Crystal ball - 2013

Environmental Microbiology Reports

Volumn 5, Issue 1, 2013, Pages 1-16

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EID: 84873297480     PISSN: None     EISSN: 17582229     Source Type: Journal    
DOI: 10.1111/1758-2229.12021     Document Type: Article

References (82)

1. 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: 1254-1262.
2. McDonald, K.L., and Auer, M. (2006) High-pressure freezing, cellular tomography and structural cell biology. Biotechniques 41: 137-141.
3. Palsdottir, H., Remis, J.P., Schaudinn, C., O'Toole, E., Lux, R., Shi, W., etal. (2009) Three-dimensional macromolecular organization of cryo-fixed Myxococcus xanthus biofilms, as revealed by electron microscopic tomography. J Bacteriol 191: 2077-2082.
4. Caporaso, J.G., Lauber, C.L., Costello, E.K., Berg-Lyons, D., Gonzalez, A., Stombaugh, J., etal. (2011) Moving pictures of the human microbiome. Genome Biol 12: R50.
5. Gilbert, J.A., Field, D., Swift, P., Newbold, L., Oliver, A., Smyth, T., etal. (2009) The seasonal structure of microbial communities in the Western English Channel. Environ Microbiol 11: 3132-3139.
6. Ottesen, E.A., Marin, R., 3rd, Preston, C.M., Young, C.R., Ryan, J.P., Scholin, C.A., and DeLong, E.F. (2011) Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton. ISME J 5: 1881-1895.
7. Ottesen, E.A., Young, C.R., Eppley, J.M., Ryan, J.P., Chavez, F.P., Scholin, C., and DeLong, E.F. (2012) Pattern and synchrony of gene expression among sympatric marine microbial populations. Proc Natl Acad Sci USA (in press).
8. Pace, N.R. (1997) A molecular view of microbial diversity and the biosphere. Science 276: 734-740.
9. Rinta-Kanto, J.M., Sun, S., Sharma, S., Kiene, R.P., and Moran, M.A. (2012) Bacterial community transcription patterns during a marine phytoplankton bloom. Environ Microbiol 14: 228-239.
10. Stahl, D.A. (1993) The natural history of microorganisms. ASM News 59: 609-613.
11. Teeling, H., Fuchs, B.M., Becher, D., Klockow, C., Gardebrecht, A., Bennke, C.M., etal. (2012) Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science 336: 608-611.
12. Woese, C.R. (1994) Microbiology in transition. Proc Natl Acad Sci USA 91: 1601-1603.
13. 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: 4909-4912.
14. 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: 941-956.
15. 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.
16. 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: 503-528.
17. Attard, E., Poly, F., Commeaux, C., Laurent, F., Terada, A., Smets, B.F., etal. (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: 315-326.
18. 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).
19. 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: 5371-5382.
20. 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: 82-89.
21. Chain, P., Lamerdin, J., Larimer, F., Regala, W., Lao, V., Land, M., etal. (2003) Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J Bacteriol 185: 2759-2773.
22. Ettwig, K.F., Shima, S., van de Pas-Schoonen, K.T., Kahnt, J., Medema, M.H., Op den Camp, H.J M., etal. (2008) Denitrifying bacteria anaerobically oxidize methane in the absence of Archaea. Environ Microbiol 10: 3164-3173.
23. Ettwig, K.F., Butler, M.K., Le Paslier, D., Pelletier, E., Mangenot, S., Kuypers, M.M.M., etal. (2010) Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature 464: 543-548.
24. Fleischmann, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R., etal. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496-512.
25. Harhangi, H.R., Le Roy, M., van Alen, T., Hu, B.-l., Groen, J., Kartal, B., etal. (2012) Hydrazine synthase, a unique phylomarker with which to study the presence and biodiversity of anammox bacteria. Appl Environ Microbiol 78: 752-758.
26. Hatzenpichler, R. (2012) Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea. Appl Environ Microbiol 78: 7501-7510.
