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In Search of a Bacterial Spedes Definition

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In Search of a Bacterial Spedes Definition Rev. Biol. Trop.,45(2): 753-771,1997 SPECIAL PAPER In search of a bacterial spedes definition EdgardoMoreno Programa de Investigación en Enfermedades Tropicales (PIET), Escuela de Medicina Veterinaria,Universidad Nacional, Heredia,Costa Rica. Fax: (506) 2381298,E-mail: [email protected] (Received14-IV-1996. Corrected 9-X-1996. Accepted30-X-1996.) Abstraet: The bacterial species concept was ¡;¡xamined within the framework of plant and animal associated a-2 proteobacteria,taking into consideration the phylogenetic, taxonomic and biological approaches as well as the microbiologists' perception. The virtue of the phylogenetic approach is that it gi.ves an evolutionary perspective of the bacterial lineage; however the methods used possess low resolution for defining species located at the terminal branches of lhe phylogenetic trees. The merit of the taxonomic approach.is that species are defined on the basis of multiple characteristicS allowing high resolution at the terminal branches of dendograms; its disadvantage is the inaccuracy in the earliet nodes. Onan individual level, the qualitative biological characteristics used for the definition of species frequently reveal shortcomings because many of these properties are the result of coevolution, parallel evolution or the horizontal transfer of genes. Nevertheless, when considered together with the phylogenetic and taxonomic approaches,important uncertainties are discovered: these must be weighed if a practical definition of bacterial species is conceived. The microbiologi.sts' perception is thecriterion expressed by a group of sponsors who, basedon scientific and practical grounds, propose a new bacterial species. The success of this new .proposal is measured by its widespread acceptance and itspermanence. A difficult pr(jblem con cerned with definingbacterial species is how to distinguishif tbey are independent evolutionary units or if they are reticulateevolutionary units. In the first case the inherenceis verticallytransmilted as a result of binary fission andclonal expansiono Thismay be the case of sorne animal ceIl associated bacteriain which recombinationappears to be precIuded or exceptional. In the second case adaptive changesoccurring within anindividual canbe horizontally transferredto many or a11 group members. This seems to be the conditión of many intestinal and plant associated bacteria. Genetic drift and speciationin c10nal bacteria will depend a1most .exclusively (jn mutation and intemal genetic rearrangement processes, whereas speciation in reticulate bacteria will depend not only on the�e processes bút in their genetic rre o to interactions wíth other bacterial strains. This uncertainty, wruch co sp nds . the evolutionary process,is at the same time one of the key factors in defininga bacterial species. Key words: Bacterial speci¡;:s,Proteobacteria, review, Brucella, Bartonella, Ochrobactrum, Afipia, Agrobacterium, Rhizobium, Phyllobacterium, Rhodopseudomonas. Bradyrhizobium. "They, and every beast after his kind, and calculate how to accommoqate all species of all the cattle after theirkind, and every animals in afinite ark size (300 cubits long x creeping thingthat creepeth upon theearth . 50 cubits wíde x 30 cubits high) but also due to after his kind, and everyfowl after his kind, the enonnous and exhausting duty of sorting every bird of every sort,GENESIS 7: 14 And and identifying in a brief death line (two theywent in unto N04h into the ark, two and months and seventeen days) thedifferent two ·of all flesh, wherein is the breath of species oí animals, their sexes, their feeding life.GENESIS 7: 15 And they that went in, went habits and aboye aH, to estimate theirchances in male and female of al! flesh, as God had for survival. Conveniently for Noah, his work commanded him: and the Lord shut him in systematics concluded after the ark's door in.GENESIS 7: 16". was closed. However, Noah's task is far from The job assigned to the mythical Noah was complete and the question concerning the monumental, not only because he had to 754 REVISTA DE BIOLOGIA TROPICAL correct identificatíon of species and where to Since the publicatíon of Darwin's locate them is still a major puzzle. masterpiece "On the Origin of Species" in The proximity of an ecologicaJ catac1ysm, 1859, the definitíon of species concerning where human beings actively participate in the animals and plants has been extensively extínction of a considerable number of species, debated by a great number of scientists has alerted many instances in the relevance of (O'Hara 1993 and 1994, Avise 1994,). In sampling and c1assification of living creatures. contrast, the bacterial world was not subjected Due to the fact that