Phylogeny of Actinobacteria Small Subunit (SSU) rRNA Gene Clones Recovered From Marine Bacterioplankton

Abstract

Summary Recent analyses of PCR-generated SSU rRNA gene clone libraries have revealed the presence of previously unidentified members of the class Actinobacteria (high G+C Gram positive bacteria) in a diverse array of natural environments. From terrestrial soil samples, Actinobacteria-related gene clones form several phylogenetic clusters, distantly related to their nearest cultivated relatives. Actinobacteria-related clones have also been discovered in SSU rRNA gene clone libraries from sea water, though a lack of representative clones with complete sequences has lead to uncertainties regarding their potential affiliation with terrestrial soil environmental gene clones, as well as uncertain phylogenetic relationships with reference strains from the class Actinobacteria . Herein, we show the phylogenetic position of PCR-generated SSU rRNA gene clones related to the class Actinobacteria recovered from three diverse populations of marine bacterioplankton, including a sample from a depth of 80 m in the Sargasso Sea and samples from a depth of 10 m over the eastern and western continental shelves of the United States. Employing phylogenetic methods which take into consideration potential bias due to unequal nucleotide frequencies between taxa, the nearly complete SSU rRNA gene sequence data presented here place the closely related marine clones (>97.4% similar) as deep branching members of the class Actinobacteria , distantly related to their nearest cultivated relatives. In addition, the clade of marine Actinobacteria gene clones did not demonstrate phylogenetically robust affiliations with any environmental gene clone sequences from terrestrial soil habitats. Based on their early divergence from the base of the Actinobacteria radiation and phylogenetic distance from other members of this class, microorganisms which possess SSU rRNA genes belonging to the marine Actinobacteria clade probably represent a previously unidentified subclass or order within the class Actinobacteria .