Microdiversity of culturable diazotrophs from the rhizoplanes of the salt marsh grasses Spartina alterniflora and Juncus roemerianus

Microbial Ecology

Volumn 39, Issue 2, 2000, Pages 128-136

  Bagwell, C E ^a   Lovell, C R ^a  

^a UNIVERSITY OF SOUTH CAROLINA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIAZOTROPH; DNA DNA HYBRIDIZATION; NITROGEN FIXATION; PHYLOGENY; RHIZOSPHERE; SEQUENCE HOMOLOGY; STRAIN DIFFERENCE;

FUNCTIONAL GROUP; MICROBIAL COMMUNITY; NITROGEN FIXATION; RHIZOSPHERE; SALTMARSH; SPECIES DIVERSITY;

JUNCUS ROEMERIANUS; SPARTINA ALTERNIFLORA;

EID: 0034078003     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002480000017     Document Type: Article

References (69)

1. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143-169
2. Bagwell CE, Piceno YM, Ashburne-Lucas A, Lovell CR (1998) Physiological diversity of the rhizosphere diazotroph assemblages of selected salt marsh grasses. Appl Environ Microbiol 64:4276-4282
3. Barber DA, Gunn KB (1974) The effect of mechanical forces on the exudation of organic substances by the roots of cereal plants grown under sterile conditions. New Phytol 73:39-45
4. Barber DA, Lynch JM (1977) Microbial growth in the rhizosphere. Soil Biol Biochem 9:305-308
5. Barber DA, Martin JK (1976) The release of organic substances by cereal roots into the soil. New Phytol 76:69-80
6. Bauld J, Brock TD (1973) Ecological studies of Chloroflexis, a gliding photosynthetic bacterium. Arch Microbiol 92:267-284
7. Benson DA, Boguski MS, Lipman DJ, Ostell J, Ouellette BFF, Rapp BA, Wheeler DL (1999) Genbank. Nucleic Acids Res 27:12-17
8. Biodini M, Klein DA, Redente EF (1988) Carbon and nitrogen losses through root exudation by Agropyron cristatum, A. smithii and Bouteloua gracilis. Soil Biol Biochem 20:477-482
9. Borneman J, Skroch PW, O'Sullivan KM, Palus JA, Rumjankek NG, Jansen JL, Nienhuis J, Triplett EW (1996) Molecular microbial diversity of an agricultural soil in Wisconsin. Appl Environ Microbiol 62:1935-1943
10. Bowen GD (1980) Misconceptions, concepts and approaches in rhizosphere biology. In: Ellwood DC, Latham MI, Hedger JN, Lynch JM, Slater JH (eds) Contemporary Microbial Ecology. Academic Press, New York, pp 283-304
11. Bradley PM, Morris JT (1990) Influence of oxygen and sulfide concentration on nitrogen uptake kinetics in Spartina alterniflora. Ecology 71:282-287
12. 4 uptake in Spartina alterniflora. Oecologia 85:375-380
13. Brock TD (1987) The study of microorganisms in situ: Progress and problems. In: Fletcher M, Gray TRG, Jones JG, (eds) Ecology of Microbial Communities. 41st Symposium of the Society for General Microbiology. Cambridge University Press, New York, pp 1-17
14. Capone DG, Budin JM (1982) Nitrogen fixation associated with rinsed roots and rhizomes of the eelgrass Zostera marina. Plant Physiol 70:1601-1604
15. 2) fixation in a Thalassia testudinum community. Limnol Oceanogr 24:117-125
16. Dang H, CR, Lovell (2000) Bacterial primary colonization and early succession on surfaces in marine waters as determined using ARDRA and sequence analysis of 16S rRNA genes. Appl Environ Microbiol 66:467-475
17. Delong EF, Wu KY, Prezelin BB, Jovine RVM (1994) High abundance of Archaea in Antarctic marine picoplankton. Nature 371:695-697
18. 2 incorporation. Soil Biol Biochem 9:119-123
19. Feinberg AP, Vogelstein B (1983) A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem 132:6-13
20. Ferris MJ, Muyzer G, Ward DM (1996) Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl Environ Microbiol 62:340-346
21. Ferris MJ, Ward DM (1997) Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis. Appl Environ Microbiol 63:1375-1381
