The hologenome: A new view of evolution
14 January 2013 by Carrie Arnold
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Far from being passive hangers-on, symbiotic microbes may shape the evolution of the plants and animals that play host to them
DISPOSING of corpses can be tricky. Bury them in a shallow grave and hungry animals are liable to dig them up. Our body faces a somewhat similar problem when it comes to disposing of unwanted substances. One of the ways the liver purifies blood is by adding the equivalent of a “chuck this out” label to molecules, but this label is made of a kind of sugar – and the bugs in our gut have a sweet tooth. Some produce a special enzyme that allows them to cut off the sugar and eat it, which often results in compounds being recycled within the body rather than disposed of.
Back in the 1980s, Richard Jefferson used the enzyme to develop a powerful technique now relied upon by thousands of genetic engineers around the world. At the same time, he was intrigued by the enzyme’s normal role. Its recycling effect helps determine the blood levels of many compounds, including important substances such as sex hormones. Jefferson realised that the bacteria within us, far from being passive hangers-on, must affect us in profound ways.
In the past decade, this view has started to become mainstream. Study after study has shown how the microbes living in us and on us – the microbiome – can affect our health and even happiness. But back in the 1980s, Jefferson took this idea even further. If microbes are so important, he reasoned, they must play a big role in evolution too. He came up with what he called the hologenome theory of evolution. “The hologenome is the biggest breakthrough in thinking I’ve had in my life,” he says.
But Jefferson was busy perfecting his genetic technique and helping organise the first field trial of a genetically engineered plant, in 1987. Later he left academia and became famous for his efforts to make biotechnology open source, so it could be used for the benefit of all rather than a few wealthy corporations. He never got around to formally writing up the hologenome theory, though he often spoke about it at meetings.
A couple of decades later, another researcher come up with much the same idea, even giving it the same name. And although this approach is only starting to be explored, hints are beginning to emerge that symbiotic microbes can indeed play a much bigger role in evolution than anyone thought.
What struck Jefferson is that our microbiome plays a critical role in some key processes. Levels of sex hormones obviously affect us in many ways, for instance – and yet as much as 65 per cent of circulating testosterone cycles through microbes, according to one study Jefferson came across at the time.
Microbes are also important in the production of the small, aromatic molecules that give us each a unique, if not always socially acceptable, odour. The body does not secrete these molecules directly. Instead, it secretes precursors called androstenes that bacteria living on our skin convert into the volatile androstenols sometimes referred to as pheromones. Although the role of these molecules in human sexual attraction is highly controversial, they do play a role in some animals. “Fertility, fecundity and mate choice – the great troika in Darwinian selection – are all impacted by the microbiome,” Jefferson says.
This suggests that the reproductive success of plants and animals may depend in part on the particular set of microbes harboured by each individual. Of course, we know parasites and diseases have a huge negative impact on fitness, but Jefferson recognised that microbes can boost fitness too. In fact, he came to the conclusion that they are so important that instead of thinking about an individual plant or animal, we should think about the overall collective including the microbiome – the “performance unit”.
“This unit comprises the contributions of many, sometimes thousands, of individual genomes, in varying combinations and numbers,” Jefferson told a meeting in Cold Spring Harbor, New York in 1994, during which he briefly outlined his ideas. And it is this performance unit, Jefferson argued, that is the unit of selection.
Meanwhile, microbiologist Eugene Rosenberg of Tel Aviv University, Israel, was studying corals in the eastern Mediterranean. A rise in sea temperatures had led to outbreaks of bleaching, which occurs when corals lose the algae that produce most of their food. In the invasive coral Oculina patagonica, Rosenberg found that higher temperatures led to infection by the bacteriumVibrio shiloi, triggering bleaching.
He thought these widespread Vibrio infections would sound the death knell for the coral. These animals do not really have an adaptive immune system for fighting off diseases, and they cannot survive prolonged or repeated bleaching. He was wrong. By the early 2000s, the corals had become resistant to Vibrio. Since neither the bacterium nor the coral seemed to have changed, Rosenberg and his colleagues proposed that a change in the coral’s microbiome must be responsible. Corals house numerous microbes along with the photosynthetic algae, and a change in this assemblage might enable them to kill off invading Vibrio.
This idea is controversial – some researchers think the coral immune system can adapt. What matters is how it shaped Rosenberg’s thinking. He knew most animals play host to a large array of microbes that are usually passed down from generation to generation, directly or indirectly. His work on corals made him realise, like Jefferson before him, that an animal’s survival – or fitness – often depends not just on its own genes, but also on those of the microbes it inherits. If a change in the microbiome can make corals resistant to infection, and this change can be passed down through the generations, then these corals have effectively evolved a new ability, even though their genome is unchanged.
