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Publications Marine Microbiology

2012
  1. Drigo, B., Van Veen, J.A., Boschker, H.T.S. & Kowalchuk, G.A. (2012). Tracking microbial responses in the rhizosphere of plants subjected to elevated CO2. Ecology Letters, in press.
  2. Eelderink, C., Moerdijk-Poortvliet, T.C.W., Wang, H.W., Schepers, M., Preston, T., Boer, T., Vonk, R.J., Schierbeek, H. & Priebe, M.G. (2012). The glycemic response does not reflect the in vivo starch digestibility of fiber-rich wheat products in healthy men. Journal of Nutrition, 142(2), 258-263.
  3. Hannula, S.E., Boschker, H.T.S., De Boer, W. & Van Veen, J.A. (2012). 13C pulse-labeling assessment of fungal community structure and activity in the rhizosphere of a genetically starch-modified potato cultivar and its parental isoline. New Phytologist, 194(3), 784-799.
  4. Ismail-Ben Ali, A., El Bour, M., Ktari, L., Bolhuis, H., Ahmed, M., Boudabbous, A. & Stal, L.J. (2012). Jania rubens-associated bacteria: molecular identification and antimicrobial activity. Journal of Applied Phycology, 24(3), 525-534.
  5. Miyatake, T., MacGregor, B.J. & Boschker, H.T.S. (2012). Linking microbial community structure and function in marine intertidal sediment by stable isotope probing combined with magnetic bead capture hybridization. ISME Journal, in press.
  6. Salama, M.S., Van der Velde, R., Van der Woerd, H.J., Kromkamp, J.C., Philippart, C.J.M., Joseph, A.T., O'Neill, P.E., Lang, R.H., Gish, T., Werdell, P.J. & Su, Z. (2012). Technical Note: Calibration and validation of geophysical observation models. Biogeosciences, 9(6), 2195-2201.
  7. Severin, I., Confurius-Guns, V. & Stal, L.J. (2012). Effect of salinity on nitrogenase activity and composition of the active diazotrophic community in intertidal microbial mats. Archives of Microbiology, 194(6), 483-491.
  8. Witte, F., Silsbe, G., Hecky, R.E., Goudswaard, P.C., Guildford, S.J., Kishe-Machumu, M.A. & Wanink, J.H. (2012). Did the loss of phytoplanktivorous fish contribute to algal blooms in the Mwanza Gulf of Lake Victoria? Hydrobiologia, 679(1), 283-296.
2011
  1. Agawin, N.S.R., Tovar-Sanchez, A., Stal, L.J., Alvarez, M., Agusti, S. & Duarte, C.M. (2011). Low water column nitrogen fixation in the Mediterranean Sea: basin-wide experimental evidence. Aquatic Microbial Ecology, 64(2), 135-147.
  2. Ahmed, M., Stal, L.J. & Hasnain, S. (2011). DTAF: an efficient probe to study cyanobacterial-plant interaction using confocal laser scanning microscopy (CLSM). Journal of Industrial Microbiology and Biotechnology, 38(1), 249-255.
  3. Bauersachs, T., Compaore, J., Severin, I., Hopmans, E.C., Schouten, S., Stal, L.J. & Sinninghe Damsté, J.S. (2011). Diazotrophic microbial community of coastal microbial mats of the southern North Sea. Geobiology, 9(4), 349-359.
  4. Benavides, M., Agawin, N.S.R., Arístegui, J., Ferrio, P. & Stal, L.J. (2011). Nitrogen fixation by Trichodesmium and small diazotrophs in the subtropical northeast Atlantic. Aquatic Microbial Ecology, 65(1), 43-53.
  5. Bolhuis, H. & Stal, L.J. (2011). Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing. ISME Journal, 5, 1701-1712.
  6. Gazeau, F.P.H., Gattuso, J.P., Greaves, M., Elderfield, H., Peene, J., Heip, C.H.R. & Middelburg, J.J. (2011). Effect of carbonate chemistry alteration on the early embryonic development of the pacific pyster (Crassostrea gigas). PLoS One, 6(8), e23010.
  7. Hackenberg, C., Kern, R., Hüge, J., Stal, L.J., Tsuji, Y., Kopka, J., Shiraiwa, Y., Bauwe, H. & Hagemann, M. (2011). Cyanobacterial lactate oxidases serve as essential partners of N2-fixation and evolved to photorespiratory glycolate oxidases in plants. Plant Cell, 23(8), 2978-2990.
  8. Ihnken, S., Kromkamp, J.C. & Beardall, J. (2011). Photoacclimation in Dunaliella tertiolecta reveals a unique NPQ pattern upon exposure to irradiance. Photosynthesis Research, 110(2), 123-137.
  9. Meisner, A., De Boer, W., Verhoeven, K.J.F., Boschker, H.T.S. & Van der Putten, W.H. (2011). Comparison of nutrient acquisition in exotic plant species and congeneric natives. Journal of Ecology, 99(6), 1308-1315.
  10. Miyatake, T. (2011, januari 25). Linking microbial community structure to biogeochemical function in coastal marine sediments. UvA. Prom./coprom.: prof. dr. L.J. Stal & ir. H.T.S. Boschker.
  11. Piquet, A.M-T., Bolhuis, H., Meredith, M.P. & Buma, A.G.J. (2011). Shifts in coastal Antarctic marine microbial communities during and after melt water-related surface stratification. FEMS Microbiology Ecology, 76(3), 413-427.
  12. Van der Wal, D., Forster, R.M., Rossi, F., Hummel, H., Ysebaert, T., Roose, F. & Herman, P.M.J. (2011). Ecological evaluation of an experimental beneficial use scheme for dredged sediment disposal in shallow tidal waters. Marine Pollution Bulletin, 62(1), 99-108.
