1887

Microbiology Society logo

Volume 148, Issue 1

Differentiation of plasmids in marine diazotroph assemblages determined by randomly amplified polymorphic DNA analysis Free

Abstract

Nitrogen fixation by diazotrophic bacteria is a significant source of new nitrogen in salt marsh ecosystems. Recent studies have characterized the physiological and phylogenetic diversity of oxygen-utilizing diazotrophs isolated from the rhizoplanes of spatially separated intertidal macrophyte habitats. However, there is a paucity of information regarding the traits encoded by and the diversity of plasmids occurring in this key ecological functional group. Five-hundred and twenty-one isolates cultivated from the rhizoplanes of , and different growth forms (short-form and tall-form) of were screened for the presence of plasmids. One-hundred and thirty-four diazotrophs carrying plasmids that ranged in size from 2 to >100 kbp were identified. The majority of the marine bacteria contained one plasmid. Diazotrophs from the short-form rhizoplane contained significantly fewer plasmids relative to isolates from tall-form , and . Although some plasmids exhibited homology to a gene probe, the majority of the plasmids were classified as cryptic. Two oligonucleotide primers were developed to facilitate genotypic typing of the endogenously isolated marine plasmids by the randomly amplified polymorphic DNA (RAPD)-PCR technique. These primers proved to be more effective than 21 commercially available primers tested to generate RAPD-PCR patterns. Analysis of the RAPD-PCR patterns indicated as many as 71 different plasmid genotypes occurring in diazotroph bacterial assemblages within and between the four different salt marsh grass rhizoplane habitats investigated in this study.

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): endogenous isolation , extrachromosomal element , RAPD, randomly amplified polymorphic DNA , RAPD-PCR and rhizoplane
© Microbiology Society
Loading

Article metrics loading...

/content/journal/micro/10.1099/00221287-148-1-179
2002-01-01
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/micro/148/1/1480179a.html?itemId=/content/journal/micro/10.1099/00221287-148-1-179&mimeType=html&fmt=ahah

