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Gately JA, Kim SM, Jin B, Brzezinski MA, Iglesias-Rodriguez MD. Coccolithophores and diatoms resilient to ocean alkalinity enhancement: A glimpse of hope? Sci Adv 2023; 9:eadg6066. [PMID: 37315127 DOI: 10.1126/sciadv.adg6066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/09/2023] [Indexed: 06/16/2023]
Abstract
It is increasingly apparent that adequately mitigating anthropogenic climate interference will require ocean carbon dioxide removal (CDR) strategies. Ocean alkalinity enhancement (OAE) is an abiotic ocean CDR approach that aims to increase the ocean's CO2 uptake capacity through the dispersal of pulverized mineral or dissolved alkali into the surface ocean. However, OAE's effect on marine biota is largely unexplored. Here, we investigate the impacts of moderate (~700 μmol kg-1) and high (~2700 μmol kg-1) limestone-inspired alkalinity additions on two biogeochemically and ecologically important phytoplankton functional group representatives: Emiliania huxleyi (calcium carbonate producer) and Chaetoceros sp. (silica producer). The growth rate and elemental ratios of both taxa showed a neutral response to limestone-inspired alkalinization. While our results are encouraging, we also observed abiotic mineral precipitation, which removed nutrients and alkalinity from solution. Our findings offer an evaluation of biogeochemical and physiological responses to OAE and provide evidence supporting the need for continued research into how OAE strategies affect marine ecosystems.
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Affiliation(s)
- James A Gately
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara; Santa Barbara, CA 93106, USA
- Marine Science Institute, University of California, Santa Barbara, CA 93106, USA
| | - Sylvia M Kim
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara; Santa Barbara, CA 93106, USA
- Marine Science Institute, University of California, Santa Barbara, CA 93106, USA
| | - Benjamin Jin
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara; Santa Barbara, CA 93106, USA
| | - Mark A Brzezinski
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara; Santa Barbara, CA 93106, USA
- Marine Science Institute, University of California, Santa Barbara, CA 93106, USA
| | - Maria D Iglesias-Rodriguez
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara; Santa Barbara, CA 93106, USA
- Marine Science Institute, University of California, Santa Barbara, CA 93106, USA
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Maniscalco MA, Brzezinski MA, Lampe RH, Cohen NR, McNair HM, Ellis KA, Brown M, Till CP, Twining BS, Bruland KW, Marchetti A, Thamatrakoln K. Diminished carbon and nitrate assimilation drive changes in diatom elemental stoichiometry independent of silicification in an iron-limited assemblage. ISME Commun 2022; 2:57. [PMID: 37938259 PMCID: PMC9723790 DOI: 10.1038/s43705-022-00136-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/12/2022] [Accepted: 06/09/2022] [Indexed: 06/17/2023]
Abstract
In the California Current Ecosystem, upwelled water low in dissolved iron (Fe) can limit phytoplankton growth, altering the elemental stoichiometry of the particulate matter and dissolved macronutrients. Iron-limited diatoms can increase biogenic silica (bSi) content >2-fold relative to that of particulate organic carbon (C) and nitrogen (N), which has implications for carbon export efficiency given the ballasted nature of the silica-based diatom cell wall. Understanding the molecular and physiological drivers of this altered cellular stoichiometry would foster a predictive understanding of how low Fe affects diatom carbon export. In an artificial upwelling experiment, water from 96 m depth was incubated shipboard and left untreated or amended with dissolved Fe or the Fe-binding siderophore desferrioxamine-B (+DFB) to induce Fe-limitation. After 120 h, diatoms dominated the communities in all treatments and displayed hallmark signatures of Fe-limitation in the +DFB treatment, including elevated particulate Si:C and Si:N ratios. Single-cell, taxon-resolved measurements revealed no increase in bSi content during Fe-limitation despite higher transcript abundance of silicon transporters and silicanin-1. Based on these findings we posit that the observed increase in bSi relative to C and N was primarily due to reductions in C fixation and N assimilation, driven by lower transcript expression of key Fe-dependent genes.