2010
  1. Ahmed, M., Stal, L.J. & Hasnain, S. (2010). Association of non-heterocystous cyanobacteria with crop plants. Plant and Soil, 336(1-2), 363-375.
  2. Ahmed, M., Stal, L.J. & Hasnain, S. (2010). Production of indole-3-acetic acid by the cyanobacterium Arthrospira platensis strain MMG-9. Journal of Microbiology and Biotechnology, 20(9), 1259-1265.
  3. Amaral-Zettler, L., Artigas, L.F., Baross, J., Boetius, A. Antje, Chandramohan, D., Herndl, G., Kogure, K., Neal, P., Pedrós-Alió, C., Ramette, A., Schouten, S., Stal, L.J., Thessen, A., Leeuw, J.W. De & Sogin, M. (2010). A global census of marine microbes. In A. McIntyre (Ed.), Life in the World's Oceans: Diversity, Distribution, and Abundance (pp. 223-245). Wiley.
  4. Bauersachs, T., Schouten, S., Compaore, J., Stal, L.J. & Damsté, J.S. Sinninghe (2010). Occurrence of C35-C45 polyprenols in filamentous and unicellular cyanobacteria. Organic Geochemistry, 41(9), 867-870.
  5. Bolhuis, H., Severin, I., Confurius-Guns, V., Wollenzien, U.I.A. & Stal, L.J. (2010). Horizontal transfer of the nitrogen fixation gene cluster in the cyanobacterium Microcoleus chthonoplastes. ISME Journal, 4, 121-130.
  6. Compaore, J. (2010, oktober 21). Oxygen and temperature in relation to nitrogen fixation in cyanobacteria. UvA. Prom./coprom.: prof. dr. L.J. Stal & ir. H.T.S. Boschker.
  7. Compaore, J. & Stal, L.J. (2010). Oxygen and the light-dark cycle of nitrogenase activity in two unicellular cyanobacteria. Environmental Microbiology, 12, 54-62.
  8. Compaore, J. & Stal, L.J. (2010). The effect of temperature on the sensitivity of nitrogenase to oxygen in two heterocystous cyanobacteria. Journal of Phycology, 46 (6), 1172-1179.
  9. Cox, T.J.S., Soetaert, K.E.R., Vanderborght, J. P., Kromkamp, J.C. & Meire, P. (2010). Modelling photosynthesis-irradiance curves: effects of temperature, dissolved silica depletion and changing community assemblage on community photosynthesis. Limnology and Oceanography Methods, 8, 424-440.
  10. Dijkman, N.A., Boschker, H.T.S., Stal, L.J. & Kromkamp, J.C. (2010). Composition and heterogeneity of the microbial community in a coastal microbial mat as revealed by the analysis of pigments and phospholipid-derived fatty acids. Journal of Sea Research, 63, 62-70.
  11. Drigo, B., Pijl, A.S., Duyts, H., Kielak, A.M., Gamper, H.A., Houtekamer, M.J., Boschker, H.T.S., Bodelier, P.L.E., Whiteley, A.S., Van Veen, J.A. & Kowalchuk, G.A. (2010). Shifting carbon flow from roots into associated microbial communities in response to elevated atmospheric CO2. Proceedings of the National Academy of Sciences of the United States of America, 107(24), 10938-10942.
  12. Gazeau, F.P.H., Gattuso, J.P., Dawber, C., Pronker, A.E., Peene, F., Peene, J., Heip, C.H.R. & Middelburg, J.J. (2010). Effect of ocean acidification on the early life stages of the blue mussel Mytilus edulis. Biogeosciences, 7(7), 2051-2060.
  13. Kromkamp, J.C. & Van Engeland, T. (2010). Changes in phytoplankton biomass in the Western Scheldt estuary during the period 1978-2006. Estuaries and Coasts, 33(2), 270-285.
  14. Kromkamp, J.C. & Van Engeland, T. (2010). Long term changes in phytoplankton biomass in the Western Scheldt Estuary. In . Seattle, WA, USA.
  15. Kromkamp, J.C., Van Engeland, T. & Peene, J. (2010). Long term changes in phytoplankton biomass in the Western Scheldt estuary (the Netherlands). In . Seattle, WA, USA.
  16. Oakes, J.M., Eyre, B.D., Middelburg, J.J. & Boschker, H.T.S. (2010). Composition, production, and loss of carbohydrates in subtropical shallow subtidal sandy sediments: Rapid processing and long-term retention revealed by 13C-labeling. Limnology and Oceanography, 55(5), 2126-2138.
  17. Perkins, R., Kromkamp, J.C., Serôdio, J., Lavaud, J., Jesus, B., Mouget, J.L., Lefebvre, S. & Forster, R.M. (2010). The application of variable chlorophyll fluorescence to microphytobenthic biofilms. In D.J. Suggett, O. Prášil & M.A. Borowitzka (Eds.), Chlorophyll a fluorescence in aquatic sciences: methods and applications (Developments in applied phycology, 4) (pp. 237-276). Dordrecht: Springer.
  18. Piquet, A.M-T., Bolhuis, H., Davidson, A.T. & Buma, A.G.J. (2010). Seasonal succession and UV sensitivity of marine bacterioplankton at an Antarctic coastal site. FEMS Microbiology Ecology, 73(1), 68-82.
  19. Piquet, A.M-T., Scheepens, J.F., Bolhuis, H., Wiencke, C. & Buma, A.G.J. (2010). Variability of protistan and bacterial communities in two Arctic fjords (Spitsbergen). Polar Biology, 33(11), 1521-1536.
  20. Severin, I. (2010, april 27). Nitrogen fixation in microbial mats: Complexity and dynamics of a small-scale ecosystem. University of Amsterdam. Prom./coprom.: prof. dr. L.J. Stal & dr. H. Bolhuis.
