 This time on Partners, it's an adventure underground with the Soil Explorers. From bioremediation efforts to improved sediments of New Jersey's industrial metalands to probing experimental gadgets that offer California wine growers a competitive edge in growing grapes to microbial observatories offering insight into the use of streptomycin in Wisconsin apple orchards. These bold explorers are reshaping the way we think about our most fundamental natural resource, Soil. Welcome to Partners. In the next half hour, we'll travel the nation and see breakthrough work in research, education and extension. That's what CSREES is all about, helping universities generate valuable knowledge for those who need it and educating our next generation of Americans. And now it's time for Partners. Soil. Perhaps no other substance in our natural world is as important as it is unappreciated. Most people understand the importance of Soil in the growing of food, but beyond that, it is frequently viewed as something that we merely tread upon. Others see it as a convenient dumping ground. If neglected, it can discreetly wash away a lost treasure to the local ecosystem. This underappreciated resource comes in many forms, and because of that diversity serves many functions. Soil provides homes for animals, material for constructing buildings, foundations for our grand structures. It acts as a filter for the planet's precious water, an anchor for our majestic forests, and a storehouse for Earth's basic elements. For instance, carbon may be stored deep in the soil for thousands, even tens of thousands of years. The largest terrestrial stock of carbon is in the soil. But when soil is disturbed, much of its carbon may be released into the atmosphere. This is causing concern as increased carbon dioxide has been linked to global warming. As a result, scientists are now studying the mechanisms of carbon sequestration, how carbon remains underground. They are among a group of modern-day explorers, those dedicated to unlocking the secrets of Earth's living skin. In the next half hour, we'll follow three intrepid scientists in their quest to learn more about this amazing natural wonder, one that is vital to us all. And now, the Cooperative State Research Education and Extension Service of USDA presents The Soil Explorers. We have a legacy of contamination in the district. Organic pollution is very prevalent. We are coming out of a cycle of 60, 70 years. I could go even further back in industrialization. I mean, this is the quintessential post-industrial landscape in New Jersey. Lowlands, you know, people just dumped here. Francisco Artigas is talking about the Carney Marsh, located in the meadowlands of northern New Jersey. Once a saltwater marsh, it was drained and used as a landfill. Later, a freshwater marsh was established on top of a dump. And while wildlife still remains here today, Carney Marsh faces other threats than those from below. During rainy periods, sewage overflows into the swamp. Runoff from nearby landfills is also a problem. The result is a marsh laden with toxins. For Donna Fennell, this is a perfect place, for she is a soil explorer. A lot of people have heard about PCBs. That's polychlorinated biphenyls. These are compounds that were produced as industrial chemicals and used for electrical insulators. They were used in carbonless copy paper. Their production was banned in the late 70s after it became apparent that these things were an environmental problem. PCBs are very hydrophobic, so they like to stick to soil particles. Those soil particles are the recipients of many types of pollutants. Some of these soil particles get washed into aquatic systems and form the basis of the sediment that forms in the bottoms of rivers, lakes, harbors, and coastal areas. Organic matter contained in soil is sort of an attractant for some of these more problematic pollutants, like PCBs and dioxins. Today, Fennell and assistant Val Crumins are going against convention. The standard method for eliminating such toxins is to dredge, physically remove the polluted sediments from the aquatic environment. This is not only costly, but the muck collected then needs to find a safe home so that the toxins don't spread further. But Donna and her Rutgers colleagues believe they have a better idea. Our techniques are intended to work naturally within the sediment. We're focused on really treating the pollutants where they are. We're looking at microorganisms that occur naturally in the sediment or which we may introduce to the sediment to transform and detoxify these compounds. That way we can detoxify the sediment in place and then the excavation or dredging if it occurs later as a normal course of management of aquatic sediments would not result in redistribution of those pollutants. The microbes that the Rutgers staff inject into the polluted sediments are tiny bacteria, ones that, in order to live, absorb chlorine from toxins like PCBs. What these microorganisms do is they use the chlorinated compound as their oxygen. They're breathing chlorine, so to speak. The Marsh experiment has several steps. First, a barrel is set down