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Liu HW, Urzica EI, Gallaher SD, Schmollinger S, Blaby-Haas CE, Iwai M, Merchant SS. Chlamydomonas cells transition through distinct Fe nutrition stages within 48 h of transfer to Fe-free medium. PHOTOSYNTHESIS RESEARCH 2024; 161:213-232. [PMID: 39017982 DOI: 10.1007/s11120-024-01103-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/15/2024] [Indexed: 07/18/2024]
Abstract
Low iron (Fe) bioavailability can limit the biosynthesis of Fe-containing proteins, which are especially abundant in photosynthetic organisms, thus negatively affecting global primary productivity. Understanding cellular coping mechanisms under Fe limitation is therefore of great interest. We surveyed the temporal responses of Chlamydomonas (Chlamydomonas reinhardtii) cells transitioning from an Fe-rich to an Fe-free medium to document their short and long-term adjustments. While slower growth, chlorosis and lower photosynthetic parameters are evident only after one or more days in Fe-free medium, the abundance of some transcripts, such as those for genes encoding transporters and enzymes involved in Fe assimilation, change within minutes, before changes in intracellular Fe content are noticeable, suggestive of a sensitive mechanism for sensing Fe. Promoter reporter constructs indicate a transcriptional component to this immediate primary response. With acetate provided as a source of reduced carbon, transcripts encoding respiratory components are maintained relative to transcripts encoding components of photosynthesis and tetrapyrrole biosynthesis, indicating metabolic prioritization of respiration over photosynthesis. In contrast to the loss of chlorophyll, carotenoid content is maintained under Fe limitation despite a decrease in the transcripts for carotenoid biosynthesis genes, indicating carotenoid stability. These changes occur more slowly, only after the intracellular Fe quota responds, indicating a phased response in Chlamydomonas, involving both primary and secondary responses during acclimation to poor Fe nutrition.
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Affiliation(s)
- Helen W Liu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 99354, USA
| | - Eugen I Urzica
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- Competence Network IBD, Hopfenstrasse 60, 24103, Kiel, Germany
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
| | - Stefan Schmollinger
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
- Plant Research Laboratory, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Crysten E Blaby-Haas
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Masakazu Iwai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sabeeha S Merchant
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 99354, USA.
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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Foresi N, De Marco MA, Del Castello F, Ramirez L, Nejamkin A, Calo G, Grimsley N, Correa-Aragunde N, Martínez-Noël GMA. The tiny giant of the sea, Ostreococcus's unique adaptations. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108661. [PMID: 38735153 DOI: 10.1016/j.plaphy.2024.108661] [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: 12/17/2023] [Revised: 04/14/2024] [Accepted: 04/23/2024] [Indexed: 05/14/2024]
Abstract
Ostreococcus spp. are unicellular organisms with one of the simplest cellular organizations. The sequencing of the genomes of different Ostreococcus species has reinforced this status since Ostreococcus tauri has one most compact nuclear genomes among eukaryotic organisms. Despite this, it has retained a number of genes, setting it apart from other organisms with similar small genomes. Ostreococcus spp. feature a substantial number of selenocysteine-containing proteins, which, due to their higher catalytic activity compared to their selenium-lacking counterparts, may require a reduced quantity of proteins. Notably, O. tauri encodes several ammonium transporter genes, that may provide it with a competitive edge for acquiring nitrogen (N). This characteristic makes it an intriguing model for studying the efficient use of N in eukaryotes. Under conditions of low N availability, O. tauri utilizes N from abundant proteins or amino acids, such as L-arginine, similar to higher plants. However, the presence of a nitric oxide synthase (L-arg substrate) sheds light on a new metabolic pathway for L-arg in algae. The metabolic adaptations of O. tauri to day and night cycles offer valuable insights into carbon and iron metabolic configuration. O. tauri has evolved novel strategies to optimize iron uptake, lacking the classic components of the iron absorption mechanism. Overall, the cellular and genetic characteristics of Ostreococcus contribute to its evolutionary success, making it an excellent model for studying the physiological and genetic aspects of how green algae have adapted to the marine environment. Furthermore, given its potential for lipid accumulation and its marine habitat, it may represent a promising avenue for third-generation biofuels.
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Affiliation(s)
- Noelia Foresi
- Instituto de Investigaciones Biológicas-UNMdP-CONICET, Mar del Plata, Argentina.
| | - María Agustina De Marco
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC)-CONICET-FIBA, Mar del Plata, Argentina
| | | | - Leonor Ramirez
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, SE-901 87, Umeå, Sweden
| | - Andres Nejamkin
- Instituto de Investigaciones Biológicas-UNMdP-CONICET, Mar del Plata, Argentina
| | - Gonzalo Calo
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC)-CONICET-FIBA, Mar del Plata, Argentina
| | - Nigel Grimsley
- CNRS, LBBM, Sorbonne Université OOB, 1 Avenue de Pierre Fabre, 66650, Banyuls-sur-Mer, France
| | | | - Giselle M A Martínez-Noël
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC)-CONICET-FIBA, Mar del Plata, Argentina.
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3
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Dellisanti W, Zhang Q, Ferrier-Pagès C, Kühl M. Contrasting effects of increasing dissolved iron on photosynthesis and O 2 availability in the gastric cavity of two Mediterranean corals. PeerJ 2024; 12:e17259. [PMID: 38699194 PMCID: PMC11064864 DOI: 10.7717/peerj.17259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/27/2024] [Indexed: 05/05/2024] Open
Abstract
Iron (Fe) plays a fundamental role in coral symbiosis, supporting photosynthesis, respiration, and many important enzymatic reactions. However, the extent to which corals are limited by Fe and their metabolic responses to inorganic Fe enrichment remains to be understood. We used respirometry, variable chlorophyll fluorescence, and O2 microsensors to investigate the impact of increasing Fe(III) concentrations (20, 50, and 100 nM) on the photosynthetic capacity of two Mediterranean coral species, Cladocora caespitosa and Oculina patagonica. While the bioavailability of inorganic Fe can rapidly decrease, we nevertheless observed significant physiological effects at all Fe concentrations. In C. caespitosa, exposure to 50 nM Fe(III) increased rates of respiration and photosynthesis, while the relative electron transport rate (rETR(II)) decreased at higher Fe(III) exposure (100 nM). In contrast, O. patagonica reduced respiration, photosynthesis rates, and maximum PSII quantum yield (Fv/Fm) across all iron enrichments. Both corals exhibited increased hypoxia (<50 µmol O2 L-1) within their gastric cavity at night when exposed to 50 and 100 nM Fe(III), leading to increased polyp contraction time and reduced O2 exchange with the surrounding water. Our results indicate that C. caespitosa, but not O. patagonica, might be limited in Fe for achieving maximal photosynthetic efficiency. Understanding the multifaceted role of iron in corals' health and their response to environmental change is crucial for effective coral conservation.
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Affiliation(s)
- Walter Dellisanti
- Department of Biology, Marine Biology Section, University of Copenhagen, Helsingør, Denmark
| | - Qingfeng Zhang
- Department of Biology, Marine Biology Section, University of Copenhagen, Helsingør, Denmark
| | - Christine Ferrier-Pagès
- Coral Ecophysiology Laboratory, Center Scientifique de Monaco, Principality of Monaco, Monaco
| | - Michael Kühl
- Department of Biology, Marine Biology Section, University of Copenhagen, Helsingør, Denmark
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4
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González-Dávila M, Maldonado MT, González AG, Guo J, González-Santana D, Martel A, Santana-Casiano JM. Cu transport and complexation by the marine diatom Phaeodactylum tricornutum: Implications for trace metal complexation kinetics in the surface ocean. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170752. [PMID: 38340864 DOI: 10.1016/j.scitotenv.2024.170752] [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: 10/26/2023] [Revised: 01/30/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Elucidating whether dissolved Cu uptake is kinetically or thermodynamically controlled, and the effects of speciation on Cu transport by phytoplankton will allow better modeling of the fate and impact of dissolved Cu in the ocean. To address these questions, we performed Cu physiological and physicochemical experiments using the model diatom, Phaeodactylum tricornutum, grown in natural North Atlantic seawater (0.44 nM Cu). Using competitive ligand equilibration-cathodic stripping voltammetry (CLE-CSV), we measured two organic ligand types released by P. tricornutum to bind Cu (L1 and L2) at concentrations of ~0.35 nM L1 and 1.3 nM L2. We also established the presence of two putative Cu-binding sites at the cell surface of P. tricornutum (S1 and S2) with log K differing by ~5 orders of magnitude (i.e., 12.9 vs. 8.1) and cell surface densities by 9-fold. Only the high-affinity binding sites, S1, exhibit reductase activity. Using voltammetric kinetic measurements and a theoretical kinetic model, we calculated the forward and dissociation rate constants of L1 and S1. Complementary 67Cu uptake experiments identified a high- and a low-affinity Cu uptake system in P. tricornutum, with half-saturation constant (Km) of 154 nM and 2.63 μM dissolved Cu, respectively. In the P. tricornutum genome, we identified a putative high-affinity Cu transporter (PtCTR49224) and a putative ZIP-like, low-affinity Cu transporter (PtZIP49400). PtCTR49224 has high homology to Homo sapiens hCTR1, which depending on the accessibility to extracellular reducing agents, the hCTR1 itself is involved in the reduction of Cu2+ to Cu+ before internalization. We combined these physiological and physicochemical data to calculate the rate constants for the internalization of Cu, and established that while the high-affinity Cu uptake system (S1) is borderline between a kinetically or thermodynamically controlled system, the low-affinity Cu transporters, S2, is thermodynamically-controlled. We revised the inverse relationship between the concentrations of inorganic complexes of essential metals (i.e., Ni, Fe, Co, Zn, Cd, Mn and Cu) in the mixed layer and the formation rate constant of metal transporters in phytoplankton, highlighting the link between the chemical properties of phytoplankton metal transporters and the availability and speciation of trace metals in the surface ocean.
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Affiliation(s)
- Melchor González-Dávila
- Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Spain.
| | - Maria T Maldonado
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia Vancouver, BC, Canada.
| | - Aridane G González
- Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Spain.
| | - Jian Guo
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia Vancouver, BC, Canada.
| | - David González-Santana
- Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Spain.
| | - Antera Martel
- Banco Español de Algas, Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Spain.
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5
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Gao S, Yang W, Li X, Zhou L, Liu X, Wu S, Wang L, Wang G. Cryptochrome PtCPF1 regulates high temperature acclimation of marine diatoms through coordination of iron and phosphorus uptake. THE ISME JOURNAL 2024; 18:wrad019. [PMID: 38365245 PMCID: PMC10837835 DOI: 10.1093/ismejo/wrad019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 02/18/2024]
Abstract
Increasing ocean temperatures threaten the productivity and species composition of marine diatoms. High temperature response and regulation are important for the acclimation of marine diatoms to such environments. However, the molecular mechanisms behind their acclimation to high temperature are still largely unknown. In this study, the abundance of PtCPF1 homologs (a member of the cryptochrome-photolyase family in the model diatom Phaeodactylum tricornutum) transcripts in marine phytoplankton is shown to increase with rising temperature based on Tara Oceans datasets. Moreover, the expression of PtCPF1 in P. tricornutum at high temperature (26 °C) was much higher than that at optimum temperature (20 °C). Deletion of PtCPF1 in P. tricornutum disrupted the expression of genes encoding two phytotransferrins (ISIP2A and ISIP1) and two Na+/P co-transporters (PHATRDRAFT_47667 and PHATRDRAFT_40433) at 26 °C. This further impacted the uptake of Fe and P, and eventually caused the arrest of cell division. Gene expression, Fe and P uptake, and cell division were restored by rescue with the native PtCPF1 gene. Furthermore, PtCPF1 interacts with two putative transcription factors (BolA and TF IIA) that potentially regulate the expression of genes encoding phytotransferrins and Na+/P co-transporters. To the best of our knowledge, this is the first study to reveal PtCPF1 as an essential regulator in the acclimation of marine diatoms to high temperature through the coordination of Fe and P uptake. Therefore, these findings help elucidate how marine diatoms acclimate to high temperature.
