SEARCH

SEARCH BY CITATION

References

  • Dohnalkova, A.C., Marshall, M.J., Areay, B.W., Williams, K.H., Buck, E.C., and Fredrickson, J.K. (2011) Imaging hydrated microbial extracellular polymers: comparative analysis by electron microscopy. Appl Environ Microbiol 77: 12541262.
  • McDonald, K.L., and Auer, M. (2006) High-pressure freezing, cellular tomography and structural cell biology. Biotechniques 41: 137141.
  • Palsdottir, H., Remis, J.P., Schaudinn, C., O'Toole, E., Lux, R., Shi, W., et al. (2009) Three-dimensional macromolecular organization of cryo-fixed Myxococcus xanthus biofilms, as revealed by electron microscopic tomography. J Bacteriol 191: 20772082.

References

References

  • Cadel-Six, S., Iteman, I., Peyraud-Thomas, C., Mann, S., Ploux, O., and Méjean, A. (2009) Identification of a polyketide synthase coding sequence specific for anatoxin-a producing Oscillatoria. Appl Environ Microbiol 75: 49094912.
  • Corringer, P.J., Poitevin, F., Prevost, M.S., Sauguet, L., Delarue, M., and Changeux, J.P. (2012) Structure and pharmacology of pentameric receptor channels: from bacteria to brain. Structure 20: 941956.
  • Wang, H., Fewer, D.P., and Sivonen, K. (2011) Genome mining demonstrates the widespread occurrence of gene clusters encoding bacteriocins in cyanobacteria. PLoS ONE 6: e22384.

