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The Hidden Biodiversity of the Ocean Realm

Genetic tools reveal new species and insights into why diversity matters

The Hidden Biodiversity of the Ocean Realm

To get a sense of how marine biology has evolved in the last century, consider USC’s Allan Hancock Foundation building. From its construction in the 1930s until the last decade, wooden shelves holding hundreds upon hundreds of glass specimen jars filled much of the red-brick building’s core. The collection revealed the great diversity of form, color, geographies and habitats of ocean life.

Today, the jars are gone. The rooms have been gutted and remodeled. The long shelves have given way to laboratory benches, gene amplifying machines, centrifuges, computers and other equipment of a modern molecular lab. These are the tools driving a new era of discovery, allowing scientists to describe the biological diversity of the sea in greater detail than ever before.

“A huge amount of biological diversity has been totally undetectable without genetic tools,” said marine microbiologist Jed Fuhrman, the McCulloch-Crosby Chair in Marine Biology in USC College and a member of the USC Wrigley Institute for Environmental Studies. “That’s been especially true for microbes, the most abundant kind of life on Earth.”

Using state-of-the-art genetic tools, Fuhrman and his colleagues have begun to reveal the heretofore hidden diversity among marine plankton and microbes, as well as the unexpected ways these microscopic organisms make a living. Others are exploring another frontier of biological diversity — the genetic diversity of individuals within a species — in studies of marlin, oysters and other larger creatures.

“Biodiversity runs the natural world,” Fuhrman said. “Human beings don’t exist in a vacuum. Everything’s connected. So if we want to understand our world, we have to understand all of the other organisms in it.”

To many, biodiversity refers simply to the number of different species on Earth. “Biologists think of biodiversity more broadly, not only as the diversity of organisms, but also of their functions and abilities, their appearances, their roles in the system,” Fuhrman said.

Geneticist Dennis Hedgecock believes biodiversity contributes to a healthy environment, but says hard evidence supporting that belief has only just started to emerge. He points to a 2006 study in the journal Science showing that both species and genetic biodiversity increase the productivity and stability of the ocean ecosystem, making it more resilient to major disturbances, both natural and human.

“This is some of the first evidence showing that biodiversity matters, at least for large species,” said Hedgecock, the Paxson H. Offield Professor of Fisheries Ecology in the College.


Using genetics, Jed Fuhrman has identified hundreds of new species of marine bacteria and provided new insights into global microbial diversity.
Photo credit: Phil Channing
Click here for high-resolution photo.

The report also found that the ecological impacts of overfishing are lessened in areas with high biodiversity. The study concludes that, although the ocean’s biodiversity is dropping fast, and bringing with it many negative effects on water quality and the fish stocks humans rely on for food, the trend can still be reversed.

Hedgecock’s studies of genetic diversity in oysters, sea bass and salmon have helped to promote more thoughtful management of commercial and recreational fisheries, as well as conservation breeding programs. He and Donal Manahan, professor of biological sciences, study oysters and recently published a paper pinpointing the genes that gives a breed of hybrid oysters an advantage over others. “We’re studying which genes allow one individual to successfully reproduce or grow larger than others in the same population,” Hedgecock said.

Suzanne Edmands, an associate professor of biological sciences, also investigates genetic variation in marine creatures. Her aim is to better understand the mechanisms by which new species form, as well as the implications of genetic biodiversity for fishery management and conservation efforts.

“Diversity within populations allows adaptation to new circumstances or stresses, like infection or the increasing sea temperatures associated with global warming,” said Edmands.

In one project, Edmands and marine biology doctoral student Catherine Purcell are looking at the genetics of striped marlin populations in the Pacific. Their results show surprisingly large genetic differences in the absence of obvious geographic barriers. For example, they find a genetic break between Southern California and Mexico marlin populations, which both spend time in the fall near the tip of Baja California. Meanwhile, populations in Japan and Hawaii, though separated by thousands of miles, show no genetic differences between each other or the Southern California group.

Their work may have direct implications for the management of this species. Currently, the striped marlin fishery is classified and managed as one stock extending throughout the Pacific. If this is not the case, as Edmands and Purcell’s results suggest, the discrete populations are more susceptible to overfishing. Managing the fish as separate stocks will protect the genetic biodiversity of the species as a whole, Edmands said.

“Genetic diversity is key to a species’ ability to respond to evolutionary challenges,” said Edmands. “And in the big picture, biological diversity — and the conservation of it — is important for many utilitarian reasons. Many pharmaceuticals begin as compounds isolated from ocean species, for example. But there’s a moral aspect to this, too. These species have been around for eons. What right do we have to extinguish any of them before their time?”

Considering the essential role marine microbes play in the ocean’s health — they form the base of the entire ocean food web, recycle nutrients and help balance the planet’s atmosphere — scientists like Fuhrman think that maintaining microbial diversity may be just as important as that of better-known marine life. Yet, understanding of microbial diversity lags decades behind what’s known about larger land and sea organisms, said Fuhrman.

“We’re still largely in the exploratory, discovery phase where we’re just trying to see what’s out there,” said Fuhrman, whose team has developed a number of new molecular identification techniques for bacteria, viruses and a distinct group of ancient microbes called Archaea.

Microbes make up some 90 percent of the biomass in the sea. Despite their abundance, the microbes’ small size, non-descript features and the fact that most will not grow in dishes in the lab have meant that the majority of species have eluded efforts to identify them.

In the last five years, however, Fuhrman and microbial ecologist David Caron have identified hundreds of new species by examining their genetic makeup. The work is part of the USC Microbial Observatory project, a National Science Foundation-funded study of microbial diversity and its fluctuations over time.

