Many marine bacteria have evolved to grow optimally at either high (copiotrophic) or low (oligotrophic) nutrient concentrations, enabling different species to colonize distinct trophic habitats in the oceans. Here, we compare the genome sequences of two bacteria, Photobacterium angustum S14 and Sphingopyxis alaskensis RB2256, that serve as useful model organisms for copiotrophic and oligotrophic modes of life and specifically relate the genomic features to trophic strategy for these organisms and define their molecular mechanisms of adaptation. We developed a model for predicting trophic lifestyle from genome sequence data and tested >400,000 proteins representing >500 million nucleotides of sequence data from 126 genome sequences with metagenome data of whole environmental samples. When applied to available oceanic metagenome data (e.g., the Global Ocean Survey data) the model demonstrated that oligotrophs, and not the more readily isolatable copiotrophs, dominate the ocean's free-living microbial populations. Using our model, it is now possible to define the types of bacteria that specific ocean niches are capable of sustaining.microbial adaptation and ecology ͉ microbial genomics and metagenomics ͉ monitoring environmental health ͉ trophic adaptation T he marine environment is the largest habitat on Earth, accounting for Ͼ90% of the biosphere by volume and harboring microorganisms responsible for Ϸ50% of total global primary production. Within this environment, marine bacteria (and archaea) play a pivotal role in biogeochemical cycles while constantly assimilating, storing, transforming, exporting, and remineralizing the largest pool of organic carbon on the planet (1).Nutrient levels in pelagic waters are not uniform. Large expanses of water are relatively nutrient depleted (e.g., oligotrophic open ocean water), whereas other zones are relatively nutrient rich (e.g., copiotrophic coastal and estuarine waters). Local variations in nutrient content can occur because of physical processes, including upwelling of nutrient rich deep waters or aeolian and riverine deposition, or biological processes such as phytoplankton blooms or aggregation of particulate organic matter. In addition, heterogeneity in ocean waters is not limited to gross differences in nutrient concentrations, but extends to microscale patchiness that occurs throughout the continuum of ocean nutrient concentrations (2).In ecological terms, bacteria are generally defined as rstrategists, having a small body, short generation time, and highly dispersible offspring. Although this strategy is broadly true compared with macroorganisms, bacteria have evolved a wide range of growth and survival strategies to maximize reproductive success. In particular, nutrient type and availability have provided strong selective pressure for defining lifestyle strategies among marine bacteria. However, although a large number of copiotrophic marine organisms (and fewer oligotrophs) have been cultured, the study of trophic strategy has been impaired by a lack of unders...

Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat. V. cholerae serogroup O1 is responsible for the previous two cholera pandemics, in which classical and El Tor biotypes were dominant in the sixth and the current seventh pandemics, respectively. Cholera researchers continually face newly emerging and reemerging pathogenic clones carrying diverse combinations of phenotypic and genotypic properties, which significantly hampered control of the disease. To elucidate evolutionary mechanisms governing genetic diversity of pandemic V. cholerae, we compared the genome sequences of 23 V. cholerae strains isolated from a variety of sources over the past 98 years. The genome-based phylogeny revealed 12 distinct V. cholerae lineages, of which one comprises both O1 classical and El Tor biotypes. All seventh pandemic clones share nearly identical gene content. Using analogy to influenza virology, we define the transition from sixth to seventh pandemic strains as a ''shift'' between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages. In contrast, transition among clones during the present pandemic period is characterized as a ''drift'' between clones, differentiated mainly by varying composition of laterally transferred genomic islands, resulting in emergence of variants, exemplified by V. cholerae O139 and V. cholerae O1 El Tor hybrid clones. Based on the comparative genomics it is concluded that V. cholerae undergoes extensive genetic recombination via lateral gene transfer, and, therefore, genome assortment, not serogroup, should be used to define pathogenic V. cholerae clones.genomic islands ͉ cholera toxin prophage ͉ lateral gene transfer

Background: Clostridium botulinum is a taxonomic designation for at least four diverse species that are defined by the expression of one (monovalent) or two (bivalent) of seven different C. botulinum neurotoxins (BoNTs, A-G). The four species have been classified as C. botulinum Groups I-IV. The presence of bont genes in strains representing the different Groups is probably the result of horizontal transfer of the toxin operons between the species.