A simple cleaning and fluorescent staining protocol for recent and fossil diatom frustules

References

• Abrantes , F. , Gil , I. , Lopes , C. and Castro , M. 2005 . Quantitative diatom analyses–a faster cleaning procedure . Deep Sea Research Part I: Oceanographic Research Papers , 52 : 189 – 198 .
   Google Scholar
• Acker , F. , Russel , B. and Hagan , E. 2002 . “ Protocol P-13-42 diatom cleaning by nitric acid digestion with a microwave apparatus ” . In Protocols for the analysis of algal samples collected as part of the U.S. Geological Survey National Water–Quality Assessment Program. Report No. 02-06 , Edited by: Charles , D. F. , Knowles , C. and Davis , R. S. 27 – 39 . The Academy of Natural Sciences, Philadelphia .
   Google Scholar
• Benton , M. J. and Pearson , P. N. 2001 . Speciation in the fossil record . Trends in Ecology & Evolution , 16 : 405 – 411 .
   PubMed Web of Science ®Google Scholar
• Blanco , S. , Aacute;lvarez , I. and Cejudo , C. 2008 . A test on different aspects of diatom processing techniques . Journal of Applied Phycology , 20 : 445 – 450 .
   Google Scholar
• Bradbury , J. 2004 . Nature's nanotechnologists: unveiling the secrets of diatoms . PLoS Biology , 2 ( e306 )
   Google Scholar
• Carr , J. M. , Hergenrader , G. L. and Troelstrup , N. H. Jr. 1986 . A simple, inexpensive method for cleaning diatoms . Transactions of the American Microscopical Society , 105 : 152 – 157 .
   Google Scholar
• Cortese , G. and Gersonde , R. 2007 . Morphometric variability in the diatom . Fragilariopsis kerguelensis: Implications for Southern Ocean paleoceanography. Earth and Planetary Science Letters , 257 : 526 – 544 .
   Web of Science ®Google Scholar
• Cymbola , J. , Ogdahl , M. and Steinman , A. D. 2008 . Phytoplankton response to light and internal phosphorus loading from sediment release . Freshwater Biology , 53 : 2530 – 2542 .
   Google Scholar
• Descles , J. , Vartanian , M. and El Harrak , A. 2008 . New tools for labeling silica in living diatoms . New Phytologist , 177 : 822 – 829 .
   PubMedGoogle Scholar
• Desikachary , T. and Dweltz , N. 1961 . The chemical composition of the diatom frustule . Proceedings: Plant Sciences , 53 : 157 – 165 .
   Google Scholar
• Douglas , M. S.V. , Ludlam , S. and Feeney , S. 1996 . Changes in diatom assemblages in Lake C2 (Ellesmere Island, Arctic Canada): response to basin isolation from the sea and to other environmental changes . Journal of Paleolimnology , 16 : 217 – 226 .
   Web of Science ®Google Scholar
• Falciatore , A. and Bowler , C. 2002 . Revealing the molecular secrets of marine diatoms . Annual Review of Plant Biology , 53 : 109 – 130 .
   PubMed Web of Science ®Google Scholar
• Finkel , Z. V. , Katz , M. E. , Wright , J. D. , Schofield , O. M.E. and Falkowski , P. G. 2005 . Climatically driven macroevolutionary patterns in the size of marine diatoms over the Cenozoic . Proceedings of the National Academy of Sciences of the United States of America , 102 : 8927 – 8932 .
   PubMed Web of Science ®Google Scholar
• Francoeur , S. N. , Biggs , B. and Lowe , R. 1998 . Microform bed clusters as refugia for periphyton in a flood–prone headwater stream . New Zealand Journal of Marine and Freshwater Research , 32 : 363 – 374 .
   Web of Science ®Google Scholar
• Friedrichs , L. , Maier , M. and Hamm , C. 2012 . A new method for exact three-dimensional reconstructions of diatom frustules . Journal of Microscopy , 248 : 208 – 217 .
   PubMed Web of Science ®Google Scholar
• Gersonde , R. and Harwood , D. M. 1990 . “ Lower Cretaceous diatoms from ODP Leg 113 Site 693 (Weddell Sea), Part 1. Vegetative cells ” . In Proceedings of the ocean drilling program, scientific results , Edited by: Barker , P. F. , Kennett , J. P. , O'Connell , S. B. , Berkowitz , S. , Bryant , W. R. , Burckle , L. H. , Egeberg , P. K. , Fuetterer , D. K. , Gersonde , R. E. , Golovchenko , X. , Hamilton , N. , Lawver , L. , Lazarus , D. B. , Lonsdale , M. J. , Mohr , B. A.R. , Nagao , T. , Pereira , C. P.G. , Pudsey , C. J. , Robert , C. M. , Schandl , E. S. , Spiess , V. , Stott , L. D. , Thomas , E. , Thompson , K. F.M. , Wise , S. W. Jr. , Kennett , D. M. , Masterson , A. and Stewart , N. J. Vol. 113 , 403 – 425 . A & M University, Texas .