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Affiliation(s)
- Shan Gao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266071, China
| | - Wenting Yang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xin Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266071, China
- College of Earth Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Zhou
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xuehua Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266071, China
| | - Songcui Wu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266071, China
| | - Lijun Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266071, China
| | - Guangce Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266071, China
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6
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Gomes KM, Nunn BL, Chappell PD, Jenkins BD. Subcellular proteomics for determining iron-limited remodeling of plastids in the model diatom Thalassiosira pseudonana (Bacillariophyta). JOURNAL OF PHYCOLOGY 2023; 59:1085-1099. [PMID: 37615442 DOI: 10.1111/jpy.13379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 08/25/2023]
Abstract
Diatoms are important primary producers in the world's oceans, yet their growth is constrained in large regions by low bioavailable iron (Fe). Low-Fe stress-induced limitation of primary production is due to requirements for Fe in components of essential metabolic pathways including photosynthesis and other chloroplast plastid functions. Studies have shown that under low-Fe stress, diatoms alter plastid-specific processes, including components of electron transport. These physiological changes suggest changes of protein content and in protein abundances within the diatom plastid. While in silico predictions provide putative information on plastid-localized proteins, knowledge of diatom plastid proteins remains limited in comparison to well-studied model photosynthetic organisms. To address this, we employed shotgun proteomics to investigate the proteome of subcellular plastid-enriched fractions from Thalassiosira pseudonana to gain a better understanding of how the plastid proteome is remodeled in response to Fe limitation. Using mass spectrometry-based peptide identification and quantification, we analyzed T. pseudonana grown under Fe-replete and -limiting conditions. Through these analyses, we inferred the relative quantities of each protein, revealing that Fe limitation regulates major metabolic pathways in the plastid, including the Calvin cycle. Additionally, we observed changes in the expression of light-harvesting proteins. In silico localization predictions of proteins identified in this plastid-enriched proteome allowed for an in-depth comparison of theoretical versus observed plastid-localization, providing evidence for the potential of additional protein import pathways into the diatom plastid.
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Affiliation(s)
- Kristofer M Gomes
- Department of Biological Sciences, University of Rhode Island, Rhode Island, Kingston, USA
| | - Brook L Nunn
- Department of Genome Sciences, University of Washington, Washington, Seattle, USA
| | - P Dreux Chappell
- College of Marine Science, University of South Florida, Florida, St. Petersburg, USA
| | - Bethany D Jenkins
- Department of Cell and Molecular Biology, University of Rhode Island, Rhode Island, Kingston, USA
- Graduate School of Oceanography, University of Rhode Island, Rhode Island, Narragansett, USA
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7
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Ban H, Sato S, Yoshikawa S, Yamada K, Nakamura Y, Ichinomiya M, Sato N, Blanc-Mathieu R, Endo H, Kuwata A, Ogata H. Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs. Commun Biol 2023; 6:697. [PMID: 37420035 PMCID: PMC10328945 DOI: 10.1038/s42003-023-05002-x] [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: 10/13/2022] [Accepted: 05/31/2023] [Indexed: 07/09/2023] Open
Abstract
The order Parmales (class Bolidophyceae) is a minor group of pico-sized eukaryotic marine phytoplankton that contains species with cells surrounded by silica plates. Previous studies revealed that Parmales is a member of ochrophytes and sister to diatoms (phylum Bacillariophyta), the most successful phytoplankton group in the modern ocean. Therefore, parmalean genomes can serve as a reference to elucidate both the evolutionary events that differentiated these two lineages and the genomic basis for the ecological success of diatoms vs. the more cryptic lifestyle of parmaleans. Here, we compare the genomes of eight parmaleans and five diatoms to explore their physiological and evolutionary differences. Parmaleans are predicted to be phago-mixotrophs. By contrast, diatoms have lost genes related to phagocytosis, indicating the ecological specialization from phago-mixotrophy to photoautotrophy in their early evolution. Furthermore, diatoms show significant enrichment in gene sets involved in nutrient uptake and metabolism, including iron and silica, in comparison with parmaleans. Overall, our results suggest a strong evolutionary link between the loss of phago-mixotrophy and specialization to a silicified photoautotrophic life stage early in diatom evolution after diverging from the Parmales lineage.
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Affiliation(s)
- Hiroki Ban
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Shinya Sato
- Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama City, Fukui, 917-0003, Japan
| | - Shinya Yoshikawa
- Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama City, Fukui, 917-0003, Japan
| | - Kazumasa Yamada
- Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama City, Fukui, 917-0003, Japan
| | - Yoji Nakamura
- Bioinformatics and Biosciences Division, Fisheries Stock Assessment Center, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fuku-ura, Kanazawa, Yokohama, Kanagawa, 236-8648, Japan
| | - Mutsuo Ichinomiya
- Prefectural University of Kumamoto, 3-1-100 Tsukide, Kumamoto, 862-8502, Japan
| | - Naoki Sato
- Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Romain Blanc-Mathieu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, IRIG, Grenoble, France
| | - Hisashi Endo
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Akira Kuwata
- Shiogama field station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 3-27-5 Shinhama-cho, Shiogama, Miyagi, Japan.
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
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8
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Cruz-López R, Carrano CJ. Iron uptake, transport and storage in marine brown algae. Biometals 2023; 36:371-383. [PMID: 36930341 DOI: 10.1007/s10534-023-00489-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/10/2023] [Indexed: 03/18/2023]
Abstract
Iron is a vital although biologically inaccessible trace nutrient for nearly all forms of life but "free" iron can be deleterious to cells and thus iron uptake and storage must be carefully controlled. The marine environment is particularly iron poor making mechanisms for its uptake and storage even more imperative. In this brief review we explore the known and potential iron uptake and storage pathways for the biologically and economically important marine brown macroalgae (seaweeds/kelps).
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Affiliation(s)
- Ricardo Cruz-López
- Instituto de Investigaciones Oceanológicas (IIO), Universidad Autónoma de Baja California (UABC), Ensenada, Baja California, México.
| | - Carl J Carrano
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182-1030, USA
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9
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Brownlee C, Helliwell KE, Meeda Y, McLachlan D, Murphy EA, Wheeler GL. Regulation and integration of membrane transport in marine diatoms. Semin Cell Dev Biol 2023; 134:79-89. [PMID: 35305902 DOI: 10.1016/j.semcdb.2022.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/18/2022] [Accepted: 03/04/2022] [Indexed: 12/27/2022]
Abstract
Diatoms represent one of the most successful groups of marine phytoplankton and are major contributors to ocean biogeochemical cycling. They have colonized marine, freshwater and ice environments and inhabit all regions of the World's oceans, from poles to tropics. Their success is underpinned by a remarkable ability to regulate their growth and metabolism during nutrient limitation and to respond rapidly when nutrients are available. This requires precise regulation of membrane transport and nutrient acquisition mechanisms, integration of nutrient sensing mechanisms and coordination of different transport pathways. This review outlines transport mechanisms involved in acquisition of key nutrients (N, C, P, Si, Fe) by marine diatoms, illustrating their complexity, sophistication and multiple levels of control.
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Affiliation(s)
- Colin Brownlee
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK; School of Ocean and Earth Sciences, University of Southampton, Southampton SO14 3ZH, UK
| | - Katherine E Helliwell
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK; Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Yasmin Meeda
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Deirdre McLachlan
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK; School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Eleanor A Murphy
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Glen L Wheeler
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
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10
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Kazamia E, Mach J, McQuaid JB, Gao X, Coale TH, Malych R, Camadro J, Lesuisse E, Allen AE, Bowler C, Sutak R. In vivo localization of iron starvation induced proteins under variable iron supplementation regimes in Phaeodactylum tricornutum. PLANT DIRECT 2022; 6:e472. [PMID: 36582220 PMCID: PMC9792268 DOI: 10.1002/pld3.472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/03/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
UNLABELLED The model pennate diatom Phaeodactylum tricornutum is able to assimilate a range of iron sources. It therefore provides a platform to study different mechanisms of iron processing concomitantly in the same cell. In this study, we follow the localization of three iron starvation induced proteins (ISIPs) in vivo, driven by their native promoters and tagged by fluorophores in an engineered line of P. tricornutum. We find that the localization patterns of ISIPs are dynamic and variable depending on the overall iron status of the cell and the source of iron it is exposed to. Notwithstanding, a shared destination of the three ISIPs both under ferric iron and siderophore-bound iron supplementation is a globular compartment in the vicinity of the chloroplast. In a proteomic analysis, we identify that the cell engages endocytosis machinery involved in the vesicular trafficking as a response to siderophore molecules, even when these are not bound to iron. Our results suggest that there may be a direct vesicle traffic connection between the diatom cell membrane and the periplastidial compartment (PPC) that co-opts clathrin-mediated endocytosis and the "cytoplasm to vacuole" (Cvt) pathway, for proteins involved in iron assimilation. Proteomics data are available via ProteomeXchange with identifier PXD021172. HIGHLIGHT The marine diatom P. tricornutum engages a vesicular network to traffic siderophores and phytotransferrin from the cell membrane directly to a putative iron processing site in the vicinity of the chloroplast.
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Affiliation(s)
- Elena Kazamia
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERMUniversité PSLParisFrance
| | - Jan Mach
- Department of Parasitology, Faculty of ScienceCharles UniversityVestecCzech Republic
| | - Jeffrey B. McQuaid
- Microbial and Environmental GenomicsJ. Craig Venter InstituteLa JollaCaliforniaUSA
- The Alfred Wegener InstituteHelmholtz Centre for Polar and Marine ResearchBremerhavenGermany
| | - Xia Gao
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERMUniversité PSLParisFrance
| | - Tyler H. Coale
- Scripps Institution of Oceanography, Integrative Oceanography DivisionUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Ronald Malych
- Department of Parasitology, Faculty of ScienceCharles UniversityVestecCzech Republic
| | | | | | - Andrew E. Allen
- Microbial and Environmental GenomicsJ. Craig Venter InstituteLa JollaCaliforniaUSA
- Scripps Institution of Oceanography, Integrative Oceanography DivisionUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Chris Bowler
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERMUniversité PSLParisFrance
| | - Robert Sutak
- Department of Parasitology, Faculty of ScienceCharles UniversityVestecCzech Republic
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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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Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence. Commun Biol 2022; 5:983. [PMID: 36114260 PMCID: PMC9481584 DOI: 10.1038/s42003-022-03939-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
The smallest phytoplankton species are key actors in oceans biogeochemical cycling and their abundance and distribution are affected with global environmental changes. Among them, algae of the Pelagophyceae class encompass coastal species causative of harmful algal blooms while others are cosmopolitan and abundant. The lack of genomic reference in this lineage is a main limitation to study its ecological importance. Here, we analysed Pelagomonas calceolata relative abundance, ecological niche and potential for the adaptation in all oceans using a complete chromosome-scale assembled genome sequence. Our results show that P. calceolata is one of the most abundant eukaryotic species in the oceans with a relative abundance favoured by high temperature, low-light and iron-poor conditions. Climate change projections based on its relative abundance suggest an extension of the P. calceolata habitat toward the poles at the end of this century. Finally, we observed a specific gene repertoire and expression level variations potentially explaining its ecological success in low-iron and low-nitrate environments. Collectively, these findings reveal the ecological importance of P. calceolata and lay the foundation for a global scale analysis of the adaptation and acclimation strategies of this small phytoplankton in a changing environment. Genomic inference reveals potential climate change-driven range expansion of the phytoplankton species Pelagomonas calceolata.