  21. Severin, I. & Stal, L.J. (2010). Diazotrophic Microbial Mats. In J. Seckbach & A. Oren (Eds.), Microbial Mats : Modern and Ancient Microorganisms in Stratified Systems (Cellular Origin, Life in Extreme Habitats and Astrobiology, 14) (pp. 321-339). Springer.
  22. Severin, I., Acinas, S.G. & Stal, L.J. (2010). Diversity of nitrogen-fixing bacteria in cyanobacterial mats. FEMS Microbiology Ecology, 73(3), 514-525.
  23. Severin, I. & Stal, L.J. (2010). NifH expression by five groups of phototrophs compared with nitrogenase activity in coastal microbial mats. FEMS Microbiology Ecology, 73(1), 55-67.
  24. Severin, I. & Stal, L.J. (2010). Spatial and temporal variability in nitrogenase activity and diazotrophic community composition in coastal microbial mats. Marine Ecology Progress Series, 417, 13-25.
  25. Severin, I. & Stal, L.J. (2010). Temporal and spatial variability of nifH expression in three filamentous Cyanobacteria in coastal microbial mats. Aquatic Microbial Ecology, 60, 59-70.
  26. Stal, L.J. (2010). Microbial mats and stromatolites. In The Ecology of Cyanobacteria.
  27. Stal, L.J., Severin, I. & Bolhuis, H. (2010). The ecology of nitrogen fixation in cyanobacterial mats. In P.C. Hallenbeck (Ed.), Recent advances in phototrophic prokaryotes (Advances in Experimental Medicine and Biology, 675) (pp. 31-45). New York: Springer.
  28. Stal, L.J. (2010). Microphytobenthos as a biogeomorphological force in intertidal sediment stabilization. Ecological Engineering, 36(2 Sp. Iss.), 236-245.
  29. Stal, L.J. & Severin, I. (2010). Diversity of diazotrophic microorganisms in a microbial mat. In . Seattle, USA.
  30. Weirdt, R. De, Possemiers, S., Vermeulen, G., Moerdijk-Poortvliet, T.C.W., Boschker, H.T.S., Verstraete, W. & Wiele, T. Van de (2010). Human faecal microbiota display variable patterns of glycerol. FEMS Microbiology Ecology, 74(3), 601-611.
2009
  1. Acinas, S.G., Haverkamp, T.H.A., Huisman, J. & Stal, L.J. (2009). Phenotypic and genetic diversification of Pseudanabaena spp. (cyanobacteria). ISME Journal, 3, 31-46.
  2. Ahmed, M., Stal, L.J. & Hasnain, S. (2009). Comparative studies of cyanobacterial associations with crop plants. New Biotechnology, 25(suppl.1), S310.
  3. Bauersachs, T., Compaore, J., Hopmans, E.C., Stal, L.J., Schouten, S. & Damsté, J.S. Sinninghe (2009). Distribution of heterocyst glycolipids in cyanobacteria. Phytochemistry, 70, 2034-2039.
  4. Bauersachs, T., Scouten, S., Compaore, J., Wollenzien, U.I.A., Stal, L.J. & Damsté, J.S. Sinninghe (2009). Nitrogen isotopic fractionation associated with growth on dinitrogen gas and nitrate by cyanobacteria. Limnology and Oceanography, 54, 1403-1411.
  5. Bauersachs, T., Compaore, J., Hopmans, E.C., Stal, L.J., Schouten, S. & Damsté, J.S. Sinninghe (2009). Rapid analysis of long-chain glycolipids in heterocystous cyanobacteria using high-performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry. Rapid Communications in Mass Spectrometry, 23, 1387-1394.
  6. Borin, S., Brusetti, L., Mapelli, F., D'Auria, G., Brusa, T., Marzorati, M., Rizzi, A., Yakimov, M., Marty, D., Lange, G.J. de, Wielen, P. Van der, Bolhuis, H., McGenity, T.J., Polymenakou, P.N., Malinverno, E., Giuliano, L., Corselli, C. & Daffonchio, D. (2009). Sulfur cycling and methanogenesis primarily drive microbial colonization of the highly sulfidic Urania deep hypersaline basin. Proceedings of the National Academy of Sciences of the United States of America, 106, 9151-9156.
  7. Dijkman, N.A., Boschker, H.T.S., Middelburg, J.J. & Kromkamp, J.C. (2009). Group-specific primary production based on stable-isotope labeling of phospholipid-derived fatty acids. Limnology and Oceanography Methods, 7, 612-625.
  8. Ferreira, D., Stal, L.J., Moradas-Ferreira, P., Mendes, M. Vaz & Tamagnini, P. (2009). The relation between N2 fixation and H2 metabolism in the marine filamentous nonheterocystous cyanobacterium Lyngbya aestuarii CCY 96161. Journal of Phycology, 45, 898-905.
  9. Fewer, D.P., Jokela, J., Rouhiainen, L., Wahsten, M., Koskenniemi, K., Stal, L.J. & Sivonen, K. (2009). The non-ribosomal assembly and frequent occurrence of the protease inhibitors spumigins in the bloom-forming cyanobacterium Nodularia spumigena. Molecular Microbiology, 5, 924-937.
  10. Gribsholt, B., Veuger, B., Tramper, A., Middelburg, J.J. & Boschker, H.T.S. (2009). Long-term 15N-nitrogen retention in tidal freshwater marsh sediment: Elucidating the microbial contribution. Limnology and Oceanography, 54, 13-22.
