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 rDNArRNA 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 rDNAand 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
Resale or republication not permitted without written consent of the publisherAquat Microb Ecol 69: [247][248][249][250][251][252][253][254][255][256][257][258][259][260][261] 2013 viral lysis (Thingstad & Lignell 1997). Determining the relative importance of these factors is challenging, particularly in estuaries, which experience large and frequent changes in environmental conditions. In these systems, tidal-driven exchanges with the marine environment and episodic riverine inputs alter salinity, inorganic nutrients, and the quality and quantity of organic matter along the longitudinal axis of the estuary. Mechanisms of bacterial community response to these factors are poorly understood, but can include shifts in bacterial abundance, community composition, and activity state.The analysis of whole-community DNA extracts from environmental samples has been used to characterize variation in estuarine bacterioplankton in response to changes in resources and physicalchemical conditions (Troussellier et al. 2002, Crump et al. 2004, Henriques et al. 2004, Kirchman et al. 2005. However, DNA is present in dormant ...