Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization

We determined the compositions of bacterioplankton communities in surface w aters of coastal California using clone libraries of 16S rRNA genes and flu orescence in situ hybridization (FISH) in order to compare the community st ructures inferred from these two culture-independent approaches. The compos itions of two clone libraries were quite similar to those of clone librarie s of marine bacterioplankton examined by previous studies. Clones from gamm a -proteobacteria comprised ca. 28% of the libraries, while approximately 5 5% of the clones came from cr-proteobacteria, which dominated the clone lib raries. The Cytophaga-Flavobacter group and three others each comprised 10% or fewer of the clone libraries. The community composition determined by F ISH differed substantially from the composition implied by the clone librar ies. The Cytophaga-Flavobacter group dominated 8 of the II communities assa yed by FISH, including the two communities assayed using clone libraries. O n average only 10% of DAPI (4',6'-diamidino-2-phenylindole)-stained bacteri a 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. ol-Proteobacteria were greatly overrepresented in clone libraries compared to their relative abundance determined by FISH, while t he Cytophaga-Flavobacter group was underrepresented in clone libraries. Our data show that the Cytophaga-Flavobacter group can be a numerically domina nt component of coastal marine bacterioplankton communities.