27. Hou, S., Makarova, K., Saw, J., Senin, P., Ly, B., Zhou, Z., etal. (2008) Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct 3: 26-51.
28. 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).
29. 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: 1534-1545.
30. Islam, T., Jensen, S., Reigstad, L.J., Larsen, O., and Birkeland, N.-K. (2008) Methane oxidation at 55°C and pH2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum. Proc Natl Acad Sci USA 105: 300-304.
31. Kartal, B., Geerts, W., and Jetten, M.S.M. (2011a) Cultivation, detection, and ecophysiology of anaerobic ammonium-oxidizing bacteria. Methods Enzymol 486: 89-108.
32. Kartal, B., Maalcke, W.J., de Almeida, N.M., Cirpus, I., Gloerich, J., Geerts, W., etal. (2011b) Molecular mechanism of anaerobic ammonium oxidation. Nature 479: 127-130.
33. 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: 1515-1530.
34. 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: 303-311.
35. Klotz, M.G., and Stein, L.Y. (2008) Nitrifier genomics and evolution of the nitrogen cycle. FEMS Microbiol Lett 278: 146-156.
36. 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. 57-93.
37. 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: 3150-3163.
38. 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: 543-546.
39. 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: 781-790.
40. Lücker, S., Wagner, M., Maixner, F., Pelletier, E., Koch, H., Vacherie, B., etal. (2010) A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc Natl Acad Sci USA 107: 13479-13484.
41. Luesken, F.A., Wu, M.L., Op den Camp, H.J.M., Keltjens, J.T., Stunnenberg, H., Francoijs, K.-J., etal. (2012) Effect of oxygen on the anaerobic methanotroph Candidatus 'Methylomirabilis oxyfera': kinetic and transcriptional analysis. Environ Microbiol 14: 1024-1034.
42. 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: 4704-4712.
43. Schmid, M.C., Hooper, A.B., Klotz, M.G., Woebken, D., Lam, P., Kuypers, M.M., etal. (2008) Environmental detection of octahaem cytochrome c hydroxylamine/hydrazine oxidoreductase genes of aerobic and anaerobic ammonium-oxidizing bacteria. Environ Microbiol 10: 3140-3149.
44. 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: 114-135.
45. Sorokin, D.Y., Lucker, S., Vejmelkova, D., Kostrikina, N.A., Kleerebezem, R., Rijpstra, W.I.C., etal. (2012) Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi. ISME J 6: 2245-2256.
46. Spang, A., Poehlein, A., Offre, P., Zumbrägel, S., Haider, S., Rychlik, N., etal. (2012) The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations. Environ Microbiol 14: 3122-3145.
47. 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).
48. Stein, L.Y., and Klotz, M.G. (2011) Nitrifying and denitrifying pathways of methanotrophic bacteria. Biochem Soc Trans 39: 1826-1831.
49. 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: 329-356.
50. Strous, M., Pelletier, E., Mangenot, S., Rattei, T., Lehner, A., Taylor, M.W., etal. (2006) Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 440: 790-794.
51. 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: 91-100.
52. Walker, C.B., de la Torre, J.R., Klotz, M.G., Urakawa, H., Pinel, N., Arp, D.J., etal. (2010) Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc Natl Acad Sci USA 107: 8818-8823.
53. Zumft, W.G. (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev 61: 522-616.
54. Barron, A.R., Wurzburger, N., Bellenger, J.P., Wright, S.J., Kraepiel, A.M.L., and Hedin, L.O. (2009) Molybdenum limitation of asymbiotic nitrogen fixation in tropical forest soils. Nat Geosci 2: 42-45. doi: 10.1038/NGEO366.
55. Martin, J.H., Coale, K.H., Johnson, K.S., Fitzwater, S.E., Gordon, R.M., Tanner, S.J., etal. (1994) Testing the iron hypothesis in ecosystems of the equatorial Pacific Ocean. Nature 371: 123-129. doi: 10.1038/371123a0.
56. Sandy, M., and Butler, A. (2009) Microbial iron acquisition: marine and terrestrial siderophores. Chem Rev 109: 4580-4595. doi: 10.1021/cr9002787.
