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Nieves-Morión M, Camargo S, Bardi S, Ruiz MT, Flores E, Foster RA. Heterologous expression of genes from a cyanobacterial endosymbiont highlights substrate exchanges with its diatom host. PNAS NEXUS 2023; 2:pgad194. [PMID: 37383020 PMCID: PMC10299089 DOI: 10.1093/pnasnexus/pgad194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/02/2023] [Indexed: 06/30/2023]
Abstract
A few genera of diatoms are widespread and thrive in low-nutrient waters of the open ocean due to their close association with N2-fixing, filamentous heterocyst-forming cyanobacteria. In one of these symbioses, the symbiont, Richelia euintracellularis, has penetrated the cell envelope of the host, Hemiaulus hauckii, and lives inside the host cytoplasm. How the partners interact, including how the symbiont sustains high rates of N2 fixation, is unstudied. Since R. euintracellularis has evaded isolation, heterologous expression of genes in model laboratory organisms was performed to identify the function of proteins from the endosymbiont. Gene complementation of a cyanobacterial invertase mutant and expression of the protein in Escherichia coli showed that R. euintracellularis HH01 possesses a neutral invertase that splits sucrose producing glucose and fructose. Several solute-binding proteins (SBPs) of ABC transporters encoded in the genome of R. euintracellularis HH01 were expressed in E. coli, and their substrates were characterized. The selected SBPs directly linked the host as the source of several substrates, e.g. sugars (sucrose and galactose), amino acids (glutamate and phenylalanine), and a polyamine (spermidine), to support the cyanobacterial symbiont. Finally, transcripts of genes encoding the invertase and SBPs were consistently detected in wild populations of H. hauckii collected from multiple stations and depths in the western tropical North Atlantic. Our results support the idea that the diatom host provides the endosymbiotic cyanobacterium with organic carbon to fuel N2 fixation. This knowledge is key to understanding the physiology of the globally significant H. hauckii-R. euintracellularis symbiosis.
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Affiliation(s)
- Mercedes Nieves-Morión
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm SE-106 91, Sweden
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville E-41092, Spain
| | - Sergio Camargo
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville E-41092, Spain
| | - Sepehr Bardi
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm SE-106 91, Sweden
| | - María Teresa Ruiz
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville E-41092, Spain
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Foster RA, Tienken D, Littmann S, Whitehouse MJ, Kuypers MMM, White AE. The rate and fate of N 2 and C fixation by marine diatom-diazotroph symbioses. THE ISME JOURNAL 2022; 16:477-487. [PMID: 34429522 PMCID: PMC8776783 DOI: 10.1038/s41396-021-01086-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 11/08/2022]
Abstract
N2 fixation constitutes an important new nitrogen source in the open sea. One group of filamentous N2 fixing cyanobacteria (Richelia intracellularis, hereafter Richelia) form symbiosis with a few genera of diatoms. High rates of N2 fixation and carbon (C) fixation have been measured in the presence of diatom-Richelia symbioses. However, it is unknown how partners coordinate C fixation and how the symbiont sustains high rates of N2 fixation. Here, both the N2 and C fixation in wild diatom-Richelia populations are reported. Inhibitor experiments designed to inhibit host photosynthesis, resulted in lower estimated growth and depressed C and N2 fixation, suggesting that despite the symbionts ability to fix their own C, they must still rely on their respective hosts for C. Single cell analysis indicated that up to 22% of assimilated C in the symbiont is derived from the host, whereas 78-91% of the host N is supplied from their symbionts. A size-dependent relationship is identified where larger cells have higher N2 and C fixation, and only N2 fixation was light dependent. Using the single cell measures, the N-rich phycosphere surrounding these symbioses was estimated and contributes directly and rapidly to the surface ocean rather than the mesopelagic, even at high estimated sinking velocities (<10 m d-1). Several eco-physiological parameters necessary for incorporating symbiotic N2 fixing populations into larger basin scale biogeochemical models (i.e., N and C cycles) are provided.
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Affiliation(s)
- Rachel A Foster
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA.
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany.
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.
| | - Daniela Tienken
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sten Littmann
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Martin J Whitehouse
- Department of Geosciences, Swedish Museum of Natural History, Stockholm, Sweden
| | - Marcel M M Kuypers
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Angelicque E White
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
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Pyle AE, Johnson AM, Villareal TA. Isolation, growth, and nitrogen fixation rates of the Hemiaulus-Richelia (diatom-cyanobacterium) symbiosis in culture. PeerJ 2020; 8:e10115. [PMID: 33083143 PMCID: PMC7548074 DOI: 10.7717/peerj.10115] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/16/2020] [Indexed: 11/20/2022] Open
Abstract
Nitrogen fixers (diazotrophs) are often an important nitrogen source to phytoplankton nutrient budgets in N-limited marine environments. Diazotrophic symbioses between cyanobacteria and diatoms can dominate nitrogen-fixation regionally, particularly in major river plumes and in open ocean mesoscale blooms. This study reports the successful isolation and growth in monocultures of multiple strains of a diatom-cyanobacteria symbiosis from the Gulf of Mexico using a modified artificial seawater medium. We document the influence of light and nutrients on nitrogen fixation and growth rates of the host diatom Hemiaulus hauckii Grunow together with its diazotrophic endosymbiont Richelia intracellularis Schmidt, as well as less complete results on the Hemiaulus membranaceus-R. intracellularis symbiosis. The symbioses rates reported here are for the joint diatom-cyanobacteria unit. Symbiont diazotrophy was sufficient to support both the host diatom and cyanobacteria symbionts, and the entire symbiosis replicated and grew without added nitrogen. Maximum growth rates of multiple strains of H. hauckii symbioses in N-free medium with N2 as the sole N source were 0.74-0.93 div d-1. Growth rates followed light saturation kinetics in H. hauckii symbioses with a growth compensation light intensity (EC) of 7-16 µmol m-2s-1and saturation light level (EK) of 84-110 µmol m-2s-1. Nitrogen fixation rates by the symbiont while within the host followed a diel pattern where rates increased from near-zero in the scotophase to a maximum 4-6 h into the photophase. At the onset of the scotophase, nitrogen-fixation rates declined over several hours to near-zero values. Nitrogen fixation also exhibited light saturation kinetics. Maximum N2 fixation rates (84 fmol N2 heterocyst-1h-1) in low light adapted cultures (50 µmol m-2s-1) were approximately 40-50% of rates (144-154 fmol N2 heterocyst-1h-1) in high light (150 and 200 µmol m-2s-1) adapted cultures. Maximum laboratory N2 fixation rates were ~6 to 8-fold higher than literature-derived field rates of the H. hauckii symbiosis. In contrast to published results on the Rhizosolenia-Richelia symbiosis, the H. hauckii symbiosis did not use nitrate when added, although ammonium was consumed by the H. hauckii symbiosis. Symbiont-free host cell cultures could not be established; however, a symbiont-free H. hauckii strain was isolated directly from the field and grown on a nitrate-based medium that would not support DDA growth. Our observations together with literature reports raise the possibility that the asymbiotic H. hauckii are lines distinct from an obligately symbiotic H. hauckii line. While brief descriptions of successful culture isolation have been published, this report provides the first detailed description of the approaches, handling, and methodologies used for successful culture of this marine symbiosis. These techniques should permit a more widespread laboratory availability of these important marine symbioses.
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Affiliation(s)
- Amy E Pyle
- Department of Marine Science and Marine Science Institute, The University of Texas at Austin, Port Aransas, TX, USA
| | | | - Tracy A Villareal
- Department of Marine Science and Marine Science Institute, The University of Texas at Austin, Port Aransas, TX, USA
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Foster RA, Zehr JP. Diversity, Genomics, and Distribution of Phytoplankton-Cyanobacterium Single-Cell Symbiotic Associations. Annu Rev Microbiol 2020; 73:435-456. [PMID: 31500535 DOI: 10.1146/annurev-micro-090817-062650] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cyanobacteria are common in symbiotic relationships with diverse multicellular organisms (animals, plants, fungi) in terrestrial environments and with single-celled heterotrophic, mixotrophic, and autotrophic protists in aquatic environments. In the sunlit zones of aquatic environments, diverse cyanobacterial symbioses exist with autotrophic taxa in phytoplankton, including dinoflagellates, diatoms, and haptophytes (prymnesiophytes). Phototrophic unicellular cyanobacteria related to Synechococcus and Prochlorococcus are associated with a number of groups. N2-fixing cyanobacteria are symbiotic with diatoms and haptophytes. Extensive genome reduction is involved in the N2-fixing endosymbionts, most dramatically in the unicellular cyanobacteria associated with haptophytes, which have lost most of the photosynthetic apparatus, the ability to fix C, and the tricarboxylic acid cycle. The mechanisms involved in N2-fixing symbioses may involve more interactions beyond simple exchange of fixed C for N. N2-fixing cyanobacterial symbioses are widespread in the oceans, even more widely distributed than the best-known free-living N2-fixing cyanobacteria, suggesting they may be equally or more important in the global ocean biogeochemical cycle of N.Despite their ubiquitous nature and significance in biogeochemical cycles, cyanobacterium-phytoplankton symbioses remain understudied and poorly understood.
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Affiliation(s)
- Rachel A Foster
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden;
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, California 95064, USA;
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Nieves-Morión M, Flores E, Foster RA. Predicting substrate exchange in marine diatom-heterocystous cyanobacteria symbioses. Environ Microbiol 2020; 22:2027-2052. [PMID: 32281201 DOI: 10.1111/1462-2920.15013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 11/27/2022]
Abstract
In the open ocean, some phytoplankton establish symbiosis with cyanobacteria. Some partnerships involve diatoms as hosts and heterocystous cyanobacteria as symbionts. Heterocysts are specialized cells for nitrogen fixation, and a function of the symbiotic cyanobacteria is to provide the host with nitrogen. However, both partners are photosynthetic and capable of carbon fixation, and the possible metabolites exchanged and mechanisms of transfer are poorly understood. The symbiont cellular location varies from internal to partial to fully external, and this is reflected in the symbiont genome size and content. In order to identify the membrane transporters potentially involved in metabolite exchange, we compare the draft genomes of three differently located symbionts with known transporters mainly from model free-living heterocystous cyanobacteria. The types and numbers of transporters are directly related to the symbiont cellular location: restricted in the endosymbionts and wider in the external symbiont. Three proposed models of metabolite exchange are suggested which take into account the type of transporters in the symbionts and the influence of their cellular location on the available nutrient pools. These models provide a basis for several hypotheses that given the importance of these symbioses in global N and C budgets, warrant future testing.