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13
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Maniscalco MA, Brzezinski MA, Lampe RH, Cohen NR, McNair HM, Ellis KA, Brown M, Till CP, Twining BS, Bruland KW, Marchetti A, Thamatrakoln K. Diminished carbon and nitrate assimilation drive changes in diatom elemental stoichiometry independent of silicification in an iron-limited assemblage. ISME COMMUNICATIONS 2022; 2:57. [PMID: 37938259 PMCID: PMC9723790 DOI: 10.1038/s43705-022-00136-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/12/2022] [Accepted: 06/09/2022] [Indexed: 06/17/2023]
Abstract
In the California Current Ecosystem, upwelled water low in dissolved iron (Fe) can limit phytoplankton growth, altering the elemental stoichiometry of the particulate matter and dissolved macronutrients. Iron-limited diatoms can increase biogenic silica (bSi) content >2-fold relative to that of particulate organic carbon (C) and nitrogen (N), which has implications for carbon export efficiency given the ballasted nature of the silica-based diatom cell wall. Understanding the molecular and physiological drivers of this altered cellular stoichiometry would foster a predictive understanding of how low Fe affects diatom carbon export. In an artificial upwelling experiment, water from 96 m depth was incubated shipboard and left untreated or amended with dissolved Fe or the Fe-binding siderophore desferrioxamine-B (+DFB) to induce Fe-limitation. After 120 h, diatoms dominated the communities in all treatments and displayed hallmark signatures of Fe-limitation in the +DFB treatment, including elevated particulate Si:C and Si:N ratios. Single-cell, taxon-resolved measurements revealed no increase in bSi content during Fe-limitation despite higher transcript abundance of silicon transporters and silicanin-1. Based on these findings we posit that the observed increase in bSi relative to C and N was primarily due to reductions in C fixation and N assimilation, driven by lower transcript expression of key Fe-dependent genes.
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Affiliation(s)
- Michael A Maniscalco
- Marine Science Institute and The Department of Ecology Evolution and Marine Biology, University of California, Santa Barbara, CA, USA.
| | - Mark A Brzezinski
- Marine Science Institute and The Department of Ecology Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Robert H Lampe
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Natalie R Cohen
- Skidaway Institute of Oceanography, University of Georgia, Savannah, GA, USA
| | - Heather M McNair
- University of Rhode Island, Graduate School of Oceanography, Narragansett, RI, USA
| | - Kelsey A Ellis
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | | | - Claire P Till
- Chemistry Department, California State Polytechnic University, Humboldt, Arcata, CA, USA
| | | | - Kenneth W Bruland
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA
| | - Adrian Marchetti
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, USA
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14
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Concentration, Spatial-Temporal Distribution, and Bioavailability of Dissolved Reactive Iron in Northern Coastal China Seawater. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10070890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The concentrations of total dissolved iron (TdFe) and dissolved reactive iron (DrFe) in the Northern coastal China seawater (Yantai Sishili Bay) in 2018 were determined using cathodic stripping voltammetry (CSV). It was found that while the concentrations of TdFe ranged from 27.8 to 82.0 nM, DrFe concentrations changed in a much narrower range from 6.8 to 13.3 nM. The annual mean concentrations of DrFe also ranged from 7.1 to 12.6 nM at the 12 sites monitored over the 4 years of the study (2017–2020). Considering the obvious changes in temperature (T), chlorophyll a (Chl a) concentrations (Chl a contents were higher in May, July and September than in March and November), and nutrients over a year in this zone, the consumption of DrFe was expected; the supplement of DrFe observed may have resulted from the transformation of strong organically complexed iron by photoreduction and cell surface reduction. Additionally, a pre-liminary conclusion was drawn based on the theoretical calculation of Fe* that the concentration of DrFe was sufficient to meet the phytoplankton demand.
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15
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Krämer LC, Wasser D, Haitz F, Sabel B, Büchel C. Heterologous expression of HUP1 glucose transporter enables low-light mediated growth on glucose in Phaeodactylum tricornutum. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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16
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Kellogg RM, Moosburner MA, Cohen NR, Hawco NJ, McIlvin MR, Moran DM, DiTullio GR, Subhas AV, Allen AE, Saito MA. Adaptive responses of marine diatoms to zinc scarcity and ecological implications. Nat Commun 2022; 13:1995. [PMID: 35422102 PMCID: PMC9010474 DOI: 10.1038/s41467-022-29603-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/23/2022] [Indexed: 01/16/2023] Open
Abstract
AbstractScarce dissolved surface ocean concentrations of the essential algal micronutrient zinc suggest that Zn may influence the growth of phytoplankton such as diatoms, which are major contributors to marine primary productivity. However, the specific mechanisms by which diatoms acclimate to Zn deficiency are poorly understood. Using global proteomic analysis, we identified two proteins (ZCRP-A/B, Zn/Co Responsive Protein A/B) among four diatom species that became abundant under Zn/Co limitation. Characterization using reverse genetic techniques and homology data suggests putative Zn/Co chaperone and membrane-bound transport complex component roles for ZCRP-A (a COG0523 domain protein) and ZCRP-B, respectively. Metaproteomic detection of ZCRPs along a Pacific Ocean transect revealed increased abundances at the surface (<200 m) where dZn and dCo were scarcest, implying Zn nutritional stress in marine algae is more prevalent than previously recognized. These results demonstrate multiple adaptive responses to Zn scarcity in marine diatoms that are deployed in low Zn regions of the Pacific Ocean.
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17
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Walworth NG, Saito MA, Lee MD, McIlvin MR, Moran DM, Kellogg RM, Fu FX, Hutchins DA, Webb EA. Why Environmental Biomarkers Work: Transcriptome-Proteome Correlations and Modeling of Multistressor Experiments in the Marine Bacterium Trichodesmium. J Proteome Res 2021; 21:77-89. [PMID: 34855411 DOI: 10.1021/acs.jproteome.1c00517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ocean microbial communities are important contributors to the global biogeochemical reactions that sustain life on Earth. The factors controlling these communities are being increasingly explored using metatranscriptomic and metaproteomic environmental biomarkers. Using published proteomes and transcriptomes from the abundant colony-forming cyanobacterium Trichodesmium (strain IMS101) grown under varying Fe and/or P limitation in low and high CO2, we observed robust correlations of stress-induced proteins and RNAs (i.e., involved in transport and homeostasis) that yield useful information on the nutrient status under low and/or high CO2. Conversely, transcriptional and translational correlations of many other central metabolism pathways exhibit broad discordance. A cellular RNA and protein production/degradation model demonstrates how biomolecules with small initial inventories, such as environmentally responsive proteins, achieve large increases in fold-change units as opposed to those with a higher basal expression and inventory such as metabolic systems. Microbial cells, due to their immersion in the environment, tend to show large adaptive responses in both RNA and protein that result in transcript-protein correlations. These observations and model results demonstrate multi-omic coherence for environmental biomarkers and provide the underlying mechanism for those observations, supporting the promise for global application in detecting responses to environmental stimuli in a changing ocean.
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Affiliation(s)
- Nathan G Walworth
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Mak A Saito
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Michael D Lee
- Blue Marble Space Institute of Science, Seattle, Washington 98104, United States.,Exobiology Branch, NASA Ames Research Center, Moffett Field, California 94035, United States
| | - Matthew R McIlvin
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Dawn M Moran
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Riss M Kellogg
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Fei-Xue Fu
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - David A Hutchins
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Eric A Webb
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
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18
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Liu X, Xie X, Gao S, Wang L, Zhou L, Liu Y, Hu Q, Gu W, Wang G. Chlorophyll fluorescence as a light signal enhances iron uptake by the marine diatom Phaeodactylum tricornutum under high-cell density conditions. BMC Biol 2021; 19:249. [PMID: 34814917 PMCID: PMC8609858 DOI: 10.1186/s12915-021-01177-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
Background Diatoms usually dominate phytoplankton blooms in open oceans, exhibiting extremely high population densities. Although the iron uptake rate of diatoms largely determines the magnitude and longevity of diatom blooms, the underlying mechanisms regulating iron uptake remain unclear. Results The transcription of two iron uptake proteins, ISIP2a and ISIP1, in the marine diatom Phaeodactylum tricornutum was enhanced with increasing cell density, whereas the cellular iron content showed the opposite trend. When compared with the wild-type strain, knockdown of ISIP2a resulted in 43% decrease in cellular iron content, implying the involvement of ISIP2a in iron uptake under high-cell density conditions. Incubation of the diatom cells with sonicated cell lysate conditioned by different cell densities did not affect ISIP2a and ISIP1 expression, ruling out regulation via chemical cues. In contrast, ISIP2a and ISIP1 transcription were strongly induced by red light. Besides, chlorophyll fluorescence excited from the blue light was also positively correlated with population density. Subsequently, a “sandwich” illumination incubator was designed to filter out stray light and ensure that the inner layer cells only receive the emitted chlorophyll fluorescence from outer layers, and the results showed that the increase in outer cell density significantly elevated ISIP2a and ISIP1 transcription in inner layer cells. In situ evidence from Tara oceans also showed positively correlated between diatom ISIP transcripts and chlorophyll content. Conclusions This study shows that chlorophyll fluorescence derived from neighboring cells is able to upregulate ISIP2a and ISIP1 expression to facilitate iron assimilation under high-cell density. These results provide novel insights into biotic signal sensing in phytoplankton, which can help to elucidate the underlying mechanisms of marine diatom blooms. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01177-z.
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Affiliation(s)
- Xuehua Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiujun Xie
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shan Gao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lepu Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lu Zhou
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yao Liu
- Public Technology Service Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Qiang Hu
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Wenhui Gu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Guangce Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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19
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Phytate as a phosphorus nutrient with impacts on iron stress-related gene expression for phytoplankton: insights from diatom Phaeodactylum tricornutum. Appl Environ Microbiol 2021; 88:e0209721. [PMID: 34757820 DOI: 10.1128/aem.02097-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phytoplankton have evolved a capability to acquire phosphorus (P) from dissolved organic phosphorus (DOP) since the preferred form, dissolved inorganic phosphate (DIP, or Pi), is often limited in parts of the ocean. Phytic acid (PA) is abundantly synthesized in plants and rich in excreta of animals, potentially enriching the DOP pool in coastal oceans. However, whether and how PA may be used by phytoplankton are poorly understood. Here, we investigated PA utilization and underlying metabolic pathways in the diatom model Phaeodactylum tricornutum. The physiological results showed that P. tricornutum could utilize PA as a sole source of P nutrient to support growth. Meanwhile, the replacement of PA for DIP also caused changes in multiple cellular processes such as inositol phosphate metabolism, photosynthesis, and signal transduction. These results suggest that PA is bioavailable to P. tricornutum and can directly participate the metabolic pathways of PA-grown cells. However, our data showed that the utilization of PA was markedly less efficient than that of DIP, and PA-grown cells exhibited P and iron (Fe) nutrient stress signals. Implicated in these findings is the potential of complicated responses of phytoplankton to an ambient DOP species, which calls for more systematic investigation. IMPORTANCE PA is abundant in plants, and cannot be digested by non-ruminant animals. Hence, it is potentially a significant component of the DOP pool in the coastal waters. Despite the potential importance, there is little information about its bioavailability to phytoplankton as a source of P nutrient and if so what molecular mechanisms are involved. In this study, we found that part of PA could be utilized by the diatom P. tricornutum to support growth, and another portion of PA can act as a substrate directly participating in various metabolism pathways and cellular processes. However, our physiological and transcriptomic data show that PA-grown cells still exhibited signs of P stress and potential Fe stress. These results have significant implications in phytoplankton P nutrient ecology and provide a novel insight into multi-faceted impacts of DOP utilization on phytoplankton nutrition and metabolism.
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20
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Molecular underpinnings and biogeochemical consequences of enhanced diatom growth in a warming Southern Ocean. Proc Natl Acad Sci U S A 2021; 118:2107238118. [PMID: 34301906 PMCID: PMC8325266 DOI: 10.1073/pnas.2107238118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Phytoplankton contribute to the Southern Ocean’s (SO) ability to absorb atmospheric CO2 and shape the stoichiometry of northward macronutrient delivery. Climate change is altering the SO environment, yet we know little about how resident phytoplankton will react to these changes. Here, we studied a natural SO community and compared responses of two prevalent, bloom-forming diatom groups to changes in temperature and iron that are projected to occur by 2100 to 2300. We found that one group, Pseudo-nitzschia, grows better under warmer low-iron conditions by managing cellular iron demand and efficiently increasing photosynthetic capacity. This ability to grow and draw down nutrients in the face of warming, regardless of iron availability, has major implications for ocean ecosystems and global nutrient cycles. The Southern Ocean (SO) harbors some of the most intense phytoplankton blooms on Earth. Changes in temperature and iron availability are expected to alter the intensity of SO phytoplankton blooms, but little is known about how these changes will influence community composition and downstream biogeochemical processes. We performed light-saturated experimental manipulations on surface ocean microbial communities from McMurdo Sound in the Ross Sea to examine the effects of increased iron availability (+2 nM) and warming (+3 and +6 °C) on nutrient uptake, as well as the growth and transcriptional responses of two dominant diatoms, Fragilariopsis and Pseudo-nitzschia. We found that community nutrient uptake and primary productivity were elevated under both warming conditions without iron addition (relative to ambient −0.5 °C). This effect was greater than additive under concurrent iron addition and warming. Pseudo-nitzschia became more abundant under warming without added iron (especially at 6 °C), while Fragilariopsis only became more abundant under warming in the iron-added treatments. We attribute the apparent advantage Pseudo-nitzschia shows under warming to up-regulation of iron-conserving photosynthetic processes, utilization of iron-economic nitrogen assimilation mechanisms, and increased iron uptake and storage. These data identify important molecular and physiological differences between dominant diatom groups and add to the growing body of evidence for Pseudo-nitzschia’s increasingly important role in warming SO ecosystems. This study also suggests that temperature-driven shifts in SO phytoplankton assemblages may increase utilization of the vast pool of excess nutrients in iron-limited SO surface waters and thereby influence global nutrient distribution and carbon cycling.
