Nitrogen-fixing phylotypes of Chesapeake Bay and neuse river estuary sediments

Microbial Ecology

Volumn 44, Issue 4, 2002, Pages 336-343

  Burns, J A ^a   Zehr, J P ^b   Capone, D G ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ESTUARINE SEDIMENT; METHANOGENESIS; MICROBIAL ACTIVITY; NITROGEN FIXATION; PHYLOGENETICS; REDUCTION; SULFATE;

UNITED STATES;

ARCHAEA; SPARTINA;

BACTERIAL DNA; PRIMER DNA;

AEROBIC BACTERIUM; ARTICLE; BACTERIAL GENE; ECOSYSTEM; GENE AMPLIFICATION; GENETICS; MICROBIOLOGY; NITROGEN FIXATION; PHYLOGENY; PHYSIOLOGY; PLANT ROOT; POACEAE; SEDIMENT; UNITED STATES;

BACTERIA, AEROBIC; DNA PRIMERS; DNA, BACTERIAL; ECOSYSTEM; GENE AMPLIFICATION; GENES, BACTERIAL; GEOLOGIC SEDIMENTS; MARYLAND; NITROGEN FIXATION; PHYLOGENY; PLANT ROOTS; POACEAE; WATER MICROBIOLOGY;

EID: 0036835633     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-002-1000-9     Document Type: Article

References (45)

