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Zhao N, Liu F, Dong W, Yu J, Halverson LJ, Xie B. Quantitative proteomics insights into Chlamydomonas reinhardtii thermal tolerance enhancement by a mutualistic interaction with Sinorhizobium meliloti. Microbiol Spectr 2024:e0021924. [PMID: 39012118 DOI: 10.1128/spectrum.00219-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/21/2024] [Indexed: 07/17/2024] Open
Abstract
Interactions between photosynthetic microalgae and bacteria impact the physiology of both partners, which influence the fitness and ecological trajectories of each partner in an environmental context-dependent manner. Thermal tolerance of Chlamydomonas reinhardtii can be enhanced through a mutualistic interaction with vitamin B12 (cobalamin)-producing Sinorhizobium meliloti. Here, we used label-free quantitative proteomics to reveal the metabolic networks altered by the interaction under normal and high temperatures. We created a scenario where the growth of Sinorhizobium requires carbon provided by Chlamydomonas for growth in co-cultures, and survival of Chlamydomonas under high temperatures relies on cobalamin and possibly other metabolites produced by Sinorhizobium. Differential abundance analysis identified proteins produced by each partner in co-cultures compared to mono-cultures at each temperature. Proteins involved in cobalamin production by Sinorhizobium increased in the presence of Chlamydomonas under elevated temperatures, whereas in Chlamydomonas, there was an increase in cobalamin-dependent methionine synthase and certain proteins associated with methylation reactions. Co-cultivation and heat stress strongly modulated the central metabolism of both partners as well as various transporters that could facilitate nutrient cross-utilization. Co-cultivation modulated expression of various components of two- or one-component signal transduction systems, transcriptional activators/regulators, or sigma factors, suggesting complex regulatory networks modulate the interaction in a temperature-dependent manner. Notably, heat and general stress-response and antioxidant proteins were upregulated in co-cultures, suggesting that the interaction is inherently stressful to each partner despite the benefits of mutualism. Our results shed insight into the metabolic tradeoffs required for mutualism and how metabolic networks are modulated by elevated temperature. IMPORTANCE Photosynthetic microalgae are key primary producers in aquatic ecosystems, playing an important role in the global carbon cycle. Nearly every alga lives in association with a diverse community of microorganisms that influence each other and their metabolic activities or survival. One chemical produced by bacteria that influence algae is vitamin B12, an enzyme cofactor used for a variety of metabolic functions. The alga Chlamydomonas reinhardtii benefits from vitamin B12 produced by Sinorhizobium meliloti by producing the amino acid methionine under high temperatures which are required for Chlamydomonas thermotolerance. Yet, our understanding of this interaction under normal and stressful temperatures is poor. Here, we used quantitative proteomics to identify differentially expressed proteins to reveal metabolic adjustments made by Chlamydomonas and Sinorhizobium that could facilitate this mutualism. These findings will enhance our understanding of how photosynthetic algae and their associated microbiomes will respond as global temperatures increase.
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Affiliation(s)
- Na Zhao
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
- Translational Medicine Research Center, Guizhou Medical University, Guiyang, China
| | - Fei Liu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
| | - Wenxiu Dong
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
| | - Jie Yu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
| | - Larry J Halverson
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Bo Xie
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
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Martínez-Pérez C, Zweifel ST, Pioli R, Stocker R. Space, the final frontier: The spatial component of phytoplankton-bacterial interactions. Mol Microbiol 2024. [PMID: 38970428 DOI: 10.1111/mmi.15293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 07/08/2024]
Abstract
Microscale interactions between marine phytoplankton and bacteria shape the microenvironment of individual cells, impacting their physiology and ultimately influencing global-scale biogeochemical processes like carbon and nutrient cycling. In dilute environments such as the ocean water column, metabolic exchange between microorganisms likely requires close proximity between partners. However, the biological strategies to achieve this physical proximity remain an understudied aspect of phytoplankton-bacterial associations. Understanding the mechanisms by which these microorganisms establish and sustain spatial relationships and the extent to which spatial proximity is necessary for interactions to occur, is critical to learning how spatial associations influence the ecology of phytoplankton and bacterial communities. Here, we provide an overview of current knowledge on the role of space in shaping interactions among ocean microorganisms, encompassing behavioural and metabolic evidence. We propose that characterising phytoplankton-bacterial interactions from a spatial perspective can contribute to a mechanistic understanding of the establishment and maintenance of these associations and, consequently, an enhanced ability to predict the impact of microscale processes on ecosystem-wide phenomena.
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Affiliation(s)
- Clara Martínez-Pérez
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Sophie T Zweifel
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Roberto Pioli
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
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Dupuis S, Lingappa UF, Mayali X, Sindermann ES, Chastain JL, Weber PK, Stuart R, Merchant SS. Scarcity of fixed carbon transfer in a model microbial phototroph-heterotroph interaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577492. [PMID: 38328118 PMCID: PMC10849638 DOI: 10.1101/2024.01.26.577492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Although the green alga Chlamydomonas reinhardtii has long served as a reference organism, few studies have interrogated its role as a primary producer in microbial interactions. Here, we quantitatively investigated C. reinhardtii's capacity to support a heterotrophic microbe using the established coculture system with Mesorhizobium japonicum , a vitamin B 12 -producing α-proteobacterium. Using stable isotope probing and nanoscale secondary ion mass spectrometry (nanoSIMS), we tracked the flow of photosynthetic fixed carbon and consequent bacterial biomass synthesis under continuous and diurnal light with single-cell resolution. We found that more 13 C fixed by the alga was taken up by bacterial cells under continuous light, invalidating the hypothesis that the alga's fermentative degradation of starch reserves during the night would boost M. japonicum heterotrophy. 15 NH 4 assimilation rates and changes in cell size revealed that M. japonicum cells reduced new biomass synthesis in coculture with the alga but continued to divide - a hallmark of nutrient limitation often referred to as reductive division. Despite this sign of starvation, the bacterium still synthesized vitamin B 12 and supported the growth of a B 12 -dependent C. reinhardtii mutant. Finally, we showed that bacterial proliferation could be supported solely by the algal lysis that occurred in coculture, highlighting the role of necromass in carbon cycling. Collectively, these results reveal the scarcity of fixed carbon in this microbial trophic relationship (particularly under environmentally relevant light regimes), demonstrate B 12 exchange even during bacterial starvation, and underscore the importance of quantitative approaches for assessing metabolic coupling in algal-bacterial interactions.
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Swaney MH, Henriquez N, Campbell T, Handelsman J, Kalan LR. Skin-associated Corynebacterium amycolatum shares cobamides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.28.591522. [PMID: 38712214 PMCID: PMC11071462 DOI: 10.1101/2024.04.28.591522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The underlying interactions that occur to maintain skin microbiome composition, function, and overall skin health are largely unknown. Often, these types of interactions are mediated by microbial metabolites. Cobamides, the vitamin B12 family of cofactors, are essential for metabolism in many bacteria, but are only synthesized by a small fraction of prokaryotes, including certain skin-associated species. Therefore, we hypothesize that cobamide sharing mediates skin community dynamics. Preliminary work predicts that several skin-associated Corynebacterium species encode de novo cobamide biosynthesis and that their abundance is associated with skin microbiome diversity. Here, we show that commensal Corynebacterium amycolatum produces cobamides and that this synthesis can be tuned by cobalt limitation. To demonstrate cobamide sharing by C. amycolatum, we employed a co-culture assay using an E. coli cobamide auxotroph and show that C. amycolatum produces sufficient cobamides to support E. coli growth, both in liquid co-culture and when separated spatially on solid medium. We also generated a C. amycolatum non-cobamide-producing strain (cob-) using UV mutagenesis that contains mutated cobamide biosynthesis genes cobK and cobO and confirm that disruption of cobamide biosynthesis abolishes support of E. coli growth through cobamide sharing. Our study provides a unique model to study metabolite sharing by microorganisms, which will be critical for understanding the fundamental interactions that occur within complex microbiomes and for developing approaches to target the human microbiota for health advances.
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Affiliation(s)
- M H Swaney
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin, Madison, WI, USA
| | - N Henriquez
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, CAN
| | - T Campbell
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, CAN
| | - J Handelsman
- Wisconsin Institute for Discovery, Madison, WI, USA
- Department of Plant Pathology, University of Wisconsin, Madison, WI, USA
| | - L R Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, CAN
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, CAN
- David Braley Centre for Antibiotic Discovery, Hamilton, ON, CAN
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5
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Carrasco Flores D, Hotter V, Vuong T, Hou Y, Bando Y, Scherlach K, Burgunter-Delamare B, Hermenau R, Komor AJ, Aiyar P, Rose M, Sasso S, Arndt HD, Hertweck C, Mittag M. A mutualistic bacterium rescues a green alga from an antagonist. Proc Natl Acad Sci U S A 2024; 121:e2401632121. [PMID: 38568970 PMCID: PMC11009677 DOI: 10.1073/pnas.2401632121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024] Open
Abstract
Photosynthetic protists, known as microalgae, are key contributors to primary production on Earth. Since early in evolution, they coexist with bacteria in nature, and their mode of interaction shapes ecosystems. We have recently shown that the bacterium Pseudomonas protegens acts algicidal on the microalga Chlamydomonas reinhardtii. It secretes a cyclic lipopeptide and a polyyne that deflagellate, blind, and lyse the algae [P. Aiyar et al., Nat. Commun. 8, 1756 (2017) and V. Hotter et al., Proc. Natl. Acad. Sci. U.S.A. 118, e2107695118 (2021)]. Here, we report about the bacterium Mycetocola lacteus, which establishes a mutualistic relationship with C. reinhardtii and acts as a helper. While M. lacteus enhances algal growth, it receives methionine as needed organic sulfur and the vitamins B1, B3, and B5 from the algae. In tripartite cultures with the alga and the antagonistic bacterium P. protegens, M. lacteus aids the algae in surviving the bacterial attack. By combining synthetic natural product chemistry with high-resolution mass spectrometry and an algal Ca2+ reporter line, we found that M. lacteus rescues the alga from the antagonistic bacterium by cleaving the ester bond of the cyclic lipopeptide involved. The resulting linearized seco acid does not trigger a cytosolic Ca2+ homeostasis imbalance that leads to algal deflagellation. Thus, the algae remain motile, can swim away from the antagonistic bacteria and survive the attack. All three involved genera cooccur in nature. Remarkably, related species of Pseudomonas and Mycetocola also act antagonistically against C. reinhardtii or as helper bacteria in tripartite cultures.
