark
- Arctic Research CenterAarhus UniversityAarhusDenmark
| | | | - Samuel Starko
- Department of BiologyUniversity of VictoriaVictoriaCanada
| | - Heroen Verbruggen
- School of BioSciencesUniversity of MelbourneParkvilleVictoriaAustralia
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12
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Seki S, Nakaniwa T, Castro-Hartmann P, Sader K, Kawamoto A, Tanaka H, Qian P, Kurisu G, Fujii R. Structural insights into blue-green light utilization by marine green algal light harvesting complex II at 2.78 Å. BBA ADVANCES 2022; 2:100064. [PMID: 37082593 PMCID: PMC10074980 DOI: 10.1016/j.bbadva.2022.100064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022] Open
Abstract
Light-harvesting complex II (LHCII) present in plants and green algae absorbs solar energy to promote photochemical reactions. A marine green macroalga, Codium fragile, exhibits the unique characteristic of absorbing blue-green light from the sun during photochemical reactions while being underwater owing to the presence of pigment-altered LHCII called siphonaxanthin-chlorophyll a/b-binding protein (SCP). In this study, we determined the structure of SCP at a resolution of 2.78 Å using cryogenic electron microscopy. SCP has a trimeric structure, wherein each monomer containing two lutein and two chlorophyll a molecules in the plant-type LHCII are replaced by siphonaxanthin and its ester and two chlorophyll b molecules, respectively. Siphonaxanthin occupies the binding site in SCP having a polarity in the trimeric inner core, and exhibits a distorted conjugated chain comprising a carbonyl group hydrogen bonded to a cysteine residue of apoprotein. These features suggest that the siphonaxanthin molecule is responsible for the characteristic green absorption of SCP. The replaced chlorophyll b molecules extend the region of the stromal side chlorophyll b cluster, spanning two adjacent monomers.
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Affiliation(s)
- Soichiro Seki
- Division of Molecular Materials Science, Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Sumiyoshi-ku, Osaka 558–8585, Japan
| | - Tetsuko Nakaniwa
- Institute for Protein Research, Osaka University, Suita, Osaka 565–0871, Japan
| | - Pablo Castro-Hartmann
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands
| | - Kasim Sader
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands
| | - Akihiro Kawamoto
- Institute for Protein Research, Osaka University, Suita, Osaka 565–0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka 565–9871, Japan
| | - Hideaki Tanaka
- Institute for Protein Research, Osaka University, Suita, Osaka 565–0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka 565–9871, Japan
| | - Pu Qian
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, Suita, Osaka 565–0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka 565–9871, Japan
| | - Ritsuko Fujii
- Division of Molecular Materials Science, Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Sumiyoshi-ku, Osaka 558–8585, Japan
- Department of Chemistry, Graduate School of Science, Osaka Metropolitan University, 3-3-138, Sugimoto, Sumiyoshi-ku, Osaka 558–8585, Japan
- Research Center for Artificial Photosynthesis (ReCAP), Osaka Metropolitan University, 3-3-138, Sugimoto, Sumiyoshi-ku, Osaka 558–8585, Japan
- Corresponding author.
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13
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Pérez-Rosales G, Hernández-Agreda A, Bongaerts P, Rouzé H, Pichon M, Carlot J, Torda G, Parravicini V, Hédouin L. Mesophotic depths hide high coral cover communities in French Polynesia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 844:157049. [PMID: 35780903 DOI: 10.1016/j.scitotenv.2022.157049] [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: 04/14/2022] [Revised: 06/17/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
The rapid decline of shallow coral reefs has increased the interest in the long-understudied mesophotic coral ecosystems (MCEs). However, MCEs are usually characterised by rather low to moderate scleractinian coral cover, with only a few descriptions of high coral cover at depth. Here, we explored eight islands across French Polynesia over a wide depth range (6 to 120 m) to identify coral cover hotspots at mesophotic depths and the co-occurrent biotic groups and abiotic factors that influence such high scleractinian cover. Using Bayesian modelling, we found that 20 out of 64 of studied deep sites exhibited a coral cover higher than expected in the mesophotic range (e.g. as high as 81.8 % at 40 m, 74.5 % at 60 m, 53 % at 90 m and 42 % at 120 m vs the average expected values based on the model of 31.2 % at 40 m, 22.8 % at 60 m, 14.6 % at 90 m and 9.8 % at 120 m). Omitting the collinear factors light-irradiance and depth, these 'hotspots' of coral cover corresponded to mesophotic sites and depths characterised by hard substrate, a steep to moderate slope, and the dominance of laminar corals. Our work unveils the presence of unexpectedly and unique high coral cover communities at mesophotic depths in French Polynesia, highlighting the importance of expanding the research on deeper depths for the potential relevance in the conservation management of tropical coral reefs.
