Tag: fungus

Pocket science – swordfish and flatfish are close kin, and ancient death-grip scars

By Ed Yong | August 17, 2010 7:00 pm


Flatfish are the closest living relatives to swordfish and marlins

At first glance, a swordfish and a flounder couldn’t seem more different. One is a fast, streamlined hunter with a pointy nose, and the other is an oddly shaped bottom-dweller with one distorted eye on the opposite side of its face. Their bodies are worlds apart, but their genes tell a different story.

Alex Little from Queen’s University, Canada, has found that billfishes, like swordfish and marlin, are some of the closest living relatives to the flatfishes, like plaice, sole, flounder and halibut. This result was completely unexpected; Little was originally trying to clarify the relationship between billfishes and their supposed closest relatives – the tunas. That connection seems to make more sense. Both tunas and billfishes are among a handful of fish that are partially warm-blooded. They can heat specific body parts, such as eyes and swimming muscles, to continuously swim after their prey at extremely fast speeds with keen eyesight.

But it turns out that these similarities are superficial. Little sequenced DNA from three species of billfishes and three tunas, focusing on three parts of their main genome and nine parts of their mitochondrial one (a small accessory genome that all animal cells have). By comparing these sequences to those of other fish, Little found that the billfishes’ closest kin are the flatfish and jacks. Indeed, if you look past the most distinctive features like the long bills and bizarre eyes, the skeletons of these groups share features that tunas lack. Indeed, billfish and tuna proved to be only distant relatives. Their ability to heat themselves must have evolved independently and indeed, their bodies product and retain heat in quite different ways.

Little’s work is testament to the power of natural selection. Even closely related species, like marlins are flounders, can end up looking vastly different if they adapt to diverse lifestyles. And distantly related species like tuna and swordfish can end up looking incredibly similar because they’ve adapted to similar challenges – pursuing fast-swimming prey. This shouldn’t come as a surprise – a few months ago, a French team found that prehistoric predatory sea reptiles were probably also warm-blooded.

Reference: Molecular Phylogenetics and Evolution: http://dx.doi.org/10.1016/j.ympev.2010.04.022; images by Luc Viatour and NAOA


Ancient death-grip scars caused by fungus-controlled ants

Forty-eight million years ago, some ants marched up to a leaf and gripped it tight in their jaws. It would be the last thing they would ever do. Their bodies had already been corrupted by a fungus that, over the next few days, fatally erupted from their heads. The fungus produced a long stalk tipped with spores, which eventually blew away, presumably to infect more ants. In time, all that was left of this grisly scene were the scars left by the ants’ death-grip. Today, David Hughes from Harvard University has found such scars in a fossilised leaf from Germany.

Today, hundreds of species of Cordyceps fungi infect a wide variety of insects, including ants. Like many parasites, they can manipulate the way their hosts behave. One species, Cordyceps unilateralis, changes the brains of its ant hosts so that they find and bite into leaves, some 25cm above the forest floor. The temperature and humidity in this zone are just right for the fungus to develop its spore capsules. In its dying act, the ant leaves a distinctive bite mark that’s always on one of the leaf’s veins on its underside. And that’s exactly what Hughes saw in his fossil leaf.

Hughes originally thought that the marks were made by an insect cutting the veins of the leaf to drain away any potential poisons, something that modern insects also do. But these marks look very different – those on the fossil leaf bear a much closer resemblance to those of Cordyceps-infected ants. This is the first fossil trace of a parasite manipulating its host, but it’s not the oldest evidence for such a relationship. In 2008, another American group found a 105-million-year-old piece of amber containing a scale insect, with two Cordyceps stalks sticking out of its head. The war between insects and their Cordyceps nemeses is an ancient one indeed.

Reference: Biology Letters http://dx.doi.org/10.1098/rsbl.2010.0521
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Pocket Science – lessons from spongy genomes, and a deadly bat-killing disease

By Ed Yong | August 6, 2010 9:00 am

Not Exactly Pocket Science is a set of shorter write-ups on new stories with links to more detailed takes. It is meant to complement the usual fare of detailed pieces that are typical for this blog.


Spongebob’s genome reveals the secrets of building an animal

Sponges are animals but, outside of children’s cartoons, they’re about as different from humans as you can imagine. These immobile creatures lie on the very earliest branch on the animal family tree. They have no tissues or organs – their bodies are made of just two layers of cells, twisted and folded into simple shapes. But despite this simplicity, the first complete sponge genome tells us a lot about what it takes to build an animal.

The genome was sequenced from an Australian species called Amphimedon queenslandica by a large team of scientists led by Mansi Strivastava from the University of California, Berkeley. It tells us that sponges share a ‘genetic toolkit’ with humans and all other animals. This includes 4,670 families of genes that are universal to all animals, 1,286 of which separate us from our closest single-celled relatives, the choanoflagellates. Within these families lie the keys to a multicellular existence.