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Affiliation(s)
- David Carrasco Flores
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
| | - Vivien Hotter
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
| | - Trang Vuong
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
| | - Yu Hou
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
| | - Yuko Bando
- Institute for Organic Chemistry and Macromolecular Chemistry, Organic Chemistry, Friedrich Schiller University Jena, Jena07743, Germany
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knöll Institute), Jena07745, Germany
| | - Bertille Burgunter-Delamare
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
| | - Ron Hermenau
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knöll Institute), Jena07745, Germany
| | - Anna J. Komor
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knöll Institute), Jena07745, Germany
| | - Prasad Aiyar
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
| | - Magdalena Rose
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
- Institute of Biology, Plant Physiology, Leipzig University, Leipzig04103, Germany
| | - Severin Sasso
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
- Institute of Biology, Plant Physiology, Leipzig University, Leipzig04103, Germany
| | - Hans-Dieter Arndt
- Institute for Organic Chemistry and Macromolecular Chemistry, Organic Chemistry, Friedrich Schiller University Jena, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knöll Institute), Jena07745, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena 07743, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena07743, Germany
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena 07743, Germany
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6
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Burgunter-Delamare B, Shetty P, Vuong T, Mittag M. Exchange or Eliminate: The Secrets of Algal-Bacterial Relationships. PLANTS (BASEL, SWITZERLAND) 2024; 13:829. [PMID: 38592793 PMCID: PMC10974524 DOI: 10.3390/plants13060829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024]
Abstract
Algae and bacteria have co-occurred and coevolved in common habitats for hundreds of millions of years, fostering specific associations and interactions such as mutualism or antagonism. These interactions are shaped through exchanges of primary and secondary metabolites provided by one of the partners. Metabolites, such as N-sources or vitamins, can be beneficial to the partner and they may be assimilated through chemotaxis towards the partner producing these metabolites. Other metabolites, especially many natural products synthesized by bacteria, can act as toxins and damage or kill the partner. For instance, the green microalga Chlamydomonas reinhardtii establishes a mutualistic partnership with a Methylobacterium, in stark contrast to its antagonistic relationship with the toxin producing Pseudomonas protegens. In other cases, as with a coccolithophore haptophyte alga and a Phaeobacter bacterium, the same alga and bacterium can even be subject to both processes, depending on the secreted bacterial and algal metabolites. Some bacteria also influence algal morphology by producing specific metabolites and micronutrients, as is observed in some macroalgae. This review focuses on algal-bacterial interactions with micro- and macroalgal models from marine, freshwater, and terrestrial environments and summarizes the advances in the field. It also highlights the effects of temperature on these interactions as it is presently known.
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Affiliation(s)
- Bertille Burgunter-Delamare
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany; (P.S.); (T.V.)
| | - Prateek Shetty
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany; (P.S.); (T.V.)
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Trang Vuong
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany; (P.S.); (T.V.)
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany; (P.S.); (T.V.)
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany
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7
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Rao D, Füssy Z, Brisbin MM, McIlvin MR, Moran DM, Allen AE, Follows MJ, Saito MA. Flexible B 12 ecophysiology of Phaeocystis antarctica due to a fusion B 12-independent methionine synthase with widespread homologues. Proc Natl Acad Sci U S A 2024; 121:e2204075121. [PMID: 38306482 PMCID: PMC10861871 DOI: 10.1073/pnas.2204075121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 11/13/2023] [Indexed: 02/04/2024] Open
Abstract
Coastal Antarctic marine ecosystems are significant in carbon cycling because of their intense seasonal phytoplankton blooms. Southern Ocean algae are primarily limited by light and iron (Fe) and can be co-limited by cobalamin (vitamin B12). Micronutrient limitation controls productivity and shapes the composition of blooms which are typically dominated by either diatoms or the haptophyte Phaeocystis antarctica. However, the vitamin requirements and ecophysiology of the keystone species P. antarctica remain poorly characterized. Using cultures, physiological analysis, and comparative omics, we examined the response of P. antarctica to a matrix of Fe-B12 conditions. We show that P. antarctica is not auxotrophic for B12, as previously suggested, and identify mechanisms underlying its B12 response in cultures of predominantly solitary and colonial cells. A combination of proteomics and proteogenomics reveals a B12-independent methionine synthase fusion protein (MetE-fusion) that is expressed under vitamin limitation and interreplaced with the B12-dependent isoform under replete conditions. Database searches return homologues of the MetE-fusion protein in multiple Phaeocystis species and in a wide range of marine microbes, including other photosynthetic eukaryotes with polymorphic life cycles as well as bacterioplankton. Furthermore, we find MetE-fusion homologues expressed in metaproteomic and metatranscriptomic field samples in polar and more geographically widespread regions. As climate change impacts micronutrient availability in the coastal Southern Ocean, our finding that P. antarctica has a flexible B12 metabolism has implications for its relative fitness compared to B12-auxotrophic diatoms and for the detection of B12-stress in a more diverse set of marine microbes.
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Affiliation(s)
- Deepa Rao
- Earth Atmospheric Planetary Sciences Department, Massachusetts Institute of Technology, Cambridge, MA02139
- Marine Chemistry and Geochemistry Department, Woods Hole, MA02543
| | - Zoltán Füssy
- Microbial and Environmental Genomics Department, J.C. Venter Institute, La Jolla, CA92037
| | | | | | - Dawn M. Moran
- Marine Chemistry and Geochemistry Department, Woods Hole, MA02543
| | - Andrew E. Allen
- Microbial and Environmental Genomics Department, J.C. Venter Institute, La Jolla, CA92037
- Integrative Oceanography Division, Scripps Instition of Oceanography, University of California San Diego, La Jolla, CA92037
| | - Michael J. Follows
- Earth Atmospheric Planetary Sciences Department, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Mak A. Saito
- Marine Chemistry and Geochemistry Department, Woods Hole, MA02543
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8
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Sayer AP, Llavero-Pasquina M, Geisler K, Holzer A, Bunbury F, Mendoza-Ochoa GI, Lawrence AD, Warren MJ, Mehrshahi P, Smith AG. Conserved cobalamin acquisition protein 1 is essential for vitamin B12 uptake in both Chlamydomonas and Phaeodactylum. PLANT PHYSIOLOGY 2024; 194:698-714. [PMID: 37864825 PMCID: PMC10828217 DOI: 10.1093/plphys/kiad564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/01/2023] [Accepted: 08/18/2023] [Indexed: 10/23/2023]
Abstract
Microalgae play an essential role in global net primary productivity and global biogeochemical cycling. Despite their phototrophic lifestyle, over half of algal species depend for growth on acquiring an external supply of the corrinoid vitamin B12 (cobalamin), a micronutrient produced only by a subset of prokaryotic organisms. Previous studies have identified protein components involved in vitamin B12 uptake in bacterial species and humans. However, little is known about its uptake in algae. Here, we demonstrate the essential role of a protein, cobalamin acquisition protein 1 (CBA1), in B12 uptake in Phaeodactylum tricornutum using CRISPR-Cas9 to generate targeted knockouts and in Chlamydomonas reinhardtii by insertional mutagenesis. In both cases, CBA1 knockout lines could not take up exogenous vitamin B12. Complementation of the C. reinhardtii mutants with the wild-type CBA1 gene restored B12 uptake, and regulation of CBA1 expression via a riboswitch element enabled control of the phenotype. When visualized by confocal microscopy, a YFP-fusion with C. reinhardtii CBA1 showed association with membranes. Bioinformatics analysis found that CBA1-like sequences are present in all major eukaryotic phyla. In algal taxa, the majority that encoded CBA1 also had genes for B12-dependent enzymes, suggesting CBA1 plays a conserved role. Our results thus provide insight into the molecular basis of algal B12 acquisition, a process that likely underpins many interactions in aquatic microbial communities.
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Affiliation(s)
- Andrew P Sayer
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Marcel Llavero-Pasquina
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Katrin Geisler
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Andre Holzer
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Freddy Bunbury
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Gonzalo I Mendoza-Ochoa
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Andrew D Lawrence
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UA, UK
| | - Payam Mehrshahi
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
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9
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Craig RJ, Gallaher SD, Shu S, Salomé PA, Jenkins JW, Blaby-Haas CE, Purvine SO, O’Donnell S, Barry K, Grimwood J, Strenkert D, Kropat J, Daum C, Yoshinaga Y, Goodstein DM, Vallon O, Schmutz J, Merchant SS. The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory. THE PLANT CELL 2023; 35:644-672. [PMID: 36562730 PMCID: PMC9940879 DOI: 10.1093/plcell/koac347] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 10/12/2022] [Accepted: 12/16/2022] [Indexed: 05/20/2023]
Abstract
Five versions of the Chlamydomonas reinhardtii reference genome have been produced over the last two decades. Here we present version 6, bringing significant advances in assembly quality and structural annotations. PacBio-based chromosome-level assemblies for two laboratory strains, CC-503 and CC-4532, provide resources for the plus and minus mating-type alleles. We corrected major misassemblies in previous versions and validated our assemblies via linkage analyses. Contiguity increased over ten-fold and >80% of filled gaps are within genes. We used Iso-Seq and deep RNA-seq datasets to improve structural annotations, and updated gene symbols and textual annotation of functionally characterized genes via extensive manual curation. We discovered that the cell wall-less classical reference strain CC-503 exhibits genomic instability potentially caused by deletion of the helicase RECQ3, with major structural mutations identified that affect >100 genes. We therefore present the CC-4532 assembly as the primary reference, although this strain also carries unique structural mutations and is experiencing rapid proliferation of a Gypsy retrotransposon. We expect all laboratory strains to harbor gene-disrupting mutations, which should be considered when interpreting and comparing experimental results. Collectively, the resources presented here herald a new era of Chlamydomonas genomics and will provide the foundation for continued research in this important reference organism.
