Category Archives: Microscopic life

Wine-delivering wasps

By John Upton

Yeast is a salubrious if invisible vintner, and scientists have discovered an important role that wasps have played in its spread and evolution in vineyards around the world.

Species of the single-celled fungal genus Saccharomyces feast on grape sugar and break it down to create alcohol molecules.

(That’s not all, of course. By shearing carbon and oxygen atoms away from carbohydrates in decomposing barley, the yeast produces booze while shaking loose pockets of carbon dioxide that manifest as bubbles in a freshly cracked beer. When the yeast produces those bubbles inside dough, the result is bread’s delightfully airy texture. Other genera of yeast fashion hard liquor, chocolate, soy sauce and scores of life’s other routine gastronomic indulgences from otherwise questionably-edible ingredients.)

Most modern wine, beer and bread makers purchase Saccharomyces and pour the yeast directly into their concoctions. But wine, beer and bread emerged as staples long before anybody understood their microbiotic secrets — in various continents and countless cultures over at least the last 9,000 years. Many of these early vintners, brewers and bakers relied on nature to deposit the mystical ingredient into their potions.

Where did this yeast come from, if not from a packet? How could nature be so dependably relied upon to provide this ingredient, apparently from thin air?

Illustrated by Perry Shirley
Illustrated by Perry Shirley

The answer rests in fungi’s remarkable ability to flood the environment with its own microscopic spores and then to lay low, requiring little to no sustenance, until it settles on food that allows it to quickly flourish.

A team of French and Italian scientists reported in 2012 in Proceedings of the National Academy of Sciences that vineyard-visiting social wasps in Italy were found to be both vectors and natural reservoirs of S. cerevisiae. The group, which expects to publish follow-up research in the same journal shortly, concluded that the wasps served as a “key environmental niche for the evolution” of a yeast used for winemaking — a yeast that cannot spread through the air unaided.

The group found the yeast inside the guts and nests of wasps, suggesting that the insects inadvertently gather the yeast while foraging in vineyards for food. Hibernating queens provide the yeast with a warm and safe winter home, and then the progenies of the queens help deposit the fungus back onto grapes as the fruit comes into season.

“Our work suggests that wasps could move wine strains and maintain diversity, favoring crosses between strains involved in wine making and wild strains,” Duccio Cavalieri, a microbiology professor at the  University of Florence who was involved with the research.

(A version of this post originally appeared on Wonk on the Wildlife in 2012.)

Fairy wasps unleashed to protect Eucalypts

By John Upton

Eucalyptus trees are the scraggly kings of Australian landscapes, growing hard and fast, resilient to fire and sundry other stresses. After their crowned heads were plucked from native wildlands and thrust into monoculture plantations in continents far afield, though, pests began sucking the antipodean puissance out of the botanical emperors.

Cue scientific tinkling and hopes for a tiny-winged salvation.

A healthy Eucalyptus plantation in Hawaii. Photo by Forest and Kim Starr.
A healthy Eucalyptus plantation in Hawaii. Photo by Forest and Kim Starr.

Natural forests and other ecosystems are being cleared the world over to make space for Eucalyptus plantations. They sprawl over millions of acres, from the American Southeast to Africa to New Zealand.

The trees are largely being grown to be pulped for paper and, more recently, to be burned to produce energy. Sometimes they’re just planted along paths and roads and as forests because they’re easy to grow, and they look nice.

Amid this upheaval, a biological chink has been gouged from the trees’ armors of hitherto resilience. Across the globe, Eucalypts in plantations and neighborhoods alike are being attacked by tiny sap-sucking bugs.

The culprits are called bronze bugs — because their victims’ hues change from green to bronze as their leaves dry out. As the sap is sucked from the trees, their growth is crippled. The heaviest of attacks can leave the trees dead.

Bronze bugs
Bronze bugs on a Eucalyptus leaf. Photo by Simon Lawson.