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Affiliation(s)
- Michael A Maniscalco
- Marine Science Institute and The Department of Ecology Evolution and Marine Biology, University of California, Santa Barbara, CA, USA.
| | - Mark A Brzezinski
- Marine Science Institute and The Department of Ecology Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Robert H Lampe
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Natalie R Cohen
- Skidaway Institute of Oceanography, University of Georgia, Savannah, GA, USA
| | - Heather M McNair
- University of Rhode Island, Graduate School of Oceanography, Narragansett, RI, USA
| | - Kelsey A Ellis
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | | | - Claire P Till
- Chemistry Department, California State Polytechnic University, Humboldt, Arcata, CA, USA
| | | | - Kenneth W Bruland
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA
| | - Adrian Marchetti
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, USA
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McNair HM, Brzezinski MA, Krause JW. Diatom populations in an upwelling environment decrease silica content to avoid growth limitation. Environ Microbiol 2018; 20:4184-4193. [PMID: 30253028 DOI: 10.1111/1462-2920.14431] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 11/30/2022]
Abstract
A mix of adaptive strategies enable diatoms to sustain rapid growth in dynamic ocean regions, making diatoms one of the most productive primary producers in the world. We illustrate one such strategy off coastal California that facilitates continued, high, cell division rates despite silicic acid stress. Using a fluorescent dye to measure single-cell diatom silica production rates, silicification (silica per unit area) and growth rates we show diatoms decrease silicification and maintain growth rate when silicon concentration limits silica production rates. While this physiological response to silicon stress was similar across taxa, in situ silicic acid concentration limited silica production rates by varying degrees for taxa within the same community. Despite this variability among taxa, silicon stress did not alter the contribution of specific taxa to total community silica production or to community composition. Maintenance of division rate at the expense of frustule thickness decreases cell density which could affect regional biogeochemical cycles. The reduction in frustule silicification also creates an ecological tradeoff: thinner frustules increase susceptibility to predation but reducing Si quotas maximizes cell abundance for a given pulse of silicic acid, thereby favouring a larger eventual population size which facilitates diatom persistence in habitats with pulsed resource supplies.
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Affiliation(s)
- Heather M McNair
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Mark A Brzezinski
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA.,Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Jeffrey W Krause
- Dauphin Island Sea Lab, University of South Alabama, Mobile, AL, USA.,Department of Marine Sciences, University of South Alabama, Mobile, AL, USA
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Lampe RH, Cohen NR, Ellis KA, Bruland KW, Maldonado MT, Peterson TD, Till CP, Brzezinski MA, Bargu S, Thamatrakoln K, Kuzminov FI, Twining BS, Marchetti A. Divergent gene expression among phytoplankton taxa in response to upwelling. Environ Microbiol 2018; 20:3069-3082. [DOI: 10.1111/1462-2920.14361] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/15/2018] [Accepted: 07/16/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Robert H. Lampe
- Department of Marine Sciences; University of North Carolina at Chapel Hill; Chapel Hill NC USA
| | - Natalie R. Cohen
- Department of Marine Sciences; University of North Carolina at Chapel Hill; Chapel Hill NC USA
| | - Kelsey A. Ellis
- Department of Marine Sciences; University of North Carolina at Chapel Hill; Chapel Hill NC USA
| | - Kenneth W. Bruland
- Department of Ocean Sciences; University of California; Santa Cruz CA USA
| | - Maria T. Maldonado
- Department of Earth, Ocean, and Atmospheric Sciences; University of British Columbia; Vancouver BC Canada
| | - Tawnya D. Peterson
- Institute of Environmental Health, Oregon Health & Science University; Portland OR USA
| | - Claire P. Till
- Department of Ocean Sciences; University of California; Santa Cruz CA USA
- Department of Chemistry; Humboldt State University; Arcata CA USA
| | - Mark A. Brzezinski
- The Marine Science Institute and the Department of Ecology Evolution and Marine Biology; University of California; Santa Barbara CA USA
| | - Sibel Bargu
- Department of Oceanography and Coastal Sciences, School of the Coast and Environment; Louisiana State University; Baton Rouge LA USA
| | - Kimberlee Thamatrakoln
- Department of Marine and Coastal Sciences, Rutgers; the State University of New Jersey; New Brunswick NJ USA
| | - Fedor I Kuzminov