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Affiliation(s)
- Rory J Craig
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sean D Gallaher
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
| | - Shengqiang Shu
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - Patrice A Salomé
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, USA
| | - Jerry W Jenkins
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Crysten E Blaby-Haas
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Samuel O’Donnell
- Laboratory of Computational and Quantitative Biology, UMR 7238, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris 75005, France
| | - Kerrie Barry
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - Jane Grimwood
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Daniela Strenkert
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
| | - Janette Kropat
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Chris Daum
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - Yuko Yoshinaga
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - David M Goodstein
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - Olivier Vallon
- Unité Mixte de Recherche 7141, CNRS, Institut de Biologie Physico-Chimique, Sorbonne Université, Paris 75005, France
| | - Jeremy Schmutz
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Sabeeha S Merchant
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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10
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Calatrava V, Tejada-Jimenez M, Sanz-Luque E, Fernandez E, Galvan A, Llamas A. Chlamydomonas reinhardtii, a Reference Organism to Study Algal-Microbial Interactions: Why Can't They Be Friends? PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12040788. [PMID: 36840135 PMCID: PMC9965935 DOI: 10.3390/plants12040788] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 05/13/2023]
Abstract
The stability and harmony of ecological niches rely on intricate interactions between their members. During evolution, organisms have developed the ability to thrive in different environments, taking advantage of each other. Among these organisms, microalgae are a highly diverse and widely distributed group of major primary producers whose interactions with other organisms play essential roles in their habitats. Understanding the basis of these interactions is crucial to control and exploit these communities for ecological and biotechnological applications. The green microalga Chlamydomonas reinhardtii, a well-established model, is emerging as a model organism for studying a wide variety of microbial interactions with ecological and economic significance. In this review, we unite and discuss current knowledge that points to C. reinhardtii as a model organism for studying microbial interactions.
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Affiliation(s)
- Victoria Calatrava
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama St., Stanford, CA 94305, USA
| | - Manuel Tejada-Jimenez
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
| | - Emanuel Sanz-Luque
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
| | - Emilio Fernandez
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
| | - Aurora Galvan
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
| | - Angel Llamas
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
- Correspondence: ; Tel.: +34-957-218352
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11
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Nef C, Madoui MA, Pelletier É, Bowler C. Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros. PLoS Biol 2022; 20:e3001893. [PMID: 36441816 PMCID: PMC9731442 DOI: 10.1371/journal.pbio.3001893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 12/08/2022] [Accepted: 10/27/2022] [Indexed: 11/30/2022] Open
Abstract
Diatoms form a diverse and abundant group of photosynthetic protists that are essential players in marine ecosystems. However, the microevolutionary structure of their populations remains poorly understood, particularly in polar regions. Exploring how closely related diatoms adapt to different environments is essential given their short generation times, which may allow rapid adaptations, and their prevalence in marine regions dramatically impacted by climate change, such as the Arctic and Southern Oceans. Here, we address genetic diversity patterns in Chaetoceros, the most abundant diatom genus and one of the most diverse, using 11 metagenome-assembled genomes (MAGs) reconstructed from Tara Oceans metagenomes. Genome-resolved metagenomics on these MAGs confirmed a prevalent distribution of Chaetoceros in the Arctic Ocean with lower dispersal in the Pacific and Southern Oceans as well as in the Mediterranean Sea. Single-nucleotide variants identified within the different MAG populations allowed us to draw a landscape of Chaetoceros genetic diversity and revealed an elevated genetic structure in some Arctic Ocean populations. Gene flow patterns of closely related Chaetoceros populations seemed to correlate with distinct abiotic factors rather than with geographic distance. We found clear positive selection of genes involved in nutrient availability responses, in particular for iron (e.g., ISIP2a, flavodoxin), silicate, and phosphate (e.g., polyamine synthase), that were further supported by analysis of Chaetoceros transcriptomes. Altogether, these results highlight the importance of environmental selection in shaping diatom diversity patterns and provide new insights into their metapopulation genomics through the integration of metagenomic and environmental data.
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Affiliation(s)
- Charlotte Nef
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
| | - Mohammed-Amin Madoui
- Service d’Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, Dijon, 21000, France
| | - Éric Pelletier
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Metabolic Genomics, Genoscope, Institut de Biologie François-Jacob, CEA, CNRS, Université Evry, Université Paris Saclay, Evry, France
| | - Chris Bowler
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- * E-mail:
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12
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Lin S, Hu Z, Song X, Gobler CJ, Tang YZ. Vitamin B 12-auxotrophy in dinoflagellates caused by incomplete or absent cobalamin-independent methionine synthase genes ( metE). FUNDAMENTAL RESEARCH 2022; 2:727-737. [PMID: 38933134 PMCID: PMC11197592 DOI: 10.1016/j.fmre.2021.12.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 12/17/2021] [Accepted: 12/28/2021] [Indexed: 10/19/2022] Open
Abstract
Dinoflagellates are responsible for most marine harmful algal blooms (HABs) and play vital roles in many ocean processes. More than 90% of dinoflagellates are vitamin B12 auxotrophs and that B12 availability can control dinoflagellate HABs, yet the genetic basis of B12 auxotrophy in dinoflagellates in the framework of the ecology of dinoflagellates and particularly HABs, which was the objective of this work. Here, we investigated the presence, phylogeny, and transcription of two methionine synthase genes (B12-dependent metH and B12-independent metE) via searching and assembling transcripts and genes from transcriptomic and genomic databases, cloning 38 cDNA isoforms of the two genes from 14 strains of dinoflagellates, measuring the expression at different scenarios of B12, and comprehensive phylogenetic analyses of more than 100 organisms. We found that 1) metH was present in all 58 dinoflagellates accessible and metE was present in 40 of 58 species, 2) all metE genes lacked N-terminal domains, 3) metE of dinoflagellates were phylogenetically distinct from other known metE genes, and 4) expression of metH in dinoflagellates was responsive to exogenous B12 levels while expression of metE was not responding as that of genuine metE genes. We conclude that most, hypothetically all, dinoflagellates have either non-functional metE genes lacking N-terminal domain for most species, or do not possess metE for other species, which provides the genetic basis for the widespread nature of B12 auxotrophy in dinoflagellates. The work elucidated a fundamental aspect of the nutritional ecology of dinoflagellates.
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Affiliation(s)
- Siheng Lin
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Current address: Department of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou 363000, China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xiaoying Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Ying Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
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13
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Song X, Lin S, Hu Z, Liu Y, Deng Y, Tang YZ. Possible functions of CobW domain-containing (CBWD) genes in dinoflagellates using Karlodinium veneficum as a representative. HARMFUL ALGAE 2022; 117:102274. [PMID: 35944961 DOI: 10.1016/j.hal.2022.102274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 05/30/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Since > 91% of dinoflagellates are proven auxotrophs of vitamin B12 and the cobalamin synthetase W (CobW) is a key gene involved in vitamin B12 synthesis pathway, a number of CobW domain-containing (CBWD) genes in dinoflagellates (DinoCBWDs) were surprisedly found from our transcriptomic and meta-transcriptomic studies. A total of 88 DinoCBWD genes were identified from the genomes and transcriptomes of four dinoflagellates, with five being cloned for full-lengths and characterized using the cosmopolitan and ecologically-important dinoflagellates Karlodinium veneficum and Scrippsiella trochoidea (synonym of Scrippsiella acuminata). DinoCBWDs were verified being irrelevant to vitamin B12 biosynthesis due to their transcriptions irresponsive to vitamin B12 levels and their phylogenetic positions. A comprehensive phylogenetic analysis demonstrated 75 out of the 88 DinoCBWD genes identified belong to three subfamilies of COG0523 protein family, of which most prokaryotic members are reported to be metallochaperones and the eukaryotic members are ubiquitously found but mostly unknown for their functions. Our results from K. veneficum demonstrated DinoCBWDs are associated with metal homeostasis and other divergent functions, with four KvCBWDs involving in zinc homeostasis and KvCBWD1 likely functioning as Fe-type nitrile hydratase activator. In addition, conserved motif analysis revealed the structural foundation of KvCBWD proteins that are consistent with previously described CBWD proteins with GTPase activity and metal binding. Our results provide a stepping-stone toward better understanding the functions of DinoCBWDs and the COG0523 family.
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Affiliation(s)
- Xiaoying Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Siheng Lin
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yuyang Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yunyan Deng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Ying Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
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14
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Bunbury F, Deery E, Sayer AP, Bhardwaj V, Harrison EL, Warren MJ, Smith AG. Exploring the onset of B 12 -based mutualisms using a recently evolved Chlamydomonas auxotroph and B 12 -producing bacteria. Environ Microbiol 2022; 24:3134-3147. [PMID: 35593514 PMCID: PMC9545926 DOI: 10.1111/1462-2920.16035] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/28/2022] [Accepted: 04/29/2022] [Indexed: 12/01/2022]
Abstract
Cobalamin (vitamin B12 ) is a cofactor for essential metabolic reactions in multiple eukaryotic taxa, including major primary producers such as algae, and yet only prokaryotes can produce it. Many bacteria can colonize the algal phycosphere, forming stable communities that gain preferential access to photosynthate and in return provide compounds such as B12 . Extended coexistence can then drive gene loss, leading to greater algal-bacterial interdependence. In this study, we investigate how a recently evolved B12 -dependent strain of Chlamydomonas reinhardtii, metE7, forms a mutualism with certain bacteria, including the rhizobium Mesorhizobium loti and even a strain of the gut bacterium E. coli engineered to produce cobalamin. Although metE7 was supported by B12 producers, its growth in co-culture was slower than the B12 -independent wild-type, suggesting that high bacterial B12 provision may be necessary to favour B12 auxotrophs and their evolution. Moreover, we found that an E. coli strain that releases more B12 makes a better mutualistic partner, and although this trait may be more costly in isolation, greater B12 release provided an advantage in co-cultures. We hypothesize that, given the right conditions, bacteria that release more B12 may be selected for, particularly if they form close interactions with B12 -dependent algae.
