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Voolstra CR, Raina JB, Dörr M, Cárdenas A, Pogoreutz C, Silveira CB, Mohamed AR, Bourne DG, Luo H, Amin SA, Peixoto RS. The coral microbiome in sickness, in health and in a changing world. Nat Rev Microbiol 2024; 22:460-475. [PMID: 38438489 DOI: 10.1038/s41579-024-01015-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2024] [Indexed: 03/06/2024]
Abstract
Stony corals, the engines and engineers of reef ecosystems, face unprecedented threats from anthropogenic environmental change. Corals are holobionts that comprise the cnidarian animal host and a diverse community of bacteria, archaea, viruses and eukaryotic microorganisms. Recent research shows that the bacterial microbiome has a pivotal role in coral biology. A healthy bacterial assemblage contributes to nutrient cycling and stress resilience, but pollution, overfishing and climate change can break down these symbiotic relationships, which results in disease, bleaching and, ultimately, coral death. Although progress has been made in characterizing the spatial-temporal diversity of bacteria, we are only beginning to appreciate their functional contribution. In this Review, we summarize the ecological and metabolic interactions between bacteria and other holobiont members, highlight the biotic and abiotic factors influencing the structure of bacterial communities and discuss the impact of climate change on these communities and their coral hosts. We emphasize how microbiome-based interventions can help to decipher key mechanisms underpinning coral health and promote reef resilience. Finally, we explore how recent technological developments may be harnessed to address some of the most pressing challenges in coral microbiology, providing a road map for future research in this field.
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Affiliation(s)
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia.
| | - Melanie Dörr
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Anny Cárdenas
- Department of Biology, American University, Washington, DC, USA
| | - Claudia Pogoreutz
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, Perpignan, France
| | | | - Amin R Mohamed
- Marine Microbiomics Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - David G Bourne
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Haiwei Luo
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, State Key Laboratory of Agrobiotechnology and Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Shady A Amin
- Marine Microbiomics Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Raquel S Peixoto
- Red Sea Research Center (RSRC) and Computational Biology Research Center (CBRC), Biological, Environmental Sciences, and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Kang W, Mu L, Hu X. Marine Colloids Boost Nitrogen Fixation in Trichodesmium erythraeum by Photoelectrophy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:9236-9249. [PMID: 38748855 DOI: 10.1021/acs.est.4c01849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Nitrogen fixation by the diazotrophic cyanobacterium Trichodesmium contributes up to 50% of the bioavailable nitrogen in the ocean. N2 fixation by Trichodesmium is limited by the availability of nutrients, such as iron (Fe) and phosphorus (P). Although colloids are ubiquitous in the ocean, the effects of Fe limitation on nitrogen fixation by marine colloids (MC) and the related mechanisms are largely unexplored. In this study, we found that MC exhibit photoelectrochemical properties that boost nitrogen fixation by photoelectrophy in Trichodesmium erythraeum. MC efficiently promote photosynthesis in T. erythraeum, thus enhancing its growth. Photoexcited electrons from MC are directly transferred to the photosynthetic electron transport chain and contribute to nitrogen fixation and ammonia assimilation. Transcriptomic analysis revealed that MC significantly upregulates genes related to the electron transport chain, photosystem, and photosynthesis, which is consistent with elevated photosynthetic capacities (e.g., Fv/Fm and carboxysomes). As a result, MC increase the N2 fixation rate by 67.5-89.3%. Our findings highlight a proof-of-concept electron transfer pathway by which MC boost nitrogen fixation, broadening our knowledge on the role of ubiquitous colloids in marine nitrogen biogeochemistry.
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Affiliation(s)
- Weilu Kang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Carbon Neutrality Interdisciplinary Science Centre, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Li Mu
- Tianjin Key Laboratory of Agro-Environment and Product Safety, Key Laboratory for Environmental Factors Controlling Agro-Product Quality Safety (Ministry of Agriculture and Rural Affairs), Institute of Agro-Environmental Protection, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Carbon Neutrality Interdisciplinary Science Centre, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
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Kuhlisch C, Shemi A, Barak-Gavish N, Schatz D, Vardi A. Algal blooms in the ocean: hot spots for chemically mediated microbial interactions. Nat Rev Microbiol 2024; 22:138-154. [PMID: 37833328 DOI: 10.1038/s41579-023-00975-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2023] [Indexed: 10/15/2023]
Abstract
The cycling of major nutrients in the ocean is affected by large-scale phytoplankton blooms, which are hot spots of microbial life. Diverse microbial interactions regulate bloom dynamics. At the single-cell level, interactions between microorganisms are mediated by small molecules in the chemical crosstalk that determines the type of interaction, ranging from mutualism to pathogenicity. Algae interact with viruses, bacteria, parasites, grazers and other algae to modulate algal cell fate, and these interactions are dependent on the environmental context. Recent advances in mass spectrometry and single-cell technologies have led to the discovery of a growing number of infochemicals - metabolites that convey information - revealing the ability of algal cells to govern biotic interactions in the ocean. The diversity of infochemicals seems to account for the specificity in cellular response during microbial communication. Given the immense impact of algal blooms on biogeochemical cycles and climate regulation, a major challenge is to elucidate how microscale interactions control the fate of carbon and the recycling of major elements in the ocean. In this Review, we discuss microbial interactions and the role of infochemicals in algal blooms. We further explore factors that can impact microbial interactions and the available tools to decipher them in the natural environment.
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Affiliation(s)
- Constanze Kuhlisch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Adva Shemi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Barak-Gavish
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
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Matthews JL, Hoch L, Raina JB, Pablo M, Hughes DJ, Camp EF, Seymour JR, Ralph PJ, Suggett DJ, Herdean A. Symbiodiniaceae photophysiology and stress resilience is enhanced by microbial associations. Sci Rep 2023; 13:20724. [PMID: 38007500 PMCID: PMC10676399 DOI: 10.1038/s41598-023-48020-9] [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: 06/01/2023] [Accepted: 11/21/2023] [Indexed: 11/27/2023] Open
Abstract
Symbiodiniaceae form associations with extra- and intracellular bacterial symbionts, both in culture and in symbiosis with corals. Bacterial associates can regulate Symbiodiniaceae fitness in terms of growth, calcification and photophysiology. However, the influence of these bacteria on interactive stressors, such as temperature and light, which are known to influence Symbiodiniaceae physiology, remains unclear. Here, we examined the photophysiological response of two Symbiodiniaceae species (Symbiodinium microadriaticum and Breviolum minutum) cultured under acute temperature and light stress with specific bacterial partners from their microbiome (Labrenzia (Roseibium) alexandrii, Marinobacter adhaerens or Muricauda aquimarina). Overall, bacterial presence positively impacted Symbiodiniaceae core photosynthetic health (photosystem II [PSII] quantum yield) and photoprotective capacity (non-photochemical quenching; NPQ) compared to cultures with all extracellular bacteria removed, although specific benefits were variable across Symbiodiniaceae genera and growth phase. Symbiodiniaceae co-cultured with M. aquimarina displayed an inverse NPQ response under high temperatures and light, and those with L. alexandrii demonstrated a lowered threshold for induction of NPQ, potentially through the provision of antioxidant compounds such as zeaxanthin (produced by Muricauda spp.) and dimethylsulfoniopropionate (DMSP; produced by this strain of L. alexandrii). Our co-culture approach empirically demonstrates the benefits bacteria can deliver to Symbiodiniaceae photochemical performance, providing evidence that bacterial associates can play important functional roles for Symbiodiniaceae.
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Affiliation(s)
- Jennifer L Matthews
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia.
| | - Lilian Hoch
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Marine Pablo
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
- Sorbonne University, Paris, France
| | - David J Hughes
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
- Australian Institute of Marine Sciences, Townsville, QLD, Australia
| | - Emma F Camp
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Peter J Ralph
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - David J Suggett
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
- KAUST Reefscape Restoration Initiative (KRRI) and Red Sea Reseach Centre (RSRC), King Abdullah University of Science & Technology, 23955, Thuwal, Saudi Arabia
| | - Andrei Herdean
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
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Villela H, Modolon F, Schultz J, Delgadillo-Ordoñez N, Carvalho S, Soriano AU, Peixoto RS. Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host. Sci Rep 2023; 13:12273. [PMID: 37507453 PMCID: PMC10382565 DOI: 10.1038/s41598-023-38512-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
Here we report the oil degradation genetic potential of six oil-degrading bacteria (ODB), previously used as a bioremediation consortium, isolated from the hydrocoral Millepora alcicornis and seawater. The strains were identified as Halomonas sp. (LC_1), Cobetia sp. (LC_6), Pseudoalteromonas shioyasakiensis (LC_2), Halopseudomonas aestusnigri (LC_3), Shewanella algae (LC_4), and Brucella intermedia (LC_5). The taxonomic identification differed from that of the original paper when we used whole genome gene markers instead of just 16S rRNA gene. Genes responsible for the degradation of aromatic hydrocarbons and n-alkanes were found in all genomes, although different (and complementary) steps of the metabolic pathways were unique to each strain. Genes for naphthalene and toluene degradation were found in various strains. We annotated quinate degradation genes in LC_6, while LC_3 and LC_5 presented genes for biosurfactant and rhamnolipid biosynthesis. We also annotated genes related to beneficial mechanisms for corals, such as genes involved in nitrogen and DMSP metabolism, cobalamin biosynthesis and antimicrobial compounds production. Our findings reinforce the importance of using bacterial consortia for bioremediation approaches instead of single strains, due to their complementary genomic arsenals. We also propose a genome-based framework to select complementary ODB that can provide additional benefits to coral health.
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Affiliation(s)
- Helena Villela
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Flúvio Modolon
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Júnia Schultz
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Computational Biology Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Nathalia Delgadillo-Ordoñez
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Marine Science and Bioscience Programs, Biological, Environmental and Engineering Sciences Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | | | - Raquel Silva Peixoto
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
- Computational Biology Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
- Marine Science and Bioscience Programs, Biological, Environmental and Engineering Sciences Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
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Tong H, Zhang F, Sun J, McIlroy SE, Zhang W, Wang Y, Huang H, Zhou G, Qian PY. Meta-organism gene expression reveals that the impact of nitrate enrichment on coral larvae is mediated by their associated Symbiodiniaceae and prokaryotic assemblages. MICROBIOME 2023; 11:89. [PMID: 37101227 PMCID: PMC10131396 DOI: 10.1186/s40168-023-01495-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/16/2023] [Indexed: 05/12/2023]
Abstract
BACKGROUND Coral meta-organisms consist of the coral, and its associated Symbiodiniaceae (dinoflagellate algae), bacteria, and other microbes. Corals can acquire photosynthates from Symbiodiniaceae, whilst Symbiodiniaceae uses metabolites from corals. Prokaryotic microbes provide Symbiodiniaceae with nutrients and support the resilience of corals as meta-organisms. Eutrophication is a major cause of coral reef degradation; however, its effects on the transcriptomic response of coral meta-organisms remain unclear, particularly for prokaryotic microbes associated with corals in the larval stage. To understand acclimation of the coral meta-organism to elevated nitrate conditions, we analyzed the physiological and transcriptomic responses of Pocillopora damicornis larvae, an ecologically important scleractinian coral, after 5 days of exposure to elevated nitrate levels (5, 10, 20, and 40 µM). RESULTS The major differentially expressed transcripts in coral, Symbiodiniaceae, and prokaryotic microbes included those related to development, stress response, and transport. The development of Symbiodiniaceae was not affected in the 5 and 20 µM groups but was downregulated in the 10 and 40 µM groups. In contrast, prokaryotic microbe development was upregulated in the 10 and 40 µM groups and downregulated in the 5 and 20 µM groups. Meanwhile, coral larval development was less downregulated in the 10 and 40 µM groups than in the 5 and 20 µM groups. In addition, multiple larval, Symbiodiniaceae, and prokaryotic transcripts were significantly correlated with each other. The core transcripts in correlation networks were related to development, nutrient metabolism, and transport. A generalized linear mixed model, using least absolute shrinkage and selection operator, demonstrated that the Symbiodiniaceae could both benefit and cost coral larval development. Furthermore, the most significantly correlated prokaryotic transcripts maintained negative correlations with the physiological functions of Symbiodiniaceae. CONCLUSIONS Results suggested that Symbiodiniaceae tended to retain more nutrients under elevated nitrate concentrations, thereby shifting the coral-algal association from mutualism towards parasitism. Prokaryotic microbes provided Symbiodiniaceae with essential nutrients and may control Symbiodiniaceae growth through competition, whereby prokaryotes can also restore coral larval development inhibited by Symbiodiniaceae overgrowth. Video Abstract.
