FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2126278064> ?p ?o ?g. }

• W2126278064 endingPage "R386" @default.
• W2126278064 startingPage "R373" @default.
• W2126278064 abstract "Bacterial systematists face unique challenges when trying to identify ecologically meaningful units of biological diversity. Whereas plant and animal systematists are guided by a theory-based concept of species, microbiologists have yet to agree upon a set of ecological and evolutionary properties that will serve to define a bacterial species. Advances in molecular techniques have given us a glimpse of the tremendous diversity present within the microbial world, but significant work remains to be done in order to understand the ecological and evolutionary dynamics that can account for the origin, maintenance, and distribution of that diversity. We have developed a conceptual framework that uses ecological and evolutionary theory to identify the DNA sequence clusters most likely corresponding to the fundamental units of bacterial diversity. Taking into account diverse models of bacterial evolution, we argue that bacterial systematics should seek to identify ecologically distinct groups with evidence of a history of coexistence, as based on interpretation of sequence clusters. This would establish a theory-based species unit that holds the dynamic properties broadly attributed to species outside of microbiology. Bacterial systematists face unique challenges when trying to identify ecologically meaningful units of biological diversity. Whereas plant and animal systematists are guided by a theory-based concept of species, microbiologists have yet to agree upon a set of ecological and evolutionary properties that will serve to define a bacterial species. Advances in molecular techniques have given us a glimpse of the tremendous diversity present within the microbial world, but significant work remains to be done in order to understand the ecological and evolutionary dynamics that can account for the origin, maintenance, and distribution of that diversity. We have developed a conceptual framework that uses ecological and evolutionary theory to identify the DNA sequence clusters most likely corresponding to the fundamental units of bacterial diversity. Taking into account diverse models of bacterial evolution, we argue that bacterial systematics should seek to identify ecologically distinct groups with evidence of a history of coexistence, as based on interpretation of sequence clusters. This would establish a theory-based species unit that holds the dynamic properties broadly attributed to species outside of microbiology. “The sure and definite determination (of species of bacteria) requires so much time, so much acumen of eye and judgment, so much of perseverance and patience that there is hardly anything else so difficult.”— Otto F. Müller For decades, the International Journal of Systematic Bacteriology featured on its cover this testimonial to the challenge of studying bacterial diversity. Indeed, compared to zoologists and botanists, bacterial systematists face unique difficulties when beholding a small phylogenetic group to identify its ecologically distinct populations and the different roles that the populations play within a community. Bacterial systematists are handicapped to some extent by the paucity of morphological differences that could help us demarcate closely related species. More profoundly, bacteriologists cannot predict with confidence what will be the traits determining the ecological differences between closely related species; this is because prokaryotes often adapt to new niches by acquiring genes from distant relatives through horizontal genetic transfer [1Gogarten J.P. Doolittle W.F. Lawrence J.G. Prokaryotic evolution in light of gene transfer.Mol. Biol. Evol. 2002; 19: 2226-2238Crossref PubMed Scopus (665) Google Scholar]. Consequently, the ecological differences among closely related bacteria are often invisible to systematists. We can imagine how evolutionary biology might have fared if Charles Darwin had arrived on the Galapagos Islands with the handicaps of a bacterial systematist. Would he have noticed 13 distinct finch species, each with a bill morphology adapted for consuming a different set of seeds or insects? Or would these birds