Astronomers have just discovered two Earth-size, rocky planets around a nearby star. Though the planets are way too broilsome for life, they suggest that steady improvements in telescope technology has made the discovery of habitable planets just a matter of time.

But as astrobiologists continue to search for life in space, geo-biologists (ok, we coined that) continue to find bizarre life in strange places on Earth: in the dark ocean depths, between grains of sand, and at roasty-toasty temperatures once considered deadly.

Hot, humid, and totally alive!

Fifty years ago, nobody believed organisms could survive near the boiling point of water. When Thomas Brock started probing the hot springs in Yellowstone in the 1960s, he was not looking to overthrow a ground rule of biology. Instead, the University of Wisconsin-Madison professor, then at Indiana University, sought to study bacteria in a simplified, real-world environment.

At the time, and even today, precious little was known about how bacteria live their lives — unless they cause disease.

As Brock sampled his way up a hot stream, he approached its source in a hot spring, and the water temperature rose steadily.

At the time, biologists thought life would not tolerate temperatures near 80° C. But Brock kept finding bacteria, so he kept looking. Eventually, he found some that could live and reproduce near the temperature of boiling water — 100° C.

The prize of his collection was a bacterium he named Thermus aquaticus (for its hot-water habitat) and placed in a public repository for study by other scientists.

Over the years, T. aquaticus proved interesting indeed. For one thing, it was the first of more than 50 species of thermophilic bacteria known to tolerate or require temperatures near water’s boiling point.

For another, it was the first of the Archaea (ancient ones), primitive microorganisms that scientists now regard as a separate and highly primitive kingdom of life.

Deep roots indeed

Because thermophiles are Archaeans, and prefer the steamy conditions typical of early Earth, many scientists think they may tell us about the origin of life itself.

To any basic scientist, those contributions would be enough. But because their enzymes work in high temperatures, where chemical reactions are faster, the thermophiles have proven to be extraordinarily useful.

Today, enzymes derived from thermophiles are used to convert millions of pounds of corn (maize) into sugar to sweeten soft drinks.

But more important, at least to scientists who don’t guzzle fizzy pop at the lab bench, T. aquaticus supplied TAQ polymerase, the essential enzyme for polymerase chain reaction, AKA PCR.

PCR is an artificial technique that does what living critters do every day — replicate DNA. But PCR is the rocket ship of replication, since it allows you to multiply a piece of DNA a billion times in a few hours. That produces enough DNA to analyze to your heart’s content — for genetic engineering, biotechnology and forensic purposes.

PCR depends on TAQ polymerase.

Aware that PCR and soda pop are both billion-dollar industries, corporations and scientists around the world have frantically searched for other thermophiles that may have equally useful enzymes. They’re looking in odd places — not just hot springs and volcanoes, but also deep-sea vents, hot petroleum-bearing rock, the outflow of geothermal power plants, and smoldering piles of garbage.

Prowling for glow-in-the-dark squid

Call me Bob.

Short for bobtail squid. (Did I mention that I’m a 3-4 centimeter cephalopod, formally Euprymna Scolopes?)

Anyway, I hang out in shallow waters around Hawaii. Save your crocodile tears — somebody’s got to live in the sunny, tropical ocean. Anyway, here’s my problem: Even though I have 10 tentacles, I don’t have spines, poisons, or any other decent defense.

So I spend my days burrowed in sand at the ocean bottom, trying to keep out of mischief. Still, a fellow’s got to eat, don’tcha know, so I cruise at night, looking to grab a bite.

Here’s the snag: All sorts of nocturnal predators seem to have this thing about calamari sushi.

Light before flashlights

A long time ago, my ancestors evolved a nifty defense against their big teeth: stealth. Even their tiny squid brains figured out that predators could see them from below, as tasty dark blobs against the bright ocean surface.

Since this was before flashlights, my relatives had to improvise. So they press-ganged billions of luminescent bacteria into making light for them. The idea was to make us just as bright as the ocean surface — and hence invisible.

At least, this is how my great-aunt Tentacla tells it. To tell the truth, I think it had more to do with the evolutionary advantage of being hard to see.

Anyway, my ancestors fed the bacteria, and gave them a home in two specialized light-emitting organs. These “photophores” have a reflective membrane to shine all their light down, toward the hungry predators. They use a diaphragm to control brightness, and even have a lens to spread the light.

The photophore reminds me of a backwards eye — one that makes light rather than detects it.

My folks even figured out how to switch the bacteria “on” when needed.

In return, the bacteria got room and board, in the biological deal they call “symbiosis” or “mutualism.” Sometimes I think people could learn from this cooperative spirit….

But that’s enough thinking for today. My squid brain is squashed.

As I burrow into the sand for another daytime nap, permit me to introduce somebody who considers me almost as fascinating as I do.

Seriously speaking…

Margaret McFall-Ngai, a biologist at University of Wisconsin-Madison, says the bobtail squid may pretend it’s cooperating in a symbiosis with those light-making bacteria, but the reality is more ominous.

She says there’s evidence that this may be slavery, not symbiosis, since the squid, “inhibits the growth of the bacteria to enhance their luminescence.” The bacteria, Vibrio fischeri, could make a better living drifting in the ocean, or in the gut of another marine animal, McFall-Ngai observes.

The concept of bacterial enslavement broadens our perspective on the many possible relationships in the living world.

