Mapping the Microbiome

<section class="entry-content instapaper_body clearfix" itemprop="articleBody">
<div class="add-container clearfix" id="add-block-placer">
</div>
<p>
  You probably think you know who shares your home. But other than the very largest organisms—your family, your pets, some occasional unwelcome rodents, perhaps the odd earwig or cockroach—the truth is, you really have no idea. For thousands of years, humans have lived indoors, spending the bulk of our time in an environment we built ourselves. And yet, it turns out, we know virtually nothing about the organisms with whom we interact every day, in our living rooms, kitchens, bedrooms, and bathrooms.
 </p>
<p>
  Rob Dunn and Noah Fierer are out to change this. Dunn, a biologist at North Carolina State University, and Fierer, an ecologist at the University of Colorado, are cataloging the diversity of our houseguests—those of the microscopic variety. Their project, called “
  <a href="http://www.yourwildlife.org/projects/wild-life-of-our-homes/">
   The Wild Life of Your Home
  </a>
  ,” is exploring the microbial makeup of 1,000 homes around the country.
 </p>
<figure class="richtext-image full-width">
<img alt="Kitchen sink faucet" class="richtext-image full-width" src="https://www.pbs.org/wgbh/nova/media/images/kitchen-sink-faucet.width-990_Khls7UJ.jpg"/>
<figcaption>We know little about what microbes live in our homes.
        
    </figcaption>
</figure>
<p>
  The technology fueling the project is distinctly 21
  <sup>
   st
  </sup>
  -century—genetic sequencing at a scale which wouldn’t have been feasible just a couple of years ago—but the questions at its heart are far more basic. “We’re doing 19
  <sup>
   th
  </sup>
  -century ecology,” Fierer says. By which he means basic natural history: What are the species that live with us?
 </p>
<p>
  “How have they evolved to live here?” Dunn wonders. “What are they doing to us, and how do our decisions affect which ones we’re exposed to?” It’s a series of questions Dunn’s been asking repeatedly in his lab. “Consistently,” he says, “we find we know extremely little about these species. Unless they kill us, we don’t study them.”
 </p>
<h2>
  Finding New Frontiers
 </h2>
<p>
  In their search to catalog the invisible world around us, Dunn and Fierer are a bit like modern-day Lewis and Clarks. Except unlike that long-ago duo who traversed the West together, Dunn and Fierer, despite several collaborations, have never met in person.
 </p>
<aside class="pulledquote">
  Imagine the gazillions of microscopic life forms that might be sharing our beds and cutting boards.
 </aside>
<p>
  They have, though, traveled together into America’s biodiversity frontiers. In a pilot project involving 40 homes, their team found three main trends: that the presence of dogs had a big influence on the dominant types of microbes, that frequently cleaned surfaces had lower diversity than their less-clean counterparts, and that microbes living outdoors directly influenced those living indoors.
 </p>
<p>
  Not long ago, Dunn surveyed the insects in 50 houses in the Raleigh-Durham area. “In one house,” he says proudly, “we found 50 species of arthropods just in the living room.” That number included one extremely rare species in which “the only way larvae becomes a male is if it eats its own mother.” Dunn says he has not yet told the homeowners.
 </p>
<p>
  If we’re that in the dark about housemates we can see, imagine the gazillions of microscopic life forms that might be sharing our beds and cutting boards. “If we don’t know what’s going on with the visible stuff,” Dunn says, “once we get to the invisible, all bets are out the door. So part of what we want to do is get a sense of what the heck is living with us.”
 </p>
<h2>
  Swabbing for Species
 </h2>
<p>
  Eager to participate, I signed up for the study, which relies on citizen scientists to collect the data. A few days later, my swabbing kit arrived in the mail: four extra-long Q-Tip-style swabs each encased in its own plastic tube. Following the instructions, I swabbed a kitchen countertop, a pillowcase from my bed, and the tops of the doorframes inside and outside my front door. Then I mailed my embarrassingly dirty—and presumably microbe-coated—swabs to North Carolina.
 </p>
<p>
  I also filled out a detailed questionnaire that covered things like how often I vacuum, whether I have pets (and what kind and how many), whether I’ve recently suffered from dry skin or fatigue. That information will help the team begin to understand how microbes affect us—and vice versa.
 </p>
<p>
  My samples will eventually come back to Colorado, where Fierer’s lab (which happens to be down the street from my house) will extract the DNA from all 4,000 swabs in the study and run them through DNA sequencing machines. Ultimately, the genetic information will show what groups of microbes are present in each home and at what concentration. The results will show the genus of microbes, though not the exact species, which might prove frustrating for participants hoping to know
  <em>
   exactly
  </em>
  what’s living in their homes and how good or bad those neighbors might be.
  <em>
   Staphylococcus
  </em>
  , for instance, is a genus of bacteria that’s common on our skin and around our homes, and many types of staph are completely harmless. But the genus also contains MRSA (methicillin-resistant
  <em>
   Staphylococcus aureus
  </em>
  ), which causes dangerous and potentially deadly infections.
 </p>
<aside class="pulledquote">
  Is a house in Phoenix, say, filled with different creatures than one in Miami?
 </aside>
<p>
  “There’s a disconnect,” Fierer admits, “between what people want to know and the information scientists can give them.” What the researchers can do, though, is start making correlations between types of microbes and practical implications—like, for example, how the presence of certain bugs affects asthma rates.
 </p>
<p>
  “Studies show that people with dogs have a lower risk of allergies,” Fierer says. “So now maybe we can show that it’s because they’re exposed to these specific bugs.”
 </p>
<h2>
  Mapping the Microbiome
 </h2>
<p>
  The researchers also want to understand regional differences in our microbial neighbors: Is a house in Phoenix, say, filled with different creatures than one in Miami? If you move from Los Angeles to Cleveland, do you take your household microbes with you? And how do our daily actions—the cleaning products we use, for instance—impact our home microbiome?
 </p>
<p>
  A study released last year found that in one community in Finland, the plants people grew in their backyards affected their children’s health. When scientists compared the microbes on the skin of teenagers whose yards contained native plants with those whose yards grew nonnatives, they found completely different diversity. What’s more, teens growing up with native plants were at four times lower risk for allergies than their exotic-plant peers. “We’re seeing more and more associations between particular groups of microbes and health issues,” Dunn says.
 </p>
<p>
  Over the next few years, he hopes to help unravel and clarify those associations with the ultimate goal of understanding how we can create healthier homes. “We know that some microbial taxa are really drought tolerant,” Dunn says. So in desert houses, he expects to see different groups of bacteria than in wetter environments. That finding could help the team focus on health impacts. Imagine that the abundance of
  <em>
   Staphylococcus
  </em>
  varies based on local climate (outside, not inside). That could influence the risk of finding a harmful strain of staph that’s resistant to antibiotics. “It tests what we know about where these resistant strains are evolving,” Dunn says.
 </p>
<p>
  Once the more mundane environments of our homes are conquered and chronicled, Fierer plans to push on to new frontiers. He wants to know what lives in extreme environments of the domestic variety: your dishwasher, your salt shaker, your soap dish. He’s beginning to sample these places, curious to learn what they’ll yield.
 </p>
<p>
  “You don’t have to travel to some alkali hot spot in Kenya to find novel environments,” Fierer says. “They’re mimicked by your dishwasher. The biomass is low, but there might be some interesting diversity.”
 </p>
</section>