1. Affourtit J, Zehr JP, Paerl HW (2001) Distributions of nitrogen-fixing microorganisms along the Neuse River Estuary, North Carolina. Microb Ecol 41:114-123
2. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143-169
3. Bagwell CE, Lovell CR (2000) Microdiversity of culturable diazotrophs from the rhizoplanes of salt marsh grasses Spartina alterniflora and Juncus roemerianus. Microb Ecol 39:128-136
4. Ben-Porath J, Zehn JP (1994) Detection and characterization of cyanobacterial nifH genes. Appl Environ Microbiol 60:880-887
5. Brooks RH, Brezonik PL, Putnam HD, Keirn MA (1971) Nitrogen fixation in an estuarine environment: The Waccasassa on the Florida gulf coast. Limnol Oceanogr 16:701-710
6. Boudreau BP, Westrich JT (1984) The dependence of bacterial sulfate reduction on sulfate concentration in marine sediments. Geochem Cosmochem Acta 48:2503-2516
7. Burdidge DJ, Zheng S (1998) The biogeochemical cycling of dissolved organic nitrogen in estuarine sediments. Limnol Oceanogr 43:1796-1813
8. Capone DG (1982) Nitrogen fixation (acetylene reduction) by rhizosphere sediments of the eelgrass, Zostera marina. Mar Ecol Prog Ser 10:67-75
9. Capone DG (1983) Benthic nitrogen fixation. In: Carpenter DG, Capone DG (eds) Nitrogen in the Marine Environment. Academic Press, New York pp 105-137
10. Capone DG (1988) Benthic nitrogen fixation. In: Blackburn J, Sorensen J (eds) Nitrogen Cycling in Coastal Marine Environments. John Wiley and Sons, New York pp 85-123
11. Capone DG (1993) Determination of nitrogenase activity in aquatic samples using the acetylene reduction procedure. In: Kemp PF, Sherr BF, Sherr EB, Cle JJ (eds) Handbook of Methods in Aquatic Microbial Ecology. Lewis Publishers, Boca Raton, FL pp 621-631
12. 2 fixation by acetylene reduction. Appl Environ Microbiol 43:1400-1405
13. Capone DG, Carpenter EJ (1999) Nitrogen fixation by marine cyanobacteria: historical and global perspectives. In: Charpy L, Larkum AWD (eds) Marine Cyanobacteria. Bulletin de l'Institue Oceanographique, Monaco pp 235-236
14. Christian RR, Boyer JN, Stanley DW (1991) Multi-year distribution patterns of nutrients within the Neuse River Estuary, NC. Mar Ecol Prog Ser 71:259-274
15. Fulton RS, Paerl HW (1988) Effects of the blue-green algae Microcystis aeruginosa on zooplankton competitive relations. Oecologia 76:383-389
16. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:63-69
17. 2. New Phytol 122:571-609
18. Glandy EL, Yoch DC (1988) Relationship between nitrogen-fixing sulfate reducers and fermenters in salt marsh sediments and roots of Spartina alterniflora. Appl Environ Microbiol 54:2031-2036
19. 2-fixing bacteria from seawater. Appl Environ Microbiol 50:350-355
20. Hanson RB, Gunderson K (1976) Influence of sewage discharge on nitrogen fixation and nitrogen flux from coral reefs in Kaneohe Bay, Hawaii. Appl Environ Microbiol 31:942-948
21. Howarth RW, Marino R, Cole JJ (1988) Nitrogen fixation in freshwater, estuaries and marine ecosystems. 2. Biogeochemical controls. Am Soc Limnol Oceanogr 33:688-701
22. Kirshtein JD, Paerl HW, Zehr JP (1991) Amplification, cloning and sequencing of a nifH segment from aquatic microorganisms and natural populations. Appl Environ Microbiol 57:2645-2650
23. Lovell CR, Piceno YM, Quattro JM, Bagwell CE (2000) Molecular analysis of diazotroph diversity in the rhizosphere of the smooth cordgrass, Spartina alterniflora. Appl Environ Microbiol 66:3814-3822
24. Marsho TV, Burchard RP, Fleming R (1975) Nitrogen fixation in Rhode River Estuary of Chesapeake Bay. Can J Microbiol 21:1348-1356
25. Marvin-DiPasquale MC, Capone DG (1998) Benthic sulfate reduction along the Chesapeake Bay central channel. I. Spatial trends and controls. Mar Ecol Prog Ser 168:213-228
26. Nicholas KB, Nicholas Jr HB (1997) GeneDoc: a tool for editing and annotating multiple sequence alignments. Distributed by author
27. O'Neil JM, Capone DG (1989) Nitrogenase activity in tropical carbonate marine sediments. Mar Ecol Prog Ser 56:145-156
28. Oremland RS, Capone DG (1988) Use of specific inhibitors in biogeochemistry and microbial ecology. In: Marshal KC (ed) Advances in Microbial Ecology, vol 10. Plenum Publishing, pp 285-283
29. Piceno YM, Lovell CR (2000) Stability in natural bacterial communities: I. Nutrient addition effects on rhizosphere diazotroph assemblage composition. Microb Ecol 39:32-40
30. Postgate JR (1998) Nitrogen Fixation, 3rd ed. Cambridge University Press, Cambridge, UK
31. Ripka R, Waterbury JB (1977) The synthesis of nitrogenase by non-heterocystic cyanobacteria. FEMS Microbiol Lett 2:83-86
32. Ruvkun GB, Ausubel FM (1980) Interspecies homology of nitrogenase genes. Proc Natl Acad Sci USA 77:191-195
33. 2 calibration of the acetylene reduction assay in coastal marine sediments. Mar Ecol Prog Ser 37:65-73
34. Skyring GW (1987) Sulfate reduction in coastal ecosystems. Geomicrobiol J 5:295-374
35. Thompson JD, Higgins DG, Gibson JJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
36. Tsai Y, Olson BH (1992) Rapid method for direct extraction of DNA from soil and sediments. Appl Environ Microbiol 57:1070-1074
37. Van de Peer Y, De Wachter R (1994) TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows Environment. Comput Appl Biosci 10:569-570
38. Ward DM, Weller R, Bateson MM (1990) 16S rRNA sequence reveal numerous uncultured microorganisms in a natural community. Nature 345:63-65
39. + switch-off regulation of nitrogenase activity by bacteria in salt marsh sediments and roots of Spartina alterniflora. Appl Environ Microbiol 51:143-149
40. Young JPW (1992) Phylogenetic classification of nitrogen-fixing organisms. In: G Stacey, RH Burris, HJ Evans (eds) Biological Nitrogen Fixation. Chapman and Hall, New York pp 43-86
41. Zani S, Mellon MT, Collier JL, Zehr JP (2000) Expression of nifH genes in natural microbial assemblages in Lake George, New York, detected by reverse transcriptase PCR. Appl Environ Microbiol 66:3119-3124
42. Zehr JP, Capone DG (1996) Problems and promises of assaying the genetic potential for nitrogen fixation in the marine environment. Microb Ecol 32:263-281
43. Zehr JP, MacReynolds LA (1989) Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium spp. Appl Environ Microbiol 55:2522-2526
44. Zehr JP, Mellon M, Braun S, Litaker W, Steppe J, Paerl HW (1995) Diversity of heterotrophic nitrogen fixation genes in a marine cyanobacterial mat. Appl Environ Microbiol 61:2527-2532
45. 2 in the subtropical North Pacific Ocean. Nature 412:635-638