plants and animals are to the same detailed analysis for more than one more conspicuous and in consequence more century. This unfortunate fact was mainly due unveiled to our prejudices regarding beauty, to the absence of data sustaining the ugliness and usefulness, most of the new evolutíonary history of bacteria (Woese 1987). "Noah's arks" have been devoted to the census The advent, during the last two decades, of of these biodiversities with little or marginal concise phylogenetic and taxonomic studies attentíon to the microbial world. If we consider based on molecular sequences and structures that the primordial living systems (and very has definitívely contributed to incorporating probably the ultimate) were assembled almost the bacterial world within the constraints of exc1usively by bacteria or bacteria-like evolutionary studies (Woese 1994). As with organisms,and that practically al! the genetics other organisms,the distinctiveness of bacteria as well as the synthetic, catabolic and requires an idiosyncratic analysis for the regulatory biochemical reactions were concept of species. However, we must developed by these organisms and are still distinguish between the various bacterial concentrated in bacteria,then it is obvious that species concepts and the different character we must give to this world its place in our sets used to define species in that the former "modern arks". Furthermore, by considering refers to a phílosophical position and the latter the simple but relevant fact that practicalIy al! refers to the characteristics used by the the eukaryotic systems studied possess or cIassification methods. Furthermore, the interact with at least one unique eubacteria different systems of classification force us to a (including endosymbíonts), it is reasonable to particular model for representing the propose that the bacterial world is not only the dispersion of species which in most cases most abundant but the most diverse of al!. overIap with the different definitions (O' Hara Shortcomings on the isolation and culture 1993). In order to obtain a correct perspective of a great number of bacteria (mainly the on this, 1 will fírst of all discuss the bacterial intracellular and the "extremist") have species concept within the framework of the restricted the correct quantification and different species views which at the same time characterisation of these organisms. Even are related to the different character sets used though this problems have been partially to distinguish the various species. Up to the solved by the advent of recent molecular present, three different views on that which techniques devoted to the amplification and constitutes a species and two perceptions sequencing of genes from bacteria which are dominate our present knowledge: the difficult to isolate or to cultivate under phylogenetic species concept championed by controlled conditíons, the truth is that Cracraft (1983),the taxonomic specíes concept classification of bacteria into species is a (Staley and Krieg 1984), the biological species constant drawback (Krieg, and Holt. 1984). concept (Dobzhansky1937), the Today it is clear (at least for sorne of us) that microbiologists' perception (Pitt 1994, Sneath the success of all conservation programs, 1984 b) and the fixed specíes' perception biodiversíty projects, bacterial collections, reviewed by Schadewald (1986). The three microbial ecologists, medical microbiologists, concepts have strengths and weaknesses, each plant pathologists, food microbiologists, emphasises different aspects of the epidemiologists and geneticists depends on the evolutionary process and are within the correct ídentífication of those extant units boundaries of science. Because the taxonomic known as bacterial species for which and phylogenetic concepts are based on protection, compilation, conservation, control, numerical analysis (Sneath 1984a, Woese destructionor selection is being sought. 1994,Williams et al. 1995), they are the most Moreno: In search of a bacterial species defmition 755 distinctly understood. The biological species THEPHYLOGENETIC APPROACH concept may be considered the ultimate definition, but due to the complexity involved A phylogenetic species may be understood in understanding the biology of a bacteria as 'the smallest diagnosable cluster of regarded as qualitative characters, it has been individual organisms within which there is a relegated to last among the three scientific parental pattem of ancestry and descendent" views (Krieg and Holt 1984). In tbis essay I (Cracraft 1983). This concept has the attempt to rescue the value of the biological advantage that species are defined as the species concept in the framework of the terminal organism in a lineage which has an bacterial population structure. Other ancestor common to other terminal organisms,
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