Heliophage

Here’s something which follows on from this post about what happens when viruses infect photosynthetic bacteria in the oceans and also from this post about Craig Venter, I guess, in that he is one of the authors of the paper I’m talking about, and the fishing of vast numbers of DNA sequences out of the ocean on which this work depends is something that he has pioneered.

As I was saying in that previous post, viruses which attack photosynthetic bacteria don’t just carry “viral” genes — genes that code for the components of the virus. They code their own versions of “bacterial” genes — genes that the bacteria use in their everyday existence — too. Why bother? Obviously the bacteria already have their own copies of the bacterial genes, and by carrying these genes the viruses are making their genomes bigger and thus more costly to reproduce, which you would think was a bad thing. The answer must be that getting the bacteria to read the viral versions of the genes and thus produce the proteins they encode helps the virus reproduce.

Now a paper by Itai Sharon and a number of co-authors, mostly at the Technion in Israel, published in the new ISME Journal offers further evidence on the matter. They worked with DNA samples from the open ocean, and one of the things they were looking for was those which contained parts of the D1 protein, which is central to photosynthesis. They found a great many copies of versions of the D1 protein from viruses (which could be identified because they were flanked by viral, as opposed to bacterial, genes), and found that they differed systematically from the normally expressed native bacterial versions in two particular parts of the sequence.

The researchers interpret this in the same way that the authors of the Nature paper I blogged about before (people from Penny Chisholm’s lab at MIT, largely) do in a paper they published last year in PLoS Biology. That study showed that in some cases there is a marked preference among the viruses for forms of the D1 protein that look like the forms which some of their hosts keep in reserve for times of stress. It looks quite likely that these viral proteins undergo less turnover than the normal proteins. I imagine they probably pay for this in terms of increased damage and lower efficiency in the long run, but make up for that by requiring less maintenance effort. That’s a good short-term trade-off for a cell with other stresses to deal with — and its a neat trick to steal if you’re a virus that wants to devote as much of your host cell’s capabilities as possible to making more virus. The details of the differences between viral forms of the protein and the common bacterial forms seem to bear this analysis out.

This is not just a quirky thing. Bacterial photosynthesis counts for a significant part of total ocean productivity, and a few percent of those bacteria will, at any given time, be under viral control, and probably expressing viral photosynthesis proteins. The idea that a measurable chunk of the earth’s primary productivity is in the hands of the viruses strikes me as quite a cool one.

About a day after I posted on excited geology my esteemed colleague Phil Ball pointed out this paper in GRL to me about the possibility that soil bacteria share electrons with each other through networks of nanowires — an idea that would always seem extremely cool and in the circumstances seemed steeped in syncronicity too. Phil looked into the work and wrote us a fine news story for this week’s Nature. Excerpt:

Last year, Gorby and his colleagues discovered that Shewanella oneidensis bacteria can grow long filaments, just 100 nanometres (a hundred millionths of a millimetre) thick, which conduct electricity (Y. A. Gorby et al. Proc. Natl Acad. Sci. USA 103, 11358–11363; 2006). The researchers presented evidence that the microbes use these ‘nanowires’ to shunt electrons produced during metabolic reactions onto the surface of mineral grains in the soil, to be taken up by metal ions. Without an electron acceptor, the bacteria cannot function properly and die. The researchers found that several other bacterial species also produce such nanowires.

Oxygen molecules act as convenient electron dumps for bacteria that lie near the soil surface. But little air penetrates to some environments, such as deep lake sediments or waterlogged soils. Now, Gorby and his team think they have found evidence that the bacterial nanowires can link up into a network, conducting electrons to the aerated surface. The researchers filled plastic columns with wet sand infiltrated with a nutrient compound (lactate), and allowed S. oneidensis to grow in this ‘fake soil’. Only the top of the column was in contact with air.

Electrodes inserted at various heights up the columns revealed that, after about ten days, electrical charge was coursing up the column. Gorby’s team examined the sand under a microscope and found that it was threaded by a web of filaments between the bacterial cells. These are wires that provide the pathways for electron transport up to the surface, they suggest.

In contrast, when the team grew a colony of mutant cells that could spawn only very thin, frail and non-conducting filaments, the electrodes in the column remained uncharged.

Phil goes on to note some caveats about the work, notably from Derek Lovley at University of Massachusetts, Amherst, and it does seem quite possible that this sort of wiring is not a major feature of the real world. Redox shuttles in biofilms may be a much more central phenomenon. But it’s definitely thought provoking. For some context to that thought, try “Microbial ecology meets electrochemistry: electricity-driven and driving communities“, a recent review in the ISME journal by many hands, including that of Ken Nealson, quoted in Phil’s piece. And if this wired-up stuff is for real, what are the implications, not just for natural phenomena, but for technologies like the microbial fuel cells (subscription) my colleague Charlotte Schubert wrote about last year? (This blog is not devoted to bigging up Nature; but we do do a pretty good job.)

