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Davenport EJ, Neudeck MJ, Matson PG, Bullerjahn GS, Davis TW, Wilhelm SW, Denney MK, Krausfeldt LE, Stough JMA, Meyer KA, Dick GJ, Johengen TH, Lindquist E, Tringe SG, McKay RML. Metatranscriptomic Analyses of Diel Metabolic Functions During a Microcystis Bloom in Western Lake Erie (United States). Front Microbiol 2019; 10:2081. [PMID: 31551998 PMCID: PMC6746948 DOI: 10.3389/fmicb.2019.02081] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 08/23/2019] [Indexed: 12/02/2022] Open
Abstract
This study examined diel shifts in metabolic functions of Microcystis spp. during a 48-h Lagrangian survey of a toxin-producing cyanobacterial bloom in western Lake Erie in the aftermath of the 2014 Toledo Water Crisis. Transcripts mapped to the genomes of recently sequenced lower Great Lakes Microcystis isolates showed distinct patterns of gene expression between samples collected across day (10:00 h, 16:00 h) and night (22:00 h, 04:00 h). Daytime transcripts were enriched in functions related to Photosystem II (e.g., psbA), nitrogen and phosphate acquisition, cell division (ftsHZ), heat shock response (dnaK, groEL), and uptake of inorganic carbon (rbc, bicA). Genes transcribed during nighttime included those involved in phycobilisome protein synthesis and Photosystem I core subunits. Hierarchical clustering and principal component analysis (PCA) showed a tightly clustered group of nighttime expressed genes, whereas daytime transcripts were separated from each other over the 48-h duration. Lack of uniform clustering within the daytime transcripts suggested that the partitioning of gene expression in Microcystis is dependent on both circadian regulation and physicochemical changes within the environment.
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Affiliation(s)
- Emily J. Davenport
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States,Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, MI, United States
| | - Michelle J. Neudeck
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States
| | - Paul G. Matson
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States
| | - George S. Bullerjahn
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States,*Correspondence: George S. Bullerjahn,
| | - Timothy W. Davis
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States
| | - Steven W. Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Maddie K. Denney
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Lauren E. Krausfeldt
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Joshua M. A. Stough
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Kevin A. Meyer
- Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, MI, United States,Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, United States
| | - Gregory J. Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, United States
| | - Thomas H. Johengen
- Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, MI, United States
| | - Erika Lindquist
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Susannah G. Tringe
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Robert Michael L. McKay
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States,Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
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Simultaneous quantification of active carbon- and nitrogen-fixing communities and estimation of fixation rates using fluorescence in situ hybridization and flow cytometry. Appl Environ Microbiol 2014; 80:6750-9. [PMID: 25172848 DOI: 10.1128/aem.01962-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Understanding the interconnectivity of oceanic carbon and nitrogen cycles, specifically carbon and nitrogen fixation, is essential in elucidating the fate and distribution of carbon in the ocean. Traditional techniques measure either organism abundance or biochemical rates. As such, measurements are performed on separate samples and on different time scales. Here, we developed a method to simultaneously quantify organisms while estimating rates of fixation across time and space for both carbon and nitrogen. Tyramide signal amplification fluorescence in situ hybridization (TSA-FISH) of mRNA for functionally specific oligonucleotide probes for rbcL (ribulose-1,5-bisphosphate carboxylase/oxygenase; carbon fixation) and nifH (nitrogenase; nitrogen fixation) was combined with flow cytometry to measure abundance and estimate activity. Cultured samples representing a diversity of phytoplankton (cyanobacteria, coccolithophores, chlorophytes, diatoms, and dinoflagellates), as well as environmental samples from the open ocean (Gulf of Mexico, USA, and southeastern Indian Ocean, Australia) and an estuary (Galveston Bay, Texas, USA), were successfully hybridized. Strong correlations between positively tagged community abundance and (14)C/(15)N measurements are presented. We propose that these methods can be used to estimate carbon and nitrogen fixation in environmental communities. The utilization of mRNA TSA-FISH to detect multiple active microbial functions within the same sample will offer increased understanding of important biogeochemical cycles in the ocean.
