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Appl Environ Microbiol. Mar 1997; 63(3): 888–895.
PMCID: PMC168381

Plasmids isolated from marine sediment microbial communities contain replication and incompatibility regions unrelated to those of known plasmid groups.


Two hundred ninety-seven bacteria carrying plasmids that range in size from 5 to 250 kb were identified from more than 1,000 aerobic heterotrophic bacteria isolated from coastal California marine sediments. While some isolates contained numerous (three to five) small (5- to 10-kb) plasmids, the majority of the natural isolates typically contained one large (40- to 100-kb) plasmid. By the method of plasmid isolation used in this study, the frequency of plasmid incidence ranged from 24 to 28% depending on the samples examined. Diversity of the plasmids occurring in the marine sediment bacterial populations was examined at the molecular level by hybridization with 14 different DNA probes specific for the incompatibility and replication (inc/rep) regions of a number of well-characterized plasmid incompatibility groups (repB/O, FIA, FII, FIB, HI1, HI2, I1, L/M, X, N, P, Q, W, and U). Interestingly, we found no DNA homology between the plasmids isolated from the culturable bacterial population of marine sediments and the replicon probes specific for numerous incompatibility groups developed by Couturier et al. (M. F. Couturier, F. Bex, P. L. Bergquist, and W. K. Maas, Microbiol. Rev. 52:375-395, 1988). Our findings suggest that plasmids in marine sediment microbial communities contain novel, as-yet-uncharacterized, incompatibility and replication regions and that the present replicon typing system, based primarily on plasmids derived from clinical isolates, may not be representative of the plasmid diversity occurring in some marine environments. Since the vast majority of marine bacteria are not culturable under laboratory conditions, we also screened microbial community DNA for the presence of broad- and narrow-host-range plasmid replication sequences. Although the replication origin of the conjugally promiscuous broad-host-range plasmid RK2 (incP) was not detectable in any of the plasmid-containing culturable marine isolates, DNA extracted from the microbial community and amplified by PCR yielded a positive signal for RK2 oriV replication sequences. The strength of the signal suggests the presence of a low level of the incP replicon within the marine microbial community. In contrast, replication sequences specific for the narrow-host-range plasmid F were not detectable in DNA extracted from marine sediment microbial communities. With the possible exception of mercuric chloride, phenotypic analysis of the 297 plasmid-bearing isolates did not demonstrate a correlation between plasmid content and antibiotic or heavy metal resistance traits.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Amuthan G, Mahadevan A. Replicon typing of plasmids of phytopathogenic xanthomonads. Plasmid. 1994 Nov;32(3):328–332. [PubMed]
  • Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol. 1966 Apr;45(4):493–496. [PubMed]
  • Baumann L, Baumann P, Mandel M, Allen RD. Taxonomy of aerobic marine eubacteria. J Bacteriol. 1972 Apr;110(1):402–429. [PMC free article] [PubMed]
  • Belliveau BH, Starodub ME, Trevors JT. Occurrence of antibiotic and metal resistance and plasmids in Bacillus strains isolated from marine sediment. Can J Microbiol. 1991 Jul;37(7):513–520. [PubMed]
  • Benson S, Shapiro J. TOL is a broad-host-range plasmid. J Bacteriol. 1978 Jul;135(1):278–280. [PMC free article] [PubMed]