There’s an interesting paper in Proceedings of the National Academy of Sciences this week which adds a small new twist to a great double-headed mystery concerning the beginning the history of photosynthesis on earth (which thus comes pretty near the middle of Eating the Sun: it’s a book with a rather arcane relation to chronology.) When did photosynthesis of the oxygen producing persuasion start, and why did the oxygen produced not immediately turn up in the atmosphere?

There’s pretty hard-to-doubt evidence that the earth’s atmosphere did not have a significant amount of oxygen in it on a permanent basis before about 2.45 billion years ago. (Some people do manage to doubt this, but they have to work fairly hard in order to do so — most people in the field accept it.) At the same time, shales dug out of a borehole in Australia contain various chemicals that suggest a) that there were cyanobacteria, which produce oxygen, living 2.7 billion years ago and b) that some other creatures were using this oxygen for their own metabolic needs. There are persistent rumours of similar results from even older shales, but as far as I know they haven’t actually made it to publication.

This creates a seeming paradox: how can it be possible to have a biosphere that produces oxygen through photosynthesis and at the same time see no oxygen in the atmosphere. And how can such a state of affairs go on for at least 250 million years, and quite possibly a lot longer. The bottomline of most of the answers to this conundrum is that there was enough other stuff — organic carbon and reduced gases from the mantle — for the oxygen to react with that it could never build up stably in the atmosphere. Only when the supply of this “other stuff” was changed, through some mixture of an increased rate of burial of organic carbon, a lessened flux of reduced gases from the mantle, and an increased oxidation of the atmosphere as a whole due to the escape of hydrogen into space, did it become possible for oxygen levels to rise, at least a little. This fascinating interplay between life and the planet it enlivens is gone into in some detail in the book: David Catling has provided a helpful pdf update on the state of the debate for those who want more.

The new paper, Biosynthesis of 2-methylbaceriohopanepolyols by an anoxygenic phototroph (PNAS doi/10.1073/pnas.0704912104), comes out of the labs of Alex Sessions and Dianne Newman at CalTech, of and from which many good things are heard. The lead author is Sky Rashby, for more on whom see this post; also on the team is Roger Summons of MIT, who with colleagues published the evidence for cyanobacteria at 2.7 billion years ago (Newman has just moved to MIT, too). To some extent this new paper challenges that evidence, in that it removes one strand from it. Cyanobacteria make chemicals called 2-methyhopanes, and until now nothing else has seemed to do so, and so the presence of those chemicals in the ancient shales seemed good evidence for cyanobacteria. The new paper shows that a bacterium called Rhodopseudomonas palustris also makes the molecules in question. R. palustris is a photosynthesiser, too — but not an oxygen producing one (there is a wide range of bacteria that use sunlight this way without producing oxygen). So the idea that there were cyanobacteria present long before there was atmospheric oxygen can no longer rely on the methyhopanes for support.

At first blush, this might seem to give comfort to those who, like Joe Kirschvink, also at Caltech, want to argue that oxygen-producing photosynthesis led to the oxygenation of the atmosphere directly — that an evolutionary transition led directly to a geological one, as outlined in this PNAS paper. But the methyhopanes aren’t the only evidence for an earlier origin. What was particularly interesting about the 2.7 billion year old shales Summons and his colleagues studied was that they contained both what seemed to be evidence of oxygen producing cyanobacteria and what seemed to be evidence of oxygen consumption, in the form of molecules called steranes. Producing steranes is thought by most people to require oxygen. And so it’s not special pleading to say that while cyanobacteria are no longer the only possible source for the 2.7 billion year old 2-methyhopanes, the oxygen requiring steranes in the same sample make them the most likely source, and pretty much require that something photosynthetic somewhere was producing oxygen at the time. (There is also, as I understand it, evidence elsewhere that oxygen-requiring methane eating bugs were around before the oxygen hit the atmosphere. Not all methane eaters require oxygen — but some do, and apparently there are molecular markers that can tell you which sort was present where.)

So the idea of a lag between the evolution of oxygen production and the arrival of free oxygen in the atmosphere has at worst only taken a minor knock; from what I can gather most people in the field are still fairly convinced on the matter. It would take a second dramatic finding — for instance evidence that the steranes in the 2.7 billion year old samples are contaminants — to really throw things into doubt. As far as I know there is no indication that any such second shoe is about to drop.