To protect hulking gum tree plantations from bronze bugs, scientists are starting to release even tinier critters. Their newest weapon is a species so small that it lays its eggs inside the eggs of the marauding pests, which hatch to feast on the meat of an egg that was laid for another, killing the unborn.

Eucalyptus trees, the bronze bugs that steal their sap, and the fairy wasps that hijack the bronze bugs’ eggs are all Australian natives. But until the turn of the century, few people had given the bronze bugs any thought. That’s when they started attacking trees in Sydney — possibly infesting tree species that had been transplanted outside their native ranges.

“There were very few records of it until it started outbreaking in Sydney in the early 2000s,” said Simon Lawson, a University of the Sunshine Coast entomologist who studies Eucalyptus pests.

From Sydney, the bronze bugs spread, hitchhiking with world trade to South America and South Africa, where the invasive populations made themselves at home amid their native prey. More recently, they’ve have been spreading through Europe and the Middle East. They’re also in New Zealand.

A fairy fly
A fairy fly. Illustrated by Perry Shirley.

The bronze bug outbreaks have coincided with a substantial rise since the 1990s in the spread of exotic pests in general — and, more recently, with a rise in the spread of Eucalyptus pests.

“Just in the last ten to 15 years or so, there’s been a real increase in the number of Australian-origin Eucalyptus insects that have been moving around the world into Eucalyptus plantations,” Lawson said.

To try to relieve the problem, Lawson and other researchers across the planet are turning to the pests’ natural predators. The main predator tested in laboratories and dispatched in the wild so far has been Cleruchoides noackae. C. noackae are from a family of wasp and ant relatives called fairyflies — or fairy wasps. As the name suggests, the family includes some of the tiniest insects ever discovered.

C. noackae
C. noackae. Photo by Samantha Bush, University of Pretoria.

Fairy wasps are often used as biological controls — as sentient insecticides.  They’re all parasitoids. That’s similar to a parasite, but dialed to a different equilibrium: parasites generally let their hosts live; parasitoids do not.

Following quarantine and tests that convinced them C. noackae was safe for native bugs, Brazilian agriculture officials released swarms of  them in the state of Minas Gerais in 2011. Two years later, field research found that about half the bronze bug eggs in local Eucalyptus plantations had been parasitized by the fairy wasps.

The results, which will be detailed in an upcoming scientific paper that’s still being finalized by Brazilian agriculture officials, are “quite a bit better than what we’ve seen in the native populations in Sydney that they’re derived from,” Lawson said.

Similar releases are planned or already underway in other South American countries and in South Africa.

Cracking the bronze bug problem, which was set off when Eucalypts were introduced to exotic environments, might mean doubling down on the number of species that are introduced to patch the problem over.

Ongoing research to identify alternative biological control agents, such as other species of fairy wasps, will also be critical for controlling the pests, Lawson said. “You’re better off having more than one agent.”

Bronze bug eggs on an infested leaf. Photo by Simon Lawson.
Bronze bug eggs on an infested leaf. Photo by Simon Lawson.

Heterokaryosis hypothesis: Could it help feed the world?

By John Upton

As scientists have started to figure out what a mycorrhizal fungus really is, they’ve discovered that it might be a really fun guy.

I mean, ahem. They’ve discovered that it might really be fungi.

Genetic sequencing is revealing surprising secrets of arbuscular mycorrhizae. The discoveries are casting doubt on notions of fungal individuality and offering new ways of boosting the amount of food that’s grown the world over.

Mycorrhizal fungi, aka myco, are soil dwellers that forage for water and nutrients, which they exchange for sugars produced by photsynthesizing plants. As I explained recently in Grist, they cool the globe and boost crop yields.

Research during the past decade suggests that what many of us would assume was a single myco fungus might actually be lots of mini fungi bits — genetically diverse nuclei that live and work together inside what we would logically perceive to be a fungus. There, the nuclei collaborate to create long mycelia and hyphae that stretch from root to root, delivering water and nutrients up to the plants, and passing carbon from the plants down into the soil.