Bugs R Us
The separation of an organism from its microbiome is artificial, Rosenberg argues. In the eyes of natural selection, he says, they are a single organism. What’s selected for is the combination of the genome of the host and the genomes of the microbiome. Like Jefferson, Rosenberg dubbed this the hologenome, from holobiont – a term that describes the collective entity formed by symbionts. The holobiont can be seen as a superorganism, he argued in a 2007 paper.
Similarly, Jefferson argues that all the bacteria doing useful jobs in and on our body are not just symbionts. Rather, they are part of us, like distant workers for a giant company that outsources manufacturing jobs. The work being done remains just as important for the company even though it is carried out by overseas workers it does not employ directly. “Bugs R Us,” as Jefferson puts it. Recent studies support this idea, such as one in 2011 showing that mice need their gut flora for their brains to develop normally.
Crucially, of course, our microbes can change. Based on his hologenome theory, Rosenberg predicted that most animals inherit much the same microbes as the previous generation, and that closely related species will have closely related microbiomes. But changes in the microbiome – from a shift in the ratio of different microbes to the acquisition of new ones – can allow the holobiont to adapt quickly to changing circumstances and even acquire new abilities during its lifetime. Thinking in these terms, Rosenberg argued, will lead to new insights.
These ideas have found a receptive audience among microbiologists. After all, as Rosenberg notes, “they have been forever saying that ‘bacteria come first’ “. Microbial ecologist Seth Bordenstein of Vanderbilt University in Nashville, Tennessee, says eukaryotes – like plants and animals – are superorganisms. “We should be looking at the total repertoire of genetic information that makes a eukaryote function,” he says.
In one recent study, for instance, Bordenstein’s team treated termites with the antibiotic rifampicin to kill off some of their microbes. They found that colonies founded by antibiotic-treated termites produced far fewer offspring than other colonies. One possible reason is that disrupting the termites’ gut microbiota reduces the insects’ ability to extract nutrients from food.
Bordenstein has also found that among parasitic Nasonia wasps, species with closer evolutionary relationships have a more similar microbiota, just as Rosenberg predicted. But despite such findings, the hologenome concept has not been warmly welcomed in evolutionary biology circles.
“I would say that most evolutionary biologists would agree that there’s definitely a lot of cooperation, but there’s also room for conflict as well,” says Andy Gardner of the University of Oxford, who studies collective evolution. “So I would be less inclined to bundle all of these cells together as a single, integrated organism because sometimes the microbial cells will be doing things that aren’t good for the host.”
Another reason for scepticism is that there is a Lamarckian dimension to the hologenome theory. Early in the 19th century, Jean-Baptiste Lamarck devised a theory of evolution incorporating the then-popular idea that organisms could pass on adaptive traits acquired during their lifetime. Thus, giraffes evolved their long necks because they were in the habit of stretching their necks. Darwin believed something similar, but such ideas became discredited with the development of modern genetics. The hologenome theory does suggest that animals can sometimes evolve via the inheritance of acquired characteristics, Rosenberg says, but it does so in a way that can be verified by experiment.
After he published his ideas, he and his wife Ilana Zilber-Rosenberg began combing the literature to find related studies. They stumbled across a 1989 paper by Diane Dodd, then a postdoc at Yale University, who had found that changing the diet of a fruit fly could alter the flies’ mating choices after just two generations.
“When I read this, I started jumping up and down,” Rosenberg said. “It had to be the microbes. I just knew it. Nothing else could explain such a rapid change.”
To prove this, Rosenberg got his PhD student Gil Sharon to try replicate Dodd’s results. Sure enough, after two generations, flies fed on molasses would no longer mate with flies on a regular starch. Next, Sharon gave the flies rifampicin to kill off their bacteria. Afterwards, starch flies happily copulated with molasses flies, showing that bacteria were indeed responsible (PNAS, vol 107, p 20051).
As Rosenberg was writing up these results, Jefferson finally got around to posting a synopsis of his hologenome theory on the blog of Cambia, the non-profit organisation he runs in Australia. This led to a spate of web searching during which he came across Rosenberg’s work. Jefferson now faced a dilemma. On the one hand, he wanted to contact Rosenberg to find out how he had come up with the idea. On the other hand, as Jefferson puts it: “Scientists can be pricks.” His curiosity got the upper hand, and on 10 March 2010, Jefferson sat down and began writing. “Dear Professor Rosenberg,” the email began, “I am writing to compliment you and Professor Zilber-Rosenberg on your clear, lucid and compelling writing in the last years on the hologenome theory.”
Rosenberg opened the email the following morning. Who the hell was this Richard Jefferson, he wondered? At first, he wasn’t sure how to respond, thinking Jefferson might be an oddball. After reading the email several times, though, he decided that oddball or not, he certainly knew his stuff. So Rosenberg wrote back: “Dear Richard, wow. What a joy to read your email and blog.”
