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Appl Environ Microbiol. 1995 March; 61(3): 944–952.
PMCID: PMC1388377

Comparison of Free-Living and Particle-Associated Bacterial Communities in the Chesapeake Bay by Stable Low-Molecular-Weight RNA Analysis


Free-living and particle-associated bacterial communities in the Chesapeake Bay estuary were analyzed and compared by using acridine orange direct counts and low-molecular-weight (LMW) RNA analysis. Samples were taken from top and bottom waters at upper- and mid-bay sites in December 1992. Free-living bacteria dominated the bacterial numbers at all sampling sites, although particle-associated bacteria increased in areas with greater particle loads. LMW RNAs (5S rRNA and tRNA) obtained directly from free-living, particle-associated, and total bacterioplankton communities were analyzed by high-resolution electrophoresis. There were distinct differences in the migration distances between LMW RNAs of free-living and particle-associated communities taken from the same site, indicating that the two communities differ in composition. In addition, LMW RNA profiles differed minimally with depth for all of the communities examined, presumably because of vertical mixing. 5S rRNAs of free-living communities from the upper- and mid-bay regions differed considerably. Particle-associated RNAs, on the other hand, were very similar, suggesting consistent environmental conditions on particles that select for similar community members. Lastly, several isolated bacteria had 5S rRNAs that were not detected in their respective extracted community 5S rRNAs, indicating that these isolated organisms were not representative of dominant members.

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Selected References

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  • Amann R, Springer N, Ludwig W, Görtz HD, Schleifer KH. Identification in situ and phylogeny of uncultured bacterial endosymbionts. Nature. 1991 May 9;351(6322):161–164. [PubMed]
  • Caron DA, Davis PG, Madin LP, Sieburth JM. Heterotrophic bacteria and bacterivorous protozoa in oceanic macroaggregates. Science. 1982 Nov 19;218(4574):795–797. [PubMed]
  • England TE, Bruce AG, Uhlenbeck OC. Specific labeling of 3' termini of RNA with T4 RNA ligase. Methods Enzymol. 1980;65(1):65–74. [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]
  • Giovannoni SJ, Britschgi TB, Moyer CL, Field KG. Genetic diversity in Sargasso Sea bacterioplankton. Nature. 1990 May 3;345(6270):60–63. [PubMed]
  • Hobbie JE, Daley RJ, Jasper S. Use of nuclepore filters for counting bacteria by fluorescence microscopy. Appl Environ Microbiol. 1977 May;33(5):1225–1228. [PMC free article] [PubMed]
  • Höfle MG. Bacterioplankton community structure and dynamics after large-scale release of nonindigenous bacteria as revealed by low-molecular-weight-RNA analysis. Appl Environ Microbiol. 1992 Oct;58(10):3387–3394. [PMC free article] [PubMed]
  • Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol. 1981 Feb 15;146(1):1–21. [PubMed]
  • Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol. 1985 Jan;2(1):13–34. [PubMed]
  • Iriberri J, Unanue M, Ayo B, Barcina I, Egea L. Bacterial production and growth rate estimation from [h]thymidine incorporation for attached and free-living bacteria in aquatic systems. Appl Environ Microbiol. 1990 Feb;56(2):483–487. [PMC free article] [PubMed]
  • Kirchman D, Mitchell R. Contribution of particle-bound bacteria to total microheterotrophic activity in five ponds and two marshes. Appl Environ Microbiol. 1982 Jan;43(1):200–209. [PMC free article] [PubMed]
  • Kolodny GM. An improved method for increasing the resolution and sensitivity of silver staining of nucleic acid bands in polyacrylamide gels. Anal Biochem. 1984 Apr;138(1):66–67. [PubMed]
  • Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stahl DA. Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol. 1986;40:337–365. [PubMed]
  • Schmidt TM, DeLong EF, Pace NR. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol. 1991 Jul;173(14):4371–4378. [PMC free article] [PubMed]
  • Simon M. Specific uptake rates of amino acids by attached and free-living bacteria in a mesotrophic lake. Appl Environ Microbiol. 1985 May;49(5):1254–1259. [PMC free article] [PubMed]
  • Slade PJ, Collins-Thompson DL. Differentiation of the genus Listeria from other gram-positive species based on low molecular weight (LMW) RNA profiles. J Appl Bacteriol. 1991 Apr;70(4):355–360. [PubMed]
  • Somerville CC, Knight IT, Straube WL, Colwell RR. Simple, rapid method for direct isolation of nucleic acids from aquatic environments. Appl Environ Microbiol. 1989 Mar;55(3):548–554. [PMC free article] [PubMed]
  • Specht T, Wolters J, Erdmann VA. Compilation of 5S rRNA and 5S rRNA gene sequences. Nucleic Acids Res. 1990 Apr 25;18 (Suppl):2215–2230. [PMC free article] [PubMed]
  • Sprinzl M, Moll J, Meissner F, Hartmann T. Compilation of tRNA sequences. Nucleic Acids Res. 1985;13 (Suppl):r1–49. [PMC free article] [PubMed]
  • Stahl DA, Lane DJ, Olsen GJ, Pace NR. Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences. Appl Environ Microbiol. 1985 Jun;49(6):1379–1384. [PMC free article] [PubMed]
  • Wommack KE, Hill RT, Kessel M, Russek-Cohen E, Colwell RR. Distribution of viruses in the Chesapeake Bay. Appl Environ Microbiol. 1992 Sep;58(9):2965–2970. [PMC free article] [PubMed]

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