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Affiliation(s)
- Gonzalo Pérez-Rosales
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, 98729 Moorea, French Polynesia; PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 66860 Perpignan Cedex, France.
| | | | - Pim Bongaerts
- California Academy of Sciences, San Francisco, CA 94118, USA
| | - Héloïse Rouzé
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, 98729 Moorea, French Polynesia; Marine Laboratory, University of Guam, Mangilao, Guam 96923, USA
| | - Michel Pichon
- Biodiversity Section, Queensland Museum, Townsville 4811, Australia
| | - Jérémy Carlot
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, 98729 Moorea, French Polynesia
| | - Gergely Torda
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4811, Australia
| | - Valeriano Parravicini
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 66860 Perpignan Cedex, France
| | - Laetitia Hédouin
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, 98729 Moorea, French Polynesia; PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 66860 Perpignan Cedex, France
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14
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Kavazos CRJ, Ricci F, Leggat W, Casey JM, Choat JH, Ainsworth TD. Intestinal Microbiome Richness of Coral Reef Damselfishes ( Actinopterygii: Pomacentridae). Integr Org Biol 2022; 4:obac026. [PMID: 36136736 PMCID: PMC9486986 DOI: 10.1093/iob/obac026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/13/2022] [Indexed: 12/03/2022] Open
Abstract
Fish gastro-intestinal system harbors diverse microbiomes that affect the host's
digestion, nutrition, and immunity. Despite the great taxonomic diversity of fish, little
is understood about fish microbiome and the factors that determine its structure and
composition. Damselfish are important coral reef species that play pivotal roles in
determining algae and coral population structures of reefs. Broadly, damselfish belong to
either of two trophic guilds based on whether they are planktivorous or algae-farming. In
this study, we used 16S rRNA gene sequencing to investigate the intestinal microbiome of 5
planktivorous and 5 algae-farming damselfish species (Pomacentridae) from
the Great Barrier Reef. We detected Gammaproteobacteria ASVs belonging to
the genus Actinobacillus in 80% of sampled individuals across the 2
trophic guilds, thus, bacteria in this genus can be considered possible core members of
pomacentrid microbiomes. Algae-farming damselfish had greater bacterial alpha-diversity, a
more diverse core microbiome and shared 35 ± 22 ASVs, whereas planktivorous species shared
7 ± 3 ASVs. Our data also highlight differences in microbiomes associated with both
trophic guilds. For instance, algae-farming damselfish were enriched in
Pasteurellaceae, whilst planktivorous damselfish in
Vibrionaceae. Finally, we show shifts in bacterial community
composition along the intestines. ASVs associated with the classes Bacteroidia,
Clostridia, and Mollicutes bacteria were predominant in the
anterior intestinal regions while Gammaproteobacteria abundance was
higher in the stomach. Our results suggest that the richness of the intestinal bacterial
communities of damselfish reflects host species diet and trophic guild.