simply have appeared as a flock of related organisms — all much of a muchness of finchdom? The challenge of not seeing bacterial species — with the help of morphology — has been surmounted by systematists in several ways, but we shall see that bacterial systematics still suffers deeply for not readily sensing the ecological differences among close relatives. Closely related bacterial species were first distinguished by careful analysis of phenotype (typically metabolism). In recent decades, systematists have adopted molecular approaches that have allowed standardized species demarcation and have ensured that each taxon is a monophyletic group — a true evolutionary group, including all and only the descendants of a given ancestor [2Gevers D. Cohan F.M. Lawrence J.G. Spratt B.G. Coenye T. Feil E.J. Stackebrandt E. Van de Peer Y. Vandamme P. Thompson F.L. et al.Opinion: Re-evaluating prokaryotic species.Nat. Rev. Microbiol. 2005; 3: 733-739Crossref PubMed Scopus (759) Google Scholar]. Ironically, just as these molecular techniques have promised a more efficient and confident systematics, they have also revealed a daunting task ahead. Surveys of gene sequence diversity from environmental DNA have indicated that fewer than 1% of bacterial species are cultivable at present [3Giovannoni S.J. Stingl U. Molecular diversity and ecology of microbial plankton.Nature. 2005; 437: 343-348Crossref PubMed Scopus (310) Google Scholar]; so traditional, laboratory-based studies of pure-culture isolates have been blind to over 99% of bacterial diversity. Recently, cultivation-independent molecular methods have indirectly estimated that bacterial species may number in the millions or even billions [4Dykhuizen D.E. Santa Rosalia revisited: why are there so many species of bacteria?.Antonie Van Leeuwenhoek. 1998; 73: 25-33Crossref PubMed Scopus (217) Google Scholar, 5Gans J. Wolinsky M. Dunbar J. Computational improvements reveal great bacterial diversity and high metal toxicity in soil.Science. 2005; 309: 1387-1390Crossref PubMed Scopus (806) Google Scholar]. This massive expansion of the scope of systematics, following on the heels of molecular promise, may strike us as a Sisyphusian curse. However, we will show how molecular and genomic approaches, when combined with advances in ecological and evolutionary theory, can bring us critical steps forward in the venture to fully characterize our planet's biological diversity. The key to molecular discovery of biodiversity is to find organisms that fall into highly distinct sequence clusters for a given gene or set of genes. Because such clusters have each had a long history of separate evolution, they are likely to have evolved unique adaptations shared by the entire cluster. Systematists have applied this sequence-based approach to discover prokaryote diversity at all levels — from the urkingdoms, such as the Archaea, to species, and to even lower levels of diversity [6Pace N.R. A molecular view of microbial diversity and the biosphere.Science. 1997; 276: 734-740Crossref PubMed Scopus (1927) Google Scholar, 7Palys T. Nakamura L.K. Cohan F.M. Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data.Int. J. Syst. Bacteriol. 1997; 47: 1145-1156Crossref PubMed Scopus (311) Google Scholar]. By identifying and then characterizing ever smaller phylogenetic groups, each with its unique history and adaptations, systematists have reached a fuller understanding of the ways that bacteria can make a living. But how far must we delve up the tree of life, identifying smaller and smaller clades, before we have fully characterized ecological diversity within the bacterial world? A comprehensive study of any type of biological diversity would be complicated beyond feasibility if nearly every individual organism were ecologically unique. Fortunately, organisms from all walks of life — including bacteria, fungi, plants, and animals — and from every known community, appear to fall into discrete clusters of ecologically interchangeable individuals [8Claridge M.F. Dawah H.A. Wilson M.R. Species: The Units of Biodiversity. Chapman & Hall, London1997Google Scholar, 9Ward D.M. Cohan F.M. Microbial diversity in hot spring cyanobacterial mats: pattern and prediction.in: Inskeep W.P. McDermott T. Geothermal Biology and Geochemistry in Yellowstone