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

Aquatic Microbial Ecology

Paul A. Bukaveckas¹  Luiz Shozo Ozaki¹  Rima B. Franklin¹  Catherine Luria¹ 

关键词: Activity state;    Bacteria;    Community composition;    Estuary;    Pyrosequencing;    Chesapeake Bay;   

DOI  :  10.3354/ame01635

学科分类：生物科学（综合）

来源: Inter-Research

【 摘 要 】

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.

【 授权许可】

Unknown