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Affiliation(s)
- Christopher R J Kavazos
- Biological, Earth and Environmental Sciences, The University of New South Wales , Kensington, NSW 2052 , Australia
| | - Francesco Ricci
- Biological, Earth and Environmental Sciences, The University of New South Wales , Kensington, NSW 2052 , Australia
- Centre of Marine Bio-Innovation, The University of New South Wales , Kensington, NSW 2052 , Australia
| | - William Leggat
- School of Environmental and Life Sciences, The University of Newcastle , 10 Chittaway Dr, Ourimbah, NSW 2258 , Australia
| | - Jordan M Casey
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University , Townsville, QLD 4811 , Australia
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan , Perpignan 66100 , France
- Laboratoire d'Excellence “CORAIL,” Université de Perpignan , Perpignan 66100 , France
| | - J Howard Choat
- College of Science and Engineering, James Cook University , Townsville QLD 4814 , Australia
| | - Tracy D Ainsworth
- Biological, Earth and Environmental Sciences, The University of New South Wales , Kensington, NSW 2052 , Australia
- Centre of Marine Bio-Innovation, The University of New South Wales , Kensington, NSW 2052 , Australia
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15
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Chen Y, Shah S, Dougan KE, van Oppen MJH, Bhattacharya D, Chan CX. Improved Cladocopium goreaui Genome Assembly Reveals Features of a Facultative Coral Symbiont and the Complex Evolutionary History of Dinoflagellate Genes. Microorganisms 2022; 10:microorganisms10081662. [PMID: 36014080 PMCID: PMC9412976 DOI: 10.3390/microorganisms10081662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Dinoflagellates of the family Symbiodiniaceae are crucial photosymbionts in corals and other marine organisms. Of these, Cladocopium goreaui is one of the most dominant symbiont species in the Indo-Pacific. Here, we present an improved genome assembly of C. goreaui combining new long-read sequence data with previously generated short-read data. Incorporating new full-length transcripts to guide gene prediction, the C. goreaui genome (1.2 Gb) exhibits a high extent of completeness (82.4% based on BUSCO protein recovery) and better resolution of repetitive sequence regions; 45,322 gene models were predicted, and 327 putative, topologically associated domains of the chromosomes were identified. Comparison with other Symbiodiniaceae genomes revealed a prevalence of repeats and duplicated genes in C. goreaui, and lineage-specific genes indicating functional innovation. Incorporating 2,841,408 protein sequences from 96 taxonomically diverse eukaryotes and representative prokaryotes in a phylogenomic approach, we assessed the evolutionary history of C. goreaui genes. Of the 5246 phylogenetic trees inferred from homologous protein sets containing two or more phyla, 35–36% have putatively originated via horizontal gene transfer (HGT), predominantly (19–23%) via an ancestral Archaeplastida lineage implicated in the endosymbiotic origin of plastids: 10–11% are of green algal origin, including genes encoding photosynthetic functions. Our results demonstrate the utility of long-read sequence data in resolving structural features of a dinoflagellate genome, and highlight how genetic transfer has shaped genome evolution of a facultative symbiont, and more broadly of dinoflagellates.
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Affiliation(s)
- Yibi Chen
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sarah Shah
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Katherine E. Dougan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Madeleine J. H. van Oppen
- School of Bioscience, The University of Melbourne, Parkville, VIC 3010, Australia
- Australian Institute of Marine Science, Townsville, QLD 4810, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Correspondence:
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16
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Kong L, Feng Y, Sun J, Rong K, Zhou J, Zheng R, Ni S, Liu S. Cross-feeding among microalgae facilitates nitrogen recovery at low C/N. ENVIRONMENTAL RESEARCH 2022; 211:113052. [PMID: 35276187 DOI: 10.1016/j.envres.2022.113052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/18/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Although co-culture of microalgae has been found as a feasible strategy to improve biomass production, their interspecies relationships are not fully understood. Here, two algae taxa, Chlorella sp. and Phormidium sp., were mono-cultured and co-cultured in three photobioreactors for 70 days with periodically harvesting to investigate how dual-species interaction influence nitrogen recovery. Results showed that the co-culture system achieved a significantly higher protein production and nitrogen removal rate than those in the individual cultures at a C/N ratio of 3:1 (p < 0.05). Genome-Centered metagenomic analysis revealed their cooperative relationship exemplified by cross-feeding. Phormidium sp. had the ability to synthesize pseudo-cobalamin, and Chlorella sp. harbored the gene for remodeling the pseudo-cobalamin to bioavailable vitamin B12. Meanwhile, Chlorella sp. could contribute the costly amino acid and cofactors for Phormidium sp. Their symbiotic interaction facilitated extracellular polymeric substances (EPS) production and nitrogen recovery. The EPS concentration in co-culture was positively related to the settling efficiency (R2 = 0.774), which plays an essential role in nitrogen recovery. This study provides new insights into microbial interactions among the photoautotrophic community and emphasizes the importance of algal interspecies interaction in algae-based wastewater treatment.