National Park. Thermal Biology Institute, Bozeman2005: 185-202Google Scholar]. We will argue that systematics should seek to recognize and characterize all these irreducible, ecologically distinct groups within a clade or within a community, as these are the fundamental units playing unique roles in community assembly, ecosystem function and biotic interactions [10Ward D.M. Bateson M.M. Ferris M.J. Kühl M. Wieland A. Koeppel A. Cohan F.M. Cyanobacterial ecotypes in the microbial mat community of Mushroom Spring (Yellowstone National Park, Wyoming) as species-like units linking microbial community composition, structure and function.Phil. Trans. Roy. Soc. Ser. B. 2006; 361: 1997-2008Crossref PubMed Scopus (115) Google Scholar, 11Staley J.T. The bacterial species dilemma and the genomic-phylogenetic species concept.Philos. Trans. R. Soc. Lond. B. Biol. Sci. 2006; 361: 1899-1909Crossref PubMed Scopus (164) Google Scholar]. We will explain that this is not the present aim of bacterial systematics, and that the recognized ‘species’ of bacterial systematics frequently contain a diversity of populations that are distinct in their biochemistry, physiology, genome content and ecology; classifying an unknown organism to its species thus tells us only vaguely about the organism's way of life. Here we propose a systematics that demarcates and names the fundamental, ecologically distinct groups within the bacteria. This approach aims to satisfy Hutchinson's central mission of systematics — to ensure that the taxonomic name of an organism can inform us precisely about the organism's ecological and physiological properties [12Hutchinson G.E. When are species necessary?.in: Lewontin R.C. Population Biology and Evolution. Syracuse University Press, Syracuse1968: 177-186Google Scholar]. Species demarcation in bacteria has been historically handicapped by lacking a theory-based conceptual framework. Systematists have yet to agree upon a set of ecological and evolutionary properties that can be expected for the set of organisms within a bacterial species. Instead, bacterial species have been demarcated empirically as clusters of similar organisms. Bacterial species were first demarcated as phenotypic clusters based largely on metabolic capabilities [13Jones D. Sackin M.J. Sneath P.H. A numerical taxonomic study of streptococci of serological group D.J. Gen. Microbiol. 1972; 72: 439-450Crossref PubMed Scopus (17) Google Scholar]. In the 1970s, bacterial systematics began incorporating molecular methods to help distinguish closely related species. Beginning with whole-genome comparisons via DNA–DNA hybridization, systematists established molecular criteria that would correspond to the species groups that had already been defined by their metabolic characteristics. Through whole-genome hybridization, members of different named species were usually found to share less than 70% of their genome content, while members of the same species share greater than 70% of their genome content [14Johnson J. Use of nucleic-acid homologies in the taxonomy of anaerobic bacteria.Int. J. Syst. Bacteriol. 1973; 23: 308-315Crossref Scopus (85) Google Scholar]. In 1987, this molecular cutoff became part of the canon of species demarcation [15Wayne L.G. Brenner D.J. Colwell R.R. Grimont P.A.D. Kandler O. Krichevsky M.I. Moore W.E.C. Murray R.G.E. Stackebrandt E. Starr M.P. et al.Report of the ad hoc committee on reconciliation of approaches to bacterial systematics.Int. J. Syst. Bacteriol. 1987; 37: 463-464Crossref Google Scholar]. Systematists have recently sought to replace the DNA hybridization standard of divergence with criteria based on sequence divergence of homologous genes [2Gevers D. Cohan F.M. Lawrence J.G. Spratt B.G. Coenye T. Feil E.J. Stackebrandt E. Van de Peer Y. Vandamme P. Thompson F.L. et al.Opinion: Re-evaluating prokaryotic species.Nat. Rev. Microbiol. 2005; 3: 733-739Crossref PubMed Scopus (759) Google Scholar]. One principal advantage to a sequence-based criterion is that any newly discovered organism can be compared, in silico, to every existing sequence in a growing data base for 16S ribosomal (r)RNA sequences [16Harris J.K. Kelley S.T. Pace N.R. New perspective on uncultured bacterial phylogenetic division OP11.Appl. Environ. Microbiol. 