Most people, if they think about bacteria at all, conjure up disease and decay, but people would be dead without bacteria, since the little critters play essential roles in producing vitamins and preventing disease.

Since the bacteria in our guts vastly outnumber the cells in our bodies, it helps that they’re helpful!

Nevertheless, and for understandable reasons, bacteriologists have traditionally focused on disease-causing organisms, and, for simplicity, on one species at a time. But that skews our view of how bacteria actually live, says McFall-Ngai.

Three cheers for complexity!

Complexity and subtlety may be the hallmarks of these interactions, and the complexity begins by recognizing that V. fischeri is closely related to V. cholerae, which causes the human intestinal disease, cholera.

Cholera is caused by a V. cholera toxin similar to a toxin produced by the light-emitting bacterium. But far from harming the poor little bobtail, that toxin signals it to secrete food for V. fischeri, so the toxin is really a chemical “dinner bell.”

And this raises the intriguing notion that a cholera bug secretes toxins not to kill its host but to discuss its menu. If so, our whole notion of pathogenesis may need rewriting, McFall-Ngai suggests. “Maybe when we’ve been studying cholera pathogenesis we’ve been studying an aspect of a normal conversation that’s gone wrong.”

Indeed, the traditional bacteriological view of bacteria as pathogens to be studied in pure culture may be “like trying to understand the complexity of all the cultures that lived in Paris by studying the activity of the Nazi occupiers,” McFall-Ngai suggests. “You are studying groups that don’t belong there, and have disrupted the normal activities.”

Want more on how the flashlight squid bullies its bacterial brethren?

Between the grains

(1996 story, only photos have been updated)

To zoologist Robert Higgins, small is beautiful. His infatuation with small creatures — “meiofauna” — dates to a student job in a biology lab that paid 35 cents an hour. Instead of quitting for more lucrative work, Higgins was intrigued.

He’d heard about tiny, amazingly diverse creatures, and put grains of sand and muck through a fine mesh, and used a microscope to find hundreds of organisms.

Forty-four years later, Higgins has retired from the Smithsonian Institution, but he’s still goggling at meiofauna — a complex group of animals found in most Earthly environments.

Indeed, a handful of wet sand could contain more biological diversity than a whole rain forest, Higgins says.

In the course of peering through countless microscopes, Higgins has discovered hundreds of species. With Danish biologist Reinhardt Kristensen, he found an entire phylum, called Loricifera.

Phyla are the broadest categories of organisms, based on structure, and according to the International Association of Meiobenthologists, “The majority of recognized phyla have meiofaunal representatives. Currently, 20 phyla considered to be meiofaunal from the 34 recognized phyla of the Kingdom Animalia. Out of these 20 phyla, five are exclusively meiofaunal in size.”

Photo: Giulio Melone, department of biology, Milan University.

A bdelloid (a type of meiofauna) shrinks when it undergoes anhydrobiosis. The dormant, dehydrated bdelloid has greater resistance to environmental stress but is ready to spring back to the active form in conducive conditions.

Meiofauna living between grains of sand have made some fancy adaptations to their harsh environment. Some have hooks on their feet, used to grab the sand. Others have hooked mouthparts, also useful for locomotion.

Beyond freeze-dried

To survive a difficult environment, meiofauna called tartigrades have evolved an amazing adaptation called “anhydrobiosis.” In this form of suspended animation, the animals replace water in their cell membranes with sugar, protecting the membrane from destruction through radiation and freezing. Microorganisms die when their cell membrane ruptures.

During anhydrobiosis, organisms are rather like plant seeds or bacterial spores, Higgins explains. “They can dry up for 100 years, and be rewetted, and come right back to active metabolism.”

Fun is fun. But what is the practical importance of studying stuff that can hardly be seen, doesn’t seem to cause disease, and is — at least to some — utterly ugly?

In other word, who cares about microscopic beach crud?

Meet the beach-cleaning crew

Anybody who likes to hang on the sand should be interested, Higgins says. “This is the system that helps keep our beaches clean.” Plankton, bacteria, all sorts of dead material is continually washing ashore, and a lot of people love to sit on beaches.

There’s a public-health angle here. Hookworms occur on beaches where dogs defecate, but meiofauna may consume hookworms, along with other nematodes. “So if we upset that, we could upset beach cleanliness,” Higgins says.

Higgins notes that meiofauna comprise a basic part of the food web, and disturbing them could have unforeseen consequences for the entire system.

Still, it’s hard to escape the notion that most of the motivation here is the pure scientific urge to discover, to classify, to understand. Meiofauna, Higgins notes, were seen under the microscope Anton van Leeuwenhoek invented in 1683.

The key to finding these things, Higgins indicates, in patience, technology, curiosity — and institutional support. “If you stare through a microscope for hour after hour, you have a chance of finding these things, but if you need to get out a certain number of papers each year, you have to take shortcuts and you won’t find as much.”

Fantastic freak show

Poke deep inside an insect cell, and you may be in for a shock. At least we were startled to learn that bacteria live inside many insects, including the fruit fly, one of the workhorses of biology.

Photo: Biodiversity Institute of Ontario

The star of the study, Drosophila mauritiana.

Today, we hear how bacteria of the genus Wolbachia boost egg production in certain fruit flies. The mechanism, says Horacio Frydman, an assistant professor of biology at Boston University, involves a two-step: first the fly makes more egg cells, and then it blocks a process that would normally prune away extra eggs.