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Affiliation(s)
- Mercedes Nieves-Morión
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
| | - Enrique Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Américo Vespucio 49, Seville, E-41092, Spain
| | - Rachel A Foster
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
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Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics. Genome Res 2020; 30:647-659. [PMID: 32205368 PMCID: PMC7197479 DOI: 10.1101/gr.253070.119] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 03/18/2020] [Indexed: 11/25/2022]
Abstract
Large-scale metagenomic and metatranscriptomic data analyses are often restricted by their gene-centric approach, limiting the ability to understand organismal and community biology. De novo assembly of large and mosaic eukaryotic genomes from complex meta-omics data remains a challenging task, especially in comparison with more straightforward bacterial and archaeal systems. Here, we use a transcriptome reconstruction method based on clustering co-abundant genes across a series of metagenomic samples. We investigated the co-abundance patterns of ∼37 million eukaryotic unigenes across 365 metagenomic samples collected during the Tara Oceans expeditions to assess the diversity and functional profiles of marine plankton. We identified ∼12,000 co-abundant gene groups (CAGs), encompassing ∼7 million unigenes, including 924 metagenomics-based transcriptomes (MGTs, CAGs larger than 500 unigenes). We demonstrated the biological validity of the MGT collection by comparing individual MGTs with available references. We identified several key eukaryotic organisms involved in dimethylsulfoniopropionate (DMSP) biosynthesis and catabolism in different oceanic provinces, thus demonstrating the potential of the MGT collection to provide functional insights on eukaryotic plankton. We established the ability of the MGT approach to capture interspecies associations through the analysis of a nitrogen-fixing haptophyte-cyanobacterial symbiotic association. This MGT collection provides a valuable resource for analyses of eukaryotic plankton in the open ocean by giving access to the genomic content and functional potential of many ecologically relevant eukaryotic species.
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Inomura K, Follett CL, Masuda T, Eichner M, Prášil O, Deutsch C. Carbon Transfer from the Host Diatom Enables Fast Growth and High Rate of N 2 Fixation by Symbiotic Heterocystous Cyanobacteria. PLANTS (BASEL, SWITZERLAND) 2020; 9:E192. [PMID: 32033207 PMCID: PMC7076409 DOI: 10.3390/plants9020192] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/20/2020] [Accepted: 01/30/2020] [Indexed: 12/25/2022]
Abstract
Diatom-diazotroph associations (DDAs) are symbioses where trichome-forming cyanobacteria support the host diatom with fixed nitrogen through dinitrogen (N2) fixation. It is inferred that the growth of the trichomes is also supported by the host, but the support mechanism has not been fully quantified. Here, we develop a coarse-grained, cellular model of the symbiosis between Hemiaulus and Richelia (one of the major DDAs), which shows that carbon (C) transfer from the diatom enables a faster growth and N2 fixation rate by the trichomes. The model predicts that the rate of N2 fixation is 5.5 times that of the hypothetical case without nitrogen (N) transfer to the host diatom. The model estimates that 25% of fixed C from the host diatom is transferred to the symbiotic trichomes to support the high rate of N2 fixation. In turn, 82% of N fixed by the trichomes ends up in the host. Modeled C fixation from the vegetative cells in the trichomes supports only one-third of their total C needs. Even if we ignore the C cost for N2 fixation and for N transfer to the host, the total C cost of the trichomes is higher than the C supply by their own photosynthesis. Having more trichomes in a single host diatom decreases the demand for N2 fixation per trichome and thus decreases their cost of C. However, even with five trichomes, which is about the highest observed for Hemiaulus and Richelia symbiosis, the model still predicts a significant C transfer from the diatom host. These results help quantitatively explain the observed high rates of growth and N2 fixation in symbiotic trichomes relative to other aquatic diazotrophs.
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Affiliation(s)
- Keisuke Inomura
- School of Oceanography, University of Washington, 1492 NE Boat St., Seattle, WA 98105, USA;
| | - Christopher L. Follett
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
- School of Earth and Ocean Sciences, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK
| | - Takako Masuda
- Institute of Microbiology, The Czech Academy of Sciences, 379 81b Třeboň, Czech Republic; (T.M.); (M.E.); (O.P.)
| | - Meri Eichner
- Institute of Microbiology, The Czech Academy of Sciences, 379 81b Třeboň, Czech Republic; (T.M.); (M.E.); (O.P.)
| | - Ondřej Prášil
- Institute of Microbiology, The Czech Academy of Sciences, 379 81b Třeboň, Czech Republic; (T.M.); (M.E.); (O.P.)
| | - Curtis Deutsch
- School of Oceanography, University of Washington, 1492 NE Boat St., Seattle, WA 98105, USA;
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Devassy RP, El-Sherbiny MM, Al-Sofyani AA, Crosby MP, Al-Aidaroos AM. Seasonality and latitudinal variability in the diatom-cyanobacteria symbiotic relationships in the coastal waters of the Red Sea, Saudi Arabia. Symbiosis 2019. [DOI: 10.1007/s13199-019-00610-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Sánchez-Baracaldo P, Bianchini G, Di Cesare A, Callieri C, Chrismas NAM. Insights Into the Evolution of Picocyanobacteria and Phycoerythrin Genes ( mpeBA and cpeBA). Front Microbiol 2019; 10:45. [PMID: 30761097 PMCID: PMC6363710 DOI: 10.3389/fmicb.2019.00045] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/11/2019] [Indexed: 11/13/2022] Open
Abstract
Marine picocyanobacteria, Prochlorococcus and Synechococcus, substantially contribute to marine primary production and have been the subject of extensive ecological and genomic studies. Little is known about their close relatives from freshwater and non-marine environments. Phylogenomic analyses (using 136 proteins) provide strong support for the monophyly of a clade of non-marine picocyanobacteria consisting of Cyanobium, Synechococcus and marine Sub-cluster 5.2; this clade itself is sister to marine Synechococcus and Prochlorococcus. The most basal lineage within the Syn/Pro clade, Sub-Cluster 5.3, includes marine and freshwater strains. Relaxed molecular clock (SSU, LSU) analyses show that while ancestors of the Syn/Pro clade date as far back as the end of the Pre-Cambrian, modern crown groups evolved during the Carboniferous and Triassic. Comparative genomic analyses reveal novel gene cluster arrangements involved in phycobilisome (PBS) metabolism in freshwater strains. Whilst PBS genes in marine Synechococcus are mostly found in one type of phycoerythrin (PE) rich gene cluster (Type III), strains from non-marine habitats, so far, appear to be more diverse both in terms of pigment content and gene arrangement, likely reflecting a wider range of habitats. Our phylogenetic analyses show that the PE genes (mpeBA) evolved via a duplication of the cpeBA genes in an ancestor of the marine and non-marine picocyanobacteria and of the symbiotic strains Synechococcus spongiarum. A 'primitive' Type III-like ancestor containing cpeBA and mpeBA had thus evolved prior to the divergence of the Syn/Pro clade and S. spongiarum. During the diversification of Synechococcus lineages, losses of mpeBA genes may explain the emergence of pigment cluster Types I, II, IIB, and III in both marine and non-marine habitats, with few lateral gene transfer events in specific taxa.
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Affiliation(s)
| | - Giorgio Bianchini
- School of Geographical Sciences, University of Bristol, Bristol, United Kingdom
| | - Andrea Di Cesare
- Institute of Ecosystem Study–Consiglio Nazionale delle Ricerche, Verbania, Italy
- Department of Earth, Environment and Life Sciences, University of Genoa, Genoa, Italy
| | - Cristiana Callieri
- Institute of Ecosystem Study–Consiglio Nazionale delle Ricerche, Verbania, Italy
| | - Nathan A. M. Chrismas
- School of Geographical Sciences, University of Bristol, Bristol, United Kingdom
- The Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, United Kingdom
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Caputo A, Nylander JAA, Foster RA. The genetic diversity and evolution of diatom-diazotroph associations highlights traits favoring symbiont integration. FEMS Microbiol Lett 2019; 366:5281432. [PMID: 30629176 PMCID: PMC6341774 DOI: 10.1093/femsle/fny297] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/23/2019] [Indexed: 11/25/2022] Open
Abstract
Diatom diazotroph associations (DDAs) are a widespread marine planktonic symbiosis between several diatom genera and di-nitrogen (N2)-fixing bacteria. Combining single cell confocal microscopy observations and molecular genetic approaches on individual field collected cells, we determined the phylogenetic diversity, distribution and evolution of the DDAs. Confocal analyses coupled with 3-D imaging re-evaluated the cellular location of DDA symbionts. DDA diversity was resolved by paired gene sequencing (18S rRNA and rbcL genes, 16S rRNA and nifH genes). A survey using the newly acquired sequences against public databases found sequences with high similarity (99-100%) to either host (18S rRNA) or symbiont (16S rRNA) in atypical regions for DDAs (high latitudes, anoxic basin and copepod gut). Concatenated phylogenies were congruent for the host and cyanobacteria sequences and implied co-evolution. Time-calibrated trees dated the appearance of N2 fixing planktonic symbiosis from 100-50Mya and were consistent with the symbiont cellular location: symbioses with internal partners are more ancient. An ancestral state reconstruction traced the evolution of traits in DDAs and highlight that the adaptive radiation to the marine environment was likely facilitated by the symbiosis. Our results present the evolutionary nature of DDAs and provide new genetic and phenotypic information for these biogeochemically relevant populations.