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Faster growth of the major prokaryotic versus eukaryotic CO2 fixers in the oligotrophic ocean. Nat Commun 2014; 5:3776. [PMID: 24777140 PMCID: PMC4015317 DOI: 10.1038/ncomms4776] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 04/01/2014] [Indexed: 01/10/2023] Open
Abstract
Because maintenance of non-scalable cellular components—membranes and chromosomes—requires an increasing fraction of energy as cell size decreases, miniaturization comes at a considerable energetic cost for a phytoplanktonic cell. Consequently, if eukaryotes can use their superior energetic resources to acquire nutrients with more or even similar efficiency compared with prokaryotes, larger unicellular eukaryotes should be able to achieve higher growth rates than smaller cyanobacteria. Here, to test this hypothesis, we directly compare the intrinsic growth rates of phototrophic prokaryotes and eukaryotes from the equatorial to temperate South Atlantic using an original flow cytometric 14CO2-tracer approach. At the ocean basin scale, cyanobacteria double their biomass twice as frequently as the picoeukaryotes indicating that the prokaryotes are faster growing CO2 fixers, better adapted to phototrophic living in the oligotrophic open ocean—the most extensive biome on Earth. After the energetically superior eukaryotes had evolved, prokaryotes appeared to lose control over biological CO2 fixation in all major biomes on Earth. Here the author shows that in the oligotrophic ocean, the most extensive biome on Earth, the prokaryotes fix CO2 twice as fast as eukaryotes.
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Tandem repeats, high copy number and remarkable diel expression rhythm of form II RuBisCO in Prorocentrum donghaiense (Dinophyceae). PLoS One 2013; 8:e71232. [PMID: 23976999 PMCID: PMC3747160 DOI: 10.1371/journal.pone.0071232] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 06/27/2013] [Indexed: 11/24/2022] Open
Abstract
Gene structure and expression regulation of form II RuBisCO (rbcII) in dinoflagellates are still poorly understood. Here we isolated this gene (Pdrbc) and investigated its diel expression pattern in a harmful algal bloom forming dinoflagellate Prorocentrum donghaiense. We obtained cDNA sequences with triple tandem repeats of the coding unit (CU); the 5′ region has the sequence of a typical dinoflagellate plastid gene, encoding an N-terminus with two transmembrane regions separated by a plastid transit peptide. The CUs (1,455 bp except 1464 bp in last CU) are connected through a 63 bp spacer. Phylogenetic analysis showed that rbcII CUs within species formed monophyletic clusters, indicative of intraspecific gene duplication or purifying evolution. Using quantitative PCR (qPCR) we estimated 117±40 CUs of Pdrbc in the P. donghaiense genome. Although it is commonly believed that most dinoflagellate genes lack transcriptional regulation, our RT-qPCR analysis on synchronized cultures revealed remarkable diel rhythm of Pdrbc expression, showing significant correlations of transcript abundance with the timing of the dark-to-light transition and cell cycle G2M-phase. When the cultures were shifted to continuous light, Pdrbc expression remained significantly correlated with the G2M-phase. Under continuous darkness the cell cycle was arrested at the G1 phase, and the rhythm of Pdrbc transcription disappeared. Our results suggest that dinoflagellate rbcII 1) undergoes duplication or sequence purification within species, 2) is organized in tandem arrays in most species probably to facilitate efficient translation and import of the encoded enzyme, and 3) is regulated transcriptionally in a cell cycle-dependent fashion at least in some dinoflagellates.
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Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana. Proc Natl Acad Sci U S A 2013; 110:7518-23. [PMID: 23596211 DOI: 10.1073/pnas.1300962110] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Marine diatoms are important primary producers that thrive in diverse and dynamic environments. They do so, in theory, by sensing changing conditions and adapting their physiology accordingly. Using the model species Thalassiosira pseudonana, we conducted a detailed physiological and transcriptomic survey to measure the recurrent transcriptional changes that characterize typical diatom growth in batch culture. Roughly 40% of the transcriptome varied significantly and recurrently, reflecting large, reproducible cell-state transitions between four principal states: (i) "dawn," following 12 h of darkness; (ii) "dusk," following 12 h of light; (iii) exponential growth and nutrient repletion; and (iv) stationary phase and nutrient depletion. Increases in expression of thousands of genes at the end of the reoccurring dark periods (dawn), including those involved in photosynthesis (e.g., ribulose-1,5-bisphosphate carboxylase oxygenase genes rbcS and rbcL), imply large-scale anticipatory circadian mechanisms at the level of gene regulation. Repeated shifts in the transcript levels of hundreds of genes encoding sensory, signaling, and regulatory functions accompanied the four cell-state transitions, providing a preliminary map of the highly coordinated gene regulatory program under varying conditions. Several putative light sensing and signaling proteins were associated with recurrent diel transitions, suggesting that these genes may be involved in light-sensitive and circadian regulation of cell state. These results begin to explain, in comprehensive detail, how the diatom gene regulatory program operates under varying environmental conditions. Detailed knowledge of this dynamic molecular process will be invaluable for new hypothesis generation and the interpretation of genetic, environmental, and metatranscriptomic data from field studies.