References

  1. Arber W. 2000; Genetic variation: molecular mechanisms and impact on microbial evolution. FEMS Microbiol Rev 24:1–7 [CrossRef]
     [Google Scholar]
  2. Armstrong J., Gibbs A., Peakall R., Weiller G. 1996; RAPDistance programs; version 1.04. http://life.anu.edu.au/molecular/software/rapd.html
  3. Aviles M., Codina J. C., Perez-Garcia A., Cazorla F., Romero P., de Vicente A. 1993; Occurrence of resistance to antibiotics and metals and of plasmids in bacterial strains isolated from marine environments. Water Sci Technol 27:475–478
     [Google Scholar]
  4. Bagwell C. E., Lovell C. R. 2000; Microdiversity of culturable diazotrophs from the rhizoplanes of the salt marsh grasses Spartina alterniflora and Juncus roemerianus . Microb Ecol 39:128–136 [CrossRef]
     [Google Scholar]
  5. Bagwell C. E., Piceno Y. M., Ashburne-Lucas A., Lovell C. R. 1998; Physiological diversity of the rhizosphere diazotroph assemblages of selected salt marsh grasses. Appl Environ Microbiol 64:4276–4282
     [Google Scholar]
  6. Bagwell C. E., Dantzler M., Bergholz P. W., Lovell C. R. 2001; Host-specific ecotype diversity of rhizoplane diazotrophs of the perennial glasswort Salicornia virginica and selected salt marsh grasses. Aquat Micro Ecol 23:293–300 [CrossRef]
     [Google Scholar]
  7. Bale M. J., Fry J. C., Day M. J. 1987; Plasmid transfer between strains of Pseudomonas aeruginosa on membrane filters attached to river stones. J Gen Microbiol 133:3099–3107
     [Google Scholar]
  8. Bale M. J., Fry J. C., Day M. J. 1988; Transfer and occurrence of large mercury resistance plasmids in river epilithon. Appl Environ Microbiol 54:972–978
     [Google Scholar]
  9. Bauer A. W., Kirby M. M., Sherris J. C., Turck M. 1966; Antibiotic susceptibility testing by a standard single disk method. Am J Clin Pathol 45:493–496
     [Google Scholar]
  10. Belliveau B. H., Starodub M. E., Trevors J. T. 1991; Occurrence of antibiotic and metal resistance and plasmids in Bacillus strains isolated from marine sediment. Can J Microbiol 37:513–520 [CrossRef]
     [Google Scholar]
  11. Bergholz P. W., Bagwell C. E., Lovell C. R. 2001; Physiological diversity of rhizoplane diazotrophs of the saltmeadow cordgrass, Spartina patens : implications for host specific ecotypes. Microb Ecol 42: in press
    [Google Scholar]
  12. Bradley P. M., Morris J. T. 1990; Influence of oxygen and sulfide concentration on nitrogen uptake kinetics in Spartina alterniflora . Ecology 71:282–287 [CrossRef]
     [Google Scholar]
  13. Brønstad K., Drønen K., Ovreaas L., Torsvik V. L. 1996; Phenotypic diversity and antibiotic resistance in soil bacterial communities. J Ind Microbiol Technol 17:253–259
     [Google Scholar]
  14. Caetano-Anollés G., Bassam B. J., Gresshoff P. M. 1991; DNA amplification fingerprinting using very short arbitrary oligonucleotide primers. Bio-Technology 9:553–557 [CrossRef]
     [Google Scholar]
  15. Cook M. A., Osborn A. M., Bettandorff J., Sobecky P. A. 2001; Endogenous isolation of replicon probes for assessing plasmid ecology of marine sediment microbial communities. Microbiology 147:2089–2101
     [Google Scholar]
  16. Coplin D. L. 1989; Plasmids and their role in the evolution of plant pathogenic bacteria. Annu Rev Phytopathol 27:187–212 [CrossRef]
     [Google Scholar]
  17. Dahlberg C., Linberg C., Torsvik V. L., Hermansson M. 1997; Conjugative plasmids isolated from bacteria in marine environments show various degrees of homology to each other and are not closely related to well-characterized plasmids. Appl Environ Microbiol 63:4692–4697
     [Google Scholar]
  18. Dahlberg C., Bergstrom M., Hermansson M. 1998; In situ detection of high levels of horizontal plasmid transfer in marine bacterial communities. Appl Environ Microbiol 64:2670–2675
     [Google Scholar]
  19. Ditta G., Stanfield S., Corbin D., Helinski D. R. 1980; Broad host range DNA cloning system for gram-negative bacteria: construction of a gene bank of Rhizobium meliloti . Proc Natl Acad Sci USA 77:7347–7351 [CrossRef]
     [Google Scholar]
  20. Drønen A. K., Torsvik V. L., Top E. M. 1999; Comparison of the plasmid types obtained by two distantly related recipients in bi-parental exogenous plasmid isolations from soil. FEMS Microbiol Lett 176:105–110 [CrossRef]
     [Google Scholar]
  21. Dye M., Skøt L., Mytton L. R., Harrison S. P., Dooley J. J., Cresswell A. 1995; A study of Rhizobium leguminosarum biovar trifolii populations from soil extracts using randomly amplified polymorphic DNA profiles. Can J Microbiol 41:336–344 [CrossRef]
