Problems and promises of assaying the genetic potential for nitrogen fixation in the marine environment

Microbial Ecology

Volumn 32, Issue 3, 1996, Pages 263-281

  Zehr, J P ^a   Capone, D G ^b  

^a RENSSELAER POLYTECHNIC INSTITUTE   (United States)

^b UNIVERSITY OF MARYLAND CENTER FOR ENVIRONMENTAL SCIENCE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL TECHNIQUES; MOLECULAR APPROACH; NITROGEN FIXATIOIN;

EID: 0030303003     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF00183062     Document Type: Article

References (93)

1. Altabet MA, Francois R (1994) Sedimentary nitrogen isotopic ratio as a recorder of surface ocean nitrate utilization. Global Biogeochem Cycles 8:103-106
2. Altabet MA, Francois R, Murray DW, Prell WL (1995) Climate-related variations in denitrification in denitrification in the Arabian Sea from sediment N-15/N-14 ratios. Nature 373:506-509
3. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Revs 59:143-169
4. 2 fixation and physiological characterization of nitrogen-fixing members of a marine microbial mat community. Appl Environ Microbiol 59:1495-1503
5. Bej AK, Mahbubani MH (1992) Applications of the polymerase chain reaction in environmental microbiology. PCR Meth Appl 1:151-159
6. Ben-Porath J, Zehr JP (1994) Detection and characterization of cyanobacterial mfH genes. Appl Environ Microbiol 60:880-887
7. Ben-Porath J, Carpenter EJ, Zehr JP (1993) Genotypic relationships in Trichodesmium (cyanophyceae) based on nifH sequence comparisons. J Phycol 29:806-810
8. Berger WH, Herguera JC (1992) Primary productivity and biogeochemical cycles in the sea. In: Falkowski PG, Woodhead AD (eds) Reading the sedimentary record of the ocean's productivity. Plenum Press, New York, pp 455-486
9. Berger WH, Smaetacek VS, Wefer G (1989) Productivity of the oceans: present and past. In: Berger WH, Smaetacek VS, Wefer G (eds) Ocean productivity and paleoproductivity - an overview. J. Wiley, Chichester, pp 1-34
10. 2 cycle from ice core studies. Radiocarbon 22:227-269
11. 2 fixation. Chapman and Hall, New York, pp 736-762
12. 2 fixation systems in Azotobacter vinelandii. Chapman and Hall, New York, pp 789-795
13. Broecker WS, Peng TH ( 1986) Carbon cycle: 1985. Glacial to interglacial changes in the operation of the global carbon cycle. Radicarbon 28:309-327
14. Burckle LH, Cirilli J (1987) Origin of diatom ooze belt in the Southern Ocean: implications for late quaternary paleooceanograph. Micropaleont 33:86-86
15. Cano RJ, Poinar H, Pieniazek N, Acra A, Poinar Jr. GO (1993) Amplification and sequencing of DNA from a 120-135 million-year-old weevil. Nature 363:536-539
16. 2 fixation. In: Carpenter EJ, Capone DG (eds) Nitrogen in the marine environment. Academic Press, New York, pp 105-137
17. 2 fixation in seagrass communities. Mar Tech Soc J 17:32-37
18. 2 fixation. In: Blackburn TH, Sorensen J (eds) Nitrogen cycling in coastal marine environments. John Wiley and Sons, pp 85-123
19. 2 fixation associated with rinsed roots and rhizomes of the eelgrass, Zostera marina. Plant Physiol 70:1601-1604
20. 2 fixation in the marine environment. Science 217:1140-1142
21. 2 reduction. Appl Environ Microbiol 43:1400-1405
22. Capone DG, O'Neil JM, Zehr J, Carpenter EJ (1990) Basis for diel variation in nitrogenase activity in the marine planktonic cyanobacterium Trichodesmium thiebautii. Appl Environ Microbiol 56:3532-3536
23. Carpenter EJ (1982) Physiology and ecology of marine planktonic Oscillatoria (Trichodesmium). Mar Biol Lett 4:69-85
24. Carpenter EJ, Romans K (1991) Major role of the cyanobacterium Trichodesmium in nutrient cycling in the North Atlantic Ocean. Science 254:1356-1358.
25. Chisholm FP, Frankel SL, Goericke R, Olson RJ, Palenik B, Waterbury, JB, West-Johnsrud L, Zettler ER (1992) Prochlorococcus marinus nov. gen. nov. sp.: an oxyphototrophic marine prokaryote containing divinylchlorophyll a and b. Arch Microbiol 157:297-300
26. Codispotti L (1989) Phosphorus vs. nitrogen limitation of new and export production. In: Berger WH, Smetacek VS, Wefer G (eds) Productivity of the ocean: present and past. S Bernhard, Dahlem Konferenzen, pp 377-394
27. 2-fixing microorganisms from aquatic environments. Limnol Oceanogr 35:59-71