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Affiliation(s)
- A Caputo
- Stockholm University, Department of Ecology, Environment and Plant Sciences, Stockholm, 10691, Sweden
| | - J A A Nylander
- NBIS/Swedish Museum of Natural History, Dept of Bioinformatics and Genetics, Stockholm, 10405, Sweden
| | - R A Foster
- Stockholm University, Department of Ecology, Environment and Plant Sciences, Stockholm, 10691, Sweden
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11
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Elhai J, Khudyakov I. Ancient association of cyanobacterial multicellularity with the regulator HetR and an RGSGR pentapeptide-containing protein (PatX). Mol Microbiol 2018; 110:931-954. [PMID: 29885033 DOI: 10.1111/mmi.14003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2018] [Indexed: 12/14/2022]
Abstract
One simple model to explain biological pattern postulates the existence of a stationary regulator of differentiation that positively affects its own expression, coupled with a diffusible suppressor of differentiation that inhibits the regulator's expression. The first has been identified in the filamentous, heterocyst-forming cyanobacterium, Anabaena PCC 7120 as the transcriptional regulator, HetR and the second as the small protein, PatS, which contains a critical RGSGR motif that binds to HetR. HetR is present in almost all filamentous cyanobacteria, but only a subset of heterocyst-forming strains carry proteins similar to PatS. We identified a third protein, PatX that also carries the RGSGR motif and is coextensive with HetR. Amino acid sequences of PatX contain two conserved regions: the RGSGR motif and a hydrophobic N-terminus. Within 69 nt upstream from all instances of the gene is a DIF1 motif correlated in Anabaena with promoter induction in developing heterocysts, preceded in heterocyst-forming strains by an apparent NtcA-binding site, associated with regulation by nitrogen-status. Consistent with a role in the simple model, PatX is expressed dependent on HetR and acts to inhibit differentiation. The acquisition of the PatX/HetR pair preceded the appearance of both PatS and heterocysts, dating back to the beginnings of multicellularity.
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Affiliation(s)
- Jeff Elhai
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Ivan Khudyakov
- All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, 196608, Russia
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12
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Occurrence of Diatom – Diazotrophic association in the coastal surface waters of south Andaman, India. Symbiosis 2018. [DOI: 10.1007/s13199-018-0559-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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13
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Stenegren M, Berg C, Padilla CC, David SS, Montoya JP, Yager PL, Foster RA. Piecewise Structural Equation Model (SEM) Disentangles the Environmental Conditions Favoring Diatom Diazotroph Associations (DDAs) in the Western Tropical North Atlantic (WTNA). Front Microbiol 2017; 8:810. [PMID: 28536565 PMCID: PMC5423296 DOI: 10.3389/fmicb.2017.00810] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/20/2017] [Indexed: 01/01/2023] Open
Abstract
Diatom diazotroph associations (DDAs) are important components in the world’s oceans, especially in the western tropical north Atlantic (WTNA), where blooms have a significant impact on carbon and nitrogen cycling. However, drivers of their abundances and distribution patterns remain unknown. Here, we examined abundance and distribution patterns for two DDA populations in relation to the Amazon River (AR) plume in the WTNA. Quantitative PCR assays, targeting two DDAs (het-1 and het-2) by their symbiont’s nifH gene, served as input in a piecewise structural equation model (SEM). Collections were made during high (spring 2010) and low (fall 2011) flow discharges of the AR. The distributions of dissolved nutrients, chlorophyll-a, and DDAs showed coherent patterns indicative of areas influenced by the AR. A symbiotic Hemiaulus hauckii-Richelia (het-2) bloom (>106 cells L-1) occurred during higher discharge of the AR and was coincident with mesohaline to oceanic (30–35) sea surface salinities (SSS), and regions devoid of dissolved inorganic nitrogen (DIN), low concentrations of both DIP (>0.1 μmol L-1) and Si (>1.0 μmol L-1). The Richelia (het-1) associated with Rhizosolenia was only present in 2010 and at lower densities (10-1.76 × 105nifH copies L-1) than het-2 and limited to regions of oceanic SSS (>36). The het-2 symbiont detected in 2011 was associated with H. membranaceus (>103nifH copies L-1) and were restricted to regions with mesohaline SSS (31.8–34.3), immeasurable DIN, moderate DIP (0.1–0.60 μmol L-1) and higher Si (4.19–22.1 μmol L-1). The piecewise SEM identified a profound direct negative effect of turbidity on the het-2 abundance in spring 2010, while DIP and water turbidity had a more positive influence in fall 2011, corroborating our observations of DDAs at subsurface maximas. We also found a striking difference in the influence of salinity on DDA symbionts suggesting a niche differentiation and preferences in oceanic and mesohaline salinities by het-1 and het-2, respectively. The use of the piecewise SEM to disentangle the complex and concomitant hydrography of the WTNA acting on two biogeochemically relevant populations was novel and underscores its use to predict conditions favoring abundance and distributions of microbial populations.
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Affiliation(s)
- Marcus Stenegren
- Department of Ecology, Environment and Plant Sciences, Stockholm UniversityStockholm, Sweden
| | - Carlo Berg
- Science for Life Laboratory, Department of Biology and Environmental Science, Linnaeus UniversityKalmar, Sweden
| | - Cory C Padilla
- School of Biology, Georgia Institute of Technology, AtlantaGA, USA
| | - Stefan-Sebastian David
- Max Planck Institute for Biophysical ChemistryGöttingen, Germany.,Max Planck Institute for Marine MicrobiologyBremen, Germany
| | - Joseph P Montoya
- School of Biology, Georgia Institute of Technology, AtlantaGA, USA
| | - Patricia L Yager
- Department of Marine Sciences, University of Georgia, AthensGA, USA
| | - Rachel A Foster
- Department of Ecology, Environment and Plant Sciences, Stockholm UniversityStockholm, Sweden.,Max Planck Institute for Marine MicrobiologyBremen, Germany.,Ocean Sciences, University of California, Santa CruzSanta Cruz, CA, USA
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14
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Sánchez-Baracaldo P. Origin of marine planktonic cyanobacteria. Sci Rep 2015; 5:17418. [PMID: 26621203 PMCID: PMC4665016 DOI: 10.1038/srep17418] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 10/29/2015] [Indexed: 11/09/2022] Open
Abstract
Marine planktonic cyanobacteria contributed to the widespread oxygenation of the oceans towards the end of the Pre-Cambrian and their evolutionary origin represents a key transition in the geochemical evolution of the Earth surface. Little is known, however, about the evolutionary events that led to the appearance of marine planktonic cyanobacteria. I present here phylogenomic (135 proteins and two ribosomal RNAs), Bayesian relaxed molecular clock (18 proteins, SSU and LSU) and Bayesian stochastic character mapping analyses from 131 cyanobacteria genomes with the aim to unravel key evolutionary steps involved in the origin of marine planktonic cyanobacteria. While filamentous cell types evolved early on at around 2,600-2,300 Mya and likely dominated microbial mats in benthic environments for most of the Proterozoic (2,500-542 Mya), marine planktonic cyanobacteria evolved towards the end of the Proterozoic and early Phanerozoic. Crown groups of modern terrestrial and/or benthic coastal cyanobacteria appeared during the late Paleoproterozoic to early Mesoproterozoic. Decrease in cell diameter and loss of filamentous forms contributed to the evolution of unicellular planktonic lineages during the middle of the Mesoproterozoic (1,600-1,000 Mya) in freshwater environments. This study shows that marine planktonic cyanobacteria evolved from benthic marine and some diverged from freshwater ancestors during the Neoproterozoic (1,000-542 Mya).
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15
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Momper LM, Reese BK, Carvalho G, Lee P, Webb EA. A novel cohabitation between two diazotrophic cyanobacteria in the oligotrophic ocean. ISME JOURNAL 2015; 9:882-93. [PMID: 25343510 DOI: 10.1038/ismej.2014.186] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 07/24/2014] [Accepted: 07/30/2014] [Indexed: 11/09/2022]
Abstract
The cyanobacterial genus Trichodesmium is biogeochemically significant because of its dual role in nitrogen and carbon fixation in the oligotrophic ocean. Trichodesmium species form colonies that can be easily enriched from the water column and used for shipboard rate measurements to estimate their contribution to oceanic carbon and nitrogen budgets. During a July 2010 cruise near the Hawaiian Islands in the oligotrophic North Pacific Subtropical Gyre, a specific morphology of Trichodesmium puff-form colonies were examined under epifluorescent microscopy and found to harbor a colonial endobiont, morphologically identified as the heterocystous diazotrophic cyanobacterium Calothrix. Using unialgal enrichments obtained from this cruise, we show that these Calothrix-like heterocystous cyanobionts (hetDA for 'Trichodesmium-associated heterocystous diazotroph') fix nitrogen on a diurnal cycle (maximally in the middle of the light cycle with a detectable minimum in the dark). Gene sequencing of nifH from the enrichments revealed that this genus was likely not quantified using currently described quantitative PCR (qPCR) primers. Guided by the sequence from the isolate, new hetDA-specific primers were designed and subsequent qPCR of environmental samples detected this diazotroph from surface water to a depth of 150 m, reaching densities up to ∼ 9 × 10(3) l(-1). Based on phylogenetic relatedness of nifH and 16S rRNA gene sequences, it is predicted that the distribution of this cyanobiont is not limited to subtropical North Pacific but likely reaches to the South Pacific and Atlantic Oceans. Therefore, this previously unrecognized cohabitation, if it reaches beyond the oligotrophic North Pacific, could potentially influence Trichodesmium-derived nitrogen fixation budgets in the world ocean.
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Affiliation(s)
- Lily M Momper
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
| | - Brandi Kiel Reese
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
| | - Gustavo Carvalho
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
| | - Patrick Lee
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
| | - Eric A Webb
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
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16
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Hilton JA, Satinsky BM, Doherty M, Zielinski B, Zehr JP. Metatranscriptomics of N2-fixing cyanobacteria in the Amazon River plume. ISME JOURNAL 2014; 9:1557-69. [PMID: 25514535 DOI: 10.1038/ismej.2014.240] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 11/04/2014] [Accepted: 11/10/2014] [Indexed: 11/09/2022]
Abstract
Biological N2 fixation is an important nitrogen source for surface ocean microbial communities. However, nearly all information on the diversity and gene expression of organisms responsible for oceanic N2 fixation in the environment has come from targeted approaches that assay only a small number of genes and organisms. Using genomes of diazotrophic cyanobacteria to extract reads from extensive meta-genomic and -transcriptomic libraries, we examined diazotroph diversity and gene expression from the Amazon River plume, an area characterized by salinity and nutrient gradients. Diazotroph genome and transcript sequences were most abundant in the transitional waters compared with lower salinity or oceanic water masses. We were able to distinguish two genetically divergent phylotypes within the Hemiaulus-associated Richelia sequences, which were the most abundant diazotroph sequences in the data set. Photosystem (PS)-II transcripts in Richelia populations were much less abundant than those in Trichodesmium, and transcripts from several Richelia PS-II genes were absent, indicating a prominent role for cyclic electron transport in Richelia. In addition, there were several abundant regulatory transcripts, including one that targets a gene involved in PS-I cyclic electron transport in Richelia. High sequence coverage of the Richelia transcripts, as well as those from Trichodesmium populations, allowed us to identify expressed regions of the genomes that had been overlooked by genome annotations. High-coverage genomic and transcription analysis enabled the characterization of distinct phylotypes within diazotrophic populations, revealed a distinction in a core process between dominant populations and provided evidence for a prominent role for noncoding RNAs in microbial communities.