Insects, like other animals, are frequently “married” to bacteria in a relationship that benefits one or both parties. This is common: Bacteria in the cow’s rumen break down cellulose eaten by the cow. Bacteria in the human gut form vitamin K, necessary for blood clotting.

And bacteria in aphids synthesize essential amino acids that the aphids cannot make by themselves.
Wolbachia are not essential to the fruit flies, but their presence can quadruple egg production.

Speeding breeding

Producing four times as many offspring “is a powerful driver of infection,” Frydman says. “Wolbachia manipulate their host reproduction to favor their own spread in nature,” noting that in less than 20 years after Wolbachia was detected in fruit flies in southern California, the infection had spread as far as Canada. “It’s considered one of the largest pandemics in the recent evolution of life. Because Wolbachia influence their host reproduction, they also impact the evolutionary history of innumerable hosts.”

Wolbachia have been linked with a wide variety of effects in the insect realm. Wolbachia “lives in at least 20 percent of the world’s arthropods, including insects, spiders, mites, and crustaceans,” according to the Wolbachia project, making them an active area of investigation.

How could this symbiosis work to increase the number of offspring?

Using sophisticated microscopy, Frydman, Ph.D. student Eva Fast and colleagues tracked the location of Wolbachia in fruit flies. In D. mauritiana, a species native to the Mauritius Islands in the Indian Ocean, the bacteria congregate in the germline stem cell niche — a structure that supports stem cells that develop into eggs. In D. melanogaster, the bacteria accumulate in the niche that harbors a different type of stem cell, which produces the eggshell.

In the germline stem cell niche, the bacteria actually outnumber mitochondria, organelles involved in making energy for the fly.

Having the bacteria in the germline stem cell niche doubled the rate of division among those stem cells. Further investigation showed that the bacteria later also halved the rate of programmed cell death.
So the bottom line was a four-fold increase in egg production.

The virtue of pruning

“It’s remarkable that there are two mechanisms being manipulated by the bacteria, the rate of egg production and the rate of programmed cell death,” says Frydman.

Hitting both systems makes sense, Frydman adds, although the mechanisms remain unclear. “It is not surprising that Wolbachia would evolve to manipulate those two process, because they are key in controlling the rate of egg production, and therefore it has a profound impact in the reproductive success of the infected host and in spreading of bacteria in nature.”

Anything that increases the number of eggs and offspring is likely to be favored by natural selection, Frydman adds.

Photo: CDC, #373

Parasitic worms cause elephantiasis, which afflicts this man from the Philippines. Could killing Wolbachia prevent this disfiguring disease?

A healthy thing?

Beyond an insight into the fascinating biology of symbiosis, the finding could also have health implications. Parasitic worms that cause diseases like elephantiasis seem to benefit from Wolbachia infection.

And Wolbachia can affect insect immunity: Tests have shown that infected fruit flies are more resistant to some viruses, for example. And a recent paper in Nature found that mosquitoes in Australia could not transmit dengue fever if they carried a Wolbachia strain derived from Drosophila.

Mosquitoes also transmit malaria. Conceivably, better knowledge of the interaction between Wolbachia and insects might convert mosquitoes from a carrier of this ancient scourge into a defense against it.

– David J. Tenenbaum

Image: M.J. Grimson & R.L. Blanton

The single-celled amoeba Dictyostelium discoideum has no brain, but its complicated social cycle enables farming.

Amoeba, single-cell, shape-shifters that eat bacteria and live in the dirt, don’t get much respect. When they run out of food, they gang up and move their sorry selves to greener pastures.

Pastures with edible bacteria, that is.

If ever a creature needed re-branding, this is it.

Could labeling amoeba as farmers boost their brand? In the human realm, farming gave rise to cities, writing, metallurgy and the computer in front of your face.

Amoeba don’t use the Internet. And although they do have a cell nucleus, nobody claims they have an ounce of smarts.

But now we know that some amoeba move “seeds” of bacteria to a new location and plant them as a food source. In other words, they farm.

Ants grow fungus. Termites and some saltwater snails do ditto. Damselfish grow algae. But until now, nobody has identified any life form that “farms” bacteria, and nobody has identified any single-celled farmers, says Debra Brock, a graduate student in ecology and evolutionary biology at Rice University.

Adds Brock, whose report on farming amoeba appears in Nature tomorrow, “Certainly there has never been an amoeba that’s known to farm.”

Bring on the rebranding!

Working with the well-studied amoeba Dictyostelium discoideum (“dicty” to you and me) Brock noticed that the fruiting bodies — reproductive structures that distribute the amoeba in new habitat — seemed to contain bacteria. That was odd, Brock admits. “To get anybody to believe me, I had to prove that the little spots were bacteria, and not an infection.”

When she spotted the sorus (mass of spores) on growth medium, colonies of bacteria grew on some of the plates — showing that about one dicty in three transports bacteria. The bacteria didn’t seem to be a harmful infection, since amoebas with and without bacteria grew similarly, she says.

She fed the shape-shifters antibiotic to kill their bacterial cargo, but when the amoebas resumed eating bacteria, some bacteria showed up in the sorus. Since this only happened with amoebas that had originally carried bacteria, Brock concluded that this was normal, healthy behavior for those amoeba, although she’s can’t yet say whether the bacteria are inside or alongside the amoeba spores.