This shared toolkit controls all the fundamental processes that allow individual cells to cooperate as part of a single creature, including how to divide, die, grow together, stick to one another, send signals to one another, take up different functions, and tell the difference between each other and outsiders. They also include many genes that are implicated in cancer, a disease where individual cells go rogue and multiply out of control at the expense of the collective. The presence of cancer-related genes in the sponge genome tells us that as long as cells have been cooperating within a single body, they have needed to guard against the threat of cancer.

Srivastava estimates that the foundations of multicellular life were laid between 600 and 800 million years ago. More than a quarter of the big genetic changes that separate humans from the single-celled choanoflagellates took place during this window, before sponges split off from the ancestors of all other animals. The last common ancestor of all animals emerged during this period and it was a creature of remarkable complexity – a multicellular species that could sense, react to and exploit its environment.

Read more from Adam Mann at Nature, Bob Holmes at New Scientist and an earlier post from me on how sponges provide clues to origin of nervous system

Reference: Nature http://dx.doi.org/10.1038/nature09201; Image by Adamska et al


Holy extinction, Batman! One of America’s most common bats could be wiped out in 16 years by new disease

The little brown bat is one of the most common bats in North America but in 16 years, people on the East Coast will be lucky to see any. The bat is being massacred and the culprit is a new disease known as white-nose syndrome caused by the ominously named fungus Geomyces destructans. The fungus grows on the wings, ears and muzzles of hibernating bats, rousing them too early from their deep sleep, sapping their fat reserves and causing strange behaviour.

White-nose syndrome was first identified in a New York cave in February 2006, but it spreads fast. In the last four years, it has covered over 1200 km and contaminated wintering roosts throughout the north-eastern US and its neighbouring Canadian provinces. In infected areas, the fungus is slaughtering bats at a rate of around 45% a year. Cave floors are littered with carcasses.

Five years ago, the little brown bat was thriving, thanks to the installation of bat boxes, conservation efforts and a reduction in pesticide use. The eastern seaboard alone was home to 6.5 million of them. But all of that good is being undone by a single disease. Using a mathematical model, Winifred Frick from Boston University calculated a 99% chance that the species will become locally extinct within 16 years. Even if the current death rate slows to just 5% a year – a highly optimistic target– the population will still collapse to around 65,000 individuals. These last survivors would be just 1% of the previous total, with a 60% chance of dying off by the end of the century. At this stage, the question isn’t if the little brown bat will go locally extinct, but when.

This is just the tip of the iceberg. White-nose syndrome is spreading across North American and at least six other bat species are affected. These animals eat such a large volume of insects that their disappearance would have severe economic and ecological consequences. There’s a desperate need for more research to understand the disease, to keep a track of it, to find ways of fighting it, and to ensure that something like it doesn’t happen again. Frick thinks that white-nose syndrome spread so quickly with such devastating results that it must have been introduced from another part of the world, hitting species whose immune systems were totally unprepared for it. This problem of “pathogen pollution” is a neglected issue in conservation – perhaps the demise of the little brown bat will provide the impetus to take it seriously.

Read more from Brandon Keim at Wired and more from me on bats and how wind turbines burst their lungs

Reference: Science http://dx.doi.org/10.1126/science.1188594

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Attack of the killer tomato fungus driven by mobile weapons package

By Ed Yong | March 17, 2010 5:25 pm

In Robert Louis Stevenson’s classic story, Dr Henry Jekyll drinks a mysterious potion that transforms him from an upstanding citizen into the violent, murderous Edward Hyde. We might think that such an easy transformation would be confined to the pages of fiction, but a similar fate regularly befalls a common fungus called Fusarium oxysporum.

A team of scientists led by Li-Jun Ma and Charlotte van der Does have found that the fungus can swap four entire chromosomes form one individual to another. This package is the genetic equivalent of Stevenson’s potion. It has everything a humble, Jekyll-like fungus needs to transform from a version that coexists harmlessly with plants into a Hyde-like agent of disease. In this guise, it infects so many plant species so virulently that it has earned the nickname of Agent Green and has been considered for use as a biological weapon. It can even infect humans.

These disease-making chromosomes came to light after Ma and van der Does sequenced the genome of a variety of F.oxysporum called lycopersici (or ‘Fol’), which infects tomatoes. Its genome was unexpectedly massive, 44% bigger than its closest relative, the cereal-infecting F.verticillioides. Looking closer, Ma and van der Does found that most of this excess DNA lies within four extra chromosomes, which Fol has and its relative lacks. Together, they make up a quarter of Fol’s genome.

