Genome Streamlining in a Cosmopolitan Oceanic Bacterium

  title={Genome Streamlining in a Cosmopolitan Oceanic Bacterium},
  author={Stephen J. Giovannoni and H. James Tripp and Scott A. Givan and Mircea Podar and Kevin L. Vergin and Damon Baptista and Lisa Bibbs and Jonathan R Eads and Toby H. Richardson and Michiel O. Noordewier and Michael S. Rapp{\'e} and Jay M. Short and James C. Carrington and Eric J. Mathur},
  pages={1242 - 1245}
The SAR11 clade consists of very small, heterotrophic marine α-proteobacteria that are found throughout the oceans, where they account for about 25% of all microbial cells. Pelagibacter ubique, the first cultured member of this clade, has the smallest genome and encodes the smallest number of predicted open reading frames known for a free-living microorganism. In contrast to parasitic bacteria and archaea with small genomes, P. ubique has complete biosynthetic pathways for all 20 amino acids… 

Microbial mariners

This month, we have a maritime theme, highlighting three very different strategies for adaptation and specialization in diverse oceanic niches: Pelagibacter ubique is omnipresent but docile, Vibrio

New light on an important microbe in the ocean

  • D. Kirchman
  • Biology
    Proceedings of the National Academy of Sciences
  • 2008
The genome sequence of a marine bacterium is discussed in this issue of PNAS with a prominent example being Pelagibacter, the cultured representative of the SAR11 clade.

The α-proteobacteria: the Darwin finches of the bacterial world

By physically separating genes for information processing from genes involved in interactions with the surrounding environment, the rate of evolutionary change can be substantially enhanced for genes underlying adaptation to new growth habitats, possibly explaining the ecological success of the α-proteo-bacterial subdivision.

The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle

Pan-genome analysis indicates a broad genotypic diversity and perhaps a highly fluid gene complement, indicating historical adaptation to a wide range of growth environments and a high degree of specialization.

Whole genome analysis of the marine Bacteroidetes'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter.

Functional analysis of the predicted proteome disclosed several traits which in joint consideration suggest a clear adaptation of this marine Bacteroidetes representative to the degradation of high molecular weight organic matter, such as a substantial suite of genes encoding hydrolytic enzymes, a predicted preference for polymeric carbon sources and a distinct capability for surface adhesion.

The unique metabolism of SAR11 aquatic bacteria

The metabolism of the SAR11 type strain Candidatus “Pelagibacter ubique” str.

Genome organisation of the marine Roseobacter clade member Marinovum algicola

The genome structure and extrachromosomal DNA content of four strains of the roseobacter species Marinovumalgicola are analysed by pulsed-field gel electrophoresis, indicating that recombination and conjugative gene transfer are dominant mechanisms for microevolution within the Roseobacter clade.

Genomic and functional adaptation in surface ocean planktonic prokaryotes

The sequencing of 137 diverse marine isolates collected from around the world is analysed to gain insights into the ecology of the surface ocean prokaryotic picoplankton and suggests that one method used to avoid predation by viruses and/or bacterivores is by means of slow growth and the maintenance of low biomass.

Ecological Genomics of Marine Roseobacters

Comparative genome sequence analysis of three cultured Roseobacter representatives suggests that cellular requirements for nitrogen are largely provided by regenerated ammonium and organic compounds, while typical sources of carbon include amino acids, glyoxylate, and aromatic metabolites.



A small and compact genome in the marine cyanobacterium Prochlorococcus marinus CCMP 1375: lack of an intron in the gene for tRNA(Leu)(UAA) and a single copy of the rRNA operon.

The absence of an intron in the gene for tRNA(Leu)(UAA), which otherwise is widespread among cyanobacteria, and the additional finding that the ribosomal operon exists as a single copy suggest that the deletion of non-essential sequences played a major role in the evolution of P. marinus.

Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment

The genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade, is described, indicating that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds to supplement heterotrophy.

The marine bacterium Pseudoalteromonas haloplanktis has a complex genome structure composed of two separate genetic units.

The genome size of Pseudoalteromonas haloplanktis, a ubiquitous and easily cultured marine bacterium, was measured as a step toward estimating the genome complexity of marine bacterioplankton and is shown to have a complex genome structure.

Complete genome sequence of Vibrio fischeri: a symbiotic bacterium with pathogenic congeners.

The genome sequence of V. fischeri ES114 is reported, which enters into a mutualistic symbiosis in the light organ of the bobtail squid, Euprymna scolopes, and analysis of this sequence has revealed surprising parallels with V. cholerae and other pathogens.

Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation

The genomes of two Prochlorococcus strains that span the largest evolutionary distance within the Pro chlorococcus lineage are compared and reveal dynamic genomes that are constantly changing in response to myriad selection pressures.

SAR11 clade dominates ocean surface bacterioplankton communities

Quantitative measurements of the cellular abundance of the SAR11 clade in northwestern Sargasso Sea waters to 3,000 m and in Oregon coastal surface waters support the conclusion that this microbial group is among the most successful organisms on Earth.

Environmental Genome Shotgun Sequencing of the Sargasso Sea

Over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors are identified, suggesting substantial oceanic microbial diversity.

The genome sequence of Rickettsia prowazekii and the origin of mitochondria

The complete genome sequence of the obligate intracellular parasite Rickettsia prowazekii, the causative agent of epidemic typhus, is described, which contains 834 protein-coding genes and is more closely related to mitochondria than is any other microbe studied so far.

rRNA Operon Copy Number Reflects Ecological Strategies of Bacteria

It is found that the number of rRNA genes correlates with the rate at which phylogenetically diverse bacteria respond to resource availability, and phenotypic effects associated with rRNA gene copy number are indicative of ecological strategies influencing the structure of natural microbial communities.

Distribution and phylogenies of enzymes of the Embden-Meyerhof-Parnas pathway from archaea and hyperthermophilic bacteria support a gluconeogenic origin of metabolism.

The universal distribution of the trunk pathway enzymes, in combination with their phylogenies, supports the notion that the EMP pathway evolved in the direction of gluconeogenesis, i.e., from the bottom up.