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Despite challenges, microbial taxonomy is on solid footing because of international cooperation and widening uses of modern analytic tools Hans G. Trüper hree international agreements, the International Codes on Botanical, Zoological, and Prokaryote Nomenclature, provide a basis for effective practices in bacterial taxonomy. Although these agreements were long in coming, steadily improving means of communication should make it easier to move toward a unified nomenclature code for all biological taxa, which will provide an even stronger basis for future biodiversity and taxonomy research. Taxonomy originates in our desire to differentiate among living beings, providing humans a better means for understanding life around us. Our very early ancestors, who surely encountered unexpected environmental conditions while they roamed the continents, needed to determine which animals or plants they could safely eat, which they had to fear, which they could T International agreements provide the current basis for effective taxonomic practices in biology. Unlike the Botanical and Zoological Codes the International Code of Nomenclature of Prokaryotes is based on living type strains that carry the species names. Y Initial efforts to classify microorganisms depended on the 19th century Botanical Code where rivalries led to a cross-Atlantic split in approaches until about 1930, when a new system for microbes based on living cultures was developed. Y Ribosomal gene-based and broader genomicsbased and polyphasic approaches to classifying microbes suggest a bright and more incisive future for taxonomics. Y domesticate or cultivate, and which were otherwise valuable to them. Those practical classification schemes were an early form of taxonomy. Ancient Philosophers and Major Religions Saw Taxonomy as Stable The Greek philosopher Aristotle (384 –322 BC) was among the first to conceptualize the signal differences between animals and plants while building a more refined means for classifying species. In recognizing that there are (at least) two principally different groups of living beings, Aristotle characterized the motile ones as animals and the nonmotile as plants. Within the animals, he assigned individual species to higher and lower orders, while his student Theophrastos (371–287 BC) started a descriptive botany. Their classical view of biology prevailed for many centuries, and was embraced by medieval scholars such as Thomas Aquinus (died 1274) and Albertus Magnus (died 1280). Aristotle and other Greeks believed in spontaneous generation, considering it a genuine property of nature and one that did not require involvement of the gods. They also believed in the constancy of species without evolution, despite believing that spontaneous generation continued to happen. In this era, as Judaism and then Christianity spread into Europe, the biblical creation story, in which God produced all living species within a six-day period about 4,000 BC, came to replace ancient Greek views about the origins of living beings. These religious dogmas further strengthened the concept of the constancy of species. Perspective International Perspectives on Taxonomy: from the Past to the Future Hans G. Trüper is an Emeritus Professor of Microbiology at the University of Bonn, Germany. He is Chairman of the Judicial Commission of the International Committee on Systematics of Prokaryotes, and a former president of the Federation of European Microbiological Societies (FEMS). This article is adapted from a lecture presented at the 2004 ASM General Meeting in New Orleans, La. Volume 71, Number 6, 2005 / ASM News Y 273 A more detailed view of biology developed during the Renaissance when scholars rediscovered the works of the Greek philosophers, and these efforts continued through the following period of humanism. Scientists, then called natural philosophers, began to collect and to describe in detail many different plants, animals, and also fossils, recording their findings mainly in Latin, which provided a valuable degree of internationality to these early efforts in the natural sciences. Microorganisms and, Later, Latin Nomenclature Enter the Picture These efforts expanded into another dimension following the development in 1660 by the Dutchman Antonie van Leeuwenhoek (1632– 1726) of what came to be called the microscope. He began describing very small but previously unrecognized living beings that are invisible to the naked eye. Because of their motility, he called them “animalcula,” meaning little animals. Some of these animalcula were later recognized to be bacteria. Large tracts containing botanical and zoological names and descriptions were compiled for several centuries. To regulate the naming of biological species, the Swedish physician and biologist Carolus Linnaeus (1707–1778; also Carl von Linné) in his Systema Naturae (1735, with many updates) proposed a binomial Latin system for naming genera and species. This prerequisite for a meaningful taxonomy became the basis for our uniform biological nomenclature. Linnaeus, who strictly adhered to the concept of the constancy of species, devised systems for categorizing plants, animals, and—today it looks strange—minerals. Within the two recognized kingdoms of animals and plants, he differentiated only four levels: class, order, genus, and species. Of these, he considered genus the most important level. Strictly on the basis of morphology, Linnaeus classified and named as many plants and animals as he could obtain. He did not accept the classification system, devised in 1764 by Michel Adanson, that relied on many different traits and included microscopic species. Indeed, Linnaeus doubted the value of microscopy and, citing their “lack of morphological characters,” refused to classify the animalcules described by van Leeuwenhoek and his 274 Y ASM News / Volume 71, Number 6, 2005 followers. Instead, he placed them in a class of invertebrate animals that he called “Chaos.” Although the Linnaean proposals were widely accepted, that acceptance came amid continuing strict adherence to the notion that any species, once created, maintained its constancy. With this new Latin nomenclature to provide structure and consistency, efforts to classify plants— including fungi—and animals based purely on their morphological descriptions increased enormously. Ideas about evolution began to take shape during the early part of the 19th century through the investigations of Friedrich T. Kützing and Jean-Baptiste Lamarck. A few decades later, the publication of Charles Darwin’s Origin of Species in 1859 led to a major upheaval in biology and long-held notions about species constancy. By now, biologists accept evolution as the explanation for how new species arise. By Mid-19th Century, Biology Becomes an International Enterprise Even while such fundamental changes were under way, biologists began to convene international conferences to amend and augment the Linnaeus-based nomenclature systems then at hand. For instance, the first International Code of Zoological Nomenclature was approved in 1901 and published in 1903. Although microscopists meticulously described numerous infusion “animalcules” in the 17th and 18th century, for a long time they did not attempt to classify them. However, later during the 19th century, the formal naming of fungi and bacteria fell under the Botanical Code. Its early version, called “Laws of Botanical Nomenclature,” was published in 1867 following the Second International Botanical Congress in Paris. Despite those efforts, however, national and personal rivalries split the world community of botanists. Thus, a renegade group several decades later proposed an alternative naming system, the “American Code of Botanical Nomenclature,” that included innovations such as the type rule. These alternative approaches were not reconciled until 1930 during the International Congress in Cambridge. Further developments in bacterial taxonomy came early during the 20th century (see box, p. 275). For instance, during the first half of the century, neither the fungal nature of bacteria nor the algal nature of blue-green algae were held in doubt because both were seen as part of the botanical system. Bacterial names that still end with the suffix –myces remind us that these species were named according to the rules of that earlier botanical system. Moreover, the myxobacteria were originally considered to be fungi and retained that status until the American mycologist Roland Thaxter (1858 –1932) recognized their bacterial nature. Ferdinand Cohn in 1872 described Bacillus anthracis not long after Robert Koch (1843–1910) identified it as the cause of the infectious disease anthrax. The very first pure cultures of bacteria—a new concept— came from Koch’s laboratory in Germany and that of Joseph Lister (1827–1912) in Britain during the 1870s, leading to a burst in such research, particularly from Louis Pasteur (1822–1895) and collaborators in Paris and Koch in Berlin. Between 1880 and 1950 there was a decline of interest in phylogenetic problems in bacteriology. After 1950, Peter H. A. Sneath in Britain and R. R. Sokal in Kansas developed phenetic taxonomy, also known as numerical taxonomy, while W. Hennig in Urbana, Ill., developed cladistic taxonomy around 1966. Modern Microbial Taxonomy Practices Emerge Enormous progress in microbiology occurred as researchers in Europe continued to isolate and describe new microbal species of all metabolic categories. These included the Dutch group led by Martinus W. Beijerinck 1851–1931) and the Russian group led by Sergei N. Winogradsky (1856 –1953). Their efforts and contributions from many others were included in the first edition of Bergey’s Manual, whose publication was strongly supported by the International Committee for Systematic Bacteriology (ICSB), which was founded in 1930. Bergey’s Manual eventually outcompeted two rival systems for classifying microorganisms, one led by François Prévot in France and the other by Nikolai A. Krassilnikov in the Soviet Union until the 1950s. During the first International Congress of Microbiology, held in Paris during 1930, the founders of the ICSB concluded that the prevail- Partial Chronology of Taxonomy, Systematics for Prokaryotes Earliest taxonomic descriptions O. F. Müller, Denmark 1786 (posthumous): genera Monas and Vibrio. F. T. Kützing , Germany 1833: Micraloa rosea (syn: Lamprocystis roseopersicina). C. G. Ehrenberg, Germany 1838: Spirillum volutans, Spirochaeta plicatilis, Ophidomonas jenensis (syn. Thiospirillum jenense) and Monas (syn. Chromatium) okenii. V. Trevisan, Italy 1842: Beggiatoa punctata and Beggiatoa leptomitiformis. Systematics O. F. Müller, Denmark 1773–1774: Based on morphology only; lacked clear distinction between bacteria and protozoa. F. Cohn, Germany 1872 and 1875: First purely bacterial system, still based on morphology only. Genera: Micrococcus, Bacterium, Vibrio, Spirillum, Bacillus and Spirochaeta, forming the higher taxon Schizomycetes, i. e., “fungi dividing by splitting” (binary fission). First to realize their similarity with certain “bluegreen algae” which he named Schizophycetes, i.e., “algae dividing by splitting.” K. B. Neumann and R. Lehmann, Germany 1896: Based on morphology, Atlas of Bacteria. W. Migula, Germany 1897: Still based on morphology, System of the Bacteria. S. Orla-Jensen, Denmark 1909: Predominant use of physiological criteria to describe bacterial species, The main lines of the natural system of bacteria. D. H. Bergey, United States 1923: Bergey’s Manual of Determinative Bacteriology, 1st edition, combined morphology and physiology and compiled most of the hitherto described species. ing Botanical Code was no longer adequate for handling microbial taxonomy. Hence, they called for establishing an international commission to develop an international code of nomenclature for bacteria. From this commission the International Union of Microbiological Societies (IUMS)-affiliated