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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Joffe N, Kuhlisch C, Schleyer G, Ahlers NS, Shemi A, Vardi A. Cell-to-cell heterogeneity drives host-virus coexistence in a bloom-forming alga. ISME J 2024; 18:wrae038. [PMID: 38452203 PMCID: PMC10980834 DOI: 10.1093/ismejo/wrae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/25/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Algal blooms drive global biogeochemical cycles of key nutrients and serve as hotspots for biological interactions in the ocean. The massive blooms of the cosmopolitan coccolithophore Emiliania huxleyi are often infected by the lytic E. huxleyi virus, which is a major mortality agent triggering bloom demise. This multi-annual "boom and bust" pattern of E. huxleyi blooms suggests that coexistence is essential for these host-virus dynamics. To investigate host-virus coexistence, we developed a new model system from an E. huxleyi culture that recovered from viral infection. The recovered population coexists with the virus, as host cells continue to divide in parallel to viral production. By applying single-molecule fluorescence in situ hybridization (smFISH) to quantify the fraction of infected cells, and assessing infection-specific lipid biomarkers, we identified a small subpopulation of cells that were infected and produced new virions, whereas most of the host population could resist infection. To further assess population heterogeneity, we generated clonal strain collections using single-cell sorting and subsequently phenotyped their susceptibility to E. huxleyi virus infection. This unraveled substantial cell-to-cell heterogeneity across a continuum of susceptibility to resistance, highlighting that infection outcome may vary depending on the individual cell. These results add a new dimension to our understanding of the complexity of host-virus interactions that are commonly assessed in bulk and described by binary definitions of resistance or susceptibility. We propose that phenotypic heterogeneity drives the host-virus coexistence and demonstrate how the coexistence with a lytic virus provides an ecological advantage for the host by killing competing strains.
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Affiliation(s)
- Nir Joffe
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Constanze Kuhlisch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Guy Schleyer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, 07745 Jena, Germany
| | - Nadia S Ahlers
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Adva Shemi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
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Shemi A, Ben-Dor S, Rotkopf R, Dym O, Vardi A. Phylogeny and biogeography of the algal DMS-releasing enzyme in the global ocean. ISME Commun 2023; 3:72. [PMID: 37452148 PMCID: PMC10349084 DOI: 10.1038/s43705-023-00280-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/27/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Abstract
Phytoplankton produce the volatile dimethyl sulfide (DMS), an important infochemical mediating microbial interactions, which is also emitted to the atmosphere and affecting the global climate. Albeit the enzymatic source for DMS in eukaryotes was elucidated, namely a DMSP lyase (DL) called Alma1, we still lack basic knowledge regarding its taxonomic distribution. We defined unique sequence motifs which enable the identification of DL homologs (DLHs) in model systems and environmental populations. We used these motifs to predict DLHs in diverse algae by analyzing hundreds of genomic and transcriptomic sequences from model systems under stress conditions and from environmental samples. Our findings show that the DL enzyme is more taxonomically widespread than previously thought, as it is encoded by known algal taxa as haptophytes and dinoflagellates, but also by chlorophytes, pelagophytes and diatoms, which were conventionally considered to lack the DL enzyme. By exploring the Tara Oceans database, we showed that DLHs are widespread across the oceans and are predominantly expressed by dinoflagellates. Certain dinoflagellate DLHs were differentially expressed between the euphotic and mesopelagic zones, suggesting a functional specialization and an involvement in the metabolic plasticity of mixotrophic dinoflagellates. In specific regions as the Southern Ocean, DLH expression by haptophytes and diatoms was correlated with environmental drivers such as nutrient availability. The expanded repertoire of putative DL enzymes from diverse microbial origins and geographic niches suggests new potential players in the marine sulfur cycle and provides a foundation to study the cellular function of the DL enzyme in marine microbes.