28. Delwiche CC (1981) The nitrogen cycle and nitrous oxide. In: Delwiche CC (ed) Denitrification, nitrification, and atmospheric nitrous oxide. Wiley & Sons, New York, pp 1-15
29. Dugdale RC (1967) Nutrient limitation in the sea: Dynamics, identification and significance. Limnol Oceanogr 12:685-695
30. Fanning KA (1992) Nutrient provinces in the sea: concentration ratios, reaction rate ratios, and ideal covariation. J Geophysical Res 97:5693-5712
31. Felsenstein J (1993) PHYLIP-Phylogeny Inference Package (Version 3.5c). Distributed by the author. Department of Genetics, University of Washington, Seattle
32. 15N. Paleoceanography 7:589-606
33. Fujita Y, Takahashi Y, Chuganji M, Matsubara H (1992) The m/H-like (frxC) gene is involved in the biosynthesis of chlorophyll in the filamentous cyanobacterium Plectonema boryanum. Plant Cell Physiol 33:81-92
34. Georgiadis MM, Komiya H, Chakrabarti P, Woo D, Kornuc JJ, Rees DC (1992) Crystallographic structure of the nitrogenase iron protein from Azotobacter vinelandii. Science 257:1653-1659
35. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63
36. 1. Biochem Biophys Res Comm 59:967-971
37. 2-fixing bacteria from seawater. Appl Environ Microbiol 50:350-355
38. 2 fixation in Atlantic deep-sea and coastal sediments. DeepSea Res 25:411-417
39. 2 fixation. Chapman and Hall, New York, pp 166-190
40. Hecky RE, Kilham R (1988) Nutrient limitation of phytoplankton in freshwater and marine environments: a review of recent evidence on the effects of enrichment. Limnol Oceanogr 33:796-822
41. Hecky RE, Campbell P, Hendzell LL (1993) The stoichiometry of carbon, nitrogen, and phosphorus in paniculate matter of lakes and oceans. Limnol Oceanogr 38:709-924
42. 2 fixation in freshwater estuarine and marine ecosystems. 2, Biogeochemical controls. Limnol Oceanogr 33:688-701
43. 13C variations in sedimentary organic matter. Nature 342:60-62
44. 2 fixation in aquatic environments. III. On the nitrogen-fixing bacteria in offshore regions. Bull Jpn Soc Sei Fish 37:981-985
45. King GM, Carlton RG, Sawyer TE (1990) Anaerobic metabolism and oxygen distribution in the carbonate sediments of a submarine canyon. Mar Ecol Prog Ser 58:275-285
46. Kirshtein JD, Paerl HW, Zehr J (1991) Amplification, cloning, and sequencing of a nifH segment from aquatic microorganisms and natural communities. Appl Environ Microbiol 57:2645-2650
47. Klump V, Martens C (1983) Benthic nitrogen regeneration. In: Carpenter EJ, Capone DG (eds) Nitrogen in the manne environment. Academic Press, New York, pp 411-457
48. Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362:709-715
49. Lyle MW, Prahl FG, Sparrow MA (1992) Upwelling and productivity changes inferred from a temperature record in the central equatorial Pacific. Nature 355:812-815
50. Maidak BL, Larsen N, McCaughey MJ, Overbeek R, Olsen GJ, Fogel K, Blandy J, Woese CR (1994) The ribosomal database project. Nucleic Acids Res 22:3485-3487
51. 2 fixation by floating diatom mats: a source of new nitrogen to oligotrophic ocean waters. Science 221:152-154
52. 2 and climate. Nature 302:328-329
53. 2 fixation. Chapman and Hall, New York, pp 835-876
54. Michaels A, and 8 others (1996) Inputs, losses, and transformations of nitrogen and phosphorus in the deep North Atlantic Ocean. Biogeochemistry in press.
55. Mitsui A, Kumazawa S, Takahashi A, Ikemoto H, Cao S, Arai T (1986) Strategy by which nitrogen-fixing unicellular cyanobacteria grow photoautotrophically. Nature 323:720-722
56. Mortlock RA, Charles CD, Froelich PN, Zibello MA, Saltzman J, Hays JD, Burckle LH (1991) Evidence for lower productivity in the Antarctic Ocean during the last glaciation. Nature 351:220-223
57. Mullis KB, Faloona FA (1987) Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Meth Enzymol 155:335-350
58. 2 fixation in sediments and the rhizosphere of the seagrass Zostera capricom. Microb Ecol 22:53-64
59. O'Neil JM, Capone DG (1989) Nitrogenase activity in tropical carbonate marine sediments. Mar Ecol Prog Ser 56:145-156
60. Olsen GJ, Woese CR, Overbeek R (1994) The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol 176:1-6
61. Päabo S (1989) Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc Natl Acad Sci USA 86:1939-1943
