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Tiny indicators of change: Microbes in the Texas High Plains may lead to better understanding of how changes in production,environment affect soil health


  1. Madeline Fisher
  1. science communications manager

Green circle images courtesy of EMSL’s photostream on Flickr. Backdrop image of grazing cattle courtesy of Jennifer Moore-Kucera.


This article in CSA NEWS

  1. Vol. 58 No. 8, p. 4-10
    unlockOPEN ACCESS
    Published: August 1, 2013

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Even when you know that every teaspoonful of soil teems with millions of busy microorganisms cycling nutrients, emitting gases, and carrying out other crucial functions, it’s hard to imagine such a bounty of belowground life in the Texas High Plains.

Dry, sunbaked, and sandy, the region’s soils frequently blow up into dark clouds, causing streetlights to blink on in Lubbock and other west Texas towns in the middle of the day. Decades of growing cotton continuously has robbed them of organic matter, and soil acidity is becoming a problem, as well. Yet, when Jennifer Moore-Kucera interviewed for a professorship at Texas Tech University in 2008, the young soil microbiologist knew the High Plains was where she wanted to be.

The draw was a long-term experiment in an alternative to continuous cotton: a mix of cotton, cattle, and forages on the landscape known as an integrated crop–livestock system, or ICL. In it, scientists were examining everything from yields and profitability to soil biology and quality, thanks to the vision of the project’s leader, Vivien Allen. A Texas Tech forage agronomist and animal scientist (now retired), Allen had a penchant for bringing diverse researchers together on problems. And she and Moore-Kucera seemed to share a passion.

“During my interview, one of the main people I immediately knew I wanted to work with was Vivien,” says Moore-Kucera, an SSSA member. “I thought what she was doing was great from a conservation and sustainability perspective.”

A more sustainable way of farming is urgently needed on the Texas High Plains. This region stretching from the Texas Panhandle south to the Pecos River was once a vast grassland that early settlers rejected because of its unreliable water supply. Then in the late 1880s, people figured out how to tap the region’s massive groundwater source, the Ogallala Aquifer, and “it just changed the world in terms of what you could do out there with agriculture,” says Allen, an ASA and CSSA Fellow. Today, the High Plains produces 25 to 30% of all U.S. cotton and finished beef, but that prodigious output has come at the aquifer’s expense. It’s now in fast decline, and as wells dry up and the cost of pumping the remaining ones skyrockets, the need for alternative practices that can preserve the region’s agricultural enterprise is increasingly hard to deny.

This scarcity and its unsettling consequences were the first things Allen learned about when she arrived at Texas Tech in 1995, and soon she was pondering the ICL system as a possible solution. With funding from USDA’s Sustainable Agriculture Research and Education (SARE) program, she and her team launched the ICL experiment in 1997 and have since examined nearly everything one can think of. They’ve shown the ICL system requires 25% less irrigation than continuous cotton, for example, and nearly 40% less nitrogen fertilizer. The integrated approach is also profitable—perhaps the most essential aspect of sustainability there is. “If you can’t stay in business, it’s not sustainable no matter what else you’re doing,” Allen points out.

Then there are the things most people don’t think about: the diversity of fungi and bacteria in the soil, how their activities interact with human management, and—most critically—the contributions they make to sustainability, especially as the region becomes drier. Some scientists may be skeptical that microbes really matter; Allen, Moore-Kucera, and their colleagues are not among them.

“We want to be able to predict what future management is going to do to important functions like soil stability, carbon storage, and nutrient cycling,” says Moore-Kucera. “And all of those functions are driven by the actions of microorganisms.”

Green circles: Electron microscope image of soil fungus. Photo courtesy of USDA-ARS, Electron & Confocal Microscopy Unit, Beltsville, MD. Bottom image: Soil core collected from the WW-B Dahl old world bluestem paddock of an integrated crop–livestock system at the Texas Tech University New Deal Research Farm.

Photo by Jennifer Moore-Kucera.