22. Gallagher J (1982) Physiological variation and electrophoretic banding patterns of genetically different seasonal populations of Skeletonema costatum (Bacillariophyceae). J Phycol 18:148-162
23. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63
24. Griffiths BS, Ritz K, Glover LA (1996) Broad-scale approaches to the determination of soil microbial community structure: Application of the community DNA hybridization technique. Microb Ecol 31:269-280
25. Hale MG, Moore LD, Griffin GJ (1978) Root exudates and exudation. In: Dommergues YR, Krupa SV, (eds) Interactions between Non-pathogenic Soil Microorganisms and Plants. Elsevier Scientific Publishing Co, New York, pp 163-203
26. Head IM, Saunders JR, Pickup RW (1998) Microbial evolution, diversity, and ecology: A decade of ribosomal RNA analysis of uncultivated microorganisms. Microb Ecol 35:1-21
27. Hopkinson CS, Schubauer JP (1984) Static and dynamic aspects of nitrogen cycling in the salt marsh graminoid Spartina alterniflora. Ecology 65:961-969
28. Hugenholtz P, Goebel BM, Pace NR (1998) Minireview: Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765-4774
29. Johnson JL (1986) Nucleic acids in bacterial classification. In: Sneath PHA, Mair NS, Sharpe NE, Holt JG, (eds) Bergey's Manual of Systematic Bacteriology, vol 2. Williams and Wilkins, Baltimore, pp 972-975
30. Kafatos FC, Jones CW, Efstratiadis A (1979) Determination of nucleic acid sequence homologies and relative concentrations by a dot hybridization procedure. Nuc Acid Res 7:1541-1552
31. 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
32. Kuske CR, Barns SM, Busch JD (1997) Diverse uncultivated bacterial groups from soils of the arid southwestern United States that are present in many geographic regions. Appl Environ Microbiol 63:3614-3621
33. Liesack W, Stackebrandt E (1992) Occurence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J Bacteriol 174:5072-5078
34. Lovell CR (2000) Diversity, microbial. In: Lederberg J (ed) Encyclopedia of Microbiology, 2nd ed. Academic Press, San Diego, in press
35. 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 (in review)
36. Lovell CR, Hui Y (1991) Design and testing of a functional group-specific DNA probe for the study of natural populations of acetogenic bacteria. Appl Environ Microbiol 57:2602-2609
37. Maidak BL, Cole JR, Parker CT, Garrity GM, Larsen N, Li B, Lilburn TG, McCaughey MJ, Olsen GJ, Overbeek R, Pramanik S, Schmidt TM, Tiedje JM, Woese CR (1999) A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res 27:171-173
38. Marmur J (1961) A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3:208-218
39. McArthur JV, Kovacic DA, Smith MH (1988) Genetic diversity in natural populations of a soil bacterium across a landscape gradient. Proc Natl Acad Sci USA 85:9621-9624
40. Mendum TA, Sockett RE, Hirsch PR (1999) Use of molecular and isotopic techniques to monitor the response of autotrophic ammonia-oxidizing populations of the β subdivision of the class Proteobacteria in arable soils to nitrogen fertilization. Appl Environ Microbiol 65:4155-4162
41. Moore LR, Rocap G, Chisholm SW (1998) Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature 393:464-467
42. 2 and acetylene reduction. Soil Biol Biochem 17:87-91
43. Murry HG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321-4325
44. Newell SY, Hopkinson CS, Scott LA (1992) Patterns of nitrogenase activity (acetylene reduction) associated with standing, decaying shoots of Spartina alterniflora. Estuarine, Coastal and Shelf Science 35:127-140