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21
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Kong L, Price NM. Transcriptomes of an oceanic diatom reveal the initial and final stages of acclimation to copper deficiency. Environ Microbiol 2021; 24:951-966. [PMID: 34029435 DOI: 10.1111/1462-2920.15609] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/13/2022]
Abstract
Copper (Cu) concentration is greatly reduced in the open sea so that phytoplankton must adjust their uptake systems and acclimate to sustain growth. Acclimation to low Cu involves changes to the photosynthetic apparatus and specific biochemical reactions that use Cu, but little is known how Cu affects cellular metabolic networks. Here we report results of whole transcriptome analysis of a plastocyanin-containing diatom, Thalassiosira oceanica 1005, during its initial stages of acclimation and after long-term adaptation in Cu-deficient seawater. Gene expression profiles, used to identify Cu-regulated metabolic pathways, show downregulation of anabolic and energy-yielding reactions in Cu-limited cells. These include the light reactions of photosynthesis, carbon fixation, nitrogen assimilation and glycolysis. Reduction of these pathways is consistent with reduced growth requirements for C and N caused by slower rates of photosynthetic electron transport. Upregulation of oxidative stress defence systems persists in adapted cells, suggesting cellular damage by increased reactive oxygen species (ROS) occurs even after acclimation. Copper deficiency also alters fatty acid metabolism, possibly in response to an increase in lipid peroxidation and membrane damage driven by ROS. During the initial stages of Cu-limitation the majority of differentially regulated genes are associated with photosynthetic metabolism, highlighting the chloroplast as the primary target of low Cu availability. The results provide insights into the mechanisms of acclimation and adaptation of T. oceanica to Cu deficiency.
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Affiliation(s)
- Liangliang Kong
- Department of Biology, McGill University, Montréal, QC, Canada.,College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
| | - Neil M Price
- Department of Biology, McGill University, Montréal, QC, Canada
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22
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Hanikenne M, Esteves SM, Fanara S, Rouached H. Coordinated homeostasis of essential mineral nutrients: a focus on iron. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2136-2153. [PMID: 33175167 DOI: 10.1093/jxb/eraa483] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/13/2020] [Indexed: 05/22/2023]
Abstract
In plants, iron (Fe) transport and homeostasis are highly regulated processes. Fe deficiency or excess dramatically limits plant and algal productivity. Interestingly, complex and unexpected interconnections between Fe and various macro- and micronutrient homeostatic networks, supposedly maintaining general ionic equilibrium and balanced nutrition, are currently being uncovered. Although these interactions have profound consequences for our understanding of Fe homeostasis and its regulation, their molecular bases and biological significance remain poorly understood. Here, we review recent knowledge gained on how Fe interacts with micronutrient (e.g. zinc, manganese) and macronutrient (e.g. sulfur, phosphate) homeostasis, and on how these interactions affect Fe uptake and trafficking. Finally, we highlight the importance of developing an improved model of how Fe signaling pathways are integrated into functional networks to control plant growth and development in response to fluctuating environments.
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Affiliation(s)
- Marc Hanikenne
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000 Liège, Belgium
| | - Sara M Esteves
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000 Liège, Belgium
| | - Steven Fanara
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000 Liège, Belgium
| | - Hatem Rouached
- BPMP, Univ. Montpellier, CNRS, INRA, Montpellier SupAgro, Montpellier, France
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
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23
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Gao X, Bowler C, Kazamia E. Iron metabolism strategies in diatoms. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2165-2180. [PMID: 33693565 PMCID: PMC7966952 DOI: 10.1093/jxb/eraa575] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 03/03/2021] [Indexed: 05/28/2023]
Abstract
Diatoms are one of the most successful group of photosynthetic eukaryotes in the contemporary ocean. They are ubiquitously distributed and are the most abundant primary producers in polar waters. Equally remarkable is their ability to tolerate iron deprivation and respond to periodic iron fertilization. Despite their relatively large cell sizes, diatoms tolerate iron limitation and frequently dominate iron-stimulated phytoplankton blooms, both natural and artificial. Here, we review the main iron use strategies of diatoms, including their ability to assimilate and store a range of iron sources, and the adaptations of their photosynthetic machinery and architecture to iron deprivation. Our synthesis relies on published literature and is complemented by a search of 82 diatom transcriptomes, including information collected from seven representatives of the most abundant diatom genera in the world's oceans.
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Affiliation(s)
- Xia Gao
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Chris Bowler
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Elena Kazamia
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
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24
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Turnšek J, Brunson JK, Viedma MDPM, Deerinck TJ, Horák A, Oborník M, Bielinski VA, Allen AE. Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway. eLife 2021; 10:e52770. [PMID: 33591270 PMCID: PMC7972479 DOI: 10.7554/elife.52770] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Iron is a biochemically critical metal cofactor in enzymes involved in photosynthesis, cellular respiration, nitrate assimilation, nitrogen fixation, and reactive oxygen species defense. Marine microeukaryotes have evolved a phytotransferrin-based iron uptake system to cope with iron scarcity, a major factor limiting primary productivity in the global ocean. Diatom phytotransferrin is endocytosed; however, proteins downstream of this environmentally ubiquitous iron receptor are unknown. We applied engineered ascorbate peroxidase APEX2-based subcellular proteomics to catalog proximal proteins of phytotransferrin in the model marine diatom Phaeodactylum tricornutum. Proteins encoded by poorly characterized iron-sensitive genes were identified including three that are expressed from a chromosomal gene cluster. Two of them showed unambiguous colocalization with phytotransferrin adjacent to the chloroplast. Further phylogenetic, domain, and biochemical analyses suggest their involvement in intracellular iron processing. Proximity proteomics holds enormous potential to glean new insights into iron acquisition pathways and beyond in these evolutionarily, ecologically, and biotechnologically important microalgae.
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Affiliation(s)
- Jernej Turnšek
- Biological and Biomedical Sciences, The Graduate School of Arts and Sciences, Harvard UniversityCambridgeUnited States
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
- Wyss Institute for Biologically Inspired Engineering, Harvard UniversityBostonUnited States
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
- Center for Research in Biological Systems, University of California San DiegoLa JollaUnited States
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
| | - John K Brunson
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
| | | | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, University of California San DiegoLa JollaUnited States
| | - Aleš Horák
- Biology Centre CAS, Institute of ParasitologyČeské BudějoviceCzech Republic
- University of South Bohemia, Faculty of ScienceČeské BudějoviceCzech Republic
| | - Miroslav Oborník
- Biology Centre CAS, Institute of ParasitologyČeské BudějoviceCzech Republic
- University of South Bohemia, Faculty of ScienceČeské BudějoviceCzech Republic
| | - Vincent A Bielinski
- Synthetic Biology and Bioenergy, J. Craig Venter InstituteLa JollaUnited States
| | - Andrew Ellis Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
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25
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Kotabova E, Malych R, Pierella Karlusich JJ, Kazamia E, Eichner M, Mach J, Lesuisse E, Bowler C, Prášil O, Sutak R. Complex Response of the Chlorarachniophyte Bigelowiella natans to Iron Availability. mSystems 2021; 6:e00738-20. [PMID: 33563784 PMCID: PMC7883536 DOI: 10.1128/msystems.00738-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/10/2021] [Indexed: 11/20/2022] Open
Abstract
The productivity of the ocean is largely dependent on iron availability, and marine phytoplankton have evolved sophisticated mechanisms to cope with chronically low iron levels in vast regions of the open ocean. By analyzing the metabarcoding data generated from the Tara Oceans expedition, we determined how the global distribution of the model marine chlorarachniophyte Bigelowiella natans varies across regions with different iron concentrations. We performed a comprehensive proteomics analysis of the molecular mechanisms underpinning the adaptation of B. natans to iron scarcity and report on the temporal response of cells to iron enrichment. Our results highlight the role of phytotransferrin in iron homeostasis and indicate the involvement of CREG1 protein in the response to iron availability. Analysis of the Tara Oceans metagenomes and metatranscriptomes also points to a similar role for CREG1, which is found to be widely distributed among marine plankton but to show a strong bias in gene and transcript abundance toward iron-deficient regions. Our analyses allowed us to define a new subfamily of the CobW domain-containing COG0523 putative metal chaperones which are involved in iron metabolism and are restricted to only a few phytoplankton lineages in addition to B. natans At the physiological level, we elucidated the mechanisms allowing a fast recovery of PSII photochemistry after resupply of iron. Collectively, our study demonstrates that B. natans is well adapted to dynamically respond to a changing iron environment and suggests that CREG1 and COG0523 are important components of iron homeostasis in B. natans and other phytoplankton.IMPORTANCE Despite low iron availability in the ocean, marine phytoplankton require considerable amounts of iron for their growth and proliferation. While there is a constantly growing knowledge of iron uptake and its role in the cellular processes of the most abundant marine photosynthetic groups, there are still largely overlooked branches of the eukaryotic tree of life, such as the chlorarachniophytes. In the present work, we focused on the model chlorarachniophyte Bigelowiella natans, integrating physiological and proteomic analyses in culture conditions with the mining of omics data generated by the Tara Oceans expedition. We provide unique insight into the complex responses of B. natans to iron availability, including novel links to iron metabolism conserved in other phytoplankton lineages.
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Affiliation(s)
- Eva Kotabova
- Institute of Microbiology, Academy of Sciences, Centrum Algatech, Trebon, Czech Republic
| | - Ronald Malych
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Juan José Pierella Karlusich
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Elena Kazamia
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Meri Eichner
- Institute of Microbiology, Academy of Sciences, Centrum Algatech, Trebon, Czech Republic
| | - Jan Mach
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Emmanuel Lesuisse
- Jacques Monod Institute, UMR7592 CNRS, Paris Diderot University, Paris, France
| | - Chris Bowler
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Ondřej Prášil
- Institute of Microbiology, Academy of Sciences, Centrum Algatech, Trebon, Czech Republic
| | - Robert Sutak
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
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Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean. Nat Microbiol 2021; 6:173-186. [PMID: 33398100 DOI: 10.1038/s41564-020-00814-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 10/13/2020] [Indexed: 01/28/2023]
Abstract
Marine microeukaryotes play a fundamental role in biogeochemical cycling through the transfer of energy to higher trophic levels and vertical carbon transport. Despite their global importance, microeukaryote physiology, nutrient metabolism and contributions to carbon cycling across offshore ecosystems are poorly characterized. Here, we observed the prevalence of dinoflagellates along a 4,600-km meridional transect extending across the central Pacific Ocean, where oligotrophic gyres meet equatorial upwelling waters rich in macronutrients yet low in dissolved iron. A combined multi-omics and geochemical analysis provided a window into dinoflagellate metabolism across the transect, indicating a continuous taxonomic dinoflagellate community that shifted its functional transcriptome and proteome as it extended from the euphotic to the mesopelagic zone. In euphotic waters, multi-omics data suggested that a combination of trophic modes were utilized, while mesopelagic metabolism was marked by cytoskeletal investments and nutrient recycling. Rearrangement in nutrient metabolism was evident in response to variable nitrogen and iron regimes across the gradient, with no associated change in community assemblage. Total dinoflagellate proteins scaled with particulate carbon export, with both elevated in equatorial waters, suggesting a link between dinoflagellate abundance and total carbon flux. Dinoflagellates employ numerous metabolic strategies that enable broad occupation of central Pacific ecosystems and play a dual role in carbon transformation through both photosynthetic fixation in the euphotic zone and remineralization in the mesopelagic zone.