  11. Haverkamp, T.H.A., Schouten, D., Doeleman, M.W., Wollenzien, U.I.A., Huisman, J. & Stal, L.J. (2009). Colorful microdiversity of Synechococcus strains (picocyanobacteria) isolated from the Baltic Sea. ISME Journal, 3, 397-408.
  12. Kromkamp, J.C., Beardall, J., Sukenik, A., Kopecky, J., Masojidek, J., Bergeijk, S. van, Gabai, S., Shaham, E. & Yamson, A. (2009). Short-term variations in photosynthetic parameters of Nannochloropsis cultures grown in two types of outdoor mass cultivation systems. Aquatic Microbial Ecology, 56, 309-322.
  13. Miyatake, T., MacGregor, B.J. & Boschker, H.T.S. (2009). Linking microbial community function to phylogeny of sulfate-reducing Deltaproteobacteria in marine sediments by combining stable isotope probing with magnetic-bead capture hybridization of 16S rRNA. Applied and Environmental Microbiology, 75, 4927-4935.
  14. Schierbeek, H., Moerdijk-Poortvliet, T.C.W., Akker, C.H.P. van den, Braake, F.W.J. te, Boschker, H.T.S. & Goudoever, J.B. van (2009). Analysis of [U-13C6]glucose in human plasma using liquid chromatography/isotope ratio mass spectrometry compared with two other mass spectrometry techniques. Rapid Communications in Mass Spectrometry, 23, 3824-3830.
  15. Stal, L.J. (2009). Is the distribution of nitrogen-fixing cyanobacteria in the oceans related to temperature? Environmental Microbiology, 11, 1632-1645.
  16. Sukenik, A., Beardall, J., Kromkamp, J.C., Kopecký, J., Masojídek, J., Bergeijk, S. van, Gabai, S., Shaham, E. & Yamshon, A. (2009). Photosynthetic performance of outdoor Nannochloropsis mass cultures under a wide range of environmental conditions. Aquatic Microbial Ecology, 56, 297-308.
  17. Vanelslander, B., Creach, V., Vanormelingen, P., Ernst, A., Chepurnov, V.A., Sahan, E., Muyzer, G., Stal, L.J., Vyverman, W. & Sabbe, K. (2009). Ecological differentiation between sympatric pseudocryptic species in the estuarine benthic diatom Navicula phyllepta (Bacillariophyceae). Journal of Phycology, 45, 1278-1289.
2008
  1. Babarro, J.M.F. & De Zwaan, A. (2008). Anaerobic survival potential of four bivalves from different habitats. A comparative survey. Comparative Biochemistry and Physiology A-Molecular & Integrative Physiology, 151, 108-113.
  2. Boschker, H.T.S., Moerdijk-Poortvliet, T.C.W., Van Breugel, P.A., Houtekamer, M.J. & Middelburg, J.J. (2008). A versatile method for stable carbon isotope analysis of carbohydrates by high-performance liquid chromatography/isotope ratio mass spectrometry. Rapid Communications in Mass Spectrometry, 22, 3902-3908.
  3. Caramujo, M.J., Boschker, H.T.S. & Admiraal, W. (2008). Fatty acid profiles of algae mark the development and composition of harpacticoid copepods. Freshwater Biology, 53, 77-90.
  4. Haverkamp, T.H.A., Acinas, S.G., Doeleman, M.W., Stomp, M., Huisman, J. & Stal, L.J. (2008). Diversity and phylogeny of Baltic Sea picocyanobacteria inferred from their ITS and phycobiliprotein operons. Environmental Microbiology, 10, 174-188.
  5. Janknegt, P.J., Poll, W.H. van de, Visser, R.J.W., Rijstenbil, J.W. & Buma, A.G.J. (2008). Oxidative stress responses in the marine antarctic diatom Chaetoceros brevis (Bacillariophyceae) during photoacclimation. Journal of Phycology, 44, 957-966.
  6. Kremer, B., Kazmierczak, J. & Stal, L.J. (2008). Calcium carbonate precipitation in cyanobacterial mats from sandy tidal flats of the North Sea. Geobiology, 6, 46-56.
  7. Kromkamp, J.C., Dijkman, N.A., Peene, J., Simis, J.G.H. & Gons, H.J. (2008). Estimating phytoplankton primary production in Lake IJsselmeer (The Netherlands) using variable fluorescence (PAM-FRRF) and C-uptake techniques. European Journal of Phycology, 43, 327-344.
  8. Leeuwe, M.A. Van, Brotas, V., Consalvey, M., Forster, R.M., Gillespie, D., Jesus, B., Roggeveld, J. & Gieskes, W.W.C. (2008). Photoacclimation in microphytobenthos and the role of xanthophyll pigments. European Journal of Phycology, 43, 123-132.
  9. Mes, T.H.M. (2008). Microbial diversity - insights from population genetics. Environmental Microbiology, 10, 251-264.
  10. Morris, E.P., Forster, R.M., Peene, J. & Kromkamp, J.C. (2008). Coupling between Photosystem II electron transport and carbon fixation in microphytobenthos. Aquatic Microbial Ecology, 50, 301-311.
  11. Piquet, A.M-T., Bolhuis, H., Davidson, A.T., Thomson, P.G. & Buma, A.G.J. (2008). Diversity and dynamics of Antarctic marine microbial eukaryotes under manipulated environmental UV radiation. FEMS Microbiology Ecology, 66, 352-366.
  12. Poele, E.M. Te, Bolhuis, H. & Dijkhuizen, L. (2008). Actinomycete integrative and conjugative elements. Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 94, 127-143.
  13. Poele, E.M. Te, Samborskyy, M., Oliynyk, M., Leadlay, P.F., Bolhuis, H. & Dijkhuizen, L. (2008). Actinomycete integrative and conjugative pMEA-like elements of Amycolatopsis and Saccharopolyspora decoded. Plasmid, 59, 202-216.