Illustrated by Perry Shirley.
Illustrated by Perry Shirley.

This proposed blend of different nuclei is called the heterokaryosis hypothesis (a heterokaryon is a cell containing genetically diverse nuclei) — and it’s highly controversial. A recently flurry of papers has concluded that it is flat-out wrong, but those findings have been criticized by scientists who subscribe to the hypothesis.

If correct, the hypothesis could help scientists solve a couple of longtime fungal mysteries.

For one thing, it could help explain how and why mycelia from seemingly different fungi fuse together as they snake through the soil.

It could also explain how these types of fungi reproduce. Molecular evidence tells us that the fungi exchange genes, which suggests that they are mating. But scientists have never been able to figure out quite how they’re doing it. The heterokaryosis hypothesis suggests it’s the nuclei within each fungus that are breeding. It appears that they are migrating through fusions between the hollow mycelia.

“Why this heterokaryosis thing is so important,” said Ian Sanders, a professor of evolutionary biology at the University of Lausanne, “is because — I believe — we can use these genetic differences among the nuclei to create fungi that make plants grow better.”

Sanders has been involved with research in Colombia, where fungi have been developed that boosted cassava yields by one fifth while requiring less fertilizer. The research program is being expanded to Africa, where cassava, a root vegetable similar to a potato, is a dietary staple.

The breakthroughs relied on breeding techniques that took advantage of fungal heterokaryosis. More such breakthroughs would mean bigger yields of crops, more food, and less world hunger.

(Speaking of food, it’s worth noting that the heterokaryosis theory has nothing to do with mushrooms. There are two main types of mycorrhizae. Endomycorrhizae, which are the subject of this article, are arbuscular. They pierce the roots of plants with tiny vesicles and arbuscules, which are microscopic organs that helped both kingdoms of life adapt to life on land some 460 million years ago. It is the other type of mycorrhizae, ectomycorrhizae, the less common and less ancient union that engulfs roots without penetrating them, that produces mushrooms.)

Endomycorrhizae fungi infuse the roots of nine out of ten crop varieties, yet we know precious little about them. That’s largely because of complications inherent in trying to study an organism that’s intricately woven into the body of another; the result of nearly a half billion years of interdependent evolution.

The heterokaryosis hypothesis has its detractors. They point to research, such as this paper published this month in PLOS Genetics, in which nuclei sampled from a single fungus were nearly genetically identical. Supporters of the hypothesis point to findings from other research where vast genetic diversity appears to have been discovered. Sample sizes in some of the experiments have been very low, and just a few strains have been analyzed, making all of the results highly contentious.

One believer in the hypothesis is Toby Kiers, a mycological researcher at Vrije Universiteit Amsterdam. “It’s a neat concept, because even within an individual you’ve got individuals,” she said.

Kiers will begin lab experiments next month designed to help breed mycorrhizal strains that further boost crop yields. I highlighted the planned research in a recent magazine article about myco fungus in The Ascender:

[Kiers] has secured funding to watch mycelia squeeze through tiny mazes, peering at them through microscopes as they trade nutrients with plants for sugars under different conditions. The goal, she says, is to “study their decision-making skills.”

Kiers’s research will combine cutting-edge microscopy and mycology with old-fashioned breeding techniques in a bid to select the most useful fungal strains. “They’re quite easy to select on,” she said, “because there’s so much genetic variability — even within a single hyphae, within a single spore.”

Human infections are dead ends for valley fever fungus

By John Upton

People infected with two closely-related species of fungi are dying in growing numbers in the American southwest. The Coccidioides spores are blown with dust into lungs, where they can trigger a painful and sometimes-deadly condition known as valley fever.

But any cocci that ends up in a human has hit a dead end. It will not reproduce to spawn a new generation.