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Affiliation(s)
- Haoya Tong
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Nansha, Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Fang Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institute of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Hainan Key Laboratory of Tropical Marine Biotechnology, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China
| | - Jin Sun
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Shelby E. McIlroy
- The Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Weipeng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yan Wang
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Hui Huang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institute of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Hainan Key Laboratory of Tropical Marine Biotechnology, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China
| | - Guowei Zhou
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institute of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Hainan Key Laboratory of Tropical Marine Biotechnology, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Nansha, Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Hainan Key Laboratory of Tropical Marine Biotechnology, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China
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Chemotaxis increases metabolic exchanges between marine picophytoplankton and heterotrophic bacteria. Nat Microbiol 2023; 8:510-521. [PMID: 36759754 DOI: 10.1038/s41564-023-01327-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 01/09/2023] [Indexed: 02/11/2023]
Abstract
Behaviours such as chemotaxis can facilitate metabolic exchanges between phytoplankton and heterotrophic bacteria, which ultimately regulate oceanic productivity and biogeochemistry. However, numerically dominant picophytoplankton have been considered too small to be detected by chemotactic bacteria, implying that cell-cell interactions might not be possible between some of the most abundant organisms in the ocean. Here we examined how bacterial behaviour influences metabolic exchanges at the single-cell level between the ubiquitous picophytoplankton Synechococcus and the heterotrophic bacterium Marinobacter adhaerens, using bacterial mutants deficient in motility and chemotaxis. Stable-isotope tracking revealed that chemotaxis increased nitrogen and carbon uptake of both partners by up to 4.4-fold. A mathematical model following thousands of cells confirmed that short periods of exposure to small but nutrient-rich microenvironments surrounding Synechococcus cells provide a considerable competitive advantage to chemotactic bacteria. These findings reveal that transient interactions mediated by chemotaxis can underpin metabolic relationships among the ocean's most abundant microorganisms.
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Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle. THE ISME JOURNAL 2022; 16:1883-1895. [PMID: 35444262 PMCID: PMC9296628 DOI: 10.1038/s41396-022-01226-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/23/2022] [Accepted: 03/14/2022] [Indexed: 12/11/2022]
Abstract
Endozoicomonas are prevalent, abundant bacterial associates of marine animals, including corals. Their role in holobiont health and functioning, however, remains poorly understood. To identify potential interactions within the coral holobiont, we characterized the novel isolate Endozoicomonas marisrubri sp. nov. 6c and assessed its transcriptomic and proteomic response to tissue extracts of its native host, the Red Sea coral Acropora humilis. We show that coral tissue extracts stimulated differential expression of genes putatively involved in symbiosis establishment via the modulation of the host immune response by E. marisrubri 6c, such as genes for flagellar assembly, ankyrins, ephrins, and serpins. Proteome analyses revealed that E. marisrubri 6c upregulated vitamin B1 and B6 biosynthesis and glycolytic processes in response to holobiont cues. Our results suggest that the priming of Endozoicomonas for a symbiotic lifestyle involves the modulation of host immunity and the exchange of essential metabolites with other holobiont members. Consequently, Endozoicomonas may play an important role in holobiont nutrient cycling and may therefore contribute to coral health, acclimatization, and adaptation.
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Becquart C, Stulz R, Thomen A, Dost M, Najafinobar N, Dahlén A, Andersson S, Ewing AG, Kurczy ME. Intracellular Absolute Quantification of Oligonucleotide Therapeutics by NanoSIMS. Anal Chem 2022; 94:10549-10556. [PMID: 35830231 DOI: 10.1021/acs.analchem.2c02111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antisense oligonucleotide (ASO)-based therapeutics hold great potential for the treatment of a variety of diseases. Therefore, a better understanding of cellular delivery, uptake, and trafficking mechanisms of ASOs is highly important for early-stage drug discovery. In particular, understanding the biodistribution and quantifying the abundance of ASOs at the subcellular level are needed to fully characterize their activity. Here, we used a combination of electron microscopy and NanoSIMS to assess the subcellular concentrations of a 34S-labeled GalNAc-ASO and a naked ASO in the organelles of primary human hepatocytes. We first cross-validated the method by including a 127I-labeled ASO, finding that the absolute concentration of the lysosomal ASO using two independent labeling strategies gave matching results, demonstrating the strength of our approach. This work also describes the preparation of external standards for absolute quantification by NanoSIMS. For both the 34S and 127I approaches used for our quantification methodology, we established the limit of detection (5 and 2 μM, respectively) and the lower limit of quantification (14 and 5 μM, respectively).
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Affiliation(s)
- Cécile Becquart
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Cardiovascular, Renal and Metabolism CVRM, BioPharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden.,Department of Chemistry and Molecular Biology, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Rouven Stulz
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 43138 Gothenburg, Sweden
| | | | - Maryam Dost
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Cardiovascular, Renal and Metabolism CVRM, BioPharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden
| | - Neda Najafinobar
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden
| | - Anders Dahlén
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 43138 Gothenburg, Sweden
| | - Shalini Andersson
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 43138 Gothenburg, Sweden
| | - Andrew G Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Michael E Kurczy
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Cardiovascular, Renal and Metabolism CVRM, BioPharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden
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Roik A, Reverter M, Pogoreutz C. A roadmap to understanding diversity and function of coral reef-associated fungi. FEMS Microbiol Rev 2022; 46:6615459. [PMID: 35746877 PMCID: PMC9629503 DOI: 10.1093/femsre/fuac028] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/01/2022] [Accepted: 06/14/2022] [Indexed: 01/09/2023] Open
Abstract
Tropical coral reefs are hotspots of marine productivity, owing to the association of reef-building corals with endosymbiotic algae and metabolically diverse bacterial communities. However, the functional importance of fungi, well-known for their contribution to shaping terrestrial ecosystems and global nutrient cycles, remains underexplored on coral reefs. We here conceptualize how fungal functional traits may have facilitated the spread, diversification, and ecological adaptation of marine fungi on coral reefs. We propose that functions of reef-associated fungi may be diverse and go beyond their hitherto described roles of pathogens and bioeroders, including but not limited to reef-scale biogeochemical cycles and the structuring of coral-associated and environmental microbiomes via chemical mediation. Recent technological and conceptual advances will allow the elucidation of the physiological, ecological, and chemical contributions of understudied marine fungi to coral holobiont and reef ecosystem functioning and health and may help provide an outlook for reef management actions.
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Affiliation(s)
- Anna Roik
- Corresponding author: Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstrasse 231, D-26129 Oldenburg, Germany. E-mail:
| | - Miriam Reverter
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Wilhelmshaven, 26046, Germany,School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, United Kingdom
| | - Claudia Pogoreutz
- Corresponding author: Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Federale de Lausanne (EPFL), 1015 Lausanne, Switzerland.,
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Abstract
Improving the availability of representative isolates from the coral microbiome is essential for investigating symbiotic mechanisms and applying beneficial microorganisms to improve coral health. However, few studies have explored the diversity of bacteria which can be isolated from a single species. Here, we isolated a total of 395 bacterial strains affiliated with 49 families across nine classes from the coral Pocillopora damicornis. Identification results showed that most of the strains represent potential novel bacterial species or genera. We also sequenced and assembled the genomes of 118 of these isolates, and then the putative functions of these isolates were identified based on genetic signatures derived from the genomes and this information was combined with isolate-specific phenotypic data. Genomic information derived from the isolates identified putative functions including nitrification and denitrification, dimethylsulfoniopropionate transformation, and supply of fixed carbon, amino acids, and B vitamins which may support their eukaryotic partners. Furthermore, the isolates contained genes associated with chemotaxis, biofilm formation, quorum sensing, membrane transport, signal transduction, and eukaryote-like repeat-containing and cell-cell attachment proteins, all of which potentially help the bacterium establish association with the coral host. Our work expands on the existing culture collection of coral-associated bacteria and provides important information on the metabolic potential of these isolates which can be used to refine understanding of the role of bacteria in coral health and are now available to be applied to novel strategies aimed at improving coral resilience through microbiome manipulation. IMPORTANCE Microbes underpin the health of corals which are the building blocks of diverse and productive reef ecosystems. Studying the culturable fraction of coral-associated bacteria has received less attention in recent times than using culture-independent molecular methods. However, the genomic and phenotypic characterization of isolated strains allows assessment of their functional role in underpinning coral health and identification of beneficial microbes for microbiome manipulation. Here, we isolated 395 bacterial strains from tissues of Pocillopora damicornis with many representing potentially novel taxa and therefore providing a significant contribution to coral microbiology through greatly enlarging the existing cultured coral-associated bacterial bank. Through analysis of the genomes obtained in this study for the coral-associated bacteria and coral host, we elucidate putative metabolic linkages and symbiotic establishment. The results of this study will help to elucidate the role of specific isolates in coral health and provide beneficial microbes for efforts aimed at improving coral health.
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12
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Shaw DK, Sekar J, Ramalingam PV. Recent insights into oceanic dimethylsulfoniopropionate biosynthesis and catabolism. Environ Microbiol 2022; 24:2669-2700. [PMID: 35611751 DOI: 10.1111/1462-2920.16045] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 11/29/2022]
Abstract
Dimethylsulfoniopropionate (DMSP), a globally important organosulfur compound is produced in prodigious amounts (2.0 Pg sulfur) annually in the marine environment by phytoplankton, macroalgae, heterotrophic bacteria, some corals and certain higher plants. It is an important marine osmolyte and a major precursor molecule for the production of climate-active volatile gas dimethyl sulfide (DMS). DMSP synthesis take place via three pathways: a transamination 'pathway-' in some marine bacteria and algae, a Met-methylation 'pathway-' in angiosperms and bacteria and a decarboxylation 'pathway-' in the dinoflagellate, Crypthecodinium. The enzymes DSYB and TpMMT are involved in the DMSP biosynthesis in eukaryotes while marine heterotrophic bacteria engage key enzymes such as DsyB and MmtN. Several marine bacterial communities import DMSP and degrade it via cleavage or demethylation pathways or oxidation pathway, thereby generating DMS, methanethiol, and dimethylsulfoxonium propionate, respectively. DMSP is cleaved through diverse DMSP lyase enzymes in bacteria and via Alma1 enzyme in phytoplankton. The demethylation pathway involves four different enzymes, namely DmdA, DmdB, DmdC and DmdD/AcuH. However, enzymes involved in the oxidation pathway have not been yet identified. We reviewed the recent advances on the synthesis and catabolism of DMSP and enzymes that are involved in these processes.
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Affiliation(s)
- Deepak Kumar Shaw
- Microbiology Lab, Department of Biotechnology, M. S. Swaminathan Research Foundation, Taramani, Chennai, 600113, Tamil Nadu, India
| | - Jegan Sekar
- Microbiology Lab, Department of Biotechnology, M. S. Swaminathan Research Foundation, Taramani, Chennai, 600113, Tamil Nadu, India
| | - Prabavathy Vaiyapuri Ramalingam
- Microbiology Lab, Department of Biotechnology, M. S. Swaminathan Research Foundation, Taramani, Chennai, 600113, Tamil Nadu, India
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13
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Moran MA, Kujawinski EB, Schroer WF, Amin SA, Bates NR, Bertrand EM, Braakman R, Brown CT, Covert MW, Doney SC, Dyhrman ST, Edison AS, Eren AM, Levine NM, Li L, Ross AC, Saito MA, Santoro AE, Segrè D, Shade A, Sullivan MB, Vardi A. Microbial metabolites in the marine carbon cycle. Nat Microbiol 2022; 7:508-523. [PMID: 35365785 DOI: 10.1038/s41564-022-01090-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/23/2022] [Indexed: 01/08/2023]
Abstract
One-quarter of photosynthesis-derived carbon on Earth rapidly cycles through a set of short-lived seawater metabolites that are generated from the activities of marine phytoplankton, bacteria, grazers and viruses. Here we discuss the sources of microbial metabolites in the surface ocean, their roles in ecology and biogeochemistry, and approaches that can be used to analyse them from chemistry, biology, modelling and data science. Although microbial-derived metabolites account for only a minor fraction of the total reservoir of marine dissolved organic carbon, their flux and fate underpins the central role of the ocean in sustaining life on Earth.