- Department of Marine and Coastal Sciences, Rutgers; the State University of New Jersey; New Brunswick NJ USA
| | | | - Adrian Marchetti
- Department of Marine Sciences; University of North Carolina at Chapel Hill; Chapel Hill NC USA
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McNair HM, Brzezinski MA, Till CP, Krause JW. Taxon-specific contributions to silica production in natural diatom assemblages. Limnol Oceanogr 2018; 63:1056-1075. [PMID: 29937577 PMCID: PMC6007990 DOI: 10.1002/lno.10754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The metabolic activity and growth of phytoplankton taxa drives their ecological function and contribution to biogeochemical processes. We present the first quantitative, taxon-resolved silica production rates, growth rates, and silica content estimates for co-occurring diatoms along two cross-shelf transects off the California coast using the fluorescent tracer PDMPO (2-(4-pyridyl)-5-((4-(2-dimethylaminoethylaminocarbamoyl)methoxy)phenyl)oxazole), and confocal microscopy. Taxon contribution to total diatom community silica production was predominantly a function of the surface area of new frustule that each taxon created as opposed to cell abundance or frustule thickness. The influential role of surface area made large diatoms disproportionately important to community silica production over short time scales (<1 d). In some cases, large taxa that comprised only ~15% of numerical cell abundance accounted for over 50% of total community silica production. Over longer time scales relevant to bloom dynamics, the importance of surface area declines and growth rate becomes the dominant influence on contribution to production. The relative importance of surface area and growth rate in relation to silica production was modeled as the time needed for a smaller, faster-growing taxon to create more surface area than a larger, slower-growing taxon. Differences in growth rate between the taxa effected the model outcome more than differences in surface area. Shifts in relative silica production among taxa are time restricted by finite resources that limit the duration of a bloom. These patterns offer clues as to how taxa respond to their environment and the consequences for both species succession and the potential diatom contribution to elemental cycling.
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Affiliation(s)
- Heather M McNair
- Department of Ecology Evolution and Marine Biology, University of California, Santa Barbara, California, United States of America
| | - Mark A Brzezinski
- Department of Ecology Evolution and Marine Biology, University of California, Santa Barbara, California, United States of America
- Marine Science Institute, University of California, Santa Barbara, California, United States of America
| | - Claire P Till
- Chemistry Department, Humboldt State University, Arcata, California, United States of America
| | - Jeffrey W Krause
- Marine Science Institute, University of California, Santa Barbara, California, United States of America
- Dauphin Island Sea Lab, Dauphin Island, Alabama, United States of America
- Department of Marine Sciences, University of South Alabama, Mobile, Alabama, United States of America
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Brzezinski MA, Krause JW, Baines SB, Collier JL, Ohnemus DC, Twining BS. Patterns and regulation of silicon accumulation in Synechococcus spp. J Phycol 2017; 53:746-761. [PMID: 28457002 DOI: 10.1111/jpy.12545] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 04/18/2017] [Indexed: 06/07/2023]
Abstract
Six clones of the marine cyanobacterium Synechococcus, representing four major clades, were all found to contain significant amounts of silicon in culture. Growth rate was unaffected by silicic acid, Si(OH)4 , concentration between 1 and 120 μM suggesting that Synechococcus lacks an obligate need for silicon (Si). Strains contained two major pools of Si: an aqueous soluble and an aqueous insoluble pool. Soluble pool sizes correspond to estimated intracellular dissolved Si concentrations of 2-24 mM, which would be thermodynamically unstable implying the binding of intracellular soluble Si to organic ligands. The Si content of all clones was inversely related to growth rate and increased with higher [Si(OH)4 ] in the growth medium. Accumulation rates showed a unique bilinear response to increasing [Si(OH)4 ] from 1 to 500 μM with the rate of Si acquisition increasing abruptly between 80 and 100 μM Si(OH)4 . Although these linear responses imply some form of diffusion-mediated transport, Si uptake rates at low Si (~1 μM Si) were inhibited by orthophosphate, suggesting a role of phosphate transporters in Si acquisition. Theoretical calculations imply that observed Si acquisition rates are too rapid to be supported by lipid-solubility diffusion of Si through the plasmalemma; however, facilitated diffusion involving membrane protein channels may suffice. The data are used to construct a working model of the mechanisms governing the Si content and rate of Si acquisition in Synechococcus.