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Affiliation(s)
- Freddy Bunbury
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NH, UK
| | - Andrew P Sayer
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Vaibhav Bhardwaj
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Ellen L Harrison
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NH, UK.,Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
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15
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Nowruzi B, Shishir MA, Porzani SJ, Ferdous UT. Exploring the Interactions between Algae and Bacteria. Mini Rev Med Chem 2022; 22:2596-2607. [PMID: 35507745 DOI: 10.2174/1389557522666220504141047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/01/2022] [Accepted: 03/17/2022] [Indexed: 11/22/2022]
Abstract
Humans have used algae for hundreds of years to make various products viz. agar, fertilizer, food, and pigments. Algae are also used in bioremediation to clean up polluted water and as essential laboratory tools in genomics, proteomics, and other research applications such as environmental warnings. Several special features of algae, including the oxygenic photosynthesis, higher yield in biomass, growth on the non-arable lands, their survival in a wide range of water supplies (contaminated or filtered waters), the production of necessary byproducts and biofuels, the enhancement of soil productivity, and the greenhouse gas emissions, etc. altogether rendered them as vital bio-resources in the sustainable development. Algae and bacteria have been assumed to coexist from the early stages of the development of the earth, and a wide variety of interactions were observed between them which have influenced the ecosystems ranging from the oceans to the lichens. Research has shown that bacteria and algae interact synergistically, especially roseobacter-algae interactions being the most common. These interactions are common to all ecosystems and characterize their primary efficiency. The commercialization of algae for industrial purposes, an important field, is also influenced by this interaction which frequently results in bacterial infections among the consumers. However, the recent findings have revealed that the bacteria improve algal growth and support flocculation which are very crucial in algal biotechnology. Some of the most exciting advancements in the area of algal biotic interactions and potential difficulties were reviewed in this article. Information gleaned in this study would provide a firm foundation for launching more contemporaneous research efforts in understanding and utilizing the algal species in biotechnology industries and medical sectors.
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Affiliation(s)
- Bahareh Nowruzi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Samaneh J Porzani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Umme Tamanna Ferdous
- Aquatic Animal Health and Therapeutics Laboratory (AquaHealth), Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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16
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Saxena A, Mishra B, Sindhu R, Binod P, Tiwari A. Nutrient acclimation in benthic diatoms with adaptive laboratory evolution. BIORESOURCE TECHNOLOGY 2022; 351:126955. [PMID: 35272038 DOI: 10.1016/j.biortech.2022.126955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
The growth of marine diatom algaeChaetoceros gracilisandThalassiosira weissflogiiin agricultural fertilizers and additional carbon sources were evaluated. The main objective behind the study was to increase the growth and productivity of the diatom acclimatized under adaptive laboratory culture conditions. In optimized conditions,C.gracilisshowed the highest cell density in NPK (202.5 ± 2.6 × 105 cells mL-1), maximum carbohydrate (212.8 ± 4.0 mg g-1) and protein (133.9 ± 1.5 mg g-1) in urea. In contrast,T.weissflogiishowed the highest cell density in glycerol (148.2 ± 2.5x105 cells mL-1), maximum carbohydrate in glycerol (273.7 ± 3.3 mg g-1), and protein in sucrose (126.2 ± 0.7 mg g-1). Lipid content was maximum in glycerol (73.4 ± 0.6%) and glucose (39.7 ± 0.2%) in C. gracilisand T. weissflogii respectively. Increased pigment production and chrysolaminarin concentration were obtained in both marine species. The study highlights the importance of adaptive laboratory evolution as an promising tool in enhancing productivity in diatom algae.
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Affiliation(s)
- Abhishek Saxena
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201301, India
| | - Bharti Mishra
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201301, India
| | - Raveendran Sindhu
- Department of Food Technology, T K M Institute of Technology, Kollam - 691 505, Kerala, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India
| | - Archana Tiwari
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201301, India.
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17
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The Spermidine Synthase Gene SPD1: A Novel Auxotrophic Marker for Chlamydomonas reinhardtii Designed by Enhanced CRISPR/Cas9 Gene Editing. Cells 2022; 11:cells11050837. [PMID: 35269459 PMCID: PMC8909627 DOI: 10.3390/cells11050837] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/15/2022] [Accepted: 02/24/2022] [Indexed: 01/09/2023] Open
Abstract
Biotechnological application of the green microalga Chlamydomonas reinhardtii hinges on the availability of selectable markers for effective expression of multiple transgenes. However, biological safety concerns limit the establishment of new antibiotic resistance genes and until today, only a few auxotrophic markers exist for C. reinhardtii. The recent improvements in gene editing via CRISPR/Cas allow directed exploration of new endogenous selectable markers. Since editing frequencies remain comparably low, a Cas9-sgRNA ribonucleoprotein (RNP) delivery protocol was strategically optimized by applying nitrogen starvation to the pre-culture, which improved successful gene edits from 10% to 66% after pre-selection. Probing the essential polyamine biosynthesis pathway, the spermidine synthase gene (SPD1) is shown to be a potent selectable marker with versatile biotechnological applicability. Very low levels of spermidine (0.75 mg/L) were required to maintain normal mixotrophic and phototrophic growth in newly designed spermidine auxotrophic strains. Complementation of these strains with a synthetic SPD1 gene was achieved when the mature protein was expressed in the cytosol or targeted to the chloroplast. This work highlights the potential of new selectable markers for biotechnology as well as basic research and proposes an effective pipeline for the identification of new auxotrophies in C. reinhardtii.
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18
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Jin X, Yang Y, Cao H, Gao B, Zhao Z. Eco-phylogenetic analyses reveal divergent evolution of vitamin B 12 metabolism in the marine bacterial family 'Psychromonadaceae'. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:147-163. [PMID: 34921716 DOI: 10.1111/1758-2229.13036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Cobalamin (vitamin B12 ) is an essential micronutrient required by both prokaryotes and eukaryotes. Nevertheless, with high genetic and metabolic cost, de novo cobalamin biosynthesis is exclusive to a subset of prokaryotic taxa. Many Cyanobacterial and Archaeal taxa have been implicated in de novo cobalamin biosynthesis in epi- and mesopelagic ocean respectively. However, the contributions of Gammaproteobacteria particularly the family 'Psychromonadaceae' is largely unknown. Through phylo-pangenomic analyses using concatenated single-copy proteins and homologous gene clusters respectively, the phylogenies within 'Psychromonadaceae' recapitulate both their taxonomic delineations and environmental distributions. Moreover, uneven distribution of cobalamin de novo biosynthetic operon and cobalamin-dependent light-responsive regulon were observed, and of which the linkages to the environmental conditions where cobalamin availability and light regime can be varied respectively were discussed, suggesting the impacts of ecological divergence in shaping their disparate cobalamin-related metabolisms. Functional analysis demonstrated a varying degree of cobalamin dependency for both central metabolic processes and cobalamin-mediated light-responsive regulation, and underlying sequence characteristics of cis- and trans-regulatory elements were revealed. Our findings emphasized the potential roles of cobalamin in shaping the ecological distributions and driving the metabolic evolution in the marine bacterial family 'Psychromonadaceae', and have further implications for an improved understanding of nutritional interdependencies and community metabolism modulated by cobalamin.
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Affiliation(s)
- Xingkun Jin
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yaofang Yang
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Haihang Cao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Beile Gao
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Zhe Zhao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
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19
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Vargas-Lagunas C, Mora Y, Aguilar A, Reyes-González AR, Arteaga-Ide A, Dunn MF, Encarnación S, Girard L, Peralta H, Mora J. A Tar aspartate receptor and Rubisco-like protein substitute biotin in the growth of rhizobial strains. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35077343 PMCID: PMC8914248 DOI: 10.1099/mic.0.001130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Biotin is a key cofactor of metabolic carboxylases, although many rhizobial strains are biotin auxotrophs. When some of these strains were serially subcultured in minimal medium, they showed diminished growth and increased excretion of metabolites. The addition of biotin, or genetic complementation with biotin synthesis genes resulted in full growth of Rhizobium etli CFN42 and Rhizobium phaseoli CIAT652 strains. Half of rhizobial genomes did not show genes for biotin biosynthesis, but three-quarters had genes for biotin transport. Some strains had genes for an avidin homologue (rhizavidin), a protein with high affinity for biotin but an unknown role in bacteria. A CFN42-derived rhizavidin mutant showed a sharper growth decrease in subcultures, revealing a role in biotin storage. In the search of biotin-independent growth of subcultures, CFN42 and CIAT652 strains with excess aeration showed optimal growth, as they also did, unexpectedly, with the addition of aspartic acid analogues α- and N-methyl aspartate. Aspartate analogues can be sensed by the chemotaxis aspartate receptor Tar. A tar homologue was identified and its mutants showed no growth recovery with aspartate analogues, indicating requirement of the Tar receptor in such a phenotype. Additionally, tar mutants did not recover full growth with excess aeration. A Rubisco-like protein was found to be necessary for growth as the corresponding mutants showed no recovery either with high aeration or aspartate analogues; also, diminished carboxylation was observed. Taken together, our results indicate a route of biotin-independent growth in rhizobial strains that included oxygen, a Tar receptor and a previously uncharacterized Rubisco-like protein.
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Affiliation(s)
- Carmen Vargas-Lagunas
- Programa de Genómica Funcional de Procariotes, Laboratorio de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Yolanda Mora
- Programa de Genómica Funcional de Procariotes, Laboratorio de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Alejandro Aguilar
- Programa de Genómica Funcional de Procariotes, Laboratorio de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Alma Ruth Reyes-González
- Programa de Genómica Funcional de Procariotes, Laboratorio de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Alejandra Arteaga-Ide
- Programa de Genómica Funcional de Procariotes, Laboratorio de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Michael F Dunn
- Programa de Genómica Funcional de Procariotes, Laboratorio de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Sergio Encarnación
- Programa de Genómica Funcional de Procariotes, Laboratorio de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Lourdes Girard
- Programa de Genómica Funcional de Procariotes, Laboratorio de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Humberto Peralta
- Programa de Genómica Funcional de Procariotes, Laboratorio de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Jaime Mora
- Programa de Genómica Funcional de Procariotes, Laboratorio de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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20
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Zhang B, Wu J, Meng F. Adaptive Laboratory Evolution of Microalgae: A Review of the Regulation of Growth, Stress Resistance, Metabolic Processes, and Biodegradation of Pollutants. Front Microbiol 2021; 12:737248. [PMID: 34484172 PMCID: PMC8416440 DOI: 10.3389/fmicb.2021.737248] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 07/30/2021] [Indexed: 11/27/2022] Open
Abstract
Adaptive laboratory evolution (ALE) experiments are a serviceable method for the industrial utilization of the microalgae, which can improve the phenotype, performance, and stability of microalgae to obtain strains containing beneficial mutations. In this article, we reviewed the research into the microalgae ALE test and assessed the improvement of microalgae growth, tolerance, metabolism, and substrate utilization by ALE. In addition, the principles of ALE and the key factors of experimental design, as well as the issues and drawbacks of the microalgae ALE method were discussed. In general, improving the efficiency of ALE and verifying the stability of ALE resulting strains are the primary problems that need to be solved in future research, making it a promising method for the application of microalgae biotechnology.