   Google Scholar
• Gersonde , R. and Zielinski , U. 2000 . The reconstruction of late quaternary antarctic sea-ice distribution – the use of diatoms as a proxy for sea-ice . Palaeogeography, Palaeoclimatology, Palaeoecology , 162 : 263 – 286 .
   Web of Science ®Google Scholar
• Goldman , J. C. 1993 . Potential role of large oceanic diatoms in new primary production . Deep Sea Research Part I: Oceanographic Research Papers , 40 : 159 – 168 .
   Google Scholar
• Gordon , R. , Losic , D. , Tiffany , M. A. , Nagy , S. S. and Sterrenburg , F. A.S. 2009 . The glass menagerie: diatoms for novel applications in nanotechnology . Trends in Biotechnology , 27 : 116 – 127 .
   PubMed Web of Science ®Google Scholar
• Guillard , R. R.L. and Ryther , J. H. 1962 . Studies of marine planktonic diatoms: I . Cyclotella nana Hustedt and Detonula confervacea (Ceve) Gran. Canadian Journal of Microbiology , 8 : 229 – 239 .
   PubMed Web of Science ®Google Scholar
• Guiry , M. D. 2012 . How many species of algae are there? . Journal of Phycology , 48 : 1057 – 1063 .
   PubMed Web of Science ®Google Scholar
• Hale , M. S. and Mitchell , J. G. 2001 . Functional morphology of diatom frustule microstructures: hydrodynamic control of Brownian particle diffusion and advection . Aquatic Microbial Ecology , 24 : 287 – 295 .
   Web of Science ®Google Scholar
• Hallam , A. 1997 . Speciation patterns and trends in the fossil record . Geobios , 30 : 921 – 930 .
   Google Scholar
• Hamm , C. 2005 . The evolution of advanced mechanical defenses and potential technological applications of diatom shells . Journal of Nanoscience and Nanotechnology , 5 : 108 – 119 .
   PubMed Web of Science ®Google Scholar
• Hamm , C. E. , Merkel , R , Springer , O , Jurkojc , P , Maier , C. , Prechtel , K. and Smetacek , V. 2003 . Architecture and material properties of diatom shells provide effective mechanical protection . Nature , 421 : 841 – 843 .
   PubMed Web of Science ®Google Scholar
• Harrison , P. J. , Conway , H. L. , Holmes , R. W. and Davis , C. O. 1977 . Marine diatoms grown in chemostats under silicate or ammonium limitation. III. Cellular chemical composition and morphology of . Chaetoceros debilis, Skeletonema costatum and Thalassiosira gravida. Marine Biology , 43 : 19 – 31 .
   Web of Science ®Google Scholar
• Harwood , D. M. and Gersonde , R. 1990 . “ Lower Cretaceous diatoms from ODP Leg 113 Site 693 (Weddell Sea), Part 2. Resting spores, chrysophycean cysts, an endoskeletal dinoflagellate, and notes on the origin of the diatoms ” . In Proceedings of the ocean drilling program, scientific results , Edited by: Barker , P. F. , Kennett , J. P. , O'Connell , S. B. , Berkowitz , S. , Bryant , W. R. , Burckle , L. H. , Egeberg , P. K. , Fuetterer , D. K. , Gersonde , R. E. , Golovchenko , X. , Hamilton , N. , Lawver , L. , Lazarus , D. B. , Lonsdale , M. J. , Mohr , B. A.R. , Nagao , T. , Pereira , C. P.G. , Pudsey , C. J. , Robert , C. M. , Schandl , E. S. , Spiess , V. , Stott , L. D. , Thomas , E. , Thompson , K. F.M. , Wise , S. W. Jr. , Kennett , D. M. , Masterson , A. and Stewart , N. J. Vol. 113 , 403 – 425 . A & M University, Texas .
   Google Scholar
• Hasle , G. R. and Fryxell , G. A. 1970 . Diatoms: cleaning and mounting for light and electron microscopy . Transactions of the American Microscopical Society , 89 : 469 – 474 .