  • Bravo A, Ortega S, de Torrontegui G, Díaz R. Killing of Escherichia coli cells modulated by components of the stability system ParD of plasmid R1. Mol Gen Genet. 1988 Dec;215(1):146–151. [PubMed]
  • Burlage RS, Bemis LA, Layton AC, Sayler GS, Larimer F. Comparative genetic organization of incompatibility group P degradative plasmids. J Bacteriol. 1990 Dec;172(12):6818–6825. [PMC free article] [PubMed]
  • Burton NF, Day MJ, Bull AT. Distribution of bacterial plasmids in clean and polluted sites in a South Wales river. Appl Environ Microbiol. 1982 Nov;44(5):1026–1029. [PMC free article] [PubMed]
  • Chaslus-Dancla E, Pohl P, Meurisse M, Marin M, Lafont JP. High genetic homology between plasmids of human and animal origins conferring resistance to the aminoglycosides gentamicin and apramycin. Antimicrob Agents Chemother. 1991 Mar;35(3):590–593. [PMC free article] [PubMed]
  • Couturier M, Bex F, Bergquist PL, Maas WK. Identification and classification of bacterial plasmids. Microbiol Rev. 1988 Sep;52(3):375–395. [PMC free article] [PubMed]
  • da Silva-Tatley FM, Steyn LM. Characterization of a replicon of the moderately promiscuous plasmid, pGSH5000, with features of both the mini-replicon of pCU1 and the ori-2 of F. Mol Microbiol. 1993 Mar;7(5):805–823. [PubMed]
  • Davey RB, Bird PI, Nikoletti SM, Praszkier J, Pittard J. The use of mini-Gal plasmids for rapid incompatibility grouping of conjugative R plasmids. Plasmid. 1984 May;11(3):234–242. [PubMed]
  • de Vicente A, Avilés M, Codina JC, Borrego JJ, Romero P. Resistance to antibiotics and heavy metals of Pseudomonas aeruginosa isolated from natural waters. J Appl Bacteriol. 1990 Jun;68(6):625–632. [PubMed]
  • Ferguson RL, Buckley EN, Palumbo AV. Response of marine bacterioplankton to differential filtration and confinement. Appl Environ Microbiol. 1984 Jan;47(1):49–55. [PMC free article] [PubMed]
  • Gerdes K, Rasmussen PB, Molin S. Unique type of plasmid maintenance function: postsegregational killing of plasmid-free cells. Proc Natl Acad Sci U S A. 1986 May;83(10):3116–3120. [PMC free article] [PubMed]
  • Götz A, Pukall R, Smit E, Tietze E, Prager R, Tschäpe H, van Elsas JD, Smalla K. Detection and characterization of broad-host-range plasmids in environmental bacteria by PCR. Appl Environ Microbiol. 1996 Jul;62(7):2621–2628. [PMC free article] [PubMed]
  • Guiney DG. Host range of conjugation and replication functions of the Escherichia coli sex plasmid Flac. Comparison with the broad host-range plasmid RK2. J Mol Biol. 1982 Dec 15;162(3):699–703. [PubMed]
  • Hada HS, Sizemore RK. Incidence of Plasmids in Marine Vibrio spp. Isolated from an Oil Field in the Northwestern Gulf of Mexico. Appl Environ Microbiol. 1981 Jan;41(1):199–202. [PMC free article] [PubMed]
  • Hermansson M, Jones GW, Kjelleberg S. Frequency of antibiotic and heavy metal resistance, pigmentation, and plasmids in bacteria of the marine air-water interface. Appl Environ Microbiol. 1987 Oct;53(10):2338–2342. [PMC free article] [PubMed]
  • Hill KE, Weightman AJ, Fry JC. Isolation and screening of plasmids from the epilithon which mobilize recombinant plasmid pD10. Appl Environ Microbiol. 1992 Apr;58(4):1292–1300. [PMC free article] [PubMed]
  • Kieser T. Factors affecting the isolation of CCC DNA from Streptomyces lividans and Escherichia coli. Plasmid. 1984 Jul;12(1):19–36. [PubMed]
  • Kobayashi N, Bailey MJ. Plasmids isolated from the sugar beet phyllosphere show little or no homology to molecular probes currently available for plasmid typing. Microbiology. 1994 Feb;140(Pt 2):289–296. [PubMed]
  • Kobori H, Sullivan CW, Shizuya H. Bacterial plasmids in antarctic natural microbial assemblages. Appl Environ Microbiol. 1984 Sep;48(3):515–518. [PMC free article] [PubMed]