Signaling a Shift in Soil Quality

Allen herself has always studied macroorganisms such as grasses and cattle, but her appreciation for microorganisms goes deep. “When I first took ruminant nutrition, my instructors said, ‘People feed the microbes and the microbes feed the cow,’” she says. “That’s very true, and it’s the same thing in the soil.” Speaking of soil, Allen was reminded repeatedly of its fragility during her first months in Lubbock, where strong winds frequently whip up dust storms.

“I was naïve enough to think they were something we read about in history books,” she says. “Then one day we had one, and, oh my!”

Still, when Allen spearheaded the launch of the ICL experiment, she wasn’t thinking as much about soil as the system’s impact on economics and water use. The idea was this: By returning part of the region’s immense monoculture cotton fields to grasses and other forages for cattle, producers could potentially save water, while maintaining or boosting profitability, diversifying their income stream, and lowering their vulnerability to swings in the cotton market and the weather. And, indeed, during the experiment’s first four years, the ICL system—with cattle, forages, and cotton—was more profitable than cotton alone (in the longer term, the two systems’ profitability has been equal). Moreover, the integrated system required substantially less irrigation and protected the soil, while providing the same amount of cotton per acre and excellent animal nutrition, Allen says.

The findings were just what the researchers had hoped for, but they were also itching to expand the project’s scope. “We knew from the beginning that it was a gold mine to go after all kinds of questions,” Allen says, and in 2002, an opportunity came along to do just that.

It started with a phone call. On the line one day was a researcher Allen had never met, a USDA-ARS microbiologist and ASA and SSSA member in Lubbock named Veronica Acosta-Martinez, whose own approach to sustainability centered on soil quality and function. Could she take some samples from the ICL experiment, she asked? “And I said, ‘Absolutely,’ ” Allen recalls. “How soon can you get here?’”

At the time, the project was in its fifth year and first incarnation, composed of three paddocks. One was planted to a perennial, old world bluestem grass with the unusual nickname “WW-B Dahl” for the Texas Tech range scientist, Bill Dahl, who first recognized its promise. The other two paddocks had the same rotation (but at different stages) of winter wheat followed by fallow in summer, rye in fall, and no-till cotton the following spring. Beef cattle grazed the B Dahl grass in spring and summer and then wheat, rye, and dormant grass in winter.

Having some land permanently in pasture had already shown many benefits by the time Acosta-Martinez began her work. And sure enough, the pasture soils likewise contained twice the microbial biomass of continuous cotton by year five, along with greater microbial enzyme activities and larger fungal populations. In the rotation, on the other hand, “microbial activity depended on which crop you looked at,” Acosta-Martinez says. In rye, for example, enzyme activities and other soil microbial properties generally exceeded those in continuous cotton, while these properties under wheat and continuous cotton were pretty much the same. But as Acosta-Martinez continued to sample, she observed a gradual shift. By year 7, microbial biomass and activity were also significantly higher in the rotation—regardless of the crop.

“So, by analyzing the microbes we could see that changes were happening in the soil,” she says, such as enhanced metabolic capacity and signs of soil conservation. But the question remained: Did those shifts truly signal an improvement in soil properties? The team got its answer in year 10, when the traditional measure of soil quality—total soil organic carbon (SOC)—reached significantly higher levels in the pasture than in continuous cotton for the first time.

How Do Microbes Affect the ICL System?

The work thus supported two hypotheses: ICL management has positive effects on soil microbes, and these tiny indicators of soil quality respond faster to shifts in farm practices than parameters like total SOC. Demonstrating the system’s impact on soil microbial life was a crucial step, but today, Acosta-Martinez and her colleagues are more interested in the opposite question: What effect are soil microbes having on the ICL system?

Instead of simply monitoring total microbial biomass, for example, the scientists are now asking what microbial species or assemblages make up that biomass, and how are they contributing to improved processes under ICL management, such as increased carbon storage? “If we can’t understand the parts [microbes] that are important to the functionality we want, then we can’t really predict what the final outcome of management changes or disturbances will be,” Moore-Kucera says. “So, we try to take the system apart and understand the pieces to get to the whole.”

