The Inner Lives of Sponges

**Zeno Swijtink** · 05-25-2008 05:12 PM

Science 23 May 2008:
Vol. 320. no. 5879, pp. 1028 - 1030
NEWS
The Inner Lives of Sponges
Gretchen Vogel

Symbiotic ties, bioactive compounds, and mysterious distributions of bacteria characterize these ancient invertebrates

A spongeful of bacteria is the last thing a dishwasher wants to think about. But for Jörn Piel, the more microbes he finds in a sponge, the better. Not a synthetic one, of course, but those that adorn tropical reefs and populate the ocean bottom.

One of evolution's more ancient animals, sponges at first glance seem quite simple--little more than loose consortiums of semiautonomous cells, stuck in one place filtering food from the water column. But a closer look reveals a surprising twist. "With many species, under the microscope you see almost exclusively bacteria" among the cells, says Piel, an organic chemist at the University of Bonn in Germany. Just as microbial ecologists are demonstrating the extent and importance of microbes in ecosystems as diverse as guts and glaciers (see p. 1046), Piel and others are slowly uncovering a hidden microbial world inside sponges.

It's a difficult job, as almost none of the sponges' inhabitants grow in the lab. But through genetic studies, researchers are revealing the rich diversity and unusual distribution of these microbes. Some investigators are pinning down the roles bacteria play in sponge biology and ecology. The microbes are teaching scientists about evolution, symbiosis, and the mind-boggling variety of life on our planet. "It never ceases to amaze me that a sponge, an organism that just sits there and pumps bucketfuls of water through its canals," has such a rich and varied, yet highly specific, inner life, says marine microbiologist Michael Taylor of the University of Auckland in New Zealand. The research also has a practical side: Piel and others are betting that sponge-dwelling bacteria could be the source of potentially valuable compounds for treating cancer, malaria, and other human diseases.

Sharper focus

The first hint of the sponges' pervasive inhabitants came in the 1960s and '70s, as new equipment allowed longer and deeper dives that gave researchers their first up-close look at the diversity of life on the ocean bottom. It quickly became clear that something else was living among the sponges' cells. Looking at the first electron microscope images of sponge tissue, marine biologist Jean Vacelet and his colleagues at the University of Marseille spotted what looked like a half-dozen different types of bacteria. Other researchers "took sponges and squeezed them out over culture plates to see what would grow," recalls marine ecologist Robert Thacker of the University of Alabama, Birmingham, but it was difficult to follow up on the finds. At most, 5% of sponge-dwelling species have thrived in the lab, says microbial ecologist Ute Hentschel of the University of Würzburg in Germany. And the sponges themselves "are incredibly hard to keep alive," Thacker says.

Therefore, Hentschel, Thacker, and others have been using indirect methods to piece together a picture of this reclusive community. Most of the evidence comes from studies of the gene for 16S ribosomal RNA (rRNA), a piece of the genome that scientists use to identify unknown microbes in the environment. Differences in this gene can serve as a useful measure of the kinship between two species.

These genetic studies uncovered a distinctive and extensive community, identifying more than 100 species of microbes that are found in sponges but not in the surrounding water. This distribution indicates that these bugs are long-term residents rather than passersby. An individual sponge might host dozens of different species, and overall, the molecular analyses have found an impressive variety: 14 bacterial phyla, two phyla of archaea, and several types of eukaryotic microbes.

Such diversity initially suggested multiple, independent acquisitions of microbial symbionts. But evidence is building that sponges of different types and in different oceans host strikingly similar microbial communities. Hentschel and her colleagues showed in 2002 that sponges from the coast of Japan, the Red Sea, the Mediterranean, and the Republic of Palau in the South Pacific contained microbes that are more closely related to each other than to the microbes in the seawater from which the sponges were harvested. "It's astounding," says Susanne Schmitt, a postdoc in Hentschel's lab. The different sponges the scientists sampled diverged millions of years ago, she says, but they are home to very similar, and very complex, microbial communities. In 2007, Taylor and his colleagues found the same result when they analyzed the entire database of 16S rRNA sequences available from sponge-dwelling microbes collected from all over the world--nearly 2000 sequences in all.

