AME 69:247-261 (2013)  -  DOI: https://doi.org/10.3354/ame01635

Community composition and activity state of estuarine bacterioplankton assessed using differential staining and metagenomic analysis of 16S rDNA and rRNA

Rima B. Franklin1, Catherine Luria1,4, Luiz Shozo Ozaki2, Paul A. Bukaveckas1,3,*

1Department of Biology, 2Center for the Study of Biological Complexity, Department of Microbiology and Immunology, and 3Center for Environmental Studies, Virginia Commonwealth University, Richmond, Virginia 23284, USA
4Present address: Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02906, USA
*Corresponding author. Email:

ABSTRACT: To better understand how resource availability controls estuarine microbial communities, we compared community composition at 2 sites in the tidal freshwater James River (Virginia, USA) which differed in nutrient concentrations and autochthonous production. In addition, we conducted laboratory microcosm experiments, wherein bacteria from the 2 sites received nutrient, light, and organic carbon amendments. Traditional, microscopy-based methods of staining and enumeration were used to determine the abundance of total, live, and active cells. DNA fingerprinting (terminal restriction fragment length polymorphism, TRFLP) and dual 16S rDNA-rRNA pyrosequencing were used to assess community composition and taxon-specific activity (from rRNA:rDNA). Enumeration revealed that total, live, and active (CTC+) bacteria were more abundant at the site where autochthonous production was higher, while DNA fingerprinting (TRFLP) and 16S rDNA pyrosequencing indicated high similarity in community composition at the 2 sites. In contrast, pyrosequencing results from rRNA revealed greater variation and suggest that the metabolically active fraction of the community differed between sites. Differences in rDNA- and rRNA-based libraries were also apparent in microcosm experiments, where resource amendments resulted in shifts in both the active and overall communities. In both environmental and microcosm samples, dual rDNA-rRNA pyrosequencing yielded higher estimates of the proportion of active cells (32 ± 3%) compared to differential staining and microscopy (13 ± 1%). Though characterization of active taxa was sensitive to the presumed activity threshold (rRNA:rDNA), our findings suggest that variable resource conditions can give rise to unique assemblages of active taxa despite similarities in overall community composition.


KEY WORDS: Activity state · Bacteria · Community composition · Estuary · Pyrosequencing · Chesapeake Bay


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Cite this article as: Franklin RB, Luria C, Ozaki LS, Bukaveckas PA (2013) Community composition and activity state of estuarine bacterioplankton assessed using differential staining and metagenomic analysis of 16S rDNA and rRNA. Aquat Microb Ecol 69:247-261. https://doi.org/10.3354/ame01635

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