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Affiliation(s)
- Lingrui Kong
- College of Engineering, Peking University, Beijing, 100871, China
| | - Yiming Feng
- Department of Environmental Engineering, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Peking University, Beijing, 100871, China
| | - Jingqi Sun
- Department of Environmental Engineering, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Peking University, Beijing, 100871, China
| | - Kaiyu Rong
- College of Engineering, Peking University, Beijing, 100871, China
| | - Jianhang Zhou
- Department of Environmental Engineering, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Peking University, Beijing, 100871, China
| | - Ru Zheng
- Department of Environmental Engineering, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Peking University, Beijing, 100871, China
| | - Shouqing Ni
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan, 250100, Shandong, China
| | - Sitong Liu
- Department of Environmental Engineering, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Peking University, Beijing, 100871, China.
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17
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Wu G, Huang A, Wen Y, Wang H, Wang J, Luo F, Wu M. Euendolithic Cyanobacteria and Proteobacteria Together Contribute to Trigger Bioerosion in Aquatic Environments. Front Microbiol 2022; 13:938359. [PMID: 35875561 PMCID: PMC9298513 DOI: 10.3389/fmicb.2022.938359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
Shellfish, mussels, snails, and other aquatic animals, which assimilate limestone (calcium carbonate, CaCO3) to build shells and skeletons, are effective carbon sinks that help mitigate the greenhouse effect. However, bioerosion, the dissolution of calcium carbonate and the release of carbon dioxide, hinders carbon sequestration process. The bioerosion of aquatic environments remains to be elucidated. In this study, the bioerosion of Bellamya spp. shells from the aquatic environment was taken as the research object. In situ microbial community structure analysis of the bioerosion shell from different geographical locations, laboratory-level infected culture, and validated experiments were conducted by coupling traditional observation and 16S rRNA sequencing analysis method. Results showed that bioeroders can implant into the CaCO3 layer of the snail shell, resulting in the formation of many small holes in the shell, which reduced the shell’s density and made the shell fragile. Results also showed that bioeroders were distributed in two major phyla, namely, Cyanobacteria and Proteobacteria. Cluster analysis showed that Cyanobacteria sp. and two unidentified genera (Burkholderiaceae and Raistonia) were the key bioeroders. Moreover, results suggested that the interaction of Cyanobacteria and other bacteria promoted the biological function of “shell bioerosion.” This study identified the causes of “shell bioerosion” in aquatic environments and provided some theoretical basis for preventing and controlling it in the aquatic industry. Results also provided new insights of cyanobacterial bioerosion of shells and microalgae carbon sequestration.
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Affiliation(s)
- Guimei Wu
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou, China
| | - Aiyou Huang
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou, China
| | - Yanhong Wen
- Liuzhou Aquaculture Technology Extending Station, Liuzhou, China
| | - Hongxia Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jiangxin Wang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Fuguang Luo
- Liuzhou Aquaculture Technology Extending Station, Liuzhou, China
- *Correspondence: Fuguang Luo,
| | - Mingcan Wu
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou, China
- Mingcan Wu,
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18
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Seki S, Yamano Y, Oka N, Kamei Y, Fujii R. Discovery of a novel siphonaxanthin biosynthetic precursor in Codium fragile that accumulates only by exposure to blue-green light. FEBS Lett 2022; 596:1544-1555. [PMID: 35460262 DOI: 10.1002/1873-3468.14357] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/04/2022] [Indexed: 02/02/2023]
Abstract
Photosynthetic organisms adapt to a variety of light conditions. Codium fragile, a macrosiphonous green alga, binds a unique carbonyl carotenoid, siphonaxanthin, to its major photosynthetic light-harvesting complexes, allowing it to utilize dim blue-green light for photosynthesis. Here, we describe the absolute chemical structure of a novel siphonaxanthin biosynthetic precursor, 19-deoxysiphonaxanthin, that accumulates specifically in the photosynthetic antenna only when cultivated under blue-green light. The action spectra of pigment accumulation suggest that siphonaxanthin biosynthesis is regulated by a specific wavelength profile. The results provide clues to a new acclimation mechanism to withstand hours of intense light at low tide and why siphonous algae have been growing invasively on the world's coasts for more than a century.