Meanwhile, the molecules involved in this identity parade may well prove interesting in and of themselves. The fact that they are present in two different photosynthetic bacteria suggests that they might have a photosynthetic purpose of some sort. What that might be remains to be seen, though there are already some theories. If the genes for the pathway that makes the stuff can be found, then it might be possibleto be more definitive about which bugs use it and under what conditions.

There’s a fascinating paper in this week’s Nature (Lindell et al, Nature, 449, pp 83-86 (2007) doi:10.1038/nature06130) dissecting what must be one of the most frequent fatal biological interactions in the world: the infection of the photosynthetic bacterium Prochlorococcus Med4 by the virus, or “phage”, P-SSP7.

This sounds pretty obscure, but it is a commonplace thing. In fact it is unimagineably commonplace. Prochlorococcus is perhaps the most plentiful organism on the planet — the average millilitre of surface seawater contains about 100,000 of them. A quick and doubtless very dirty calculation suggests that there are more prochlorococcus in the earth’s oceans than there are atoms in your head (sources wiki, madsci, guesswork). In parts of the ocean that are nutrient poor (which is a lot of the ocean) these peculiarly small bacteria — sometimes called picoplankton — dominate primary photosynthetic production.

And while doing so they get a lot of viral infections — perhaps 2-3% of the entire population is torn apart by phages every day (that figure is actually from a paper about synechococcus, but I’m happy to go with orders of magnitude here). This all means that a virus infects one of these bacteria a trillion times every nanosecond. And this process, or rather something functionally very similar, has presumably been happening at a similar rate for billions of years.

As I said, unimagineably commonplace.

So what goes on? A team at MIT and other institutions (including Debbie Lindell, now at the Technion, Penny Chisholm, the scientist who first discovered prochlorococcus, and George Church, high-throughput sequencing guru) has looked into the problem by stopping the process of infection at various stages (by flash freezing the bacteria involved) and then looking to see what genes were being transcribed when.

The virus forces the bacterium to produce copies of itself; if it didn’t, it would be a very poor virus. And the way it gets to work is very familiar, in that it is very like the job that the phage T-7 does on lab favourite E. coli. The deep similarities between the strategies used in the gut (natural habitat of E coli) and the open ocean on bacteria that live in entirely different ways is, the authors point out, remarkable.

At the same time as it’s doing this, though, the virus is also transcribing a small set of genes which, though carried in the viral genome, describe proteins that are used by the bacterial metabolism. One of these proteins is D1, which is the protein at the heart of photosystem II, the molecular machine that strips electrons from water using sunlight and thus drives the whole photosynthetic process. The other proteins are also involved in photosynthesis and the cell’s ability to handle its energy. By making more of these proteins, the virus is giving the bacterial cell an energy boost — at exactly the time that it is also requiring the cell to make copies of teh viral genome, which uses a fair amount of energy.

Meanwhile, control of the genomes having been taken over by the virus (and there’s an ablative absolute unknown to Caesar) most of the bacterial genes are shut off to some extent, meaning the proteins the bacteria would normally be making to keep itself in business don’t get made. But though the activity of 1,716 genes gets turned down this way, the expression of 41 others actually goes up, some immediately after infection, some about two hours later.

Some of this is the bacteria’s attempt to do something about the infection. Some may be caused by the phage for its own purposes. Some of it may be things that were once adapatations against infection but which the virus has evolved to welcome, even to promote. The story is particularly involved with the hli gene family. These genes do something (not entirely clear to me what) to help photosynthesis along and allow the bacteria to deal with high light conditions. They get turned on when the phage first strikes — and then copies carried by the phage itself get turned on. What’s more, some of the versions of hli genes seen in bacterial genomes seem to have been acquired from phages and then put to bacterial use.

This is all fascinating (at least to me). And as the authors say, further work on these lines will probably have implications for understanding how bacterial photosynthesis works at an ecological level and what factors limit it. But it also seems to hint at something bigger or stranger. It is very hard for us to see this other than in terms of one thing attacking another. Its almost impossible to describe without terms of agency on the part of the players. But reading about it in this detail brings with it a sense in which teh infectuion almost feels like a thing in itself — a process to be described in its own terms, not as a struggle between two players. I suppose this feeling is linked to the ideas that drive “systems biology” — that there is a system here, phage+bacterium, that is its own thing, and can’t be reduced to two complex components, that evolves in its own way.

I’ve no idea whether that idea has much use or room for expansion; and it carries a vaguely Cronenbergy vibe I’m not necessarily on for. It just felt hard to avoid. The paper is fascinating regardless.

Image: Lawrence Berkeley Labs