57. Velasquez, I., Nunn, B.L., Ibisanmi, E., Goodlett, D.R., Hunter, K.A., and Sander, S.G. (2011) Detection of hydroxamate siderophores in coastal and Sub-Antarctic waters off the South Eastern Coast of New Zealand. Mar Chem 126: 97-107. doi: 10.1016/j.marchem.2011.04.003.
58. Conley, D.J., Paerl, H.W., Howarth, R.W., Boesch, D.F., Seitzinger, S.P., Havens, K.E., etal. (2009) Controlling eutrophication: nitrogen and phosphorus. Science 323: 1014-1015.
59. Lunetta, R.S., Knight, J.F., Paerl, H.W., Streicher, J.J., Peierls, B.L., Gallo, T., etal. (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: 3291-3314.
60. Nixon, S.W. (1995) Coastal marine eutrophication: a definition, social causes, and future concerns. Ophelia 41: 199-219.
61. 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: 3480-3488.
62. Paerl, H.W., and Huisman, J. (2008) Blooms like it hot. Science 320: 57-58.
63. 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: 7756-7758.
64. Schindler, D.W., Hecky, R.E., Findlay, D.L., Stainton, M.P., Parker, B.R., Paterson, M., etal. (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: 11254-11258.
65. 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: 1477-1496.
66. 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: 59-69.
67. 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: 68-75.
68. 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: 420-432.
69. Ballor, N.R., and Leadbetter, J.R. (2012) Analysis of extensive [FeFe] hydrogenase gene diversity within the gut microbiota of insects representing five families of Dictyoptera. Microb Ecol 63: 586-595.
70. Colman, D.R., Toolson, E.C., and Takacs-Vesbach, C.D. (2012) Do diet and taxonomy influence insect gut bacterial communities? Mol Ecol 21: 5124-5137.
71. Leidy, J. (1881) The parasites of termites. J Acad Nat Sci Phila 8: 425-447.
72. Ley, R.E., Hamady, M., Lozupone, C., Turnbaugh, P.J., Ramey, R.R., Bircher, J.S., etal. (2008) Evolution of mammals and their gut microbes. Science 320: 1647-1651.
73. Mazmanian, S.K., Liu, C.H., Tzianabos, A.O., and Kasper, D.L. (2005) An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122: 107-118.
74. Noda, S., Hongoh, Y., Sato, T., and Ohkuma, M. (2009) Complex coevolutionary history of symbiotic Bacteroidales bacteria of various protists in the gut of termites. BMC Evol Biol 9: 158.
75. Schauer, C., Thompson, C.L., and Brune, A. (2012) The bacterial community in the gut of the cockroach Shelfordella lateralis reflects the close evolutionary relatedness of cockroaches and termites. Appl Environ Microbiol 78: 2758-2767.
76. Warnecke, F., Luginbühl, P., Ivanova, N., Ghassemian, M., Richardson, T.H., Stege, J.T., etal. (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450: 560-565.
77. Faust, K., Sathirapongsasuti, J.F., Izard, J., Segata, N., Gevers, D., Raes, J., and Huttenhower, C. (2012) Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol 8: e1002606. doi: 10.1371/journal.pcbi.1002606.
78. Friedman, J., and Alm, E.J. (2012) Inferring correlation networks from genomic survey data. PLoS Comput Biol 8: e1002687. doi: 10.1371/journal.pcbi.1002687.
79. Lawley, T.D., Clare, S., Walker, A.W., Stares, M.D., Connor, T.R., Raisen, C., etal. (2012) Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice. PLoS Pathog 8: e1002995. doi: 10.1371/journal.ppat.1002995.
80. Lovell, D., Müller, W.M., Taylor, J., Zwart, A., and Helliwell, C. (2010) Caution! Compositions! Can constraints on omics data lead analyses astray? CSIRO: 1-44.
81. Romano, J.P., Shaikh, A.M., and Wolf, M. (2008) Control of the false discovery rate under dependence using the bootstrap and subsampling. Test 17: 417-442.
82. Xia, L.C., Steele, J.A., Cram, J.A., Cardon, Z.G., Simmons, S.L., Vallino, J.J., etal. (2011) Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. BMC Syst Biol 5 (Suppl. 2): S15.