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Affiliation(s)
- Adva Shemi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ron Rotkopf
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Orly Dym
- Structural Proteomics Unit, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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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: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Frada MJ, Rosenwasser S, Ben-Dor S, Shemi A, Sabanay H, Vardi A. Morphological switch to a resistant subpopulation in response to viral infection in the bloom-forming coccolithophore Emiliania huxleyi. PLoS Pathog 2017; 13:e1006775. [PMID: 29244854 PMCID: PMC5756048 DOI: 10.1371/journal.ppat.1006775] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 01/05/2018] [Accepted: 11/27/2017] [Indexed: 11/18/2022] Open
Abstract
Recognizing the life cycle of an organism is key to understanding its biology and ecological impact. Emiliania huxleyi is a cosmopolitan marine microalga, which displays a poorly understood biphasic sexual life cycle comprised of a calcified diploid phase and a morphologically distinct biflagellate haploid phase. Diploid cells (2N) form large-scale blooms in the oceans, which are routinely terminated by specific lytic viruses (EhV). In contrast, haploid cells (1N) are resistant to EhV. Further evidence indicates that 1N cells may be produced during viral infection. A shift in morphology, driven by meiosis, could therefore constitute a mechanism for E. huxleyi cells to escape from EhV during blooms. This process has been metaphorically coined the 'Cheshire Cat' (CC) strategy. We tested this model in two E. huxleyi strains using a detailed assessment of morphological and ploidy-level variations as well as expression of gene markers for meiosis and the flagellate phenotype. We showed that following the CC model, production of resistant cells was triggered during infection. This led to the rise of a new subpopulation of cells in the two strains that morphologically resembled haploid cells and were resistant to EhV. However, ploidy-level analyses indicated that the new resistant cells were diploid or aneuploid. Thus, the CC strategy in E. huxleyi appears to be a life-phase switch mechanism involving morphological remodeling that is decoupled from meiosis. Our results highlight the adaptive significance of morphological plasticity mediating complex host-virus interactions in marine phytoplankton.
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Affiliation(s)
- Miguel José Frada
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shilo Rosenwasser
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Bioinformatics and Biological Computing Unit–Department of Biological Services, Weizmann Institute of Science, Rehovot, Israel
| | - Adva Shemi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Helena Sabanay
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
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6
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Shemi A, Schatz D, Fredricks HF, Van Mooy BAS, Porat Z, Vardi A. Phosphorus starvation induces membrane remodeling and recycling in Emiliania huxleyi. New Phytol 2016; 211:886-898. [PMID: 27111716 DOI: 10.1111/nph.13940] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 02/20/2016] [Indexed: 06/05/2023]
Abstract
Nutrient availability is an important factor controlling phytoplankton productivity. Phytoplankton contribute c. 50% of the global photosynthesis and possess efficient acclimation mechanisms to cope with nutrient stress. We investigate the cellular response of the bloom-forming coccolithophore Emiliania huxleyi to phosphorus (P) scarcity, which is often a limiting factor in marine ecosystems. We combined mass spectrometry, fluorescence microscopy, transmission electron microscopy (TEM) and gene expression analyses in order to assess diverse cellular features in cells exposed to P limitation and recovery. Early starvation-induced substitution of phospholipids in the cells' membranes with galacto- and betaine lipids. Lipid remodeling was rapid and reversible upon P resupply. The PI3K inhibitor wortmannin reduced phospholipid substitution, suggesting a possible involvement of PI3K- signaling in this process. In addition, P limitation enhanced the formation and acidification of membrane vesicles in the cytoplasm. Intracellular vesicles may facilitate the recycling of cytoplasmic content, which is engulfed in the vesicles and delivered to the main vacuole. Long-term starvation was characterized by a profound increase in cell size and morphological alterations in cellular ultrastructure. This study provides cellular and molecular basis for future ecophysiological assessment of natural E. huxleyi populations in oligotrophic regions.