into the sediment to isolate it from the rest of the bottom. The dechlorinating microbes are then injected into the sediment. Then a second blue barrel is fitted into the first. This allows the scientists to funnel in materials from the boat. The last step is to cap off the embedded barrel with a gel-like clay seal. This capping idea is something that has been used for some time for treating sediment. What we want to do is study how the microbial process under the cap could be stimulated and how it can work in conjunction with capping. Back on shore, the Rutgers team examines the sample just brought in from the boat. CSR EES helped fund this research, along with a grant from the Department of Defense. With the samples safely preserved in liquid hydrogen, the serious sediment is transferred back to Rutgers, where the rigorous lab work begins. It is here that Fennell is discovering the intricacies of the dechlorinating microbes used at Carni Marsh. Only by using molecular DNA technologies can we have a hope of detecting those microorganisms. Extracting the DNA and using molecular markers that are specific for the bacteria that we're interested in, we can pinpoint members that make up only a small percentage of that population. Right now I have a three-year-old in my house, and I'm very concerned about the impact that pollutants have. We're really starting to break down these barriers. What happens in sediments? What can degrade these pollutants? We're developing technologies to deal with these legacy pollutants, and we can sort of right the wrongs that have been done in the past. It's recovering our environmental legacy and our heritage, and making that a resource for future generations. In 2001, homeowners applied over 40% of garden chemicals used in the U.S. Land Grant University studied the impact of chemical runoff on soils and supply urbanites with guidelines for responsible care of city landscapes. It is autumn in the Napa Valley of California, and the rush is on to harvest this year's bounty of grapes. Time is of the essence. When you're growing grapes for wines, especially for reds, you're very much on the edge in terms of too much stress and too little stress, and so the push is always to do more stress. But if the weather is adverse in terms that it's too hot or it's too dry, you can go overboard. And so the risk really is, because you're always on that knife edge, you can go too far. Daniel Bosch knows the risk in the high-stakes business of vineyard production. He is the senior vina-culturalist for Robert Mondavi Wines, making crucial decisions for this 1500-acre operation, one of Napa's largest. But he also understands that water is the key. Guessing wrongly about moisture beneath the surface can lead to a bad harvest. If the soil is too moist, the grapes grow fat and flavorless. Too dry, they just wither and die. What Bosch wants is the optimum amount of H2O to reduce tiny grapes bursting with flavor. Deep blue jewels that offer the most delicious wine. Soil really determines an awful lot in quality in growing grapes, and the water relations in the soil is really the primary way that soil is involved in wine quality. But to date, determining soil moisture leaves much to be desired. Growers sometimes dig test holes to see below. This is spotty information at best. They also check the moisture inside the plant. Our current methods are all point measurements, so it's single vines or a few vines. But at the University of California, Berkeley, soil explorer Yoram Rubin thought he might have a better method. He contacted Daniel Bosch with a novel way to see below the surface. GPR stands for Ground Penetrating Radar. GPR is a system that sends an electronic signal into the ground and record it after it travels in the ground for a certain while. And we then take the recorded signals back to the lab and we interpret them. We had the instrumentation, but it had to be modified for use in vineyards and more importantly, we had to develop the methodology for interpreting of the signal. It's high-risk research. This technology was unproven when we started. It's on the interface between basic research and applied research. What we found in CSREES is openness and willingness to take the risk. They, in fact, allowed us to do it. There was no other way. Back in Napa, a prototype GPR device is put to the test. Assembling the maze of cables, connections and computers is left to the deft hands of another soil explorer, Catherine Grote. I was the primary data collector and processor here, so I would come out on a typical day and collect data. The great thing about radar is that you get really high-density data. As the unit is dragged across the surface, it sends a high-frequency electromagnetic pulse down into the soil. The signal is then reflected back to a receiver and recorded into a laptop computer. The speed of the transmitted and reflected signals varies with the soil's water content. Pulses move slower through wetter soils, faster and drier ones. Here, very quickly, we actually monitor a very large area and get a three-dimensional image of the soil, and with that, get a comprehensive