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Affiliation(s)
- Mark A Brzezinski
- Marine Science Institute and the Department of Ecology Evolution and Marine Biology, University of California, Santa Barbara, California, USA
| | - Jeffrey W Krause
- Dauphin Island Sea Lab, Dauphin Island, Alabama, USA
- Department of Marine Sciences, University of South Alabama, Mobile, Alabama, USA
| | - Stephen B Baines
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Jackie L Collier
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Daniel C Ohnemus
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
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James AK, Passow U, Brzezinski MA, Parsons RJ, Trapani JN, Carlson CA. Elevated pCO2 enhances bacterioplankton removal of organic carbon. PLoS One 2017; 12:e0173145. [PMID: 28257422 PMCID: PMC5336268 DOI: 10.1371/journal.pone.0173145] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 02/15/2017] [Indexed: 12/01/2022] Open
Abstract
Factors that affect the removal of organic carbon by heterotrophic bacterioplankton can impact the rate and magnitude of organic carbon loss in the ocean through the conversion of a portion of consumed organic carbon to CO2. Through enhanced rates of consumption, surface bacterioplankton communities can also reduce the amount of dissolved organic carbon (DOC) available for export from the surface ocean. The present study investigated the direct effects of elevated pCO2 on bacterioplankton removal of several forms of DOC ranging from glucose to complex phytoplankton exudate and lysate, and naturally occurring DOC. Elevated pCO2 (1000–1500 ppm) enhanced both the rate and magnitude of organic carbon removal by bacterioplankton communities compared to low (pre-industrial and ambient) pCO2 (250 –~400 ppm). The increased removal was largely due to enhanced respiration, rather than enhanced production of bacterioplankton biomass. The results suggest that elevated pCO2 can increase DOC consumption and decrease bacterioplankton growth efficiency, ultimately decreasing the amount of DOC available for vertical export and increasing the production of CO2 in the surface ocean.
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Affiliation(s)
- Anna K. James
- Marine Science Institute, Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California, United States of America
- * E-mail:
| | - Uta Passow
- Marine Science Institute, Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California, United States of America
| | - Mark A. Brzezinski
- Marine Science Institute, Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California, United States of America
| | | | | | - Craig A. Carlson
- Marine Science Institute, Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California, United States of America
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Abstract
Diatoms require silicic acid to construct ornately detailed cell walls called frustules. The growth and geographic distribution of diatoms is often controlled by the availability of silicic acid. Analytical methods exist to assess diatom community biogenic silica (bSiO2) production, but partitioning production among taxa has been largely qualitative. We present a method for the quantitative analysis of taxa-specific silica production through labeling diatoms with the fluorescent dye PDMPO [2-(4-pyridyl)-5-((4-(2-dimethylaminoethylaminocarbamoyl)methoxy)phenyl)oxazole]. To make PDMPO a quantitative tool: diatom frustules were solubilized to assess the total diatom community incorporation by quantitation of PDMPO fluorescence using a fluorometer, and laser confocal microscopy was used to quantify the fluorescence of PDMPO in single diatom cells. We created a fluorescence standard to intercalibrate the raw fluorescence signals of the fluorometer and microscope and to determine the fluorescence per mole of PDMPO. PDMPO incorporation was converted to silica production using diatom bSiO2:PDMPO incorporation ratios which varied systematically with silicic acid concentration. Above 3 μM Si(OH)4, bSiO2:PDMPO was constant and PDMPO incorporation was converted to silica production using a mole ratio of 2,916 as determined from cultures. Below 3 μM, the ratio was a linear function of [Si(OH)4] (bSiO2:PDMPO = 912.6 × [Si(OH)4]), as determined using data from two oceanographic cruises. Field evaluation of the method showed that total community PDMPO incorporation generally agreed to within 30% of radioisotope-determined silica production. This PDMPO method has the potential to be a powerful tool for understanding physiology, silicification and resource competition among diatom taxa.