45. Newman EI (1985) The rhizosphere: Carbon sources and microbial populations. In: Fitter AH (ed) Ecological interactions in soil, plants, microbes, and animals. British Ecological Society Special Publication 4. Blackwell Scientific Publications Ltd., Oxford, pp 107-121
46. Nold SC, Ward DM (1995) Diverse Thermus species inhabit a single hot spring microbial mat. Syst Appl Microbiol 18:274-278
47. Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR (1986) Microbial ecology and evolution: A ribosomal RNA approach. Ann Rev Microbiol 40:337-365
48. Olsen GJ, Woese CR, Overbeek R (1994) Minireview: The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol 176:1-6
49. Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276:734-740
50. Patriquin D, Knowles R (1972) Nitrogen fixation in the rhizosphere of marine angiosperms. Mar Biol 16:49-58
51. Peary JA, Castenholz RW (1964) Temperature strains of a thermophilic blue-green alga. Nature 202:720-721
52. Piceno YM, Lovell CR (2000) Stability of natural bacterial communities: I. Nutrient addition effects on rhizosphere diazotroph assemblage composition. Microb Ecol (in press)
53. Piceno YM, Lovell CR (2000) Stability of natural bacterial communities: II. Plant resource allocation effects on rhizosphere diazotroph assemblage composition. Microb Ecol (in press)
54. Piceno YM, Noble PA, Lovell CR (1999) Spatial and temporal assessment of diazotroph assemblage composition in vegetated salt marsh sediments using denaturing gradient gel electrophoresis analysis. Microb Ecol 38:157-167
55. Pichard SL, Campbell L, Paul JH (1997) Diversity of the ribulose bisphosphate carboxylase/oxygenase form I gene (rbcL) in natural phytoplankton communities. Appl Environ Microbiol 63:3600-3606
56. Rovira AD (1969) Plant root exudates. Bot Rev 35:33-57
57. Ruff-Roberts AL, Kuenen JG, Ward DM (1994) Distribution of cultivated and uncultivated cyanobacteria and Chloroflexis-like bacteria in hot spring microbial mats. Appl Environ Microbiol 60:697-704
58. Santegoeds CM, Nold SC, Ward DM (1996) Denaturing gradient gel electrophoresis used to monitor the enrichment culture of aerobic chemoorganotrophic bacteria from a hot spring cyanobacterial mat. Appl Environ Microbiol 62:3922-3928
59. Stackebrandt E, Goebel BM (1994) Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846-849
60. Turner RE (1976) Geographic variations in salt marsh macrophyte production: A review. Contrib Mar Sci 20:47-68
61. 2-fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of nifH gene sequences. J Bacteriol 177:1414-1417
62. Vancura V, Prikryl Z, Kalachova L, Wurst M (1977) Some quantitative aspects of root exudation. Ecol Bull 25:381-386
63. Ward DM, Bateson MM, Weller R, Ruff-Roberts AL (1992) Ribosomal RNA analysis of microorganisms as they occur in nature. In: Marshall KC (ed) Advances in Microbial Ecology, vol 12. Plenum Press, New York, pp 219-286
64. Ward DM, Ferris MJ, Nold SC, Bateson MM (1998) A natural view of microbial biodiversity within hot spring cyanobacterial mat communities. Microbiol Mol Biol Rev 62:1353-1370
65. Ward DM, Weller R, Bateson MM (1990) 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345:63-65
66. Ward DM, Weller R, Bateson MM (1990) 16S rRNA sequences reveal uncultured inhabitants of a well-studied thermal community. FEMS Microbiol Rev 75:105-116
67. Whittaker RH (1975) Production. In: Communities and Ecosystems, 2nd ed. MacMillan Publishing Co Inc, New York, pp 192-235
68. Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221-271
69. Wood DC, Hayasaka SS (1981) Chemotaxis of rhizoplane bacteria to amino acids comprising eelgrass (Zostera marina L) root exudate. J Exp Mar Biol Ecol 50:153-161