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Affiliation(s)
- Jason A Hilton
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA
| | | | - Mary Doherty
- Department of Biology, Rhodes College, Memphis, TN, USA
| | - Brian Zielinski
- College of Marine Science, University of South Florida, St Petersburg, FL, USA
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA
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17
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Comparative genomics reveals surprising divergence of two closely related strains of uncultivated UCYN-A cyanobacteria. ISME JOURNAL 2014; 8:2530-42. [PMID: 25226029 DOI: 10.1038/ismej.2014.167] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/05/2014] [Accepted: 08/08/2014] [Indexed: 11/08/2022]
Abstract
Marine planktonic cyanobacteria capable of fixing molecular nitrogen (termed 'diazotrophs') are key in biogeochemical cycling, and the nitrogen fixed is one of the major external sources of nitrogen to the open ocean. Candidatus Atelocyanobacterium thalassa (UCYN-A) is a diazotrophic cyanobacterium known for its widespread geographic distribution in tropical and subtropical oligotrophic oceans, unusually reduced genome and symbiosis with a single-celled prymnesiophyte alga. Recently a novel strain of this organism was also detected in coastal waters sampled from the Scripps Institute of Oceanography pier. We analyzed the metagenome of this UCYN-A2 population by concentrating cells by flow cytometry. Phylogenomic analysis provided strong bootstrap support for the monophyly of UCYN-A (here called UCYN-A1) and UCYN-A2 within the marine Crocosphaera sp. and Cyanothece sp. clade. UCYN-A2 shares 1159 of the 1200 UCYN-A1 protein-coding genes (96.6%) with high synteny, yet the average amino-acid sequence identity between these orthologs is only 86%. UCYN-A2 lacks the same major pathways and proteins that are absent in UCYN-A1, suggesting that both strains can be grouped at the same functional and ecological level. Our results suggest that UCYN-A1 and UCYN-A2 had a common ancestor and diverged after genome reduction. These two variants may reflect adaptation of the host to different niches, which could be coastal and open ocean habitats.
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18
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Thompson AW, Zehr JP. Cellular interactions: lessons from the nitrogen-fixing cyanobacteria. JOURNAL OF PHYCOLOGY 2013; 49:1024-1035. [PMID: 27007623 DOI: 10.1111/jpy.12117] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Accepted: 08/17/2013] [Indexed: 06/05/2023]
Abstract
Marine nitrogen-fixing cyanobacteria play a central role in the open-ocean microbial community by providing fixed nitrogen (N) to the ocean from atmospheric dinitrogen (N2 ) gas. Once thought to be dominated by one genus of cyanobacteria, Trichodesmium, it is now clear that marine N2 -fixing cyanobacteria in the open ocean are more diverse, include several previously unknown symbionts, and are geographically more widespread than expected. The next challenge is to understand the ecological implications of this genetic and phenotypic diversity for global oceanic N cycling. One intriguing aspect of the cyanobacterial N2 fixers ecology is the range of cellular interactions they engage in, either with cells of their own species or with photosynthetic protists. From organelle-like integration with the host cell to a free-living existence, N2 -fixing cyanobacteria represent the range of types of interactions that occur among microbes in the open ocean. Here, we review what is known about the cellular interactions carried out by marine N2 -fixing cyanobacteria and where future work can help. Discoveries related to the functional roles of these specialized cells in food webs and the microbial community will improve how we interpret their distribution and abundance patterns and contributions to global N and carbon (C) cycles.
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Affiliation(s)
- Anne W Thompson
- Department of Ocean Sciences, University of California, 1156 High Street, Santa Cruz, California, 95064, USA
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California, 1156 High Street, Santa Cruz, California, 95064, USA
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19
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Genomic deletions disrupt nitrogen metabolism pathways of a cyanobacterial diatom symbiont. Nat Commun 2013; 4:1767. [PMID: 23612308 PMCID: PMC3667715 DOI: 10.1038/ncomms2748] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 03/15/2013] [Indexed: 11/26/2022] Open
Abstract
Diatoms with symbiotic N2-fixing cyanobacteria are often abundant in the oligotrophic
open ocean gyres. The most abundant cyanobacterial symbionts form heterocysts (specialized
cells for N2 fixation) and provide nitrogen (N) to their hosts, but their
morphology, cellular locations and abundances differ depending on the host. Here we show
that the location of the symbiont and its dependency on the host are linked to the evolution
of the symbiont genome. The genome of Richelia (found inside the siliceous frustule
of Hemiaulus) is reduced and lacks ammonium transporters, nitrate/nitrite reductases
and glutamine:2-oxoglutarate aminotransferase. In contrast, the genome of the closely
related Calothrix (found outside the frustule of Chaetoceros) is more similar
to those of free-living heterocyst-forming cyanobacteria. The genome of Richelia is
an example of metabolic streamlining that has implications for the evolution of
N2-fixing symbiosis and
potentially for manipulating plant–cyanobacterial interactions. Cyanobacterial symbionts of marine diatoms can localize intracellularly or
externally to their host partners. Here Hilton et al. describe the genomes of two
diazotroph cyanobacterial symbionts of diatoms and show that the location of the symbiont
affects expression of nitrogen assimilation genes.
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20
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Occurrence and Distribution of a Diatom-Diazotrophic Cyanobacteria Association during a Trichodesmium Bloom in the Southeastern Arabian Sea. ACTA ACUST UNITED AC 2013. [DOI: 10.1155/2013/350594] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Symbiotic diatom-diazotrophic cyanobacteria association (DDA) of Rhizosolenia hebetata and Rhizosolenia formosa with endosymbiotic cyanobacteria Richelia intracellularis was noticed and documented for the first time during a bloom of the cyanobacterium Trichodesmium erythraeum in the oligotrophic shelf waters along Kochi and Mangalore transects, southeastern Arabian Sea (SEAS), during spring intermonsoon (April 2012). Although the host is frequently seen, the symbiont is rarely reported in the Indian EEZ. The presence of nitrogen-fixing symbiotic association of Rhizosolenia-Richelia along with Trichodesmium erythraeum highlights the significance of DDAs on the nutrient and energy budgets of phytoplankton in the oligotrophic environments of the Arabian Sea during spring intermonsoon.
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21
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Foster RA, Kuypers MMM, Vagner T, Paerl RW, Musat N, Zehr JP. Nitrogen fixation and transfer in open ocean diatom-cyanobacterial symbioses. THE ISME JOURNAL 2011; 5:1484-93. [PMID: 21451586 PMCID: PMC3160684 DOI: 10.1038/ismej.2011.26] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 02/08/2011] [Accepted: 02/08/2011] [Indexed: 11/17/2022]
Abstract
Many diatoms that inhabit low-nutrient waters of the open ocean live in close association with cyanobacteria. Some of these associations are believed to be mutualistic, where N(2)-fixing cyanobacterial symbionts provide N for the diatoms. Rates of N(2) fixation by symbiotic cyanobacteria and the N transfer to their diatom partners were measured using a high-resolution nanometer scale secondary ion mass spectrometry approach in natural populations. Cell-specific rates of N(2) fixation (1.15-71.5 fmol N per cell h(-1)) were similar amongst the symbioses and rapid transfer (within 30 min) of fixed N was also measured. Similar growth rates for the diatoms and their symbionts were determined and the symbiotic growth rates were higher than those estimated for free-living cells. The N(2) fixation rates estimated for Richelia and Calothrix symbionts were 171-420 times higher when the cells were symbiotic compared with the rates estimated for the cells living freely. When combined, the latter two results suggest that the diatom partners influence the growth and metabolism of their cyanobacterial symbionts. We estimated that Richelia fix 81-744% more N than needed for their own growth and up to 97.3% of the fixed N is transferred to the diatom partners. This study provides new information on the mechanisms controlling N input into the open ocean by symbiotic microorganisms, which are widespread and important for oceanic primary production. Further, this is the first demonstration of N transfer from an N(2) fixer to a unicellular partner. These symbioses are important models for molecular regulation and nutrient exchange in symbiotic systems.
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Affiliation(s)
- Rachel A Foster
- Ocean Sciences Department, University of California, Santa Cruz, CA, USA.
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22
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Zehr JP. Nitrogen fixation by marine cyanobacteria. Trends Microbiol 2011; 19:162-73. [DOI: 10.1016/j.tim.2010.12.004] [Citation(s) in RCA: 323] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 12/01/2010] [Accepted: 12/06/2010] [Indexed: 11/26/2022]
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23
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Yogev T, Rahav E, Bar-Zeev E, Man-Aharonovich D, Stambler N, Kress N, Béjà O, Mulholland MR, Herut B, Berman-Frank I. Is dinitrogen fixation significant in the Levantine Basin, East Mediterranean Sea? Environ Microbiol 2011; 13:854-71. [PMID: 21244595 DOI: 10.1111/j.1462-2920.2010.02402.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report N(2) fixation rates measured from two stations monitored monthly off the Mediterranean coast of Israel during 2006 and 2007, and along a transect from Israel to Crete in September 2008. Analyses of time-series data revealed expression of nifH genes from diazotrophs in nifH clusters I and II, including cyanobacterial bloom-formers Trichodesmium and diatom-Richelia intracellularis associations. However, nifH gene abundance and rates of N(2) fixation were very low in all size fractions measured (> 0.7 µm). Volumetric (15) N uptake ranged from below detection (∼ 36% of > 300 samples) to a high of 0.3 nmol N l(-1) d(-1) and did not vary distinctly with depth or season. Areal N(2) fixation averaged ∼ 1 to 4 µmol N m(-2) d(-1) and contributed only ∼ 1% and 2% of new production and ∼ 0.25% and 0.5% of primary production for the mixed (winter) and stratified (spring-fall) periods respectively. N(2) fixation rates along the 2008 east-west transect were also extremely low (0-0.04 nmol N l(-1) d(-1), integrated average 2.6 µmol N m(-2) d(-1) ) with 37% of samples below detection and no discernable difference between stations. We demonstrate that diazotrophy and N(2) fixation contribute only a minor amount of new N to the P impoverished eastern Mediterranean Sea.
