SCIENTIST STUDY GENETIC DIVERSITY IN OCEAN MICROBES

FROM:  NATIONAL SCIENCE FOUNDATION
Octillions of microbes in the seas: Ocean microbes show incredible genetic diversity

In a few drops of seawater, one species, hundreds of subpopulations
The smallest, most abundant marine microbe, Prochlorococcus, is a photosynthetic bacterial species essential to the marine ecosystem.

It's estimated that billions of the single-celled creatures live in the oceans, forming the center of the marine food web.

They occupy a range of ecological niches based on temperature, light, water chemistry and interactions with other species.

But the diversity within this single species remains a puzzle.

To probe this question, scientists at the Massachusetts Institute of Technology (MIT) recently performed a cell-by-cell genomic analysis of a wild population of Prochlorococcus living in a milliliter of ocean water--less than a quarter of a teaspoon--and found hundreds of distinct genetic subpopulations.

Each subpopulation in those few drops of water is characterized by a set of core gene alleles linked to a few associated flexible genes--a combination the scientists call the "genomic backbone."

This backbone gives the subpopulation a finely tuned ability to fill a particular ecological niche.

Diversity also exists within backbone subpopulations; most individual cells in the samples carried at least one set of flexible genes not found in any other cell in its subpopulation.

A report on the research by Sallie Chisholm and Nadav Kashtan at MIT, along with co-authors, appears in this week's issue of the journal Science.

The National Science Foundation (NSF), through its Divisions of Environmental Biology and Ocean Sciences, supported the research.

"In this extraordinary finding on the power of natural selection, the scientists have discovered a mosaic of genetically distinct populations of one of the most abundant organisms on Earth," says George Gilchrist, program director in NSF's Division of Environmental Biology.

"In spite of the constant mixing of the oceans," Gilchrist says, "variations in light, temperature and chemistry create unique habitats that evolution has filled with an enormous diversity of populations over millions of years."

Adds David Garrison, program director in NSF's Division of Ocean Sciences, "The results will change the way marine ecologists think about how planktonic microbes and, in turn, planktonic communities may respond to climate and environmental change."

The scientists estimate that the subpopulations diverged at least a few million years ago.

The backbone is an older, more slowly evolving, component of the genome, while the flexible genes reside in areas of the genome where gene exchange is relatively frequent, facilitating more rapid evolution.

The study also revealed that the relative abundance of the backbone subpopulations changes with the seasons at the study site near Bermuda, adding strength to the argument that each subpopulation is finely tuned for optimal growth under different conditions.

"The sheer enormity of diversity that must be in the octillion Prochlorococcus cells living in the seas is daunting to consider," Chisholm says. "It creates a robust and stable population in the face of environmental instability."

Ocean turbulence also plays a role in the evolution and diversity of Prochlorococcus.

A fluid mechanics model predicts that in typical ocean flow, just-divided daughter cells drift rapidly, placing them centimeters apart from one another in minutes, tens of meters apart in an hour, and kilometers apart in a week's time.

"The interesting question is, 'Why does such a diverse set of subpopulations exist?'" Kashtan says.

"The huge population size of Prochlorococcus suggests that this remarkable diversity and the way it is organized is not random, but is a masterpiece product of natural selection."

Chisholm and Kashtan say the evolutionary and ecological distinction among the subpopulations is probably common in other wild, free-living (not attached to particles or other organisms) bacteria species with large populations and highly mixed habitats.

Other co-authors of the paper are Sara Roggensack, Sébastien Rodrigue, Jessie Thompson, Steven Biller, Allison Coe, Huiming Ding, Roman Stocker and Michael Follows of MIT; Pekka Marttinen of the Helsinki Institute for Information Technology; Rex Malmstrom of the U.S. Department of Energy Joint Genome Institute and Ramunas Stepanauskas of the Bigelow Laboratory for Ocean Sciences.

The NSF Center for Microbial Oceanography, U.S. Department of Energy Genomics Science Program and the Gordon and Betty Moore Foundation Marine Microbiology Initiative also supported the work.

