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PNNL helps lead national microbiome initiative

May 31, 2016

RICHLAND, Wash. - Scientists at the U.S. Department of Energy's Pacific Northwest National Laboratory are playing a central role as the nation devotes more than $500 million to understand communities of microorganisms and their role in climate science, food production and human health.

Scientists Janet Jansson and Ljiljana Paša-Toli are part of a core group of scientists advising the White House on issues related to research around the microbiome, a term that describes a community of microbes in a given environment.

Both Jansson and Paša-Toli are leaders of broader scientific teams at PNNL. Jansson is chief scientist for biology in the Earth and Biological Sciences Directorate at PNNL, while Paša-Toli is lead scientist for mass spectrometry at EMSL, the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility at PNNL.

Earlier this month, the two took part in a White House briefing as the president's advisers announced more than $121 million in new funding from federal agencies for the National Microbiome Initiative. That's in addition to more than $400 million from foundations such as the Gates and Kavli foundations, organizations such as the American Chemical Society and the American Physical Society, and companies, universities, and other laboratories.

That's big money to study tiny organisms with a big impact.

Microorganisms have huge sway over environmental happenings in soil, groundwater, the ocean, the atmosphere, and our own bodies. They determine in large part how the planet stores carbon, when and how carbon is released into the environment, and what happens to contaminants and other compounds. They're important for knowing how plants take up nutrients, for helping crops sustain or develop resistance to conditions like drought, and for overall crop productivity.

Microorganisms also play a huge role in human health and disease - not just infections but in conditions like obesity, inflammatory bowel disease and diabetes. In toto, the little buggers make up an estimated one-third of all the biomass on Earth.

A lot to learn

Just a teaspoon of soil has tens of thousands of different microbial species present. While scientists have made strides sorting out which species are present in such complex samples, how those species interact remains a hugely daunting problem.

Jansson and Paša-Toli ask the same sorts of questions that an anthropologist might ask when encountering a new community. Who is present? What business do they transact with each other? What is the currency they use to get things done? What does their trash tell us about their way of life?

"We want to know not just who's there, but what they're doing," said Jansson, an expert on the role of microbes in the environment.

"We are getting pretty good at identifying some of the microorganisms present in samples, and some of what they do, but completely understanding a single microbial community, even a tiny one, is a future challenge to solve," added Jansson, president of the International Society of Microbial Ecology.

Think of an analyst confronted with the following disparate array of data: Loud buses, thousands of people, ubiquitous fast food, diesel fuel, cars, loud noises, and lots of bickering and jockeying for position. What does it all mean? The scene might be - an airport, a sporting event, a concert, an ordinary big-city work day, or an evacuation after a major disaster.

So, too, scientists like Jansson and Paša-Toli are presented an array of data about complex microbial communities, but it's very difficult to put the information together to create a coherent picture of the activity they're seeing. They can identify some microbial species; they can detect microbial nutrients and their byproducts; they see signs of their molecular doings; but putting together the big picture remains tremendously difficult.

PNNL colleague Richard Allen White III, who is working with Jansson on a project to disentangle the information about microbes that live in soil from the Kansas prairie, puts it this way:

"Imagine taking a thick book written in hundreds of different languages, chopping the book up into pieces the size of grains of rice, and then having to put it back together again," said White. "That's not unlike the challenge we face when we try to understand what's going on in even a handful of soil."

Past successes and a roadmap

Last year, Jansson and Paša-Toli were part of an elite team of scientists who, in a paper in the journal Science, called for a Unified Microbiome Initiative to understand and harness the capabilities of Earth's microbial ecosystems - a call that has largely been answered with the new White House initiative.

Last year, Jansson used an array of technologies to show the versatility of microbes that live in permafrost, which is a reservoir for a huge amount of carbon. The fate of that carbon as the climate warms and permafrost thaws is a huge issue for scientists trying to understand the planet's future. The work, published in Nature, yielded one of the most detailed looks ever at the microbes active in permafrost.

Earlier this year, Jansson and PNNL colleague Aaron Wright were among the authors of a paper in ACS Nano that discussed the technologies needed to explore the world's microbiomes. Among the technological challenges are several related to understanding the "omics" of organisms - information related to genes, protein coding and activity, and metabolism. While DNA sequencing has become very quick and relatively inexpensive, the other measurements currently take longer and are more costly.

In this month's issue of Nature Microbiology, Jansson and PNNL chemist Erin Baker discuss the importance of understanding such communities as whole entities. The pair calls for strides in technology, optimized protocols, improved databases, speedier analysis, larger sample sizes, and international collaborations.

Currently, Jansson is heading a major initiative at PNNL looking at Microbiomes in Transition, known as the MinT Initiative. More than two dozen researchers are involved in the five-year effort focusing on environmental issues, exposure science, and computational biology. Last year, one of the first actions of the MinT team, in conjunction with EMSL scientists including Paša-Toli, was to bring together nearly 200 microbiome experts from around the world to discuss the future of microbiome studies and the technologies necessary for scientists to develop to make further discoveries.

DOE/Pacific Northwest National Laboratory

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