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Affiliation(s)
- Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, USA.
| | - Elizabeth B Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - William F Schroer
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Shady A Amin
- Division of Science, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Nicholas R Bates
- Bermuda Institute of Ocean Sciences, St George's, Bermuda.,School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Erin M Bertrand
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Rogier Braakman
- Departments of Earth, Atmospheric and Planetary Sciences, and Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - C Titus Brown
- Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Scott C Doney
- Department of Environmental Sciences, University of Virginia, Charlottesville, VA, USA
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, USA.,Department of Earth and Environmental Science, Columbia University, Palisades, NY, USA
| | - Arthur S Edison
- Departments of Biochemistry and Genetics, Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - A Murat Eren
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA.,Helmholtz-Institute for Functional Marine Biodiversity (HIFMB), University of Oldenburg, Oldenburg, Germany
| | - Naomi M Levine
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada
| | - Mak A Saito
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Alyson E Santoro
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Daniel Segrè
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA, USA
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, and Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
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14
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Thatcher C, Høj L, Bourne DG. Probiotics for coral aquaculture: challenges and considerations. Curr Opin Biotechnol 2021; 73:380-386. [PMID: 34749049 DOI: 10.1016/j.copbio.2021.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/18/2021] [Accepted: 09/21/2021] [Indexed: 01/12/2023]
Abstract
Globally, coral reefs are under pressure from climate change, with concerning declines in coral abundance observed due to increasing cumulative impacts. Active intervention measures that mitigate the declines are increasingly being applied to buy time for coral reefs as the world transitions to a low-carbon economy. One such mitigation strategy is coral restoration based on large-scale coral aquaculture to provide stock for reseeding reefs, with the added potential of selecting corals that better tolerate environmental stress. Application of probiotics during production and deployment, to modulate the naturally occurring bacteria associated with corals, may confer health benefits such as disease resistance, increased environmental tolerance or improved coral nutrition. Here, we briefly describe coral associated bacteria and their role in the coral holobiont, identify probiotics traits potentially beneficial to coral, and discuss current research directions required to develop, test and verify the feasibility for probiotics to improve coral aquaculture at industrial scales.
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Affiliation(s)
- Callaway Thatcher
- College of Science and Engineering, James Cook University, 1 Angus Smith Drive, Douglas, QLD 4814, Australia; Australian Institute of Marine Science, PMB 3 Townsville MC, Townsville, QLD 4810, Australia; AIMS@JCU, James Cook University, DB17-148, Townsville, QLD 4811, Australia
| | - Lone Høj
- Australian Institute of Marine Science, PMB 3 Townsville MC, Townsville, QLD 4810, Australia; AIMS@JCU, James Cook University, DB17-148, Townsville, QLD 4811, Australia
| | - David G Bourne
- College of Science and Engineering, James Cook University, 1 Angus Smith Drive, Douglas, QLD 4814, Australia; Australian Institute of Marine Science, PMB 3 Townsville MC, Townsville, QLD 4810, Australia; AIMS@JCU, James Cook University, DB17-148, Townsville, QLD 4811, Australia.
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15
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Shemi A, Alcolombri U, Schatz D, Farstey V, Vincent F, Rotkopf R, Ben-Dor S, Frada MJ, Tawfik DS, Vardi A. Dimethyl sulfide mediates microbial predator-prey interactions between zooplankton and algae in the ocean. Nat Microbiol 2021; 6:1357-1366. [PMID: 34697459 DOI: 10.1038/s41564-021-00971-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 09/01/2021] [Indexed: 12/11/2022]
Abstract
Phytoplankton are key components of the oceanic carbon and sulfur cycles1. During bloom events, some species can emit large amounts of the organosulfur volatile dimethyl sulfide (DMS) into the ocean and consequently the atmosphere, where it can modulate aerosol formation and affect climate2,3. In aquatic environments, DMS plays an important role as a chemical signal mediating diverse trophic interactions. Yet, its role in microbial predator-prey interactions remains elusive with contradicting evidence for its role in either algal chemical defence or in the chemo-attraction of grazers to prey cells4,5. Here we investigated the signalling role of DMS during zooplankton-algae interactions by genetic and biochemical manipulation of the algal DMS-generating enzyme dimethylsulfoniopropionate lyase (DL) in the bloom-forming alga Emiliania huxleyi6. We inhibited DL activity in E. huxleyi cells in vivo using the selective DL-inhibitor 2-bromo-3-(dimethylsulfonio)-propionate7 and overexpressed the DL-encoding gene in the model diatom Thalassiosira pseudonana. We showed that algal DL activity did not serve as an anti-grazing chemical defence but paradoxically enhanced predation by the grazer Oxyrrhis marina and other microzooplankton and mesozooplankton, including ciliates and copepods. Consumption of algal prey with induced DL activity also promoted O. marina growth. Overall, our results demonstrate that DMS-mediated grazing may be ecologically important and prevalent during prey-predator dynamics in aquatic ecosystems. The role of algal DMS revealed here, acting as an eat-me signal for grazers, raises fundamental questions regarding the retention of its biosynthetic enzyme through the evolution of dominant bloom-forming phytoplankton in the ocean.
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Affiliation(s)
- Adva Shemi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Uria Alcolombri
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.,Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Viviana Farstey
- The Inter-University Institute for Marine Sciences, Eilat, Israel
| | - Flora Vincent
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Rotkopf
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Miguel J Frada
- The Inter-University Institute for Marine Sciences, Eilat, Israel.,Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
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16
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Maire J, Blackall LL, van Oppen MJH. Intracellular Bacterial Symbionts in Corals: Challenges and Future Directions. Microorganisms 2021; 9:2209. [PMID: 34835335 PMCID: PMC8619543 DOI: 10.3390/microorganisms9112209] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 02/07/2023] Open
Abstract
Corals are the main primary producers of coral reefs and build the three-dimensional reef structure that provides habitat to more than 25% of all marine eukaryotes. They harbor a complex consortium of microorganisms, including bacteria, archaea, fungi, viruses, and protists, which they rely on for their survival. The symbiosis between corals and bacteria is poorly studied, and their symbiotic relationships with intracellular bacteria are only just beginning to be acknowledged. In this review, we emphasize the importance of characterizing intracellular bacteria associated with corals and explore how successful approaches used to study such microorganisms in other systems could be adapted for research on corals. We propose a framework for the description, identification, and functional characterization of coral-associated intracellular bacterial symbionts. Finally, we highlight the possible value of intracellular bacteria in microbiome manipulation and mitigating coral bleaching.
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Affiliation(s)
- Justin Maire
- School of Biosciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (L.L.B.); (M.J.H.v.O.)
| | - Linda L. Blackall
- School of Biosciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (L.L.B.); (M.J.H.v.O.)
| | - Madeleine J. H. van Oppen
- School of Biosciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (L.L.B.); (M.J.H.v.O.)
- Australian Institute of Marine Science, Townsville, QLD 4810, Australia
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17
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Decelle J, Veronesi G, LeKieffre C, Gallet B, Chevalier F, Stryhanyuk H, Marro S, Ravanel S, Tucoulou R, Schieber N, Finazzi G, Schwab Y, Musat N. Subcellular architecture and metabolic connection in the planktonic photosymbiosis between Collodaria (radiolarians) and their microalgae. Environ Microbiol 2021; 23:6569-6586. [PMID: 34499794 DOI: 10.1111/1462-2920.15766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/27/2021] [Accepted: 09/05/2021] [Indexed: 11/28/2022]
Abstract
Photosymbiosis is widespread and ecologically important in the oceanic plankton but remains poorly studied. Here, we used multimodal subcellular imaging to investigate the photosymbiosis between colonial Collodaria and their microalga dinoflagellate (Brandtodinium). We showed that this symbiosis is very dynamic whereby symbionts interact with different host cells via extracellular vesicles within the colony. 3D electron microscopy revealed that the photosynthetic apparatus of the microalgae was more voluminous in symbiosis compared to free-living while the mitochondria volume was similar. Stable isotope probing coupled with NanoSIMS showed that carbon and nitrogen were stored in the symbiotic microalga in starch granules and purine crystals respectively. Nitrogen was also allocated to the algal nucleolus. In the host, low 13 C transfer was detected in the Golgi. Metal mapping revealed that intracellular iron concentration was similar in free-living and symbiotic microalgae (c. 40 ppm) and twofold higher in the host, whereas copper concentration increased in symbionts and was detected in the host cell and extracellular vesicles. Sulfur concentration was around two times higher in symbionts (chromatin and pyrenoid) than their host. This study improves our understanding on the functioning of this oceanic photosymbiosis and paves the way for more studies to further assess its biogeochemical significance.
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Affiliation(s)
- Johan Decelle
- Univ. Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, Grenoble, France.,Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Giulia Veronesi
- CNRS, Laboratoire de Chimie et Biologie des Métaux (LCBM), UMR 5249 CNRS-CEA-UGA, F-38054, Grenoble, France.,CEA, LCBM, F-38054, Grenoble, France.,Université Grenoble Alpes, LCBM, F-38054, Grenoble, France.,ESRF, The European Synchrotron, 71, Avenue des Martyrs, 38043, Grenoble, France
| | | | - Benoit Gallet
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France
| | - Fabien Chevalier
- Univ. Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, Grenoble, France
| | - Hryhoriy Stryhanyuk
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Sophie Marro
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'Océanographie de Villefranche (LOV), UMR 7093, Observatoire Océanologique, 06230, Villefranche-sur-Mer, France
| | - Stéphane Ravanel
- Univ. Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, Grenoble, France
| | - Rémi Tucoulou
- ESRF, The European Synchrotron, 71, Avenue des Martyrs, 38043, Grenoble, France
| | - Nicole Schieber
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany
| | - Giovanni Finazzi
- Univ. Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, Grenoble, France
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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18
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Sheraz S, Wan Y, Venter E, Verma SK, Xiong Q, Waites J, Connorton JM, Shewry PR, Moore KL, Balk J. Subcellular dynamics studies of iron reveal how tissue-specific distribution patterns are established in developing wheat grains. THE NEW PHYTOLOGIST 2021; 231:1644-1657. [PMID: 33914919 DOI: 10.1111/nph.17440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/14/2021] [Indexed: 06/12/2023]
Abstract
Understanding the mechanisms of iron trafficking in plants is key to enhancing the nutritional quality of crops. Because it is difficult to image iron in transit, we currently have an incomplete picture of the route(s) of iron translocation in developing seeds and how the tissue-specific distribution is established. We have used a novel approach, combining iron-57 (57 Fe) isotope labelling and nanoscale secondary ion mass spectrometry (NanoSIMS), to visualize iron translocation between tissues and within cells in immature wheat grain, Triticum aestivum. This enabled us to track the main route of iron transport from maternal tissues to the embryo through the different cell types. Further evidence for this route was provided by genetically diverting iron into storage vacuoles, with confirmation provided by histological staining and transmission electron microscopy energy dispersive X-ray spectroscopy (TEM-EDS). Almost all iron in both control and transgenic grains was found in intracellular bodies, indicating symplastic rather than apoplastic transport. Furthermore, a new type of iron body, highly enriched in 57 Fe, was observed in aleurone cells and may represent iron being delivered to phytate globoids. Correlation of the 57 Fe enrichment profiles obtained by NanoSIMS with tissue-specific gene expression provides an updated model of iron homeostasis in cereal grains with relevance for future biofortification strategies.