Photo: Scott Solomon

Fruiting bodies of the amoeba Dictyostelium discoideum contain bacteria and spores of amoebas. Each sorus is attached to a single slug, comprised of about 100,000 individual amoebas.

Wild about amoeba

The project began when Brock was studying wild amoeba rather than a strain that had been living in labs since the 1930s, and she noticed that some clones consistently carried bacteria.

Brock says dictys are “social amoeba” because “they have a structured society, and can exist in two states.” Individual amoebas in the soil eat bacteria, divide and eat some more. So long as edible bacteria are available, “they are perfectly happy to do this,” says Brock. “But if they use up all the food, they start talking to each other with chemical signals: ‘Wow! There’s not enough food!’ And then approximately 100,000 come together to form a slug.”

The slug serves as a truck to haul amoeba to new territory, Brock says. “During the multi-cellular part of the life cycle, they are starving, and they want to go somewhere else.”

The slug eventually shoots up a stalk containing amoeba spores, and among the farmers, bacteria. When the sorus opens, the bacteria can plant themselves as amoeba food.

Reminds us of Johnny Appleseed…

The Darwinian decision

Why does the same species of dicty use two survival strategies? Why do some farm while others don’t? “It’s a smart evolutionary strategy,” says Brock. “It’s bet-hedging. If you happen to land in a patch without bacteria, farmers have a great advantage because they bring their food with them, which allows them to grow and divide and bear a huge number of progeny while the poor non-farmers have nothing to eat.”

But while the farmers quit eating before they remove all bacteria from their old location, non-farmers can eat all those bacteria, so non-farmers do benefit if the new home already contains edible bacteria.

Apparently, both strategies work, because both have survived the evolutionary gauntlet. Brock is exploring whether a “farmer gene” causes some amoeba to hoard bacteria…

It’s enough to give a person a new respect for protozoans, which offers a firm basis for rebranding. “From quite a long time ago, we’ve thought we are so special,” says Brock, “but you can’t imagine the number of genes the amoeba has that are just like human genes. It’s scary; it takes you down a notch or two.”

– David J. Tenenbaum

When Deepwater Horizon blew up and melted down in April, the wound it tore in the Earth’s crust released a gusher of crude oil, estimated at 4.2 million barrels, into the Gulf of Mexico.

The massive microbial munching of methane during the BP spill may be the only good news from the Deepwater Horizon disaster.

The blowout also released about 160,000 tons of methane. If you counted molecules in BP’s blowout, methane (CH₄), the simple hydrocarbon that fuels stoves, furnaces and electric generators, was the single most abundant one.

But a report published in today’s Science shows that BP’s methane was totally devoured by microbes in the Gulf of Mexico, leaving less than .01 percent of the methane to enter the atmosphere. “We measured the sea-to-air flux of methane and found it was completely negligible,” says first author John Kessler, an assistant professor of oceanography at Texas A&M University.

Within four months of the April 20, 2010, blowout, a population explosion among methane-eating bacteria native to the Gulf decomposed virtually all of the methane, mainly in deep water, says Kessler.

Study author John Kessler extracts a water sample from a device that detects changes in water conductivity and temperature with depth.
NOAA Pisces.

The study offered three lines of evidence that bacteria were “eating” the released methane:

• Methane levels in the Gulf fell up to 10,000 times between June and October.
• Methane-munching microorganisms became extremely abundant downstream of the blowout. “Over the summer, the methane degraders were higher than we have ever seen at any other place in the world,” says Kessler.
• Dissolved oxygen in the water dropped as methane and oxygen reacted to form carbon dioxide and water, Kessler says. “Once we summed up all the lost oxygen in the area of the methane plume, we saw that it could only be explained by a complete [microbial] consumption of this methane.”

Although oxygen depletion is already a concern in the Gulf’s “Dead Zone,” the average loss was only 3 percent, Kessler says.

In a previous study, ethane and propane, two other natural gases that BP also released, decomposed even faster than methane, and were no higher than background levels by early fall. In both studies, Kessler collaborated with David Valentine of the University of California at Santa Barbara.

Cool news for your atmosphere

In the short term, spilled methane is less environmentally dangerous than crude oil, but it can pose a global warming problem in the long term, since a molecule of methane stores much more heat than a molecule of carbon dioxide.
Methane seeps are frequently found at ocean floors, where methane from decomposition enters the ocean. And unfathomable quantities of frozen methane are stored beneath the seabed.

So inquiring minds want to know: If and when this methane enters the ocean, could it reach the atmosphere and accelerate global warming?

Pisces, a research ship of the National Oceanic and Atmospheric Administration, was a floating laboratory to study Deepwater Horizon's aftershocks.
Photo: John D. Kessler/TAMU

The giant Deepwater spill contained too little methane to affect atmospheric levels, says Kessler, “but it does simulate a very energetic release from a seep or a methane hydrate, and so we were interested in using it as an analog for understanding how a massive submarine release of methane might behave.”

Although the microbes-eat-methane story provides a rare bright spot in BP’s ecological disaster, it’s not clear what would happen in shallow water, and in places lacking natural methane and a ready supply of methane eaters.

