Abstract
We determined the compositions of bacterioplankton communities in surface waters of coastal California using clone libraries of 16S rRNA genes and fluorescence in situ hybridization (FISH) in order to compare the community structures inferred from these two culture-independent approaches. The compositions of two clone libraries were quite similar to those of clone libraries of marine bacterioplankton examined by previous studies. Clones from gamma-proteobacteria comprised ca. 28% of the libraries, while approximately 55% of the clones came from alpha-proteobacteria, which dominated the clone libraries. The Cytophaga-Flavobacter group and three others each comprised 10% or fewer of the clone libraries. The community composition determined by FISH differed substantially from the composition implied by the clone libraries. The Cytophaga-Flavobacter group dominated 8 of the 11 communities assayed by FISH, including the two communities assayed using clone libraries. On average only 10% of DAPI (4', 6'-diamidino-2-phenylindole)-stained bacteria were detected by FISH with a probe for alpha-proteobacteria, but 30% of DAPI-stained bacteria appeared to be in the Cytophaga-Flavobacter group as determined by FISH. alpha-Proteobacteria were greatly overrepresented in clone libraries compared to their relative abundance determined by FISH, while the Cytophaga-Flavobacter group was underrepresented in clone libraries. Our data show that the Cytophaga-Flavobacter group can be a numerically dominant component of coastal marine bacterioplankton communities.
Highlights
An important first step towards understanding the roles of various bacteria in the ocean is determining the numbers and relative abundances of different bacterial groups (21)
We found that ␣-proteobacteria dominated clone libraries of 16S rRNA genes, as shown previously for marine bacterioplankton communities, whereas Fluorescence in situ hybridization (FISH) indicated that the Cytophaga-Flavobacter cluster was usually the most abundant group of bacterioplankton in coastal California waters
Our study revealed substantial differences between the community compositions of marine bacterioplankton communities determined by FISH and clone libraries of 16S rRNA genes
Summary
An important first step towards understanding the roles of various bacteria in the ocean is determining the numbers and relative abundances of different bacterial groups (21). Marine ␣-proteobacteria typically dominate 16S rRNA gene clone libraries (21), while the limited data collected using FISH suggest that members of the CytophagaFlavobacter group dominate marine bacterioplankton communities (25, 42). It is not clear if these differences reflect spatial and temporal variation or methodological differences, because no study has applied both analyses to the same community. We found that ␣-proteobacteria dominated clone libraries of 16S rRNA genes, as shown previously for marine bacterioplankton communities, whereas FISH indicated that the Cytophaga-Flavobacter cluster was usually the most abundant group of bacterioplankton in coastal California waters
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