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Storelli N, Peduzzi S, Saad MM, Frigaard NU, Perret X, Tonolla M. CO2assimilation in the chemocline of Lake Cadagno is dominated by a few types of phototrophic purple sulfur bacteria. FEMS Microbiol Ecol 2013; 84:421-32. [DOI: 10.1111/1574-6941.12074] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 01/09/2013] [Accepted: 01/10/2013] [Indexed: 11/30/2022] Open
Affiliation(s)
| | | | - Maged M. Saad
- Department of Botany and Plant Biology, Microbiology Unit; University of Geneva, Sciences III; Geneva; Switzerland
| | - Niels-Ulrik Frigaard
- Section for Marine Biology, Department of Biology; University of Copenhagen; Helsingør; Denmark
| | - Xavier Perret
- Department of Botany and Plant Biology, Microbiology Unit; University of Geneva, Sciences III; Geneva; Switzerland
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Bird C, Wyman M. Transcriptionally active heterotrophic diazotrophs are widespread in the upper water column of the Arabian Sea. FEMS Microbiol Ecol 2012; 84:189-200. [PMID: 23210855 DOI: 10.1111/1574-6941.12049] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 11/22/2012] [Accepted: 11/25/2012] [Indexed: 11/26/2022] Open
Abstract
Pelagic nitrogen fixation makes an important contribution to the fixed nitrogen budget of the world's oceans. Filamentous and unicellular cyanobacteria are significant players in this process but less is known of the potential activity of heterotrophic diazotrophs, although they are present and can be quite numerous in the nitrogen-deplete surface waters of the tropical and sub-tropical oceans. In this study we focused on the potential activity of several clades of heterotrophic nitrogen-fixers identified by phylogenetic analysis of 44 non-Trichodesmium-related, nifH (encoding the Fe-subunit of nitrogenase) clones from the Arabian Sea. Specific Northern slot blot protocols were developed to quantify nifH mRNAs from each clade and showed that two groups of Gammaproteobacteria, including the previously characterized UMB clade, and a third, novel phylotype affiliated with cluster III anaerobes, were actively expressing nitrogenase in the equatorial waters of this region. Transcripts (nifH mRNAs) from the latter clade were particularly abundant and were also detected in the suboxic waters of the oxygen minimum zone further north. Like the gammaproteobacterial groups, nifH expression by these organisms appeared to be insensitive to combined nitrogen concentrations and was readily detected in the nutrient-replete waters below the upper mixed layer as well as at shallower depths.
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Affiliation(s)
- Clare Bird
- Biological and Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling, UK
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Temporal orchestration of glycogen synthase (GlgA) gene expression and glycogen accumulation in the oceanic picoplanktonic cyanobacterium Synechococcus sp. strain WH8103. Appl Environ Microbiol 2012; 78:4744-7. [PMID: 22522678 DOI: 10.1128/aem.00254-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glycogen is accumulated during the latter half of the diel cycle in Synechococcus sp. strain WH8103 following a midday maximum in glgA (encoding glycogen synthase) mRNA abundance. This temporal pattern is quite distinct from that of Prochlorococcus and may highlight divergent regulatory control of carbon/nitrogen metabolism in these closely related picocyanobacteria.
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Ruiz-González C, Simó R, Vila-Costa M, Sommaruga R, Gasol JM. Sunlight modulates the relative importance of heterotrophic bacteria and picophytoplankton in DMSP-sulphur uptake. ISME JOURNAL 2011; 6:650-9. [PMID: 21955992 DOI: 10.1038/ismej.2011.118] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There is a large body of evidence supporting a major role of heterotrophic bacteria in dimethylsulphoniopropionate (DMSP) utilisation as a source of reduced sulphur. However, a role for phototrophic microorganisms has been only recently described and little is known about their contribution to DMSP consumption and the potential modulating effects of sunlight. In an attempt to ascertain the relative quantitative roles of heterotrophic bacteria and picophytoplankton in the osmoheterotrophic uptake of DMSP-sulphur upon exposure to natural sunlight conditions, we incubated northwestern Mediterranean waters under various optical filters and used an array of bulk and single-cell activity methods to trace the fate of added (35)S-DMSP. Flow cytometry cell sorting confirmed dark (35)S uptake by Prochlorococcus, Synechococcus and heterotrophic bacteria, the latter being the most efficient in terms of uptake on a cell volume basis. Under exposure to full sunlight, however, the relative contribution of Synechococcus was significantly enhanced, mainly because of the inhibition of heterotrophic bacteria. Microautoradiography showed a strong increase in the proportion of Synechococcus cells actively taking up (35)S-DMSP, which, after full sunlight exposure, made up to 15% of total active Bacteria. Parallel incubations with (3)H-leucine generally showed no clear responses to light. Finally, size-fractionated assimilation experiments showed greater relative cyanobacterial assimilation during the day than at night compared with that of heterotrophic bacteria. Our results show for the first time a major influence of sunlight in regulating the competition among autotrophic and heterotrophic picoplankton for DMSP uptake at both the daily and seasonal time scales.