“The Gulf of Mexico has many natural methane seeps,” says Kessler, “that probably account for why Gulf waters are populated with these microorganisms, which are ready to degrade methane once there is a massive restocking of their ‘buffet.’ How this may play out at another place, without the natural seeps, I’m not sure.”

Within four months, bacteria had spawned enough offspring to devour essentially all of the added methane in the Gulf. “But if the bacteria are at lower abundance, would this take five months or two years? We don’t know.”

– David J. Tenenbaum

Even people who can’t distinguish the periodic table from a dining table know arsenic is poisonous, although few realize why. Arsenic is chemically akin to phosphorus, one of life’s essential elements. But it’s not identical, and when arsenic substitutes for phosphorus, it produce a toxic compound instead of a protein or chunk of DNA.

So we weren’t the only ones to be surprised by a study in today’s Science that identifies a bacterium that thrives on arsenic, at least in the lab, and incorporates this normally-poisonous element into proteins, fats and DNA.

Image: Wikipedia

A more typical reaction to arsenic comes from the elderly poisoning victims in the macabre comedy “Arsenic and Old Lace.” In that play and movie, two dotty spinsters spiked elderberry wine with arsenic, strychnine and cyanide for a freelance euthanasia project.

The new study is the first to show that it is possible to substitute for one of the elite elements (carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur) that were thought to be found in all life, says Ariel Anbar, a professor of earth and space exploration at Arizona State University. “No one has previously shown that arsenic can be substituted, and I am not aware that anyone has found a substitution for any of the six essential elements. And that’s why this is a big deal.”

Arsenic: It’s what’s for dinner

Felisa Wolfe-Simon, a former post-doctoral fellow with Anbar, gathered sediment and water from salty, alkaline, arsenic-rich Mono Lake in California and placed them in cultures intended to replicate Mono Lake water.

Images courtesy of Science/AAAS

These bacteria, viewed under an electron microscope, metabolized arsenic as if it were phosphorus. Mouseover to see the same strain of bacteria growing with phosphorus but without arsenic.

“Over time we made serial dilutions, one in 10, one in 10,” always including a strain of lake microbes, says Wolfe-Simon.

Wolfe-Simon, who is now at the NASA Astrobiology Institute and U.S. Geological Survey, says the dilutions removed “essentially all” of the phosphorus. In some samples, she jacked up the arsenic roughly 2,000 times above the concentration in Mono Lake, which gets its arsenic from rocks and is already about 20,000 times above the Environmental Protection Agency standard for arsenic in drinking water.

“This is a huge amount of arsenic,” Wolfe-Simon says. “It’s surprising that they could grow, even with phosphorus, in that condition.”

Although the bacteria died in the absence of phosphorus and arsenic, they survived if only arsenic was available. “The arsenic seems to be substituting for phosphorus,” says Wolfe-Simon. “We have identified arsenic in cellular structures that are consistent with where we would expect to see phosphorus.”

Photo: ©2010 Henry Bortman

Mono Lake, California, is salty, alkaline conditions, and toxic to many organisms. The lake is ideal for the study of extremophiles, microbes that live under bizarre temperature or chemistry.

Stepping out of line

This elemental swaperoo could operate more broadly, since the elements in each column of the periodic table have chemical similarities. If one neighbor of phosphorus can sustain life without phosphorus, could the elements below carbon, nitrogen or oxygen do the same?

Photo: ©2010 Henry Bortman

“This is not just about arsenic or Mono Lake,” says Wolfe-Simon. Life on Earth and the rest of the universe will be limited if it always requires six elements, but “If microbes can use arsenic as they can use phosphorus, that opens the door. What else can life do that is not yet known?”

In searching for life in the universe, NASA has focused on liquid water, another prerequisite for known life, but Anbar asserts that a search for the chemistry of life should stay broad. “Felisa’s results say we should think harder about which elements we should follow. We don’t want to be too influenced by the particular example of life on Earth. We want to push the boundaries.”

Call it “Arsenic in a new place.” Roll cameras!

With fanfare that even snared some attention outside scientific circles, the 10-year Census of Marine Life came to a conclusion Oct. 1. The headlines and self-congratulation were deserved: our “ocean planet” is predominantly covered with salt water, and the Census had strength in numbers: 2,700 scientists from more than 80 nations spent $650 million exploring life in salt water. Working in 25 groups, the scientists sifted and collated old data and performed new studies on 540 field expeditions.

The Census also crafted the ground-breaking Ocean Biogeographic Information System. This public database contains 30 million records on more than 100,000 marine species, derived from new studies and about 800 existing databases that were harmonized for easy digital access (or so we’re told; we confess we’ve not looked up our favorite lobster in the database).

Kiwa hirsuta, Ifremer, A. Fifis, 2006

South of Easter Island in the Pacific, Census explorers discovered the yeti crab, which became the first member of a new biological family, Kiwida (Kiwa was the mythological Polynesian goddess of shellfish). The yeti crab supposedly resembles the abominable snowman, the “yeti.”

The effort was monumental, but necessary, considering that roughly 71 percent of our planet is covered by ocean. For reasons of remoteness, expense, logistics and physics, ocean science is difficult and expensive, and as a result, we know a lot less about life in the oceans than on land.

And even on land, scientists cannot agree on the total number of multicellular species, let alone count the bacteria and other one-celled critters.

The effort to explore salty sections of the planet that began in 2000 has already boosted the number of known marine species from 230,000 to 250,000. About 5,000 more candidate species await analysis in jars and freezers around the world.

