Bacterial Complexity
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thesis Bacterial complexity Life on Earth depends on photosynthesis — the This spectacular diversity has another side harvesting of light by organisms to draw For some organisms to it. The basic core genes common to the CO2 out of the air, and to harvest nutrients entire Prochlorococcus group represent a kind from the soil and water. The planet would the idea of ‘species’ of rudimentary genomic plan or simplified otherwise be barren. Phytoplankton, in theme, with every actual organism being salt or freshwater, do fully half of that may not be a some considerable elaboration upon it. As photosynthesis, fixing roughly 35–50 billion useful concept. a result, Chisholm suggests, understanding tons of carbon each year, and all this despite how Prochlorococcus thrives may require weighing, in the collective, 1,000 times less thinking about the ‘genome’ in a new way — than land plants. Phytoplankton are secretly be much more profound — for example, each and the species may not always be the right efficient photosynthesizers. ecotype thrives in conditions under which level for it. For example, another interesting Thirty years ago, biologists thought these the other would die. fact about Prochlorococcus is that it enjoys the phytoplankton ranged in size from one When sequenced, the two ecotypes presence of other bacteria. Why? Well, the millimetre to ten micrometres in diameter, shared some 1,350 of the same genes, yet basic streamlined genome of Prochlorococcus with the smallest being a tenth the width one ecotype had a total of 2,300 genes and lacks genes encoding the enzyme catalase, of a human hair. But advancing technology the other only 1,700. Even the physical which almost all organisms use to break soon uncovered a surprise — the bulk of content of the DNA was markedly different. down the toxic chemical hydrogen peroxide. oceanic photosynthesis actually depends on In one ecotype, the fraction of guanine- Prochlorococcus doesn’t need this enzyme organisms ten times smaller. The bacterium cytosine base pairs was 30%, whereas in only because the other bacteria it maintains Prochlorococcus marinus is the smallest the other it was 50%. Further study of the in its environment supply this enzyme photosynthetic organism known, at just bacterium from oceans around the globe themselves. In effect, Prochlorococcus uses 0.5 to 0.8 micrometres across, and is perhaps shows that these two ecotypes were only the genomes of other organisms. Put another the most plentiful species on Earth. In the beginning of a much deeper diversity. way, it’s as if metabolic coherence doesn’t 2013, researchers estimated that there are Researchers have now identified some exist just at the level of the single cell, but at some 1027 such cells in the oceans, mostly 39 distinct strains from different habitats. the level of an interacting group of organisms near the surface, and they account, in some They share about 1,200 ‘core’ genes, yet of many different species. ocean regions, for as much as half of the show huge variations in other ‘flexible’ One further oddity — Prochlorococcus total chlorophyll. genes that vary with environment. Estimates plays host to a variety of infecting viruses, What makes this species important, put the total number of such genes in the which, coincidentally, carry many genes that however, isn’t just its astonishing numbers. complete Prochlorococcus group at around are very close to many Prochlorococcus genes. It’s one of a number of bacteria that 80,000 — about three times the number Why would they do that? Again, Chisholm seem to break some of the fundamental of human genes (Stephen Biller et al., points to a rather unusual kind of symbiosis. rules of biology. Last month, biologist Nature Rev. Microbiol. 13, 13–27; 2015). These viruses seem to be vehicles for ferrying Sallie Chisholm of MIT gave the lead lecture These flexible genes seem to code for genes between distinct Prochlorococcus at a three-day seminar on new directions specific useful features — extra cellular organisms. So, although we’re used to in biology at the Carl Woese Institute protection for cells thriving near the thinking of the interaction of virus and host for Genomic Biology at the University of ocean surface, for example, or specific as a win–loss relationship, here it seems that Illinois. Her main message — echoed by proteins useful for defence against viruses both gain. Indeed, it’s more like the viruses the contributions of other participants common to some oceanic zone. Large- are part of a larger coherent system or meta- (see http://conferences.igb.illinois.edu/ scale meta-genomic studies of all the population of organisms. The viruses help woesenewbiology/) — was that we still have genetic content of different seawater maintain genetic diversity and, possibly, help surprisingly large gaps in our understanding samples showed that Prochlorococcus in the improve the fitness of the larger complex. of life, and some of our basic ideas about Atlantic Ocean have many more genes for These are a few of the surprises linked species and genomes may be deeply flawed. phosphorous acquisition than do those in to a bacterium that was unknown just Prochlorococcus is a prime example. the Pacific Ocean. This makes sense, as the 30 years ago. Prochlorococcus looks like a In the 1990s, Chisholm and her colleagues phosphorus concentration in the Atlantic is signpost pointing biology toward its next grew cultures from samples of ocean water some ten times smaller. challenge — to move beyond the idea of taken from different depths, and first found At finer levels of detail the diversity is ‘species’, which may not be a useful concept two distinct ‘ecotypes’ — one adapted to the even more amazing. In a study published last for some organisms. Prochlorococcus bright light very near the surface and another year, researchers from Chisholm’s lab have can’t be understood by studying a single more suited to the low-light at deeper levels. sampled individuals from the same millilitre copy, a single cell, the details of which in This isn’t so surprising, as many species of ocean water and found enormous diversity no way reflect the diversity of the entire have ecotypes adapted to slightly different even there. Hundreds of sub-populations of collection. The organism, it seems, can’t environments — humans have different organisms form clusters in genomic space, even be understood without reference to its skin colours suited to local conditions, for groups with similar ‘backbones’ of core genes environment, and the close interactions it example, and these reflect small genetic decorated with particular sets of flexible has with many other species. ❐ variations. However, the genetic differences genes. The broad ecotypes actually consist of in the Prochlorococcus ecotypes turn out to more subtle sub-populations. MARK BUCHANAN NATURE PHYSICS | VOL 11 | NOVEMBER 2015 | www.nature.com/naturephysics 887 © 2015 Macmillan Publishers Limited. All rights reserved.