image of soil moisture and control the stress irrigation process. The second advantage is related to harvesting. When they get an image or information about the soil moisture content, with that, they can control irrigation. They can control the maturation of the fruit such that the fruit from the entire block matures at around the same time. They can send the crew just one time with the strong competition, the California wine coming from the New World wine, Australia, Chile, Argentina. There's no choice. First of all, that really helps in understanding how deep the roots are, where the water is, how fast it's starting to run out, and that makes farming easier. And the ground penetrating radar, the GPR, measures multiple points, and so we can get sort of a 3D look of what's going on rather than just one point. Having that picture allows us to be more efficient in designing it so that we don't, after the fact, have to make adjustments to how we plant it. The ability to better plan new vineyards is a huge advantage for Bosch. Napa is known for its rolling hills and varied earth that rapidly change from loam to sand to gravel. Over 30 types of soil have been identified in the valley. GPR will allow viniculturalists to efficiently match their plantings to variations in the subsurface terrain. And there are environmental advantages for California, a state that uses more water than any other. The larger the pressure on water resources, there will be a growing pressure to control irrigation. And this is not just because we need to save water, but because water can actually percolate below the root zone and carry the pesticide deeper into the ground. So you really want to irrigate as much as is needed and not to drop more. And this you can do with our technology. I'm just very excited about the potentials of this technique. If you read the manuals on how to measure water content, GPR isn't even really mentioned yet. But as we develop this, say, in three to five years, I think it has very far-reaching potential for both precision agriculture and more traditional farming techniques. The future for the technology looks bright. Catherine Grote now uses GPR in Wisconsin to determine nitrate content through electric conductivity. This CSR EES-funded research helps Midwest farmers determine optimum fertilizer applications for their fields. Yoram Rubin is exploring ways to use the radar for monitoring moisture below highways with hopes of better predicting road maintenance needs. And for Dan Bosch, he remains on the land. The French have a concept of what they call terroir, and it's really the concept of the place, of the environment, of the soil, of the people, of the history. It's really all of those. A lot of it is experience. And we're hoping that with the techniques like GPR that we can make some jumps ahead. And I think we're starting to see some of the same advantages that took other people hundreds of years. With GPR, I can imagine at some point you could attach it to a tractor and go down every few rows and have a good understanding of what your various parts of the vineyards are doing. CSR EES funds soil conservation projects that improve farm tillage and cultivation to reduce soil erosion. An added benefit? Cleaner air for better human health by reducing dust particulate. Looking at this Wisconsin countryside, it's hard to imagine that much could go wrong in such a pastoral landscape. But trouble arrived here just a few years ago when a bacterial pathogen re-invaded the area, causing widespread destruction. Firelight is a disease that affects apples and pears and related crab apples, related ornamental trees. It's caused by a bacterium or winium alabra. And although it's sporadic disease, it can be really devastating taking out branches, flowers, fruit, entire trees sometimes. The most noticeable signs are that when you look at the tree it looks like a branch will be scorched by fire, so it's brown or black and the leaves are dried up and the branch might be crooked over at the end so it resembles a shepherd's crook. It's a pretty big problem. Patty McManus advised Wisconsin farmers on how best to combat the disease. One of those was Vern Forrest of Eppelgarten Farms. Very scary. I thought that the way it suddenly hit and the fact that we had it for two years in a row, I thought we might lose the orchard. The total of 200 or 300 trees maybe we've lost and then of course we've cut back on some of the infected trees. Production was lost for quite a while. From then on we've been pretty serious about trying to cut out the ugly dead stuff and to manage it and get it under control. One such control method that Vern and others use is the spraying of Streptomycin. Streptomycin comes from the bacterium Streptomyces grisius that's found in soil. It's proven to be a formidable foe against fire blight. But historically Streptomycin has been used as an antibiotic in the medical world. It was here in this building at Rutgers University that Albert Schatz and Selman Waxman first discovered the bacterium that produces Streptomycin. Streptomycin proved to be instrumental in checking the spread of tuberculosis. Today