Creator of species?
Although Rosenberg did not know it at the time, his fruit-fly results fitted in beautifully with Jefferson’s ideas about the importance of bacteria in fertility and mate choice. The findings have also made many other biologists sit up and take notice, because they hint at an intriguing possibility.
While natural selection explains how species change over time, accounting for how new species arise in the first place has proved rather trickier. Darwin’s On the Origin of Species actually said nothing at all about the origin of species. In broad terms, biologists define a species as a group of similar organisms that can reproduce only with each other. Anything that prevents groups of organisms interbreeding, then, can potentially lead to the formation of new species.
Such reproductive isolation can come about through the rise of a new mountain range, being stranded on a far-flung island, changes in mating preferences, or mutations that prevent two strains producing viable offspring if they do mate, although there is still much debate about the details. In theory, then, if a change in diet causes shifts in gut bacteria that affect a fly’s mating preferences, it could lead to one species splitting into two.
The microbiome might also lead to speciation in another way, Bordenstein thinks. When different species of the Nasonia wasp are crossed, many of the offspring die as larvae. He and graduate student Robert Brucker have just finished experiments that show, they think, that these deaths happen because the offspring have inherited incompatible bacteria. If so, it means that differences in the microbiome can prevent otherwise compatible animals interbreeding.
In a review paper published in August, Bordenstein and Brucker also point out that acquiring certain microbes can give animals the ability to consume a new kind of food or survive in a different environment. Over time, this too could, in principle, lead to speciation.
But the case remains to be proven. “I don’t think we have any evidence yet that there has been speciation caused by microbes… I’m not willing to go that far yet,” says evolutionary biologist Scott Gilbert of Swarthmore College in Pennsylvania. “I can say that symbionts are capable of giving us selectable variation.”
Jerry Coyne, an evolutionary biologist at the University of Chicago, agrees. “I know of very, very few cases in which endosymbionts cause speciation, and a ton of cases in which changes in [host] genes do, and in which those genes have been mapped,” he says.
That is true, but we have only just started looking, say Rosenberg. We do not even know which microbes are found in most animals, let alone understand their role in evolution. Given the recent flood of evidence about the importance of microbiota, it would perhaps be surprising if this role is not also bigger than previously thought.
Even if symbiotic microbes do turn out to be important in the formation of new species, however, this does not necessarily support the concept of a superorganism with a hologenome, says David Sloan Wilson of Binghamton University in New York, who studies group selection. Speciation could be a by-product of a microbe manipulating the host for its own benefit rather than of microbes and host evolving together for their collective benefit.
There is little sign of the hologenome theory winning converts among evolutionary biologists, then, but some other biologists are starting to adopt the same perspective. “We have a tendency to think of the microbes as being separate from the nuclear genes, but I think the most contemporary view is that the microbiome is as essential as the nuclear genome, and these things should be viewed together,” says Bordenstein. The discoveries about flies and wasps suggest this perspective can indeed lead to new insights as Rosenberg claimed. Bordenstein puts it more cautiously. “Terms such as ‘superorganism’ and ‘hologenome’ help to encapsulate a wide array of research,” he says. “A symbiotic concept of complex life has basic and biomedical relevance that is here to stay.”
For Jefferson, there are even wider implications. By themselves, large organisms can only evolve slowly, he points out, but by cooperating with fast-evolving microbes they can take advantage of the latest innovations, just as termites have acquired the ability to digest wood or legumes have become able to make their own nitrogen fertiliser.
He sees parallels with the modern world. When companies keep their knowledge and technology to themselves, progress is much slower than when they share it freely. Since Darwin, almost all the emphasis has been on competition as the driving force in evolution. Important as it is, Jefferson says, cooperation and collaboration are even more vital.
SMELLS like Hyena spirit
Kevin Theis smelled it before he saw it. Squinting across the vast expanse of Kenyan savannah, Theis spotted the oily brown substance that a spotted hyena had recently rubbed on the ends of the grasses with its rear end. This behaviour is the hyena equivalent of a Facebook page, providing information on the animal’s health, reproductive status and social rank.
The foul-smelling, greasy goo, known as “paste”, contains an array of chemicals secreted from anal scent pouches. Theis, of Michigan State University in East Lansing, thinks that its smell is produced by the microbes living in the scent pouches. He has shown thatdifferent groups of hyenas harbour different arrays of microbes. Since chemical communication is crucial to hyena society and reproduction, changes in the bacterial content of paste may help drive hyena evolution (see main story). It may even have played a role 4 million years ago, when the ancestor of hyenas split into two species, the spotted and striped hyenas.
Carrie Arnold is a freelance writer in the US