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10
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Levitan O, Sudhaus S, LaRoche J, Berman-Frank I. The influence of pCO2 and temperature on gene expression of carbon and nitrogen pathways in Trichodesmium IMS101. PLoS One 2010; 5:e15104. [PMID: 21151907 PMCID: PMC2997788 DOI: 10.1371/journal.pone.0015104] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 10/21/2010] [Indexed: 11/28/2022] Open
Abstract
Growth, protein amount, and activity levels of metabolic pathways in Trichodesmium are influenced by environmental changes such as elevated pCO(2) and temperature. This study examines changes in the expression of essential metabolic genes in Trichodesmium grown under a matrix of pCO(2) (400 and 900 µatm) and temperature (25 and 31°C). Using RT-qPCR, we studied 21 genes related to four metabolic functional groups: CO(2) concentrating mechanism (bicA1, bicA2, ccmM, ccmK2, ccmK3, ndhF4, ndhD4, ndhL, chpX), energy metabolism (atpB, sod, prx, glcD), nitrogen metabolism (glnA, hetR, nifH), and inorganic carbon fixation and photosynthesis (rbcL, rca, psaB, psaC, psbA). nifH and most photosynthetic genes exhibited relatively high abundance and their expression was influenced by both environmental parameters. A two to three orders of magnitude increase was observed for glnA and hetR only when both pCO(2) and temperature were elevated. CO(2) concentrating mechanism genes were not affected by pCO(2) and temperature and their expression levels were markedly lower than that of the nitrogen metabolism and photosynthetic genes. Many of the CO(2) concentrating mechanism genes were co-expressed throughout the day. Our results demonstrate that in Trichodesmium, CO(2) concentrating mechanism genes are constitutively expressed. Co-expression of genes from different functional groups were frequently observed during the first half of the photoperiod when oxygenic photosynthesis and N(2) fixation take place, pointing at the tight and complex regulation of gene expression in Trichodesmium. Here we provide new data linking environmental changes of pCO(2) and temperature to gene expression in Trichodesmium. Although gene expression indicates an active metabolic pathway, there is often an uncoupling between transcription and enzyme activity, such that transcript level cannot usually be directly extrapolated to metabolic activity.
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Affiliation(s)
- Orly Levitan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel.
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11
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Jensen SI, Steunou AS, Bhaya D, Kühl M, Grossman AR. In situ dynamics of O2, pH and cyanobacterial transcripts associated with CCM, photosynthesis and detoxification of ROS. ISME JOURNAL 2010; 5:317-28. [PMID: 20740024 DOI: 10.1038/ismej.2010.131] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The relative abundance of transcripts encoding proteins involved in inorganic carbon concentrating mechanisms (CCM), detoxification of reactive oxygen species (ROS) and photosynthesis in the thermophilic cyanobacterium Synechococcus OS-B' was measured in hot spring microbial mats over two diel cycles, and was coupled with in situ determinations of incoming irradiance and microenvironmental dynamics of O(2) and pH. Fluctuations in pH and O(2) in the mats were largely driven by the diel cycle of solar irradiance, with a pH variation from ∼7.0 to ∼9.5, and O(2) levels ranging from anoxia to supersaturation during night and day, respectively. Levels of various transcripts from mat cyanobacteria revealed several patterns that correlated with incident irradiance, O(2) and pH within the mat matrix. Transcript abundances for most genes increased during the morning dark-light transition. Some transcripts remained at a near constant level throughout the light period, whereas others showed an additional increase in abundance as the mat underwent transition from low-to-high light (potentially reflecting changes in O(2) concentration and pH), followed by either a decreased abundance in the early afternoon, or a gradual decline during the early afternoon and into the evening. One specific transcipt, psbA1, was the lowest during mid-day under high irradiance and increased when the light levels declined. We discuss these complex in situ transcriptional patterns with respect to environmental and endogenous cues that might impact and regulate transcription over the diel cycle.