2004; 70: 845-849Crossref PubMed Scopus (162) Google Scholar]. Stackebrandt and Goebbel [17Stackebrandt E. Goebel B.M. Taxonomic note: a place for DNA: DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology.Int. J. Syst. Bacteriol. 1994; 44: 846-849Crossref Scopus (5220) Google Scholar] found that, if two strains are at least 2.5% divergent in 16S rRNA, they are sure to fall into different species on the basis of DNA–DNA hybridization (although the converse is not necessarily true). More recently, a 16S divergence level of ∼1% has been deemed sufficient to consider strains as sufficiently divergent to be in different species [18Stackebrandt E. Ebers J. Taxonomic parameters revisited: tarnished gold standards.Microbiol. Today. 2006; 33: 152-155Google Scholar]. Similarly, Konstantinidis and Tiedje [19Konstantinidis K.T. Tiedje J.M. Genomic insights that advance the species definition for prokaryotes.Proc. Natl. Acad. Sci. USA. 2005; 102: 2567-2572Crossref PubMed Scopus (1142) Google Scholar] have found that a genome-wide average nucleotide identity of at least 94% in homologous protein-coding genes is typical for members of the species recognized by bacterial systematics. Efforts are now underway to make possible a universal classification based on protein-coding sequences [20Konstantinidis K.T. Ramette A. Tiedje J.M. Toward a more robust assessment of intraspecies diversity, using fewer genetic markers.Appl. Environ. Microbiol. 2006; 72: 7286-7293Crossref PubMed Scopus (144) Google Scholar, 21Santos S.R. Ochman H. Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins.Environ. Microbiol. 2004; 6: 754-759Crossref PubMed Scopus (175) Google Scholar, 22Zeigler D.R. Gene sequences useful for predicting relatedness of whole genomes in bacteria.Int. J. Syst. Evol. Microbiol. 2003; 53: 1893-1900Crossref PubMed Scopus (253) Google Scholar]. Another empirical approach is to find molecular criteria that yield clear clusters of closely related organisms, without the constraint that the clusters need to coincide with existing species. For example, Hanage et al.[23Hanage W.P. Fraser C. Spratt B.G. Sequences, sequence clusters and bacterial species.Phil. Trans. Roy. Soc. Ser. B. 2006; 361: 1917-1927Crossref PubMed Scopus (139) Google Scholar] have shown that phylogeny based on a concatenation of several genes can yield sequence clusters that are robust with respect to recombination, even within bacterial groups with relatively high recombination rates. Also, studies of genomic content may have the potential to help identify clusters of diversity. We must note that these molecular and genomic approaches, however promising, are not designed to infuse a theory of species into systematics. They are merely adding new empirical criteria for dividing organisms into clusters with little attempt to correlate clusters with the fundamental, ecologically distinct populations within a natural community. What is wrong with demarcating bacterial species without a theory-based concept of species? To illustrate the importance of theory, we turn to the systematics of animals and plants, for which a robust theory of species was developed long ago [24Mayr E. Systematics and the Origin of Species from the Viewpoint of a Zoologist. Columbia Univ. Press, New York1944Google Scholar]. While species concepts for macrobes are by no means without dispute, all modern species concepts embrace the following dynamic attributes for species [25de Queiroz K. Ernst Mayr and the modern concept of species.Proc. Natl. Acad. Sci. USA. 2005; 102: 6600-6607Crossref PubMed Scopus (378) Google Scholar]: a species is a cohesive group (there are forces that limit genetic diversity within a species); a species is monophyletic (invented only once); different species are irreversibly separate; and different species are ecologically distinct (allowing them to coexist into the future). In the case of animals and plants, there is one quintessential property that determines membership within a given species: successful interbreeding in nature. Interbreeding acts as a force of genetic and phenotypic cohesion among the members of an animal or plant species, and loss of the ability to interbreed allows two species to diverge phenotypically and to follow irreversibly separate evolutionary paths [26Coyne J.A. Orr H.A. Speciation. Sinauer