What is the big picture?

Educated guesstimates suggest that the oceans may hold 1 million multicellular species – four times the number that’s been cataloged. In total, since 2000, an average of 1650 new marine species have been named each year — proof that the age of biological discovery continues. That number includes about 150 species of fish.

Courtesy Patricia Miloslavich

Half of fish biodiversity in the Caribbean is located near venerable marine science stations (circled). “Very few samples come from the huge, deep-sea basin in the middle,” says Census scientist Patricia Miloslavich. “If you go to places where you have never been, you will find new species.”

Our view of marine biodiversity suffers from sampling bias – we find more species near scientific stations, and that is one error Census projects are trying to correct, says Patricia Miloslavich of Simon Bolivar University in Venezuela. Miloslavich, a co-senior scientist for the census and head of its Caribbean project, says biodiversity data for the Caribbean, “did not show the location of biodiversity so much as the location of marine scientific institutions. There are little hot spots around … the places where most research been carried out in the last 50 to 80 years.”

Because South America extends so far north and south, and fronts two major oceans, it posed a good test for the notion that biodiversity would peak in the tropics and taper off toward the poles. Miloslavich says Census data from South America refuted that conventional wisdom.

Near South America, at 40° to 50° south latitude, biodiversity is much higher in the Pacific than the Atlantic, probably due to the many biological niches in Chile’s convoluted coastline. Scientists traditionally expect to find more biodiversity in the tropics.

In the tropics, the expected high biodiversity did appear in the Pacific and the Atlantic, Miloslavich says. But the Pacific also showed a biodiversity hotspot between 40° to 50° south latitude. “The Chilean fjords are a very irregular coast, with a lot of biodiversity,” Miloslavich says, “but at the same latitude on the Atlantic side, off Argentina, biodiversity was low.”

No way can we summarize this huge effort to catalog and measure ocean life. Instead, we’ll encourage you to browse for yourself while we focus on new data about:

Canada’s coldest realm

The Census of Marine Life studied Canada’s Atlantic, Pacific and Arctic coasts, which by themselves account for 16 percent of the globe’s coasts, says Philippe Archambault, first author of the report on Canada’s “three oceans”.

The Census attempted to negate sampling bias, which had suggested that the Atlantic was more diverse than the enormous Arctic coast, which stretches more than 160,000 kilometers.

Colossendeis colossea, Mylène Bourque, Benthic Ecology Laboratory, Institut des sciences de la mer, Rimouski, Quebec.

This large sea spider, from the Canadian Arctic, feeds on corals and other organisms by sucking their contents through his enormous mouth, or proboscis, located at lower right. Although the sea spider has a small body, its vital organs, including gonads, are housed in its elegant legs.

On the Arctic coast, biodiversity counts covering just 53 square meters (“the size of three Canadian kitchens!” Archambault says) revealed 1,200 species (mainly animals longer than 1 millimeter). In comparison, studies of 170 square meters of the shorter Atlantic coast showed 1,300 species. We offered the conventional wisdom, that the Arctic is biologically boring. “This was not the case when we put out a similar sampling effort,” Archambault says.

The planetary warming that is melting the Arctic ice is already affecting sea life, Archambault adds. In areas that were normally covered with ice for most of the year, the summer melt allows a brief pulse of sunlight that energizes plants, starting a simple food chain in which animals graze the plants and drop to the sea floor, to be eaten by predators. But when the water remains ice-free for more time, Archambault says, small crustaceans called copepods in the water eat the grazers before they can reach the sea floor. “So you now have copepod feces going to the sea floor, and you don’t have the same animals living down below.”

Photo: Casey Debenham, University of Alaska Fairbanks

These subarctic sunflowers live in the shallow waters of Prince William Sound, Alaska; part of an Arctic that now seems unexpectedly rich in biodiversity.

The studies organized by the Census are documenting today’s conditions in the Arctic, so we can understand what happens as the climate changes. “The Arctic is almost the last pristine area on the planet,” Archambault says. “When the ice melts, there will be more shipping, more potential for oil spills, and yet we don’t have baseline information” to help track the anticipated changes. (This video shows biological exploration in the Arctic.)

The Canadian studies highlighted how biology is hobbled by a shortage of taxonomists — experts who can distinguish one species from another. “We are losing taxonomic expertise in Canada, and everywhere,” says Archambault. “We have much more technology for counting species, but this can only help us know how many species are there, it won’t tell us what they are doing.” He notes that the Census of Marine Life had to send 25 samples of polychaete worms, a common sea-bed resident, to Mexico for analysis, and one turned out to be an unknown species. “We cannot do this identification in Canada anymore,” says Archambault. “Taxonomy is not sexy enough!”

A lot of biology is at stake in the frozen realm, Archambault says, yet we don’t even know what’s living there. “Each time we send in equipment, in the Arctic, in the Pacific or the Atlantic, there is a big chance of finding something new.”

Tracking fish

Migrations always fascinate biologists, whether it’s the monarch butterfly winging thousands of miles between central Mexico and the American Midwest, or the Arctic tern, flying a round-trip of about 9,000 miles from the South Atlantic to Norway.

Whales migrate, turtles migrate, and so do fish like the salmon. Because tracking migrations, especially for smaller critters, is difficult, one Census project has laid strings of underwater microphones across rivers, straits and the continental shelf along British Columbia.