References

  • Arp, D.J., Chain, P.S., and Klotz, M.G. (2007) The impact of genome analyses on our understanding of ammonia-oxidizing bacteria. Annu Rev Microbiol 61: 503528.
  • Attard, E., Poly, F., Commeaux, C., Laurent, F., Terada, A., Smets, B.F., et al. (2010) Shifts between Nitrospira- and Nitrobacter-like nitrite oxidizers underlie the response of soil potential nitrite oxidation to changes in tillage practices. Environ Microbiol 12: 315326.
  • Bartossek, R., Spang, A., Weidler, G., Lanzen, A., and Schleper, C. (2012) Metagenomic analysis of ammonia oxidizing archaea affiliated with the soil group. Front Microbiol 3: e208 (201–214).
  • Bergmann, D.J., Hooper, A.B., and Klotz, M.G. (2005) Structure and sequence conservation of hao cluster genes of autotrophic ammonia-oxidizing bacteria: evidence for their evolutionary history. Appl Environ Microbiol 71: 53715382.
  • Campbell, M.A., Nyerges, G., Kozlowski, J.A., Poret-Peterson, A.T., Stein, L.Y., and Klotz, M.G. (2011) Model of the molecular basis for hydroxylamine oxidation and nitrous oxide production in methanotrophic bacteria. FEMS Microbiol Lett 322: 8289.
  • Chain, P., Lamerdin, J., Larimer, F., Regala, W., Lao, V., Land, M., et al. (2003) Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J Bacteriol 185: 27592773.
  • Ettwig, K.F., Shima, S., van de Pas-Schoonen, K.T., Kahnt, J., Medema, M.H., Op den Camp, H.J M., et al. (2008) Denitrifying bacteria anaerobically oxidize methane in the absence of Archaea. Environ Microbiol 10: 31643173.
  • Ettwig, K.F., Butler, M.K., Le Paslier, D., Pelletier, E., Mangenot, S., Kuypers, M.M.M., et al. (2010) Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature 464: 543548.
  • Fleischmann, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R., et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496512.
  • Harhangi, H.R., Le Roy, M., van Alen, T., Hu, B.-l., Groen, J., Kartal, B., et al. (2012) Hydrazine synthase, a unique phylomarker with which to study the presence and biodiversity of anammox bacteria. Appl Environ Microbiol 78: 752758.
  • Hatzenpichler, R. (2012) Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea. Appl Environ Microbiol 78: 75017510.
  • Hou, S., Makarova, K., Saw, J., Senin, P., Ly, B., Zhou, Z., et al. (2008) Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct 3: 2651.
  • Hu, Z., Speth, D.R., Francoijs, K.-J., Quan, Z.-X., and Jetten, M. (2012) Metagenome analysis of a complex community reveals the metabolic blueprint of anammox bacterium Candidatus Jettenia asiatica. Front Microbiol 3: e366 (361–369).
  • Hyman, M.R., and Arp, D.J. (1992) 14C2H2- and 14CO2-labeling studies of the de novo synthesis of polypeptides by Nitrosomonas europaea during recovery from acetylene and light inactivation of ammonia monooxygenase. J Biol Chem 267: 15341545.
  • Islam, T., Jensen, S., Reigstad, L.J., Larsen, O., and Birkeland, N.-K. (2008) Methane oxidation at 55°C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum. Proc Natl Acad Sci USA 105: 300304.
  • Kartal, B., Geerts, W., and Jetten, M.S.M. (2011a) Cultivation, detection, and ecophysiology of anaerobic ammonium-oxidizing bacteria. Methods Enzymol 486: 89108.
  • Kartal, B., Maalcke, W.J., de Almeida, N.M., Cirpus, I., Gloerich, J., Geerts, W., et al. (2011b) Molecular mechanism of anaerobic ammonium oxidation. Nature 479: 127130.
  • Kern, M., Klotz, M.G., and Simon, J. (2011) The Wolinella succinogenes mcc gene cluster encodes an unconventional respiratory sulphite reduction system. Mol Microbiol 82: 15151530.
  • Klotz, M.G., and Norton, J.M. (1998) Multiple copies of ammonia monooxygenase (amo) operons have evolved under biased AT/GC mutational pressure in ammonia-oxidizing autotrophic bacteria. FEMS Microbiol Lett 168: 303311.
  • Klotz, M.G., and Stein, L.Y. (2008) Nitrifier genomics and evolution of the nitrogen cycle. FEMS Microbiol Lett 278: 146156.
  • Klotz, M.G., and Stein, L.Y. (2011) Genomics of ammonia-oxidizing bacteria and insights to their evolution. In Nitrification. Ward, B.B. , Arp, D.J. , and Klotz, M.G. (eds). Washington, D.C.: ASM Press, pp. 5793.
  • Klotz, M.G., Schmid, M.C., Strous, M., op den Camp, H.J., Jetten, M.S., and Hooper, A.B. (2008) Evolution of an octahaem cytochrome c protein family that is key to aerobic and anaerobic ammonia oxidation by bacteria. Environ Microbiol 10: 31503163.
  • Könneke, M., Bernhard, A.E., de la Torre, J.R., Walker, C.B., Waterbury, J.B., and Stahl, D.A. (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437: 543546.
  • Li, M., Hong, Y., Klotz, M.G., and Gu, J.D. (2010) A comparison of primer sets for detecting 16S rRNA and hydrazine oxidoreductase genes of anaerobic ammonium-oxidizing bacteria in marine sediments. Appl Microbiol Biotechnol 86: 781790.
  • Lücker, S., Wagner, M., Maixner, F., Pelletier, E., Koch, H., Vacherie, B., et al. (2010) A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc Natl Acad Sci USA 107: 1347913484.
  • Luesken, F.A., Wu, M.L., Op den Camp, H.J.M., Keltjens, J.T., Stunnenberg, H., Francoijs, K.-J., et al. (2012) Effect of oxygen on the anaerobic methanotroph Candidatus ‘Methylomirabilis oxyfera’: kinetic and transcriptional analysis. Environ Microbiol 14: 10241034.
  • Rotthauwe, J.H., Witzel, K.P., and Liesack, W. (1997) The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl Environ Microbiol 63: 47044712.
  • Schmid, M.C., Hooper, A.B., Klotz, M.G., Woebken, D., Lam, P., Kuypers, M.M., et al. (2008) Environmental detection of octahaem cytochrome c hydroxylamine/hydrazine oxidoreductase genes of aerobic and anaerobic ammonium-oxidizing bacteria. Environ Microbiol 10: 31403149.
  • Simon, J., and Klotz, M.G. (2013) Diversity and evolution of bioenergetic systems involved in microbial nitrogen compound transformations. Biochim Biophys Acta (BBA)-Bioenergetics 1827: 114135.
  • Sorokin, D.Y., Lucker, S., Vejmelkova, D., Kostrikina, N.A., Kleerebezem, R., Rijpstra, W.I.C., et al. (2012) Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi. ISME J 6: 22452256.
  • Spang, A., Poehlein, A., Offre, P., Zumbrägel, S., Haider, S., Rychlik, N., et al. (2012) The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations. Environ Microbiol 14: 31223145.
  • Speth Daan, R., Hu, B., Bosch, N., Keltjens, J., Stunnenberg, H., and Jetten, M. (2012) Comparative genomics of two independently enriched Candidatus Kuenenia stuttgartiensis anammox bacteria. Front Microbiol 3: e307 (301–307).
  • Stein, L.Y., and Klotz, M.G. (2011) Nitrifying and denitrifying pathways of methanotrophic bacteria. Biochem Soc Trans 39: 18261831.
  • Stein, L.Y., and Yung, Y.L. (2003) Production, isotopic composition, and atmospheric fate of biologically produced nitrous oxide. Annu Rev Earth Planet Sci 31: 329356.
  • Strous, M., Pelletier, E., Mangenot, S., Rattei, T., Lehner, A., Taylor, M.W., et al. (2006) Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 440: 790794.
  • Tavormina, P.L., Orphan, V.J., Kalyuzhnaya, M.G., Jetten, M.S.M., and Klotz, M.G. (2011) A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs. Environ Microbiol Rep 3: 91100.
  • Walker, C.B., de la Torre, J.R., Klotz, M.G., Urakawa, H., Pinel, N., Arp, D.J., et al. (2010) Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc Natl Acad Sci USA 107: 88188823.
  • Zumft, W.G. (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev 61: 522616.