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Affiliation(s)
- Sadia Sheraz
- School of Materials and Photon Science Institute, University of Manchester, Manchester, M13 9PL, UK
| | - Yongfang Wan
- Department of Plant Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Eudri Venter
- Bioimaging facility, Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Shailender K Verma
- Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK
| | - Qing Xiong
- Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK
| | - Joshua Waites
- Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - James M Connorton
- Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Peter R Shewry
- Department of Plant Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Katie L Moore
- School of Materials and Photon Science Institute, University of Manchester, Manchester, M13 9PL, UK
| | - Janneke Balk
- Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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19
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Santoro EP, Borges RM, Espinoza JL, Freire M, Messias CSMA, Villela HDM, Pereira LM, Vilela CLS, Rosado JG, Cardoso PM, Rosado PM, Assis JM, Duarte GAS, Perna G, Rosado AS, Macrae A, Dupont CL, Nelson KE, Sweet MJ, Voolstra CR, Peixoto RS. Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality. SCIENCE ADVANCES 2021; 7:7/33/eabg3088. [PMID: 34389536 PMCID: PMC8363143 DOI: 10.1126/sciadv.abg3088] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 06/24/2021] [Indexed: 05/03/2023]
Abstract
Beneficial microorganisms for corals (BMCs) ameliorate environmental stress, but whether they can prevent mortality and the underlying host response mechanisms remains elusive. Here, we conducted omics analyses on the coral Mussismilia hispida exposed to bleaching conditions in a long-term mesocosm experiment and inoculated with a selected BMC consortium or a saline solution placebo. All corals were affected by heat stress, but the observed "post-heat stress disorder" was mitigated by BMCs, signified by patterns of dimethylsulfoniopropionate degradation, lipid maintenance, and coral host transcriptional reprogramming of cellular restructuration, repair, stress protection, and immune genes, concomitant with a 40% survival rate increase and stable photosynthetic performance by the endosymbiotic algae. This study provides insights into the responses that underlie probiotic host manipulation. We demonstrate that BMCs trigger a dynamic microbiome restructuring process that instigates genetic and metabolic alterations in the coral host that eventually mitigate coral bleaching and mortality.
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Affiliation(s)
- Erika P Santoro
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Ricardo M Borges
- Walter Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Josh L Espinoza
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, USA
- Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Marcelo Freire
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Infectious Diseases and Global Health, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Camila S M A Messias
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Helena D M Villela
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Leandro M Pereira
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Caren L S Vilela
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - João G Rosado
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Pedro M Cardoso
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Phillipe M Rosado
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Juliana M Assis
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gustavo A S Duarte
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gabriela Perna
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
| | - Alexandre S Rosado
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Andrew Macrae
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Christopher L Dupont
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, USA
| | - Karen E Nelson
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, USA
| | - Michael J Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, UK
| | - Christian R Voolstra
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
| | - Raquel S Peixoto
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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20
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Lin Q, Shang L, Wang X, Hu Z, Du H, Wang H. Different dimethylsulphoniopropionate-producing ability of dinoflagellates could affect the structure of their associated bacterial community. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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21
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Combining SIMS and mechanistic modelling to reveal nutrient kinetics in an algal-bacterial mutualism. PLoS One 2021; 16:e0251643. [PMID: 34014955 PMCID: PMC8136852 DOI: 10.1371/journal.pone.0251643] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/29/2021] [Indexed: 11/21/2022] Open
Abstract
Microbial communities are of considerable significance for biogeochemical processes, for the health of both animals and plants, and for biotechnological purposes. A key feature of microbial interactions is the exchange of nutrients between cells. Isotope labelling followed by analysis with secondary ion mass spectrometry (SIMS) can identify nutrient fluxes and heterogeneity of substrate utilisation on a single cell level. Here we present a novel approach that combines SIMS experiments with mechanistic modelling to reveal otherwise inaccessible nutrient kinetics. The method is applied to study the onset of a synthetic mutualistic partnership between a vitamin B12-dependent mutant of the alga Chlamydomonas reinhardtii and the B12-producing, heterotrophic bacterium Mesorhizobium japonicum, which is supported by algal photosynthesis. Results suggest that an initial pool of fixed carbon delays the onset of mutualistic cross-feeding; significantly, our approach allows the first quantification of this expected delay. Our method is widely applicable to other microbial systems, and will contribute to furthering a mechanistic understanding of microbial interactions.
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22
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Vallet M, Kaftan F, Grabe V, Ghaderiardakani F, Fenizia S, Svatoš A, Pohnert G, Wichard T. A new glance at the chemosphere of macroalgal-bacterial interactions: In situ profiling of metabolites in symbiosis by mass spectrometry. Beilstein J Org Chem 2021; 17:1313-1322. [PMID: 34136011 PMCID: PMC8182680 DOI: 10.3762/bjoc.17.91] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/28/2021] [Indexed: 12/15/2022] Open
Abstract
Symbiosis is a dominant form of life that has been observed numerous times in marine ecosystems. For example, macroalgae coexist with bacteria that produce factors that promote algal growth and morphogenesis. The green macroalga Ulva mutabilis (Chlorophyta) develops into a callus-like phenotype in the absence of its essential bacterial symbionts Roseovarius sp. MS2 and Maribacter sp. MS6. Spatially resolved studies are required to understand symbiont interactions at the microscale level. Therefore, we used mass spectrometry profiling and imaging techniques with high spatial resolution and sensitivity to gain a new perspective on the mutualistic interactions between bacteria and macroalgae. Using atmospheric pressure scanning microprobe matrix-assisted laser desorption/ionisation high-resolution mass spectrometry (AP-SMALDI-HRMS), low-molecular-weight polar compounds were identified by comparative metabolomics in the chemosphere of Ulva. Choline (2-hydroxy-N,N,N-trimethylethan-1-aminium) was only determined in the alga grown under axenic conditions, whereas ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid) was found in bacterial presence. Ectoine was used as a metabolic marker for localisation studies of Roseovarius sp. within the tripartite community because it was produced exclusively by these bacteria. By combining confocal laser scanning microscopy (cLSM) and AP-SMALDI-HRMS, we proved that Roseovarius sp. MS2 settled mainly in the rhizoidal zone (holdfast) of U. mutabilis. Our findings provide the fundament to decipher bacterial symbioses with multicellular hosts in aquatic ecosystems in an ecologically relevant context. As a versatile tool for microbiome research, the combined AP-SMALDI and cLSM imaging analysis with a resolution to level of a single bacterial cell can be easily applied to other microbial consortia and their hosts. The novelty of this contribution is the use of an in situ setup designed to avoid all types of external contamination and interferences while resolving spatial distributions of metabolites and identifying specific symbiotic bacteria.
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Affiliation(s)
- Marine Vallet
- Research Group Phytoplankton Community Interactions, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Filip Kaftan
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Veit Grabe
- Research Group Olfactory Coding, Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Fatemeh Ghaderiardakani
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Germany
| | - Simona Fenizia
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Germany.,Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Aleš Svatoš
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Georg Pohnert
- Research Group Phytoplankton Community Interactions, Max Planck Institute for Chemical Ecology, Jena, Germany.,Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Germany.,Microverse Cluster, Friedrich Schiller University Jena, Germany
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Germany
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23
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Müller E, von Gunten U, Bouchet S, Droz B, Winkel LHE. Reaction of DMS and HOBr as a Sink for Marine DMS and an Inhibitor of Bromoform Formation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:5547-5558. [PMID: 33788559 DOI: 10.1021/acs.est.0c08189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recently, we suggested that hypobromous acid (HOBr) is a sink for the marine volatile organic sulfur compound dimethyl sulfide (DMS). However, HOBr is also known to react with reactive moieties of dissolved organic matter (DOM) such as phenolic compounds to form bromoform (CHBr3) and other brominated compounds. The reaction between HOBr and DMS may thus compete with the reaction between HOBr and DOM. To study this potential competition, kinetic batch and diffusion-reactor experiments with DMS, HOBr, and DOM were performed. Based on the reaction kinetics, we modeled concentrations of DMS, HOBr, and CHBr3 during typical algal bloom fluxes of DMS and HOBr (10-13 to 10-9 M s-1). For an intermediate to high HOBr flux (≥10-11 M s-1) and a DMS flux ≤10-11 M s-1, the model shows that the DMS degradation by HOBr was higher than for photochemical oxidation, biological consumption, and sea-air gas exchange combined. For HOBr fluxes ≤10-11 M s-1 and a DMS flux of 10-11 M s-1, our model shows that CHBr3 decreases by 86% compared to a lower DMS flux of 10-12 M s-1. Therefore, the reaction between HOBr and DMS likely not only presents a sink for DMS but also may lead to suppressed CHBr3 formation.
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Affiliation(s)
- Emanuel Müller
- Department of Water Resources and Drinking Water (W+T), Eawag, Swiss Federal Institute of Aquatic Science and Technology, Ueberlandstrasse 133, CH-8600 Duebendorf, Switzerland
- Department of Environment Systems (D-USYS), ETH Zurich, Swiss Federal Institute of Technology, Institute of Biogeochemistry and Pollutant Dynamics (IBP), Universitätsstrasse 16, 8092 Zürich, Switzerland
| | - Urs von Gunten
- Department of Water Resources and Drinking Water (W+T), Eawag, Swiss Federal Institute of Aquatic Science and Technology, Ueberlandstrasse 133, CH-8600 Duebendorf, Switzerland
- Department of Environment Systems (D-USYS), ETH Zurich, Swiss Federal Institute of Technology, Institute of Biogeochemistry and Pollutant Dynamics (IBP), Universitätsstrasse 16, 8092 Zürich, Switzerland
- School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Sylvain Bouchet
- Department of Water Resources and Drinking Water (W+T), Eawag, Swiss Federal Institute of Aquatic Science and Technology, Ueberlandstrasse 133, CH-8600 Duebendorf, Switzerland
- Department of Environment Systems (D-USYS), ETH Zurich, Swiss Federal Institute of Technology, Institute of Biogeochemistry and Pollutant Dynamics (IBP), Universitätsstrasse 16, 8092 Zürich, Switzerland
| | - Boris Droz
- Department of Water Resources and Drinking Water (W+T), Eawag, Swiss Federal Institute of Aquatic Science and Technology, Ueberlandstrasse 133, CH-8600 Duebendorf, Switzerland
- Department of Environment Systems (D-USYS), ETH Zurich, Swiss Federal Institute of Technology, Institute of Biogeochemistry and Pollutant Dynamics (IBP), Universitätsstrasse 16, 8092 Zürich, Switzerland
| | - Lenny H E Winkel
- Department of Water Resources and Drinking Water (W+T), Eawag, Swiss Federal Institute of Aquatic Science and Technology, Ueberlandstrasse 133, CH-8600 Duebendorf, Switzerland
- Department of Environment Systems (D-USYS), ETH Zurich, Swiss Federal Institute of Technology, Institute of Biogeochemistry and Pollutant Dynamics (IBP), Universitätsstrasse 16, 8092 Zürich, Switzerland
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24
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Higuchi T, Tanaka K, Shirai K, Yuyama I, Mezaki T, Takahata N, Sano Y. Sulfur assimilation in corals with aposymbiotic and symbiotic zooxanthellae. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:98-103. [PMID: 33196142 DOI: 10.1111/1758-2229.12908] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 06/11/2023]
Abstract
Although sulfate ions are the main form of sulfur in the ocean, there is limited knowledge on their use by living organisms. Stable isotope labelling and NanoSIMS analysis were used in this study to clarify how sulfate, in seawater, is assimilated by corals and zooxanthellae at the cellular level. Aposymbiotic and symbiotic coral juveniles from the genus Acropora were incubated for 2 days in filtered seawater with 34 S-labelled sulfate. Further, the labelled corals were incubated for additional 2 days in natural seawater. Mapping of sulfur isotopes (34 S/32 S) showed that the 'hotspots' were enriched in 34 S on a sub-micro level and were heterogeneously distributed in the coral soft tissues. Specifically, 34 S hotspots were found in both the symbiotic zooxanthellae and coral host tissues. In aposymbiotic corals, 34 S was detected in the tissues, indicating that the host corals directly assimilated the sulfate ions without any aid from the zooxanthellae. Even after 2 days in normal seawater, the 34 S label was clearly seen in both symbiotic and aposymbiotic corals, indicating that the assimilated sulfur was retained for at least 2 days.