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Affiliation(s)
- Soichiro Seki
- Division of Molecular Materials Science, Graduate School of Science, Osaka City University, Japan
| | - Yumiko Yamano
- Comprehensive Education and Research Center, Kobe Pharmaceutical University, Japan
| | - Naohiro Oka
- Bio-innovation Research Center (Naruto Campus), Tokushima University, Naruto, Japan
| | - Yasuhiro Kamei
- Spectrography and Bioimaging Facility, National Institute for Basic Biology, Okazaki, Japan
| | - Ritsuko Fujii
- Division of Molecular Materials Science, Graduate School of Science, Osaka City University, Japan.,Research Center for Artificial Photosynthesis (ReCAP), Osaka Metropolitan University, Japan
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19
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Maire J, Buerger P, Chan WY, Deore P, Dungan AM, Nitschke MR, van Oppen MJH. Effects of Ocean Warming on the Underexplored Members of the Coral Microbiome. Integr Comp Biol 2022; 62:1700-1709. [PMID: 35259253 PMCID: PMC9801979 DOI: 10.1093/icb/icac005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 03/01/2022] [Accepted: 03/05/2022] [Indexed: 01/05/2023] Open
Abstract
The climate crisis is one of the most significant threats to marine ecosystems. It is leading to severe increases in sea surface temperatures and in the frequency and magnitude of marine heatwaves. These changing conditions are directly impacting coral reef ecosystems, which are among the most biodiverse ecosystems on Earth. Coral-associated symbionts are particularly affected because summer heatwaves cause coral bleaching-the loss of endosymbiotic microalgae (Symbiodiniaceae) from coral tissues, leading to coral starvation and death. Coral-associated Symbiodiniaceae and bacteria have been extensively studied in the context of climate change, especially in terms of community diversity and dynamics. However, data on other microorganisms and their response to climate change are scarce. Here, we review current knowledge on how increasing temperatures affect understudied coral-associated microorganisms such as archaea, fungi, viruses, and protists other than Symbiodiniaceae, as well as microbe-microbe interactions. We show that the coral-microbe symbiosis equilibrium is at risk under current and predicted future climate change and argue that coral reef conservation initiatives should include microbe-focused approaches.
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Affiliation(s)
| | - Patrick Buerger
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia,Applied BioSciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Wing Yan Chan
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Pranali Deore
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ashley M Dungan
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | | | - Madeleine J H van Oppen
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia,Australian Institute of Marine Science, Townsville, QLD 4810, Australia
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20
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Repetti SI, Iha C, Uthanumallian K, Jackson CJ, Chen Y, Chan CX, Verbruggen H. Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae. THE NEW PHYTOLOGIST 2022; 233:2144-2154. [PMID: 34923642 DOI: 10.1111/nph.17926] [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: 09/26/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
The genomic diversity underpinning high ecological and species diversity in the green algae (Chlorophyta) remains little known. Here, we aimed to track genome evolution in the Chlorophyta, focusing on loss and gain of homologous genes, and lineage-specific innovations of the core Chlorophyta. We generated a high-quality nuclear genome for pedinophyte YPF701, a sister lineage to others in the core Chlorophyta and incorporated this genome in a comparative analysis with 25 other genomes from diverse Viridiplantae taxa. The nuclear genome of pedinophyte YPF701 has an intermediate size and gene number between those of most prasinophytes and the remainder of the core Chlorophyta. Our results suggest positive selection for genome streamlining in the Pedinophyceae, independent from genome minimisation observed among prasinophyte lineages. Genome expansion was predicted along the branch leading to the UTC clade (classes Ulvophyceae, Trebouxiophyceae and Chlorophyceae) after divergence from their last common ancestor with pedinophytes, with genomic novelty implicated in a range of basic biological functions. Results emphasise multiple independent signals of genome minimisation within the Chlorophyta, as well as the genomic novelty arising before diversification in the UTC clade, which may underpin the success of this species-rich clade in a diversity of habitats.