But Taylor, Hentschel, and their colleagues are still trying to work out what the results mean. Microbes might have colonized a sponge early in the group's evolutionary history and acquired characteristics that enabled them to live in sponges full-time, Taylor proposes. Those sponge-loving microbes could have then spread to other sponges--and other oceans. And such a scenario could explain what may be a new phylum called Poribacteria, after Porifera, Latin for "sponge." Poribacteria have been found throughout the world, albeit exclusively in sponges.

Fruitful partnership

As with much of microbial ecology, the sponge specialists have been focused primarily on taking a census. "I go in just trying to figure out what's there--what people did collecting insects in the forest 100 years ago," Taylor explains. But he and his colleagues are now starting to take the next step, because census data can't tell researchers what each side gets out of the relationship. Ecologists want to know if the microbes and their hosts are obligate symbionts, unable to survive without each other, or whether the microbes are tolerated but dispensable guests, says Michael Wagner, a microbial ecologist at the University of Vienna in Austria: "If we want to understand these communities, we have to know the function each member plays."

Yet even after decades of study, scientists are still not exactly sure what sponges and their microbes are doing for each other. Living in nutrient-poor but sunlit waters in the lagoons of the Republic of Palau, sponges of the family Dysideidae are home to blue-green algae that probably provide their hosts with energy and carbon. The sheer mass of the microbes may help support the meter-high giant barrel sponge Xestospongia muta, in which bacteria can sometimes make up 40% of a sponge's volume. Microorganisms may even help defend their hosts against disease-causing bacteria.

But those are educated guesses rather than proven observations. "And there are a whole lot of other things that are going on that we just don't know about," says molecular ecologist Russell Hill of the University of Maryland Biotechnology Institute in Baltimore.

To try to get a picture of the daily goings-on inside a sponge, Wagner and his colleagues are catching sponge microbes in the act of "eating." The researchers have just started experiments on several species of sponges that host Poribacteria. No Poribacteria have ever been cultured in the lab, but the scientists are able to keep the host sponges alive in aquaria, at least for a short time. They use a technique that allows them to observe the metabolic activity of individual microbes and sponge cells. They expose the sponge to fluorescently labeled rRNA markers, which lets them know what species they are dealing with, and to radioactively labeled "food"--amino acids, bicarbonate, and other molecules. They then watch which cells take up the labeled morsels and follow how the morsels are processed, including whether the sponge consumes compounds excreted by the microbes. "We're asking not only 'Who are you?' but also 'What are you eating?' " he says.

Whatever their function, the microbes seem important enough for sponges to pass on to future generations. In the female sponge, nurse cells, which provide the "yolk" for developing eggs, also ferry blue-green algae from the sponge's outer layers to the developing oocytes located deeper in the sponge matrix. In 2005, Kayley Usher and her colleagues at the University of Western Australia in Perth even found blue-green algae in the sperm of the sponge Chondrilla australiensis. A year later, Julie Enticknap, a postdoctoral fellow in Hill's lab, was able to culture a sponge-dwelling alphaproteobacterium from the larvae of a sponge collected off the coast of Florida, another indication of possible parent-to-offspring transmission.

But that study highlights what may be the most baffling mystery in sponge microbiology. Usually when symbionts are passed from parent to offspring, the partners undergo what is called cospeciation, and the microbes develop a unique genetic signature and become confined to that particular host. "But that doesn't happen here," says Hentschel. The bacteria in the larvae proved closely related to those cultured from unrelated sponges growing in Jamaica, Indonesia, and the Chesapeake Bay in the United States. The best explanation for the broad distribution of this bacterium--and for many other species found across the globe--she says, is that sponges acquire their resident bacteria both from their parents and from the environment.

To date, no sponge-specific microbe has turned up in seawater, but scientists have a distinct disadvantage when it comes to sampling. Although a 1-kilogram sponge can filter thousands of liters of seawater a day, Hills says that "if we are lucky, we filter 200 liters," so the chances of finding an uncommon microbe, such as the larvae's alphaproteobacterium, are small.