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Affiliation(s)
- Tomihiko Higuchi
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
| | - Kentaro Tanaka
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
| | - Kotaro Shirai
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
| | - Ikuko Yuyama
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
- Faculty of Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi City, Yamaguchi, 753-8512, Japan
| | - Takuma Mezaki
- Kuroshio Biological Research Foundation, Nishidomari, Otsuki, Kochi, 788-0333, Japan
| | - Naoto Takahata
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
| | - Yuji Sano
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
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25
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Dittami SM, Arboleda E, Auguet JC, Bigalke A, Briand E, Cárdenas P, Cardini U, Decelle J, Engelen AH, Eveillard D, Gachon CMM, Griffiths SM, Harder T, Kayal E, Kazamia E, Lallier FH, Medina M, Marzinelli EM, Morganti TM, Núñez Pons L, Prado S, Pintado J, Saha M, Selosse MA, Skillings D, Stock W, Sunagawa S, Toulza E, Vorobev A, Leblanc C, Not F. A community perspective on the concept of marine holobionts: current status, challenges, and future directions. PeerJ 2021; 9:e10911. [PMID: 33665032 PMCID: PMC7916533 DOI: 10.7717/peerj.10911] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/16/2021] [Indexed: 12/19/2022] Open
Abstract
Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g., the development of controlled experimental model systems for holobionts from all major lineages and the modeling of (info)chemical-mediated interactions between organisms. Here we propose that one significant challenge is to bridge cross-disciplinary research on tractable model systems in order to address key ecological and evolutionary questions. This first step is crucial to decipher the main drivers of the dynamics and evolution of holobionts and to account for the holobiont concept in applied areas, such as the conservation, management, and exploitation of marine ecosystems and resources, where practical solutions to predict and mitigate the impact of human activities are more important than ever.
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Affiliation(s)
- Simon M Dittami
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Enrique Arboleda
- FR2424, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | | | - Arite Bigalke
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Enora Briand
- Laboratoire Phycotoxines, Ifremer, Nantes, France
| | - Paco Cárdenas
- Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Ulisse Cardini
- Integrative Marine Ecology Dept, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Johan Decelle
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRA, Grenoble, France
| | | | - Damien Eveillard
- Laboratoire des Sciences Numériques de Nantes (LS2N), Université de Nantes, CNRS, Nantes, France
| | - Claire M M Gachon
- Scottish Marine Institute, Scottish Association for Marine Science, Oban, United Kingdom
| | - Sarah M Griffiths
- School of Science and the Environment, Manchester Metropolitan University, Manchester, United Kingdom
| | | | - Ehsan Kayal
- FR2424, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | | | - François H Lallier
- Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, University Park, United States of America
| | - Ezequiel M Marzinelli
- Ecology and Environment Research Centre, The University of Sydney, Sydney, Australia.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Sydney Institute of Marine Science, Mosman, Australia
| | | | - Laura Núñez Pons
- Section Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Soizic Prado
- Molecules of Communication and Adaptation of Microorganisms (UMR 7245), National Museum of Natural History, CNRS, Paris, France
| | - José Pintado
- Instituto de Investigaciones Marinas, CSIC, Vigo, Spain
| | - Mahasweta Saha
- Benthic Ecology, Helmholtz Center for Ocean Research, Kiel, Germany.,Marine Ecology and Biodiversity, Plymouth Marine Laboratory, Plymouth, United Kingdom
| | - Marc-André Selosse
- National Museum of Natural History, Département Systématique et Evolution, Paris, France.,Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Derek Skillings
- Philosophy Department, University of Pennsylvania, Philadelphia, United States of America
| | - Willem Stock
- Laboratory of Protistology & Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Shinichi Sunagawa
- Dept. of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH, Zürich, Switzerland
| | - Eve Toulza
- IHPE, Univ. de Montpellier, CNRS, IFREMER, UPDV, Perpignan, France
| | - Alexey Vorobev
- CEA - Institut de Biologie François Jacob, Genoscope, Evry, France
| | - Catherine Leblanc
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Fabrice Not
- Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
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26
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Intracellular bacteria are common and taxonomically diverse in cultured and in hospite algal endosymbionts of coral reefs. ISME JOURNAL 2021; 15:2028-2042. [PMID: 33558689 PMCID: PMC8245515 DOI: 10.1038/s41396-021-00902-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 02/06/2023]
Abstract
Corals house a variety of microorganisms which they depend on for their survival, including endosymbiotic dinoflagellates (Symbiodiniaceae) and bacteria. While cnidarian–microorganism interactions are widely studied, Symbiodiniaceae–bacteria interactions are only just beginning to receive attention. Here, we describe the localization and composition of the bacterial communities associated with cultures of 11 Symbiodiniaceae strains from nine species and six genera. Three-dimensional confocal laser scanning and electron microscopy revealed bacteria are present inside the Symbiodiniaceae cells as well as closely associated with their external cell surface. Bacterial pure cultures and 16S rRNA gene metabarcoding from Symbiodiniaceae cultures highlighted distinct and highly diverse bacterial communities occur intracellularly, closely associated with the Symbiodiniaceae outer cell surface and loosely associated (i.e., in the surrounding culture media). The intracellular bacteria are highly conserved across Symbiodiniaceae species, suggesting they may be involved in Symbiodiniaceae physiology. Our findings provide unique new insights into the biology of Symbiodiniaceae.
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27
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He C, Migawa MT, Chen K, Weston TA, Tanowitz M, Song W, Guagliardo P, Iyer KS, Bennett CF, Fong LG, Seth PP, Young SG, Jiang H. High-resolution visualization and quantification of nucleic acid-based therapeutics in cells and tissues using Nanoscale secondary ion mass spectrometry (NanoSIMS). Nucleic Acids Res 2021; 49:1-14. [PMID: 33275144 PMCID: PMC7797060 DOI: 10.1093/nar/gkaa1112] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/27/2020] [Accepted: 11/04/2020] [Indexed: 01/19/2023] Open
Abstract
Nucleic acid therapeutics (NATs) have proven useful in promoting the degradation of specific transcripts, modifying gene expression, and regulating mRNA splicing. In each situation, efficient delivery of nucleic acids to cells, tissues and intracellular compartments is crucial—both for optimizing efficacy and reducing side effects. Despite successes in NATs, our understanding of their cellular uptake and distribution in tissues is limited. Current methods have yielded insights into distribution of NATs within cells and tissues, but the sensitivity and resolution of these approaches are limited. Here, we show that nanoscale secondary ion mass spectrometry (NanoSIMS) imaging can be used to define the distribution of 5-bromo-2′-deoxythymidine (5-BrdT) modified antisense oligonucleotides (ASO) in cells and tissues with high sensitivity and spatial resolution. This approach makes it possible to define ASO uptake and distribution in different subcellular compartments and to quantify the impact of targeting ligands designed to promote ASO uptake by cells. Our studies showed that phosphorothioate ASOs are associated with filopodia and the inner nuclear membrane in cultured cells, and also revealed substantial cellular and subcellular heterogeneity of ASO uptake in mouse tissues. NanoSIMS imaging represents a significant advance in visualizing uptake and distribution of NATs; this approach will be useful in optimizing efficacy and delivery of NATs for treating human disease.
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Affiliation(s)
- Cuiwen He
- Department of Medicine, University of California, Los Angeles, CA 90095, USA
| | | | - Kai Chen
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia
| | - Thomas A Weston
- Department of Medicine, University of California, Los Angeles, CA 90095, USA
| | | | - Wenxin Song
- Department of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth 6009, Australia
| | - K Swaminathan Iyer
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia
| | | | - Loren G Fong
- Department of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Punit P Seth
- Ionis Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Stephen G Young
- Department of Medicine, University of California, Los Angeles, CA 90095, USA.,Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
| | - Haibo Jiang
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia.,Department of Chemistry, The University of Hong Kong, Hong Kong, China
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28
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Rosset SL, Oakley CA, Ferrier-Pagès C, Suggett DJ, Weis VM, Davy SK. The Molecular Language of the Cnidarian-Dinoflagellate Symbiosis. Trends Microbiol 2020; 29:320-333. [PMID: 33041180 DOI: 10.1016/j.tim.2020.08.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/21/2020] [Accepted: 08/27/2020] [Indexed: 12/18/2022]
Abstract
The cnidarian-dinoflagellate symbiosis is of huge importance as it underpins the success of coral reefs, yet we know very little about how the host cnidarian and its dinoflagellate endosymbionts communicate with each other to form a functionally integrated unit. Here, we review the current knowledge of interpartner molecular signaling in this symbiosis, with an emphasis on lipids, glycans, reactive species, biogenic volatiles, and noncoding RNA. We draw upon evidence of these compounds from recent omics-based studies of cnidarian-dinoflagellate symbiosis and discuss the signaling roles that they play in other, better-studied symbioses. We then consider how improved knowledge of interpartner signaling might be used to develop solutions to the coral reef crisis by, for example, engineering more thermally resistant corals.
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Affiliation(s)
- Sabrina L Rosset
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Clinton A Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | | | - David J Suggett
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, PO Box 123, Broadway NSW 2007, Australia
| | - Virginia M Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand.
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29
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Hartman LM, van Oppen MJH, Blackall LL. Microbiota characterization of Exaiptasia diaphana from the Great Barrier Reef. Anim Microbiome 2020; 2:10. [PMID: 33499977 PMCID: PMC7807684 DOI: 10.1186/s42523-020-00029-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/17/2020] [Indexed: 02/04/2023] Open
Abstract
Background Coral reefs have sustained damage of increasing scale and frequency due to climate change, thereby intensifying the need to elucidate corals’ biological characteristics, including their thermal tolerance and microbial symbioses. The sea anemone, Exaiptasia diaphana, has proven an ideal coral model for many studies due to its close phylogenetic relationship and shared traits, such as symbiosis with algae of the family Symbiodiniaceae. However, established E. diaphana clonal lines are not available in Australia thus limiting the ability of Australian scientists to conduct research with this model. To help address this, the bacterial and Symbiodiniaceae associates of four Great Barrier Reef (GBR)-sourced E. diaphana genotypes established in laboratory aquaria and designated AIMS1–4, and from proxies of wild GBR E. diaphana were identified by metabarcoding of the bacterial 16S rRNA gene and eukaryotic rRNA gene ITS2 region. The relationship between AIMS1–4 and their bacterial associates was investigated, as was bacterial community phenotypic potential. Existing data from two existing anemone clonal lines, CC7 and H2, were included for comparison. Results Overall, 2238 bacterial amplicon sequence variants (ASVs) were observed in the AIMS1–4 bacterial communities, which were dominated by Proteobacteria and Bacteroidetes, together comprising > 90% relative abundance. Although many low abundance bacterial taxa varied between the anemone genotypes, the AIMS1–4 communities did not differ significantly. A significant tank effect was identified, indicating an environmental effect on the microbial communities. Bacterial community richness was lower in all lab-maintained E. diaphana compared to the wild proxies, suggesting a reduction in bacterial diversity and community phenotypic potential due to culturing. Seventeen ASVs were common to every GBR lab-cultured anemone, however five were associated with the Artemia feedstock, making their specific association to E. diaphana uncertain. The dominant Symbiodiniaceae symbiont in all GBR anemones was Breviolum minutum. Conclusion Despite differences in the presence and abundance of low abundance taxa, the bacterial communities of GBR-sourced lab-cultured E. diaphana are generally uniform and comparable to communities reported for other lab-cultured E. diaphana. The data presented here add to the global E. diaphana knowledge base and make an important contribution to the establishment of a GBR-sourced coral model organism.
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Affiliation(s)
- Leon Michael Hartman
- Swinburne University of Technology, Melbourne, Australia. .,The University of Melbourne, Melbourne, Australia.