How Water Is Reshaping the West

<div class="related"></div>
<p></p><p>On an unseasonably warm September day with a cloudless sky, I stand on a Colorado hillside, in a meadow that’s painted the ochre of early fall. Ponderosa pines stand sentry above the grass, which sways in a barely perceptible breeze. Down below, cottonwoods tower above an old streambed. All around me, birds chirp and flit among the shrubs; recent visitors spotted fresh mountain lion tracks and a black bear. It’s an almost perfect vista. Except I’m looking at a landscape that will soon disappear.</p><p></p><p>“Be careful of rattlesnakes,” Brian Werner says as we walk near what will, a few years out, become the south end of Chimney Hollow Reservoir. I try to imagine what will happen to the snakes—and the bears and birds and burrowing animals—when these 1,600 acres become a lakebed. I’d been conducting an animated interview with Werner for more than an hour as we toured the region’s waterworks–reservoirs, pipelines, diversion ditches, pumps—but now, standing here, I’m speechless. Perhaps sensing my mood, Werner tries to be upbeat. He gestures to the west, where, as part of the reservoir land-acquisition deal, another 1,800 acres will be permanently protected. But it’s hard to stand beneath those ponderosas and not feel a kind of heartbreak.</p>
<div class="pullquote">
<p>“Some people think if we don’t build those projects, people just won’t come. I wish that were the case. But it’s not gonna happen.”</p>
</div>
<p>Werner works for Northern Water, a public utility that delivers water to parts of eight northeastern Colorado counties and about 880,000 people. In conjunction with the U.S. Bureau of Reclamation, Northern Water administers the Colorado-Big Thompson Project, a sprawling collection of reservoirs and pipes built to send Colorado River water from the western part of the state across the Rockies (through a tunnel beneath Rocky Mountain National Park) the more populous—and growing—northeastern towns. Werner’s job title is public information officer, but after 34 years with the utility, he’s also its de facto historian, with an insider’s deep knowledge of the entire state’s water past and present, including the intricacies of water rights. (Western water law is an unfathomably complex beast predicated on a first-come-first-served system, which is why newer cities, late to the game, are struggling for rights to water that often flows right past them.)<br/></p>
<figure class="richtext-image full-width">
<img alt="" class="richtext-image full-width" src="https://www.pbs.org/wgbh/nova/media/images/chimney-hollow.width-990_TwicQty.jpg"/>
<figcaption>A grassy meadow sways in the breeze in Chimney Hollow.
        