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Affiliation(s)
- Sheila I Jensen
- Department of Biology, Marine Biological Laboratory, University of Copenhagen, Helsingør, Denmark.
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12
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Granum E, Roberts K, Raven JA, Leegood RC. PRIMARY CARBON AND NITROGEN METABOLIC GENE EXPRESSION IN THE DIATOM THALASSIOSIRA PSEUDONANA (BACILLARIOPHYCEAE): DIEL PERIODICITY AND EFFECTS OF INORGANIC CARBON AND NITROGEN(1). JOURNAL OF PHYCOLOGY 2009; 45:1083-92. [PMID: 27032353 DOI: 10.1111/j.1529-8817.2009.00728.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Diel periodicity and effects of inorganic carbon (Ci ) and NO3 (-) on the expression of 11 key genes for primary carbon and nitrogen metabolism, including potential C4 photosynthesis, in the marine diatom Thalassiosira pseudonana Hasle et Heimdal were investigated. Target gene transcripts were measured by quantitative reverse transcriptase-PCR, and some of the gene-encoded proteins were analyzed by Western blotting. The diatom was grown with a 12 h photoperiod at two different Ci concentrations maintained by air-equilibration with either 380 μL · L(-1) (near-ambient) or 100 μL · L(-1) (low) CO2 . Transcripts of the principal Ci and NO3 (-) assimilatory genes RUBISCO LSU (rbcL) and nitrate reductase displayed very strong diel oscillations with peaks at the end of the scotophase. Considerable diel periodicities were also exhibited by the β-carboxylase genes phosphoenolpyruvate carboxylase (PEPC1 and PEPC2) and phosphoenolpyruvate carboxykinase (PEPCK), and the Benson-Calvin cycle gene sedoheptulose-bisphosphatase (SBPase), with peaks during mid- to late scotophase. In accordance with the transcripts, there were substantial diel periodicities in PEPC1, PEPC2, PEPCK, and especially rbcL proteins, although they peaked during early to mid-photophase. Inorganic carbon had some transient effects on the β-carboxylase transcripts, and glycine decarboxylase P subunit was highly up-regulated by low Ci concentration, indicating increased capacity for photorespiration. Nitrogen-starved cells had reduced amounts of carbon metabolic gene transcripts, but the PEPC1, PEPC2, PEPCK, and rbcL transcripts increased rapidly when NO3 (-) was replenished. The results suggest that the β-carboxylases in T. pseudonana play key anaplerotic roles but show no clear support for C4 photosynthesis.
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Affiliation(s)
- Espen Granum
- Robert Hill Institute and Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UKDivision of Plant Sciences, University of Dundee at Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UKRobert Hill Institute and Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Karen Roberts
- Robert Hill Institute and Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UKDivision of Plant Sciences, University of Dundee at Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UKRobert Hill Institute and Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - John A Raven
- Robert Hill Institute and Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UKDivision of Plant Sciences, University of Dundee at Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UKRobert Hill Institute and Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Richard C Leegood
- Robert Hill Institute and Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UKDivision of Plant Sciences, University of Dundee at Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UKRobert Hill Institute and Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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John DE, Wang ZA, Liu X, Byrne RH, Corredor JE, López JM, Cabrera A, Bronk DA, Tabita FR, Paul JH. Phytoplankton carbon fixation gene (RuBisCO) transcripts and air-sea CO2 flux in the Mississippi River plume. ISME JOURNAL 2007; 1:517-31. [DOI: 10.1038/ismej.2007.70] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Bird C, Martinez Martinez J, O'Donnell AG, Wyman M. Spatial distribution and transcriptional activity of an uncultured clade of planktonic diazotrophic gamma-proteobacteria in the Arabian sea. Appl Environ Microbiol 2005; 71:2079-85. [PMID: 15812041 PMCID: PMC1082540 DOI: 10.1128/aem.71.4.2079-2085.2005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The spatial distribution of an uncultured clade of marine diazotrophic gamma-proteobacteria in the Arabian Sea was investigated by the development of a specific primer pair to amplify an internal fragment of nifH by PCR. These organisms were most readily detected in highly oligotrophic surface waters but could also be found in deeper waters below the nutricline. nifH transcripts originating from this clade were detected in oligotrophic surface waters and, in addition, in the deeper and the more productive near-coastal waters. The nifH sequences most closely related to the unidentified marine bacterial group are from environmental clones amplified from the Atlantic and Pacific Oceans. These findings suggest that these gamma-proteobacteria are widespread and likely to be an important component of the heterotrophic diazotrophic microbial community of the tropical and subtropical oceans.