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Affiliation(s)
- Bo Zhang
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, China.,College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Jiangyue Wu
- National Marine Hazard Mitigation Service, Ministry of Natural Resource of the People's Republic of China, Beijing, China
| | - Fanping Meng
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, China.,College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
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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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Yamagishi T, Yamaguchi H, Suzuki S, Yoshikawa M, Jameson I, Lorenz M, Nobles DR, Campbell C, Seki M, Kawachi M, Yamamoto H. Comparative genome analysis of test algal strain NIVA-CHL1 (Raphidocelis subcapitata) maintained in microalgal culture collections worldwide. PLoS One 2020; 15:e0241889. [PMID: 33166324 PMCID: PMC7652255 DOI: 10.1371/journal.pone.0241889] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/21/2020] [Indexed: 11/24/2022] Open
Abstract
Raphidocelis subcapitata is one of the most frequently used species for algal growth inhibition tests. Accordingly, many microalgal culture collections worldwide maintain R. subcapitata for distribution to users. All R. subcapitata strains maintained in these collections are derived from the same cultured strain, NIVA-CHL1. However, considering that 61 years have passed since this strain was isolated, we suspected that NIVA-CHL1 in culture collections might have acquired various mutations. In this study, we compared the genome sequences among NIVA-CHL1 from 8 microalgal culture collections and one laboratory in Japan to evaluate the presence of mutations. We found single-nucleotide polymorphisms or indels at 19,576 to 28,212 sites per strain in comparison with the genome sequence of R. subcapitata NIES-35, maintained at the National Institute for Environmental Studies, Tsukuba, Japan. These mutations were detected not only in non-coding but also in coding regions; some of the latter mutations may affect protein function. In growth inhibition test with 3,5-dichlorophenol, EC50 values varied 2.6-fold among the 9 strains. In the ATCC 22662-2 and CCAP 278/4 strains, we also detected a mutation in the gene encoding small-conductance mechanosensitive ion channel, which may lead to protein truncation and loss of function. Growth inhibition test with sodium chloride suggested that osmotic regulation has changed in ATCC 22662-2 and CCAP 278/4 in comparison with NIES-35.
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Affiliation(s)
- Takahiro Yamagishi
- Ecotoxicity Reference Laboratory, Risk Assessment Science Collaboration Office, Center for Health and Environmental Risk Research, National Institute for Environmental Studies (NIES), Tsukuba, Ibaraki, Japan
| | - Haruyo Yamaguchi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies (NIES), Tsukuba, Ibaraki, Japan
| | - Shigekatsu Suzuki
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies (NIES), Tsukuba, Ibaraki, Japan
| | - Mayumi Yoshikawa
- Chemicals Evaluation and Research Institute, Japan (CERI), Kurume, Fukuoka, Japan
| | - Ian Jameson
- Australian National Algae Culture Collection (ANACC), Commonwealth Scientific and Industrial Research Organisation (CSIRO), Castray Esplanade, Hobart, Tasmania, Australia
| | - Maike Lorenz
- Culture Collection of Algae at Göttingen University (SAG), Georg-August-University Göttingen, Göttingen, Germany
| | - David R. Nobles
- The University of Texas at Austin, Austin, Texas, United States of America
| | - Christine Campbell
- Culture Collection of Algae and Protozoa (CCAP), Scottish Association for Marine Science (SAMS), Oban, Argyll, United Kingdom
| | - Masanori Seki
- Chemicals Evaluation and Research Institute, Japan (CERI), Kurume, Fukuoka, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies (NIES), Tsukuba, Ibaraki, Japan
| | - Hiroshi Yamamoto
- Ecotoxicity Reference Laboratory, Risk Assessment Science Collaboration Office, Center for Health and Environmental Risk Research, National Institute for Environmental Studies (NIES), Tsukuba, Ibaraki, Japan
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23
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Sokolovskaya OM, Shelton AN, Taga ME. Sharing vitamins: Cobamides unveil microbial interactions. Science 2020; 369:369/6499/eaba0165. [PMID: 32631870 DOI: 10.1126/science.aba0165] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microbial communities are essential to fundamental processes on Earth. Underlying the compositions and functions of these communities are nutritional interdependencies among individual species. One class of nutrients, cobamides (the family of enzyme cofactors that includes vitamin B12), is widely used for a variety of microbial metabolic functions, but these structurally diverse cofactors are synthesized by only a subset of bacteria and archaea. Advances at different scales of study-from individual isolates, to synthetic consortia, to complex communities-have led to an improved understanding of cobamide sharing. Here, we discuss how cobamides affect microbes at each of these three scales and how integrating different approaches leads to a more complete understanding of microbial interactions.
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Affiliation(s)
- Olga M Sokolovskaya
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Amanda N Shelton
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
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24
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Dell'Aglio E. Overcoming Algal Vitamin B12 Auxotrophy by Experimental Evolution. PLANT PHYSIOLOGY 2020; 183:15-16. [PMID: 32385175 PMCID: PMC7210650 DOI: 10.1104/pp.20.00274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Elisa Dell'Aglio
- Institut National des Sciences Appliquées-Lyon, 69100 Villeurbanne, France
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25
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Bunbury F, Helliwell KE, Mehrshahi P, Davey MP, Salmon DL, Holzer A, Smirnoff N, Smith AG. Responses of a Newly Evolved Auxotroph of Chlamydomonas to B 12 Deprivation. PLANT PHYSIOLOGY 2020; 183:167-178. [PMID: 32079734 PMCID: PMC7210614 DOI: 10.1104/pp.19.01375] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/04/2020] [Indexed: 05/10/2023]
Abstract
The corrinoid B12 is synthesized only by prokaryotes yet is widely required by eukaryotes as an enzyme cofactor. Microalgae have evolved B12 dependence on multiple occasions, and we previously demonstrated that experimental evolution of the non-B12-requiring alga Chlamydomonas reinhardtii in media supplemented with B12 generated a B12-dependent mutant (hereafter metE7). This clone provides a unique opportunity to study the physiology of a nascent B12 auxotroph. Our analyses demonstrate that B12 deprivation of metE7 disrupts C1 metabolism, causes an accumulation of starch and triacylglycerides, and leads to a decrease in photosynthetic pigments, proteins, and free amino acids. B12 deprivation also caused a substantial increase in reactive oxygen species, which preceded rapid cell death. Survival could be improved without compromising growth by simultaneously depriving the cells of nitrogen, suggesting a type of cross protection. Significantly, we found further improvements in survival under B12 limitation and an increase in B12 use efficiency after metE7 underwent a further period of experimental evolution, this time in coculture with a B12-producing bacterium. Therefore, although an early B12-dependent alga would likely be poorly adapted to coping with B12 deprivation, association with B12-producers can ensure long-term survival whilst also providing a suitable environment for evolving mechanisms to tolerate B12 limitation better.
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Affiliation(s)
- Freddy Bunbury
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Katherine E Helliwell
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth EX4 4PY, United Kingdom
- School of Biosciences, University of Exeter, Exeter, PL1 2PB, United Kingdom
| | - Payam Mehrshahi
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Matthew P Davey
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Deborah L Salmon
- School of Biosciences, University of Exeter, Exeter, PL1 2PB, United Kingdom
| | - Andre Holzer
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Nicholas Smirnoff
- School of Biosciences, University of Exeter, Exeter, PL1 2PB, United Kingdom
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
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26
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Rastogi A, Vieira FRJ, Deton-Cabanillas AF, Veluchamy A, Cantrel C, Wang G, Vanormelingen P, Bowler C, Piganeau G, Hu H, Tirichine L. A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum. THE ISME JOURNAL 2020; 14:347-363. [PMID: 31624346 PMCID: PMC6976637 DOI: 10.1038/s41396-019-0528-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/24/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022]
Abstract
Diatoms emerged in the Mesozoic period and presently constitute one of the main primary producers in the world's ocean and are of a major economic importance. In the current study, using whole genome sequencing of ten accessions of the model diatom Phaeodactylum tricornutum, sampled at broad geospatial and temporal scales, we draw a comprehensive landscape of the genomic diversity within the species. We describe strong genetic subdivisions of the accessions into four genetic clades (A-D) with constituent populations of each clade possessing a conserved genetic and functional makeup, likely a consequence of the limited dispersal of P. tricornutum in the open ocean. We further suggest dominance of asexual reproduction across all the populations, as implied by high linkage disequilibrium. Finally, we show limited yet compelling signatures of genetic and functional convergence inducing changes in the selection pressure on many genes and metabolic pathways. We propose these findings to have significant implications for understanding the genetic structure of diatom populations in nature and provide a framework to assess the genomic underpinnings of their ecological success and impact on aquatic ecosystems where they play a major role. Our work provides valuable resources for functional genomics and for exploiting the biotechnological potential of this model diatom species.
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Affiliation(s)
- Achal Rastogi
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
- Corteva Agriscience™, The V Ascendas, Atria Block, 12th Floor, Madhapur, Hyderabad, 500081, India
| | - Fabio Rocha Jimenez Vieira
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Anne-Flore Deton-Cabanillas
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Alaguraj Veluchamy
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
- Biological and Environmental Sciences and Engineering Division, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Catherine Cantrel
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Gaohong Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, 430072, Wuhan, China
| | - Pieter Vanormelingen
- Department of Biology, Research Group Protistology and Aquatic Ecology, Ghent University, Krijgslaan 281/S8 9000, Gent, Belgium
| | - Chris Bowler
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Gwenael Piganeau
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650, Banyuls/Mer, France
| | - Hanhua Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, 430072, Wuhan, China.
| | - Leila Tirichine
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France.