That’s because of the lifecycle adopted by these varieties of cocci after evolving with the rodents that share their desert home. The coccis’ ancient ancestors lived and dined on plants. Then they evolved to feast instead on the rotting flesh of dead animals. Now they have evolved to live inside a living mammal, sometimes waiting for years for the host to die so they can pounce and quickly consume the fresh kill.

Illustrated by Perry Shirley.
Illustrated by Perry Shirley.

Mammals whose immune systems can’t control the fungus may die quickly. But as I explain in Vice’s Motherboard blog, most animals that are infected with cocci develop few symptoms — and those symptoms are normally short-lived:

Normally, [the Cocci] eek out lives as filaments called hyphae. The hyphae live in the soil and produce spores, a lucky few of which get sniffed into the lungs of desert rodents. The spores balloon in size inside the host, forming spherules. The mammal immune system kicks quickly into gear at this point, building walls around the spherules, containing them and developing immunity against further attacks.

It’s when the immune system fails to contain these spherules that the fungus can propagate throughout its victim, sometimes with deadly consequences. As an infected rodent dies, collapsing into the desert, the cocci burst out of suspended animation and unleash streamers of hyphae that eat the rotting meat. As the fungus feasts, hyphae and spores slip back into the soil, ready to start the cycle all over again.

Humans don’t slip into the desert sands when we die. We are embalmed or cremated, making any infection a waste of time for the fungus and, in some cases, a waste of life for humanity. “If a cocci spore gets into a human, it has made a big mistake,” John Taylor, a University of California at Berkeley mycologist, told me. “It’s unlikely to ever become adapted to living in humans.”

A hungry red tide is a dangerous red tide

By John Upton

When fertilizer or sewage runs into a waterway, or when phosphorous and nitrogen rise up from the ocean depths, algae can converge and feast and mushroom on the buffet of growth-inducing nutrients.

But scientists have discovered that starving a poisonous red tide of its nutrient supply can trigger a very dangerous and counterintuitive response.

Red tides are freaky types of algae blooms. They often occur in the ocean or in salty bays, and they frequently produce poisons. Scientists prefer the term “harmful algal bloom,” since a red tide isn’t always red and it is most certainly not a tide.

Illustrated by Perry Shirley
Illustrated by Perry Shirley

The most common type of algae in Gulf of Mexico red tides is a dinoflagellate called Karenia brevis. The neurotoxin produced by these single-celled creatures help protect them from predation: Would-be hunters can die if they take a mouthful. But as the red tides break down, the poison escapes from the plankton cells and it can drift through the marine environment, poisoning it. The toxin can even spray into the air, aerosolized by crashing waves, where it can get into lungs and trigger serious ailments in people and other animals. The Floridian West Coast is often the worst affected.

Concentrations of the poison in each of the algae cells varies widely — from a mild 1 picogram per cell to a treacherous 68 picograms per cell. Needless to say, figuring out what causes a bloom to be especially poisonous would be valuable for public health officials.

Since Karenia brevis uses nutrients to grow, one may assume that starving them of phosphorous and nitrogen, such as by preventing fertilizer or sewage runoff into the Gulf, would protect the environment from their poisons.

But that’s only true up to a point. If you can keep nutrients out of the water, a bloom will not materialize, so there will be no danger of the waterway being poisoned by it. But if the nutrient supplies suddenly dry up, an existing bloom will switch into a defensive mode, stop growing and become very toxic.

The ecological theory to describe this response comes to us from botany. It is called the carbon:nutrient balance hypothesis.

North Carolina scientists grew samples of the dinoflagellate in water taken from the Gulf in a laboratory. Some samples were fed plenty of phosphorous, but others received very little. The scientists found that K. brevis strains living with limited phosphorous supplies produced 2.3 to 7.3 times more poison than did those that had plenty of phosphorous available.

“Because PbTxs [K. brevis brevetoxins] are potent anti-grazing compounds, this increased investment in PbTxs should enhance cellular survival during periods of nutrient-limited growth,” the scientists wrote in their paper, published last month in PLoS ONE.

