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Stephen Joseph Giovannoni, a marine microbiologist and Distinguished Professor in the Department of Microbiology at Oregon State University, is a leader in the field of molecular microbiology, systems biology and marine microbial ecology. His innovations, including the use of PCR to recover 16S rRNA genes to characterize microbial diversity, and phylogenetic group specific rRNA probes, revolutionized microbial ecology. He was the first to discover the great diversity of uncultivated microbes in the oceans[1]. Until Giovannoni's pioneering studies using PCR (polymerase chain reaction) to directly amplify ribosomal RNA genes from environmental samples, knowledge of marine microbes was largely circumscribed by what could be learned from cultivated strains. Giovannoni and colleagues found that most microbes present in environmental samples are from previously unknown groups[1][2][3][4][5]. Giovannoni and his lab group discovered the SAR11 clade (Pelagibacteraceae)[1], a lineage of bacteria that makes up roughly one third of microbial cells in the ocean[6], suggesting that SAR11 and its relatives represent the most common cells on Earth.

Education A native of California, Giovannoni's undergraduate degree was from University of California at San Diego, where he majored in Biophysics. His master's degree was from Boston University, where he worked with noted evolutionary biologist Lynn Margulis[7][8]. For his Ph.D. at University of Oregon with Richard Castenholtz, he studied the ecology of hot springs bacteria[9][10][11]. He was an NSF Postdoctoral Fellow at Indiana University in the laboratory of Norman Pace, during the period when the Pace lab was developing methods for sequencing ribosomal RNA for phylogenetic analysis. His research there cast light on phylogenetic relationships of chloroplasts and cyanobacteria[12][13]. Giovannoni also developed the concept of using rRNA-based probes to identify specific microbial groups (phylogenetic group specific probes[14].

Research After the discovery of the SAR11 clade, Giovannoni's research group continued to characterize the group and many other lineages of previously-unknown planktonic bacteria they discovered, using both genome analysis and isolation and cultivation. Understanding these organisms has been critical to the development of local and global geochemical models, as well as socially relevant issues such as bioremediation.

Giovannoni's lab developed high-throughput methods for isolating oligotrophic bacteria previously known only from sequence data[15]. This resulted in isolation of Pelagibacter ubique, the first representative of the SAR11 clade to be cultured[16]. His lab maintains a culture collection and makes it available to other researchers. Isolates from many of the lineages represented in the collection have now had their genomes sequenced, adding greatly to understanding of the evolution, physiology and community structure of microbial communities.

Giovannoni’s genomic, metagenomic, and proteomic studies are coupled to ecological field studies, mainly in the Sargasso Sea, but also in many other environments ranging from deep subsurface basalts[17][18] to Antarctic frozen lakes[19][20]. Giovannoni and his collaborators established a Microbial Observatory in the Western Sargasso Sea (BATS, the Bermuda Atlantic Time-series Study), an example of an oligotrophic ocean gyre. Many ecological studies have resulted from this work[21][22][23].

Isolates in the SAR11 clade have the smallest genomes known from any free-living heterotrophic bacteria (1.31 -1.46 Mbp). Giovannoni’s recent studies are concentrated on elucidating principals of genomic and metabolic streamlining exemplified by these bacteria[24][25].