Ma and van der Does demonstrated the power of this extraneous quartet by incubating a harmless strain of Fol with one that causes tomato wilt. Just by sharing the same space, the inoffensive strain managed to acquire two of the extra chromosomes found in the virulent one. And, suddenly, it too could infect tomatoes. In a single event, the fungus had been loaded with a mobile armoury and changed into a killer. It seems that the fungus needs just two of the four chromosomes to cause disease; the others probably act as accessories, boosting its new pestilent powers.

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Leafcutter ants rely on bacteria to fertilise their fungus gardens

By Ed Yong | November 21, 2009 11:30 am

Hardly a natural history documentary goes by without some mention of leafcutter ants. So overexposed are these critters that I strongly suspect they’re holding David Attenborough’s relatives to ransom somewhere. But there is good reason for their fame – these charismatic insects are incredibly successful because of their skill as gardeners.

As their name suggests, the 41 species of leafcutter ants slice up leaves and carry them back to their nests in long columns of red and green. They don’t eat the leaves – they use them to grow a fungus, and it’s this crop that they feed on. It’s an old, successful alliance and the largest leafcutter colonies redefine the concept of a “super-organism”.  They include over 8 million individuals, span more than 20 cubic metres and harvest more than 240 kg of leaves every year. They’re technically plant-eaters, with the fungus acting as the super-organism’s external gut.

But the partnership between ant and fungus depends on other collaborators – bacteria. Some of these microbes help the ants to fertilise their gardens with valuable nitrogen, by capturing it from the atmosphere (a process known as “fixing”). Adrian Pinto-Tomas from the University of Wisconsin-Madison managed to isolate strains of these “nitrogen-fixing bacteria” from the gardens of 80 leafcutter colonies, throughout South and Central America.

Nitrogen is a scarce commodity for leafcutters, and the leaves they cut have too little of this vital element. And yet, they clearly get it from somewhere. The exhausted leaves they chuck into their refuse piles have higher proportions of nitrogen than those in the gardens, which have higher proportions than those that are freshly harvested or in the local leaf litter. Somewhere along the way, the cut leaves become enriched with nitrogen.

To find out how, Pinto-Tomas searched captive colonies of leafcutters for telltale signs of nitrogen-fixing bacteria. These microbes extract nitrogen from the air using an enzyme called, appropriately enough, nitrogenase. The enzyme also speeds up other chemical reactions, including converting acetylene into methane. So the fate of acetylene reveals the presence of nitrogenase, which in turn reveals the presence of nitrogen-fixing bacteria.

And that’s exactly what happened – the test showed that nitrogenase was present and active in the gardens of all the 8 leafcutter species that Pinto-Tomas analysed. The enzyme and the bacteria that wield it are particularly active in the centre of the fungus gardens and not at all on the ants themselves, or the leaves they cut. Around half of the garden’s supply of nitrogen comes from these bacteria.

But finding the bacteria wasn’t enough; Pinto-Tomas had to show that these microbes were actually beneficial partners rather than casual stowaways. He did that by sealing the colonies in airtight chambers and pumped in air containing a relatively rare form of nitrogen called nitrogen-15. He found that after a week, levels of this isotope had increased not just in the fungus, but the worker ants and their larvae too.

The ants were clearly reaping substantial rewards from their bacterial tenants. And by denying the ants access to soil or other food sources, Pinto-Tomas showed that they were indeed getting their nitrogen from these bacteria, and not from other sources.

This joint venture with fungi and bacteria must be a key part to the leafcutters’ undeniable success. It makes them a super-herbivore. The ants don’t fall prey to insecticides produced by plants because the fungus deals with those, and the fungus doesn’t have to cope with anti-fungal countermeasures because the ants break those down before plying it with leaves. As a result, both partners can exploit a massive variety of different plants, rather than specialising one any one type. A lack of nitrogen is the big limiting factor, but the ants can clearly overcome that too, with some bacterial assistance.

The partnership is probably a boon to other plants too. The leaves that the ants discard have 26 times more nitrogen than the surrounding leaf litter and they fertilise the surrounding soil. It’s no coincidence that the diversity of plants tends to skyrocket near a leafcutter garbage dump.

The nitrogen-fixers aren’t the only bacteria that cement the alliance between ant and fungus. A decade ago, Cameron Currie, who was also involved in this study, showed that leafcutters use another type of fungus as a pesticide. Their gardens are plagued by a different species of virulent, parasitic fungus and to protect their monocultures from these weeds, the ants use a type of Streptomyces bacteria. It hitches a lift on the ants’ shell and it secretes antibiotics that halt the growth of the parasite.