- Université de Nantes, CNRS, UFIP, UMR 6286, F-44000, Nantes, France.
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27
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Gude S, Taga ME. Multi-faceted approaches to discovering and predicting microbial nutritional interactions. Curr Opin Biotechnol 2019; 62:58-64. [PMID: 31597114 DOI: 10.1016/j.copbio.2019.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/08/2019] [Accepted: 08/20/2019] [Indexed: 01/07/2023]
Abstract
Nearly all microbes rely on other species in their environment to provide nutrients they are unable to produce. Nutritional interactions include not only the exchange of carbon and nitrogen compounds, but also amino acids and cofactors. Interactions involving cross-feeding of cobamides, the vitamin B12 family of cofactors, have been developed as a model for nutritional interactions across species and environments. In addition to experimental studies, new developments in culture-independent methodologies such as genomics and modeling now enable the prediction of nutritional interactions in a broad range of organisms including those that cannot be cultured in the laboratory. New insights into the mechanisms and evolution of microbial nutritional interactions are beginning to emerge by combining experimental, genomic, and modeling approaches.
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Affiliation(s)
- Sebastian Gude
- Department of Plant & Microbial Biology, University of California, Berkeley, CA USA
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, CA USA.
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28
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Nef C, Jung S, Mairet F, Kaas R, Grizeau D, Garnier M. How haptophytes microalgae mitigate vitamin B 12 limitation. Sci Rep 2019; 9:8417. [PMID: 31182768 PMCID: PMC6557843 DOI: 10.1038/s41598-019-44797-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 05/13/2019] [Indexed: 12/05/2022] Open
Abstract
Vitamin B12 (cobalamin) can control phytoplankton development and community composition, with around half of microalgal species requiring this vitamin for growth. B12 dependency is determined by the absence of cobalamin-independent methionine synthase and is unrelated across lineages. Despite their important role in carbon and sulphur biogeochemistry, little is known about haptophytes utilization of vitamin B12 and their ability to cope with its limitation. Here we report the first evaluation of B12 auxotrophy among this lineage based on molecular data of 19 species from 9 families. We assume that all species encode only a B12-dependent methionine synthase, suggesting ubiquitous B12 auxotrophy in this phylum. We further address the effect of different B12 limitations on the molecular physiology of the model haptophyte Tisochrysis lutea. By coupling growth assays in batch and chemostat to cobalamin quantification and expression analyses, we propose that haptophytes use three strategies to cope with B12 limitation. Haptophytes may assimilate dissolved methionine, finely regulate genes involved in methionine cycle and B12 transport and/or limit B12 transport to the mitochondrion. Taken together, these results provide better understanding of B12 metabolism in haptophytes and represent valuable data for deciphering how B12-producing bacteria shape the structure and dynamics of this important phytoplankton community.
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Affiliation(s)
- Charlotte Nef
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France.
| | - Sébastien Jung
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France
| | - Francis Mairet
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France
| | - Raymond Kaas
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France
| | | | - Matthieu Garnier
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France
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29
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Heal KR, Kellogg NA, Carlson LT, Lionheart RM, Ingalls AE. Metabolic Consequences of Cobalamin Scarcity in the Diatom Thalassiosira pseudonana as Revealed Through Metabolomics. Protist 2019; 170:328-348. [PMID: 31260945 DOI: 10.1016/j.protis.2019.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 05/17/2019] [Accepted: 05/19/2019] [Indexed: 02/07/2023]
Abstract
Diatoms perform an estimated 20% of global photosynthesis, form the base of the marine food web, and sequester carbon into the deep ocean through the biological pump. In some areas of the ocean, diatom growth is limited by the micronutrient cobalamin (vitamin B12), yet the biochemical ramifications of cobalamin limitation are not well understood. In a laboratory setting, we grew the diatom Thalassiosira pseudonana under replete and low cobalamin conditions to elucidate changes in metabolite pools. Using metabolomics, we show that the diatom experienced a metabolic cascade under cobalamin limitation that affected the central methionine cycle, transsulfuration pathway, and composition of osmolyte pools. In T. pseudonana, 5'-methylthioadenosine decreased under low cobalamin conditions, suggesting a disruption in the diatom's polyamine biosynthesis. Furthermore, two acylcarnitines accumulated under low cobalamin, suggesting the limited use of an adenosylcobalamin-dependent enzyme, methylmalonyl CoA mutase. Overall, these changes in metabolite pools yield insight into the metabolic consequences of cobalamin limitation in diatoms and suggest that cobalamin availability may have consequences for microbial interactions that are based on metabolite production by phytoplankton.
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Affiliation(s)
- Katherine R Heal
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Natalie A Kellogg
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Laura T Carlson
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Regina M Lionheart
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA 98195, USA.
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30
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Arora NK, Fatima T, Mishra I, Verma M, Mishra J, Mishra V. Environmental sustainability: challenges and viable solutions. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/s42398-018-00038-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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31
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Van den Bergh B, Swings T, Fauvart M, Michiels J. Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution. Microbiol Mol Biol Rev 2018; 82:e00008-18. [PMID: 30045954 PMCID: PMC6094045 DOI: 10.1128/mmbr.00008-18] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.
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Affiliation(s)
- Bram Van den Bergh
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- Douglas Lab, Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Toon Swings
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
| | - Maarten Fauvart
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- imec, Leuven, Belgium
| | - Jan Michiels
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
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32
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Role of Chemical Mediators in Aquatic Interactions across the Prokaryote-Eukaryote Boundary. J Chem Ecol 2018; 44:1008-1021. [PMID: 30105643 DOI: 10.1007/s10886-018-1004-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 07/24/2018] [Accepted: 07/30/2018] [Indexed: 10/28/2022]
Abstract
There is worldwide growing interest in the occurrence and diversity of metabolites used as chemical mediators in cross-kingdom interactions within aquatic systems. Bacteria produce metabolites to protect and influence the growth and life cycle of their eukaryotic hosts. In turn, the host provides a nutrient-enriched environment for the bacteria. Here, we discuss the role of waterborne chemical mediators that are responsible for such interactions in aquatic multi-partner systems, including algae or invertebrates and their associated bacteria. In particular, this review highlights recent advances in the chemical ecology of aquatic systems that support the overall ecological significance of signaling molecules across the prokaryote-eukaryote boundary (cross-kingdom interactions) for growth, development and morphogenesis of the host. We emphasize the value of establishing well-characterized model systems that provide the basis for the development of ecological principles that represent the natural lifestyle and dynamics of aquatic microbial communities and enable a better understanding of the consequences of environmental change and the most effective means of managing community interactions.
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33
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Berthelier J, Casse N, Daccord N, Jamilloux V, Saint-Jean B, Carrier G. A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea. BMC Genomics 2018. [PMID: 29783941 DOI: 10.17882/52231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Transposable elements (TEs) are mobile DNA sequences known as drivers of genome evolution. Their impacts have been widely studied in animals, plants and insects, but little is known about them in microalgae. In a previous study, we compared the genetic polymorphisms between strains of the haptophyte microalga Tisochrysis lutea and suggested the involvement of active autonomous TEs in their genome evolution. RESULTS To identify potentially autonomous TEs, we designed a pipeline named PiRATE (Pipeline to Retrieve and Annotate Transposable Elements, download: https://doi.org/10.17882/51795 ), and conducted an accurate TE annotation on a new genome assembly of T. lutea. PiRATE is composed of detection, classification and annotation steps. Its detection step combines multiple, existing analysis packages representing all major approaches for TE detection and its classification step was optimized for microalgal genomes. The efficiency of the detection and classification steps was evaluated with data on the model species Arabidopsis thaliana. PiRATE detected 81% of the TE families of A. thaliana and correctly classified 75% of them. We applied PiRATE to T. lutea genomic data and established that its genome contains 15.89% Class I and 4.95% Class II TEs. In these, 3.79 and 17.05% correspond to potentially autonomous and non-autonomous TEs, respectively. Annotation data was combined with transcriptomic and proteomic data to identify potentially active autonomous TEs. We identified 17 expressed TE families and, among these, a TIR/Mariner and a TIR/hAT family were able to synthesize their transposase. Both these TE families were among the three highest expressed genes in a previous transcriptomic study and are composed of highly similar copies throughout the genome of T. lutea. This sum of evidence reveals that both these TE families could be capable of transposing or triggering the transposition of potential related MITE elements. CONCLUSION This manuscript provides an example of a de novo transposable element annotation of a non-model organism characterized by a fragmented genome assembly and belonging to a poorly studied phylum at genomic level. Integration of multi-omics data enabled the discovery of potential mobile TEs and opens the way for new discoveries on the role of these repeated elements in genomic evolution of microalgae.
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Affiliation(s)
- Jérémy Berthelier
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France.