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Sutak R, Camadro JM, Lesuisse E. Iron Uptake Mechanisms in Marine Phytoplankton. Front Microbiol 2020; 11:566691. [PMID: 33250865 PMCID: PMC7676907 DOI: 10.3389/fmicb.2020.566691] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/19/2020] [Indexed: 12/20/2022] Open
Abstract
Oceanic phytoplankton species have highly efficient mechanisms of iron acquisition, as they can take up iron from environments in which it is present at subnanomolar concentrations. In eukaryotes, three main models were proposed for iron transport into the cells by first studying the kinetics of iron uptake in different algal species and then, more recently, by using modern biological techniques on the model diatom Phaeodactylum tricornutum. In the first model, the rate of uptake is dependent on the concentration of unchelated Fe species, and is thus limited thermodynamically. Iron is transported by endocytosis after carbonate-dependent binding of Fe(III)' (inorganic soluble ferric species) to phytotransferrin at the cell surface. In this strategy the cells are able to take up iron from very low iron concentration. In an alternative model, kinetically limited for iron acquisition, the extracellular reduction of all iron species (including Fe') is a prerequisite for iron acquisition. This strategy allows the cells to take up iron from a great variety of ferric species. In a third model, hydroxamate siderophores can be transported by endocytosis (dependent on ISIP1) after binding to the FBP1 protein, and iron is released from the siderophores by FRE2-dependent reduction. In prokaryotes, one mechanism of iron uptake is based on the use of siderophores excreted by the cells. Iron-loaded siderophores are transported across the cell outer membrane via a TonB-dependent transporter (TBDT), and are then transported into the cells by an ABC transporter. Open ocean cyanobacteria do not excrete siderophores but can probably use siderophores produced by other organisms. In an alternative model, inorganic ferric species are transported through the outer membrane by TBDT or by porins, and are taken up by the ABC transporter system FutABC. Alternatively, ferric iron of the periplasmic space can be reduced by the alternative respiratory terminal oxidase (ARTO) and the ferrous ions can be transported by divalent metal transporters (FeoB or ZIP). After reoxidation, iron can be taken up by the high-affinity permease Ftr1.
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Affiliation(s)
- Robert Sutak
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
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28
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The Importance of Protein Phosphorylation for Signaling and Metabolism in Response to Diel Light Cycling and Nutrient Availability in a Marine Diatom. BIOLOGY 2020; 9:biology9070155. [PMID: 32640597 PMCID: PMC7408324 DOI: 10.3390/biology9070155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/01/2020] [Accepted: 07/03/2020] [Indexed: 01/23/2023]
Abstract
Diatoms are major contributors to global primary production and their populations in the modern oceans are affected by availability of iron, nitrogen, phosphate, silica, and other trace metals, vitamins, and infochemicals. However, little is known about the role of phosphorylation in diatoms and its role in regulation and signaling. We report a total of 2759 phosphorylation sites on 1502 proteins detected in Phaeodactylum tricornutum. Conditionally phosphorylated peptides were detected at low iron (n = 108), during the diel cycle (n = 149), and due to nitrogen availability (n = 137). Through a multi-omic comparison of transcript, protein, phosphorylation, and protein homology, we identify numerous proteins and key cellular processes that are likely under control of phospho-regulation. We show that phosphorylation regulates: (1) carbon retrenchment and reallocation during growth under low iron, (2) carbon flux towards lipid biosynthesis after the lights turn on, (3) coordination of transcription and translation over the diel cycle and (4) in response to nitrogen depletion. We also uncover phosphorylation sites for proteins that play major roles in diatom Fe sensing and utilization, including flavodoxin and phytotransferrin (ISIP2A), as well as identify phospho-regulated stress proteins and kinases. These findings provide much needed insight into the roles of protein phosphorylation in diel cycling and nutrient sensing in diatoms.
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29
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Rizkallah MR, Frickenhaus S, Trimborn S, Harms L, Moustafa A, Benes V, Gäbler-Schwarz S, Beszteri S. Deciphering Patterns of Adaptation and Acclimation in the Transcriptome of Phaeocystis antarctica to Changing Iron Conditions 1. JOURNAL OF PHYCOLOGY 2020; 56:747-760. [PMID: 32068264 DOI: 10.1111/jpy.12979] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
The haptophyte Phaeocystis antarctica is endemic to the Southern Ocean, where iron supply is sporadic and its availability limits primary production. In iron fertilization experiments, P. antarctica showed a prompt and steady increase in cell abundance compared to heavily silicified diatoms along with enhanced colony formation. Here we utilized a transcriptomic approach to investigate molecular responses to alleviation of iron limitation in P. antarctica. We analyzed the transcriptomic response before and after (14 h, 24 h and 72 h) iron addition to a low-iron acclimated culture. After iron addition, we observed indicators of a quick reorganization of cellular energetics, from carbohydrate catabolism and mitochondrial energy production to anabolism. In addition to typical substitution responses from an iron-economic toward an iron-sufficient state for flavodoxin (ferredoxin) and plastocyanin (cytochrome c6 ), we found other genes utilizing the same strategy involved in nitrogen assimilation and fatty acid desaturation. Our results shed light on a number of adaptive mechanisms that P. antarctica uses under low iron, including the utilization of a Cu-dependent ferric reductase system and indication of mixotrophic growth. The gene expression patterns underpin P. antarctica as a quick responder to iron addition.
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Affiliation(s)
| | - Stephan Frickenhaus
- Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Centre for Industrial Mathematics, University of Bremen, Bibliothekstrasse 1, 28359 Postfach 330440, 28334, Bremen, Germany
| | - Scarlett Trimborn
- Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Department of Marine Botany, University of Bremen, Bibliothekstrasse 1, 28359 Postfach 330440, 28334, Bremen, Germany
| | - Lars Harms
- Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Herrstrasse 231, 26129, Oldenburg, Germany
| | - Ahmed Moustafa
- Department of Biology, American University in Cairo, P.O. Box 74, 11835, Cairo, Egypt
| | - Vladimir Benes
- European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Steffi Gäbler-Schwarz
- Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Sara Beszteri
- Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
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30
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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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31
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Suzuki S, Kataoka T, Watanabe T, Yamaguchi H, Kuwata A, Kawachi M. Depth-dependent transcriptomic response of diatoms during spring bloom in the western subarctic Pacific Ocean. Sci Rep 2019; 9:14559. [PMID: 31601926 PMCID: PMC6787086 DOI: 10.1038/s41598-019-51150-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/24/2019] [Indexed: 11/09/2022] Open
Abstract
Diatoms play important roles in primary production and carbon transportation in various environments. Large-scale diatom bloom occurs worldwide; however, metabolic responses of diatoms to environmental conditions have been little studied. Here, we targeted the Oyashio region of the western subarctic Pacific where diatoms bloom every spring and investigated metabolic response of major diatoms to bloom formation by comparing metatranscriptomes between two depths corresponding to different bloom phases. Thalassiosira nordenskioeldii and Chaetoceros debilis are two commonly occurring species at the study site. The gene expression profile was drastically different between the surface (late decline phase of the bloom; 10 m depth) and the subsurface chlorophyll maximum (SCM, initial decline phase of the bloom; 30 m depth); in particular, both species had high expression of genes for nitrate uptake at the surface, but for ammonia uptake at the SCM. Our culture experiments using T. nordenskioeldii imitating the environmental conditions showed that gene expression for nitrate and ammonia transporters was induced by nitrate addition and active cell division, respectively. These results indicate that the requirement for different nitrogen compounds is a major determinant of diatom species responses during bloom maturing.
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Affiliation(s)
- Shigekatsu Suzuki
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, Japan.
| | - Takafumi Kataoka
- Faculty of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama, Fukui, Japan
| | - Tsuyoshi Watanabe
- Tohoku National Fisheries Research Institute, Japan Fisheries Research and Education Agency, 3-27-5 Shinhama-cho, Shiogama, Miyagi, Japan
| | - Haruyo Yamaguchi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, Japan
| | - Akira Kuwata
- Tohoku National Fisheries Research Institute, Japan Fisheries Research and Education Agency, 3-27-5 Shinhama-cho, Shiogama, Miyagi, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, Japan
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32
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Scheiber IF, Pilátová J, Malych R, Kotabova E, Krijt M, Vyoral D, Mach J, Léger T, Camadro JM, Prášil O, Lesuisse E, Sutak R. Copper and iron metabolism in Ostreococcus tauri – the role of phytotransferrin, plastocyanin and a chloroplast copper-transporting ATPase. Metallomics 2019; 11:1657-1666. [DOI: 10.1039/c9mt00078j] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We have identified Ostreococcus tauri major iron uptake mediating protein, phytotransferrin (Ot-FEA1), whose expression and binding of iron is copper dependent.
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33
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Pervasive iron limitation at subsurface chlorophyll maxima of the California Current. Proc Natl Acad Sci U S A 2018; 115:13300-13305. [PMID: 30530699 PMCID: PMC6310781 DOI: 10.1073/pnas.1813192115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The vertical distribution of phytoplankton cells and chlorophyll concentrations throughout the sunlit water column is rarely uniform. In many ocean regions, chlorophyll concentrations peak in distinct and persistent layers deep below the surface called subsurface chlorophyll maximum layers (SCMLs). SCML formation is hypothesized to reflect the consequences of phytoplankton light/macronutrient colimitation, behavior, and/or photoacclimation. We discovered unexpectedly persistent and widespread phytoplankton iron limitation and iron/light colimitation in SCMLs of the California Current and at the edge of the North Pacific Subtropical Gyre using shipboard incubations, metatranscriptomics, and biogeochemical proxies. These results suggest that interactions and feedbacks between iron and light availability play an important and previously unrecognized role in controlling the productivity and biogeochemical dynamics of SCMLs. Subsurface chlorophyll maximum layers (SCMLs) are nearly ubiquitous in stratified water columns and exist at horizontal scales ranging from the submesoscale to the extent of oligotrophic gyres. These layers of heightened chlorophyll and/or phytoplankton concentrations are generally thought to be a consequence of a balance between light energy from above and a limiting nutrient flux from below, typically nitrate (NO3). Here we present multiple lines of evidence demonstrating that iron (Fe) limits or with light colimits phytoplankton communities in SCMLs along a primary productivity gradient from coastal to oligotrophic offshore waters in the southern California Current ecosystem. SCML phytoplankton responded markedly to added Fe or Fe/light in experimental incubations and transcripts of diatom and picoeukaryote Fe stress genes were strikingly abundant in SCML metatranscriptomes. Using a biogeochemical proxy with data from a 40-y time series, we find that diatoms growing in California Current SCMLs are persistently Fe deficient during the spring and summer growing season. We also find that the spatial extent of Fe deficiency within California Current SCMLs has significantly increased over the last 25 y in line with a regional climate index. Finally, we show that diatom Fe deficiency may be common in the subsurface of major upwelling zones worldwide. Our results have important implications for our understanding of the biogeochemical consequences of marine SCML formation and maintenance.