These insects really are gardeners par excellence, not only successfully growing a monoculture crop, they also use pesticides and fertilisers. Now if they’d only return David Attenborough’s family…

Reference: Science 10.1126/science.1173036

More on ants:

Images by Jarrod Scott, Cameron Currie and Bandwagonman

Tiny fungi replay the fall of the giant beasts

By Ed Yong | November 19, 2009 2:00 pm

Around 15,000 years ago, North American was home to a wide menagerie of giant mammals – mammoths and mastodons, giant ground sloths, camels, short-faced bears, American lions, dire wolves, and more. But by 10,000 years ago, these “megafauna” had been wiped out. Thirty-four entire genera went extinct, including every species that weighed over a tonne, leaving the bison as the continent’s largest animal.

In trying to explain these extinctions, the scientific prosecution has examined suspects including early human hunters, climate change and even a meteor strike. But cracking the case has proved difficult, because most of these events happened at roughly the same time. To sort out this muddled chronology, Jacquelyn Gill has approached the problem from a fresh angle. Her team have tried to understand the final days of these giant beasts by studying a tiny organism, small enough to be dwarfed by their dung – a fungus called Sporormiella.

Sporormiella grows in the droppings of large plant-eating mammals and birds, and it leaves tell-tale spores in its wake. More spores mean more dung, so Sporormiella acts as a rough indicator of the number of herbivores in a given area. The fall of these beasts is reflected in falling numbers of spores.

Gill counted these spores in the sediment of Indiana’s Appleman Lake, and compared them to counts of fossilised pollen and charcoal from the same soil. That allowed her to match the numbers of plant-eaters at any given time with the local plant species and the frequency of forest fires.

Using this fungal index, Gill has produced a detailed timeline of the changes in the Pleistocene. Her revised history argues against a role of climate change or alien rocks, but fails to clear early humans of the blame. More importantly, it suggests that many events that happened around the same time, such as an upheaval in the local plant communities and a rise in large infernos, were the result of the beasts’ decline, rather than the cause of them.

The spores revealed that the fall of the megafauna began in earnest around 14,800 years ago. By the 13,700 year mark, their numbers had fallen to less than 2% of their former glory. They never recovered, but it clearly took a few more millennia for the stragglers to succumb – the last bones of the great beasts date to around 11,500 years ago. 

Changes in the local vegetation happened after the beasts started disappearing, around 13,700 years ago. Before this point, the environment was open grassland with the odd tree. Fires were a rarity. But without the suppressive mouths of the big plant-eaters, trees grew unchecked, producing a combo of vegetation you just don’t see today. Large numbers of temperate deciduous trees like elm and ash happily coexisted with cold-loving conifers like larch and spruce.

And with them came fires, large infernos that broke out around 14,000 years ago and returned every century or so for the next few millennia. The pollen and charcoal of Appleman Lake tell the story of these changes, and also show that they came after the beasts’ disappearance.

Right away, this timeline rules out the possibility that a collision with a large space object killed the megafauna. The proponents of that theory place the collision at around 13,000 years ago, after the giants had started to decline. And it’s clear that extinctions were long, drawn-out affairs, rather than the relatively rapid annihilations you’d expect from an extraterrestrial impact. 

Likewise, changing climate becomes an unlikelier suspect. The megafaunal extinction predated a rapid, millennium-long chill called the Younger Dryas that took place around 11,500 and 12,800 years ago. When the megafauna started dying, the Earth was going through a warming phase. That might well have affected them, but it didn’t do so through the most obvious method – changing the plants they ate. After all, Gill’s work tells us that the beasts’ disappearance changed the plants, not the other way round. 

What about humans, those pesky slayers of animals? Some scientists believed that North America’s Clovis people specialised in hunting big mammals, causing a “blitzkrieg” of spear-throwing that drove many species to extinction. But these hunters only arrive in North America between 13,300 and 12,900 years ago, around a thousand years after the population crashes had begun.

If people were responsible, they must have been pre-Clovis settlers. There’s growing evidence that such humans were around, but they weren’t common or specialised. They may have contributed to the beasts’ downfall, while Clovis hunting technology delivered a coup de grace to already faltering populati0ons.

By analysing the sediment at Appleman lake – spores, pollen, charcoal and all – Gill has replayed the history of the site, spanning the last 17,000 years. Her data rule out a few theories, but as she says, they “[do] not conclusively resolve the debate” about climate causes versus human ones. It’s possible that similar studies at different sites and other continents will help to provide more clues.

Meanwhile, her study certainly tells us more about what happened in Earth’s recent history, when a large swathe of hefty plant-eaters died off – a change from savannah to woodland, and more fires. This isn’t just a matter of historical interest. The same events might be playing out today, as the largest modern land mammals suppress fires by eating flammable plants, and are facing a very real threat of extinction. History could well repeat itself.  

Reference: Science 10.1126/science.1179504

More on megafauna:


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