  • Lehnherr H, Yarmolinsky MB. Addiction protein Phd of plasmid prophage P1 is a substrate of the ClpXP serine protease of Escherichia coli. Proc Natl Acad Sci U S A. 1995 Apr 11;92(8):3274–3277. [PMC free article] [PubMed]
  • Mamun KZ, Shears P, Hart CA. The prevalence and genetics of resistance to commonly used antimicrobial agents in faecal Enterobacteriaceae from children in Bangladesh. Epidemiol Infect. 1993 Jun;110(3):447–458. [PMC free article] [PubMed]
  • Mergeay M, Nies D, Schlegel HG, Gerits J, Charles P, Van Gijsegem F. Alcaligenes eutrophus CH34 is a facultative chemolithotroph with plasmid-bound resistance to heavy metals. J Bacteriol. 1985 Apr;162(1):328–334. [PMC free article] [PubMed]
  • Novick RP. Plasmid incompatibility. Microbiol Rev. 1987 Dec;51(4):381–395. [PMC free article] [PubMed]
  • Pansegrau W, Lanka E, Barth PT, Figurski DH, Guiney DG, Haas D, Helinski DR, Schwab H, Stanisich VA, Thomas CM. Complete nucleotide sequence of Birmingham IncP alpha plasmids. Compilation and comparative analysis. J Mol Biol. 1994 Jun 24;239(5):623–663. [PubMed]
  • Perri S, Helinski DR. DNA sequence requirements for interaction of the RK2 replication initiation protein with plasmid origin repeats. J Biol Chem. 1993 Feb 15;268(5):3662–3669. [PubMed]
  • Powers EM. Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol. 1995 Oct;61(10):3756–3758. [PMC free article] [PubMed]
  • Roberts RC, Ström AR, Helinski DR. The parDE operon of the broad-host-range plasmid RK2 specifies growth inhibition associated with plasmid loss. J Mol Biol. 1994 Mar 18;237(1):35–51. [PubMed]
  • Saadi S, Maas WK, Hill DF, Bergquist PL. Nucleotide sequence analysis of RepFIC, a basic replicon present in IncFI plasmids P307 and F, and its relation to the RepA replicon of IncFII plasmids. J Bacteriol. 1987 May;169(5):1836–1846. [PMC free article] [PubMed]
  • Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA, Arnheim N. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science. 1985 Dec 20;230(4732):1350–1354. [PubMed]
  • Schmidhauser TJ, Helinski DR. Regions of broad-host-range plasmid RK2 involved in replication and stable maintenance in nine species of gram-negative bacteria. J Bacteriol. 1985 Oct;164(1):446–455. [PMC free article] [PubMed]
  • Sizemore RK, Colwell RR. Plasmids carried by antibiotic-resistant marine bacteria. Antimicrob Agents Chemother. 1977 Sep;12(3):373–382. [PMC free article] [PubMed]
  • Sobecky PA, Schell MA, Moran MA, Hodson RE. Impact of a genetically engineered bacterium with enhanced alkaline phosphatase activity on marine phytoplankton communities. Appl Environ Microbiol. 1996 Jan;62(1):6–12. [PMC free article] [PubMed]
  • Stalker DM, Thomas CM, Helinski DR. Nucleotide sequence of the region of the origin of replication of the broad host range plasmid RK2. Mol Gen Genet. 1981;181(1):8–12. [PubMed]
  • Summers AO, Jacoby GA. Plasmid-determined resistance to tellurium compounds. J Bacteriol. 1977 Jan;129(1):276–281. [PMC free article] [PubMed]
  • Tebbe CC, Vahjen W. Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast. Appl Environ Microbiol. 1993 Aug;59(8):2657–2665. [PMC free article] [PubMed]
  • Thomas CM. Recent studies on the control of plasmid replication. Biochim Biophys Acta. 1988 Mar 31;949(3):253–263. [PubMed]
  • Tsai YL, Olson BH. Rapid method for direct extraction of DNA from soil and sediments. Appl Environ Microbiol. 1991 Apr;57(4):1070–1074. [PMC free article] [PubMed]
  • Wortman AT, Colwell RR. Frequency and characteristics of plasmids in bacteria isolated from deep-sea amphipods. Appl Environ Microbiol. 1988 May;54(5):1284–1288. [PMC free article] [PubMed]

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