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Cohen NR, Gong W, Moran DM, McIlvin MR, Saito MA, Marchetti A. Transcriptomic and proteomic responses of the oceanic diatom
Pseudo‐nitzschia granii
to iron limitation. Environ Microbiol 2018; 20:3109-3126. [DOI: 10.1111/1462-2920.14386] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 08/09/2018] [Accepted: 08/12/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Natalie R Cohen
- Department of Marine Sciences University of North Carolina at Chapel Hill Chapel Hill NC 27514 USA
- Marine Chemistry and Geochemistry Department Woods Hole Oceanographic Institution Woods Hole MA 02543 USA
| | - Weida Gong
- Department of Marine Sciences University of North Carolina at Chapel Hill Chapel Hill NC 27514 USA
| | - Dawn M. Moran
- Marine Chemistry and Geochemistry Department Woods Hole Oceanographic Institution Woods Hole MA 02543 USA
| | - Matthew R. McIlvin
- Marine Chemistry and Geochemistry Department Woods Hole Oceanographic Institution Woods Hole MA 02543 USA
| | - Mak A. Saito
- Marine Chemistry and Geochemistry Department Woods Hole Oceanographic Institution Woods Hole MA 02543 USA
| | - Adrian Marchetti
- Department of Marine Sciences University of North Carolina at Chapel Hill Chapel Hill NC 27514 USA
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Kazamia E, Sutak R, Paz-Yepes J, Dorrell RG, Vieira FRJ, Mach J, Morrissey J, Leon S, Lam F, Pelletier E, Camadro JM, Bowler C, Lesuisse E. Endocytosis-mediated siderophore uptake as a strategy for Fe acquisition in diatoms. SCIENCE ADVANCES 2018; 4:eaar4536. [PMID: 29774236 PMCID: PMC5955625 DOI: 10.1126/sciadv.aar4536] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/29/2018] [Indexed: 05/20/2023]
Abstract
Phytoplankton growth is limited in vast oceanic regions by the low bioavailability of iron. Iron fertilization often results in diatom blooms, yet the physiological underpinnings for how diatoms survive in chronically iron-limited waters and outcompete other phytoplankton when iron becomes available are unresolved. We show that some diatoms can use siderophore-bound iron, and exhibit a species-specific recognition for siderophore types. In Phaeodactylum tricornutum, hydroxamate siderophores are taken up without previous reduction by a high-affinity mechanism that involves binding to the cell surface followed by endocytosis-mediated uptake and delivery to the chloroplast. The affinity recorded is the highest ever described for an iron transport system in any eukaryotic cell. Collectively, our observations suggest that there are likely a variety of iron uptake mechanisms in diatoms besides the well-established reductive mechanism. We show that iron starvation-induced protein 1 (ISIP1) plays an important role in the uptake of siderophores, and through bioinformatics analyses we deduce that this protein is largely diatom-specific. We quantify expression of ISIP1 in the global ocean by querying the Tara Oceans atlas of eukaryotic genes and show a link between the abundance and distribution of diatom-associated ISIP1 with ocean provinces defined by chronic iron starvation.
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Affiliation(s)
- Elena Kazamia
- Institut de Biologie de l’Ecole normale supérieure, Ecole normale supérieure, CNRS, INSERM, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Robert Sutak
- Department of Parasitology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic
| | - Javier Paz-Yepes
- Institut de Biologie de l’Ecole normale supérieure, Ecole normale supérieure, CNRS, INSERM, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Richard G. Dorrell
- Institut de Biologie de l’Ecole normale supérieure, Ecole normale supérieure, CNRS, INSERM, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Fabio Rocha Jimenez Vieira
- Institut de Biologie de l’Ecole normale supérieure, Ecole normale supérieure, CNRS, INSERM, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Jan Mach
- Department of Parasitology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic
| | - Joe Morrissey
- Institut de Biologie de l’Ecole normale supérieure, Ecole normale supérieure, CNRS, INSERM, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Sébastien Leon
- Université Paris Diderot (Paris 07), Centre National de la Recherche Scientifique, Institut Jacques Monod, F-75013 Paris, France
| | - France Lam
- Université Paris Diderot (Paris 07), Centre National de la Recherche Scientifique, Institut Jacques Monod, F-75013 Paris, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives, CNRS, Univ Evry, Univ Paris-Saclay, 91000 Evry, France
| | - Jean-Michel Camadro
- Université Paris Diderot (Paris 07), Centre National de la Recherche Scientifique, Institut Jacques Monod, F-75013 Paris, France
| | - Chris Bowler
- Institut de Biologie de l’Ecole normale supérieure, Ecole normale supérieure, CNRS, INSERM, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
- Corresponding author. (E.L.); (C.B.)
| | - Emmanuel Lesuisse
- Université Paris Diderot (Paris 07), Centre National de la Recherche Scientifique, Institut Jacques Monod, F-75013 Paris, France
- Corresponding author. (E.L.); (C.B.)
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36
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McQuaid JB, Kustka AB, Oborník M, Horák A, McCrow JP, Karas BJ, Zheng H, Kindeberg T, Andersson AJ, Barbeau KA, Allen AE. Carbonate-sensitive phytotransferrin controls high-affinity iron uptake in diatoms. Nature 2018. [DOI: 10.1038/nature25982] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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37
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Zhao P, Gu W, Huang A, Wu S, Liu C, Huan L, Gao S, Xie X, Wang G. Effect of iron on the growth of Phaeodactylum tricornutum via photosynthesis. JOURNAL OF PHYCOLOGY 2018; 54:34-43. [PMID: 29159944 DOI: 10.1111/jpy.12607] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 10/14/2017] [Indexed: 06/07/2023]
Abstract
Iron is a limiting factor that controls the phytoplankton biomass in the modern ocean, and iron fertilization of the ocean could lead to blooms dominated by diatoms. Thus, iron plays an important role in controlling the distribution of diatoms. In this study, we measured the growth rate and photosynthetic activity of the model diatom Phaeodactylum tricornutum cultured under different iron concentrations and found that it grew more rapidly and had a much higher photosynthetic efficiency under higher iron concentrations. In order to explore the unique mechanism of the response of diatoms to iron, a proteomic analysis was carried out, and the results indicated that iron promotes the Calvin cycle of P. tricornutum. Diatoms can tolerate the pressure of iron limitation by replacing iron-rich proteins with flavodoxin, and so on. Moreover, we found that the photosystem I (PSI) activity of iron-limited algae that were treated by N',N',N',N'-tetramethyl-p-phenylenediamine (TMPD) was increased significantly. As TMPD plays the role of a cytochrome b6 /f complex that transfers electrons from photosystem II to PSI, the cytochrome b6 /f complex is the key to photosynthesis regulation. Iron could influence the growth of P. tricornutum by regulating its biosynthesis. All of the results suggest that iron might affect the growth of diatoms through the Calvin cycle and the cytochrome b6 /f complex.
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Affiliation(s)
- Peipei Zhao
- Institute of Oceanology, Key Laboratory of Experimental Biology, Chinese Academy of Sciences, Qingdao, 266071, China
- Qingdao National Lab for Marine Science and Technology, Qingdao, 266200, China
- Biology Institute of Shandong Academy of Sciences, Jinan, 250014, China
| | - Wenhui Gu
- Institute of Oceanology, Key Laboratory of Experimental Biology, Chinese Academy of Sciences, Qingdao, 266071, China
- Qingdao National Lab for Marine Science and Technology, Qingdao, 266200, China
| | - Aiyou Huang
- Institute of Oceanology, Key Laboratory of Experimental Biology, Chinese Academy of Sciences, Qingdao, 266071, China
- Qingdao National Lab for Marine Science and Technology, Qingdao, 266200, China
| | - Songcui Wu
- Institute of Oceanology, Key Laboratory of Experimental Biology, Chinese Academy of Sciences, Qingdao, 266071, China
- Qingdao National Lab for Marine Science and Technology, Qingdao, 266200, China
| | - Changheng Liu
- Biology Institute of Shandong Academy of Sciences, Jinan, 250014, China
| | - Li Huan
- Institute of Oceanology, Key Laboratory of Experimental Biology, Chinese Academy of Sciences, Qingdao, 266071, China
- Qingdao National Lab for Marine Science and Technology, Qingdao, 266200, China
| | - Shan Gao
- Institute of Oceanology, Key Laboratory of Experimental Biology, Chinese Academy of Sciences, Qingdao, 266071, China
- Qingdao National Lab for Marine Science and Technology, Qingdao, 266200, China
| | - Xiujun Xie
- Institute of Oceanology, Key Laboratory of Experimental Biology, Chinese Academy of Sciences, Qingdao, 266071, China
- Qingdao National Lab for Marine Science and Technology, Qingdao, 266200, China
| | - Guangce Wang
- Institute of Oceanology, Key Laboratory of Experimental Biology, Chinese Academy of Sciences, Qingdao, 266071, China
- Qingdao National Lab for Marine Science and Technology, Qingdao, 266200, China
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38
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Moreno CM, Lin Y, Davies S, Monbureau E, Cassar N, Marchetti A. Examination of gene repertoires and physiological responses to iron and light limitation in Southern Ocean diatoms. Polar Biol 2017. [DOI: 10.1007/s00300-017-2228-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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39
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Blaby-Haas CE, Merchant SS. Regulating cellular trace metal economy in algae. CURRENT OPINION IN PLANT BIOLOGY 2017; 39:88-96. [PMID: 28672168 PMCID: PMC5595633 DOI: 10.1016/j.pbi.2017.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/09/2017] [Accepted: 06/12/2017] [Indexed: 05/05/2023]
Abstract
As indispensable protein cofactors, Fe, Mn, Cu and Zn are at the center of multifaceted acclimation mechanisms that have evolved to ensure extracellular supply meets intracellular demand. Starting with selective transport at the plasma membrane and ending in protein metalation, metal homeostasis in algae involves regulated trafficking of metal ions across membranes, intracellular compartmentalization by proteins and organelles, and metal-sparing/recycling mechanisms to optimize metal-use efficiency. Overlaid on these processes are additional circuits that respond to the metabolic state as well as to the prior metal status of the cell. In this review, we focus on recent progress made toward understanding the pathways by which the single-celled, green alga Chlamydomonas reinhardtii controls its cellular trace metal economy. We also compare these mechanisms to characterized and putative processes in other algal lineages. Photosynthetic microbes continue to provide insight into cellular regulation and handling of Cu, Fe, Zn and Mn as a function of the nutritional supply and cellular demand for metal cofactors. New experimental tools such as RNA-Seq and subcellular metal imaging are bringing us closer to a molecular understanding of acclimation to supply dynamics in algae and beyond.
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Affiliation(s)
- Crysten E Blaby-Haas
- Biology Department, Brookhaven National Laboratory, 50 Bell Avenue, Building 463, Upton, NY 11973, USA.
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, USA; Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, USA
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40
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Marchetti A, Moreno CM, Cohen NR, Oleinikov I, deLong K, Twining BS, Armbrust EV, Lampe RH. Development of a molecular-based index for assessing iron status in bloom-forming pennate diatoms. JOURNAL OF PHYCOLOGY 2017; 53:820-832. [PMID: 28394444 DOI: 10.1111/jpy.12539] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 03/09/2017] [Indexed: 06/07/2023]
Abstract
Iron availability limits primary productivity in large areas of the world's oceans. Ascertaining the iron status of phytoplankton is essential for understanding the factors regulating their growth and ecology. We developed an incubation-independent, molecular-based approach to assess the iron nutritional status of specific members of the diatom community, initially focusing on the ecologically important pennate diatom Pseudo-nitzschia. Through a comparative transcriptomic approach, we identified two genes that track the iron status of Pseudo-nitzschia with high fidelity. The first gene, ferritin (FTN), encodes for the highly specialized iron storage protein induced under iron-replete conditions. The second gene, ISIP2a, encodes an iron-concentrating protein induced under iron-limiting conditions. In the oceanic diatom Pseudo-nitzschia granii (Hasle) Hasle, transcript abundance of these genes directly relates to changes in iron availability, with increased FTN transcript abundance under iron-replete conditions and increased ISIP2a transcript abundance under iron-limiting conditions. The resulting ISIP2a:FTN transcript ratio reflects the iron status of cells, where a high ratio indicates iron limitation. Field samples collected from iron grow-out microcosm experiments conducted in low iron waters of the Gulf of Alaska and variable iron waters in the California upwelling zone verify the validity of our proposed Pseudo-nitzschia Iron Limitation Index, which can be used to ascertain in situ iron status and further developed for other ecologically important diatoms.