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Affiliation(s)
- Tali Yogev
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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24
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Fiore CL, Jarett JK, Olson ND, Lesser MP. Nitrogen fixation and nitrogen transformations in marine symbioses. Trends Microbiol 2010; 18:455-63. [PMID: 20674366 DOI: 10.1016/j.tim.2010.07.001] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 06/28/2010] [Accepted: 07/02/2010] [Indexed: 10/19/2022]
Abstract
Many marine organisms have coevolved symbiotic relationships with nitrogen-fixing bacteria in nitrogen limited environments such as coral reefs. In addition, some of these organisms also harbor microbes that carry out nitrification and denitrification. Prokaryotes involved in nitrogen fixation and other nitrogen transformations are symbionts in a range of eukaryotic hosts in the marine environment including shipworms, diatoms, corals and sponges. Molecular genetic approaches, and other analytical techniques, have provided exciting new insights into symbiont diversity and the relationship between host and symbiont. We review the current state of knowledge of these symbioses and highlight important avenues for future studies.
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Affiliation(s)
- Cara L Fiore
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
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25
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Wouters J, Raven JA, Minnhagen S, Janson S. The luggage hypothesis: Comparisons of two phototrophic hosts with nitrogen-fixing cyanobacteria and implications for analogous life strategies for kleptoplastids/secondary symbiosis in dinoflagellates. Symbiosis 2009. [DOI: 10.1007/s13199-009-0020-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Ramachandra TV, Mahapatra DM, B K, Gordon R. Milking Diatoms for Sustainable Energy: Biochemical Engineering versus Gasoline-Secreting Diatom Solar Panels. Ind Eng Chem Res 2009. [DOI: 10.1021/ie900044j] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- T. V. Ramachandra
- Energy & Wetlands Research Group, Centre for Ecological Sciences/Centre for Sustainable Technologies, Indian Institute of Science, Bangalore 560 012, India
| | - Durga Madhab Mahapatra
- Energy & Wetlands Research Group, Centre for Ecological Sciences/Centre for Sustainable Technologies, Indian Institute of Science, Bangalore 560 012, India
| | - Karthick B
- Energy & Wetlands Research Group, Centre for Ecological Sciences/Centre for Sustainable Technologies, Indian Institute of Science, Bangalore 560 012, India
| | - Richard Gordon
- Department of Radiology, University of Manitoba, Room GA216, HSC, 820 Sherbrook Street, Winnipeg MB R3A 1R9, Canada
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27
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Beardall J, Allen D, Bragg J, Finkel ZV, Flynn KJ, Quigg A, Rees TAV, Richardson A, Raven JA. Allometry and stoichiometry of unicellular, colonial and multicellular phytoplankton. THE NEW PHYTOLOGIST 2009; 181:295-309. [PMID: 19121029 DOI: 10.1111/j.1469-8137.2008.02660.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Phytoplankton life forms, including unicells, colonies, pseudocolonies, and multicellular organisms, span a huge size range. The smallest unicells are less than 1 microm3 (e.g. cyanobacteria), while large unicellular diatoms may attain 10(9) microm3, being visible to the naked eye. Phytoplankton includes chemo-organotrophic unicells, colonies and multicellular organisms that depend on symbionts or kleptoplastids for their capacity to photosynthesize. Analyses of physical (transport within cells, diffusion boundary layers, package effect, turgor, and vertical movements) and biotic (grazing, viruses and other parasitoids) factors indicate potential ecological constraints and opportunities that differ among the life forms. There are also variations among life forms in elemental stoichiometry and in allometric relations between biovolume and specific growth. While many of these factors probably have ecological and evolutionary significance, work is needed to establish those that are most important, warranting explicit description in models. Other factors setting limitations on growth rate (selecting slow-growing species) await elucidation.
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Affiliation(s)
- John Beardall
- School of Biological Sciences, PO Box 18, Monash University, Clayton, Vic 3800, Australia;National Center for Ecological Analysis and Synthesis, 735 State St, Suite 300, Santa Barbara, CA 93101, USA;Civil and Environmental Engineering, MIT 48-208, 18 Vassar St, Cambridge, MA 02139, USA;Environmental Science Program, Mount Allison University, Avard-Dixon, 144 Main Street, Sackville, Canada E4L 1A7;Institute of Environmental Sustainability, Wallace Building, University of Swansea, Swansea SA2 8PP, UK;Department of Oceanography, Texas A&M University, 5007 Avenue U, TX 77551, USA;Leigh Marine Laboratory, University of Auckland, PO Box 349, Warkworth, New Zealand;Climate Adaptation Flagship, CSIRO Marine and Atmospheric Research, Cleveland, Qld 4163, Australia;University of Queensland, School of Physical Sciences, St Lucia, Qld 4072, Australia;Division of Plant Sciences, University of Dundee at SCRI, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Drew Allen
- School of Biological Sciences, PO Box 18, Monash University, Clayton, Vic 3800, Australia;National Center for Ecological Analysis and Synthesis, 735 State St, Suite 300, Santa Barbara, CA 93101, USA;Civil and Environmental Engineering, MIT 48-208, 18 Vassar St, Cambridge, MA 02139, USA;Environmental Science Program, Mount Allison University, Avard-Dixon, 144 Main Street, Sackville, Canada E4L 1A7;Institute of Environmental Sustainability, Wallace Building, University of Swansea, Swansea SA2 8PP, UK;Department of Oceanography, Texas A&M University, 5007 Avenue U, TX 77551, USA;Leigh Marine Laboratory, University of Auckland, PO Box 349, Warkworth, New Zealand;Climate Adaptation Flagship, CSIRO Marine and Atmospheric Research, Cleveland, Qld 4163, Australia;University of Queensland, School of Physical Sciences, St Lucia, Qld 4072, Australia;Division of Plant Sciences, University of Dundee at SCRI, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Jason Bragg
- School of Biological Sciences, PO Box 18, Monash University, Clayton, Vic 3800, Australia;National Center for Ecological Analysis and Synthesis, 735 State St, Suite 300, Santa Barbara, CA 93101, USA;Civil and Environmental Engineering, MIT 48-208, 18 Vassar St, Cambridge, MA 02139, USA;Environmental Science Program, Mount Allison University, Avard-Dixon, 144 Main Street, Sackville, Canada E4L 1A7;Institute of Environmental Sustainability, Wallace Building, University of Swansea, Swansea SA2 8PP, UK;Department of Oceanography, Texas A&M University, 5007 Avenue U, TX 77551, USA;Leigh Marine Laboratory, University of Auckland, PO Box 349, Warkworth, New Zealand;Climate Adaptation Flagship, CSIRO Marine and Atmospheric Research, Cleveland, Qld 4163, Australia;University of Queensland, School of Physical Sciences, St Lucia, Qld 4072, Australia;Division of Plant Sciences, University of Dundee at SCRI, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Zoe V Finkel
- School of Biological Sciences, PO Box 18, Monash University, Clayton, Vic 3800, Australia;National Center for Ecological Analysis and Synthesis, 735 State St, Suite 300, Santa Barbara, CA 93101, USA;Civil and Environmental Engineering, MIT 48-208, 18 Vassar St, Cambridge, MA 02139, USA;Environmental Science Program, Mount Allison University, Avard-Dixon, 144 Main Street, Sackville, Canada E4L 1A7;Institute of Environmental Sustainability, Wallace Building, University of Swansea, Swansea SA2 8PP, UK;Department of Oceanography, Texas A&M University, 5007 Avenue U, TX 77551, USA;Leigh Marine Laboratory, University of Auckland, PO Box 349, Warkworth, New Zealand;Climate Adaptation Flagship, CSIRO Marine and Atmospheric Research, Cleveland, Qld 4163, Australia;University of Queensland, School of Physical Sciences, St Lucia, Qld 4072, Australia;Division of Plant Sciences, University of Dundee at SCRI, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Kevin J Flynn
- School of Biological Sciences, PO Box 18, Monash University, Clayton, Vic 3800, Australia;National Center for Ecological Analysis and Synthesis, 735 State St, Suite 300, Santa Barbara, CA 93101, USA;Civil and Environmental Engineering, MIT 48-208, 18 Vassar St, Cambridge, MA 02139, USA;Environmental Science Program, Mount Allison University, Avard-Dixon, 144 Main Street, Sackville, Canada E4L 1A7;Institute of Environmental Sustainability, Wallace Building, University of Swansea, Swansea SA2 8PP, UK;Department of Oceanography, Texas A&M University, 5007 Avenue U, TX 77551, USA;Leigh Marine Laboratory, University of Auckland, PO Box 349, Warkworth, New Zealand;Climate Adaptation Flagship, CSIRO Marine and Atmospheric Research, Cleveland, Qld 4163, Australia;University of Queensland, School of Physical Sciences, St Lucia, Qld 4072, Australia;Division of Plant Sciences, University of Dundee at SCRI, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Antonietta Quigg