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Affiliation(s)
- Sonja I Repetti
- School of BioSciences, University of Melbourne, Melbourne, Vic, 3010, Australia
| | - Cintia Iha
- School of BioSciences, University of Melbourne, Melbourne, Vic, 3010, Australia
| | | | | | - Yibi Chen
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Cheong Xin Chan
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, Vic, 3010, Australia
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21
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Bringloe TT, Zaparenkov D, Starko S, Grant WS, Vieira C, Kawai H, Hanyuda T, Filbee-Dexter K, Klimova A, Klochkova TA, Krause-Jensen D, Olesen B, Verbruggen H. Whole-genome sequencing reveals forgotten lineages and recurrent hybridizations within the kelp genus Alaria (Phaeophyceae). JOURNAL OF PHYCOLOGY 2021; 57:1721-1738. [PMID: 34510441 DOI: 10.1111/jpy.13212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/20/2021] [Accepted: 09/05/2021] [Indexed: 05/22/2023]
Abstract
The genomic era continues to revolutionize our understanding of the evolution of biodiversity. In phycology, emphasis remains on assembling nuclear and organellar genomes, leaving the full potential of genomic datasets to answer long-standing questions about the evolution of biodiversity largely unexplored. Here, we used whole-genome sequencing (WGS) datasets to survey species diversity in the kelp genus Alaria, compare phylogenetic signals across organellar and nuclear genomes, and specifically test whether phylogenies behave like trees or networks. Genomes were sequenced from across the global distribution of Alaria (including Alaria crassifolia, A. praelonga, A. crispa, A. marginata, and A. esculenta), representing over 550 GB of data and over 2.2 billion paired reads. Genomic datasets retrieved 3,814 and 4,536 single-nucleotide polymorphisms (SNPs) for mitochondrial and chloroplast genomes, respectively, and upwards of 148,542 high-quality nuclear SNPs. WGS revealed an Arctic lineage of Alaria, which we hypothesize represents the synonymized taxon A. grandifolia. The SNP datasets also revealed inconsistent topologies across genomic compartments, and hybridization (i.e., phylogenetic networks) between Pacific A. praelonga, A. crispa, and putative A. grandifolia, and between some lineages of the A. marginata complex. Our analysis demonstrates the potential for WGS data to advance our understanding of evolution and biodiversity beyond amplicon sequencing, and that hybridization is potentially an important mechanism contributing to novel lineages within Alaria. We also emphasize the importance of surveying phylogenetic signals across organellar and nuclear genomes, such that models of mixed ancestry become integrated into our evolutionary and taxonomic understanding.
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Affiliation(s)
- Trevor T Bringloe
- School of BioSciences, University of Melbourne, Parkville Campus, Parkville, Victoria, 3010, Australia
| | - Dani Zaparenkov
- School of BioSciences, University of Melbourne, Parkville Campus, Parkville, Victoria, 3010, Australia
| | - Samuel Starko
- Department of Biology, University of Victoria, Victoria, British Columbia, V8W 2Y2, Canada
| | - William Stewart Grant
- School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Juneau, Alaska, USA
| | - Christophe Vieira
- Kobe University Research Center for Inland Seas, Kobe University, Rokkodai, Nada, Kobe, Japan
| | - Hiroshi Kawai
- Kobe University Research Center for Inland Seas, Kobe University, Rokkodai, Nada, Kobe, Japan
| | - Takeaki Hanyuda
- Kobe University Research Center for Inland Seas, Kobe University, Rokkodai, Nada, Kobe, Japan
| | - Karen Filbee-Dexter
- ArcticNet, Québec Océan, Départment de biologie, Université Laval, Québec, Canada
- Institute of Marine Research, His, Norway
| | - Anna Klimova
- Kamchatka State Technical University, Petropavlovsk-Kamchatsky, 683003, Russia
| | - Tatyana A Klochkova
- Kamchatka State Technical University, Petropavlovsk-Kamchatsky, 683003, Russia
| | - Dorte Krause-Jensen
- Department of Bioscience, Aarhus University, Vejlsøvej 25, Silkeborg, DK-8600, Denmark
- Arctic Research Center, Aarhus University, Ole Worms Allé 1, Arhus C, DK-8000, Denmark
| | - Birgit Olesen
- Department of Biology, Aarhus University, Ole Worms Allé 1, Aarhus C, 8000, Denmark
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville Campus, Parkville, Victoria, 3010, Australia
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