    </figcaption>
</figure>
<p>Up and down Colorado’s Front Range—the string of cities perched along the Rocky Mountains’ eastern flanks—it’s a boom time. Fort Collins, the northernmost city, has doubled its population since the 1980s, with no sign of stopping. Farther to the east, in former rural communities like Frederick, Dacono, and Evans, pavement is spreading like weeds, subdivisions are sprouting in place of corn. The reservoir soon to drown the spectacular landscape under my feet that afternoon would deliver water to these bustling communities.</p>
<p>Nearby, another proposed reservoir would submerge a highway to store water from the Poudre River, which flows through downtown Fort Collins; this project will serve those same growing towns. “Some people think if we don’t build those projects, people just won’t come,” Werner says. “I wish that were the case. But it’s not gonna happen. People are going to keep moving here, because it’s a great place to live.”</p><p>Across much of the West, the story is similar. As cities and states grapple with urban growth alongside the impacts of global warming—crippling drought, a shifted timeline of snowmelt and stream flows, uncertainty about future water supplies—nothing is off the table when it comes to securing access to water. These days, the stories that make national news are more likely to be about old dams coming down than about new ones rising. That’s partly because dams coming down are still a rarity. But across the West, the local news is far more likely to be about smaller dams going up. The era of water mega-projects may be behind us, but engineers are still transforming landscapes to deliver water—an increasingly elusive and valuable commodity.</p><p>In Colorado, planning for the next phase in the perpetual quest for water is nearing completion. The statewide water plan, mandated by Governor John Hickenlooper, is a massive document, two and a half years in the making, that details how the state will provide water to its expected population of 10 million people by midcentury and make up an anticipated 163-billion-gallon-a-year water deficit. A final version of the plan is due to the governor by December 10; officials are scrambling to respond to new demands by some Front Range cities, including Denver, Colorado Springs, and the towns that Northern Water supplies, for new reservoir capacity. The Denver Post reported last month that “46 staffers are scrambling to fix the plan and include a massive new commitment for new reservoir storage of 130 billion gallons.”</p><h2>Smaller Projects</h2><p>“The Reclamation era”—roughly the 1930s to the 1970s—“was big monster projects, massive dams that totally reshaped the watershed, rivers, and ecology,” says Reagan Waskom, director of the Colorado Water Institute at Colorado State University in Fort Collins. Today’s projects, Waskom says, are a series of “expansions and enlargements,” smaller-scale efforts meant to complement or shore up existing systems. About an hour south of Chimney Hollow, in the mountains west of Boulder, Denver’s water utility is planning to enlarge a reservoir built in the 1940s, raising the dam by 100 feet, doubling the lake’s surface area and tripling its storage capacity.</p><p>The dams being built today, Werner agrees, are “not the Hoovers and the Meads. We’re not doing that anymore.” Still, he adds, “I don’t want to rule them out totally.” As recently as the 1990s, he notes, California built Diamond Valley, the biggest reservoir constructed in the western U.S. in 50 years. But in his three-plus decades with Northern Water, he’s worked on the construction of just one reservoir.</p><p>Certainly, Chimney Hollow is no Diamond Valley or Lake Mead. The country’s largest reservoir, Mead can store roughly 26 million acre-feet, or 8.47 trillion gallons, of water. (Water storage is often measured in acre-feet, or the amount of water needed to flood one acre of land one foot deep.) The Hoover Dam, which stops the Colorado River in its tracks to create the lake, is 726 feet high. Chimney Hollow will hold 90,000 acre-feet, or about 29.3 billion gallons, with a 300-foot-high dam.</p><p>A subsidiary of Northern Water, called the Municipal Subdistrict, runs the Windy Gap project, which was built in the early 1980s to provide water for Boulder, Fort Collins, and four other Front Range cities. The system pulls water from the Colorado River and stores it in the Windy Gap reservoir on the west side of the Rockies then delivers it to Lake Granby, where it is pumped through the Big Thompson system to the eastern side. But in wet years, Lake Granby, the main reservoir for that Big Thompson system, is already full—leaving no room to store the Windy Gap water. That means in dry years, when the customers really need it, the water isn’t there.</p>
<div class="ad"></div>
<p>Chimney Hollow is the solution, a way to stabilize the Windy Gap water supply. Water managers call it “firming.” Imagine that you are technically entitled to ten units of water out of a reservoir that stores 100 units. But in a dry year, the reservoir might only contain 30 units, and there are other customers besides you. In such a system, you couldn’t really depend on the reservoir for your water. That worst-case scenario is what water people call “firm yield.”</p><p>On the Windy Gap system, the firm yield is currently zero. “In the dry years, there’s no water available,” explains Werner, “and in the wet years, there’s nowhere to put it. You can’t rely on a project with zero firm yield.” Chimney Hollow, the utility contends, will give customers—the city of Erie, say— guaranteed annual delivery of their legally allotted water.</p><p>“Even with climate change, we know that there will be high flow years,” Waskom says. “When those come along, you’ve either got a place to store that water or you don’t.”</p><p>Storage offers a safety measure, a way to even out the inconsistencies and help ensure a more stable water supply. That’s no small thing when you’re coping with climate change. Floods that scientists used to consider 100-year events—with a 1% chance of occurring in any given year—are now being called 20-year events—with a 5% chance of occurring in any given year. Droughts are different than they used to be, too: today’s droughts, which coincide with warmer temperatures, bring more wildfires, earlier snowmelt, and greater rates of evaporation—transferring water from soil, plants, lakes, and reservoirs to the air.</p><h2>Zombie Projects</h2><p>But not everyone thinks that means we should keep building reservoirs.</p><p>“One of the things you see all over the West is that people think they need more water to serve more people,” says John Fleck, an adjunct professor and writer-in-residence at the University of New Mexico’s Water Resources Program. “But when push comes to shove, communities are really successful at using a lot less water. There’s this notion that if our population goes up, our water use has to go up. That’s really not the case.” Albuquerque, notes Fleck, who is writing a book about the future of the Colorado River, uses less water today than it did in the late 1980s even as it grew by 45%.</p>
<p>Fleck believes some new reservoir and pipeline construction falls into a category he calls “zombie projects”: yet-to-be-built portions of long-ago-conceived storage systems. Decades ago, he says, “we got these projects in our minds, the idea that they were going to be built. People continue to think they want to build them, without recognizing the changing water-use realities.”</p><p>Fleck points to a federal project called the Ute Lake Pipeline in eastern New Mexico as the “classic zombie”: A dam and reservoir were built back in the early 1960s, but a pipeline to deliver the water to the Clovis area—150 miles away—remains, well, a pipe dream. “The backers want to build it, homeowners around the lake and environmentalists want to stop it. The water just sits in the lake.” Fleck doubts it will ever be built. “But it limps along, because everybody’s incentives are well fed.”</p>
<figure class="richtext-image full-width">
<img alt="flatiron reservoir" class="richtext-image full-width" src="https://www.pbs.org/wgbh/nova/media/images/flatiron-reservoir.width-990_i76flM5.jpg"/>
<figcaption>Baseline Reservoir stores 760 acre-feet, or 247 million gallons, of water southwest of Loveland, Colorado.
        