   Google Scholar
• Hendey , N. I. 1938 . An efficient technique for cleaning diatoms . Journal of the Royal Microscopical Society , 58 : 49 – 52 .
   Google Scholar
• Hoffmann , L. , Peeken , I. and Lochte , K. 2008 . Iron, silicate, and light co-limitation of three Southern Ocean diatom species . Polar Biology , 31 : 1067 – 1080 .
   Google Scholar
• Jablonski , D. 1999 . The future of the fossil record . Science , 284 : 2114 – 2116 .
   PubMedGoogle Scholar
• Johnson , B. R. and Remeikis , N. A. 1993 . Effective shelf-life of prepared sodium hypochlorite solution . Journal of Endodontics , 19 : 40 – 43 .
   PubMedGoogle Scholar
• Kaczmarska , I. , Beaton , M. , Benoit , A. C. and Medlin , L. K. 2006 . Molecular phylogeny of selected members of the order . Thalassiosirales (Bacillariophyta) and evolution of the fultoportula. Journal of Phycology , 42 : 121 – 138 .
   Web of Science ®Google Scholar
• Katz , M. E. , Finkel , Z. V. , Grzebyk , D , Knoll , A. H. and Falkowski , P. G. 2004 . Evolutionary trajectories and biogeochemical impacts of marine eukaryotic phytoplankton . Annual Review of Ecology, Evolution, and Systematics , 35 : 523 – 556 .
   Web of Science ®Google Scholar
• Kooistra , W. H.C.F. and Medlin , L. K. 1996 . Evolution of the diatoms (Bacillariophyta): IV. A reconstruction of their age from small subunit rRNA coding regions and the fossil record . Molecular Phylogenetics and Evolution , 6 : 391 – 407 .
   PubMed Web of Science ®Google Scholar
• Krammer , K. , Lange-Bertalot , H. and Schiller , W. 1997 . Miosira rhoenana n. gen. n. sp. (Bacillariophyceae) aus miozänen limnischen Sedimenten der Rhön im Vergleich mit anderen zentrischen Diatomeen. Paläontologische Zeitschrift , 71 : 5 – 18 .
   Google Scholar
• Kröger , N. , Bergsdorf , C. and Sumper , M. 1996 . Frustulins: domain conservation in a protein family associated with diatom cell walls . European Journal of Biochemistry , 239 : 259 – 264 .
   Google Scholar
• Kucki , M. 2009 . Biological photonic crystals: diatoms . Universität Kassel, Kassel. , 171 Ph.D. Thesis
   Google Scholar
• Lewin , J. 1961 . The dissolution of silica from diatom walls . Geochimica et Cosmochimica Acta , 21 : 182 – 198 .
   Web of Science ®Google Scholar
• Lopez , P. J. , Desclés , J , Allen , A. E. and Bowler , C. 2005 . Prospects in diatom research . Current Opinion in Biotechnology , 16 : 180 – 186 .
   PubMed Web of Science ®Google Scholar
• Mann , D. and Droop , S. 1996 . Biodiversity, biogeography and conservation of diatoms . Hydrobiologia , 336 : 19 – 32 .
   Web of Science ®Google Scholar
• March , J. G. , Pringle , C. M. , Townsend , M. J. and Wilson , A. I. 2002 . Effects of freshwater shrimp assemblages on benthic communities along an altitudinal gradient of a tropical island stream . Freshwater Biology , 47 : 377 – 390 .
   Web of Science ®Google Scholar
• Marchetti , A. and Cassar , N. 2009 . Diatom elemental and morphological changes in response to iron limitation: a brief review with potential paleoceanographic applications . Geobiology , 7 : 419 – 431 .
   PubMed Web of Science ®Google Scholar
• Nelson , D. M. , Tréguer , P. , Brzezinski , M. A. , Leynaert , A. and Quéguiner , B. 1995 . Production and dissolution of biogenic silica in the ocean: revised global estimates, comparison with regional data and relationship to biogenic sedimentation . Global Biogeochemical Cycles , 9 : 359 – 372 .
   Web of Science ®Google Scholar
• Paasche , E. and Ostergren , I. 1980 . The annual cycle of plankton diatom growth and silica production in the Inner Oslofjord . Limnology and Oceanography , 25 : 481 – 494 .
   Web of Science ®Google Scholar
• Philippe , H. , Sörhannus , U. , Baroin , A. , Perasso , R. , Gasse , F. and Adoutte , A. 1994 . Comparison of molecular and paleontological data in diatoms suggests a major gap in the fossil record . Journal of Evolutionary Biology , 7 : 247 – 265 .