The strings can be used to track fish or other animals that carry tiny noisemakers.

On the continental shelf, receivers spaced 800 meters apart can detect 90 percent of the fish swimming past, says Jim Bolger, executive director of POST, the Pacific Ocean Shelf Tracking project. Because the network can identify individual animals, remote-control migration tracking becomes possible once the noisemakers are in place.

Scientists who use the network “are not only looking at where they go and how fast they traveling, but are identifying bottlenecks for survival, where fish fail to show up,” says Bolger, who also directs the Vancouver Aquarium. Such information can abet management measures designed to make life easier for many types of marine creatures.

2004 photo, POST

Acoustic units prepare for a swim in the Strait of Georgia, British Columbia, to prove that these arrays of microphones can track animals bearing distinctive noisemakers.

Salmon in the Northwest have been a focus of concern for many years — as their spawning rivers are dammed, fewer are returning to the ocean to mature. Fish tagging can be used to track salmon, if you can find the fish later on, but POST works much quicker, Bolger says. “We don’t have to wait four or five years to see how they survive; we can measure survival almost in real time.”

Bolger says salmon swim complex routes. A POST study of four salmon species in British Columbia found major variations in swimming speed and route.

A second study of young salmon in British Columbia linked survival to the timing of migration: young salmon that hit the ocean when plankton were blooming had 150 percent to 300 percent better survival.

This type of data could help conservation groups and hatcheries trying to restore salmon, but . “There is no one-size-fits-all strategy,” Bolger says. “Even within the same species, on the same river, we have tremendous complexity in how they swim and where they go. Some go north, others to the south. This could be a survival strategy; they don’t send all their progeny in one direction.”

Photo: POST

The new noisemakers are so small they can even be placed inside young salmon, before they start their migration down rivers and into the ocean.

Information from the acoustic array can also be melded with data on genetics and physiology, Bolger says. “We can see whether fish with high levels of stress hormone behave differently than those with low levels. Scientists can examine the blood chemistry and genetics when the tag is implanted,” and then correlate the data with their subsequent movement.

The magic of microbes

Perhaps the biggest single question about ocean life concerns microbes — bacteria, their primitive relatives called Archaea, and other single-celled organisms such as protists and ameba. Species are difficult to define in bacteria and Archaea, which is why scientists use “taxa” instead, but the numbers are daunting: the oceans could contain tens of millions of taxa, and the exploration has just begun.

“Small” does not mean insignificant: the approximately 10²⁹ microbes in the sea weigh one trillion (1,000,000,000,000) tons, and comprise an estimated 90 percent of life in the ocean, by weight. Not only are microbes critical to the food chain, but they also engineer many of the basic chemical reactions that move fundamental elements like carbon and nitrogen through the oceans.

Global Seafloor Biomass

Photo: Chih-Lin Wei and Gilbert T. Rowe

By measuring carbon, scientists estimated biomass, including creatures from bacteria to plants and the biggest animals, at the seafloor. Generally, the tropics seafloor is low in biomass compared to temperate and polar regions.

Scientists long ago gave up trying to distinguish microbes by growing them in culture, and now count them with genetic techniques nick-named “molecular bar-coding.” These methods evaluate similarities and difference in a specific section of the genes, then use the data to build an evolutionary tree. Bar-coding applies to all life, and is widely used to assess evolutionary relationships in higher organisms as well as bacteria.

Ten years ago, scientists using molecular bar-coding concluded that a single liter of ocean water might contain 3,000 types of microbe, says Mitch Sogin, of the Marine Biological Laboratory in Woods Hole, Massachusetts, and a leader of the International Census of Marine Microbes, “But what blew the doors off that estimate was a very deep molecular sampling effort in 2005 … which revealed that the number is at least an order of magnitude higher.”

Today, it’s estimated that a liter of seawater may have 30,000 to 40,000 types of microbes, Sogin says, “so if we take all 1,200 samples [from the microbial wing of the ocean census], we very conservatively estimate that they contain one-half million kinds of microbes.”

There are reasons to suspect that the actual number may be much higher, Sogin says, but even using this definition, “Every time we look at a new sample, we identify new taxa, and yet we have only sampled 1,200 liters, which is 1 in 10 ¹⁸ parts of the total ocean.”

when bacteria make rock

Loihi Seamount, courtesy Katrina Edwards

An iron-processing bacteria (bean-shaped object) forming iron-oxide needles.

Unfortunately, molecular bar-coding does not show what newfound microbes are eating, or how they affect their surroundings. At Loihi Seamount, a submarine volcano near Hawaii, marine census scientists have explored microbial iron-mongers. Katrina Edwards, a professor of marine and environmental biology at the University of Southern California, says, “At Loihi, we could dig our heels in to study a particular class of microbes that we think are pretty ubiquitous at the seafloor.”

These bacteria “play a very large role in iron oxidation and the deposition of enormous quantities of iron oxide,” which eventually becomes rock, Edwards says. “If we can understand how these rocks are formed in the modern world, and can understand the physiology, genome and ecology of the bacteria, we can interpret” old rocks found in other locations.

Microbes: Why so many?

Linda Amaral-Zettler, a microbial ecologist and program manager for the International Census of Marine Microbes, has a question: “Why are there so many different kinds of microbes living in this environment, that at first blush, seems uniform?”