it is still used to fight TB of other diseases including bubonic plague. And herein lies the problem. Some in the medical community are alarmed by the spraying of Streptomycin for agriculture. They fear its overuse will lead to a biological weakening of the medicine. If true, this could have serious health implications. What Streptomycin does is it inhibits the making of the protein from the RNA. So basically it shuts down almost all metabolism in the bacteria. If Streptomycin is used extensively in their high concentrations then I think bugs which are in soil which will be exposed to high concentrations will become resistant. So yes it will have human implications. At least at this point in time one of the diseases that we really need to curb is TB and if for any reason mycobacterium tuberculosis becomes resistant to Streptomycin which it is becoming I think it would be a problem because we will lose what people consider a second line drug for TB. We should be very careful with how we use our antimicrobials. They spray with Streptomycin during bloom to prevent infections and growers are under scrutiny from people who don't understand why they're using it but there's really no data to help us figure out what the effects are. Microbiologist Jo Handelsman and her team are trying to get answers to this pressing question. With CSREES funding they are exploring the soils in orchards and other places for clues establishing what she calls a microbial observatory. We all think of observatories as being places that we look at the very very largest parts of our universe and microbial observatories are places where we look at the tiniest parts of our universe, the microorganisms that live around us. It is in this world of microbes that Handelsman believes the answers may lie. No question about it, microbes rule, they run all of the major chemical cycles on the earth, they make most of the oxygen that's available to us, they clean the systems that we live in, they clean the soil, they clean the waters but perhaps the most important use of the microbes is their production of antibiotics that are used in medicine. In fact, most of the antibiotics we use today in medicine are derived from microorganisms that live in the soil. It's in this vast new frontier of uncultured bacteria where Handelsman and her soil explorers work. Back at the lab the samples are sifted. The hard part comes when we try to extract the DNA from all of the microorganisms in the soil. This is the technology that we now know as metagenomics which involves studying all of the genomes of the organisms in an entire community. But Handelsman's microbial observatory extends far beyond the borders of Wisconsin. This is the Tanana River of the Alaskan interior. Today, researcher Roger Rousse guides his boat down these wild waters toward a remote island in the stream. His destination? The Bonanza Creek Experimental Forest, one of the more biologically pristine environments in the world. This is a braided river channel. It's a large river. It's one of the largest rivers in Alaska. The landscape is a mosaic of islands interrupted by back slews and the vegetation represents stages of development in response to disturbances, principally fire and flood dynamics. It's incredibly pristine relative to the lower 48. These forests are undisturbed by humans essentially. The very foundation of this laboratory under the sky is why Roger Rousse has traveled here. He is in search of soil, samples that may offer clues to the streptomycin issue back in Wisconsin. Roger has a fantastic ecological understanding of the whole ecosystem. The Alaskan soils are very interesting because of their geologic history, because of the climate and the vegetation in the islands that we study. But they also provide a very unusual habitat that has been exposed to very little human effects. That gives us a baseline of antibiotic resistance in an environment that has not been perturbed by humans and provides a nice contrast to the site in Wisconsin that has been managed by humans for quite a long time. It offers her an unusual set of conditions in the soils. The soils are characterized by extremely cold adapted organisms that are capable of dealing with very recalcitrant organic matter. Ultimately, we hope that by comparing the two soils we'll have a sense of what antibiotic resistance genes are present even when humans have not intervened. And that will give us some perspective on the apple orchard because we won't know in the apple orchard if any of those genes would have been discoverable in the absence of antibiotic use. Over 3,000 miles to the south the work continues at the University of Wisconsin's Microbial Observatory. Perhaps the answer to the streptomycin issue will be found in one of the Alaska samples sent by Roger Ruse. We simply don't know if streptomycin is going to have an effect on streptomycin resistance in the orchard. That's exactly what we want to find out. Now, as land-grant scientists meet the challenge of fueling America that's next time on Partners. Or on the Soil Explorers or other episodes of Partners' Video Magazine log on to this website.