If sponges are taking microbes in from the surrounding environment, they need to be able to tell friend from foe from food. And the microbes need a way to protect themselves against accidental or intentional rebuff by their hosts. Electron microscope images reveal that most sponge-dwelling bacteria have either thickened cell walls or slime capsules that might prevent the sponge cells from digesting them. Once established, these resident microbes, or the sponge itself, seem to produce chemicals that discourage interlopers. Several antibiotic compounds isolated from sponges efficiently kill bacteria found in the water column but do not affect sponge-dwelling organisms.

Sea-based drugs

Those antibiotic compounds are driving at least some of the interest in sponges. For bio-prospectors looking for potential new drugs from the sea, "sponges are one of the best sources of bioactive compounds," says Hill. The chemical from which the antiretroviral drug AZT was derived was first found in a Caribbean sponge. In the lab, other compounds from sponges kill cancer cells and malaria parasites.

AIDS, cancer, and malaria are not the sponge's concern, but a powerful chemical defense arsenal is, points out microbial ecologist Julie Olson of the University of Alabama, Tuscaloosa: "Sponges can't evade predators, and if something blocks their [water-filtering] passages, it's a death sentence." To protect against unfriendly microbes, a successful sponge probably needs a range of chemical weapons, she says.

Initially, marine biochemists using the "grind and find" approach assumed that most of those chemicals came from the sponge itself. But as the diversity of the sponges' residents became clear, many began to suspect that at least some of the compounds might come from the lodgers rather than the hosts. The quest to come up with enough of a bioactive compound for clinical testing is proving that these suspicions are well-founded.

To date, few sea-based drugs have made it to the clinic. "Supply is the primary reason there is no blockbuster so far," says Piel. It's been almost impossible to purify a compound in quantities large enough for animal and human testing, and the chemical structures are often too complex for large-scale chemical synthesis. Halichondrin B, for example, is a powerful antitumor compound in lab tests. But scientists calculated that clinical trials would require at least 10 grams of the substance. The best producer, a New Zealand sponge group called Lissodendoryx, yielded 300 milligrams per metric ton of sponges. Because the entire population of Lissodendoryx was estimated at 280 metric tons, it was clear that harvesting from the wild was not sustainable, Piel says.

Piel is trying to get around that problem. His lab is fishing for genes involved in making promising compounds. The goal is to find the set of genes that codes for the potential drug's synthesis, and if the original host won't grow in the lab, to transfer those genes to a microbe that is happy in an artificial environment. The designer microbe would then pump out enough of the drug for testing.

The technique is pointing to bacteria as the source of many of the compounds. "So far, every time we've found a gene cluster, we found typical bacterial genes" nearby, Piel says. In 2004, the group reported that they had pinned down the genes responsible for producing compounds called polyketides in a dark-red sponge called Theonella swinhoei that lives in coral reefs. (In the lab, polyketides can kill tumor cells, and several types are in clinical trials.)

Based on the genes' similarity to known genes, Piel and his colleagues concluded that the genes most likely come from a still-uncultured microbe. What's odd, however, is that these genes are quite similar to polyketide genes belonging to a bacterium that lives in the guts of beetles. The researchers are currently working to transfer the sponge microbe's genes to a lab-friendly host.

Hill and his group have focused on trying to harness the original bacteria producers. "Part of the problem is that people have in their heads that all symbionts are difficult to grow," Hill says. But patience and hard work can pay off. "Sometimes we get new colonies after months of incubation."

In recent work, Hill's lab has homed in on the source of a particularly promising compound called manzamine A. In lab tests, manzamines kill malaria parasites more efficiently than either chloroquine or artemisinin, two of the leading antimalarial drugs. The compound was first identified in a sponge collected off the coast of Okinawa, but related compounds have since turned up in dozens of unrelated sponge species all over the world--a strong hint, Hill says, that they are produced by a microbe shared by all these species.

In as-yet-unpublished work, his group has isolated the bacterium that produces manzamine A. The microbe should give scientists their first steady supply of the compound, allowing them to make and test new derivatives, Hill says. Such studies led to the eventual development of AZT, Hill points out. And he is hoping sponges--or at least their microbes--will again lend a hand in the fight against deadly disease.