Different bacterial communities associated with the roots and bulk sediment of the seagrass Zostera marina

FEMS Microbiology Ecology

Volumn 62, Issue 1, 2007, Pages 108-117

  Jensen, Sheila Ingemann ^a   Kühl, Michael ^a   Priemé, Anders ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Bacteria; Radial oxygen loss; Seagrass; Zostera marina

Indexed keywords

ANOXIC CONDITIONS; BACTERIUM; GENETIC ANALYSIS; MARINE SEDIMENT; MICROBIAL COMMUNITY; POLYMERASE CHAIN REACTION; RELATIVE ABUNDANCE; ROOT COLONIZATION; SEAGRASS; SENSOR;

ACTINOBACTERIA; ALPHAPROTEOBACTERIA; ARTICLE; BACTERIAL COLONIZATION; BACTERIAL FLORA; BACTERIAL GROWTH; BACTERIODETES; CLOSTRIDIA; CYANOBACTERIUM; DELTAPROTEOBACTERIA; EPSILONPROTEOBACTERIA; FUSOBACTERIA; GAMMAPROTEOBACTERIA; GROWTH INHIBITION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANCTOMYCETES; PLANT ROOT; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SEAGRASS; SEDIMENT; SULFATE REDUCING BACTERIUM; SULFURIMONAS; THIOMICROSPIRA;

BACTERIA; BIODIVERSITY; DNA FINGERPRINTING; DNA, BACTERIAL; DNA, RIBOSOMAL; ECOSYSTEM; GEOLOGIC SEDIMENTS; MOLECULAR SEQUENCE DATA; OXYGEN; PHYLOGENY; PLANT ROOTS; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; ZOSTERACEAE;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); DELTAPROTEOBACTERIA; EPSILONPROTEOBACTERIA; GAMMAPROTEOBACTERIA; ZOSTERA MARINA;

EID: 34848898806     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2007.00373.x     Document Type: Article

References (46)

