Manifesto for a New Bacteriology Rev. Can. Biol.  35: 158 - 167 Sorin Sonea (EBR emphasis in bold) It is surprising to note that, in spite of the increasing amount of data on bacteria, there is a lack of a coherent view embracing the entire bacterial world. This attitude is in contrast with the marked interest in this field shown one hundred years ago, especially the two opposing concepts of pleomorphism verses monomorphism or fixism. We put forward the hypothesis that all bacteria of our planet form a single clonal entity, as is a single oak or a horse, only far more complex. A series of uninterrupted divisions ensured a physical continuity between the present living bacterial cells and that of their first ancestor. One should remember that in bacteria the mother cell never dies, it only changes generation after each division. Furthermore, ecological and epidemiological evidence suggest that the simple planet-wide bacterial clone is able to perform many complex functions. One clear example is the widespread appearance of bacterial resistance to sulfa drugs and to the many existing anti-biotics. Our general view has a superficial likeness to the now disreputed hypothesis of pleomorphism, which unleashed a particularly bitter controversy around the end of the 19th century until it was definitely rejected. In some cases, the observation that any bacterial strain could change completely under modified external circumstances had been proven to be the product of the contamination of the culture. It is thus understandable that this ideological dispute resulted in a hostility against every unifying concept in bacteriology, considered almost as a heresy. Only entirely new and decisive evidence could overcome the long-lasting scientific anathema for any speculation resembling pleomorphism. This decisive evidence was recently found by bacterial genetics, which provides an overwhelming support for a unifying view through what we consider the genetic solidarity of all bacteria. Each bacterial cell can easily benefit in nature from genes derived from other bacterial strains, a phenomenon unlike anything occurring in eukaryotes. Genetic exchanges between bacteria are realized partially by transformation and mainly by transfer of small replicons: plasmids and prophanges. Some of them will "visit" mostly very similar strains, others have a larger spectrum. Through intermediate strains all genetic exchanges seem possible, even between Gram positive and negative bacteria. The transfer of small replicons happens at random and at an optimal rate, due to the large concentrations of bacteria in every favorable circumstance. Many biologists will not accept the general occurrence of genetic exchanges in nature among bacteria, basing their hesitation on either its apparent low frequency or on the phenomenon of specific DNA restriction; they overlook the fact that restriction enzymes have also modification activities which finally permit many DNA exchanges. Once we accept the fact that exchange of bacterial genes is a general and frequent phenomenon in nature we understand also that clonal or rather sub-clonal episodes take place every time that "visiting" genes are favorable. The favorable gene and the cell that is carrying it, are replicating more often and its chances to reach other strains are increased. This is a general mechanism in bacteria and marks every important aspect and major function of the planet-wide bacterial clone. We suggest that, as a consequence, all the genes present in all bacteria on Earth constitute a single enormous potential genome, shared by all living bacterial cells of the planet-wide clone. Access to this total potential genome for each one of the bacterial cells shows the existence of an unexpected solidarity of all bacterial cells. It also offers the means for the planetary clone to perform highly complex and major actions that no other bacterial entity could attain, except mankind. Evolution of bacteria followed, for all these reasons, an entirely different pattern than the more familiar eukaryotic model. The total potential genome of all the clone being available through gene exchanges, any new favorable gene formed or improved by successive mutations in a strain could be shared by all the cells of the immense clone of all the bacteria, enriching its genetic pool. This means that the genes present in the other bacteria that could be favorable in any particular strain, may have been acquired by exchange at any moment of the evolution of a strain. In the planetary bacterial clone, in at least in its first two billion years of existence, there was a constant increase of the total and common potential genome. Even if these infinite possibilities for exchange of genes suggest a high instability of the genetic arrangements in any bacterial strain, in fact, the bacteria seemed to have slowly and stably evolved from the first living cell toward different possibilities of metabolism, as they appeared with the changing conditions of earth. Each different line of evolution kept its general direction, with the ever present possibility for minor genetic corrections, by reverse evolution, if necessary.  In general, the different strains have specialized so that they finally covered together a complete spectrum. However, each strain kept improving its general orientation without outbursts of unexpected permutations in the inter-cellular genomes of different bacteria. Progressive specialization at successive branching by these germinating cells was probably the general pattern of bacterial evolution. The different bacterial strains ended all up as highly specialized cells lacking even a minimal amount of supplementary intracellular genes which might have constituted a reserve for future evolution. From the first moment the first cell settled all our planet as a primitive bacteria-like strain, this clone changed slowly to contain an increased variety of cells and this planet-wide biological entity became progressively more complex and as its efficiency increased, the total number of its cells increased also. Continuity was such a dominate factor of