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Affiliation(s)
- Heather M. McNair
- Department of Ecology Evolution and Marine Biology, University of
California, Santa Barbara, California 93106, United States of America
| | - Mark A. Brzezinski
- Department of Ecology Evolution and Marine Biology, University of
California, Santa Barbara, California 93106, United States of America
- Marine Science Institute, University of California, Santa Barbara,
California 93106, United States of America
| | - Jeffrey W. Krause
- Marine Science Institute, University of California, Santa Barbara,
California 93106, United States of America
- Dauphin Island Sea Lab, Dauphin Island, Alabama 36528, United States
of America
- Department of Marine Sciences, University of South Alabama, Mobile,
Alabama 36688, United States of America
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Brzezinski MA, Washburn L. Phytoplankton primary productivity in the Santa Barbara Channel: Effects of wind-driven upwelling and mesoscale eddies. ACTA ACUST UNITED AC 2011. [DOI: 10.1029/2011jc007397] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
Marine macroalgae are believed to be among the most productive autotrophs in the world. However, relatively little information exists about spatial and temporal variation in net primary production (NPP) by these organisms. The data presented here are being collected to investigate patterns and causes of variation in NPP by the giant kelp, Macrocystis pyrifera, which is believed to be one of the fastest growing autotrophs on earth. The standing crop and loss rates of M. pyrifera have been measured monthly in permanent plots at three sites in the Santa Barbara Channel, USA. Collection of these data began in June 2002 and is ongoing. Seasonal estimates of NPP and growth rate are made by combining the field data with a model of kelp dynamics. The purpose of this Data Paper is to make available a time series of M. pyrifera NPP, growth, and standing crop that is appropriate for examining seasonal and interannual patterns across multiple sites. Data on plant density in each plot and censuses of fronds on tagged plants at each site are also made available here. NPP, mass-specific growth rate, and standing crop are presented in four different metrics (wet mass, dry mass, carbon mass, and nitrogen mass) to facilitate comparisons with previous studies of M. pyrifera and with NPP measured in other ecosystems. Analyses of these data reveal seasonal cycles in growth and standing crop as well as substantial differences in M. pyrifera NPP among sites and years.
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Affiliation(s)
- Andrew Rassweiler
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California 93106, USA.
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Anderson CR, Siegel DA, Brzezinski MA, Guillocheau N. Controls on temporal patterns in phytoplankton community structure in the Santa Barbara Channel, California. ACTA ACUST UNITED AC 2008. [DOI: 10.1029/2007jc004321] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Brzezinski MA, Jones JL, Beucher CP, Demarest MS, Berg HL. Automated Determination of Silicon Isotope Natural Abundance by the Acid Decomposition of Cesium Hexafluosilicate. Anal Chem 2006; 78:6109-14. [PMID: 16944891 DOI: 10.1021/ac0606406] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A procedure for the automated determination of isotopic abundances of silicon from biogenic and lithogenic particulate matter and from dissolved silicon in fresh or saltwaters is reported. Samples are purified using proven procedures through the reaction of Si with acidified ammonium molybdate, followed by precipitation with triethylamine and combustion of the precipitate to yield silicon dioxide. The silicon dioxide is converted to cesium hexafluosilicate by dissolution in hydrogen fluoride and the addition of cesium chloride. Isotopic analysis is accomplished by decomposing the cesium hexafluosilicate with concentrated sulfuric acid to generate silicon tetrafluoride gas. Silicon tetrafluoride is purified cryogenically and analyzed on a gas source isotope ratio mass spectrometer. Yields of silicon tetrafluoride are >99.5%. The procedure can be automated by modifying commercial inlet systems designed for carbonate analysis. The procedure is free of memory effects and isotopic biases. Reproducibility is +/-0.03-0.10 per thousand for a variety of natural and synthetic materials.
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Affiliation(s)
- Mark A Brzezinski
- Marine Science Institute and the Department of Ecology Evolution and Marine Biology, University of California-Santa Barbara, Santa Barbara, CA 93106, USA.
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Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt KE, Bechner M, Brzezinski MA, Chaal BK, Chiovitti A, Davis AK, Demarest MS, Detter JC, Glavina T, Goodstein D, Hadi MZ, Hellsten U, Hildebrand M, Jenkins BD, Jurka J, Kapitonov VV, Kröger N, Lau WWY, Lane TW, Larimer FW, Lippmeier JC, Lucas S, Medina M, Montsant A, Obornik M, Parker MS, Palenik B, Pazour GJ, Richardson PM, Rynearson TA, Saito MA, Schwartz DC, Thamatrakoln K, Valentin K, Vardi A, Wilkerson FP, Rokhsar DS. The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism. Science 2004; 306:79-86. [PMID: 15459382 DOI: 10.1126/science.1101156] [Citation(s) in RCA: 1158] [Impact Index Per Article: 57.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for approximately 20% of global carbon fixation. We report the 34 million-base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair plastid and 44 thousand-base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.
