Past projects

Those are my latest completed projects from the Giovannoni lab. See list of publications for more.

Improvements of high-throughput-culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site (Stingl et al., ISME journal, in press)

 

The introduction of high throughput dilution-to-extinction culturing (HTC) of marine bacterioplankton using sterilized natural seawater as media yielded isolates of many abundant but previously uncultured marine bacterial clades. In early experiments bacteria from the SAR11 cluster (class Alphaproteobacteria), which are presumed to be the most abundant prokaryotes on earth, were cultured. Although many additional attempts were made, no further strains of the SAR11 clade were obtained. Here, we describe improvements to the HTC technique, which led to the isolation of 17 new SAR11 strains from the Oregon coast and the Sargasso Sea, accounting for 28% and 31% of all isolates in these experiments. Phylogenetic analysis of the ITS region showed that the isolates from the Oregon coast represent three different subclusters of SAR11, while isolates from the Sargasso Sea were more uniform and represent a single ITS cluster. A PCR assay proved the presence of proteorhodopsin (PR) in nearly all SAR11 isolates. Analysis of PR amino acid sequences indicated that isolates from the Oregon coast were tuned to either green or blue light, while PRs from strains obtained from the Sargasso Sea were exclusively tuned to maximum absorbance in the blue. Interestingly, phylogenies based on PR and ITS did not correlate, suggesting lateral gene transfer. In addition to the new SAR11 strains, many novel strains belonging to clusters of previously uncultured or undescribed species of different bacterial phyla, including the first strain of the highly abundant alphaproteobacterial SAR116 clade, were isolated using the modified methods.

 

The SAR92 clade: An abundant coastal clade of culturable marine bacteria possessing proteorhodopsin   

(Stingl et al. AEM 2007)    

Proteorhodopsin (PR) is a protein that is abundant in marine bacterioplankton. PR is hypothesized to a light-dependent proton thus creating a proton gradient that can be used for energy production without electron transport. Currently, the only culture published that possesses PR is the highly abundant Alphaproteobacterium Candidatus Pelagibacter ubique (SAR11 clade), but, surprisingly, its growth in batch culture was not enhanced by light. Here, we present the first cultured Gammaproteobacterium that possesses a PR gene. Genome sequencing and analysis of HTCC2207 showed that the PR gene is present as a lone transcriptional unit directly followed by an operon containing genes that are presumably involved in the synthesis of retinal, the chromophore of PR. Half-time decay times of different PR intermediates in native HTCC2207 cells ranged between 2 and 15 ms, the absorbance maximum of PR was determined to be 528 nm. Proteorhodopsin was identified in three additional strains using a specific PCR assay on other cultured members of the SAR92 clade. Phylogenetic analysis of the PR genes determined that they form a deeply-rooting cluster not closely related to any PR genes recovered so far. Fluorescence in situ hybridization (FISH) and RNA blots show that the SAR92 clade reaches up to 10% of the total bacterial population in surface waters close to the < xml="true" ns="urn:schemas-microsoft-com:office:smarttags" prefix="st1" namespace="">Oregon coast and decreases over depth and distance from the shore. Although being carbon-limited in the applied media, also these cultures do not grow at higher growth rate nor have better growth yields when incubated under light.< xml="true" ns="urn:schemas-microsoft-com:office:office" prefix="o" namespace="">

 

Molecular Diversity and Ecology of Microbial Plankton  (Giovannoni and Stingl, Nature 2005)

 

The history of microbial evolution in the oceans is probably as old as the history of life itself. In contrast to terrestrial ecosystems, microorganisms are the major form of biomass in the oceans. The microorganisms that succeeded in capturing key resources in the ocean food web now form some of the largest populations on the planet (2-4).  Heterotrophic prokaryotes, which are the main focus of this review, process about 50% of oceanic primary production. As pointed out by Kimura, size matters with populations. His theory predicts that selection should act efficiently in large microbial plankton populations, producing organisms that are models of adaptive sophistication.  Whether this prediction is correct remains to be seen. Genome sequence data is piling up, but most of the key microbial plankton clades have no cultivated representatives, and information about their ecological activities is sparse. Below we review current knowledge about marine bacterial and archaeal diversity, as inferred from phylogenies of genes recovered from the ocean water column, and consider the implications of microbial diversity for understanding the ecology of the oceans. Although some of the studies referred to extend into the abyssal ocean, our comments are focused on the surface layer (0-300 m), the region of highest biological activity.