by Roberto and Elio
Exactly forty years ago to the day (as we sit down to write this post on November 3, 2017) the front page of the New York Times displayed a large photograph of Carl Woese followed by a full length article describing his discovery that "living systems represent one of three aboriginal lines of descent." The press coverage in this and many other newspapers around the world had stemmed from the publication in PNAS, two days earlier, of the landmark paper by Woese and Fox, "Phylogenetic structure of the prokaryotic domain: The primary kingdoms." But despite the publicity and the momentous nature of the publication, most scientists – microbiologists included – initially ignored this tripartite view of the tree of life.
Woese explained this initial lack of interest in his work with these words: "People didn't understand the size of my contribution. They had no appreciation for what not having a microbial phylogeny meant and therefore no appreciation for what having one would mean." (From a 1997 interview with Virginia Morell).
To many microbiologists today, it is difficult to imagine how it could have been that Woese's discovery and its implications to our understanding of evolution were initially ignored. Looking back forty years and analyzing both the state of molecular biology at the time and the methodologies available, in part helps explain the initial reaction that Woese's findings received. For one, molecular biology had brought forth the remarkable unity in biology through the reductionist discoveries that lead to "the central dogma," best epitomized in Jacques Monod's quote: "Tout ce qui est vrai pour E. coli est vrai pour l'éléphant." (All that is true for E. coli is true for the elephant.) That phrase alone indicates how many of us, deeply enamored with the universality of DNA and its functions, had little appreciation for what it meant to not have a microbial phylogeny. But there was more. A quick look at Woese's 1977 PNAS paper reveals only one table of results, showing "association coefficients between representative members of the three primary kingdoms." These coefficients themselves had been derived from extensive 16S or 18S rRNA oligonucleotide catalogs. And the sequences of those oligonucleotides had been obtained using RNAse T1 digests of 32PO4-labeled rRNA that had been separated using two-dimensional paper electrophoresis. Woese and Fox were way, way ahead of the times; very few people knew how to carry out such experiments and analyze the results. In today's world of fast, inexpensive and automated deep DNA sequencing, it is nearly impossible to conceive just how incredibly difficult and time-consuming the work Woese and Fox carried out really was. As a result, relatively few microbiologists back in 1977 understood the methodology and the meaning of those tables containing association coefficients. But the significance of Woese's discovery is ignored no more and the vast majority of us today (though not all) operate under the "Woesian paradigm."
There is little doubt that the microbial sciences have evolved dramatically since Woese initially turned our worldview upside down with his discovery of the three-domain universal phylogeny. As a way to celebrate this fortieth anniversary, and to honor Woese and his contribution, we have been discussing between ourselves the many remarkable new insights that microbiology has continued to provide since 1977. We offer our list of what we consider the three major changes in worldview that have occurred since then. Clearly, this list of dramatic changes is based on our personal opinions. We invite STC readers to discuss these and to add their items of choice to the list.
A. Microbes comprise a huge proportion of the earth's biomass.
Had we been asked what proportion of the planet's biomass is bacterial any time before 1977, we might have guessed somewhere around 1%. But in 1998 Whitman et al. published the first census of the number of bacteria on Earth. They proposed that the microbial biomass consists of about 1030 cells, amounting to perhaps half of the total weight of all living things on the planet. The number of bacteriophages in the oceans and marine sediments is thought to exceed that of bacteria and archaea by a factor of 10 or so. The figure for the total microbial mass becomes substantially greater when we include the eukaryotic microbes, such as the protists and small algae of the picoplankton. Indeed, microbes in the oceans account for about 90% of the total oceanic biomass. Although the figures are variable (witness, for example, the gigantic but ephemeral algal blooms of the coccolithophore Emiliania huxleyi ), it is generally agreed that a large proportion of the biosphere by weight is microbial. Being small, microbes vastly exceed the number of all other living entities.
