Robert Belas

Since the recognition of prokaryotes as essential components of the oceanic food web, bacterioplankton have been acknowledged as catalysts of most major biogeochemical processes in the sea. Studying heterotrophic bacterioplankton has been challenging, however, as most major clades have never been cultured or have only been grown to low densities in sea water. Here we describe the genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade (Fig. 1), the relatives of which comprise approximately 10-20% of coastal and oceanic mixed-layer bacterioplankton. This first genome sequence from any major heterotrophic clade consists of a chromosome (4,109,442 base pairs) and megaplasmid (491,611 base pairs). Genome analysis indicates that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds (carbon monoxide and sulphide) to supplement heterotrophy. Silicibacter pomeroyi also has genes advantageous for associations with plankton and suspended particles, including genes for uptake of algal-derived compounds, use of metabolites from reducing microzones, rapid growth and cell-density-dependent regulation. This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean.

Bacterioplankton of the marine Roseobacter clade have genomes that reflect a dynamic environment and diverse interactions with marine plankton. Comparative genome sequence analysis of three cultured representatives suggests that cellular requirements for nitrogen are largely provided by regenerated ammonium and organic compounds (polyamines, allophanate, and urea), while typical sources of carbon include amino acids, glyoxylate, and aromatic metabolites. An unexpectedly large number of genes are predicted to encode proteins involved in the production, degradation, and efflux of toxins and metabolites. A mechanism likely involved in cell-to-cell DNA or protein transfer was also discovered: vir-related genes encoding a type IV secretion system typical of bacterial pathogens. These suggest a potential for interacting with neighboring cells and impacting the routing of organic matter into the microbial loop. Genes shared among the three roseobacters and also common in nine draft Roseobacter genomes include those for carbon monoxide oxidation, dimethylsulfoniopropionate demethylation, and aromatic compound degradation. Genes shared with other cultured marine bacteria include those for utilizing sodium gradients, transport and metabolism of sulfate, and osmoregulation.

Two distinctly different organelles of locomotion are produced by Vibrio parahaemolyticus. The polar flagellum is responsible for motility in a liquid environment (swimming), and the lateral flagella enable the bacteria to move over surfaces (swarming). Synthesis of lateral flagella occurs when V. parahaemolyticus is grown on agar media but not when it is grown in liquid media. We used lux (luminescence gene) fusions to conveniently and sensitively analyze the factors which influence transcription of lateral flagella genes (laf). Transposon mini-Mu lux was used to mutagenize V. parahaemolyticus and to generate laf::lux transcriptional fusions. Mutants with insertions of mini-Mu lux in laf genes were defective in the swarming phenotype and produced light when the bacteria were propagated on agar media, but not when cells were grown in liquid media. Thus, surface-dependent expression of lateral flagella synthesis is controlled by regulation of transcription. Such fusion strains were also used to further define the environmental conditions which induce laf gene expression. Cultivation on media solidified by gelling agents other than agar also induced light production in fusion strains, as did growth on a variety of hydrophilic membrane filters suspended over liquid media. Growth at an air-surface interface was not necessary for expression since embedding the fusion strains in agar was also effective. Furthermore, induction of laf gene transcription could also be accomplished by increasing the viscosity of the liquid medium by the addition of a high-molecular-weight polymer such as polyvinylpyrrolidone. Increase in luminescence of the fusion strains was detected within 30 min of initiation of the inducing circumstance, and reversal of induction, e.g., by dilution of the viscous medium, resulted in a rapid decline in the rate of increase in luminescence. Conditions that induced luminescence in the fusion strains also induced the synthesis of lateral flagella in wild-type V. parahaemolyticus. The growth environment of the genes, and it appears that the signal that triggers laf expression is physical rather than chemical in nature. Possibilities for a sensing mechanism are discussed.