DIVERSITY AND DEPTH-SPECIFIC DISTRIBUTION OF SAR11 CLUSTER RIBOSOMAL-RNA GENES FROM MARINE PLANKTONIC BACTERIA

Small-subunit (SSU) ribosomal DNA (rDNA) gene clusters are phylogeneti cally related sets of SSU rRNA genes, commonly encountered in genes am plified from natural populations. Genetic variability in gene clusters could result from artifacts (polymerase error or PCR chimera formatio n), microevolution (variation among rrn copies within strains), or mac roevolution (genetic divergence correlated with long-term evolutionary divergence). To better understand gene clusters, this study assessed genetic diversity and distribution of a single environmental SSU rDNA gene cluster, the SAR11 cluster. SAR11 cluster genes, from an uncultur ed group of the a subclass of the class Proteobacteria, have been reco vered from coastal and midoceanic waters of the North Atlantic and Pac ific. We cloned and bidirectionally sequenced 23 new SAR11 cluster 16S rRNA genes, from 80 and 250 m in the Sargasso Sea and from surface co astal waters of the Atlantic and Pacific, and analyzed them with previ ously published sequences. Two SAR11 genes were obviously PCR chimeras , but the biological (nonchimeric) origins of most subgroups, within t he cluster were confirmed by independent recovery from separate gene l ibraries. Using group-specific oligonucleotide probes, we analyzed dep th profiles of nucleic acids, targeting both amplified rDNAs and bulk RNAs. Two subgroups within the SAR11 cluster showed different highly d epth-specific distributions. We conclude that some of the genetic dive rsity, within the SAR11 gene cluster represents macroevolutionary dive rgence correlated with niche specialization. Furthermore, we demonstra te the utility for marine microbial ecology of oligonucleotide probes based on gene sequences amplified from natural populations and show th at a detailed knowledge of sequence variability may be needed to effec tively design these probes.