   Web of Science ®Google Scholar
• Pondaven , P. , Gallinari , M. , Chollet , S. , Bucciarelli , E. , Sarthou , G. , Schultes , S. and Jean , F. 2007 . Grazing-induced changes in cell wall silicification in a marine diatom . Protist , 158 : 21 – 28 .
   PubMed Web of Science ®Google Scholar
• Pringle , C. M. , Hemphill , N , McDowell , W. H. , Bednarek , A. and March , J. G. 1999 . Linking species and ecosystems: different biotic assemblages cause interstream differences in organic matter . Ecology , 80 : 1860 – 1872 .
   Web of Science ®Google Scholar
• Rogall , E. 1939 . Über den Feinbau der Kieselmembran der Diatomeen . Planta , 29 : 279 – 291 .
   Google Scholar
• Rothpletz , A. 1896 . Über die Flysch–Fucoiden und einige andere fossile Algen, sowie über liasische, Diatomeen führende Hornschwämme . Zeitschrift der Deutschen Geologischen Gesellschaft , 48 : 854 – 914 .
   Google Scholar
• Round , F. E. , Crawford , R. M. and Mann , D. G. 1990 . The diatoms. Biology and morphology of the genera , 758 Cambridge : Cambridge Universtity Press .
   Google Scholar
• Siemiñska , J. 2000 . The discoveries of diatoms older than the Cretaceous. In: . The origin and early evolution of the diatoms , : 55 – 74 . Szafer Institute of Botany, Polish Academy of Sciences, Kraków.
   Google Scholar
• Siever , R. 1962 . Silica solubility, 0 °–200 °C and the diagenesis of siliceous sediments . The Journal of Geology , 70 : 127 – 150 .
   Web of Science ®Google Scholar
• Smetacek , V. 1999 . Diatoms and the ocean carbon cycle . Protist , 150 : 25 – 32 .
   PubMed Web of Science ®Google Scholar
• Sorhannus , U. 2004 . Diatom phylogenetics inferred based on direct optimization of nuclear-encoded SSU rRNA sequences . Cladistics , 20 : 487 – 497 .
   PubMed Web of Science ®Google Scholar
• Spaulding , S. A. , McKnight , D. M. , Stanish , L , Van de Vijver , B. and Hodgson , D. 2010 . “ Diatoms as indicators of environmental change in Antarctic and Sub-Antarctic freshwaters ” . In The diatoms: applications for the environmental and earth sciences , Edited by: Smol , J. and Stoermer , E. F. 267 – 286 . Cambridge : Cambridge University Press .
   Google Scholar
• Swift , E. 1967 . Cleaning diatom frustules with ultraviolet radiation and peroxide . Phycologia , 6 : 161 – 163 .
   Google Scholar
• Tiffany , M. A. , Gordon , R. and Gebeshuber , I. C. 2010 . Hyalodiscopsis plana, a sublittoral centric marine diatom, and its potential for nanotechnology as a natural zipper-like nanoclasp. Polish Botanical Journal , 55 : 27 – 41 .
   Google Scholar
• Uitz , J. , Claustre , H. , Gentili , B. and Stramski , D. 2010 . Phytoplankton class-specific primary production in the world's oceans: seasonal and interannual variability from satellite observations . Global Biogeochemical Cycle , 24 : 1 – 19 .
   Google Scholar
• Van Blaaderen , A. and Vrij , A. 1992 . Synthesis and characterization of colloidal dispersions of fluorescent, monodisperse silica spheres . Langmuir , 8 : 2921 – 2931 .
   Web of Science ®Google Scholar
• Watanabe , T. , Kodama , Y. and Mayama , S. 2010 . Application of a novel cleaning method using low-temperature plasma on tidal flat diatoms with heterovalvy or delicate frustule structure . Proceedings of the Academy of Natural Sciences of Philadelphia , 160 : 83 – 87 .
   Web of Science ®Google Scholar
• Wefer , G. and Berger , W. H. 2001 . “ Reconstruction of productivity from the sedimentary record ” . In Encyclopedia of ocean sciences , 2 , Edited by: Steele , J. H. , Thorpe , S. A. and Turekian , K. K. 2713 – 2724 . Academic Press, London .
   Google Scholar
• Wilken , S. , Hoffmann , B. , Hersch , N. , Kirchgessner , N. , Dieluweit , S. , Rubner , W. , Hoffmann , L. J. , Merkel , R. and Peeken , I. 2011 . Diatom frustules show increased mechanical strength and altered valve morphology under iron limitation . Limnology and Oceanography , 56 : 1399 – 1410 .
   Web of Science ®Google Scholar