  14. Roncarati, F., Rijstenbil, J.W. & Pistocchi, R. (2008). Photosynthetic performance, oxidative damage and antioxidants in Cylindrotheca closterium in response to high irradiance, UVB radiation and salinity. Marine Biology, 153, 965-973.
  15. Severin, I. & Stal, L.J. (2008). Light dependency of nitrogen fixation in a coastal cyanobacterial mat. ISME Journal, 2, 1077-1088.
  16. Stal, L.J. & Zehr, J.P. (2008). Cyanobacterial nitrogen fixation in the ocean: Diversity, regulation and ecology. In A. Herrero & E.            Flores (Eds.), The Cyanobacteria: Molecular Biology, Genomics and Evolution (pp. 423-446). Norfolk, UK: Caister Academic Press.
  17. Stal, L.J. (2008). Nitrogen Fixation in Cyanobacteria. In Encyclopedia of Life Sciences (ELS) (pp. 1-8). Chichester: John Wiley & Sons.
  18. Van der Wal, D., Ysebaert, T., Forster, R.M., Rossi, F., Bouma, T.J. & Herman, P.M.J. (2008). Synoptic techniques for monitoring the response of intertidal benthic biota to an alternative dredging strategy. In C.M. Dohmen-Janssen & J.M.H. Hulscher (Eds.), River, Coastal and Estuarine Morphodynamics (pp. 307-311). London: Taylor & Francis Group.
  19. Van der Wal, D., Herman, P.M.J., Forster, R.M., Ysebaert, T., Rossi, F., Knaeps, E., Plancke, Y.M.G. & Ides, S.J. (2008). Distribution and dynamics of intertidal macrobenthos predicted from remote sensing: response to microphytobenthos and environment. Marine Ecology Progress Series, 367, 57-72.
2007
  1. Alderkamp, A-C., Rijssel, M. van & Bolhuis, H. (2007). Characterization of marine bacteria and the activity of their enzyme systems involved in degradation of the algal storage glucan laminarin. FEMS Microbiology Ecology, 59, 108-117.
  2. Becker, S., Richl, P. & Ernst, A. (2007). Seasonal and habitat-related distribution pattern of Synechococcus genotypes in Lake Constance. FEMS Microbiology Ecology, 62, 64-77.
  3. Burns, D.G., Janssen, P.H., Itoh, T., Kamekura, M., Li, Z., Jensen, G., Rodríguez-Valera, F., Bolhuis, H. & Dyall-Smith, M.L. (2007). Haloquadratum walsbyi gen. nov., sp. nov., the square haloarchaeon of Walsby, isolated from saltern crystallizers in Australia and Spain. International Journal of Systematic and Evolutionary Microbiology, 57, 387-392.
  4. Drigo, B., Kowalchuk, G.A., Yergeau, E., Bezemer, T.M., Boschker, H.T.S. & Van Veen, J.A. (2007). Impact of elevated carbon dioxide on the rhizosphere communities of Carex arenaria and Festuca rubra. Global Change Biology, 13, 2396-2410.
  5. Gribsholt, B., Struyf, E., Tramper, A., Brabandere, L. De, Brion, N., Damme, S. Van, Meire, P., Dehairs, F., Middelburg, J.J. & Boschker, H.T.S. (2007). Nitrogen assimilation and short term retention in a nutrient-rich tidal freshwater marsh - a whole ecosystem 15N enrichment study. Biogeosciences, 4, 11-26.
  6. Herlory, O., Richard, P. & Blanchard, G.F. (2007). Methodology of light response curves: application of chlorophyll fluorescence to microphytobenthic biofilms. Marine Biology, 153, 91-101.
  7. Janknegt, P.J., Rijstenbil, J.W., Poll, W.H. van de, Gechev, T.S. & Buma, A.G.J. (2007). A comparison of quantitative and qualitative superoxide dismutase assays for application to low temperature microalgae. Journal of Photochemistry and Photobiology B: Biology, 87, 218-226.
  8. Kromkamp, J.C., Perkins, R., Dijkman, N.A., Consalvey, M., Andres, R. P. & Reid, R.P. (2007). Resistance to burial of cyanobacteria in stromatolites. Aquatic Microbial Ecology, 48, 123-130.
  9. Mes, T.H.M., Eysker, M. & Ploeger, H.W. (2007). A simple, robust and semi-automated parasite egg isolation protocol. Nature Protocols, 2(3), 486-489.
  10. Mes, T.H.M. & Putten, J.P.M. Van (2007). Positively selected codons in immune-exposed loops of the vaccine candidate OMP-P1 of Haemophilus influenzae. Journal of Molecular Evolution, 64, 411-422.
  11. Perkins, R., Kromkamp, J.C. & Reid, R.P. (2007). Importance of light and oxygen for photochemical reactivation in photosynthetic stromatolite communities after natural sand burial. Marine Ecology Progress Series, 349, 23-32.
  12. Poele, E.M. Te, Habets, M.N., Tan, G.Y.A., Ward, A.C., Goodfellow, M., Bolhuis, H. & Dijkhuizen, L. (2007). Prevalence and distribution of nucleotide sequences typical for pMEA-like accessory genetic elements in the genus Amycolatopsis. FEMS Microbiology Ecology, 61, 285-294.
  13. Roeselers, G., Stal, L.J. & Loosdrecht, C.M. van (2007). Development of a PCR for the detection and identification of cyanobacterial nifD genes. Journal of Microbiological Methods, 70, 550-556.
  14. Sahan, E., Sabbe, K., Creach, V., Hernandez-Raquet, G., Vyverman, W., Stal, L.J. & Muyzer, G. (2007). Community structure and seasonal dynamics of diatom biofilms and associated grazers in intertidal mudflats. Aquatic Microbial Ecology, 47, 253-266.