    </figcaption>
</figure>
<p>There’s also the issue of whether there will continue to be enough water in the rivers to make these efforts worthwhile. “Whether you have a big reservoir or just a straw where you’re sucking water out of the river and sending it somewhere else, the question is, will the water be there?” says Jeff Lukas, a researcher with the Western Water Assessment, a research program based at the University of Colorado. “Just because you’ve done the modeling and your scheme would’ve worked under the hydrology of last 50 years doesn’t mean it’ll work in the next 50 years.”</p><p>A new reservoir for the swelling Denver suburb of Parker, for instance, completed in 2011, has managed to fill to only a third of capacity, thanks to dry spells, evaporation, and junior water rights that allow Parker to draw water only after more senior rights holders are done. The project took 30 years to build, and currently only provides a year’s worth of water for 75 families.</p><p>New water storage projects may also amount to a zero-sum game. “If you take more water out of the Colorado River basin,” Fleck says, “you’re taking water out of an overstressed system that can’t afford to lose water without someone else having less.”</p>
<div class="pullquote">
<p>“In this new world, you don’t do things from strictly engineering standpoint.”</p>
</div>
<p>Or, as Douglas Kenney puts it, “It’s not like there’s some new water we can capture and the region is better off.” Kenney directs the Western Water Policy Program at the University of Colorado School of Law. When I visited him in his office, he picked up a manila envelope from a pile of mail on his desk. Sent by someone he’s never met, it contained a proposal for a “veterans memorial pipeline” that would carry water from the Mississippi River to the West. Kenney says these things land in his mailbox on a regular basis. Nutty as it sounds, it’s an idea that repeatedly surfaces, most notably pushed by former Nevada water czar Patricia Mulroy. Before she retired last year, Mulroy was the head of the Southern Nevada Water Authority, which supplies water to Las Vegas; during her 25-year tenure, the city slashed per capita water use by a third. Yet Mulroy frequently said that no option was too outrageous to consider. In addition to suggesting the West siphon water from the Mississippi, she applied for federal permits to tap vast quantities of groundwater from beneath 20,000 square miles of eastern Nevada sagebrush country. (The project is bogged down in lawsuits.)</p><p>Some critics believe that new water projects are proceeding from a faulty premise: the idea that you develop as much water as you possibly can while you can, and then only conserve water when you absolutely have to. But it’s hard to tell that to cities that may simply not have enough water for their booming populations. “You look at the big cities of the West, and they’re pretty much all using the same or less water than 30 years ago,” Kenney says. “But they can do that because they had a big enough base to start from. It’s pretty easy to go to a city of one million and say you can conserve your way to the next 50 years of growth. It’s hard to go to a city of 500 people that’s growing rapidly, and say that conservation is the way you’re going to grow for the next couple of decades.”</p><h2>Tradeoffs</h2><p>At some level, decisions about how to plan for the future of Western water supplies come down to both values and inertia. As Werner says, it’s not feasible to stop people from moving to Colorado’s Front Range and other booming parts of the Western U.S. While environmental conditions—unbearably hot summers or persistent extreme drought—might ultimately make both the Front Range and the entire West far less attractive, for the moment, they’re still desirable places to live. It’s hard to stop progress.</p><p>“I see all of these Front Range projects as tradeoffs for society, just like building another freeway or power plant,” Waskom tells me when I call him on his cell phone one morning. “They are the costs of growth to live the way we live. I think there will be an effort to do the best we can for the environment, but everything has an impact, and I think we all have to take some personal responsibility for that.”</p>
<figure class="richtext-image full-width">
<img alt="" class="richtext-image full-width" src="https://www.pbs.org/wgbh/nova/media/images/carter_chim_hollow.width-990_R8fUWvB.jpg"/>
<figcaption>A view of Chimney Hollow with Carter Lake Reservoir in the background
        