The algae samples living without much phosphorous put their carbon to a defensive use, since it couldn’t be used as effectively for growth. The proportion of carbon that each cell used to produce poison as much as doubled when phosphorous was limited.

This is consistent with the carbon:nutrient balance hypothesis. When vegetation has lots of carbon and lots of nutrients available, it invests those building blocks of life into fast growth. But when nutrients, be they phosphorous or nitrogen, are in short supply, the carbon is put to a different use: Defense against predators.

It also helps explain some of the late season bursts in toxicity noticed in the red tides: They become poisonous after they have greedily slurped down the last of the available nutrients.

This research was limited to phosphorous. But previous research uncovered a similar red tide response when nitrogen was limited.

The discovery could help public health managers predict the potency of red tides in the Gulf of Mexico. By measuring the amount of phosphorous in the ecosystem, it could become possible to determine how dangerous the red tides will become.

Cicada wings rip bacteria apart

Illustrated by Perry Shirley

By John Upton

Forget sanitary hand wipes. Scientists have discovered that cicada wings have evolved to kill bacteria without using any chemicals.

The wing are coated with tiny blunt bumps that are so small and plentiful that when a bacterium lands on them, it becomes skewered through multiple parts of its tiny writhing cell wall.

The bacterium doesn’t pop — it is torn open, shredded to pieces by the bumpy wing.

The Australian and Spanish scientists, who published their findings in Biophysical Journal, say the discovery could lead to antibacterial materials “incorporating cicada wing nanopatterns.”

Watch a simulation of a bacterium that was unlucky enough to land on a cicada wing:

When T7 attacks — watch a virus infect a cell

Illustration by Perry Shirley

By John Upton

The E. coli was doomed. This gut-dwelling microbe was trapped in the company of a predator. A T7 bacteriophage, a virus that propagates by inserting its DNA into bacteria, had been deposited nearby.

As the T7 landed on the surface of its prey, it was being watched by University of Texas Medical School researchers. They were watching the attack using cryo-electron tomography – a technique that creates 3-dimensional pictures from multiple microscopic images taken at freezing cold temperatures. They watched in graphic close-up detail as a virus infected a cell.

The virus was smaller than its prey. It looked like a bloated tick, with six folded legs made of protein at one end of its body. The legs formed a circle around a retracted tail. As the T7 landed on the bacterium, it extended some of its fibrous legs. It used the legs to walk along the surface of its prey, feeling for a suitable place to attack. Once it found the right location, it stopped walking and stood still. It planted its legs, extended its retracted tail and jammed it through the cell wall and into the victim. It pumped in its DNA. Then it retracted the tail, and the hole in the cell wall healed back over.

The attack was complete. The hapless bacterium now harbored the virus.

“The complete process we describe is unique to T7 and its relatives,” Ian Molineux, one of the researchers, told me. The study was published Thursday in the journal Science. “But some aspects, in particular fibers binding to the head and walking over the cell surface, are probably quite general.”

Parasite hijacks cells, dulls fear

Cats, such as Poppy here in Oakland, are the definitive hosts of Toxoplasma gondii / Kamala Kelkar

By John Upton

Toxoplasma gondii is a wily parasite that’s beautifully adapted to the urban environment. The protozoans pass between rats, house cats and humans with aplomb.

Once inside a rat, the single-celled stalker diminishes its host’s fear of cats, which helps it spread from the hunted to the hunter. From the cat, the parasite passes into kitty litter, where it can infect new rats and enter humans through litter-tainted food or licked fingers.

Perhaps one quarter of the world’s human population is infected. Consequences are seemingly slight: Temporary flu symptoms and a lifetime of benign infection. But inside the central nervous system the disease could trigger depression and schizophrenia and reduce reaction times. Infected humans are more likely to crash their vehicles than those who are uninfected.