bacterial evolution that we have to accept that, for the bacterial clone, phylogeny is the equivalent of phylogeny and ontogeny in a superior animal. Bacterial evolution took place at the level of the small replicons, as much or more at the level of the large one, the "chromosome". As the genes can be exchanged easily between the small and large replicons every "mini-evolution" in one of them could finally represent possibilities of evolution for the others. There is no genetic isolation in bacteria, therefore there is no speciation, no irreversible evolution and probably no extinction for over specialized groups, as in eukaryotes. This might be considered as a tremendous advantage, since it confers a sort of immortality on all the strains of the bacterial clone. However there is a high price to pay: clonal selection being an ever present mechanism in all the general functions of bacteria, only very competitive cells are surviving. They also have to remain mostly dispersed and with different strains intermingled as it helps genetic exchanges and mutually supporting metabolisms. No room was left for cells with complex higher functions. Evolution, as a means of synthesizing new genes or improving old ones ended long ago for the bacterial world as most of the possible genes were finally produced by different subclones. The same mechanism of generalized random exchange of genes followed by occasional subclonal selection, are being used today in a very high degree of the superior functions of the general bacterial clone. Instead of accepting the existence of species, genera or families in the bacterial world we consider that the planetary clone consists of many differentiated cells, as is the case of an individual tree or an individual mammal. The superior eukaryotes show differentiation in the mortal somatic cells which use mostly selective transcription and modification of the latter steps in the synthesis of proteins as its mechanism. In the bacterial world-wide entity differentiation is involving "immortal" germinating cells and is obtained mostly by the arrival or the disparition of different genes in cells open for genetic exchange. When a bacterial cell gains or loses a small replicon (plasmid or prophage) the phenomenon should be considered as a short term differentiation and when the large replicon changes its gene composition it correspond to a long term differentiation. As we stressed the point in the case of the prokaryotic evolution, we have to admit that the isolated bacterial cells are also genetically incomplete for the process of differentiation. Almost all intracellular genes of every bacterium are derepressed and there is no intracellular equivalent to the pool of available repressed genes of the eukaryotic cells. In the planet wide bacterial clone, practically all the genes that can be used for differentiation are in the other strains than the one involved, that is in the potential, common genome of the entire clone.  There is however a certain similarity between this way of seeing differentiation in the bacterial world and that more familiar, of a higher animal: in both, only a fraction of the total potential genome is expressed in any cell. The rest of the total genome is available but permanently repressed in a eukaryotic cell and present in other strains in the case of bacteria. As the bacterial planetary clone is three billion years old , the differentiation of many of its subclones is evidently very old and can be seen also as one of its evolutionary episodes. Evolution and differentiation have been for bacteria two aspects of the same phenomenon . Many experimental or natural short term differentiations that we observe may be considered "mini-evolutions", for the strains involved. This only confirms that the same phenomenon: exchange of genes and clonal selection is responsible for the evolution of the different subclones of the bacterial subclone and also for the countless episodes of reversible differentiation. Compared to the clone of a mammal or a tree, the planetary bacterial clone has a much larger variety of differentiated cells. As we have seen, in general, mostly the long term differentiation and even some of the short-term examples are very stable in bacteria, even more so that the epigenetic stability of the mammal cells. This stability was not accepted by the supporters of pleomorphism but encouraged their adversaries. It is one of the reasons that bacteriologists have for so long accepted the notion of  "species ", "genera" and "families" for what we consider to be distinctly differentiated groups of a single planet-wide clone. These currently used names should probably be kept for practical purposes, even if we know now that no speciation exists among bacteria. In a similar way the mammal or human lymph or epithelial cells which keep their differentiation in artificial cultures behave as different species, although belonging to the same clone. For the mammalian cells involved in the immune response, we have even a closer similarity with bacteria: one of their main mechanisms in realizing their function is clonal selection, showing a partial convergent evolution for this with subclones of the planetary bacterial clone. Another factor that probably contributes to the stability of the specialized differentiation in most bacterial strains is the symbiotic tendency that many of them have acquired, by reaching an equilibrium, after hundred of millions years of savage competition. Their present reciprocal supplementary metabolism has taken the form of team work that is visible in soils, in the intestinal flora and mostly so in the rumen of the ruminants. The general symbiotic characteristic is less obvious for the activity of the total bacterial entity on Earth but we know that the biosphere benefits from an optimal general equilibrium between plants, animals and bacteria. We begin to have at least incomplete picture of what really represents this single bacterial clone. Since its cells are mostly isolated and dispersed, they could not produce tissues, organs and a stabilized internal environment. In fact, the bacterial