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Affiliation(s)
- Adva Shemi
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Helen F Fredricks
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Benjamin A S Van Mooy
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Ziv Porat
- Biological Services Department, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, 7610001, Israel
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Abstract
Aquatic photosynthetic eukaryotes represent highly diverse groups (green, red, and chromalveolate algae) derived from multiple endosymbiosis events, covering a wide spectrum of the tree of life. They are responsible for about 50% of the global photosynthesis and serve as the foundation for oceanic and fresh water food webs. Although the ecophysiology and molecular ecology of some algal species are extensively studied, some basic aspects of algal cell biology are still underexplored. The recent wealth of genomic resources from algae has opened new frontiers to decipher the role of cell signaling pathways and their function in an ecological and biotechnological context. Here, we took a bioinformatic approach to explore the distribution and conservation of TOR and autophagy-related (ATG) proteins (Atg in yeast) in diverse algal groups. Our genomic analysis demonstrates conservation of TOR and ATG proteins in green algae. In contrast, in all 5 available red algal genomes, we could not detect the sequences that encode for any of the 17 core ATG proteins examined, albeit TOR and its interacting proteins are conserved. This intriguing data suggests that the autophagy pathway is not conserved in red algae as it is in the entire eukaryote domain. In contrast, chromalveolates, despite being derived from the red-plastid lineage, retain and express ATG genes, which raises a fundamental question regarding the acquisition of ATG genes during algal evolution. Among chromalveolates, Emiliania huxleyi (Haptophyta), a bloom-forming coccolithophore, possesses the most complete set of ATG genes, and may serve as a model organism to study autophagy in marine protists with great ecological significance.
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Key Words
- ATG, autophagy related
- ATG8
- ATG9
- DUF, domain of unknown function
- EST, expressed sequence tag
- EhV, Emiliania huxleyi virus
- GABARAP, GABA(A) receptor-associated protein
- PtdIns3K, phosphatidylinositol 3-kinase
- RPTOR, regulatory associated protein of MTOR, complex 1
- TOR, target of rapamycin
- TORC, target of rapamycin complex
- Ubl, ubiquitin-like
- Vps, vacuolar protein sorting
- algae
- autophagy
- blooms
- chromalveolata
- phylogenetics
- phytoplankton
- rhodophyta
- stress
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Affiliation(s)
- Adva Shemi
- a Department of Plant Sciences ; Weizmann Institute of Science ; Rehovot , Israel
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Schatz D, Shemi A, Rosenwasser S, Sabanay H, Wolf SG, Ben-Dor S, Vardi A. Hijacking of an autophagy-like process is critical for the life cycle of a DNA virus infecting oceanic algal blooms. New Phytol 2014; 204:854-63. [PMID: 25195618 PMCID: PMC4233938 DOI: 10.1111/nph.13008] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 07/27/2014] [Indexed: 05/04/2023]
Abstract
Marine photosynthetic microorganisms are the basis of marine food webs and are responsible for nearly 50% of the global primary production. Emiliania huxleyi forms massive oceanic blooms that are routinely terminated by large double-stranded DNA coccolithoviruses. The cellular mechanisms that govern the replication cycle of these giant viruses are largely unknown. We used diverse techniques, including fluorescence microscopy, transmission electron microscopy, cryoelectron tomography, immunolabeling and biochemical methodologies to investigate the role of autophagy in host-virus interactions. Hallmarks of autophagy are induced during the lytic phase of E. huxleyi viral infection, concomitant with up-regulation of autophagy-related genes (ATG genes). Pretreatment of the infected cells with an autophagy inhibitor causes a major reduction in the production of extracellular viral particles, without reducing viral DNA replication within the cell. The host-encoded Atg8 protein was detected within purified virions, demonstrating the pivotal role of the autophagy-like process in viral assembly and egress. We show that autophagy, which is classically considered as a defense mechanism, is essential for viral propagation and for facilitating a high burst size. This cellular mechanism may have a major impact on the fate of the viral-infected blooms, and therefore on the cycling of nutrients within the marine ecosystem.
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Affiliation(s)
- Daniella Schatz
- Department of Plant Sciences, Weizmann Institute of ScienceRehovot, 76100, Israel
| | - Adva Shemi
- Department of Plant Sciences, Weizmann Institute of ScienceRehovot, 76100, Israel
| | - Shilo Rosenwasser
- Department of Plant Sciences, Weizmann Institute of ScienceRehovot, 76100, Israel
| | - Helena Sabanay
- Department of Chemical Research Support, Weizmann Institute of ScienceRehovot, 76100, Israel
| | - Sharon G Wolf
- Department of Chemical Research Support, Weizmann Institute of ScienceRehovot, 76100, Israel
| | - Shifra Ben-Dor
- Department of Biological Services, Weizmann Institute of ScienceRehovot, 76100, Israel
| | - Assaf Vardi
- Department of Plant Sciences, Weizmann Institute of ScienceRehovot, 76100, Israel
- Author for correspondence: Assaf Vardi, Tel: +972 8 934 2914,
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