Researchers have honed in on a deft trick used by the parasite to spread through the body and commandeer parts of its hosts’ brains. By affecting brain function, the protozoans could help cats catch infected rats.

T. gondii under a microscope / Flickr: OmarCerna

The protozoans bust into dendritic cells, which play major roles in the immune system. Research published last week in PLOS Pathogens reveals that the protozoans trick the infected cells into producing a compound dubbed GABA.

Production of GABA excites the infected cell, encouraging it to move around the body and aiding in the parasite’s migration into the brain.

GABA is also a neurotransmitter; it stifles sensations such as fear and anxiety.

“For toxoplasma to make cells in the immune defence secrete GABA was as surprising as it was unexpected,” said Antonio Barragan, researcher at the Center for Infectious Medicine at Karolinska Institute and the Swedish Institute for Communicable Disease Control, “and is very clever of the parasite.”

Oil dispersant upshot — bacteria feasted after BP spill

By John Upton

During its Deepwater Horizon oil spill, BP wickedly used 1.8 million gallons of oil dispersants to hide the slick. The chemical cocktail known as COREXIT 9500 caused the crude oil to dissolve in water instead of float on its surface. Among other things, the move destroyed plankton communities and threw the Gulf of Mexico’s food chain into chaos.

But one of life’s most primitive forms benefited greatly from this poisonous approach.

Hydrocarbon-eating bacteria feasted on the oil and methane as it swirled around in the gulf’s water column. New research published in Environmental Science and Technology reveals that the bacteria consumed at least 200,000 tons of the stuff, converting some of it into biomass that passed up the food-chain while also releasing the greenhouse gas carbon dioxide. The feeding frenzy reached its peak nearly three months after the oil rig explosion killed 11 workers, the scientists found.

“Certainly, some of the hydrocarbons were respired to CO2,” John Kessler, a Rochester University professor who co-authored the paper, told me in an email. “But some of that oily food had to go into supporting an increase in the microbial population.”

TV news report on the impacts of oil dispersants on gulf plankton communities:

Pumice — rad wildlife raft

Pumice for $4.49.

By John Upton

Natural rock rafts are normally way too small for us humans to ride. But the fragments of lightweight pumice that form after waterlogged volcanoes explode are surfed around the world’s oceans by everything from algae and barnacles to nudibranchs and crabs.

Pumice, normally found in bathroom cabinets and beauty salons, is an extraordinary type of rock: It’s light enough to float on water. It forms when searing hot lava strikes water, which cools the material suddenly and freezes pockets of air inside. Following a marine eruption, ribbons of pumice can float all around an ocean, directed by currents and winds, until they eventually settle on far-flung shorelines. New Zealand’s Navy stumbled across 10,000 square miles of the stuff floating in the southern Pacific Ocean last month.

Research published in July revealed that extraordinarily diverse communities of wildlife quickly set their roots on these floating substrates, helping otherwise sedentary marine species travel great distances in short periods.

Life teems on this chunk of pumice, formed when Home Reef Volcano exploded in waters near Tonga / Courtesy: PLoS ONE.

Scientists monitored pumice formed by a 2006 underwater volcanic eruption near the Pacific Islands nation of Tonga. They discovered more than 80 species using the floating rock as a raft, some of them hitchhiking a ride of more than 3,000 miles in less than nine months.

“The rafted community exhibits a variety of feeding strategies: photosynthetic, filter feeding, grazing and scavenging to predation, but with photosynthesising organisms and filter feeders most dominant,” the Australian researchers wrote in their paper, which was published in the online journal PloS ONE.

The pores that help the rock float also offered shelter for many of the species, the researchers found: “Vesicles and surface depressions offer protection from predation for obligate rafting organisms and for facultative species during initial growth.”

The Tongan pumice was still washing up on Australian beaches 20 months after the explosion, revealing that the wacky substance provides wildlife with more than just a means of jetting across an ocean: It can provide a mini-ecosystem with a seafaring home that lasts for years.