- Mer Molécules Santé, EA 2160 IUML - FR 3473 CNRS, Le Mans University, Le Mans, France.
| | - Nathalie Casse
- Mer Molécules Santé, EA 2160 IUML - FR 3473 CNRS, Le Mans University, Le Mans, France
| | - Nicolas Daccord
- Institut de Recherche en Horticulture et Semences, INRA of Angers, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d'Angers, Angers, France
- Université Bretagne Loire, Angers, France
| | | | - Bruno Saint-Jean
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France
| | - Grégory Carrier
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France
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Berthelier J, Casse N, Daccord N, Jamilloux V, Saint-Jean B, Carrier G. A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea. BMC Genomics 2018; 19:378. [PMID: 29783941 PMCID: PMC5963040 DOI: 10.1186/s12864-018-4763-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 05/07/2018] [Indexed: 01/01/2023] Open
Abstract
Background Transposable elements (TEs) are mobile DNA sequences known as drivers of genome evolution. Their impacts have been widely studied in animals, plants and insects, but little is known about them in microalgae. In a previous study, we compared the genetic polymorphisms between strains of the haptophyte microalga Tisochrysis lutea and suggested the involvement of active autonomous TEs in their genome evolution. Results To identify potentially autonomous TEs, we designed a pipeline named PiRATE (Pipeline to Retrieve and Annotate Transposable Elements, download: 10.17882/51795), and conducted an accurate TE annotation on a new genome assembly of T. lutea. PiRATE is composed of detection, classification and annotation steps. Its detection step combines multiple, existing analysis packages representing all major approaches for TE detection and its classification step was optimized for microalgal genomes. The efficiency of the detection and classification steps was evaluated with data on the model species Arabidopsis thaliana. PiRATE detected 81% of the TE families of A. thaliana and correctly classified 75% of them. We applied PiRATE to T. lutea genomic data and established that its genome contains 15.89% Class I and 4.95% Class II TEs. In these, 3.79 and 17.05% correspond to potentially autonomous and non-autonomous TEs, respectively. Annotation data was combined with transcriptomic and proteomic data to identify potentially active autonomous TEs. We identified 17 expressed TE families and, among these, a TIR/Mariner and a TIR/hAT family were able to synthesize their transposase. Both these TE families were among the three highest expressed genes in a previous transcriptomic study and are composed of highly similar copies throughout the genome of T. lutea. This sum of evidence reveals that both these TE families could be capable of transposing or triggering the transposition of potential related MITE elements. Conclusion This manuscript provides an example of a de novo transposable element annotation of a non-model organism characterized by a fragmented genome assembly and belonging to a poorly studied phylum at genomic level. Integration of multi-omics data enabled the discovery of potential mobile TEs and opens the way for new discoveries on the role of these repeated elements in genomic evolution of microalgae. Electronic supplementary material The online version of this article (10.1186/s12864-018-4763-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jérémy Berthelier
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France. .,Mer Molécules Santé, EA 2160 IUML - FR 3473 CNRS, Le Mans University, Le Mans, France.
| | - Nathalie Casse
- Mer Molécules Santé, EA 2160 IUML - FR 3473 CNRS, Le Mans University, Le Mans, France
| | - Nicolas Daccord
- Institut de Recherche en Horticulture et Semences, INRA of Angers, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d'Angers, Angers, France.,Université Bretagne Loire, Angers, France
| | | | - Bruno Saint-Jean
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France
| | - Grégory Carrier
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France
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Experimental evolution in photoautotrophic microorganisms as a means of enhancing chloroplast functions. Essays Biochem 2018; 62:77-84. [PMID: 28887328 DOI: 10.1042/ebc20170010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 08/13/2017] [Accepted: 08/15/2017] [Indexed: 01/11/2023]
Abstract
The term 'experimental evolution' refers to short-term evolutionary experiments with microorganisms under controlled conditions in which selection is expected to occur. In combination with whole-genome sequencing and genetic engineering, the method has become a powerful tool to study evolutionary mechanisms and engineer new microbial variants. It has been most extensively used in the model species Escherichia coli and Saccharomyces cerevisiae, but more recently photosynthetic microorganisms have been subjected to experimental evolution. In such assays, strains were generated that had become more tolerant to certain abiotic environmental factors or evolved new traits during co-propagation with other organisms. These strains were viable under conditions that were lethal to the non-adapted progenitor and in a few cases, the causative mutations were identified. Because cyanobacteria like Synechocystis or green algae like Chlamydomonas reinhardtii share many features with crop plants - which are not amenable to such experiments - experimental evolution with photosynthetic microorganisms has the potential to identify novel targets for improving the capacity of plants to acclimate to environmental change. Here, I provide a survey of the experiments performed so far in cyanobacteria and green algae, focusing on Synechocystis and C. reinhardtii, and discuss the promise and the challenges of such approaches.
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Srivastava A, Seo SH, Ko SR, Ahn CY, Oh HM. Bioflocculation in natural and engineered systems: current perspectives. Crit Rev Biotechnol 2018; 38:1176-1194. [DOI: 10.1080/07388551.2018.1451984] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ankita Srivastava
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Seong-Hyun Seo
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - So-Ra Ko
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Chi-Yong Ahn
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
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Helliwell KE, Pandhal J, Cooper MB, Longworth J, Kudahl UJ, Russo DA, Tomsett EV, Bunbury F, Salmon DL, Smirnoff N, Wright PC, Smith AG. Quantitative proteomics of a B 12 -dependent alga grown in coculture with bacteria reveals metabolic tradeoffs required for mutualism. THE NEW PHYTOLOGIST 2018; 217:599-612. [PMID: 29034959 PMCID: PMC5765456 DOI: 10.1111/nph.14832] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/31/2017] [Indexed: 05/02/2023]
Abstract
The unicellular green alga Lobomonas rostrata requires an external supply of vitamin B12 (cobalamin) for growth, which it can obtain in stable laboratory cultures from the soil bacterium Mesorhizobium loti in exchange for photosynthate. We investigated changes in protein expression in the alga that allow it to engage in this mutualism. We used quantitative isobaric tagging (iTRAQ) proteomics to determine the L. rostrata proteome grown axenically with B12 supplementation or in coculture with M. loti. Data are available via ProteomeXchange (PXD005046). Using the related Chlamydomonas reinhardtii as a reference genome, 588 algal proteins could be identified. Enzymes of amino acid biosynthesis were higher in coculture than in axenic culture, and this was reflected in increased amounts of total cellular protein and several free amino acids. A number of heat shock proteins were also elevated. Conversely, photosynthetic proteins and those of chloroplast protein synthesis were significantly lower in L. rostrata cells in coculture. These observations were confirmed by measurement of electron transfer rates in cells grown under the two conditions. The results indicate that, despite the stability of the mutualism, L. rostrata experiences stress in coculture with M. loti, and must adjust its metabolism accordingly.
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Affiliation(s)
| | - Jagroop Pandhal
- Department of Chemical and Biological EngineeringUniversity of SheffieldMappin StreetSheffieldS1 3JDUK
| | - Matthew B. Cooper
- Department of Plant SciencesUniversity of CambridgeCambridgeCB2 3EAUK
| | - Joseph Longworth
- Department of Chemical and Biological EngineeringUniversity of SheffieldMappin StreetSheffieldS1 3JDUK
| | | | - David A. Russo
- Department of Chemical and Biological EngineeringUniversity of SheffieldMappin StreetSheffieldS1 3JDUK
| | | | - Freddy Bunbury
- Department of Plant SciencesUniversity of CambridgeCambridgeCB2 3EAUK
| | - Deborah L. Salmon
- BiosciencesCollege of Life and Environmental SciencesUniversity of ExeterExeterEX4 4QDUK
| | - Nicholas Smirnoff
- BiosciencesCollege of Life and Environmental SciencesUniversity of ExeterExeterEX4 4QDUK
| | - Phillip C. Wright
- Department of Chemical and Biological EngineeringUniversity of SheffieldMappin StreetSheffieldS1 3JDUK
| | - Alison G. Smith
- Department of Plant SciencesUniversity of CambridgeCambridgeCB2 3EAUK
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Helliwell KE. The roles of B vitamins in phytoplankton nutrition: new perspectives and prospects. THE NEW PHYTOLOGIST 2017; 216:62-68. [PMID: 28656633 DOI: 10.1111/nph.14669] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/05/2017] [Indexed: 06/07/2023]
Abstract
Contents 62 I. 62 II. 63 III. 63 IV. 66 V. 66 VI. 67 67 References 67 SUMMARY: B vitamins play essential roles in central metabolism. These organic water-soluble molecules act as, or as part of, coenzymes within the cell. Unlike land plants, many eukaryotic algae are auxotrophic for certain B vitamins. Recent progress in algal genetic resources and environmental chemistry have promoted a renewal of interest in the role of vitamins in governing phytoplankton dynamics, and illuminated amazing versatility in phytoplankton vitamin metabolism. Accumulating evidence demonstrates metabolic complexity in the production and bioavailability of different vitamin forms, coupled with specialized acquisition strategies to salvage and remodel vitamin precursors. Here, I describe recent advances and discuss how they redefine our view of the way in which vitamins are cycled in aquatic ecosystems and their importance in structuring phytoplankton communities.
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Affiliation(s)
- Katherine E Helliwell
- The Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
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Hippmann AA, Schuback N, Moon KM, McCrow JP, Allen AE, Foster LJ, Green BR, Maldonado MT. Contrasting effects of copper limitation on the photosynthetic apparatus in two strains of the open ocean diatom Thalassiosira oceanica. PLoS One 2017; 12:e0181753. [PMID: 28837661 PMCID: PMC5570362 DOI: 10.1371/journal.pone.0181753] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 07/06/2017] [Indexed: 11/25/2022] Open
Abstract
There is an intricate interaction between iron (Fe) and copper (Cu) physiology in diatoms. However, strategies to cope with low Cu are largely unknown. This study unveils the comprehensive restructuring of the photosynthetic apparatus in the diatom Thalassiosira oceanica (CCMP1003) in response to low Cu, at the physiological and proteomic level. The restructuring results in a shift from light harvesting for photochemistry—and ultimately for carbon fixation—to photoprotection, reducing carbon fixation and oxygen evolution. The observed decreases in the physiological parameters Fv/Fm, carbon fixation, and oxygen evolution, concomitant with increases in the antennae absorption cross section (σPSII), non-photochemical quenching (NPQ) and the conversion factor (φe:C/ηPSII) are in agreement with well documented cellular responses to low Fe. However, the underlying proteomic changes due to low Cu are very different from those elicited by low Fe. Low Cu induces a significant four-fold reduction in the Cu-containing photosynthetic electron carrier plastocyanin. The decrease in plastocyanin causes a bottleneck within the photosynthetic electron transport chain (ETC), ultimately leading to substantial stoichiometric changes. Namely, 2-fold reduction in both cytochrome b6f complex (cytb6f) and photosystem II (PSII), no change in the Fe-rich PSI and a 40- and 2-fold increase in proteins potentially involved in detoxification of reactive oxygen species (ferredoxin and ferredoxin:NADP+ reductase, respectively). Furthermore, we identify 48 light harvesting complex (LHC) proteins in the publicly available genome of T. oceanica and provide proteomic evidence for 33 of these. The change in the LHC composition within the antennae in response to low Cu underlines the shift from photochemistry to photoprotection in T. oceanica (CCMP1003). Interestingly, we also reveal very significant intra-specific strain differences. Another strain of T. oceanica (CCMP 1005) requires significantly higher Cu concentrations to sustain both its maximal and minimal growth rate compared to CCMP 1003. Under low Cu, CCMP 1005 decreases its growth rate, cell size, Chla and total protein per cell. We argue that the reduction in protein per cell is the main strategy to decrease its cellular Cu requirement, as none of the other parameters tested are affected. Differences between the two strains, as well as differences between the well documented responses to low Fe and those presented here in response to low Cu are discussed.