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Affiliation(s)
- Clare Bird
- School of Biological and Environmental Sciences, University of Stirling, Stirling FK9 4LA United Kingdom
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15
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Wyman M, Davies JT, Hodgson S, Tarran GA, Purdie DA. Dynamics of ribulose 1,5-bisphosphate carboxylase/oxygenase gene expression in the coccolithophorid Coccolithus pelagicus during a tracer release experiment in the Northeast Atlantic. Appl Environ Microbiol 2005; 71:1659-61. [PMID: 15746374 PMCID: PMC1065161 DOI: 10.1128/aem.71.3.1659-1661.2005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report a pronounced diel rhythm in ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) gene expression in a natural population of the coccolithophorid Coccolithus pelagicus sampled during a Lagrangian experiment in the Northeast Atlantic. Our observations show that there is greater heterogeneity in the temporal regulation of RubisCO expression among planktonic chromophytes than has been reported hitherto.
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Affiliation(s)
- Michael Wyman
- School of Biological and Environmental Sciences, University of Stirling, Stirling FK9 4LA, United Kingdom.
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16
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Nanba K, King GM, Dunfield K. Analysis of facultative lithotroph distribution and diversity on volcanic deposits by use of the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase. Appl Environ Microbiol 2004; 70:2245-53. [PMID: 15066819 PMCID: PMC383153 DOI: 10.1128/aem.70.4.2245-2253.2004] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A 492- to 495-bp fragment of the gene coding for the large subunit of the form I ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) (rbcL) was amplified by PCR from facultatively lithotrophic aerobic CO-oxidizing bacteria, colorless and purple sulfide-oxidizing microbial mats, and genomic DNA extracts from tephra and ash deposits from Kilauea volcano, for which atmospheric CO and hydrogen have been previously documented as important substrates. PCR products from the mats and volcanic sites were used to construct rbcL clone libraries. Phylogenetic analyses showed that the rbcL sequences from all isolates clustered with form IC rbcL sequences derived from facultative lithotrophs. In contrast, the microbial mat clone sequences clustered with sequences from obligate lithotrophs representative of form IA rbcL. Clone sequences from volcanic sites fell within the form IC clade, suggesting that these sites were dominated by facultative lithotrophs, an observation consistent with biogeochemical patterns at the sites. Based on phylogenetic and statistical analyses, clone libraries differed significantly among volcanic sites, indicating that they support distinct lithotrophic assemblages. Although some of the clone sequences were similar to known rbcL sequences, most were novel. Based on nucleotide diversity and average pairwise difference, a forested site and an 1894 lava flow were found to support the most diverse and least diverse lithotrophic populations, respectively. These indices of diversity were not correlated with rates of atmospheric CO and hydrogen uptake but were correlated with estimates of respiration and microbial biomass.
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Affiliation(s)
- K Nanba
- Laboratory of Aquatic Biology and Environmental Science, Graduate School of Agricultural Life Sciences, University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
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Bird C, Wyman M. Nitrate/nitrite assimilation system of the marine picoplanktonic cyanobacterium Synechococcus sp. strain WH 8103: effect of nitrogen source and availability on gene expression. Appl Environ Microbiol 2004; 69:7009-18. [PMID: 14660343 PMCID: PMC310010 DOI: 10.1128/aem.69.12.7009-7018.2003] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genes encoding the structural components of the nitrate/nitrite assimilation system of the oceanic cyanobacterium Synechococcus sp. strain WH 8103 were cloned and characterized. The genes encoding nitrate reductase (narB) and nitrite reductase (nirA) are clustered on the chromosome but are organized in separate transcriptional units. Upstream of narB is a homologue of nrtP that encodes a nitrate/nitrite-bispecific permease rather than the components of an ABC-type nitrate transporter found in freshwater cyanobacteria. Unusually, neither nirA nor ntcA (encoding a positive transcription factor of genes subject to nitrogen control) were found to be tightly regulated by ammonium. Furthermore, transcription of glnA (encoding glutamine synthetase) is up-regulated in ammonium-grown cells, highlighting significant differences in nitrogen control in this cyanobacterium. Nitrogen depletion led to the transient up-regulation of ntcA, nirA, nrtP, narB, and glnA in what appears to be an NtcA-dependent manner. The NtcA-like promoters found upstream of nirA, nrtP, and narB all differ in sequence from the canonical NtcA promoter established for other cyanobacteria, and in the case of nirA, the NtcA-like promoter was functional only in cells deprived of combined nitrogen. The ecological implications of these findings are discussed in the context of the oligotrophic nature of oceanic surface waters in which Synechococcus spp. thrive.