ICSB (now the International Committee for Systematics of Prokaryotes, or ICSP) arose. Volume 71, Number 6, 2005 / ASM News Y 275 Future Critical Tasks in Prokaryote Taxonomy Keep isolating new species, increase teaching of systematics. At least 3 million prokaryote species may someday be characterized, named, and classified. A prerequisite for understanding and exploiting this biodiversity is to continue educating microbiologists to understand taxonomy and systematics, including the international rules of nomenclature, and to continue to advance the art of isolating and culturing microbes. Improve taxonomic practices by including genomics and proteomics. Microbial taxonomists need to develop a better understanding of phylogeny by intensively making full use of genomics and proteomics. For example, multilocus sequence analyses of genomes should allow taxonomists to identify genetically stable “housekeeping genes” that will help them to understand internal structures of species and to overcome the species definition dilemma. Genome-based comparisons could turn out to be a better tool than are ribosomal RNA comparisons for resolving the key unsettled questions about “Bacteria versus Archaea.” Include the Cyanophyceae, or Cyanobacteria, under the ICNP. The taxonomy of the Cyanobacteria remains unsettled, with botanists classifying them as algae (Cyanophyceae, Myxophyceae) under the Botanical Code of Nomenclature, together with eukaryotic algae, all other plants, and fungi. Yet these organisms are bacteria and should be classified under the ICNP, following its key principle of preserving living type cultures. Complete the unified biocode for all species of living and extinct beings. For the sake of biodiversity research, international taxonomists should continue to develop a unified “biocode,” to ensure that names for biological taxa are properly assigned. For instance, some eucaryotic genera now carry bacterial names, such as the green walking stick insect that is named Bacillus and the blind cave amphibium called Proteus. A prerequisite for such a biocode is to compile a list of all valid names for living and extinct beings. Ensure access to type strains and their taxonomic data. Prokaryote taxonomy is based on living type strains as stipulated by the ICNP. It also requires that type strains are deposited in two internationally acknowledged culture collections in different countries. Regardless of intellectual property considerations, access to type strains must be ensured for doing comparative taxonomic and other scholarly studies. Delayed by World War II, the first edition of the International Code of Nomenclature of Bacteria appeared in 1948. It declared that bacteria would be described under its rules and no longer under those of the Botanical Code. The key principle that distinguishes this code from those of botany and zoology is that it is based upon living type strains deposited in type culture collections. These efforts led to publication in 1966 of The Index Bergeyana, which was compiled by Robert E. Buchanan and coworkers. It and later supplements collected all extent names for bacteria to establish the Approved Lists of Names. In 1980 the ICSB abandoned those names that were not represented by a living type strain. This rigorous ICSB policy put prokaryote taxonomy on a basis that remains the envy of botanists and zoologists. The Approved Lists are continued as Validation Lists in every issue of the International Journal of Systematic and Evolutionary Microbiology (IJSEM). Names do 276 Y ASM News / Volume 71, Number 6, 2005 not have standing in nomenclature unless they have been included in those Lists. A fourth edition of the Code, is scheduled to appear later this year during the IUMS Congress in San Francisco. Meanwhile, the French biologist Emile Chatton in 1937 introduced the terms eukaryotes and prokaryotes. Taxonomists who specialize in classifying eukaryotes often have claimed the species concept for themselves, arguing philosophically that prokaryote species do not exist. Bacterial taxonomists indeed remain aware of the less-than-satisfying definition of prokaryote species. Nonetheless, they have continued to name prokaryotes as species ever since microbiology enabled them to do so. In 1968 British taxonomist S. T. Cowan humorously wrote: “a bacterial species is a group of organisms defined more or less subjectively by the criteria chosen by the taxonomist to show—to best advantage as far as possible and putting into practice— his individual concept, what a species is.” Rita Colwell and several collaborators reformulated the bacterial species concept about a decade ago: “A prokaryote species is a group of strains that show a high degree of overall similarity and differs considerably from related strain groups with respect to many independent characteristics.” In 1962, Roger Stanier and Cornelis van Niel published The Concept of a Bacterium, lamenting the state of bacterial systematics but declaring faith in developments that appeared favorable for its future. They said that bacteria are prokaryotes and vice versa and included the blue-green algae in this category. Meanwhile, George Fox, Carl Woese, Erko Stackebrandt, and others championed the se- quencing of ribosomal RNA molecules and, later, genes encoding those molecules as a way of establishing the phylogeny of prokaryotes. Subsequent classification methods helped to show that rRNA sequences alone cannot meet this challenge. Today, a majority of taxonomists seem to adhere to a “polyphasic” approach that Rita Colwell proposed initially in 1970 and that the Belgian Peter Vandamme refined in 1996. This approach calls for combining phenotypic and genotypic markers as a way of classifying microbial species. Of course, genomic sequencing is now a powerful tool that is becoming a part of our continuing, cooperative, and international taxonomic efforts. Those efforts appear to have a bright future (see box, page 276). Volume 71, Number 6, 2005 / ASM News Y 277