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Coale KH, Johnson KS, Chavez FP, Buesseler KO, Barber RT, Brzezinski MA, Cochlan WP, Millero FJ, Falkowski PG, Bauer JE, Wanninkhof RH, Kudela RM, Altabet MA, Hales BE, Takahashi T, Landry MR, Bidigare RR, Wang X, Chase Z, Strutton PG, Friederich GE, Gorbunov MY, Lance VP, Hilting AK, Hiscock MR, Demarest M, Hiscock WT, Sullivan KF, Tanner SJ, Gordon RM, Hunter CN, Elrod VA, Fitzwater SE, Jones JL, Tozzi S, Koblizek M, Roberts AE, Herndon J, Brewster J, Ladizinsky N, Smith G, Cooper D, Timothy D, Brown SL, Selph KE, Sheridan CC, Twining BS, Johnson ZI. Southern Ocean Iron Enrichment Experiment: Carbon Cycling in High- and Low-Si Waters. Science 2004; 304:408-14. [PMID: 15087542 DOI: 10.1126/science.1089778] [Citation(s) in RCA: 465] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The availability of iron is known to exert a controlling influence on biological productivity in surface waters over large areas of the ocean and may have been an important factor in the variation of the concentration of atmospheric carbon dioxide over glacial cycles. The effect of iron in the Southern Ocean is particularly important because of its large area and abundant nitrate, yet iron-enhanced growth of phytoplankton may be differentially expressed between waters with high silicic acid in the south and low silicic acid in the north, where diatom growth may be limited by both silicic acid and iron. Two mesoscale experiments, designed to investigate the effects of iron enrichment in regions with high and low concentrations of silicic acid, were performed in the Southern Ocean. These experiments demonstrate iron's pivotal role in controlling carbon uptake and regulating atmospheric partial pressure of carbon dioxide.
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Affiliation(s)
- Kenneth H Coale
- Moss Landing Marine Laboratories, 8272 Moss Landing Road, Moss Landing, CA 95039-9647, USA.
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Gebeshuber IC, Kindt JH, Thompson JB, Del Amo Y, Stachelberger H, Brzezinski MA, Stucky GD, Morse DE, Hansma PK. Atomic force microscopy study of living diatoms in ambient conditions. J Microsc 2004; 212:292-9. [PMID: 14629555 DOI: 10.1111/j.1365-2818.2003.01275.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We present the first in vivo study of diatoms using atomic force microscopy (AFM). Three chain-forming, benthic freshwater species -Eunotia sudetica, Navicula seminulum and a yet unidentified species - are directly imaged while growing on glass slides. Using the AFM, we imaged the topography of the diatom frustules at the nanometre range scale and we determined the thickness of the organic case enveloping the siliceous skeleton of the cell (10 nm). Imaging proved to be stable for several hours, thereby offering the possibility to study long-term dynamic changes, such as biomineralization or cell movement, as they occur. We also focused on the natural adhesives produced by these unicellular organisms to adhere to other cells or the substratum. Most man-made adhesives fail in wet conditions, owing to chemical modification of the adhesive or its substrate. Diatoms produce adhesives that are extremely strong and robust both in fresh- and in seawater environments. Our phase-imaging and force-pulling experiments reveal the characteristics of these natural adhesives that might be of use in designing man-made analogues that function in wet environments. Engineering stable underwater adhesives currently poses a major technical challenge.
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Affiliation(s)
- I C Gebeshuber
- Austrian Center of Competence for Tribology AC 2T Research GmbH, Viktor-Kaplan-Strasse 2, A-2700 Wiener Neustadt, Austria.
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Sarmiento JL, Gruber N, Brzezinski MA, Dunne JP. High-latitude controls of thermocline nutrients and low latitude biological productivity. Nature 2004; 427:56-60. [PMID: 14702082 DOI: 10.1038/nature02127] [Citation(s) in RCA: 154] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2003] [Accepted: 10/08/2003] [Indexed: 11/08/2022]
Abstract
The ocean's biological pump strips nutrients out of the surface waters and exports them into the thermocline and deep waters. If there were no return path of nutrients from deep waters, the biological pump would eventually deplete the surface waters and thermocline of nutrients; surface biological productivity would plummet. Here we make use of the combined distributions of silicic acid and nitrate to trace the main nutrient return path from deep waters by upwelling in the Southern Ocean and subsequent entrainment into subantarctic mode water. We show that the subantarctic mode water, which spreads throughout the entire Southern Hemisphere and North Atlantic Ocean, is the main source of nutrients for the thermocline. We also find that an additional return path exists in the northwest corner of the Pacific Ocean, where enhanced vertical mixing, perhaps driven by tides, brings abyssal nutrients to the surface and supplies them to the thermocline of the North Pacific. Our analysis has important implications for our understanding of large-scale controls on the nature and magnitude of low-latitude biological productivity and its sensitivity to climate change.