References

References

  • Conley, D.J., Paerl, H.W., Howarth, R.W., Boesch, D.F., Seitzinger, S.P., Havens, K.E., et al. (2009) Controlling eutrophication: nitrogen and phosphorus. Science 323: 10141015.
  • Lunetta, R.S., Knight, J.F., Paerl, H.W., Streicher, J.J., Peierls, B.L., Gallo, T., et al. (2009) Measurement of water color using AVIRIS Imagery to assess the potential for an operational monitoring capability in the Pamlico Sound Estuary, USA. Int J Remote Sens 30: 32913314.
  • Nixon, S.W. (1995) Coastal marine eutrophication: a definition, social causes, and future concerns. Ophelia 41: 199219.
  • Otten, T.G., Xu, H., Qin, B., Zhu, G., and Paerl, H.W. (2012) Spatiotemporal patterns and ecophysiology of toxigenic Microcystis blooms in Lake Taihu, China: implications for water quality management. Environ Sci Technol 46: 34803488.
  • Paerl, H.W., and Huisman, J. (2008) Blooms like it hot. Science 320: 5758.
  • Paerl, H.W., and Scott, J.T. (2010) Throwing fuel on the fire: synergistic effects of excessive nitrogen inputs and global warming on harmful algal blooms. Environ Sci Technol 44: 77567758.
  • Schindler, D.W., Hecky, R.E., Findlay, D.L., Stainton, M.P., Parker, B.R., Paterson, M., et al. (2008) Eutrophication of lakes cannot be controlled by reducing nitrogen input: results of a 37 year whole ecosystem experiment. Proc Natl Acad Sci USA 105: 1125411258.
  • Schofield, O., Grzymski, J., Bissett, W.P., Kirkpatrick, G.J., Millie, D.F., Moline, M., and Roesler, C.S. (1999) Optical monitoring and forecasting systems for harmful algal blooms: possibility or pipe dream? J Phycol 35: 14771496.
  • Singh, D. (2011) Generation and evaluation of gross primary productivity using Landsat data through blending with MODIS data. Int J Appl Earth Obs Geoinf 13: 5969.
  • Wheeler, S.M., Morrissey, L.A., Levine, S.N., Livingston, G.P., and Vincent, W.F. (2012) Mappingcyanobacterial blooms in Lake Champlain's Missisquoi Bay using QuickBird and MERIS satellite data. J Great Lakes Res 38: 6875.
  • Xu, H., Paerl, H.W., Qin, B., Zhu, G., and Gao, G. (2010) Nitrogen and phosphorus inputs control phytoplankton growth in eutrophic Lake Taihu, China. Limnol Oceanogr 55: 420432.

References

References