1. ¹College of Oceanic and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
2. ²Department of Biological Sciences, Rowan University, Glassboro, NJ, USA
3. ³Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
4. ⁴Department of Microbiology, Oregon State University, Corvallis, OR, USA

Correspondence: SJ Giovannoni, Department of Microbiology, Oregon State University, Nash Hall, Corvallis, OR 97331, USA. E-mail: steve.giovannoni@oregonstate.edu

Received 10 June 2008; Revised 1 September 2008; Accepted 2 September 2008; Published online 9 October 2008.

Abstract

We used molecular techniques to analyze basalts of varying ages that were collected from the East Pacific Rise, 9° N, from the rift axis of the Juan de Fuca Ridge and from neighboring seamounts. Cluster analysis of 16S rDNA terminal restriction fragment polymorphism data revealed that basalt endoliths are distinct from seawater and that communities clustered, to some degree, based on the age of the host rock. This age-based clustering suggests that alteration processes may affect community structure. Cloning and sequencing of bacterial and archaeal 16S rRNA genes revealed 12 different phyla and subphyla associated with basalts. These include the Gemmatimonadetes, Nitrospirae, the candidate phylum SBR1093 in the bacteria, and in the Archaea Marine Benthic Group B, none of which have been previously reported in basalts. We delineated novel ocean crust clades in the -Proteobacteria, Planctomycetes and Actinobacteria that are composed entirely of basalt-associated microflora, and may represent basalt ecotypes. Finally, microarray analysis of functional genes in basalt revealed that genes coding for previously unreported processes such as carbon fixation, methane oxidation, methanogenesis and nitrogen fixation are present, suggesting that basalts harbor previously unrecognized metabolic diversity. These novel processes could exert a profound influence on ocean chemistry.