  15. Staal, M.J., Thar, R., Kühl, M., Loosdrecht, M.C.M. van, Wolf, G., Brouwer, J.F.C. De & Rijstenbil, J.W. (2007). Different carbon isotope fractionation in developing natural phototrophic biofilms. Biogeosciences, 4, 613-626.
  16. Staal, M.J., Hekkert, S. te Lintel, Brummer, G.J., Veldhuis, M., Sikkens, C., Persijn, S. & Stal, L.J. (2007). Nitrogen fixation along a north-south transect in the eastern Atlantic Ocean. Limnology and Oceanography, 52, 1305-1316.
  17. Staal, M.J., Rabouille, S.A.M. & Stal, L.J. (2007). On the role of oxygen for nitrogen fixation in the marine cyanobacterium Trichodesmium sp. Environmental Microbiology, 9, 727-736.
  18. Stal, L.J. (2007). Cyanobacteria: Diversity and versatility, Clues to Life in Extreme Environments. In J. Seckbach (Ed.), Algae and Cyanobacteria in Extreme Environments (pp. 659-680). Dordrecht: Springer.
  19. Stal, L.J. & Défarge, C. (2007). ERRATUM to: Structure and Dynamics of Exopolymers in an Intertidal Diatom Biofilm [Geomicrobiology Journal 22: 341-352, 2005]. Geomicrobiology Journal, 24, 77-77.
  20. Stomp, M., Huisman, J., Vörös, L., Pick, F.R., Laamanen, M., Haverkamp, T.H.A. & Stal, L.J. (2007). Colourful coexistence of red and green picocyanobacteria in lakes and seas. Ecology Letters, 10, 290-298.
  21. Stomp, M., Huisman, J., Stal, L.J. & Matthijs, H.C.P. (2007). Colourful niches of phototrophic microorganisms shaped by vibrations of the water molecule. ISME Journal, 1, 271–282.
  22. Veuger, B., Middelburg, J.J., Boschker, H.T.S. & Houtekamer, M.J. (2007). UPDATE of Analysis of 15N incorporation into D-alanine: A new method for tracing nitrogen uptake by bacteria (Veuger et al. 2005, Limnology and Oceanography Methods 3: 230-240). Limnology and Oceanography Methods, 5, 192-194.
  23. Yergeau, E., Bokhorst, S.F., Huiskes, A.H.L., Boschker, H.T.S., Aerts, R.A.M. & Kowalchuk, G.A. (2007). Size and structure of bacterial, fungal and nematode communities along an Antarctic environmental gradient. FEMS Microbiology Ecology, 59, 436-451.
  24. Zippel, B., Rijstenbil, J.W. & Neu, T.R. (2007). A flow-lane incubator for studying freshwater and marine phototrophic biofilms. Journal of Microbiological Methods, 70, 336-345.
2006
  1. Boison, G., Steingen, C., Stal, L.J. & Bothe, H. (2006). The rice field cyanobacteria Anabaena azotica and Anabaena sp. CH1 express vanadium-dependent nitrogenase. Archives of Microbiology, 186, 367-376.
  2. Bontes, B.M., Pel, R., Ibelings, B.W., Boschker, H.T.S., Middelburg, J.J. & Van Donk, E. (2006). The effects of biomanipulation on the biogeochemistry, carbon isotopic composition and pelagic food web relations of a shallow lake. Biogeosciences, 3, 69-83.
  3. Bouillon, S. & Boschker, H.T.S. (2006). Bacterial carbon sources in coastal sediments: a cross-system analysis based on stable isotope data of biomarkers. Biogeosciences, 3, 175-185.
  4. Brouwer, J.F.C. De, Neu, T.R. & Stal, L.J. (2006). On the function of secreation of extracellular polymeric substances by benthic diatoms and their role in intertidal mudflats: A review of recent insights and views. In J.C. Kromkamp, J.F.C. De Brouwer, G.F. Blanchard, R.M. Forster & V. Créach (Eds.), Functioning of Microphytobenthos in Estuaries : Proceedings of the Colloquium, Amsterdam, 21-23 August 2003 (pp. 45-61). Amsterdam: Royal Netherlands Academy of Arts and Sciences.
  5. Brouwer, J.F.C. De, Cooksey, K.E., Wigglesworth-Cooksey, B., Staal, M.J., Stal, L.J. & Avci, R. (2006). Time of FLight-Secondary Ion Mass Spectrometry on isolated extracellular fractions and intact biofilms of three species of benthic diatoms. Journal of Microbiological Methods, 65, 562-572.
  6. Créach, V., Ernst, A., Sabbe, K., Stal, L.J., Vanelslander, B. & Vyverman, W. (2006). Using quantitative PCR to determine the distribution of a semicryptic benthic diatom, Navicula phyllepta (Bacillariophyceae). Journal of Phycology, 42, 1142-1154.
  7. Deronde, B., Kempeneers, P. & Forster, R.M. (2006). Imaging spectroscopy as a tool to study sediment characteristics on a tidal sandbank in the Westerschelde. Estuarine Coastal and Shelf Science, 69, 580-590.
  8. Dijkman, N.A. & Kromkamp, J.C. (2006). Phospholipid-derived fatty acids as chemotaxonomic markers for phytoplankton: application for inferring phytoplankton composition. Marine Ecology Progress Series, 324, 113-125.
  9. Dijkman, N.A. & Kromkamp, J.C. (2006). Photosynthetic characteristics of the phytoplankton in the Scheldt estuary: community and single-cell fluorescence measurements. European Journal of Phycology, 41, 425-434.