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Affiliation(s)
- Anna A. Hippmann
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail: (AAH); (MTM)
| | - Nina Schuback
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kyung-Mee Moon
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - John P. McCrow
- Department of Microbial & Environmental Genomics, J. Craig Venter Institute, La Jolla, California, United States of America
| | - Andrew E. Allen
- Department of Microbial & Environmental Genomics, J. Craig Venter Institute, La Jolla, California, United States of America
| | - Leonard J. Foster
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Beverley R. Green
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Maria T. Maldonado
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail: (AAH); (MTM)
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Danchin A, Braham S. Coenzyme B12 synthesis as a baseline to study metabolite contribution of animal microbiota. Microb Biotechnol 2017; 10:688-701. [PMID: 28612402 PMCID: PMC5481537 DOI: 10.1111/1751-7915.12722] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Microbial communities thrive in a number of environments. Exploration of their microbiomes – their global genome – may reveal metabolic features that contribute to the development and welfare of their hosts, or chemical cleansing of environments. Yet we often lack final demonstration of their causal role in features of interest. The reason is that we do not have proper baselines that we could use to monitor how microbiota cope with key metabolites in the hosting environment. Here, focusing on animal gut microbiota, we describe the fate of cobalamins – metabolites of the B12 coenzyme family – that are essential for animals but synthesized only by prokaryotes. Microbiota produce the vitamin used in a variety of animals (and in algae). Coprophagy plays a role in its management. For coprophobic man, preliminary observations suggest that the gut microbial production of vitamin B12 plays only a limited role. By contrast, the vitamin is key for structuring microbiota. This implies that it is freely available in the environment. This can only result from lysis of the microbes that make it. A consequence for biotechnology applications is that, if valuable for their host, B12‐producing microbes should be sensitive to bacteriophages and colicins, or make spores.
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Affiliation(s)
- Antoine Danchin
- Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié-Salpêtrière, 47 Boulevard de l'Hôpital, 75013, Paris, France
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Simon M, Scheuner C, Meier-Kolthoff JP, Brinkhoff T, Wagner-Döbler I, Ulbrich M, Klenk HP, Schomburg D, Petersen J, Göker M. Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. THE ISME JOURNAL 2017; 11:1483-1499. [PMID: 28106881 PMCID: PMC5437341 DOI: 10.1038/ismej.2016.198] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/29/2016] [Accepted: 11/19/2016] [Indexed: 12/31/2022]
Abstract
Marine Rhodobacteraceae (Alphaproteobacteria) are key players of biogeochemical cycling, comprise up to 30% of bacterial communities in pelagic environments and are often mutualists of eukaryotes. As 'Roseobacter clade', these 'roseobacters' are assumed to be monophyletic, but non-marine Rhodobacteraceae have not yet been included in phylogenomic analyses. Therefore, we analysed 106 genome sequences, particularly emphasizing gene sampling and its effect on phylogenetic stability, and investigated relationships between marine versus non-marine habitat, evolutionary origin and genomic adaptations. Our analyses, providing no unequivocal evidence for the monophyly of roseobacters, indicate several shifts between marine and non-marine habitats that occurred independently and were accompanied by characteristic changes in genomic content of orthologs, enzymes and metabolic pathways. Non-marine Rhodobacteraceae gained high-affinity transporters to cope with much lower sulphate concentrations and lost genes related to the reduced sodium chloride and organohalogen concentrations in their habitats. Marine Rhodobacteraceae gained genes required for fucoidan desulphonation and synthesis of the plant hormone indole 3-acetic acid and the compatible solutes ectoin and carnitin. However, neither plasmid composition, even though typical for the family, nor the degree of oligotrophy shows a systematic difference between marine and non-marine Rhodobacteraceae. We suggest the operational term 'Roseobacter group' for the marine Rhodobacteraceae strains.
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Affiliation(s)
- Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Carmen Scheuner
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P Meier-Kolthoff
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Irene Wagner-Döbler
- Helmholtz Centre for Infection Research, Research Group Microbial Communication, Braunschweig, Germany
| | - Marcus Ulbrich
- Institute of Biochemical Engineering, Technical University Braunschweig, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Dietmar Schomburg
- Institute of Biochemical Engineering, Technical University Braunschweig, Braunschweig, Germany
| | - Jörn Petersen
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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42
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Kazamia E, Helliwell KE, Purton S, Smith AG. How mutualisms arise in phytoplankton communities: building eco-evolutionary principles for aquatic microbes. Ecol Lett 2017; 19:810-22. [PMID: 27282316 PMCID: PMC5103174 DOI: 10.1111/ele.12615] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/03/2016] [Accepted: 04/07/2016] [Indexed: 01/05/2023]
Abstract
Extensive sampling and metagenomics analyses of plankton communities across all aquatic environments are beginning to provide insights into the ecology of microbial communities. In particular, the importance of metabolic exchanges that provide a foundation for ecological interactions between microorganisms has emerged as a key factor in forging such communities. Here we show how both studies of environmental samples and physiological experimentation in the laboratory with defined microbial co‐cultures are being used to decipher the metabolic and molecular underpinnings of such exchanges. In addition, we explain how metabolic modelling may be used to conduct investigations in reverse, deducing novel molecular exchanges from analysis of large‐scale data sets, which can identify persistently co‐occurring species. Finally, we consider how knowledge of microbial community ecology can be built into evolutionary theories tailored to these species’ unique lifestyles. We propose a novel model for the evolution of metabolic auxotrophy in microorganisms that arises as a result of symbiosis, termed the Foraging‐to‐Farming hypothesis. The model has testable predictions, fits several known examples of mutualism in the aquatic world, and sheds light on how interactions, which cement dependencies within communities of microorganisms, might be initiated.
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Affiliation(s)
- Elena Kazamia
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | | | - Saul Purton
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Alison Gail Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
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Bussard A, Corre E, Hubas C, Duvernois-Berthet E, Le Corguillé G, Jourdren L, Coulpier F, Claquin P, Lopez PJ. Physiological adjustments and transcriptome reprogramming are involved in the acclimation to salinity gradients in diatoms. Environ Microbiol 2016; 19:909-925. [DOI: 10.1111/1462-2920.13398] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adrien Bussard
- UMR Biologie des Organismes et des Ecosystèmes Aquatiques, CNRS 7208-MNHN-UPMC-IRD 207-UCN-UA; 43 rue Cuvier Paris 75005 France
| | - Erwan Corre
- CNRS, UPMC, FR2424, ABiMS, Station Biologique; Roscoff 29680 France
| | - Cédric Hubas
- UMR Biologie des Organismes et des Ecosystèmes Aquatiques, CNRS 7208-MNHN-UPMC-IRD 207-UCN-UA; 43 rue Cuvier Paris 75005 France
| | | | | | - Laurent Jourdren
- Ecole Normale Supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Plateforme Génomique; Paris 75005 France
| | - Fanny Coulpier
- Ecole Normale Supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Plateforme Génomique; Paris 75005 France
| | - Pascal Claquin
- UMR Biologie des Organismes et des Ecosystèmes Aquatiques, CNRS 7208-MNHN-UPMC-IRD 207-UCN-UA, Esplanade de la paix; Caen 14032 France
| | - Pascal Jean Lopez
- UMR Biologie des Organismes et des Ecosystèmes Aquatiques, CNRS 7208-MNHN-UPMC-IRD 207-UCN-UA; 43 rue Cuvier Paris 75005 France
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Helliwell KE, Lawrence AD, Holzer A, Kudahl UJ, Sasso S, Kräutler B, Scanlan DJ, Warren MJ, Smith AG. Cyanobacteria and Eukaryotic Algae Use Different Chemical Variants of Vitamin B12. Curr Biol 2016; 26:999-1008. [PMID: 27040778 PMCID: PMC4850488 DOI: 10.1016/j.cub.2016.02.041] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/15/2016] [Accepted: 02/17/2016] [Indexed: 01/04/2023]
Abstract
Eukaryotic microalgae and prokaryotic cyanobacteria are the major components of the phytoplankton. Determining factors that govern growth of these primary producers, and how they interact, is therefore essential to understanding aquatic ecosystem productivity. Over half of microalgal species representing marine and freshwater habitats require for growth the corrinoid cofactor B12, which is synthesized de novo only by certain prokaryotes, including the majority of cyanobacteria. There are several chemical variants of B12, which are not necessarily functionally interchangeable. Cobalamin, the form bioavailable to humans, has as its lower axial ligand 5,6-dimethylbenzimidazole (DMB). Here, we show that the abundant marine cyanobacterium Synechococcus synthesizes only pseudocobalamin, in which the lower axial ligand is adenine. Moreover, bioinformatic searches of over 100 sequenced cyanobacterial genomes for B12 biosynthesis genes, including those involved in nucleotide loop assembly, suggest this is the form synthesized by cyanobacteria more broadly. We further demonstrate that pseudocobalamin is several orders of magnitude less bioavailable than cobalamin to several B12-dependent microalgae representing diverse lineages. This indicates that the two major phytoplankton groups use a different B12 currency. However, in an intriguing twist, some microalgal species can use pseudocobalamin if DMB is provided, suggesting that they are able to remodel the cofactor, whereas Synechococcus cannot. This species-specific attribute implicates algal remodelers as novel and keystone players of the B12 cycle, transforming our perception of the dynamics and complexity of the flux of this nutrient in aquatic ecosystems. Dominant marine cyanobacteria synthesize only pseudocobalamin Pseudocobalamin is orders of magnitude less bioavailable to eukaryotic algae Certain algae can remodel pseudocobalamin to a bioavailable form This implies a complex B12 cycle between microbes in the photic zone
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Affiliation(s)
| | | | - Andre Holzer
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK; Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls University Heidelberg, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Ulrich Johan Kudahl
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Severin Sasso
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Bernhard Kräutler
- Institute of Organic Chemistry and Centre of Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | | | | | - Alison Gail Smith
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK.
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