62. 2 fixation in natural waters. In: Marshall KC (ed) Advances in microbial ecology. Plenum Publishing, pp 305-344
63. 2 fixation in a marine microbial mat: physiological and ecological ramifications. In: Cohen Y, Rosenberg E (eds) Microbial mats: physiological ecology of benthic microbial communities. Am Soc Microbiol, pp 326-341
64. Parks RJ, Cragg BA, Bale SJ, Getliff JM, Goodman K, Rochelle PA, Fry JC. Weightman AJ, Harvey SM (1994) Deep bacterial biosphere in Pacific Ocean sediment. Nature 371:410-413
65. 2 fixation in the rhizosphere of marine angiosperms. Mar Biol 16:49-58
66. Pichard SL, Paul JH (1993) Gene expression per gene dose, a specific measure of gene expression in aquatic microorganisms. Appl Environ Microbiol 59:451-457
67. Pope MR, Murrell SA, Ludden PW (1985) Convalent modification of the iron protein of nitrogenase from Rhodospirillum rubrum by adenosine diphoshoribosylation of a specific arginine residue. Proc Natl Acad Sci USA 82:3173-3177
68. 2 fixation. Cambridge University Press, Cambridge. Massachusetts, pp 252
69. Redfield AC (1958) The biological control of chemical factors in the environment. Am Sci 46:205-222
70. Revsbech NP, Sorensen J, Blackburn TH, Lomholt J (1981) Distribution of oxygen in marine sediments measured with microelectrodes. Limnol Oceanogr 25:403-411
71. Reysenbach AL, Giver LJ, Wickham GS, Pace NR (1992) Differential amplification of rRNA genes by polymerase chain reaction. Appl Environ Microbiol 58:3417-3418
72. 2 fixation. Chapman and Hall. New York, pp 135-165
73. 18O and alkenone records. Nature 364:319-323
74. Ruvkun GB, Ausubel FM (1980) Interspecies homology of nitrogenase genes. Proc Natl Acad Sei USA 77:191-195
75. Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487-491
76. Sancetta C (1992) Primary production in the glacial North Atlantic and North Pacific oceans. Nature 360:249-251
77. 2 calibration of the acetylene reduction assay in coastal marine sediments. Mar Ecol Prog Ser 37:65-73
78. Short FT (1983) The seagrass Zostera marina L.: plant morphology and bed structure in relation to sediment ammonium in Izembeck lagoon Alaska. Aquat Bot 16:149-161
79. Simonet P, Grosjean MC, Misra AK, Nazaret S, Cournoyer B, Normand P (1991) Frankia genusspecific characterization by polymerase chain reaction. Appl Environ Microbiol 57:3278-3286
80. 2-fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of nifH gene sequences. J Bacteriol 177:1414-1417
81. Vitousek PM, Howarth RW (1991) Nitrogen limitation on land and in the sea: how can it occur? Biogeochemistry 13:87-115
82. Ward DM, Weiler R, Bateson MM (1990) 16S rRNA sequences reveal numberous uncultured inhabitants in a natural community. Nature 345:63-65
83. Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221-271
84. Woodward SR, Weyand NJ, Bunnell M (1994) DNA sequence from Cretaceous period bone fragments. Nature 266:1229-1231
85. 2 fixation in seawater. J Appl Bacteriol 37:203-216
86. - switch-off regulation of nitrogenase activity by bacteria in salt marsh sediments and roots of the grass Sparina alterniflora. Appl Environ Microbiol 51, 143-149
87. 2 fixation. Chapman and Hall, New York, pp 43-86
88. Zehr JP (1992) Molecular biology of nitrogen fixation in natural populations of marine cyanobacteria. In: Carpenter EJ, Capone DG, Rueter JG (eds) Marine pelagic cyanobacteria Trichodesmium and other diszotrophs. Kluwer Academic Publishers, Dordrecht, The Netherlands, pp 249-264
89. 2 fixation in the sea: why only trichodesmium? In: Joint I, Carr N, Falkowski P (eds) NATO ASI series. Springer-Verlag.
90. Zehr JP, McReynolds LA ( 1989) Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium thiebautii. Appl Environ Microbiol 55:2522-2526
91. Zehr JP, Ohki K, Fujita Y (1991) Arrangement of nitrogenase structural genes in an aerobic filamentous nonheterocystous cyanobacterium. J Bacteriol 173:7055-7058
92. Zehr JP, Wyman M, Miller V, Duguay L, Capone DG (1993) Modification of the Fe protein of nitrogenase in natural populations of Trichodesmium thiebautii. Appl Environ Microbiol 59:669-676
93. 2 fixation genes in a marine cyanobacterial mat. App] Environ Microbiol 61:2527-2532