    </figcaption>
</figure>
<p>At Northern Water’s headquarters in Berthoud—another rapidly growing Front Range town—a series of experimental garden plots occupy several acres behind the building. There, the utility is growing scores of different kinds of grasses and perennials using varying amounts of water and types of irrigation systems and soil amendments. New signs detail the watering needs of various landscapes and link, via QR codes, to web pages filled with water-conserving information for homeowners and professional landscapers. “I’m a huge believer that you better be able to convince people you’re doing everything you can do to save every last drop of water before you go out and build that next water project,” Werner says.</p><p>Still, this is the same utility that, back in the mid 1980s, immediately after the Cache La Poudre became the state’s first river to receive an official Wild and Scenic designation, proposed building a 300-foot-high dam in the Poudre Canyon, west of Fort Collins. (The designation tied up 90 percent of the river above the canyon mouth from future development but left a seven-mile stretch through the canyon open.) “From a strict engineering sense, it made the most sense,” Werner says. “Run-of-the-river reservoirs are the best way to do it, in canyons. Part of what I’m saying about the new world is, you don’t do things from strictly engineering standpoint.”</p><p>The new world is nothing if not complex. It’s a world of tradeoffs, a world without easy answers. Still, standing on the hillside at Chimney Hollow, I’m sure of one thing: I wish there was some way to spare this spectacular place.</p>
<div class="newsletter"></div>
<p>Photo credits: <a href="https://www.flickr.com/photos/kairologic/">Bombaci Photography/Flickr (CC BY-NC-ND)</a> , Cassyt (CC BY-NC), <a href="https://www.flickr.com/photos/question_everything/4114858561/">Let Ideas Compete/Flickr (CC BY-NC-ND)</a> , U.S. Bureau of Reclamation</p>

<p data-block-key="esuew">New dams and reservoirs are unmistakably altering the American West’s iconic landscapes.</p>

Hillary Rosner

Articles

Mapping the Microbiome

How Water Is Reshaping the West

Support Provided By