     [Google Scholar]
  22. Eberhard W. G. 1990; Evolution in bacterial plasmids and levels of selection. Q Rev Biol 65:3–22 [CrossRef]
     [Google Scholar]
  23. Elaichouni A., Claeys G., Vershraegen G., Verhelst R., Vaneechoutte M., van Emmelo J. 1994; Study of the influence of plasmids on the arbitrary primer polymerase chain reaction fingerprint of Escherichia coli strains. FEMS Microbiol Lett 115:335–340 [CrossRef]
     [Google Scholar]
  24. van Elsas J. D., Gardener B. B. M., Wolters A. C., Smit E. 1998; Isolation, characterization, and transfer of cryptic gene-mobilizing plasmids in the wheat rhizosphere. Appl Environ Microbiol 64:880–889
     [Google Scholar]
  25. Fislage R., Berceanu M., Humboldt Y., Wendt M., Oberender H. 1997; Primer design for a prokaryotic differential display RT-PCR. Nucleic Acids Res 25:1830–1835 [CrossRef]
     [Google Scholar]
  26. Franklin R. B., Taylor D. R., Mills A. L. 1999; Characterization of microbial communities using randomly amplified polymorphic DNA (RAPD). J Microbiol Methods 35:225–235 [CrossRef]
     [Google Scholar]
  27. Freiberg C., Fellay R., Bairoch A., Broughton W. J., Rosenthal A., Perret X. 1997; Molecular basis of symbiosis between Rhizobium and legumes. Nature 387:394–401 [CrossRef]
     [Google Scholar]
  28. Harrison S. P., Mytton L. R., Skøt L., Dye M., Cresswell A. 1992; Characterization of Rhizobium isolates by amplification of DNA polymorphisms using random primers. Can J Microbiol 38:1009–1015 [CrossRef]
     [Google Scholar]
  29. Hermansson M., Jones G. W., Kjelleberg S. 1987; Frequency of antibiotic and heavy metal resistance, pigmentation, and plasmids in bacteria of the marine air–water interface. Appl Environ Microbiol 53:2338–2342
     [Google Scholar]
  30. Hyytia E., Hielm S., Bjorkroth J., Korkeala H. 1999; Biodiversity of Clostridium botulinum type E strains isolated from fish and fishery products. Appl Environ Microbiol 65:2057–2064
     [Google Scholar]
  31. Kobayashi N., Bailey M. J. 1994; Plasmids isolated from the sugar beet phyllosphere show little or no homology to molecular probes currently available for plasmid typing. Microbiology 140:289–296 [CrossRef]
     [Google Scholar]
  32. Kobori H., Sullivan C. W., Shizuya H. 1984; Bacterial plasmids in Antarctic natural assemblages. Appl Environ Microbiol 48:515–518
     [Google Scholar]
  33. Lilley A. K., Bailey M. J., Day M. J., Fry J. C. 1996; Diversity of mercury resistance plasmids obtained by exogenous isolation from the bacteria of sugar beet in three successive years. FEMS Microbiol Ecol 20:211–227 [CrossRef]
     [Google Scholar]
  34. Maniatis T., Fritsch E. F., Sambrook J. 1982 Molecular Cloning: a Laboratory Manual Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
     [Google Scholar]
  35. Moenne-Loccoz Y., Weaver R. W. 1995; Plasmids influence growth of rhizobia in the rhizosphere of clover. Soil Biol Biochem 27:1001–1004 [CrossRef]
     [Google Scholar]
  36. Mori E., Lio P., Daly S., Damiani G., Perito B., Fani R. 1999; Molecular nature of RAPD markers from Haemophilus influenzae Rd genome. Res Microbiol 150:83–93 [CrossRef]
     [Google Scholar]
  37. Morris J. T., Haskin B. 1990; A 5-yr record of aerial primary production and stand characteristics of Spartina alterniflora . Ecology 71:2209–2217 [CrossRef]
     [Google Scholar]
  38. Moschetti G., Blaiotta G., Villani F., Coppola S., Parente E. 2001; Comparison of statistical methods for identification of Streptococcus thermophilus , Enterococcus faecalis , and Entercoccus faecium from randomly amplified polymorphic DNA patterns. Appl Environ Microbiol 67:2156–2166 [CrossRef]
     [Google Scholar]
  39. Oakey H. J., Gibson L. F., George A. M. 1999; DNA probes specific for Aeromonas hydrophila (HG1). J Appl Microbiol 86:187–193 [CrossRef]
     [Google Scholar]
  40. Osborn A. M., Pickup R. W., Saunders J. R. 2000; Development and application of molecular tools in the study of IncN -related plasmids from lakewater sediments. FEMS Microbiol Lett 186:203–208 [CrossRef]
     [Google Scholar]
  41. Pansegrau W., Lanka E., Barth P. T. 7 other authors 1994; Complete nucleotide-sequence of Birmingham IncP-α plasmids – compilation and comparative analysis. J Mol Biol 239:623–663 [CrossRef]
     [Google Scholar]