-NSF-

NSF: GAME OF HEARTS, QUEEN OF SPADES AND A NEW EVOLUTIONARY THEORY

FROM:  NATIONAL SCIENCE FOUNDATION
Queen of Spades Key to New Evolutionary Hypothesis 
May 10, 2012
Sleight of hand is a trait that belongs mainly to humans.
Or so scientists thought.

Studies of common, microscopic ocean plankton named Prochlorococcus show that humans aren't the only ones who can play a mean game of cards.

Their method lurks in the Black Queen Hypothesis, as it's called, after the Queen of Spades in the card game Hearts.

Scientists Jeffrey Morris and Richard Lenski of Michigan State University and the BEACON Center for the Study of Evolution in Action, and Erik Zinser of the University of Tennessee, Knoxville, knew that smaller genomes were the norm in symbiotic microbes--those that have reciprocally beneficial relationships--but wondered how non-symbionts got away with cutting out functions it appeared they needed.

These non-symbiotic microbes, the researchers found, may be getting others to do the hard work of living for them.

The biologists published their results in a recent issue of the journal mBio, in a paper titled: "The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss."

"Black Queen" sets forth the notion that eliminating a necessary function confers an evolutionary advantage--as long as your neighbors continue to do the work. "It would make sense for a microbe to 'want' to lose a gene that's a burden," says Morris, "and get someone else to pick it up."

In the game of Hearts, the winning strategy involves avoiding the Queen of Spades.
"A microbe stuck carrying the load for another is, in effect, holding the Queen of Spades," Morris says. "But the Queen of Spades is a card that, while a drag, is necessary--whether in the hand or in the sea. If everyone threw out the Queen of Spades, it would be 'game over.' The whole community would suffer."

To test the Black Queen Hypothesis, the researchers applied it to a genus of microbes that has been the source of scientific confusion. Prochlorococcus, one of the most common groups of plankton in the open ocean, has a much smaller genome than biologists would expect in free-living bacteria.

How has Prochlorococcus been so successful in colonizing the sea while jettisoning seemingly important genes, including the gene for catalase-peroxidase, which lets the microbes neutralize hydrogen peroxide, a compound that can damage or kill cells?
Prochlorococcus, it turns out, relies on other microorganisms to remove hydrogen peroxide from the environment, says Zinser, "allowing it to dump its responsibilities on the unlucky card-holders floating around nearby."

It's a clear instance, Zinser says, of one species making out like a bandit while letting other members of the community carry the load.

The Black Queen Hypothesis offers a new way of looking at complex, linked communities of microbes, says Lenski.

"People often think about evolution as leading to more and more complex organisms, and that's often, but not always, the case," he says. "Sometimes organisms evolve to become simpler if that saves time or energy."

Under the Black Queen Hypothesis, these simpler organisms take advantage of "helpers" that perform essential functions. In that sense, beneficiaries are "cheaters" that exploit what might be called a public service.

Sometimes they contribute in other ways. Prochlorococcus, which benefits from the peroxide clean-up performed by other microbes, contributes energy through photosynthesis that supports the larger community.

The Black Queen Hypothesis describes an evolutionary process that may include cheating, but in other ecological contexts, may result in neutral or positive interactions between species.

Take Shooting the Moon, an alternate route to victory in Hearts. This risky move requires a player to capture all the point-scoring cards, including the Queen of Spades, the opposite of the usual strategy of minimizing one's points.

Shooting the Moon may be an analog to the Black Queen Hypothesis. Might a species, having become a helper for one function, therefore be more likely to become a helper for other, unrelated functions?

"Such an outcome would involve evolution toward a niche with high resource requirements," write the scientists in their paper, "but with the advantage of high 'job security' for the helper owing to the dependence of the community on its continued well-being."

The scientists ask, what forces lead to the reliance of communities on keystone organisms, whose extinction can lead to instability and potential catastrophe?
"The Black Queen Hypothesis has far-reaching implications for understanding the evolutionary forces behind diverse, interconnected ecological communities," says George Gilchrist, program director in the National Science Foundation's Division of Environmental Biology, which co-funded the research with NSF's Division of Ocean Sciences.

In the game of Hearts--or the game of life--the Queen of Spades, it turns out, may be the most important card.