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30
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McParland EL, Wright A, Art K, He M, Levine NM. Evidence for contrasting roles of dimethylsulfoniopropionate production in Emiliania huxleyi and Thalassiosira oceanica. THE NEW PHYTOLOGIST 2020; 226:396-409. [PMID: 31850524 PMCID: PMC7154784 DOI: 10.1111/nph.16374] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/27/2019] [Indexed: 05/28/2023]
Abstract
Dimethylsulfoniopropionate (DMSP) is a globally abundant marine metabolite and a significant source of organic carbon and sulfur for marine microbial ecosystems with the potential to influence climate regulation. However, the physiological function of DMSP has remained enigmatic for >30 yr. Recent insight suggests that there are different physiological roles for DMSP based on the cellular DMSP concentrations in producers. Differential production of DMSP was tested with multiple physiological experiments that altered nitrate availability, salinity and temperature to create stressed growth and target different metabolic conditions in Emiliania huxleyi, a high DMSP producer and Thalassiosira oceanica, a low DMSP producer. Emiliania huxleyi intracellular DMSP did not respond to metabolically imbalanced conditions, while Thalassiosira oceanica intracellular DMSP was significantly correlated to stressed growth rate across all conditions tested and exhibited a plastic response on a timescale of hours in nonsteady-state. The previous assumption that proposed DMSP mechanism(s) can be universally applied to all producers is shown to be unlikely. Rather, two distinct ecological roles for DMSP likely exist that differ by producer type, where: (1) the primary role of DMSP in high producers is a constitutive compatible solute; and (2) DMSP production in low producers is a finely tuned stress response.
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Affiliation(s)
- Erin L. McParland
- Department of Marine Chemistry and GeochemistryWoods Hole Oceanographic InstitutionWoods HoleMA02543USA
- Department of Marine and Environmental BiologyUniversity of Southern CaliforniaLos AngelesCA90089USA
| | - Anna Wright
- Department of Marine and Environmental BiologyUniversity of Southern CaliforniaLos AngelesCA90089USA
| | - Kristin Art
- Department of Marine and Environmental BiologyUniversity of Southern CaliforniaLos AngelesCA90089USA
| | - Meagan He
- Department of Marine and Environmental BiologyUniversity of Southern CaliforniaLos AngelesCA90089USA
| | - Naomi M. Levine
- Department of Marine and Environmental BiologyUniversity of Southern CaliforniaLos AngelesCA90089USA
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31
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Damjanovic K, Menéndez P, Blackall LL, van Oppen MJH. Early Life Stages of a Common Broadcast Spawning Coral Associate with Specific Bacterial Communities Despite Lack of Internalized Bacteria. MICROBIAL ECOLOGY 2020; 79:706-719. [PMID: 31435691 DOI: 10.1007/s00248-019-01428-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 08/13/2019] [Indexed: 06/10/2023]
Abstract
Coral-associated bacteria are critical for the well-being of their host and may play essential roles during ontogeny, as suggested by the vertical transmission of some bacteria in brooding corals. Bacterial acquisition patterns in broadcast spawners remain uncertain, as 16S rRNA gene metabarcoding of coral early life stages suggests the presence of bacterial communities, which have not been detected by microscopic examinations. Here, we combined 16S rRNA gene metabarcoding with fluorescence in situ hybridization (FISH) microscopy to analyze bacterial assemblages in Acropora tenuis egg-sperm bundles, embryos, and larvae following a spawning event. Metabarcoding results indicated that A. tenuis offspring ≤ 4-day-old were associated with diverse and dynamic bacterial microbiomes, dominated by Rhodobacteraceae, Alteromonadaceae, and Oceanospirillaceae. While FISH analyses confirmed the lack of internalized bacteria in A. tenuis offspring, metabarcoding showed that even the earliest life stages examined (egg-sperm bundles and two-cell stages) were associated with a diverse bacterial community, suggesting the bacteria were confined to the mucus layer. These results can be explained by vertical transmission of certain taxa (mainly Endozoicomonas) in the mucus surrounding the gametes within bundles, or by horizontal bacterial transmission through the release of bacteria by spawning adults into the water column.
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Affiliation(s)
- Katarina Damjanovic
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Australian Institute of Marine Science, PMB No 3, Townsville MC, QLD, 4810, Australia.
| | - Patricia Menéndez
- Australian Institute of Marine Science, PMB No 3, Townsville MC, QLD, 4810, Australia
- Department of Econometrics and Business Statistics, Monash University, Clayton, VIC, 3800, Australia
| | - Linda L Blackall
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Madeleine J H van Oppen
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
- Australian Institute of Marine Science, PMB No 3, Townsville MC, QLD, 4810, Australia
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Response of dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO) cell quotas to salinity and temperature shifts in the sea-ice diatom Fragilariopsis cylindrus. Polar Biol 2020. [DOI: 10.1007/s00300-020-02651-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Subcellular Chemical Imaging: New Avenues in Cell Biology. Trends Cell Biol 2020; 30:173-188. [DOI: 10.1016/j.tcb.2019.12.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/10/2019] [Accepted: 12/17/2019] [Indexed: 12/31/2022]
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Phylogenomic Analyses of Members of the Widespread Marine Heterotrophic Genus Pseudovibrio Suggest Distinct Evolutionary Trajectories and a Novel Genus, Polycladidibacter gen. nov. Appl Environ Microbiol 2020; 86:AEM.02395-19. [PMID: 31811036 PMCID: PMC6997731 DOI: 10.1128/aem.02395-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 12/04/2019] [Indexed: 12/16/2022] Open
Abstract
Bacteria belonging to the Pseudovibrio genus are widespread, metabolically versatile, and able to thrive as both free-living and host-associated organisms. Although more than 50 genomes are available, a comprehensive comparative genomics study to resolve taxonomic inconsistencies is currently missing. We analyzed all available genomes and used 552 core genes to perform a robust phylogenomic reconstruction. This in-depth analysis revealed the divergence of two monophyletic basal lineages of strains isolated from polyclad flatworm hosts, namely, Pseudovibrio hongkongensis and Pseudovibrio stylochi These strains have reduced genomes and lack sulfur-related metabolisms and major biosynthetic gene clusters, and their environmental distribution appears to be tightly associated with invertebrate hosts. We showed experimentally that the divergent strains are unable to utilize various sulfur compounds that, in contrast, can be utilized by the type strain Pseudovibrio denitrificans Our analyses suggest that the lineage leading to these two strains has been subject to relaxed purifying selection resulting in great gene loss. Overall genome relatedness indices (OGRI) indicate substantial differences between the divergent strains and the rest of the genus. While 16S rRNA gene analyses do not support the establishment of a different genus for the divergent strains, their substantial genomic, phylogenomic, and physiological differences strongly suggest a divergent evolutionary trajectory and the need for their reclassification. Therefore, we propose the novel genus Polycladidibacter gen. nov.IMPORTANCE The genus Pseudovibrio is commonly associated with marine invertebrates, which are essential for ocean health and marine nutrient cycling. Traditionally, the phylogeny of the genus has been based on 16S rRNA gene analysis. The use of the 16S rRNA gene or any other single marker gene for robust phylogenetic placement has recently been questioned. We used a large set of marker genes from all available Pseudovibrio genomes for in-depth phylogenomic analyses. We identified divergent monophyletic basal lineages within the Pseudovibrio genus, including two strains isolated from polyclad flatworms. These strains showed reduced sulfur metabolism and biosynthesis capacities. The phylogenomic analyses revealed distinct evolutionary trajectories and ecological adaptations that differentiate the divergent strains from the other Pseudovibrio members and suggest that they fall into a novel genus. Our data show the importance of widening the use of phylogenomics for better understanding bacterial physiology, phylogeny, and evolution.
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Matthews JL, Raina J, Kahlke T, Seymour JR, Oppen MJH, Suggett DJ. Symbiodiniaceae‐bacteria interactions: rethinking metabolite exchange in reef‐building corals as multi‐partner metabolic networks. Environ Microbiol 2020; 22:1675-1687. [DOI: 10.1111/1462-2920.14918] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Jennifer L. Matthews
- Climate Change Cluster University of Technology Sydney 2007 New South Wales Australia
| | - Jean‐Baptiste Raina
- Climate Change Cluster University of Technology Sydney 2007 New South Wales Australia
| | - Tim Kahlke
- Climate Change Cluster University of Technology Sydney 2007 New South Wales Australia
| | - Justin R. Seymour
- Climate Change Cluster University of Technology Sydney 2007 New South Wales Australia
| | - Madeleine J. H. Oppen
- The University of Melbourne Parkville 3010 Victoria Australia
- Australian Institute of Marine Science PMB No 3 Townsville MC 4810 QLD Australia
| | - David J. Suggett
- Climate Change Cluster University of Technology Sydney 2007 New South Wales Australia
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Mayali X. NanoSIMS: Microscale Quantification of Biogeochemical Activity with Large-Scale Impacts. ANNUAL REVIEW OF MARINE SCIENCE 2020; 12:449-467. [PMID: 31299167 DOI: 10.1146/annurev-marine-010419-010714] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
One major objective of aquatic microbial ecology is to understand the distribution of microbial populations over space and time and in response to environmental factors. Perhaps more importantly, it is crucial to quantify how those microbial cells affect biogeochemical processes of interest, such as primary production, nitrogen cycling, or the breakdown of pollutants. One valuable approach to link microbial identity to activity is to carry out incubations with stable-isotope-labeled substrates and then quantify the isotope incorporation by individual microbial cells using nanoscale secondary ion mass spectrometry (NanoSIMS). This review summarizes recent efforts in this field, highlights novel methods, describes studies investigating rare metabolisms as well as widespread microbial activity, and hopes to provide a framework to increase the use and capabilities of NanoSIMS for microbial biogeochemical studies in the future.
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Affiliation(s)
- Xavier Mayali
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA;
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A genomic view of the reef-building coral Porites lutea and its microbial symbionts. Nat Microbiol 2019; 4:2090-2100. [DOI: 10.1038/s41564-019-0532-4] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 07/05/2019] [Indexed: 11/09/2022]
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Cooke I, Mead O, Whalen C, Boote C, Moya A, Ying H, Robbins S, Strugnell JM, Darling A, Miller D, Voolstra CR, Adamska M. Molecular techniques and their limitations shape our view of the holobiont. ZOOLOGY 2019; 137:125695. [PMID: 31759226 DOI: 10.1016/j.zool.2019.125695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/08/2019] [Accepted: 07/12/2019] [Indexed: 11/26/2022]
Abstract
It is now recognised that the biology of almost any organism cannot be fully understood without recognising the existence and potential functional importance of associated microbes. Arguably, the emergence of this holistic viewpoint may never have occurred without the development of a crucial molecular technique, 16S rDNA amplicon sequencing, which allowed microbial communities to be easily profiled across a broad range of contexts. A diverse array of molecular techniques are now used to profile microbial communities, infer their evolutionary histories, visualise them in host tissues, and measure their molecular activity. In this review, we examine each of these categories of measurement and inference with a focus on the questions they make tractable, and the degree to which their capabilities and limitations shape our view of the holobiont.
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Affiliation(s)
- Ira Cooke
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia.
| | - Oliver Mead
- ARC Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, ACT, 2601, Australia; Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Casey Whalen
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Chloë Boote
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Aurelie Moya
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Hua Ying
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Steven Robbins
- Australian Center for Ecogenomics, University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Jan M Strugnell
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia; Centre of Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, 4810, QLD, Australia; Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Melbourne, 3083, Australia
| | - Aaron Darling
- The ithree institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - David Miller
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | | | - Maja Adamska
- ARC Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, ACT, 2601, Australia; Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
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Zhang XH, Liu J, Liu J, Yang G, Xue CX, Curson ARJ, Todd JD. Biogenic production of DMSP and its degradation to DMS-their roles in the global sulfur cycle. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1296-1319. [PMID: 31231779 DOI: 10.1007/s11427-018-9524-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/16/2019] [Indexed: 01/08/2023]
Abstract
Dimethyl sulfide (DMS) is the most abundant form of volatile sulfur in Earth's oceans, and is mainly produced by the enzymatic clevage of dimethylsulfoniopropionate (DMSP). DMS and DMSP play important roles in driving the global sulfur cycle and may affect climate. DMSP is proposed to serve as an osmolyte, a grazing deterrent, a signaling molecule, an antioxidant, a cryoprotectant and/or as a sink for excess sulfur. It was long believed that only marine eukaryotes such as phytoplankton produce DMSP. However, we recently discovered that marine heterotrophic bacteria can also produce DMSP, making them a potentially important source of DMSP. At present, one prokaryotic and two eukaryotic DMSP synthesis enzymes have been identified. Marine heterotrophic bacteria are likely the major degraders of DMSP, using two known pathways: demethylation and cleavage. Many phytoplankton and some fungi can also cleave DMSP. So far seven different prokaryotic and one eukaryotic DMSP lyases have been identified. This review describes the global distribution pattern of DMSP and DMS, the known genes for biosynthesis and cleavage of DMSP, and the physiological and ecological functions of these important organosulfur molecules, which will improve understanding of the mechanisms of DMSP and DMS production and their roles in the environment.
