Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia river, its estuary, and the adjacent coastal ocean

The Columbia River estuary is a dynamic system in which estuarine turbidity maxims trap and extend the residence time of particles and particle-attach ed bacteria over those of the water and free-living bacteria. Particle-atta ched bacteria dominate bacterial activity in the estuary and are an importa nt part of the estuarine food web. PCR-amplified 16S rRNA genes from partic le-attached and free-living bacteria in the Columbia River, its estuary, an d the adjacent coastal ocean were cloned, and 239 partial sequences were de termined. A wide diversity was observed at the species level within at leas t six different bacterial phyla, including most subphyla of the class Prote obacteria. In the estuary, most particle-attached bacterial clones (75%) we re related to members of the genus Cytophaga or of the alpha, gamma, or bet a subclass of the class Proteobacteria. These same clones, however, were ra re in or absent from either the particle-attached or the free-living bacter ial communities of the river and the coastal ocean. In contrast, about half (48%) of the free-living estuarine bacterial clones were similar to clones from the river or the coastal ocean. These free-living bacteria were relat ed to groups of cosmopolitan freshwater bacteria (beta-proteobacteria, gram -positive bacteria, and Verrucomicrobium spp,) and groups of marine organis ms (gram-positive bacteria and alpha-proteobacteria [SAR11 and Rhodobacter spp.]). These results suggest that rapidly growing particle-attached bacter ia develop into a uniquely adapted estuarine community and that free-living estuarine bacteria are similar to members of the river and the coastal oce an microbial communities. The high degree of diversity in the estuary is th e result of the mixing of bacterial communities from the river, estuary, an d coastal ocean.