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Affiliation(s)
- Adrian Marchetti
- Department of Marine Sciences, University of North Carolina at Chapel Hill, CB 3300, Chapel Hill, North Carolina, 27599, USA
| | - Carly M Moreno
- Department of Marine Sciences, University of North Carolina at Chapel Hill, CB 3300, Chapel Hill, North Carolina, 27599, USA
| | - Natalie R Cohen
- Department of Marine Sciences, University of North Carolina at Chapel Hill, CB 3300, Chapel Hill, North Carolina, 27599, USA
| | - Irina Oleinikov
- Department of Biomedical Science, Florida Atlantic University, 777 Glades Road, BC-71, Boca Raton, Florida, 33431, USA
| | - Kimberly deLong
- Department of Marine Sciences, University of North Carolina at Chapel Hill, CB 3300, Chapel Hill, North Carolina, 27599, USA
| | - Benjamin S Twining
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Dr., PO Box 380, East Boothbay, Maine, 04544, USA
| | - E Virginia Armbrust
- School of Oceanography, University of Washington, Benjamin Hall IRB, 616 NE Northlake Place, Seattle, Washington, 98105, USA
| | - Robert H Lampe
- Department of Marine Sciences, University of North Carolina at Chapel Hill, CB 3300, Chapel Hill, North Carolina, 27599, USA
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41
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Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta). Proc Natl Acad Sci U S A 2017; 114:E6361-E6370. [PMID: 28716924 DOI: 10.1073/pnas.1703088114] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Porphyra umbilicalis (laver) belongs to an ancient group of red algae (Bangiophyceae), is harvested for human food, and thrives in the harsh conditions of the upper intertidal zone. Here we present the 87.7-Mbp haploid Porphyra genome (65.8% G + C content, 13,125 gene loci) and elucidate traits that inform our understanding of the biology of red algae as one of the few multicellular eukaryotic lineages. Novel features of the Porphyra genome shared by other red algae relate to the cytoskeleton, calcium signaling, the cell cycle, and stress-tolerance mechanisms including photoprotection. Cytoskeletal motor proteins in Porphyra are restricted to a small set of kinesins that appear to be the only universal cytoskeletal motors within the red algae. Dynein motors are absent, and most red algae, including Porphyra, lack myosin. This surprisingly minimal cytoskeleton offers a potential explanation for why red algal cells and multicellular structures are more limited in size than in most multicellular lineages. Additional discoveries further relating to the stress tolerance of bangiophytes include ancestral enzymes for sulfation of the hydrophilic galactan-rich cell wall, evidence for mannan synthesis that originated before the divergence of green and red algae, and a high capacity for nutrient uptake. Our analyses provide a comprehensive understanding of the red algae, which are both commercially important and have played a major role in the evolution of other algal groups through secondary endosymbioses.
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42
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Intraspecific variability in Phaeocystis antarctica's response to iron and light stress. PLoS One 2017; 12:e0179751. [PMID: 28692685 PMCID: PMC5503234 DOI: 10.1371/journal.pone.0179751] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 06/02/2017] [Indexed: 12/13/2022] Open
Abstract
Phaeocystis antarctica is an abundant phytoplankton species in the Southern Ocean, where growth is frequently limited by iron and light. Being able to grow under low iron conditions is essential to the species’ success, but there have been hints that this ability differs among clones. Here, we compare the growth, cell size and chlorophyll a concentrations of four P. antarctica clones cultured under different iron and light conditions. Iron was provided either as unchelated iron (Fe′) or bound to the bacterial siderophore desferrioxamine B, representing, respectively, the most and least bioavailable forms of iron which phytoplankton encounter in the marine environment. The growth rate data demonstrate that the clones vary in their ability to grow using organically bound iron, and that this ability is not related to their ability to grow at low inorganic iron concentrations. These results are consistent at low and high light. Physiologically, only three of the four clones shrink or decrease the concentration of chlorophyll a in response to iron limitation, and only one clone decreases colony formation. Together, our data show that P. antarctica clones 1) respond to the same degree of iron limitation using different acclimation strategies, and 2) vary in their ability to grow under the same external iron and light conditions. This physiological diversity is surprisingly large for isolates of a single phytoplankton species.
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43
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Shoenfelt EM, Sun J, Winckler G, Kaplan MR, Borunda AL, Farrell KR, Moreno PI, Gaiero DM, Recasens C, Sambrotto RN, Bostick BC. High particulate iron(II) content in glacially sourced dusts enhances productivity of a model diatom. SCIENCE ADVANCES 2017; 3:e1700314. [PMID: 28691098 PMCID: PMC5482553 DOI: 10.1126/sciadv.1700314] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/08/2017] [Indexed: 05/31/2023]
Abstract
Little is known about the bioavailability of iron (Fe) in natural dusts and the impact of dust mineralogy on Fe utilization by photosynthetic organisms. Variation in the supply of bioavailable Fe to the ocean has the potential to influence the global carbon cycle by modulating primary production in the Southern Ocean. Much of the dust deposited across the Southern Ocean is sourced from South America, particularly Patagonia, where the waxing and waning of past and present glaciers generate fresh glaciogenic material that contrasts with aged and chemically weathered nonglaciogenic sediments. We show that these two potential sources of modern-day dust are mineralogically distinct, where glaciogenic dust sources contain mostly Fe(II)-rich primary silicate minerals, and nearby nonglaciogenic dust sources contain mostly Fe(III)-rich oxyhydroxide and Fe(III) silicate weathering products. In laboratory culture experiments, Phaeodactylum tricornutum, a well-studied coastal model diatom, grows more rapidly, and with higher photosynthetic efficiency, with input of glaciogenic particulates compared to that of nonglaciogenic particulates due to these differences in Fe mineralogy. Monod nutrient accessibility models fit to our data suggest that particulate Fe(II) content, rather than abiotic solubility, controls the Fe bioavailability in our Fe fertilization experiments. Thus, it is possible for this diatom to access particulate Fe in dusts by another mechanism besides uptake of unchelated Fe (Fe') dissolved from particles into the bulk solution. If this capability is widespread in the Southern Ocean, then dusts deposited to the Southern Ocean in cold glacial periods are likely more bioavailable than those deposited in warm interglacial periods.
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Affiliation(s)
- Elizabeth M Shoenfelt
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, NY 10964, USA
- Department of Earth and Environmental Sciences, Columbia University, New York, NY 10027, USA
| | - Jing Sun
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, NY 10964, USA
- Department of Earth and Environmental Sciences, Columbia University, New York, NY 10027, USA
| | - Gisela Winckler
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, NY 10964, USA
- Department of Earth and Environmental Sciences, Columbia University, New York, NY 10027, USA
| | - Michael R Kaplan
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, NY 10964, USA
| | - Alejandra L Borunda
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, NY 10964, USA
- Department of Earth and Environmental Sciences, Columbia University, New York, NY 10027, USA
| | - Kayla R Farrell
- Department of Environmental Science, Barnard College at Columbia University, New York, NY 10027, USA
| | - Patricio I Moreno
- Department of Ecological Sciences, University of Chile, Av. Libertador Bernardo O'Higgins 1058, Santiago, Chile
| | - Diego M Gaiero
- Center for Earth Science Research, National University of Córdoba, Av. Haya de la Torre s/n, Córdoba, Argentina
| | - Cristina Recasens
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, NY 10964, USA
| | - Raymond N Sambrotto
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, NY 10964, USA
| | - Benjamin C Bostick
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, NY 10964, USA
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Tirichine L, Rastogi A, Bowler C. Recent progress in diatom genomics and epigenomics. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:46-55. [PMID: 28226268 DOI: 10.1016/j.pbi.2017.02.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 01/31/2017] [Accepted: 02/02/2017] [Indexed: 06/06/2023]
Abstract
Diatoms are one of the most diverse and successful groups of phytoplankton at the base of the food chain, sustaining life in the ocean and performing vital biogeochemical functions. The last fifteen years have witnessed the comprehensive analysis of several diatom genomes, revealing that they bear traces of their endosymbiotic origins from algal and heterotrophic ancestors, as well as significant gene transfer from bacteria. Their chimeric genomes are further regulated by a range of chromatin-based processes that are characteristic of both plant and animal genomes. We discuss the conservation of gene regulatory mechanisms in diatoms and propose that epigenetic processes may have a significant role in mediating responses to a highly dynamic and unpredictable environment in these organisms.
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Affiliation(s)
- Leila Tirichine
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005 Paris, France.
| | - Achal Rastogi
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005 Paris, France
| | - Chris Bowler
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005 Paris, France
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45
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Iron incorporation in biosilica of the marine diatom Stephanopyxis turris: dispersed or clustered? Biometals 2017; 30:71-82. [PMID: 28064420 DOI: 10.1007/s10534-016-9987-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 12/21/2016] [Indexed: 01/08/2023]
Abstract
Iron incorporation into diatom biosilica was investigated for the species Stephanopyxis turris. It is known that several "foreign" elements (e.g., germanium, titanium, aluminum, zinc, iron) can be incorporated into the siliceous cell walls of diatoms in addition to silicon dioxide (SiO2). In order to examine the amount and form of iron incorporation, the iron content in the growth medium was varied during cultivation. Fe:Si ratios of isolated cell walls were measured by ICP-OES. SEM studies were performed to examine of a possible influence of excess iron during diatom growth upon cell wall formation. The chemical state of biosilica-attached iron was characterized by a combination of infrared, 29Si MAS NMR, and EPR spectroscopy. For comparison, synthetic silicagels of variable iron content were studied. Our investigations show that iron incorporation in biosilica is limited. More than 95% of biosilica-attached iron is found in the form of iron clusters/nanoparticles. In contrast, iron is preferentially dispersedly incorporated within the silica framework in synthetic silicagels leading to Si-O-Fe bond formation.
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46
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Smith SR, Gillard JTF, Kustka AB, McCrow JP, Badger JH, Zheng H, New AM, Dupont CL, Obata T, Fernie AR, Allen AE. Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation. PLoS Genet 2016; 12:e1006490. [PMID: 27973599 PMCID: PMC5156380 DOI: 10.1371/journal.pgen.1006490] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 11/16/2016] [Indexed: 11/23/2022] Open
Abstract
Environmental fluctuations affect distribution, growth and abundance of diatoms in nature, with iron (Fe) availability playing a central role. Studies on the response of diatoms to low Fe have either utilized continuous (24 hr) illumination or sampled a single time of day, missing any temporal dynamics. We profiled the physiology, metabolite composition, and global transcripts of the pennate diatom Phaeodactylum tricornutum during steady-state growth at low, intermediate, and high levels of dissolved Fe over light:dark cycles, to better understand fundamental aspects of genetic control of physiological acclimation to growth under Fe-limitation. We greatly expand the catalog of genes involved in the low Fe response, highlighting the importance of intracellular trafficking in Fe-limited diatoms. P. tricornutum exhibited transcriptomic hallmarks of slowed growth leading to prolonged periods of cell division/silica deposition, which could impact biogeochemical carbon sequestration in Fe-limited regions. Light harvesting and ribosome biogenesis transcripts were generally reduced under low Fe while transcript levels for genes putatively involved in the acquisition and recycling of Fe were increased. We also noted shifts in expression towards increased synthesis and catabolism of branched chain amino acids in P. tricornutum grown at low Fe whereas expression of genes involved in central core metabolism were relatively unaffected, indicating that essential cellular function is protected. Beyond the response of P. tricornutum to low Fe, we observed major coordinated shifts in transcript control of primary and intermediate metabolism over light:dark cycles which contribute to a new view of the significance of distinctive diatom pathways, such as mitochondrial glycolysis and the ornithine-urea cycle. This study provides new insight into transcriptional modulation of diatom physiology and metabolism across light:dark cycles in response to Fe availability, providing mechanistic understanding for the ability of diatoms to remain metabolically poised to respond quickly to Fe input and revealing strategies underlying their ecological success. Oceanic diatoms live in constantly fluctuating environments to which they must adapt in order to survive. During sunlit hours, photosynthesis occurs allowing diatoms to store energy used at night to sustain energy demands. Cellular and molecular mechanisms for regulation of phytoplankton growth are important to understand because of their environmental roles at the base of food webs and in regulating carbon flux out of the atmosphere. In ocean ecosystems, the availability of iron (Fe) commonly limits phytoplankton growth and diatoms typically outcompete other phytoplankton when Fe is added, indicating they have adaptations allowing them to both survive at low Fe and rapidly respond to Fe additions. These adaptations may be unique depending on isolation from coastal or oceanic locations. To identify adaptive strategies, we characterized the response of a model diatom, Phaeodactylum tricornutum, to limiting Fe conditions over day:night cycles using a combination of gene expression analyses, metabolite, and physiology measurements. Major coordinated shifts in metabolism and growth were documented over diel cycles, with peak expression of low Fe expressed genes in the dark phase. Diatoms respond to limiting Fe by increasing Fe acquisition, while decreasing growth rate through slowed cell cycle progression, reduced energy acquisition, and subtle metabolic remodeling.
