The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity

The Bacteria and Archaea are the most genetically diverse superkingdoms of life, and techniques for exploring that diversity are only just becoming widespread. Taxonomists classify these organisms into species in much the same way as they classify eukaryotes, but differences in their biology—including horizontal gene transfer between distantly related taxa and variable rates of homologous recombination—mean that we still do not understand what a bacterial species is. This is not merely a semantic question; evolutionary theory should be able to explain why species exist at all levels of the tree of life, and we need to be able to define species for practical applications in industry, agriculture, and medicine. Recent studies have emphasized the need to combine genetic diversity and distinct ecology in an attempt to define species in a coherent and convincing fashion. The resulting data may help to discriminate among the many theories of prokaryotic species that have been produced to date.

[1]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[2]  Vincent J. Denef,et al.  The dynamic genetic repertoire of microbial communities , 2008, FEMS microbiology reviews.

[3]  Raymond K. Auerbach,et al.  Genomic islands from five strains of Burkholderia pseudomallei , 2008, BMC Genomics.

[4]  C. Viboud,et al.  Explorer The genomic and epidemiological dynamics of human influenza A virus , 2016 .

[5]  D. Gevers,et al.  Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton , 2008, Science.

[6]  M. Wagner,et al.  Microbial diversity and the genetic nature of microbial species , 2008, Nature Reviews Microbiology.

[7]  D. Falush,et al.  Convergence of Campylobacter Species: Implications for Bacterial Evolution , 2008, Science.

[8]  D. M. Ward,et al.  Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics , 2008, Proceedings of the National Academy of Sciences.

[9]  H. Owen,et al.  New Phytol , 2008 .

[10]  J. Lawrence,et al.  Temporal Fragmentation of Speciation in Bacteria , 2007, Science.

[11]  Florent E. Angly,et al.  Power law rank-abundance models for marine phage communities. , 2007, FEMS microbiology letters.

[12]  F. Cohan,et al.  A Systematics for Discovering the Fundamental Units of Bacterial Diversity , 2007, Current Biology.

[13]  C. Knight,et al.  Adaptive Divergence in Experimental Populations of Pseudomonas fluorescens. III. Mutational Origins of Wrinkly Spreader Diversity , 2007, Genetics.

[14]  A. Halpern,et al.  The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific , 2007, PLoS biology.

[15]  C. Fraser,et al.  Recombination and the Nature of Bacterial Speciation , 2007, Science.

[16]  Sarah P Preheim,et al.  Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

[17]  C. Fraser,et al.  Sequences, sequence clusters and bacterial species , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

[18]  W. Doolittle,et al.  Genomics and the bacterial species problem , 2006, Genome Biology.

[19]  D. Gevers,et al.  Re-evaluating prokaryotic species , 2005, Nature Reviews Microbiology.

[20]  刘金明,et al.  IL-13受体α2降低血吸虫病肉芽肿的炎症反应并延长宿主存活时间[英]/Mentink-Kane MM,Cheever AW，Thompson RW，et al//Proc Natl Acad Sci U S A , 2005 .

[21]  N. Goldenfeld,et al.  Global divergence of microbial genome sequences mediated by propagating fronts. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[22]  J. Handelsman.  Metagenomics: Application of Genomics to Uncultured Microorganisms , 2004, Microbiology and Molecular Biology Reviews.

[23]  A. Steigerwalt,et al.  Accuracy of Phenotypic and Genotypic Testing for Identification of Streptococcus pneumoniae and Description of Streptococcus pseudopneumoniae sp. nov , 2004, Journal of Clinical Microbiology.

[24]  M. Polz,et al.  Diversity and Dynamics of a North Atlantic Coastal Vibrio Community , 2004, Applied and Environmental Microbiology.

[25]  Ulrich Dobrindt,et al.  Genomic islands in pathogenic and environmental microorganisms , 2004, Nature Reviews Microbiology.

[26]  F. Blattner,et al.  Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[27]  R. Facklam,et al.  What Happened to the Streptococci: Overview of Taxonomic and Nomenclature Changes , 2002, Clinical Microbiology Reviews.

[28]  W. Whitman,et al.  Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. , 2002, International journal of systematic and evolutionary microbiology.

[29]  F. Cohan.  What are bacterial species? , 2002, Annual review of microbiology.

[30]  B. Spratt,et al.  Recombination and the population structures of bacterial pathogens. , 2001, Annual review of microbiology.

[31]  Christopher G. Dowson,et al.  Barriers to Genetic Exchange between Bacterial Species: Streptococcus pneumoniae Transformation , 2000, Journal of bacteriology.

[32]  J. Majewski,et al.  DNA sequence similarity requirements for interspecific recombination in Bacillus. , 1999, Genetics.

[33]  F. Cohan,et al.  Adapt globally, act locally: the effect of selective sweeps on bacterial sequence diversity. , 1999, Genetics.

[34]  F. Maytag.  Evolution , 1996, Arch. Mus. Informatics.

[35]  J. M. Smith,et al.  How clonal are bacteria? , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[36]  John Maynard Smith,et al.  The population genetics of bacteria , 1991, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[37]  B. Levin.  Periodic selection, infectious gene exchange and the genetic structure of E. coli populations. , 1981, Genetics.

[38]  M. Slatkin.  Gene flow and genetic drift in a species subject to frequent local extinctions. , 1977, Theoretical population biology.

[39]  B. Bainbridge,et al.  Genetics , 1981, Experientia.

[40]  K. Atwood,et al.  Periodic selection in Escherichia coli. , 1951, Proceedings of the National Academy of Sciences of the United States of America.

[41]  R A Fisher,et al.  The spread of a gene in natural conditions in a colony of the moth Panaxia dominula L. , 1947, Heredity.

[42]  Sarah Mae Sincero.  Heredity , 1875, Nature.