“It’s a major deal when someone finds a new species of fish, or even a new kind of worm. Now we are doing that every day. It’s just astounding,” said Caron, who studies protists, a group of single-celled microbes that includes marine algae and zooplankton called the protozoa. “Now, instead of just looking at these microbes under microscopes, we’re looking at genes to identify species.”

Adding to their interest is that they have “no clue” about many of these new microbes’ morphology, physiology or ecological role, said Caron, a professor of biological sciences in the College.

Their project piggybacked on the USC Wrigley Institute’s San Pedro Ocean Time Series, an ongoing study led by Anthony Michaels, professor of biological sciences and director of the Wrigley Institute. The Time Series allows institute scientists to study long-term changes in environmental factors such as temperature, salinity, nutrient concentrations and ocean ecology at a spot in the San Pedro Channel, about halfway between the coast and Catalina Island.

Fuhrman’s team made a major discovery last year, when they found annual repeating patterns in the kinds and abundance of microbes at the site. They were able to relate these patterns to changing environmental factors.

Who’s there, Fuhrman said, “doesn’t change a huge amount from month to month. But two, three months later, the community has changed. And by six months, it’s a very different group. But by 12 months, the [original microbe groups] are back.”

That pattern, he said, supports the idea that microbes, like animals and plants, each have a specific biological niche.

“This conclusion shouldn’t be that earthshaking, but it actually is for some people,” said Fuhrman, who published the findings in the Proceedings of the National Academy of Sciences. “Microbes have their own, unique place in the world. It’s not the ‘if you lose one, another one’s fine, a dime-a-dozen’ kind of thing. They all have their own job. You wouldn’t see a repeating pattern if any one could do the job. It would just be random and change unpredictably.”

From Caron’s point of view, discovering the diversity of microbial life — the who — is one of the two most pressing questions in his field. The other is the where: Are some marine microbes found only in specific locales, or does the open nature of the oceans give most microbes a global reach, what he calls “cosmopolitan” presence? His work suggests it may be a mix. “I think that some organisms will have a discrete distribution, but we’ve already found that quite a few species do have a global distribution.”

Caron expects that, even for cosmopolitan species, their relative abundance will differ from place to place, depending on specific local conditions. “There’s usually a large suite of organisms at low abundance that can backfill (become more abundant) when and if environmental conditions change.”

In that way, the functions of the ecosystem can be maintained, even if the individual species shift. Caron likens it to a soccer game, with players substituting in and out. The individual players may change, yet the game goes on.

That’s why, Caron said, maintaining biodiversity — even of tiny microbes — is so important to marine health. “Microbes do the majority of the biological work in the oceans. They produce most of the energy and organic matter, and they decompose all of the dead organic matter. They support a wonderful and charismatic macrofauna, from shrimp to dolphins. What microbes do is fundamental to the way the oceans, and our entire planet, works.”

College research efforts in these crucial areas are set to expand. In fall 2006, seven new marine scientists joined the College faculty, recruited as part of an innovative “cluster hire” in environmental genomics and biogeochemistry coordinated by Michaels of the Wrigley Institute.

Among the new faculty are John Heidelberg, an associate professor of biological sciences, and his wife and colleague Karla Heidelberg, an assistant professor of biological sciences, who now live at the Wrigley Marine Science Center on Catalina Island with their two children. Both scientists have played key roles in large-scale, genomic studies of microbial diversity.

In March, the Heidelbergs and geobiologist Ken Nealson, the Wrigley Chair in Environmental Studies in the College, were among some two dozen co-authors of a report on the largest-ever global census of marine microbial life. The genomic study, published in the Public Library of Science Biology, revealed thousands of new and astonishingly diverse species. The team also described millions of new genes and proteins, some of which may prove useful in the creation of new antibiotics and alternative energy sources and in furthering our understanding of the role of microbes in global climate change.

New hire Katrina Edwards also studies microbial diversity, but in a largely unknown terrain — the rock below the sea floor. Since 2003, Edwards, an associate professor of biological sciences who was among the first anywhere to earn an interdisciplinary doctorate in geobiology, has been preparing to probe the biosphere scientists believe thrives underneath the ocean. In 2008, she will begin drilling to depths of 500 meters at a site in the tropical Atlantic Ocean.

Considering that soil holds the most diverse group of microbes on land, most believe that she will find a mother lode of new species in the sea subfloor. “No one’s ever done this before, so we really don’t know,” Edwards said.

Describing the extent of microbial diversity is not the only goal of these researchers. Most also want to apply what they learn to solve urgent environmental problems facing the oceans, and there are immediate practical applications too.

“So many of these microbial systems are incredibly important all over the planet,” said Michaels, listing pollution, bioremediation, climate change, corrosion, sewage treatment and biofuels as some areas where research on microbes may prove pivotal.

For example, Caron’s new insights into the workings of normal marine communities will aid his research monitoring harmful algal blooms off the California coast. Algal blooms, which can prove fatal to marine life and cause millions of dollars in economic damage, begin when one species becomes overly dominant. Caron hopes to understand what factors tip the ecological balance.

Fuhrman’s genetic tests are already being used to test coastal waters for the presence of potentially harmful viruses — including enteroviruses and hepatitis viruses — and other human contaminants. “People have asked me for a long time, ‘Is it safe to go into the water?’

“If we understand how the natural ecology works, then we’ll have a better idea of what’s happening with these pathogens — in terms of how long they’ll survive in the water, what conditions promote them and what conditions inhibit them,” Fuhrman said.

College marine scientists still do much of their work at the old Hancock building at the center of campus — as well as aboard sea-going research vessels and in the labs at the Wrigley Institute’s island campus. In many ways, they are asking the same kinds of questions about biodiversity and the marine world posed by earlier faculty. But now, they’ve got better tools — and an ocean that needs help more urgently than ever before.