1. Armstrong J Armstrong W (2001) Rice and Phragmites: effects of organic acids on growth, root permeability, and radial oxygen loss to the rhizosphere. Am J Bot 88 : 1359 1370.
2. 2+ and water uptake, and lateral root emergence. Ann Bot 96 : 625 638.
3. Avaniss-Aghajani E, Jones K, Chapman D Brunk C (1994) A molecular technique for identification of bacteria using small subunit ribosomal RNA sequences. BioTechniques 17 : 144 149.
4. Bagarinao T (1992) Sulfide as an environmental factor and toxicant: tolerance and adaptations in aquatic organisms. Aquat Toxicol 24 : 21 62.
5. Bagwell CE, La Rocque JR, Smith GW, Polson SW, Friez MJ, Longshore JW Lovell CR (2002) Molecular diversity of diazotrophs in oligotrophic tropical seagrass bed communities. FEMS Microb Ecol 39 : 113 119.
6. Borum J, Pedersen O, Greve TM, Frankovich TA, Zieman JC, Fourqurean JW Madden CJ (2005) The potential role of plant oxygen and sulphide dynamics in die-off events of the tropical seagrass, Thalassia testudinum. J Ecol 93 : 148 158.
7. Bray JR Curtis JT (1957) An ordination of the upland forest communities of southern Wisconsin. Ecol Monogr 27 : 325 349.
8. Callaham D, Del Tredici P Torrey JG (1978) Isolation and cultivation in vitro of the actinomycete causing root nodulation in Comptonia. Science 199 : 899 902.
9. Campbell BJ, Engel AS, Porter ML Takai K (2006) The versatile ε-proteobacteria: key players in sulphidic habitats. Nat Rev Microbiol 4 : 458 468.
10. Cifuentes A, Antón J, Benlloch S, Donnelly A, Herbert RA Rodríguez-Valera F (2000) Prokaryotic diversity in Zostera noltii-colonized marine sediments. Appl Environ Microbiol 66 : 1715 1719.
11. Clarke KR (1993) Non-parametric multivariate analyses of changes in community structure. Aust J Ecol 18 : 117 143.
12. Clarke KR Warwick RM (2001) Change in Marine Communities: An Approach to Statistical Analysis and Interpretation. Primer-E, Plymouth, UK.
13. Connell EL, Colmer TD Walker DI (1999) Radial oxygen loss from intact roots of Halophila ovalis as a function of distance behind the root tip and shoot illumination. Aquat Bot 63 : 219 228.
14. Dunbar J, Ticknor LO Kuske CR (2000) Assessment of microbial diversity in four southwestern united states soils by 16S rRNA gene terminal restriction fragment analysis. Appl Environ Microbiol 66 : 2943 2950.
15. Finster K, Thomsen TR Ramsing NB (2001) Desulfomusa hansenii gen. nov., sp. nov., a novel marine propionate-degrading, sulfate-reducing bacterium isolated from Zostera marina roots. Int J Syst Evol Microbiol 151 : 2055 2061.
16. Frederiksen MS Glud RN (2006) Oxygen dynamics in the rhizosphere of Zostera marina: a two-dimensional planar optode study. Limnol Oceanogr 51 : 1072 1083.
17. Goodfellow M Williams ST (1983) Ecology of actinomycetes. Annu Rev Microbiol 37 : 189 216.
18. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucl Acids Symp Ser 41 : 95 98.
19. Holmer M Nielsen SL (1997) Sediment sulfur dynamics related to biomass - density patterns in Zostera marina (eelgrass) beds. Mar Ecol Prog Ser 146 : 163 171.
20. Holmer M, Pedersen O Ikejima K (2006) Sulfur cycling and sulfide intrusion in mixed southeast Asian tropical seagrass meadows. Bot Mar 49 : 91 102.
21. James JB, Sherman TD Devereux R (2006) Analysis of bacterial communities in seagrass bed sediments by double-gradient denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA genes. Microb Ecol 52 : 655 661.
22. Jensen SI, Kühl M, Glud RN, Jørgensen LB Priemé A (2005) Oxic microzones and radial oxygen loss from roots of Zostera marina. Mar Ecol Prog Ser 293 : 49 58.
23. Jørgensen BB (1982) Mineralization of organic matter in the sea bed - the role of sulphate reduction. Nature 296 : 643 645.
24. 2S microgradients. Appl Environ Microbiol 45 : 1261 1270.
25. Jukes TH Cantor CR (1969) Evolution of protein molecules. Mammalian Protein Metabolism (Murano HN, ed pp. 21 132. Academic Press, New York.
26. Koch MS Erskine JM (2001) Sulfide as a phytotoxin to the tropical seagrass Thalassia testudinum: interactions with light, salinity and temperature. J Exp Mar Biol Ecol 266 : 81 95.
27. Küsel K, Pinkart HC, Drake HL Devereux R (1999) Acetogenic and sulfate-reducing bacteria inhabiting the rhizoplane and deep cortex cells of the seagrass Halodule wrightii. Appl Environ Microbiol 65 : 5117 5123.
28. Küsel K, Trinkwalter T, Drake HL Devereux R (2006) Comparative evaluation of anaerobic bacterial communities associated with roots of submerged macrophytes growing in marine or brackish water sediments. J Exp Mar Biol Ecol 337 : 49 58.
29. Lane DJ (1991) 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematis (Stackebrandt E Goodfellow M, eds), pp. 115 175. Wiley, New York.
30. Lee K-S Dunton KH (2000) Diurnal changes in pore water sulfide concentrations in the seagrass Thalassia testudinum beds: the effects of seagrasses on sulfide dynamics. J Exp Mar Biol Ecol 255 : 201 214.
31. Lee RW, Kraus DW Doeller JE (1999) Oxidation of sulfide by Spartina alterniflora roots. Limnol Oceanogr 44 : 1155 1159.
32. Loria R, Kers J Joshi M (2006) Evolution of plant pathogenicity in Streptomyces. Annu Rev Phytopathol 44 : 469 487.
33. McClung CR, Patriquin DG Davis RE (1983) Campylobacter nitrofigilis sp. nov., a nitrogen-fixing bacterium associated with roots of Spartina alterniflora loisel. Int J Syst Bacteriol 33 : 605 612.
34. Nielsen JT, Liesack W Finster K (1999) Desulfovibrio zosterae sp. nov., a new sulfate reducer isolated from surface-sterilized roots of the seagrass Zostera marina. Int J Syst Bacteriol 49 : 859 865.
35. Pedersen O, Binzer T Borum J (2004) Sulphide intrusion in eelgrass (Zostera marina L.). Plant Cell Environ 27 : 595 602.
36. Revsbech NP (1989) An oxygen microsensor with a guard cathode. Limnol Oceanogr 34 : 474 478.
37. Saitou N Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 : 406 425.
38. Smith AC, Kostka JE, Devereux R Yates DF (2004) Seasonal composition and activity of sulfate-reducing prokaryotic communities in seagrass bed sediments. Aquat Microb Ecol 37 : 183 195.
39. Thompson JD, Higgins DG Gibson TJ (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.
40. 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.
41. Ward AC Bora N (2006) Diversity and biogeography of marine Actinobacteria. Curr Opin Microbiol 9 : 279 286.
42. Weinbauer MG, Fritz I, Wenderoth DF Höfle MG (2002) Simultaneous extraction from bacterioplankton of total RNA and DNA suitable for quantitative structure and function analyses. Appl Environ Microbiol 68 : 1082 1087.
43. Welsh DT (2000) Nitrogen fixation in seagrass meadows: regulation, plant-bacteria interactions and significance to primary productivity. Ecol Lett 3 : 58 71.
44. Wintzingerode FV, Göbel UB Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21 : 213 229.
45. Wirsen CO, Sievert SM, Cavanaugh CM, Molyneaux SJ, Ahmad A, Taylor LT, DeLong EF Taylor CD (2002) Characterization of an autotrophic sulfide-oxidizing marine Arcobacter sp. that produces filamentous sulfur. Appl Environ Microbiol 68 : 316 325.
46. Yu Z Mohn WW (1999) Killing two birds with one stone: simultaneous extraction of DNA and RNA from activated sludge biomass. Can J Microbiol 45 : 269 272.