Associates, Sunderland2004Google Scholar]. Different macrobial species, so defined, are typically distinct in morphology, behavior, physiology and ecology; organisms of the same species are expected to be functionally interchangeable. Thus, zoologists and botanists benefit from a systematics that satisfies Hutchinson's [12Hutchinson G.E. When are species necessary?.in: Lewontin R.C. Population Biology and Evolution. Syracuse University Press, Syracuse1968: 177-186Google Scholar] fundamental mission of systematics — classifying an organism to an animal or plant species yields detailed and specific information about the organisms' physiology, biochemistry, and ecology. Regrettably, lacking a concept of species, bacterial systematics has failed to identify taxa that might satisfy this mission. That is, a typical named bacterial species contains huge diversity at all levels of analysis; so species identification does not provide specific ecological information about any of its members. Even though bacterial species were originally demarcated as phenotypic (usually metabolic) clusters, named bacterial species hold an enormous amount of phenotypic diversity [27De Clerck E. Rodriguez-Diaz M. Forsyth G. Lebbe L. Logan N.A. DeVos P. Polyphasic characterization of Bacillus coagulans strains, illustrating heterogeneity within this species, and emended description of the species.Syst. Appl. Microbiol. 2004; 27: 50-60Crossref PubMed Scopus (56) Google Scholar, 28Logan N.A. Berkeley R.C. Identification of Bacillus strains using the API system.J. Gen. Microbiol. 1984; 130: 1871-1882PubMed Google Scholar, 29Bochner B.R. Gadzinski P. Panomitros E. Phenotype microarrays for high-throughput phenotypic testing and assay of gene function.Genome Res. 2001; 11: 1246-1255Crossref PubMed Scopus (459) Google Scholar]. Species also show a significant amount of genomic diversity. DNA–DNA hybridization studies have demonstrated that members of a named species frequently share only 80–90% of their genes [30Feldgarden M. Byrd N. Cohan F.M. Gradual evolution in bacteria: evidence from Bacillus systematics.Microbiology. 2003; 149: 3565-3573Crossref PubMed Scopus (35) Google Scholar]. These results have been more recently corroborated by physical mapping of genomes [31Bergthorsson U. Ochman H. Distribution of chromosome length variation in natural isolates of Escherichia coli.Mol. Biol. Evol. 1998; 15: 6-16Crossref PubMed Scopus (163) Google Scholar, 32Thompson J.R. Pacocha S. Pharino C. Klepac-Ceraj V. Hunt D.E. Benoit J. Sarma-Rupavtarm R. Distel D.L. Polz M.F. Genotypic diversity within a natural coastal bacterioplankton population.Science. 2005; 307: 1311-1313Crossref PubMed Scopus (274) Google Scholar], and by genome sequence comparisons [33Boucher Y. Douady C.J. Sharma A.K. Kamekura M. Doolittle W.F. Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes.J. Bacteriol. 2004; 186: 3980-3990Crossref PubMed Scopus (98) Google Scholar, 34Lindsay J.A. Holden M.T. Staphylococcus aureus: superbug, super genome?.Trends Microbiol. 2004; 12: 378-385Abstract Full Text Full Text PDF PubMed Scopus (286) Google Scholar, 35Nelson K.E. Fouts D.E. Mongodin E.F. Ravel J. DeBoy R.T. Kolonay J.F. Rasko D.A. Angiuoli S.V. Gill S.R. Paulsen I.T. et al.Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species.Nucleic Acids Res. 2004; 32: 2386-2395Crossref PubMed Scopus (363) Google Scholar, 36Goris J. Konstantinidis K.T. Klappenbach J.A. Coenye T. Vandamme P. Tiedje J.M. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities.Int. J. Syst. Evol. Microbiol. 2007; 57: 81-91Crossref PubMed Scopus (2347) Google Scholar]. Even for genes shared across an entire named species, there exists a great deal of sequence variation within the species. At the 16S rRNA locus, sequence diversity within a recognized bacterial species is frequently at 1%. This is equal to the level of divergence typically found between orders of mammals at the homologous nuclear gene 18S rRNA [37Staley J.T. Speciation and bacterial phylospecies.in: Bull A.T. Microbial Diversity and Bioprospecting. American Society for Microbiology Press, Washington, D.C.2003: 40-48Google Scholar]. When we correct for the faster rate of molecular evolution in bacteria, we can estimate the time of divergence among conspecific bacteria to be about five times greater than that for eukaryotic species [38Cohan F.M. Toward a conceptual and operational union of bacterial systematics, ecology, and evolution.Proc. Roy. Soc. Lond. Series B. 2006; 361: 1985-1996PubMed Google Scholar]. Recent ecological studies show that a named bacterial species is typically an assemblage of closely related but ecologically distinct populations [39Lopez-Lopez A. Bartual S.G. Stal L. Onyshchenko O. Rodriguez-Valera F. Genetic analysis of housekeeping genes reveals a deep-sea ecotype of Alteromonas macleodii in the Mediterranean Sea.Environ. Microbiol. 