Because of their large numbers, their diverse metabolic capacities and their usually fast metabolic rates, microbes carry out much of the metabolism of this planet, as is readily revealed by their key role in the geochemical cycling of carbon, nitrogen, oxygen, and sulfur. Microbes carry out the bulk of photosynthesis in the oceans and virtually all of the non-industrial fixation of nitrogen.
B. Microbes are enormously diverse
It has been known for some time that every inhabitable corner of Earth is populated by microbes. This include sites with extremes of temperature, osmotic and atmospheric pressures, and pH. But what was completely unexpected what the gargantuan scale of the genetic diversity of microbes. It was not until the pioneering work of Vigdis Torsvik, showing that the DNA present in a gram of soil was 10,000 times more complex than the genome of E. coli (interpreted loosely as containing 10,000 different species) and Norman Pace's exploring of genetic diversity using culture-independent methodologies that we got some initial glimpses of the extent of microbial diversity. The discovery of an entirely new huge cluster of phyla just last year (the largely uncultured 'Candidate Phyla Radiation' (CPR) covered here in STC) is a sign that we still have not fully assessed the extent of the genetic diversity of microbes. The fact that most of the members of the candidate phyla radiation may live in extremely close associations with other organisms adds to the growing sense that mutualistic symbiosis as a way of life may be the rule rather than the exception in the microbial world.
It has been proposed that there are 1 trillion (1012 ) microbial 'species' on Earth. Since the definition of what constitutes a microbial species remains elusive, this figure simply reflects differences that can be perceived at a genomic level. Whatever the deeper meaning, the actual number of distinct entities is likely to be gigantic and much larger than suspected before the availability of deep sequencing and metagenomic analyses. Thus, the perception of microbial diversity has shifted from very large to colossal.
C. Evolution takes place by two mechanisms
The two mechanisms are gene mutation and the transfer of packets of information from one organism to another via horizontal gene transfer (HGT). Although knowledge that genetic material could be transferred laterally among microbes had been obtained in the 1940s, its importance as likely the main driver of microbial evolution came mostly after the advent of full genome sequencing. The amount of genetic material transferred ranges from parts of a gene to whole operons or more, and, in the case of eukaryogenesis, to the genomes of entire organisms. Because HGT gene transfer varies quantitatively over such a vast range, its effect on evolution may be small, affecting a single trait, or huge, creating new species across taxonomic chasms. HGT is common, if not rampant (see STC's excursion into this topic here). Many pathogens owe their virulence to genes present in phages, plasmids or in chromosomsal fragments of chromosomal DNA (islands) that arrived via HGT.
Organellogenesis is curiously limited to two cases, mitochondria and plastids, plus a few related ones. Perhaps there may be yet others in the making (might rhizobia, which differentiate into bacteroids in plants, not become "nitroplasts" in the distant future?). Symbioses where the genome of the microbe is not incorporated into that of the host (at least not en masse ), occur widely, as in bacterial endosymbionts of insects and clams. Although not widespread among vertebrates and other groups, symbioses of this sort are yet another important class of HGT events that are driving evolution.
D. Other examples of leaps in understanding
Clearly, many advances beyond those three discussed have changed our view of the lives of microbes. Take the example of microbial sociality. While before we largely saw microbes as unicellular entities living separate lives, we now recognize microbes as generally living in organized communities where intercellular communication is common. However, much of the groundwork leading to the concepts of microbial multicellularity, sociality and communication (now everywhere referred to as quorum sensing) had already been laid down prior to 1977. Take another example, the current knowledge of the extent of subcellular organization among microbes is astounding. And most of the tools to study this organization were certainly developed after 1977, the prime example perhaps being the use of fluorescent proteins. But, arguably, there were numerous indications that microbial cells contained elaborate subcellular organization prior to that time. But, as we said at the outset, our list is based on our opinions and we would love to hear from you, our readers, what other changes in worldview you perceive as having occurred in the forty years since Woese's seminal discovery of the three domains of life. Regardless of what we include on the list, the explosion of new knowledge about microbes during the last forty years makes these arguably the most exciting times in the history of microbiology.