Biology's next revolution

The emerging picture of microbes as gene-swapping collectives demands a revision of such concepts as organism, species and evolution itself. Will the traditional units of biology — the organism and the species — be swept away in the flood of new genomics data? In the first of a new Essay series, Nigel Goldenfeld and Carl Woese argue that, for microbes at least, it could happen. Free-living marine microbes, unlike their lab-grown 'clonal' cousins, are adept at acquiring useful characteristics from a shared pool of genetic material. It's beginning to look as if a genetic continuum, rather than a series of discrete species, is the natural condition in many instances.

[1]  P. Forterre,et al.  The role played by viruses in the evolution of their hosts: a view based on informational protein phylogenies. , 2003, Research in microbiology.

[2]  L. Mcdaniel,et al.  Seasonal Variation in Lysogeny as Depicted by Prophage Induction in Tampa Bay, Florida , 2002, Applied and Environmental Microbiology.

[3]  E. Delong,et al.  Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea , 2006, Nature.

[4]  Antoine Laurent Lavoisier,et al.  Traite élémentaire de chimie , 1967 .

[5]  Laurence D. Hurst,et al.  A quantitative measure of error minimization in the genetic code , 1991, Journal of Molecular Evolution.

[6]  Wolf-Dietrich Hardt,et al.  Phages and the Evolution of Bacterial Pathogens: from Genomic Rearrangements to Lysogenic Conversion , 2004, Microbiology and Molecular Biology Reviews.

[7]  C. Suttle Viruses in the sea , 2005, Nature.

[8]  M. Weinbauer,et al.  Are viruses driving microbial diversification and diversity? , 2003, Environmental microbiology.

[9]  Gary J. Olsen,et al.  Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process , 2000, Microbiology and Molecular Biology Reviews.

[10]  N. Goldenfeld,et al.  Collective evolution and the genetic code. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[11]  M Mergeay,et al.  Retrotransfer or gene capture: a feature of conjugative plasmids, with ecological and evolutionary significance. , 1999, Microbiology.

[12]  A. Salyers,et al.  Why are antibiotic resistance genes so resistant to elimination? , 1997, Antimicrobial agents and chemotherapy.

[13]  Susan M. Huse,et al.  Microbial diversity in the deep sea and the underexplored “rare biosphere” , 2006, Proceedings of the National Academy of Sciences.

[14]  D. Grogan,et al.  Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus. , 2005, Molecular biology and evolution.

[15]  J. V. Van Etten,et al.  Chlorella virus PBCV-1 encodes a homolog of the bacteriophage T4 UV damage repair gene denV , 1997, Applied and environmental microbiology.

[16]  M. G. Lorenz,et al.  Bacterial gene transfer by natural genetic transformation in the environment. , 1994, Microbiological reviews.

[17]  S. Sonea A bacterial way of life , 1988, Nature.

[18]  Jillian F. Banfield,et al.  Community genomics in microbial ecology and evolution , 2005, Nature Reviews Microbiology.

[19]  Stefan Wuertz,et al.  Studying plasmid horizontal transfer in situ: a critical review , 2005, Nature Reviews Microbiology.

[20]  Christopher M Thomas,et al.  Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria , 2005, Nature Reviews Microbiology.

[21]  H. Ochman,et al.  Lateral gene transfer and the nature of bacterial innovation , 2000, Nature.

[22]  Maureen L. Coleman,et al.  Genomic Islands and the Ecology and Evolution of Prochlorococcus , 2006, Science.

[23]  Miroslav Radman,et al.  Reassembly of shattered chromosomes in Deinococcus radiodurans , 2006, Nature.