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Affiliation(s)
- Clare Bird
- School of Biological and Environmental Sciences, University of Stirling, Stirling FK9 4LA, United Kingdom
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El Alaoui S, Diez J, Toribio F, Gómez-Baena G, Dufresne A, García-Fernández JM. Glutamine synthetase from the marine cyanobacteria Prochlorococcus spp: characterization, phylogeny and response to nutrient limitation. Environ Microbiol 2003; 5:412-23. [PMID: 12713467 DOI: 10.1046/j.1462-2920.2003.00433.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The regulation of glutamine synthetase (EC 6.3.1.2) from Prochlorococcus was previously shown to exhibit unusual features: it is not upregulated by nitrogen starvation and it is not inactivated by darkness (El Alaoui et al. (2001) Appl Environ Microbiol 67: 2202-2207). These are probably caused by adaptations to oligotrophic environments, as confirmed in this work by the marked decrease in the enzymatic activity when cultures were subjected to iron or phosphorus starvation. In order to further understand the adaptive features of ammonium assimilation in this cyanobacterium, glutamine synthetase was purified from two Prochlorococcus strains: PCC 9511 (high-light adapted) and SS120 (low-light adapted). We obtained approximately 100-fold purified samples of glutamine synthetase electrophoretically homogeneous, with a yield of approximately 30%. The estimated molecular mass of the subunits was roughly the same for both strains: 48.3 kDa. The apparent Km constants for the biosynthetic activity were 0.30 mM for ammonium, 1.29 mM for glutamate and 1.35 mM for ATP; the optimum pH was 8.0. Optimal temperature was surprisingly high (55 degrees C). Phylogenetic analysis of glnA from three Prochlorococcus strains (MED4, MIT9313 and SS120) showed they group closely with marine Synechococcus isolates, in good agreement with other studies based on 16 S RNA sequences. All of our results suggest that the structure and kinetics of glutamine synthetase in Prochlorococcus have not been significantly modified during the evolution within the cyanobacterial radiation, in sharp contrast with its regulatory properties.
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Affiliation(s)
- Sabah El Alaoui
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, planta 1, Campus de Rabanales, 14071-Córdoba, Spain
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19
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Gillor O, Harush A, Hadas O, Post AF, Belkin S. A Synechococcus PglnA::luxAB fusion for estimation of nitrogen bioavailability to freshwater cyanobacteria. Appl Environ Microbiol 2003; 69:1465-74. [PMID: 12620830 PMCID: PMC150075 DOI: 10.1128/aem.69.3.1465-1474.2003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2002] [Accepted: 11/26/2002] [Indexed: 11/20/2022] Open
Abstract
In contrast to extensive studies of phosphorus, widely considered the main nutrient limiting phytoplankton biomass in freshwater ecosystems, there have been few studies on the role of nitrogen in controlling phytoplankton populations. This situation may be due partly to the complexity in estimating its utilization and bioavailability. In an attempt to provide a novel tool for this purpose, we fused the promoter of the glutamine synthetase-encoding gene, P glnA, from Synechococcus sp. strain PCC7942 to the luxAB luciferase-encoding genes of the bioluminescent bacterium Vibrio harveyi. The resulting construct was introduced into a neutral site on the Synechococcus chromosome to yield the reporter strain GSL. Light emission by this strain was dependent upon ambient nitrogen concentrations. The linear response range of the emitted luminescence was 1 mM to 1 micro M for the inorganic nitrogen species tested (ammonium, nitrate, and nitrite) and 10- to 50-fold lower for glutamine and urea. When water samples collected from along a depth profile in Lake Kinneret (Israel) were exposed to the reporter strain, the bioluminescence of the reporter strain mirrored the total dissolved nitrogen concentrations determined for the same samples and was shown to be a sensitive indicator of the concentration of bioavailable nitrogen.