One answer comes from the billions of years of every that have produced so many life patterns and genetics. But another answer, she says, may be “that there are a lot more niches or places to live than we have appreciated. Somehow these organisms are sensing these micro-habitats and are able to survive despite the competition.”

Photo: Enric Sala

Coral reefs serve as the perfect haven for co-habitation between microbes and sharks!

Microbes can be extremely specialized, and scientists have found that the most common microbes living on one species of sponge are not among the most common on another sponge, says Amaral-Zettler, who works at the Marine Biological Laboratory in Massachusetts. “Animals, plants and other multicellular organisms are likely to be havens for microbes, and we have barely sampled them. Essentially any surface that is out in the ocean can be colonized.”

Even trash?

Apparently. “All the signs say that even garbage is something the microbes are taking advantage of; likely they are degrading it and using it for an energy source,” says Amaral-Zettler, who is starting to examine microbes on plastic in the sea in collaboration with the Sea Education Association.

Here’s another question: Why are most of the microbial taxa discovered by the Census so rare? Having a few dominant species and plenty of rare ones is often characteristic “of an environment that is impacted in some way” Amaral-Zettler says, “but it seems to be a repeating pattern in the sea; we see it everywhere we look. We are struggling to understand the ecological consequences of having so many rare microbial species.”

Photo: Karen Gowlett-Holmes

Plant or animal? The leafy seadragon confuses predators by mimicking drifting seaweed.

This business of the “rare biosphere” fascinates Sogin, a specialist in microbial evolution, who suggests that the many rare species:

Should we worry?

If there is an uncountable diversity of microbes in the sea, should we ignore the conventional cavil about biodiversity — that too many species will go extinct? Why worry if the sea has more microbes than we can count?

Not so fast, says Sogin, who warns that we are changing the sea in ways that could harm microbes and boomerang back to harm us.

It’s not just that all multicellular organisms evolved from single-celled creatures, Sogin says. Life can survive happily without people, but life relies on microbes. “During 80 percent of the history of life, microbes transformed the planet into something that was habitable by multicellular organisms. They created an environment we can live in. This process continues, because so many microbes in the ocean carry out processes that are essential to our survival.”

People, after all, are dumping garbage, sewage and fertilizer into the ocean, warming it with greenhouse gases, and as the ocean absorbs our carbon dioxide, it becomes more acidic.

Since we don’t understand how the ocean works, we cannot predict the consequences of a major change in the environment.

However, Sogin says, “We know from lab work in microbiology that tremendous shifts can occur in population structures and lead to an imbalance and then a further change in environmental conditions. What will happen with continued ocean acidification or a dramatic shift in seawater temperature? We are going to have a disruption of the microbial community. Is that good or bad? We don’t know.”

Green background, inside circle two separate yellow lines with leaf-like growths on both.

Rivalries in nature regularly produce clashing outcomes, and a recent study proved that this can also be the case for some bacteria. Colonies of the bacterium Paenibacillus dendritiformis have been shown to produce a lethal chemical to keep their competition at a distance.

The study forced two colonies of bacteria into the same space, and the result was the formation of a distinct “no-mans land” between them. A protein was identified in the space, and subsequent testing showed it had a lethal effect on the bacteria, causing instinctive movement away from the protein.

“It supports the notion that each colony is a superorganism, a multicellular organism with it’s own identity,” said Eshel Ben-Jacob, an adjunct senior scientist at UC San Diego’s Center for Theoretical Biological Physics.  In this work, Ben-Jacobs collaborated with Avraham Be’er of the University of Texas, Austin, and others.

Eshel Ben-Jacob

Salmonella, which causes what we sometimes call “food poisoning,” can live more than 400 days in soil. And when dried on a laboratory slide, salmonella survived for almost three years, says Barak, who studies salmonella contamination on leafy greens, a growing cause of gastrointestinal illness.

However, E. coli, another resident of the intestinal tract, tends to die sooner in the environment.

Many bacteria form spores — tough, durable “seeds” that can withstand extreme abuse. Spores of respiratory anthrax, like that used in the 2001 bio-terrorism attacks, can survive for many years.

Environmental also conditions affect survival, Barak adds. For example, the bacterium that causes tuberculosis can be killed by full-spectrum lights, which contain ultraviolet light. In contrast, bacteria that live on plants have pigments that block ultraviolet rays, allowing them to thrive in sunlight.

Finally, bacteria can form communities called “biofilms” that greatly increase their ability to survive adverse conditions. Biofilms can be a major problem on catheters and other medical devices, because measures that kill the outer layers of bacteria may not affect those located deeper inside the biofilm.

At least that’s the implication of a new study from Kansas State University that indicates dog owners that kiss their pets are no more likely to be infected with dangerous strains of bacteria than those who don’t. The real risk, say the researches, is to the dog.

A close examination of dog and owner poop — the duty of a graduate student, no doubt — revealed that owners’ intestinal tracts contained far more antibiotic-resistant bacteria than did the dogs’. Don’t hold back the love though. Swapping slobber with your dog isn’t too dangerous for them. In fact, the article’s authors suggest bonding with pets through kisses and food sharing underlies many of the psychological benefits of pet ownership, for both of you. It turns out the greatest danger is in allowing your dog to lick your grubby paws.

“Halt! Wash your hands.” That’s a good human.

Photo: ktylerconk