2005; 7: 649-659Crossref PubMed Scopus (57) Google Scholar, 40Schloter M. Lebuhn M. Heulin T. Hartmann A. Ecology and evolution of bacterial microdiversity.FEMS Microbiol. Rev. 2000; 24: 647-660Crossref PubMed Google Scholar, 41Smith N.H. Kremer K. Inwald J. Dale J. Driscoll J.R. Gordon S.V. van Soolingen D. Hewinson R.G. Smith J.M. Ecotypes of the Mycobacterium tuberculosis complex.J. Theor. Biol. 2006; 239: 220-225Crossref PubMed Scopus (135) Google Scholar]. For example, a species of free-living heterotrophs may contain numerous sequence clusters that differ in the carbon sources they can utilize, as seen in the aquatic Shewanella putrefaciens[42Höfle M.G. Ziemke F. Brettar I. Niche differentiation of Shewanella putrefaciens populations from the Baltic as revealed by molecular and metabolic fingerprinting.in: Bell C.R. Brylinsky M. Johnson-Green P. Microbial Biosystems: New Frontiers, Proc. Eighth Int. Symp. Micr. Ecol. Atlantic Canada Society for Microbial Ecology, Halifax2000: 135-142Google Scholar]. Clusters within a species of free-living soil heterotrophs may differ in the solar radiation (and covarying parameters) to which they are adapted, as seen in Bacillus simplex[43Sikorski J. Nevo E. Adaptation and incipient sympatric speciation of Bacillus simplex under microclimatic contrast at “Evolution Canyons” I and II Israel.Proc. Natl. Acad. Sci. USA. 2005; 102: 15924-15929Crossref PubMed Scopus (78) Google Scholar] and in B. licheniformis[44Cohan, F.M., Perry, E., Koeppel, A., Krizanc, D., Ward, D.M., Bateson, M., Rooney, A., Sikorski, J., Nevo, E., and Ratcliff, R.M. (2007). Identifying the fundamental units of bacterial diversity. (in preparation).Google Scholar]. Very closely related phototrophs may partition resources by light quantity and spectral quality, as seen in Synechococcus[10Ward D.M. Bateson M.M. Ferris M.J. Kühl M. Wieland A. Koeppel A. Cohan F.M. Cyanobacterial ecotypes in the microbial mat community of Mushroom Spring (Yellowstone National Park, Wyoming) as species-like units linking microbial community composition, structure and function.Phil. Trans. Roy. Soc. Ser. B. 2006; 361: 1997-2008Crossref PubMed Scopus (115) Google Scholar, 44Cohan, F.M., Perry, E., Koeppel, A., Krizanc, D., Ward, D.M., Bateson, M., Rooney, A., Sikorski, J., Nevo, E., and Ratcliff, R.M. (2007). Identifying the fundamental units of bacterial diversity. (in preparation).Google Scholar], and in the mineral nutrient resources they can utilize or store, as seen in Prochlorococcus marinus[45Coleman M.L. Sullivan M.B. Martiny A.C. Steglich C. Barry K. Delong E.F. Chisholm S.W. Genomic islands and the ecology and evolution of Prochlorococcus.Science. 2006; 311: 1768-1770Crossref PubMed Scopus (334) Google Scholar]. Within a pathogen species, populations can differ in their host ranges [41Smith N.H. Kremer K. Inwald J. Dale J. Driscoll J.R. Gordon S.V. van Soolingen D. Hewinson R.G. Smith J.M. Ecotypes of the Mycobacterium tuberculosis complex.J. Theor. Biol. 2006; 239: 220-225Crossref PubMed Scopus (135) Google Scholar], their target tissues [46Enright M.C. Spratt B.G. Kalia A. Cross J.H. Bessen D.E. Multilocus sequence typing of Streptococcus pyogenes and the relationships between emm type and clone.Infect. Immun. 2001; 69: 2416-2427Crossref PubMed Scopus (253) Google Scholar], or in the mode of transmission [47Paraskevopoulos C. Bordenstein S.R. Wernegreen J.J. Werren J.H. Bourtzis K. Toward a Wolbachia multilocus sequence typing system: discrimination of Wolbachia strains present in Drosophila species.Curr. Microbiol. 