- School of Biological Sciences, PO Box 18, Monash University, Clayton, Vic 3800, Australia;National Center for Ecological Analysis and Synthesis, 735 State St, Suite 300, Santa Barbara, CA 93101, USA;Civil and Environmental Engineering, MIT 48-208, 18 Vassar St, Cambridge, MA 02139, USA;Environmental Science Program, Mount Allison University, Avard-Dixon, 144 Main Street, Sackville, Canada E4L 1A7;Institute of Environmental Sustainability, Wallace Building, University of Swansea, Swansea SA2 8PP, UK;Department of Oceanography, Texas A&M University, 5007 Avenue U, TX 77551, USA;Leigh Marine Laboratory, University of Auckland, PO Box 349, Warkworth, New Zealand;Climate Adaptation Flagship, CSIRO Marine and Atmospheric Research, Cleveland, Qld 4163, Australia;University of Queensland, School of Physical Sciences, St Lucia, Qld 4072, Australia;Division of Plant Sciences, University of Dundee at SCRI, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - T Alwyn V Rees
- School of Biological Sciences, PO Box 18, Monash University, Clayton, Vic 3800, Australia;National Center for Ecological Analysis and Synthesis, 735 State St, Suite 300, Santa Barbara, CA 93101, USA;Civil and Environmental Engineering, MIT 48-208, 18 Vassar St, Cambridge, MA 02139, USA;Environmental Science Program, Mount Allison University, Avard-Dixon, 144 Main Street, Sackville, Canada E4L 1A7;Institute of Environmental Sustainability, Wallace Building, University of Swansea, Swansea SA2 8PP, UK;Department of Oceanography, Texas A&M University, 5007 Avenue U, TX 77551, USA;Leigh Marine Laboratory, University of Auckland, PO Box 349, Warkworth, New Zealand;Climate Adaptation Flagship, CSIRO Marine and Atmospheric Research, Cleveland, Qld 4163, Australia;University of Queensland, School of Physical Sciences, St Lucia, Qld 4072, Australia;Division of Plant Sciences, University of Dundee at SCRI, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Anthony Richardson
- School of Biological Sciences, PO Box 18, Monash University, Clayton, Vic 3800, Australia;National Center for Ecological Analysis and Synthesis, 735 State St, Suite 300, Santa Barbara, CA 93101, USA;Civil and Environmental Engineering, MIT 48-208, 18 Vassar St, Cambridge, MA 02139, USA;Environmental Science Program, Mount Allison University, Avard-Dixon, 144 Main Street, Sackville, Canada E4L 1A7;Institute of Environmental Sustainability, Wallace Building, University of Swansea, Swansea SA2 8PP, UK;Department of Oceanography, Texas A&M University, 5007 Avenue U, TX 77551, USA;Leigh Marine Laboratory, University of Auckland, PO Box 349, Warkworth, New Zealand;Climate Adaptation Flagship, CSIRO Marine and Atmospheric Research, Cleveland, Qld 4163, Australia;University of Queensland, School of Physical Sciences, St Lucia, Qld 4072, Australia;Division of Plant Sciences, University of Dundee at SCRI, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - John A Raven
- School of Biological Sciences, PO Box 18, Monash University, Clayton, Vic 3800, Australia;National Center for Ecological Analysis and Synthesis, 735 State St, Suite 300, Santa Barbara, CA 93101, USA;Civil and Environmental Engineering, MIT 48-208, 18 Vassar St, Cambridge, MA 02139, USA;Environmental Science Program, Mount Allison University, Avard-Dixon, 144 Main Street, Sackville, Canada E4L 1A7;Institute of Environmental Sustainability, Wallace Building, University of Swansea, Swansea SA2 8PP, UK;Department of Oceanography, Texas A&M University, 5007 Avenue U, TX 77551, USA;Leigh Marine Laboratory, University of Auckland, PO Box 349, Warkworth, New Zealand;Climate Adaptation Flagship, CSIRO Marine and Atmospheric Research, Cleveland, Qld 4163, Australia;University of Queensland, School of Physical Sciences, St Lucia, Qld 4072, Australia;Division of Plant Sciences, University of Dundee at SCRI, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
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Foster RA, Subramaniam A, Zehr JP. Distribution and activity of diazotrophs in the Eastern Equatorial Atlantic. Environ Microbiol 2008; 11:741-50. [PMID: 19175790 PMCID: PMC2702491 DOI: 10.1111/j.1462-2920.2008.01796.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The gene abundance and gene expression of six diazotroph populations from the Eastern Equatorial Atlantic in June 2007 were examined using nifH gene quantitative polymerase chain reaction (q PCR) methods. Of all the diazotrophs, Trichodesmium spp. was the most abundant with the highest number of gene copies in the Gulf of Guinea. Trichodesmium also had the highest nitrogenase gene transcript abundance overall with the maximum in samples collected at the equator and in waters influenced by the Congo River plume (> 105 cDNA nifH copies l−1). Both cyanobacterial unicellular groups (A and B) were detected, where group A was the second most abundant in surface samples, in particular at the stations along the equator. Transcript abundance for group A, however, was at the detection limit and suggests that it was not actively fixing N2. Trichodesmium and group B nifH gene abundances co-varied (P < 0.0001). Richelia associated with Hemiaulus hauckii diatoms were detected in 9 of 10 surface samples and the highest abundances (> 104nifH copies l−1) were found north-west of the Congo River plume. In contrast, the Calothrix symbionts (het-3) of Chaetoceros had low abundances at the surface, but were present at 3.7 × 104nifH copies l−1 at 40 m depth in the equatorial upwelling. This is the first report of the Calothrix symbiont in the Atlantic Ocean. This is also the first report of nifH gene copy and transcript abundance in an Equatorial upwelling zone. Although the number of gene copies for Richelia associated with Rhizosolenia were the lowest, the transcript abundance were high (9.4 × 101−1.8 × 104 cDNA nifH copies l−1) and similar to that of Trichodesmium. The distribution of the diazotroph groups, especially the three strains of symbiotic cyanobacteria, was different, and appeared largely controlled by riverine inputs and upwelling.
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Affiliation(s)
- Rachel A Foster
- Ocean Sciences, University of California, Santa Cruz, CA 95064, USA.
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Han D, Fan Y, Hu Z. An evaluation of four phylogenetic markers in Nostoc: implications for cyanobacterial phylogenetic studies at the intrageneric level. Curr Microbiol 2008; 58:170-6. [PMID: 18972163 DOI: 10.1007/s00284-008-9302-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2006] [Accepted: 10/12/2006] [Indexed: 11/24/2022]
Abstract
The success of some phylogenetic markers in cyanobacteria owes to the design of cyanobacteria-specific primers, but a few studies have directly investigated the evolution "behavior" of the loci. In this study, we performed a case study in Nostoc to evaluate rpoC1, hetR, rbcLX, and 16S rRNA-tRNA(Ile)-tRNA(Ala)-23S rRNA internal transcribed spacer (ITS) as phylogenetic markers. The results indicated that the gene trees of these loci are not congruent with the phylogeny based on 16S rRNA gene. The mechanisms contributing to the incongruence include randomized variation and recombination. As the results suggested, one should be careful to choose the molecular markers for phylogenetic reconstruction at the intrageneric level in cyanobacteria.
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Affiliation(s)
- D Han
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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30
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Zeev EB, Yogev T, Man-Aharonovich D, Kress N, Herut B, Béjà O, Berman-Frank I. Seasonal dynamics of the endosymbiotic, nitrogen-fixing cyanobacterium Richelia intracellularis in the eastern Mediterranean Sea. ISME JOURNAL 2008; 2:911-23. [DOI: 10.1038/ismej.2008.56] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Fong AA, Karl DM, Lukas R, Letelier RM, Zehr JP, Church MJ. Nitrogen fixation in an anticyclonic eddy in the oligotrophic North Pacific Ocean. ISME JOURNAL 2008; 2:663-76. [PMID: 18309359 DOI: 10.1038/ismej.2008.22] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mesoscale physical processes (for example eddies, frontal meanders and planetary waves) can play important roles in controlling ocean biogeochemistry. We examined spatial variations in upper ocean (0-100 m) nutrient inventories, N(2) fixing microorganism diversity and abundance, and rates of N(2) fixation in an anticyclonic eddy near Station ALOHA (22 degrees 45' N, 158 degrees 00' W) in the North Pacific Subtropical Gyre (NPSG). In July 2005, satellite-based sea surface altimetry and ocean color observation revealed an anticyclonic eddy with enhanced chlorophyll in the upper ocean in the vicinity of Station ALOHA. Within the eddy, near-surface ocean chlorophyll concentrations were approximately 5-fold greater than in the surrounding waters. Inventories of nitrate and phosphate in the eddy were similar to the concentrations historically observed at Station ALOHA, while silicic acid inventories were significantly depleted (one-way analysis of variance, P<0.01). Quantitative PCR determinations of nifH gene copies revealed relatively high abundances of several N(2) fixing cyanobacteria, including Trichodesmium spp., Crocosphaera watsonii and Richelia intracellularis. Reverse transcriptase PCR (RT-PCR) amplified nitrogenase (nifH) gene transcripts were cloned and sequenced to examine the diversity of active N(2) fixing microorganisms; these clone libraries were dominated by sequence-types 97%-99% identical to the filamentous cyanobacteria Trichodesmium spp. Near-surface ocean rates of N(2) fixation were 2-18 times greater (averaging 8.6+/-5.6 nmol N per l per day) than previously reported measurements at Station ALOHA. These results suggest that mesoscale physical variability can play an important role in modifying the abundances of N(2) fixing microorganisms and associated rates of N(2) fixation in open ocean ecosystems.