clone never needs to produce special favorable conditions for tis cells (as eukaryotes did) because they already existed for them. There were large and small wet or aqueous surroundings on Earth and the physical properties of our planet are used by the bacterial clone as a giant support or skeleton. There are streams, currents and waves on Earth so no circulatory is necessary, and also the different bacteria are constantly mixed. The winds and the agitation of the surface waters brings fresh oxygen, so no lungs were necessary either. Most of the bacteria in the soil, or in the bottoms of lakes, rivers, or marshes and seas are now metabolizing the death tissues of plants and animals, to transform them into mineral substances, ready to be used again by plants. The general metabolism of the bacterial planetary clone participates in a giant symbiosis with the plants and animals to stabilize and vivify the biosphere. We find even a communication system used on a planetary scale by the bacterial clone: when new conditions in one environment are exercising a strong selective pressure, a favorable gene from another environment can be transmitted by gene exchange and spread by subclonal selection in the cells that can obtain it. This new genetic information is amplified and spread in all the places where it shows its advantages. We have the example of the appearance and the spreading over all the planet of the different bacterial resistances to a variety of anti-biotics. The pathogens and the saprophytes of the normal flora did not possess such genes fifty years ago.; these genes existed in the soil bacteria, side by side with the microbes producing the anti-biotics. As soon as the anti-biotics were generously and somewhat indiscrimately used, the pathenogenic bacteria obtained the necessary genetic information about resistance to each anti-biotic mostly from the soil bacteria through the system of communication we mentioned. We may say that somehow these reactions of the bacterial clone are similar to the problem-solving capacities of the computer. Both categories are based on a very large pool of information : all the planetary bacterial genes in the case of the bacterial clone. To this is added a system to select the right answer: it is realized through subclonal selection for bacteria. The general capacities of the entire bacterial clone are thus far more complex and efficient than the sum of of the properties of all the bacterial strains. We have already identified three general laws that bacteria respect and which help keep the small diameter of their cells, the limited intracellular genome and also the facilities for exchange of genetic material. The entity formed by all the differentiated subclones of the bacterial planetary clone represents a giant and more complex equivalent of one superior eukaryote as we have seen above. The functions that keep unified a superior eukaryotes have an equivalent in the unique genetic solidarity of all the bacterial cells. Major activities of the bacterial planetary clone, are made possible by gene exchanges and also by the complimentary of the metabolisms of it different subclones. It is now generally accepted that the ancestor of the eukaryotic cells originated from the symbiosis of at least two different bacteria, which realized a complex and efficient cell. Its descendants have evolved in an entirely different way from that of their bacterial ancestors: this is more evident when we accept the unitary view of bacteria. The eukaryotes lost their previous genetic solidarity and had to pay the price of genetic isolation by the extinction of the most highly specialized species of the past. Eukaryotes appeared when their ancestors, by an "original sin" did not respect the three laws of the bacteria we have described and, as a consequence, for their offspring, it was also a case of "lost paradise", the one of genetic solidarity, reversible evolution and near-immortality, shared now only by the "law abiding" bacteria. As the most able of the eukaryotes, we, the humans, have to reconsider our relationship with this planetary bacterial clone which only now seems to be a biological entity of indisputable major and complex possibilities. As an enemy or more often as an ally, it represents a tremendous and respectable ubiquitous neighbor, very far from the mixture of primitive cells as the reductionists see the bacteria. Through an improved knowledge of the bacterial world we might be able to use gene transfer for our bodies, benefiting from a bacterial "paradise regained", at least partially. The new bacteriology will have to introduce the methods of studying societies of cells for the subclones of bacteria. It will have to find and study the main ways and path for the exchange of genes and other communication molecules between the different bacterial subclones.  It has to realize and study better the center and essential role of the small replicons and of transformation as genetic and communication bridges and traders between strains in the important functions of the planetary bacterial clone in which genetic solidarity is thew main unifying factor. Only the ever present and lasting activities of the small replicons, and sometime transformation can compensate for the incomplete set of inter-cellular genes in every bacterium. The vocabulary of bacteriologists should change to correspond to the new concepts, closer to the scientific realities. For example, a temperate phage is in fact a spreading form of a small replicon and an essential part of the genetic solidarity of the total bacterial clone; only the exceptional, virulent phages are real viruses. The very decisive progresses obtained by studying bacteria with reductionist methods have to be supplemented by a theoretical coordination, at a higher level, of the relations among the different cells which are all part of this enormous, dispersed, planetary being; the single bacterial clone. We are at the threshold of understanding the originality of this biological entity, kept together by an unexpected genetic solidarity and able of superior and complex functions.