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

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