2006; 53: 388-395Crossref PubMed Scopus (72) Google Scholar]. Even though fine-scale ecological differences are frequently overlooked by modern systematics, we should note that these differences within named species are extremely interesting from an evolutionary point of view. These differences tell us about the kinds of ecological adaptations that can accrue over very short time periods, and that can foster coexistence among the most closely related of populations. We expect that finding the basis of coexistence among closest relatives will be a rewarding challenge for the next generation of bacterial community ecologists and systematists. There is one realm of bacteriology where systematics has been scrupulous about naming every ecologically distinct sequence cluster — medical microbiology. When one bacterial sequence cluster can kill us, but a close relative cannot, it becomes worth our while to put this distinction into our taxonomy [48Stackebrandt E. Frederiksen W. Garrity G.M. Grimont P.A. Kampfer P. Maiden M.C. Nesme X. Rossello-Mora R. Swings J. Truper H.G. et al.Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology.Int. J. Syst. Evol. Microbiol. 2002; 52: 1043-1047Crossref PubMed Scopus (1280) Google Scholar]. This is seen in the naming of Bacillus anthracis (causing anthrax) as distinct from B. cereus[49Helgason E. Okstad O.A. Caugant D.A. Johansen H.A. Fouet A. Mock M. Hegna I. Kolsto A.B. Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis–one species on the basis of genetic evidence.Appl. Environ. Microbiol. 2000; 66: 2627-2630Crossref PubMed Scopus (780) Google Scholar], and the naming of Yersinia pestis (causing plague) as distinct from Y. pseudotuberculosis. We would prefer that all bacteria be as aptly demarcated into ecologically distinct groups as are the most virulent agents of human death. We believe an understanding of bacterial population dynamics can help us identify these groups possessing the fundamental attributes of species. In contrast to most animals and plants, prokaryotes reproduce clonally, and the genetic exchange among prokaryotes proceeds by various parasexual processes that are not tied to reproduction. When genetic exchange occurs in bacteria, a short segment from a ‘donor’ individual replaces the homologous segment in a ‘recipient’ individual. Recombination in bacteria occurs at much lower frequencies than in most animals and plants, with the recombination rate ranging from less than the mutation rate (per gene segment) to about ten times the mutation rate in the most frequently recombining organisms [50Cohan F.M. Population structure and clonality of bacteria.in: Pagel M. Encyclopedia of Evolution. Volume 1. Oxford University Press, New York2002: 161-163Google Scholar, 51Feil E.J. Maiden M.C. Achtman M. Spratt B.G. The relative contributions of recombination and mutation to the divergence of clones of Neisseria meningitidis.Mol. Biol. Evol. 1999; 16: 1496-1502Crossref PubMed Scopus (238) Google Scholar, 52Maynard Smith J. Smith N. O'Rourke M. Spratt B.G. How clonal are bacteria?.Proc. Natl. Acad. Sci. USA. 1993; 90: 4384-4388Crossref PubMed Scopus (1425) Google Scholar]. Only one bacterial species, Helicobacter pylori, is known to undergo recombination many orders of magnitude more frequently than mutation [53Falush D. Kraft C. Taylor N.S. Correa P. Fox J.G. Achtman M. Suerbaum S. Recombination and mutation during long-term gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age.Proc. Natl. Acad. Sci. USA. 2001; 98: 15056-15061Crossref PubMed Scopus (316) Google Scholar]. The rarity of recombination is expected to simplify the formation of new species of bacteria. In order for adaptive divergence to occur between highly sexual animal or plant populations, gene flow must be restricted by some geographical or ecological barrier [26Coyne J.A. Orr H.A. Speciation. Sinauer Associates," @default.
• W2126278064 created "2016-06-24" @default.
• W2126278064 creator A5031234833 @default.
• W2126278064 creator A5059582524 @default.
• W2126278064 date "2007-05-01" @default.
• W2126278064 modified "2023-10-13" @default.
• W2126278064 title "A Systematics for Discovering the Fundamental Units of Bacterial Diversity" @default.
• W2126278064 cites W1485005536 @default.
• W2126278064 cites W1496547366 @default.
• W2126278064 cites W1583030352 @default.
• W2126278064 cites W1608910061 @default.
• W2126278064 cites W1798521112 @default.
• W2126278064 cites W1841452201 @default.