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Affiliation(s)
- Osnat Gillor
- Environmental Sciences, The Fredy and Nadin Herrmann Graduate School of Applied Science, The Hebrew University, Jerusalem 91904, Israel
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Abstract
During the twenty years or so since the discovery of tiny photosynthetic cells of the genus Synechococcus in marine oceanic systems, a tremendous expansion of interest has been seen in the literature pertaining to these organisms. The fact that they are ubiquitous and abundant in major oceanic regimes underlies their ecological importance as significant contributors to marine C fixation. Recent advances in the physiology and biochemistry of these organisms are presented here, focusing on strains of the MC-A and MC-B clusters; it is stressed that the data contained herein should be put into the context of the ecological niche occupied by particular genotypes in situ. This system is ripe for joining the often separate disciplines of molecular ecology and microbial physiology and provides a great opportunity to tease out the underlying processes that both mediate organism evolution and also the environmental factors that dictate this.
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Affiliation(s)
- David J Scanlan
- Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
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Wawrik B, Paul JH, Tabita FR. Real-time PCR quantification of rbcL (ribulose-1,5-bisphosphate carboxylase/oxygenase) mRNA in diatoms and pelagophytes. Appl Environ Microbiol 2002; 68:3771-9. [PMID: 12147471 PMCID: PMC123995 DOI: 10.1128/aem.68.8.3771-3779.2002] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptional activity is often used as a surrogate for gene expression in environmental microbial communities. We developed a real-time PCR assay in which the ABI-Prism (PE Applied Biosystems) detection system is used for quantification of large-subunit ribulose-1,5-bisphosphate caboxylase/oxygenase (rbcL) mRNA in diatoms and pelagophytes both in cultures and from natural phytoplankton communities. Plasmid DNA containing rbcL inserts, as well as in vitro transcribed mRNA of the plasmids, was used to generate standard curves with a dynamic range of more than 6 orders of magnitude with high accuracy and precision (R(2) = 0.998). Expression levels in a cultured diatom (Phaeodactylum tricornutum) were quantified through one light-dark cycle by using traditional 35S-labeled oligonucleotide hybridization and real-time PCR. The mRNA levels detected by the two techniques were similar and correlated well (R(2) = 0.95; slope = 1.2). The quantities obtained by hybridization were slightly, yet significantly, larger (t = 5.29; P = 0.0011) than the quantities obtained by real-time PCR. This was most likely because partially degraded transcripts were not detected by real-time PCR. rbcL mRNA detection by real-time PCR was 3 orders of magnitude more sensitive than rbcL mRNA detection by hybridization. Diatom and pelagophyte rbcL mRNAs were also quantified in a profile from an oligotrophic site in the Gulf of Mexico. We detected the smallest amount of diatom rbcL expression in the surface water and maximum expression at a depth that coincided with the depth of the subsurface chlorophyll maximum. These results indicate that real-time PCR may be utilized for quantification of microbial gene expression in the environment.
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Affiliation(s)
- B Wawrik
- College of Marine Science, University of South Florida, St. Petersburg, Florida 33701, USA
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22
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Paul JH. Gene expression by mRNA analysis. METHODS IN MICROBIOLOGY 2001. [DOI: 10.1016/s0580-9517(01)30055-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Wyman M, Davies JT, Crawford DW, Purdie DA. Molecular and physiological responses of two classes of marine chromophytic phytoplankton (Diatoms and prymnesiophytes) during the development of nutrient-stimulated blooms. Appl Environ Microbiol 2000; 66:2349-57. [PMID: 10831410 PMCID: PMC110529 DOI: 10.1128/aem.66.6.2349-2357.2000] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Generic taxon-specific DNA probes that target an internal region of the gene (rbcL) encoding the large subunit of ribulose-1, 5-bisphosphate carboxylase/oxygenase (RubisCO) were developed for two groups of marine phytoplankton (diatoms and prymnesiophytes). The specificity and utility of the probes were evaluated in the laboratory and also during a 1-month mesocosm experiment in which we investigated the temporal variability in RubisCO gene expression and primary production in response to inorganic nutrient enrichment. We found that the onset of successive bloom events dominated by each of the two classes of chromophyte algae was associated with marked taxon-specific increases in rbcL transcription rates. These observations suggest that measurements of RubisCO gene expression can provide an early indicator of the development of phytoplankton blooms and may also be useful in predicting which taxa are likely to dominate a bloom.
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Affiliation(s)
- M Wyman
- Department of Biological Sciences, University of Stirling, Stirling FK9 4LA, United Kingdom.
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