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Affiliation(s)
- Xiao-Hua Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Ji Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jingli Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Guipeng Yang
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266071, China
| | - Chun-Xu Xue
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Andrew R J Curson
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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40
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Bernasconi R, Stat M, Koenders A, Huggett MJ. Global Networks of Symbiodinium-Bacteria Within the Coral Holobiont. MICROBIAL ECOLOGY 2019; 77:794-807. [PMID: 30218130 DOI: 10.1007/s00248-018-1255-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 08/29/2018] [Indexed: 05/12/2023]
Abstract
Scleractinian corals form the framework of coral reefs and host abundant and diverse microbial communities that are fundamental to their success. A very limited number of studies have examined the co-occurrence of multiple partners within the coral 'holobiont' and their pattern of specificity over different geographical scales. In this study, we explored two molecular sequence datasets representing associations between corals and dinoflagellates in the genus Symbiodinium and between corals and bacteria, across the globe. Through a network theory approach, we characterised patterns of co-occurrences between bacteria and Symbiodinium with 13 coral genera across six water basins. The majority of the bacteria-Symbiodinium co-occurrences were specific to either a coral genus or water basin, emphasising both coral host and environment as important factors driving the diversity of coral assemblages. Yet, results also identified bacteria and Symbiodinium that were shared by multiple coral genera across several water basins. The analyses indicate that shared co-occurrences are independent of the phylogenetic and biogeographic relationship of coral hosts.
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Affiliation(s)
- Rachele Bernasconi
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, Western Australia, 6027, Australia.
| | - Michael Stat
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture Curtin University, Bentley, 6102, Western Australia
- Department of Biological Sciences, Macquarie University, Sydney, 2109, Australia
| | - Annette Koenders
- Centre for Ecosystem Management, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, Western Australia, 6027, Australia
| | - Megan J Huggett
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, Western Australia, 6027, Australia
- Centre for Ecosystem Management, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, Western Australia, 6027, Australia
- School of Environmental and Life Sciences, Faculty of Science, The University of Newcastle, PO Box 127, Ourimbah, New South Wales, 2258, Australia
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Decelle J, Stryhanyuk H, Gallet B, Veronesi G, Schmidt M, Balzano S, Marro S, Uwizeye C, Jouneau PH, Lupette J, Jouhet J, Maréchal E, Schwab Y, Schieber NL, Tucoulou R, Richnow H, Finazzi G, Musat N. Algal Remodeling in a Ubiquitous Planktonic Photosymbiosis. Curr Biol 2019; 29:968-978.e4. [PMID: 30827917 DOI: 10.1016/j.cub.2019.01.073] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 12/03/2018] [Accepted: 01/28/2019] [Indexed: 01/12/2023]
Abstract
Photosymbiosis between single-celled hosts and microalgae is common in oceanic plankton, especially in oligotrophic surface waters. However, the functioning of this ecologically important cell-cell interaction and the subcellular mechanisms allowing the host to accommodate and benefit from its microalgae remain enigmatic. Here, using a combination of quantitative single-cell structural and chemical imaging techniques (FIB-SEM, nanoSIMS, Synchrotron X-ray fluorescence), we show that the structural organization, physiology, and trophic status of the algal symbionts (the haptophyte Phaeocystis) significantly change within their acantharian hosts compared to their free-living phase in culture. In symbiosis, algal cell division is blocked, photosynthesis is enhanced, and cell volume is increased by up to 10-fold with a higher number of plastids (from 2 to up to 30) and thylakoid membranes. The multiplication of plastids can lead to a 38-fold increase of the total plastid volume in a cell. Subcellular mapping of nutrients (nitrogen and phosphorous) and their stoichiometric ratios shows that symbiotic algae are impoverished in phosphorous and suggests a higher investment in energy-acquisition machinery rather than in growth. Nanoscale imaging also showed that the host supplies a substantial amount of trace metals (e.g., iron and cobalt), which are stored in algal vacuoles at high concentrations (up to 660 ppm). Sulfur mapping reveals a high concentration in algal vacuoles that may be a source of antioxidant molecules. Overall, this study unveils an unprecedented morphological and metabolic transformation of microalgae following their integration into a host, and it suggests that this widespread symbiosis is a farming strategy wherein the host engulfs and exploits microalgae.
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Affiliation(s)
- Johan Decelle
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, 04318 Leipzig, Germany.
| | - Hryhoriy Stryhanyuk
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, 04318 Leipzig, Germany
| | - Benoit Gallet
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, 71 Avenue des Martyrs, 38044 Grenoble, France
| | - Giulia Veronesi
- Laboratoire de Chimie et Biologie des Métaux UMR 5249, Université Grenoble Alpes, CNRS, CEA, 17 Avenue des Martyrs, 38054 Grenoble, France; ESRF, The European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38043 Grenoble, France
| | - Matthias Schmidt
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, 04318 Leipzig, Germany
| | - Sergio Balzano
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, PO Box 59, 1790 AB Den Burg, the Netherlands
| | - Sophie Marro
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'Océanographie de Villefranche UMR7093, Observatoire Océanologique, 06230 Villefranche-sur-Mer, France
| | - Clarisse Uwizeye
- Cell & Plant Physiology Laboratory, University of Grenoble Alpes, CNRS, CEA, INRA, 38054 Grenoble Cedex 9, France
| | - Pierre-Henri Jouneau
- Institut Nanosciences et Cryogénie, Université Grenoble Alpes, CEA, 38054 Grenoble, France
| | - Josselin Lupette
- Cell & Plant Physiology Laboratory, University of Grenoble Alpes, CNRS, CEA, INRA, 38054 Grenoble Cedex 9, France
| | - Juliette Jouhet
- Cell & Plant Physiology Laboratory, University of Grenoble Alpes, CNRS, CEA, INRA, 38054 Grenoble Cedex 9, France
| | - Eric Maréchal
- Cell & Plant Physiology Laboratory, University of Grenoble Alpes, CNRS, CEA, INRA, 38054 Grenoble Cedex 9, France
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Nicole L Schieber
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Rémi Tucoulou
- ESRF, The European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38043 Grenoble, France
| | - Hans Richnow
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, 04318 Leipzig, Germany
| | - Giovanni Finazzi
- Cell & Plant Physiology Laboratory, University of Grenoble Alpes, CNRS, CEA, INRA, 38054 Grenoble Cedex 9, France
| | - Niculina Musat
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, 04318 Leipzig, Germany
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Ismagulova T, Shebanova A, Gorelova O, Baulina O, Solovchenko A. A new simple method for quantification and locating P and N reserves in microalgal cells based on energy-filtered transmission electron microscopy (EFTEM) elemental maps. PLoS One 2018; 13:e0208830. [PMID: 30533056 PMCID: PMC6289464 DOI: 10.1371/journal.pone.0208830] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 11/23/2018] [Indexed: 11/18/2022] Open
Abstract
We established a new simple approach to study phosphorus (P) and nitrogen (N) reserves at subcellular level potentially applicable to various types of cells capable of accumulating P- and/or N-rich inclusions. Here, we report on using this approach for locating and assessing the abundance of the P and N reserves in microalgal and cyanobacterial cells. The approach includes separation of the signal from P- or N-rich structures from noise on the energy-filtered transmission electron microscopy (EFTEM) P- or N-maps. The separation includes (i) relative entropy estimation for each pixel of the map, (ii) binary thresholding of the map, and (iii) segmenting the image to assess the inclusion relative area and localization in the cell section. The separation is based on comparing the a posteriori probability that a pixel of the map contains information about the sample vs. Gaussian a priori probability that the pixel contains noise. The difference is expressed as relative entropy value for the pixel; positive values are characteristic of the pixels containing the payload information about the sample. This is the first known method for quantification and locating at a subcellular level P-rich and N-rich inclusions including tiny (< 180 nm) structures. We demonstrated the applicability of the proposed method both to the cells of eukaryotic green microalgae and cyanobacteria. Using the new method, we elucidated the heterogeneity of the studied cells in accumulation of P and N reserves across different species. The proposed approach will be handy for any cytological and microbiological study requiring a comparative assessment of subcellular distribution of cyanophycin, polyphosphates or other type of P- or N-rich inclusions. An added value is the potential of this approach for automation of the data processing and evaluation enabling an unprecedented increase of the EFTEM analysis throughput.
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Affiliation(s)
- Tatiana Ismagulova
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- * E-mail:
| | - Anastasia Shebanova
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Olga Gorelova
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Olga Baulina
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexei Solovchenko
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Eurasian Centre for Food Security, Lomonosov Moscow State University, Moscow, Russia
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Giardina M, Cheong S, Marjo CE, Clode PL, Guagliardo P, Pickford R, Pernice M, Seymour JR, Raina JB. Quantifying Inorganic Nitrogen Assimilation by Synechococcus Using Bulk and Single-Cell Mass Spectrometry: A Comparative Study. Front Microbiol 2018; 9:2847. [PMID: 30538685 PMCID: PMC6277480 DOI: 10.3389/fmicb.2018.02847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 11/05/2018] [Indexed: 12/03/2022] Open
Abstract
Microorganisms drive most of the major biogeochemical cycles in the ocean, but the rates at which individual species assimilate and transform key elements is generally poorly quantified. One of these important elements is nitrogen, with its availability limiting primary production across a large proportion of the ocean. Nitrogen uptake by marine microbes is typically quantified using bulk-scale approaches, such as Elemental Analyzer-Isotope Ratio Mass Spectrometry (EA-IRMS), which averages uptake over entire communities, masking microbial heterogeneity. However, more recent techniques, such as secondary ion mass spectrometry (SIMS), allow for elucidation of assimilation rates at the scale at which they occur: the single-cell level. Here, we combine and compare the application of bulk (EA-IRMS) and single-cell approaches (NanoSIMS and Time-of-Flight-SIMS) for quantifying the assimilation of inorganic nitrogen by the ubiquitous marine primary producer Synechococcus. We aimed to contrast the advantages and disadvantages of these techniques and showcase their complementarity. Our results show that the average assimilation of 15N by Synechococcus differed based on the technique used: values derived from EA-IRMS were consistently higher than those derived from SIMS, likely due to a combination of previously reported systematic depletion as well as differences in sample preparation. However, single-cell approaches offered additional layers of information, whereby NanoSIMS allowed for the quantification of the metabolic heterogeneity among individual cells and ToF-SIMS enabled identification of nitrogen assimilation into peptides. We suggest that this coupling of stable isotope-based approaches has great potential to elucidate the metabolic capacity and heterogeneity of microbial cells in natural environments.