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Affiliation(s)
- Allison A Fong
- Department of Oceanography, University of Hawaii, Honolulu, HI 96822, USA
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Usher KM, Bergman B, Raven JA. Exploring Cyanobacterial Mutualisms. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2007. [DOI: 10.1146/annurev.ecolsys.38.091206.095641] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kayley M. Usher
- School of Plant Biology, The University of Western Australia, Crawley, Western Australia, 6009 Australia;
| | - Birgitta Bergman
- Department of Botany, Stockholm University, SE-106 91 Stockholm, Sweden;
| | - John A. Raven
- Plant Research Unit, University of Dundee at SCRI, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom;
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Kneip C, Lockhart P, Voß C, Maier UG. Nitrogen fixation in eukaryotes--new models for symbiosis. BMC Evol Biol 2007; 7:55. [PMID: 17408485 PMCID: PMC1853082 DOI: 10.1186/1471-2148-7-55] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Accepted: 04/04/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Nitrogen, a component of many bio-molecules, is essential for growth and development of all organisms. Most nitrogen exists in the atmosphere, and utilisation of this source is important as a means of avoiding nitrogen starvation. However, the ability to fix atmospheric nitrogen via the nitrogenase enzyme complex is restricted to some bacteria. Eukaryotic organisms are only able to obtain fixed nitrogen through their symbiotic interactions with nitrogen-fixing prokaryotes. These symbioses involve a variety of host organisms, including animals, plants, fungi and protists. RESULTS We have compared the morphological, physiological and molecular characteristics of nitrogen fixing symbiotic associations of bacteria and their diverse hosts. Special features of the interaction, e.g. vertical transmission of symbionts, grade of dependency of partners and physiological modifications have been considered in terms of extent of co-evolution and adaptation. Our findings are that, despite many adaptations enabling a beneficial partnership, most symbioses for molecular nitrogen fixation involve facultative interactions. However, some interactions, among them endosymbioses between cyanobacteria and diatoms, show characteristics that reveal a more obligate status of co-evolution. CONCLUSION Our review emphasises that molecular nitrogen fixation, a driving force for interactions and co-evolution of different species, is a widespread phenomenon involving many different organisms and ecosystems. The diverse grades of symbioses, ranging from loose associations to highly specific intracellular interactions, might themselves reflect the range of potential evolutionary fates for symbiotic partnerships. These include the extreme evolutionary modifications and adaptations that have accompanied the formation of organelles in eukaryotic cells: plastids and mitochondria. However, age and extensive adaptation of plastids and mitochondria complicate the investigation of processes involved in the transition of symbionts to organelles. Extant lineages of symbiotic associations for nitrogen fixation show diverse grades of adaptation and co-evolution, thereby representing different stages of symbiont-host interaction. In particular cyanobacterial associations with protists, like the Rhopalodia gibba-spheroid body symbiosis, could serve as important model systems for the investigation of the complex mechanisms underlying organelle evolution.
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Affiliation(s)
- Christoph Kneip
- Department of Cell Biology, Philipps-University Marburg, Marburg, Germany
- Department of Molecular Biology, Max-Planck-Institute for Infection Biology, Berlin, Germany
| | - Peter Lockhart
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand
| | - Christine Voß
- Department of Cell Biology, Philipps-University Marburg, Marburg, Germany
| | - Uwe-G Maier
- Department of Cell Biology, Philipps-University Marburg, Marburg, Germany
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Mes THM, Doeleman M, Lodders N, Nübel U, Stal LJ. Selection on protein-coding genes of natural cyanobacterial populations. Environ Microbiol 2007; 8:1534-43. [PMID: 16913914 DOI: 10.1111/j.1462-2920.2006.01044.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We examined the distribution of synonymous and non-synonymous changes in 12 protein-coding genes of natural populations of cyanobacteria to infer changes in gene functionality. By comparing mutation distributions within and across species using the McDonald-Kreitman test, we found data sets to contain evidence for purifying selection (hetR of Trichodesmium, nifH of Cylindrospermopsis raceborskii and rpoC1 of Anabaena lemmermannii) and positive selection (kaiC of Microcoleus chthonoplastes and rbcX of Anabaena and Aphanizomenon sp.). Other genes from the same set of clonal isolates (petB and rbcL in M. chthonoplastes and Anabaena/Aphanizomenon, respectively) did not harbour evidence for either form of selection. The results of branch models of codon evolution agreed fully with the results of the McDonald-Kreitman test in terms of significance and absolute value of the dN/dS estimates. The high frequency of gene-specific mutation patterns and their association with branches that separate closely related cyanobacterial genera suggest that evolutionary tests are suited to uncover gene-specific selective differentiation in cyanobacterial genomes. At the same time, given the lack of information about the history of cyanobacteria, analysis of larger numbers of protein-coding genes of clonal cyanobacterial isolates will produce more detailed pictures of the effects of natural selection.
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Affiliation(s)
- Ted H M Mes
- Netherlands Institute of Ecology (NIOO-KNAW), Centre for Estuarine and Marine Ecology, POB 140, 4400 AC, Yerseke, the Netherlands.
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Foster RA, Zehr JP. Characterization of diatom-cyanobacteria symbioses on the basis of nifH, hetR and 16S rRNA sequences. Environ Microbiol 2006; 8:1913-25. [PMID: 17014491 DOI: 10.1111/j.1462-2920.2006.01068.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Richelia intracellularis is a symbiotic heterocystous cyanobacterium that is capable of forming associations with several genera of diatoms. nifH, 16S rRNA and hetR sequences were amplified and cloned from field populations of Richelia associated with Hemiaulus hauckii (N. Atlantic), with Rhizosolenia clevei (N. Pacific), and from a cultivated isolate of Calothrix associated with Chaetoceros from station ALOHA (N. Pacific). Sequence identity was highest (98.2%) among the 16S rRNA sequences, and more divergent for the hetR (83.8%) and nifH (91.1%) sequences. The hetR and nifH DNA and amino acid sequences obtained from the symbionts associated with the three different diatom genera diverged into three separate lineages supported by high bootstrap values. The data indicate that symbionts in the different hosts are distinct species or strains. Furthermore, three previously unidentified heterocystous-like nifH sequence groups recently reported from station ALOHA in the subtropical Pacific, het-1, het-2 and het-3, were linked to Richelia associated with R. clevei, H. hauckii and the Calothrix symbiont of Chaetoceros sp. respectively.
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Affiliation(s)
- Rachel A Foster
- Institute of Marine Science, University of California, Santa Cruz, CA 95064, USA.
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36
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Abstract
Cyanobacteria such as Synechococcus elongatus PCC 7942, Thermosynechococcus elongatus BP-1, and Synechocystis species strain PCC 6803 have an endogenous timing mechanism that can generate and maintain a 24 h (circadian) periodicity to global (whole genome) gene expression patterns. This rhythmicity extends to many other physiological functions, including chromosome compaction. These rhythmic patterns seem to reflect the periodicity of availability of the primary energy source for these photoautotrophic organisms, the Sun. Presumably, eons of environmentally derived rhythmicity--light/dark cycles--have simply been mechanistically incorporated into the regulatory networks of these cyanobacteria. Genetic and biochemical experimentation over the last 15 years has identified many key components of the primary timing mechanism that generates rhythmicity, the input pathways that synchronize endogenous rhythms to exogenous rhythms, and the output pathways that transduce temporal information from the timekeeper to the regulators of gene expression and function. Amazingly, the primary timing mechanism has evidently been extracted from S. elongatus PCC 7942 and can also keep time in vitro. Mixing the circadian clock proteins KaiA, KaiB, and KaiC from S. elongatus PCC 7942 in vitro and adding ATP results in a circadian rhythm in the KaiC protein phosphorylation state. Nonetheless, many questions still loom regarding how this circadian clock mechanism works, how it communicates with the environment and how it regulates temporal patterns of gene expression. Many details regarding structure and function of the individual clock-related proteins are provided here as a basis to discuss these questions. A strong, data-intensive foundation has been developed to support the working model for the cyanobacterial circadian regulatory system. The eventual addition to that model of the metabolic parameters participating in the command and control of this circadian global regulatory system will ultimately allow a fascinating look into whole-cell physiology and metabolism and the consequential organization of global gene expression patterns.
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Affiliation(s)
- Stanly B Williams
- Department of Biology, Life Science Building, University of Utah, Salt Lake City, UT 84112, USA
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37
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Church MJ, Short CM, Jenkins BD, Karl DM, Zehr JP. Temporal patterns of nitrogenase gene (nifH) expression in the oligotrophic North Pacific Ocean. Appl Environ Microbiol 2005; 71:5362-70. [PMID: 16151126 PMCID: PMC1214674 DOI: 10.1128/aem.71.9.5362-5370.2005] [Citation(s) in RCA: 139] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2004] [Accepted: 04/04/2005] [Indexed: 11/20/2022] Open
Abstract
Dinitrogen (N(2))-fixing microorganisms (diazotrophs) play important roles in ocean biogeochemistry and plankton productivity. In this study, we examined the presence and expression of specific planktonic nitrogenase genes (nifH) in the upper ocean (0 to 175 m) at Station ALOHA in the oligotrophic North Pacific Ocean. Clone libraries constructed from reverse-transcribed PCR-amplified mRNA revealed six unique phylotypes. Five of the nifH phylotypes grouped with sequences from unicellular and filamentous cyanobacteria, and one of the phylotypes clustered with gamma-proteobacteria. The cyanobacterial nifH phylotypes retrieved included two sequence types that phylogenetically grouped with unicellular cyanobacteria (termed groups A and B), several sequences closely related (97 to 99%) to Trichodesmium spp. and Katagnymene spiralis, and two previously unreported phylotypes clustering with heterocyst-forming nifH cyanobacteria. Temporal patterns of nifH expression were evaluated using reverse-transcribed quantitative PCR amplification of nifH gene transcripts. The filamentous and presumed unicellular group A cyanobacterial phylotypes exhibited elevated nifH transcription during the day, while members of the group B (closely related to Crocosphaera watsonii) unicellular phylotype displayed greater nifH transcription at night. In situ nifH expression by all of the cyanobacterial phylotypes exhibited pronounced diel periodicity. The gamma-proteobacterial phylotype had low transcript abundance and did not exhibit a clear diurnal periodicity in nifH expression. The temporal separation of nifH expression by the various phylotypes suggests that open ocean diazotrophic cyanobacteria have unique in situ physiological responses to daily fluctuations of light in the upper ocean.
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Affiliation(s)
- Matthew J Church
- Department of Oceanography, University of Hawaii, Honolulu, HI 96822, USA.