  10. Forster, R.M. & Kromkamp, J.C. (2006). Estimating primary production: scaling up from point measurements to the whole estuary. In J.C. Kromkamp, J.F.C. De Brouwer, G.F. Blanchard, R.M. Forster & V. Créach (Eds.), Functioning of Microphytobenthos in Estuaries : Proceedings of the Colloquium, Amsterdam, 21-23 August 2003 (pp. 109-120). Amsterdam: Royal Netherlands Academy of Arts and Sciences.
  11. Forster, R.M., Créach, V., Sabbe, K., Vyverman, W. & Stal, L.J. (2006). Biodiversity-ecosystem function relationship in microphytobenthic diatoms of the Westerschelde estuary. Marine Ecology Progress Series, 311, 191-201.
  12. Forster, R.M. & Jesus, B. (2006). Field spectroscopy of estuarine intertidal habitats. International Journal of Remote Sensing, 27, 3657-3669.
  13. Gribsholt, B., Struyf, E., Tramper, A., Andersson, M.G.I., Brion, N., Brabandere, L. De, Damme, S. Van, Meire, P., Middelburg, J.J., Dehairs, F. & Boschker, H.T.S. (2006). Ammonium transformation in a nitrogen-rich tidal freshwater marsh. Biogeochemistry, 80, 289-298.
  14. Huiskes, A.H.L., Boschker, H.T.S., Lud, D. & Moerdijk-Poortvliet, T.C.W. (2006). Stable isotope ratio analysis as a tool for assessing habitat differentiation in Antarctic terrestrial ecosystems. Plant Ecology, 182, 79-86.
  15. Kromkamp, J.C., Brouwer, J.F.C. De, Blanchard, G.F., Forster, R.M. & Créach, V. (2006). Functioning of Microphytobenthos in Estuaries : Proceedings of the Colloquium Amsterdam, 21-23 August 2003. Amsterdam: Royal Netherlands Academy of Arts and Sciences.
  16. Kromkamp, J.C. & Forster, R.M. (2006). Developments in microphytobenthos primary productivity studies. In J.C. Kromkamp, J.F.C. De Brouwer, G.F. Blanchard, R.M. Forster & V. Créach (Eds.), Functioning of Microphytobenthos in Estuaries : Proceedings of the Colloquium, Amsterdam, 21-23 August 2003 (pp. 9-30). Amsterdam: Royal Netherlands Academy of Arts and Sciences.
  17. Kromkamp, J.C., Morris, E.P., Forster, R.M., Honeywill, C., Hagerthey, S. & Paterson, D.M. (2006). Relationship of intertidal surface sediment chlorophyll concentration to hyper-spectral reflectance and chlorophyll fluorescence. Estuaries and Coasts, 29, 183-196.
  18. MacGregor, B.J., Boschker, H.T.S. & Amann, R. (2006). Comparison of rRNA and Polar-Lipid-Derived fatty acid biomarkers for following 13C-substrate incorporation by microorganisms in marine sediments. Applied and Environmental Microbiology, 72, 5246-5253.
  19. Malea, P., Rijstenbil, J.W. & Haritonidis, S. (2006). Effects of cadmium, zinc and nitrogen status on nonprotein thiols in the macroalgae Enteromorpha spp. from the Scheldt Estuary (SW Netherlands, Belgium) and Thermaikos Gulf (Greece, N Aegean Sea). Marine Environmental Research, 62, 45-60.
  20. Mes, T.H.M. & Doeleman, M.W. (2006). Positive selection on transposase genes of insertion sequences in the Crocosphaera watsonii genome. Journal of Bacteriology, 188, 7176-7185.
  21. Mes, T.H.M., Doeleman, M.W., Lodders, N., Nübel, U. & Stal, L.J. (2006). Selection on protein-coding genes of natural cyanobacterial populations. Environmental Microbiology, 8, 1534-1543.
  22. Müller, L.N., Brouwer, J.F.C. De, Almeida, J.S., Stal, L.J. & Xavier, J.B. (2006). Analysis of a marine phototrophic biofilm by confocal laser scanning microscopy using the new image quantification software PHLIP. BMC Ecology, 6, 1 [1-15].
  23. Rabouille, S.A.M., Staal, M.J., Stal, L.J. & Soetaert, K.E.R. (2006). Modeling the dynamic regulation of nitrogen fixation in the cyanobacterium Trichodesmium sp. Applied and Environmental Microbiology, 72, 3217-3227.
  24. Roeselers, G., Zippel, B., Staal, M.J., Loosdrecht, M.C.M. van & Muyzer, G. (2006). On the reproducibility of microcosms experiments - different community composition in parallel phototrophic biofilm microcosms. FEMS Microbiology Ecology, 58, 169-178.
  25. Struyf, E., Dausse, A., Damme, S. Van, Bal, K., Gribsholt, B., Boschker, H.T.S. & Meire, P. (2006). Tidal marshes and biogenic silica recycling at the land-sea interface. Limnology and Oceanography, 51, 838-846.
  26. Tolhurst, T.J., Defew, E.C., Brouwer, J.F.C. De, Wolfstein, K., Stal, L.J. & Paterson, D.M. (2006). Small-scale temporal and spatial variability in the erosion threshold and properties of cohesive intertidal sediments. Continental Shelf Research, 26, 351-362.
  27. Van Bergeijk, S.A., Wollenzien, U.I.A., Schönefeldt, K. & Stal, L.J. (2006). Seasonal variation of dimethylsulfoniopropionate in related to microphytobenthos in estuarine intertidal sediments. Marine Ecology Progress Series, 320, 55-63.
  28. Van der Wal, A., Van Veen, J.A., Smant, W., Boschker, H.T.S., Bloem, J., Kardol, P., Van der Putten, W.H. & De Boer, W. (2006). Fungal biomass development in a chronosequence of land abandonment. Soil Biology & Biochemistry, 38, 51-60.