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Affiliation(s)
- Marco Giardina
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Soshan Cheong
- Mark Wainwright Analytical Centre, University of New South Wales, Kensington, NSW, Australia
| | - Christopher E. Marjo
- Mark Wainwright Analytical Centre, University of New South Wales, Kensington, NSW, Australia
| | - Peta L. Clode
- Centre for Microscopy Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia
- UWA School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
- UWA Oceans Institute, The University of Western Australia, Perth, WA, Australia
| | - Paul Guagliardo
- Centre for Microscopy Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia
| | - Russell Pickford
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, Australia
| | - Mathieu Pernice
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Justin R. Seymour
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
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Jauffrais T, LeKieffre C, Schweizer M, Geslin E, Metzger E, Bernhard JM, Jesus B, Filipsson HL, Maire O, Meibom A. Kleptoplastidic benthic foraminifera from aphotic habitats: insights into assimilation of inorganic C, N and S studied with sub-cellular resolution. Environ Microbiol 2018; 21:125-141. [PMID: 30277305 DOI: 10.1111/1462-2920.14433] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/31/2018] [Accepted: 09/24/2018] [Indexed: 10/28/2022]
Abstract
The assimilation of inorganic compounds in foraminiferal metabolism compared to predation or organic matter assimilation is unknown. Here, we investigate possible inorganic-compound assimilation in Nonionellina labradorica, a common kleptoplastidic benthic foraminifer from Arctic and North Atlantic sublittoral regions. The objectives were to identify the source of the foraminiferal kleptoplasts, assess their photosynthetic functionality in light and darkness and investigate inorganic nitrogen and sulfate assimilation. We used DNA barcoding of a ~ 830 bp fragment from the SSU rDNA to identify the kleptoplasts and correlated transmission electron microscopy and nanometre-scale secondary ion mass spectrometry (TEM-NanoSIMS) isotopic imaging to study 13 C-bicarbonate, 15 N-ammonium and 34 S-sulfate uptake. In addition, respiration rate measurements were determined to assess the response of N. labradorica to light. The DNA sequences established that over 80% of the kleptoplasts belonged to Thalassiosira (with 96%-99% identity), a cosmopolitan planktonic diatom. TEM-NanoSIMS imaging revealed degraded cytoplasm and an absence of 13 C assimilation in foraminifera exposed to light. Oxygen measurements showed higher respiration rates under light than dark conditions, and no O2 production was detected. These results indicate that the photosynthetic pathways in N. labradorica are not functional. Furthermore, N. labradorica assimilated both 15 N-ammonium and 34 S-sulfate into its cytoplasm, which suggests that foraminifera might have several ammonium or sulfate assimilation pathways, involving either the kleptoplasts or bona fide foraminiferal pathway(s) not yet identified.
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Affiliation(s)
- Thierry Jauffrais
- UMR CNRS 6112 LPG-BIAF, Université d'Angers, 2 Boulevard Lavoisier, 49045, Angers Cedex 1, France.,Ifremer, RBE/LEAD, 101 Promenade Roger Laroque, 98897, Nouméa, New Caledonia
| | - Charlotte LeKieffre
- UMR CNRS 6112 LPG-BIAF, Université d'Angers, 2 Boulevard Lavoisier, 49045, Angers Cedex 1, France.,Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Magali Schweizer
- UMR CNRS 6112 LPG-BIAF, Université d'Angers, 2 Boulevard Lavoisier, 49045, Angers Cedex 1, France
| | - Emmanuelle Geslin
- UMR CNRS 6112 LPG-BIAF, Université d'Angers, 2 Boulevard Lavoisier, 49045, Angers Cedex 1, France
| | - Edouard Metzger
- UMR CNRS 6112 LPG-BIAF, Université d'Angers, 2 Boulevard Lavoisier, 49045, Angers Cedex 1, France
| | - Joan M Bernhard
- Woods Hole Oceanographic Institution, Geology & Geophysics Department, Woods Hole, MA, USA
| | - Bruno Jesus
- EA2160, Laboratoire Mer Molécules Santé, Université de Nantes, Nantes, France.,BioISI - Biosystems & Integrative Sciences Institute, Campo Grande University of Lisboa, Faculty of Sciences, Lisbon, Portugal
| | - Helena L Filipsson
- Department of Geology, Lund University, Sölvegatan 12, 223 62, Lund, Sweden
| | - Olivier Maire
- Univ. Bordeaux, EPOC, UMR 5805, 33400, Talence, France.,CNRS, EPOC, UMR 5805, 33400, Talence, France
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.,Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, 1015, Lausanne, Switzerland
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45
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Stryhanyuk H, Calabrese F, Kümmel S, Musat F, Richnow HH, Musat N. Calculation of Single Cell Assimilation Rates From SIP-NanoSIMS-Derived Isotope Ratios: A Comprehensive Approach. Front Microbiol 2018; 9:2342. [PMID: 30337916 PMCID: PMC6178922 DOI: 10.3389/fmicb.2018.02342] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 09/12/2018] [Indexed: 11/18/2022] Open
Abstract
The nanoSIMS-based chemical microscopy has been introduced in biology over a decade ago. The spatial distribution of elements and isotopes analyzed by nanoSIMS can be used to reconstruct images of biological samples with a resolution down to tens of nanometers, and can be also interpreted quantitatively. Currently, a unified approach for calculation of single cell assimilation rates from nanoSIMS-derived changes in isotope ratios is missing. Here we present a comprehensive concept of assimilation rate calculation with a rigorous mathematical model based on quantitative evaluation of nanoSIMS-derived isotope ratios. We provide a detailed description of data acquisition and treatment, including the selection and accumulation of nanoSIMS scans, defining regions of interest and extraction of isotope ratios. Next, we present alternative methods to determine the cellular volume and the density of the element under scrutiny. Finally, to compensate for alterations of original isotopic ratios, our model considers corrections for sample preparation methods (e.g., air dry, chemical fixation, permeabilization, hybridization), and when known, for the stable isotope fractionation associated with utilization of defined growth substrates. As proof of concept we implemented this protocol to quantify the assimilation of 13C-labeled glucose by single cells of Pseudomonas putida. In addition, we provide a calculation template where all protocol-derived formulas are directly available to facilitate routine assimilation rate calculations by nanoSIMS users.
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Affiliation(s)
- Hryhoriy Stryhanyuk
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Federica Calabrese
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Steffen Kümmel
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Florin Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
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46
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Inorganic carbon and nitrogen assimilation in cellular compartments of a benthic kleptoplastic foraminifer. Sci Rep 2018; 8:10140. [PMID: 29973634 PMCID: PMC6031614 DOI: 10.1038/s41598-018-28455-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/20/2018] [Indexed: 11/08/2022] Open
Abstract
Haynesina germanica, an ubiquitous benthic foraminifer in intertidal mudflats, has the remarkable ability to isolate, sequester, and use chloroplasts from microalgae. The photosynthetic functionality of these kleptoplasts has been demonstrated by measuring photosystem II quantum efficiency and O2 production rates, but the precise role of the kleptoplasts in foraminiferal metabolism is poorly understood. Thus, the mechanism and dynamics of C and N assimilation and translocation from the kleptoplasts to the foraminiferal host requires study. The objective of this study was to investigate, using correlated TEM and NanoSIMS imaging, the assimilation of inorganic C and N (here ammonium, NH4+) in individuals of a kleptoplastic benthic foraminiferal species. H. germanica specimens were incubated for 20 h in artificial seawater enriched with H13CO3- and 15NH4+ during a light/dark cycle. All specimens (n = 12) incorporated 13C into their endoplasm stored primarily in the form of lipid droplets. A control incubation in darkness resulted in no 13C-uptake, strongly suggesting that photosynthesis is the process dominating inorganic C assimilation. Ammonium assimilation was observed both with and without light, with diffuse 15N-enrichment throughout the cytoplasm and distinct 15N-hotspots in fibrillar vesicles, electron-opaque bodies, tubulin paracrystals, bacterial associates, and, rarely and at moderate levels, in kleptoplasts. The latter observation might indicate that the kleptoplasts are involved in N assimilation. However, the higher N assimilation observed in the foraminiferal endoplasm incubated without light suggests that another cytoplasmic pathway is dominant, at least in darkness. This study clearly shows the advantage provided by the kleptoplasts as an additional source of carbon and provides observations of ammonium uptake by the foraminiferal cell.
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47
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SHAO CF, ZHAO Y, WU K, JIA FF, LUO Q, LIU Z, WANG FY. Correlated Secondary Ion Mass Spectrometry-Laser Scanning Confocal Microscopy Imaging for Single Cell-Principles and Applications. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2018. [DOI: 10.1016/s1872-2040(18)61095-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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48
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Abstract
There are more than one million microbial cells in every drop of seawater, and their collective metabolisms not only recycle nutrients that can then be used by larger organisms but also catalyze key chemical transformations that maintain Earth’s habitability. Understanding how these microbes interact with each other and with multicellular hosts is critical to reliably quantify any functional aspect of their metabolisms and to predicting their outcomes on larger scales. There are more than one million microbial cells in every drop of seawater, and their collective metabolisms not only recycle nutrients that can then be used by larger organisms but also catalyze key chemical transformations that maintain Earth’s habitability. Understanding how these microbes interact with each other and with multicellular hosts is critical to reliably quantify any functional aspect of their metabolisms and to predict their outcomes on larger scales. Following a large body of literature pioneered by Farooq Azam and colleagues more than 30 years ago, I emphasize the importance of studying microbial interactions at the appropriate scale if we want to fully decipher the roles that they play in oceanic ecosystems.
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Ecology and Biotechnological Potential of Bacteria Belonging to the Genus Pseudovibrio. Appl Environ Microbiol 2018; 84:AEM.02516-17. [PMID: 29453252 DOI: 10.1128/aem.02516-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Members of the genus Pseudovibrio have been isolated worldwide from a great variety of marine sources as both free-living and host-associated bacteria. So far, the available data depict a group of alphaproteobacteria characterized by a versatile metabolism, which allows them to use a variety of substrates to meet their carbon, nitrogen, sulfur, and phosphorous requirements. Additionally, Pseudovibrio-related bacteria have been shown to proliferate under extreme oligotrophic conditions, tolerate high heavy-metal concentrations, and metabolize potentially toxic compounds. Considering this versatility, it is not surprising that they have been detected from temperate to tropical regions and are often the most abundant isolates obtained from marine invertebrates. Such an association is particularly recurrent with marine sponges and corals, animals that play a key role in benthic marine systems. The data so far available indicate that these bacteria are mainly beneficial to the host, and besides being involved in major nutrient cycles, they could provide the host with both vitamins/cofactors and protection from potential pathogens via the synthesis of antimicrobial secondary metabolites. In fact, the biosynthetic abilities of Pseudovibrio spp. have been emerging in recent years, and both genomic and analytic studies have underlined how these organisms promise novel natural products of biotechnological value.
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50
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Rädecker N, Raina JB, Pernice M, Perna G, Guagliardo P, Kilburn MR, Aranda M, Voolstra CR. Using Aiptasia as a Model to Study Metabolic Interactions in Cnidarian- Symbiodinium Symbioses. Front Physiol 2018; 9:214. [PMID: 29615919 PMCID: PMC5864895 DOI: 10.3389/fphys.2018.00214] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/26/2018] [Indexed: 11/13/2022] Open
Abstract
The symbiosis between cnidarian hosts and microalgae of the genus Symbiodinium provides the foundation of coral reefs in oligotrophic waters. Understanding the nutrient-exchange between these partners is key to identifying the fundamental mechanisms behind this symbiosis, yet has proven difficult given the endosymbiotic nature of this relationship. In this study, we investigated the respective contribution of host and symbiont to carbon and nitrogen assimilation in the coral model anemone Aiptaisa. For this, we combined traditional measurements with nanoscale secondary ion mass spectrometry (NanoSIMS) and stable isotope labeling to investigate patterns of nutrient uptake and translocation both at the organismal scale and at the cellular scale. Our results show that the rate of carbon and nitrogen assimilation in Aiptasia depends on the identity of the host and the symbiont. NanoSIMS analysis confirmed that both host and symbiont incorporated carbon and nitrogen into their cells, implying a rapid uptake and cycling of nutrients in this symbiotic relationship. Gross carbon fixation was highest in Aiptasia associated with their native Symbiodinium communities. However, differences in fixation rates were only reflected in the δ13C enrichment of the cnidarian host, whereas the algal symbiont showed stable enrichment levels regardless of host identity. Thereby, our results point toward a "selfish" character of the cnidarian-Symbiodinium association in which both partners directly compete for available resources. Consequently, this symbiosis may be inherently instable and highly susceptible to environmental change. While questions remain regarding the underlying cellular controls of nutrient exchange and the nature of metabolites involved, the approach outlined in this study constitutes a powerful toolset to address these questions.
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Affiliation(s)
- Nils Rädecker
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Mathieu Pernice
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Gabriela Perna
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth, WA, Australia
| | - Matt R Kilburn
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth, WA, Australia
| | - Manuel Aranda
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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