• W2126278064 cites W1868768034 @default.
• W2126278064 cites W1896854451 @default.
• W2126278064 cites W1919160891 @default.
• W2126278064 cites W1922732464 @default.
• W2126278064 cites W1975738274 @default.
• W2126278064 cites W1976065917 @default.
• W2126278064 cites W1978117785 @default.
• W2126278064 cites W1984852783 @default.
• W2126278064 cites W1985048665 @default.
• W2126278064 cites W1992939342 @default.
• W2126278064 cites W1993602546 @default.
• W2126278064 cites W2008144158 @default.
• W2126278064 cites W2011847079 @default.
• W2126278064 cites W2020081610 @default.
• W2126278064 cites W2020964336 @default.
• W2126278064 cites W2024481000 @default.
• W2126278064 cites W2024602980 @default.
• W2126278064 cites W2024810689 @default.
• W2126278064 cites W2030546342 @default.
• W2126278064 cites W2045194639 @default.
• W2126278064 cites W2051727227 @default.
• W2126278064 cites W2055307142 @default.
• W2126278064 cites W2068687524 @default.
• W2126278064 cites W2069794768 @default.
• W2126278064 cites W2073925485 @default.
• W2126278064 cites W2077602917 @default.
• W2126278064 cites W2087793347 @default.
• W2126278064 cites W2089050509 @default.
• W2126278064 cites W2089290086 @default.
• W2126278064 cites W2100873784 @default.
• W2126278064 cites W2101305165 @default.
• W2126278064 cites W2101830323 @default.
• W2126278064 cites W2103129339 @default.
• W2126278064 cites W2104253405 @default.
• W2126278064 cites W2104274153 @default.
• W2126278064 cites W2105333758 @default.
• W2126278064 cites W2106205860 @default.
• W2126278064 cites W2108018752 @default.
• W2126278064 cites W2108177860 @default.
• W2126278064 cites W2109143374 @default.
• W2126278064 cites W2109268199 @default.
• W2126278064 cites W2110105435 @default.
• W2126278064 cites W2112091811 @default.
• W2126278064 cites W2113478852 @default.
• W2126278064 cites W2114363836 @default.
• W2126278064 cites W2116537276 @default.
• W2126278064 cites W2117120138 @default.
• W2126278064 cites W2126482672 @default.
• W2126278064 cites W2127036970 @default.
• W2126278064 cites W2130371740 @default.
• W2126278064 cites W2130641564 @default.
• W2126278064 cites W2130984115 @default.
• W2126278064 cites W2132598047 @default.
• W2126278064 cites W2134375163 @default.
• W2126278064 cites W2134650310 @default.
• W2126278064 cites W2135764299 @default.
• W2126278064 cites W2137207655 @default.
• W2126278064 cites W2140175819 @default.
• W2126278064 cites W2143947945 @default.
• W2126278064 cites W2144433650 @default.
• W2126278064 cites W2147029889 @default.
• W2126278064 cites W2149353640 @default.
• W2126278064 cites W2151141101 @default.
• W2126278064 cites W2154184384 @default.
• W2126278064 cites W2155047651 @default.
• W2126278064 cites W2159138215 @default.
• W2126278064 cites W2161713631 @default.
• W2126278064 cites W2163786118 @default.
• W2126278064 cites W2164177460 @default.
• W2126278064 cites W2164435125 @default.
• W2126278064 cites W2169812063 @default.
• W2126278064 cites W2170093840 @default.
• W2126278064 cites W2174328995 @default.
• W2126278064 cites W2316608916 @default.
• W2126278064 cites W3131394639 @default.
• W2126278064 cites W4237000009 @default.
• W2126278064 cites W4237231881 @default.
• W2126278064 cites W4244422285 @default.
• W2126278064 cites W4247916292 @default.
• W2126278064 cites W4253970275 @default.
• W2126278064 cites W4254341248 @default.
• W2126278064 cites W4323053702 @default.
• W2126278064 doi "https://doi.org/10.1016/j.cub.2007.03.032" @default.
• W2126278064 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/17502094" @default.
• W2126278064 hasPublicationYear "2007" @default.

• next