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38
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Finkel ZV, Katz ME, Wright JD, Schofield OME, Falkowski PG. Climatically driven macroevolutionary patterns in the size of marine diatoms over the Cenozoic. Proc Natl Acad Sci U S A 2005; 102:8927-32. [PMID: 15956194 PMCID: PMC1157017 DOI: 10.1073/pnas.0409907102] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2004] [Indexed: 11/18/2022] Open
Abstract
Numerous taxonomic groups exhibit an evolutionary trajectory in cell or body size. The size structure of marine phytoplankton communities strongly affects food web structure and organic carbon export into the ocean interior, yet macroevolutionary patterns in the size structure of phytoplankton communities have not been previously investigated. We constructed a database of the size of the silica frustule of the dominant fossilized marine planktonic diatom species over the Cenozoic. We found that the minimum and maximum sizes of the diatom frustule have expanded in concert with increasing species diversity. In contrast, the mean area of the diatom frustule is highly correlated with oceanic temperature gradients inferred from the delta18O of foraminiferal calcite, consistent with the hypothesis that climatically induced changes in oceanic mixing have altered nutrient availability in the euphotic zone and driven macroevolutionary shifts in the size of marine pelagic diatoms through the Cenozoic.
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Affiliation(s)
- Zoe V Finkel
- Institute of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Road, New Brunswick, NJ 08901, USA.
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39
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Mes THM, Stal LJ. Variable selection pressures across lineages in Trichodesmium and related cyanobacteria based on the heterocyst differentiation protein gene hetR. Gene 2005; 346:163-71. [PMID: 15716028 DOI: 10.1016/j.gene.2004.10.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2004] [Revised: 10/01/2004] [Accepted: 10/14/2004] [Indexed: 11/26/2022]
Abstract
Due to the irreversible inhibition of nitrogenase by O2, N2 fixation is incompatible with the oxygenic photosynthesis of cyanobacteria. These organisms have therefore evolved various strategies for growing diazotrophically. One group of N2-fixing cyanobacteria has specialized cells, heterocysts, which contain the nitrogenase, lack the oxygenic photosystem II, and are virtually anoxic inside as the result of respiratory activity and a thick glycolipid cell wall. The hetR gene encodes a serine protease which is thought to be involved in the regulation of heterocyst development and in DNA binding. Although hetR is also present in many non-heterocystous N2-fixing cyanobacteria, its function in these organisms is unknown. In this study, hetR sequences of the N2-fixing, non-heterocystous cyanobacterium Trichodesmium spp. and related genera were examined for signatures of selection. In parsimony- or distance-based hetR phylogenies, the filamentous non-heterocystous cyanobacteria Symploca sp. and Leptolyngbya sp. were closest to Trichodesmium sp. However, accommodating molecular attributes of hetR such as nucleotide frequencies and rate heterogeneity in phylogenetic analyses suggested that many other genera could not be excluded as sister taxa of Trichodesmium. Maximum likelihood analysis of the dN/dS ratio (omega) showed that-irrespective of the use of Symploca, Leptolyngbya, or more distant taxa as an outgroup-the lineage between an outgroup and Trichodesmium (omega1=0.02-0.05) and a lineage leading to Trichodesmium erythraeum (omega1=0.02) were under much stronger purifying selection than the other lineages in Trichodesmium (omega0=0.13-0.32). Although the results from the maximum likelihood analyses are most trustworthy because of codon usage bias in Trichodesmium, the results from a simpler tree-based McDonald-Kreitman test were in general agreement. Due to their quite different assumptions, the combination of these two methods of analysis circumvents multiple testing which, in general, is problematic when using branch models. Although the causal selective forces underlying the substitution patterns in hetR have not yet been identified, these findings parallel the variety of physiological, molecular, and behavioral differences in cyanobacteria related to N2 fixation. The heterogeneity of selection pressures in Trichodesmium is more surprising, because multiple adaptation mechanisms have not been described in this genus.
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Affiliation(s)
- T H M Mes
- Netherlands Institute of Ecology (NIOO-KNAW), Marine Microbiology, Centre for Estuarine and Marine Ecology, Korringaweg 7, 4401 NT Yerseke, The Netherlands.
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Janson S. Molecular evidence that plastids in the toxin-producing dinoflagellate genus Dinophysis originate from the free-living cryptophyte Teleaulax amphioxeia. Environ Microbiol 2004; 6:1102-6. [PMID: 15344936 DOI: 10.1111/j.1462-2920.2004.00646.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Some species of the dinoflagellate genus Dinophysis form red tides and are toxin producers with a great environmental impact. The dinoflagellates as a group display high plastid diversity. Several cases indicate that plastids have been replaced. In the case of the genus Dinophysis, the plastids show characteristics of a plastid originating from a cryptophyte. Recent molecular evidence showed that the plastid indeed originates from a cryptophyte, but the source could not be identified to species or genus level. The data presented here show that both a 799 bp region of the psbA gene and 1,221 bp region of the 16S rRNA gene from Dinophysis spp. are identical to the same loci in Teleaulax amphioxeia SCCAP K434. This strongly indicates that the plastid was acquired recently in Dinophysis and may be a so-called kleptoplastid, specifically originating from a species of Teleaulax.
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Affiliation(s)
- Sven Janson
- Department of Biology and Environmental Science, University of Kalmar, SE-391 82 Kalmar, Sweden.
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41
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Prechtl J, Kneip C, Lockhart P, Wenderoth K, Maier UG. Intracellular spheroid bodies of Rhopalodia gibba have nitrogen-fixing apparatus of cyanobacterial origin. Mol Biol Evol 2004; 21:1477-81. [PMID: 14963089 DOI: 10.1093/molbev/msh086] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Nitrogen fixation is not regarded as a eukaryotic invention. The process has only been reported as being carried out by bacteria. These prokaryotes typically interact with their eukaryotic hosts as extracellular and temporary nonobligate nitrogen-fixing symbionts. However, intracellular permanent "spheroid bodies" have been reported within the fresh-water diatom Rhopalodia gibba, and these, too, have been speculated as being able to provide nitrogen to their host diatom. These spheroid bodies have gram-negative characteristics with thylakoids. We demonstrate that they fix nitrogen under light conditions. We also show that phylogenetic analyses of their 16rRNA and nif D genes predict that their genome is closely related to that of Cyanothece sp. ATCC 51.142, a free-living diazotrophic cyanobacterium. We suggest that the intracellular spheroid bodies of Rhopalodia gibba may represent a vertically transmitted, permanent endosymbiotic stage in the transition from a free-living diazotrophic cyanobacterium to a nitrogen-fixing eukaryotic organelle.
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Affiliation(s)
- Julia Prechtl
- Cell Biology, Philipps-University Marburg, Marburg, Germany
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42
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Abstract
Cyanobacteria such as Synechococcus elongatus PCC 7942 exhibit 24-h rhythms of gene expression that are controlled by an endogenous circadian clock that is mechanistically distinct from those described for diverse eukaryotes. Genetic and biochemical experiments over the past decade have identified key components of the circadian oscillator, input pathways that synchronize the clock with the daily environment, and output pathways that relay temporal information to downstream genes. The mechanism of the cyanobacterial circadian clock that is emerging is based principally on the assembly and disassembly of a large complex at whose heart are the proteins KaiA, KaiB, and KaiC. Signal transduction pathways that feed into and out of the clock employ protein domains that are similar to those in two-component regulatory systems of bacteria.
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Affiliation(s)
- J L Ditty
- Department of Biology, University of St. Thomas, St. Paul, Minnesota 55105, USA.
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43
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Wouters J, Bergman B, Janson S. Cloning and expression of a putative cyclodextrin glucosyltransferase from the symbiotically competent cyanobacterium Nostoc sp. PCC 9229. FEMS Microbiol Lett 2003; 219:181-5. [PMID: 12620618 DOI: 10.1016/s0378-1097(02)01204-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
A polymerase chain reaction-based method was used to isolate a Nostoc sp. PCC 9229 cDNA from infected glands of Gunnera chilensis. The complete gene sequence was isolated from a genomic Nostoc sp. PCC 9229 library. Sequence analysis showed 84% amino acid similarity to a putative cyclodextrin glycosyltransferase from Nostoc sp. PCC 7120 and the gene was therefore termed cgt. Southern blot revealed that the cgt gene was present in symbiotically competent cyanobacteria. The cgt gene was expressed in free-living nitrogen-fixing cultures in light or in darkness when supplemented with fructose. This is the first expression analysis of a cgt gene from a cyanobacterium.
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Affiliation(s)
- Johanna Wouters
- Department of Biology and Environmental Science, Kalmar University, Barlastgatan 1, S-391 82, Kalmar, Sweden.
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Carpenter EJ, Janson S. INTRACELLULAR CYANOBACTERIAL SYMBIONTS IN THE MARINE DIATOM CLIMACODIUM FRAUENFELDIANUM (BACILLARIOPHYCEAE). JOURNAL OF PHYCOLOGY 2000; 36:540-544. [PMID: 29544002 DOI: 10.1046/j.1529-8817.2000.99163.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The diatom Climacodium frauenfeldianum Grunow was collected in the tropical Atlantic and Pacific Oceans. Observations with epifluorescence microscopy revealed that this diatom contained coccoid symbionts (2.5-3.5 μm) with a typical cyanobacterial fluorescence in addition to that of their own chloroplasts. Mean concentration of C. frauenfeldianum for 28 stations in the SW tropical Pacific Ocean was 530 x 103 (SE = 1372) cells·m-2 , with highest concentration (mean 17.5 cells·L-1 ) at 40-m depth. The symbiosis was only observed at water temperatures between 26.3 and 28.9° C, with highest concentrations at 27.7° C. Three almost complete 16S rDNA sequences from one sample were determined, and they were identical. The phylogenetic analysis of this 16S rDNA sequence and those from other cyanobacteria and plastids revealed that it was closely related to the 16S rDNA sequence from Cyanothece sp. ATCC 51142. Cyanothece sp. ATCC 51142 is a unicellular nitrogen-fixing cyanobacterium isolated from a coastal marine environment and has ultrastructural features similar to the symbionts of C. frauenfeldianum. The close relationship between Cyanothece sp. and the cyanobacterial symbiont in C. frauenfeldianum suggests the potential for nitrogen fixation in the symbiosis.
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Affiliation(s)
- Edward J Carpenter
- Marine Sciences Research Center, State University of New York, Stony Brook, New York 11794-5000Department of Marine Sciences, Institute of Natural Sciences, University of Kalmar, Box 905, S-391 29, Kalmar, Sweden
| | - Sven Janson
- Marine Sciences Research Center, State University of New York, Stony Brook, New York 11794-5000Department of Marine Sciences, Institute of Natural Sciences, University of Kalmar, Box 905, S-391 29, Kalmar, Sweden
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