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Affiliation(s)
- Sarah R. Smith
- Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California, United States of America
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - Jeroen T. F. Gillard
- J. Craig Venter Institute, La Jolla, California, United States of America
- Department of Biology, CSU Bakersfield, Bakersfield, California, United States of America
| | - Adam B. Kustka
- Department of Earth and Environmental Sciences, Rutgers University, Newark, New Jersey, United States of America
| | - John P. McCrow
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - Jonathan H. Badger
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - Hong Zheng
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - Ashley M. New
- Department of Earth and Environmental Sciences, Rutgers University, Newark, New Jersey, United States of America
| | - Chris L. Dupont
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - Toshihiro Obata
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
| | - Andrew E. Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California, United States of America
- J. Craig Venter Institute, La Jolla, California, United States of America
- * E-mail: ,
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Liu X, Hempel F, Stork S, Bolte K, Moog D, Heimerl T, Maier UG, Zauner S. Addressing various compartments of the diatom model organism Phaeodactylum tricornutum via sub-cellular marker proteins. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.10.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Diner RE, Schwenck SM, McCrow JP, Zheng H, Allen AE. Genetic Manipulation of Competition for Nitrate between Heterotrophic Bacteria and Diatoms. Front Microbiol 2016; 7:880. [PMID: 27375600 PMCID: PMC4899447 DOI: 10.3389/fmicb.2016.00880] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/25/2016] [Indexed: 12/13/2022] Open
Abstract
Diatoms are a dominant group of eukaryotic phytoplankton that contribute substantially to global primary production and the cycling of important elements such as carbon and nitrogen. Heterotrophic bacteria, including members of the gammaproteobacteria, are commonly associated with diatom populations and may rely on them for organic carbon while potentially competing with them for other essential nutrients. Considering that bacterioplankton drive oceanic release of CO 2 (i.e., bacterial respiration) while diatoms drive ocean carbon sequestration vial the biological pump, the outcome of such competition could influence the direction and magnitude of carbon flux in the upper ocean. Nitrate availability is commonly a determining factor for the growth of diatom populations, particularly in coastal and upwelling regions. Diatoms as well as many bacterial species can utilize nitrate, however the ability of bacteria to compete for nitrate may be hindered by carbon limitation. Here we have developed a genetically tractable model system using the pennate diatom Phaeodactylum tricornutum and the widespread heterotrophic bacteria Alteromonas macleodii to examine carbon-nitrogen dynamics. While subsisting solely on P. tricornutum derived carbon, A. macleodii does not appear to be an effective competitor for nitrate, and may in fact benefit the diatom; particularly in stationary phase. However, allochthonous dissolved organic carbon addition in the form of pyruvate triggers A. macleodii proliferation and nitrate uptake, leading to reduced P. tricornutum growth. Nitrate reductase deficient mutants of A. macleodii (ΔnasA) do not exhibit such explosive growth and associated competitive ability in response to allochthonous carbon when nitrate is the sole nitrogen source, but could survive by utilizing solely P. tricornutum-derived nitrogen. Furthermore, allocthonous carbon addition enables wild-type A. macleodii to rescue nitrate reductase deficient P. tricornutum populations from nitrogen starvation, and RNA-seq transcriptomic evidence supports nitrogen-based interactions between diatoms and bacteria at the molecular level. This study provides key insights into the roles of carbon and nitrogen in phytoplankton-bacteria dynamics and lays the foundation for developing a mechanistic understanding of these interactions using co-culturing and genetic manipulation.
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Affiliation(s)
- Rachel E. Diner
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa Jolla, CA, USA
- Microbial and Environmental Genomics Group, J. Craig Venter InstituteLa Jolla, CA, USA
| | - Sarah M. Schwenck
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa Jolla, CA, USA
- Microbial and Environmental Genomics Group, J. Craig Venter InstituteLa Jolla, CA, USA
| | - John P. McCrow
- Microbial and Environmental Genomics Group, J. Craig Venter InstituteLa Jolla, CA, USA
| | - Hong Zheng
- Microbial and Environmental Genomics Group, J. Craig Venter InstituteLa Jolla, CA, USA
| | - Andrew E. Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa Jolla, CA, USA
- Microbial and Environmental Genomics Group, J. Craig Venter InstituteLa Jolla, CA, USA
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Taddei L, Stella GR, Rogato A, Bailleul B, Fortunato AE, Annunziata R, Sanges R, Thaler M, Lepetit B, Lavaud J, Jaubert M, Finazzi G, Bouly JP, Falciatore A. Multisignal control of expression of the LHCX protein family in the marine diatom Phaeodactylum tricornutum. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3939-51. [PMID: 27225826 PMCID: PMC4915529 DOI: 10.1093/jxb/erw198] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Diatoms are phytoplanktonic organisms that grow successfully in the ocean where light conditions are highly variable. Studies of the molecular mechanisms of light acclimation in the marine diatom Phaeodactylum tricornutum show that carotenoid de-epoxidation enzymes and LHCX1, a member of the light-harvesting protein family, both contribute to dissipate excess light energy through non-photochemical quenching (NPQ). In this study, we investigate the role of the other members of the LHCX family in diatom stress responses. Our analysis of available genomic data shows that the presence of multiple LHCX genes is a conserved feature of diatom species living in different ecological niches. Moreover, an analysis of the levels of four P. tricornutum LHCX transcripts in relation to protein expression and photosynthetic activity indicates that LHCXs are differentially regulated under different light intensities and nutrient starvation, mostly modulating NPQ capacity. We conclude that multiple abiotic stress signals converge to regulate the LHCX content of cells, providing a way to fine-tune light harvesting and photoprotection. Moreover, our data indicate that the expansion of the LHCX gene family reflects functional diversification of its members which could benefit cells responding to highly variable ocean environments.
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Affiliation(s)
- Lucilla Taddei
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 15 rue de l'Ecole de Médecine, 75006 Paris, France
| | - Giulio Rocco Stella
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 15 rue de l'Ecole de Médecine, 75006 Paris, France Department of Biotechnology, University of Verona, Strada Le Grazie, I-37134 Verona, Italy
| | - Alessandra Rogato
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 15 rue de l'Ecole de Médecine, 75006 Paris, France Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, 80131 Naples, Italy Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Benjamin Bailleul
- Institut de Biologie Physico-Chimique, UMR 7141 CNRS-UPMC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Antonio Emidio Fortunato
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 15 rue de l'Ecole de Médecine, 75006 Paris, France
| | - Rossella Annunziata
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 15 rue de l'Ecole de Médecine, 75006 Paris, France
| | - Remo Sanges
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Michael Thaler
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 15 rue de l'Ecole de Médecine, 75006 Paris, France
| | - Bernard Lepetit
- Zukunftskolleg, Department of Plant Ecophysiology, University of Konstanz, D-78457 Konstanz, Germany
| | - Johann Lavaud
- UMI 3376 TAKUVIK, CNRS/Université Laval, Département de Biologie, Pavillon Alexandre-Vachon, 1045 avenue de la Médecine, Québec (Québec) G1V 0A6, Canada
| | - Marianne Jaubert
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 15 rue de l'Ecole de Médecine, 75006 Paris, France
| | - Giovanni Finazzi
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, Centre National de la Recherche Scientifique (CNRS), Institut National Recherche Agronomique (INRA), Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Biosciences et Biotechnologies de Grenoble, (BIG), CEA Grenoble, F-38054 Grenoble cedex 9, France
| | - Jean-Pierre Bouly
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 15 rue de l'Ecole de Médecine, 75006 Paris, France
| | - Angela Falciatore
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 15 rue de l'Ecole de Médecine, 75006 Paris, France
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50
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Lelandais G, Scheiber I, Paz-Yepes J, Lozano JC, Botebol H, Pilátová J, Žárský V, Léger T, Blaiseau PL, Bowler C, Bouget FY, Camadro JM, Sutak R, Lesuisse E. Ostreococcus tauri is a new model green alga for studying iron metabolism in eukaryotic phytoplankton. BMC Genomics 2016; 17:319. [PMID: 27142620 PMCID: PMC4855317 DOI: 10.1186/s12864-016-2666-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/26/2016] [Indexed: 11/17/2022] Open
Abstract
Background Low iron bioavailability is a common feature of ocean surface water and therefore micro-algae developed original strategies to optimize iron uptake and metabolism. The marine picoeukaryotic green alga Ostreococcus tauri is a very good model for studying physiological and genetic aspects of the adaptation of the green algal lineage to the marine environment: it has a very compact genome, is easy to culture in laboratory conditions, and can be genetically manipulated by efficient homologous recombination. In this study, we aimed at characterizing the mechanisms of iron assimilation in O. tauri by combining genetics and physiological tools. Specifically, we wanted to identify and functionally characterize groups of genes displaying tightly orchestrated temporal expression patterns following the exposure of cells to iron deprivation and day/night cycles, and to highlight unique features of iron metabolism in O. tauri, as compared to the freshwater model alga Chalamydomonas reinhardtii. Results We used RNA sequencing to investigated the transcriptional responses to iron limitation in O. tauri and found that most of the genes involved in iron uptake and metabolism in O. tauri are regulated by day/night cycles, regardless of iron status. O. tauri lacks the classical components of a reductive iron uptake system, and has no obvious iron regulon. Iron uptake appears to be copper-independent, but is regulated by zinc. Conversely, iron deprivation resulted in the transcriptional activation of numerous genes encoding zinc-containing regulation factors. Iron uptake is likely mediated by a ZIP-family protein (Ot-Irt1) and by a new Fea1-related protein (Ot-Fea1) containing duplicated Fea1 domains. The adaptation of cells to iron limitation involved an iron-sparing response tightly coordinated with diurnal cycles to optimize cell functions and synchronize these functions with the day/night redistribution of iron orchestrated by ferritin, and a stress response based on the induction of thioredoxin-like proteins, of peroxiredoxin and of tesmin-like methallothionein rather than ascorbate. We briefly surveyed the metabolic remodeling resulting from iron deprivation. Conclusions The mechanisms of iron uptake and utilization by O. tauri differ fundamentally from those described in C. reinhardtii. We propose this species as a new model for investigation of iron metabolism in marine microalgae. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2666-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gaëlle Lelandais
- CNRS, Institut Jacques Monod, Université Paris Diderot-Paris 7, F-75013, Paris, France
| | - Ivo Scheiber
- Department of Parasitology, Faculty of Science, Charles University in Prague, 12844, Prague, Czech Republic
| | - Javier Paz-Yepes
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Jean-Claude Lozano
- Sorbonne Universités, University Pierre et Marie Curie, University of Paris VI, CNRS, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | - Hugo Botebol
- Sorbonne Universités, University Pierre et Marie Curie, University of Paris VI, CNRS, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | - Jana Pilátová
- Department of Parasitology, Faculty of Science, Charles University in Prague, 12844, Prague, Czech Republic
| | - Vojtěch Žárský
- Department of Parasitology, Faculty of Science, Charles University in Prague, 12844, Prague, Czech Republic
| | - Thibaut Léger
- CNRS, Institut Jacques Monod, Université Paris Diderot-Paris 7, F-75013, Paris, France
| | - Pierre-Louis Blaiseau
- Sorbonne Universités, University Pierre et Marie Curie, University of Paris VI, CNRS, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | - Chris Bowler
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - François-Yves Bouget
- Sorbonne Universités, University Pierre et Marie Curie, University of Paris VI, CNRS, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | - Jean-Michel Camadro
- CNRS, Institut Jacques Monod, Université Paris Diderot-Paris 7, F-75013, Paris, France
| | - Robert Sutak
- Department of Parasitology, Faculty of Science, Charles University in Prague, 12844, Prague, Czech Republic.
| | - Emmanuel Lesuisse
- CNRS, Institut Jacques Monod, Université Paris Diderot-Paris 7, F-75013, Paris, France.
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