  42. Picard C., Di Cello F., Ventura M., Fani R., Guckert A. 2000; Frequency and biodiversity of 2,4-diacetylphloroglucinol-producing bacteria isolated from the maize rhizosphere at different stages of plant growth. Appl Environ Microbiol 66:948–955 [CrossRef]
     [Google Scholar]
  43. Piceno Y. M., Noble P. A., Lovell C. R. 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 [CrossRef]
     [Google Scholar]
  44. Powers L. G., Mallonee J. T., Sobecky P. A. 2000; Complete nucleotide sequence of a cryptic plasmid from the marine bacterium Vibrio splendidus and identification of open reading frames. Plasmid 43:99–102 [CrossRef]
     [Google Scholar]
  45. Reyes N. S., Frischer M. E., Sobecky P. A. 1999; Characterization of mercury resistance mechanisms in marine sediment microbial communities. FEMS Microbiol Ecol 30:273–284 [CrossRef]
     [Google Scholar]
  46. Roberts M. A., Crawford D. L. 2000; Use of randomly amplified polymorphic DNA as a means of developing genus- and strain-specific Streptomyces DNA probes. Appl Environ Microbiol 66:2555–2564 [CrossRef]
     [Google Scholar]
  47. Roberts R. C., Burioni R., Helinski D. R. 1990; Genetic characterization of the stabilizing functions of a region of broad-host-range plasmid RK2. J Bacteriol 172:6204–6216
     [Google Scholar]
  48. Sandaa R. A., Enger O. 1994; Transfer in marine sediments of the naturally occurring plasmid pRAS1 encoding multiple antibiotic resistance. Appl Environ Microbiol 60:4234–4238
     [Google Scholar]
  49. Sneath P. H., Sokal R. R. 1973 Numerical Taxonomy San Francisco: W. H. Freeman;
     [Google Scholar]
  50. Sobecky P. A., Mincer T. J., Chang M. C., Helinski D. R. 1997; Plasmids isolated from marine sediment microbial communities contain replication and incompatibility regions unrelated to those of known plasmid groups. Appl Environ Microbiol 63:888–895
     [Google Scholar]
  51. Sobecky P. A., Mincer T. J., Chang M. C., Toukdarian A., Helinski D. R. 1998; Isolation of broad-host-range replicons from marine sediment bacteria. Appl Environ Microbiol 64:2822–2830
     [Google Scholar]
  52. Son R., Nasreldin E. H., Zaiton H., Samuel L., Rusul G., Nimita F. 1998; Use of randomly amplified polymorphic DNA analysis to differentiate isolates of Vibrio parahaemolyticus from cockles ( Anadara granosa ). World J Microbiol Biotechnol 14:895–901 [CrossRef]
     [Google Scholar]
  53. Stalker D. M., Kolter R., Helinski D. R. 1979; Nucleotide sequence of the region of an origin of replication of the antibiotic resistance plasmid R6K. Proc Natl Acad Sci USA 76:1150–1154 [CrossRef]
     [Google Scholar]
  54. Takeyama H., Burgess J. G., Sudo H., Sode K., Matsunaga T. 1991; Salinity-dependent copy number increase of a marine cyanobacterial endogenous plasmid. FEMS Microbiol Lett 90:95–98 [CrossRef]
     [Google Scholar]
  55. Vieira J., Messing J. 1982; The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene 19:259–268 [CrossRef]
     [Google Scholar]
  56. Welsh J., McClelland M. 1990; Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18:7213–7218 [CrossRef]
     [Google Scholar]
  57. Williams J. G. K., Kubelik A. R., Livak K. J., Rafalski J. A., Tingey S. V. 1990; DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535 [CrossRef]
     [Google Scholar]
  58. Wommack K. E., Ravel J., Hill R. T., Colwell R. R. 1999; Hybridization analysis of Chesapeake Bay virioplankton. Appl Environ Microbiol 65:241–250
     [Google Scholar]
  59. Zawadzki P., Riley M. A., Cohan F. M. 1996; Homology among nearly all plasmids infecting three Bacillus species. J Bacteriol 178:191–198
     [Google Scholar]
  60. Zhang X., Kosier B., Priefer U. B. 2001; Symbiotic plasmid rearrangement in Rhizobium leguminosarum bv. viciae VF39SM. J Bacteriol 183:2141–2144 [CrossRef]
     [Google Scholar]
  61. Zillig W., Yeats S., Holz I., Bock A., Gropp E., Rettenberger M., Lutz S. 1985; Plasmid-related anaerobic autotrophy of the novel archaebacterium Sulfolobus ambivalens . Nature 313:789–791 [CrossRef]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/00221287-148-1-179
Loading
Differentiation of plasmids in marine diazotroph assemblages determined by randomly amplified polymorphic DNA analysis
Microbiology 148, 179 (2002); https://doi.org/10.1099/00221287-148-1-179
/content/journal/micro/10.1099/00221287-148-1-179
/content/journal/micro/10.1099/00221287-148-1-179
Loading

Data & Media loading...

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error