  29. Veuger, B., Van Oevelen, D., Boschker, H.T.S. & Middelburg, J.J. (2006). Fate of peptidoglycan in an intertidal sediment: an in situ 13C-labeling study. Limnology and Oceanography, 51, 1572-1580.
2005
  1. Boschker, H.T.S., Kromkamp, J.C. & Middelburg, J.J. (2005). Biomarker and carbon isotopic constraints on bacterial and algal community structure and functioning in a turbid, tidal estuary. Limnology and Oceanography, 50, 70-80.
  2. Bothe, H. & Boison, G. (2005). Electron donation and alternative nitrogenases in cyanobacterial dinitrogen fixation. In Y.-P. Wang, M. Lin, Z.-X. Tian, C. Elmerich & W.E. Newton (Eds.), Biological Nitrogen Fixation, Sustainable Agriculture and the Environment: Proceedings of the 14th International Nitrogen Fixation Congress (pp. 349-353). Dordrecht: Springer.
  3. Brouwer, J.F.C. De, Wolfstein, K., Ruddy, G.K., Jones, T.H. & Stal, L.J. (2005). Biogenic stabilization of intertidal sediments: the importance of extracellular polymeric substances produced by benthic diatoms. Microbial Ecology, 49, 501-512.
  4. Dijkman, N.A. & Kromkamp, J.C. (2005). Group-specific primary production in the Scheldt estuary. In A. Van der Est & D. Bruce (Eds.), Photosynthesis: Fundamental Aspects to Global Perspectives. Proceedings of the 13th International Congress on Photosynthesis Montreal, Canada, 2004 (pp. 993-995). International Society of Photosynthesis.
  5. Ernst, A., Deicher, M., Herman, P.M.J. & Wollenzien, U.I.A. (2005). Nitrate and Phosphate Affect Cultivability of Cyanobacteria from Environments with Low Nutrient Levels. Applied and Environmental Microbiology, 71, 3379-3383.
  6. Forster, R.M. & Martin-Jézéquel, V.R. (2005). Photophysiological variability of microphytobenthic diatoms after growth in different types of culture conditions. Phycologia, 44, 393-402.
  7. Gribsholt, B., Boschker, H.T.S., Struyf, E., Andersson, M.G.I., Tramper, A., Brabandere, L. De, Damme, S. Van, Brion, N., Meire, P., Dehairs, F., Middelburg, J.J. & Heip, C.H.R. (2005). Nitrogen processing in a tidal freshwater marsh: a whole ecosystem 15N labeling study. Limnology and Oceanography, 50, 1945-1959.
  8. Huiskes, A.H.L., Boschker, H.T.S., Lud, D., Moerdijk-Poortvliet, T.C.W. & Cannone, N. (2005). Stable isotope ratios as a tool for assessing the marine influence on Antarctic terrestrial ecosystems. In N. Cannone & M. Guglielmin (Eds.), 5th Workshop on Regional Sensitivity to Climate Change in Antarctic Terrestrial and Limnetic Ecosystems (Terra Antarctica Reports No. 11) (pp. 33-36). Siena: Terra Antarctica Publication.
  9. Kromkamp, J.C., Dijkman, N.A. & Peene, J. (2005). Estimating phytoplankton primary production by means of PAM, FRRF, oxygen exchange and c-fixation. In A. Van der Est & D. Bruce (Eds.), Photosynthesis: Fundamental Aspects to Global Perspectives. Proceedings of the 13th International Congress on Photosynthesis Montreal, Canada, 2004 (pp. 991-992). International Society of Photosynthesis.
  10. Kromkamp, J.C. & Claquin, P. (2005). Role of the cell cycle in the metabolism of marine microalgae. In D.V. Subba Rao (Ed.), Algal Cultures, Analogues of Blooms and Apllications (pp. 385-406). Enfield (NH), USA, [etc.]: Science Publishers.
  11. Kromkamp, J.C. & Peene, J. (2005). Changes in phytoplankton biomass and primary production between 1991 and 2001 in the Westerschelde estuary (Belgium/The Netherlands). Hydrobiologia, 540, 117-126.
  12. López-López, A., Bartual, S. G., Stal, L.J., Onyshchenko, O. & Rodríguez-Valera, F. (2005). Genetic analysis of housekeeping genes reveals a deep-sea ecotype of Alteromonas macleodii in the Mediterranean Sea. Environmental Microbiology, 7, 649-659.
  13. Mes, T.H.M. & Stal, L.J. (2005). Variable selection pressures across lineages in Trichodesmium and related cyanobacteria based on the heterocyst differentiation protein gene hetR. Gene, 346, 163-171.
  14. Moodley, L., Middelburg, J.J., Soetaert, K.E.R., Boschker, H.T.S., Herman, P.M.J. & Heip, C.H.R. (2005). Similar rapid response to phytodetritus deposition in shallow and deep-sea sediments. Journal of Marine Research, 63, 457-469.
  15. Rijstenbil, J.W. (2005). UV- and salinity-induced oxidative effects in the marine diatom Cylindrotheca closterium during simulated emersion. Marine Biology, 147, 1063-1073.
  16. Stal, L.J. & Défarge, C. (2005). Structure and dynamics of exopolymers in an intertidal diatom biofilm. Geomicrobiology Journal, 22, 341-352.
  17. Veuger, B., Middelburg, J.J., Boschker, H.T.S. & Houtekamer, M.J. (2005). Analysis of 15N incorporation into D-alanine: a new method for tracing nitrogen uptake by bacteria. Limnology and Oceanography Methods, 3, 230-240.
Varicolored Marine Microbiology group; Purple Sulfurs flanked by Cyanos