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Affiliation(s)
- J L Sarmiento
- Atmospheric and Oceanic Sciences Program, Princeton University, Princeton, New Jersey 08544, USA.
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Abstract
BACKGROUND Biological silica production has drawn intense attention and several molecules involved in biosilicification have been identified. Cellular mechanisms, however, remain unknown mainly due to the lack of probes required for obtaining information on live specimens. RESULTS The fluorescence spectra of the compound 2-(4-pyridyl)-5-((4-(2-dimethylaminoethylaminocarbamoyl)methoxy)phenyl)oxazole (PDMPO) are affected by the presence of >3.2 mM silicic acid. Increase in intensity and shift in the fluorescence coincide with the polymerization of Si. The unique PDMPO-silica fluorescence is explored here to visualize Si deposition in living diatoms. The fluorophore is selectively incorporated and co-deposited with Si into the newly synthesized frustules (the outer silica shells) showing an intense green fluorescence. CONCLUSIONS We suggest that a fluorescence shift is due to an interaction between PDMPO and polymeric silicic acid. PDMPO is an excellent probe for imaging newly deposited silica in living cells and has also a potential for a wide range of applications in various Si-related disciplines, including biology of living organisms as diatoms, sponges, and higher plants, clinical research (e.g. lung fibrosis and cancer, bone development, artificial bone implantation), and chemistry and physics of materials research.
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Affiliation(s)
- K Shimizu
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, 93106, USA
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Debenham P, Brzezinski MA, Foltz KR. Evaluation of sequence variation and selection in the bindin locus of the red sea urchin, Strongylocentrotus franciscanus. J Mol Evol 2000; 51:481-90. [PMID: 11080371 DOI: 10.1007/s002390010111] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Recent evidence suggests that gamete recognition proteins may be subjected to directed evolutionary pressure that enhances sequence variability. We evaluated whether diversity enhancing selection is operating on a marine invertebrate fertilization protein by examining the intraspecific DNA sequence variation of a 273-base pair region located at the 5' end of the sperm bindin locus in 134 adult red sea urchins (Strongylocentrotus franciscanus). Bindin is a sperm recognition protein that mediates species-specific gamete interactions in sea urchins. The region of the bindin locus examined was found to be polymorphic with 14 alleles. Mean pairwise comparison of the 14 alleles indicates moderate sequence diversity (p-distance = 1.06). No evidence of diversity enhancing selection was found. It was not possible to reject the null hypothesis that the sequence variation observed in S. franciscanus bindin is a result of neutral evolution. Statistical evaluation of expected proportions of replacement and silent nucleotide substitutions, observed versus expected proportions of radical replacement substitutions, and conformance to the McDonald and Kreitman test of neutral evolution all indicate that random mutation followed by genetic drift created the polymorphisms observed in bindin. Observed frequencies were also highly similar to results expected for a neutrally evolving locus, suggesting that the polymorphism observed in the 5' region of S. franciscanus bindin is a result of neutral evolution.
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Affiliation(s)
- P Debenham
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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De La Rocha CL, Brzezinski MA, DeNiro MJ. Purification, Recovery, and Laser-Driven Fluorination of Silicon from Dissolved and Particulate Silica for the Measurement of Natural Stable Isotope Abundances. Anal Chem 1996; 68:3746-50. [DOI: 10.1021/ac960326j] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christina L. De La Rocha
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California 93106
| | - Mark A. Brzezinski
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California 93106
| | - Michael J. DeNiro
- Department of Geological Sciences, University of California, Santa Barbara, California 93106
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Nelson DM, Ducklow HW, Hitchcock GL, Brzezinski MA, Cowles TJ, Garside C, Gould RW, Joyce TM, Langdon C, McCarthy JJ, Yentsch CS. Distribution and composition of biogenic particulate matter in a Gulf Stream warm-core ring. ACTA ACUST UNITED AC 1985. [DOI: 10.1016/0198-0149(85)90052-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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