Examining the pieces is no easy task, though. For one, many more ICL experiments had been launched by the time Moore-Kucera joined Texas Tech, including a dryland experiment, a deficit-irrigated one, and 30 sites run by local farmers (see sidebar, next page). On top of this, the dynamic, three-dimensional structure of soil creates countless microenvironments where different types of microorganisms reside. “So we have to go to the niche level,” says ASA, CSSA, and SSSA member Marko Davinic, who earned his Ph.D. with Moore-Kucera in 2012. “We’re not going to analyze microbes by the handful of soil.”

Former Texas Tech University (TTU) Ph.D. students, Cody Zilverberg and Lisa Fultz collecting soil samples using a tractor-mounted Giddings Probe from one of the cattle exclusion areas in a WW-B Dahl old world bluestem paddock of an integrated crop–livestock system at the TTU New Deal Research Farm.

Photo by Jennifer Moore-Kucera.

Despite these challenges, Moore-Kucera and her group dove into the research with Acosta-Martinez. With another grant from USDA-SARE, they compared three different ICL systems and two continuous cotton ones, along with various soil micro-niches for bacteria and fungi. In some cases, they even tracked changes over time. “We did a ton of work,” laughs Moore-Kucera.

A central effort has been to determine the effects of ICL management not just on total SOC, but also on the specific carbon pools that promote water retention, carbon storage, and other critical processes. In a study just published in the Soil Science Society of America Journal, Moore-Kucera’s former student, Lisa Fultz, analyzed soil samples taken from 1997 to 2010 in the ICL and continuous cotton systems. Like those before her, Fultz saw an increase in total SOC in the ICL system, but more significant was what her analysis of different soil fractions revealed. The ICL system contained larger and more stable soil aggregates than did continuous cotton, indicating greater resistance to erosion. Plus, more carbon was stored within protected, recalcitrant soil pools—such as macroaggregates—suggesting the ICL system could better sequester it long term.

Davinic, meanwhile, examined the bacterial diversity in these same fractions with an advanced DNA sequencing technique called pyro-sequencing. Each fraction contained a distinct community, he discovered. Within macroaggregates, for instance, he found a greater abundance and diversity of Actinobacteria, which are important in soil aggregation, and a-Proteobacteria, critical to nutrient cycling. Microaggregates, in contrast, were richer in the Rubrobacteriales. It was a key demonstration of which bacterial groups inhabit various soil fractions and vegetation types—something that’s often only guessed at in other studies, Davinic says.

But the most exciting result emerged when the team decided to look at the fungi. Not only did the ICL system contain more fungal diversity and activity overall, but also larger numbers specifically of arbuscular-mycorrhizal fungi that associate with plant roots. Moreover, abundance of this group correlated strongly with soil aggregate stability and enzymes involved in phosphorus cycling—linking the microbes to two vital ecosystem functions, Moore-Kucera says.

The group’s hypothesis now is that under ICL management, higher inputs of plant organic matter and a lack of tillage—which tears up fungal hyphae—allow fungi and bacteria to flourish. As these organisms increase in abundance, they boost the cycling of nutrients and help stabilize soil particles in aggregates by enmeshing them in hyphae and releasing sticky substances. Improved stability of aggregates, in turn, reduces erosion, retains soil water, and helps store soil carbon—changes that further promote microbial growth.

“So, they’re all kind of working together,” Moore-Kucera says, “to build this overall sustainable ecosystem.”

Top image: Marko Davinic in the lab. Green circles: color-enhanced digital micrograph of a black and white scanning electron microscope image of Desulfovibrio desulfuricans.

Photo by Alice Dohnalkova and courtesy of EMSL’s photostream on Flickr.

What Can We Learn about Ecosystem Functions?

Now that this connection has been made, the scientists are asking yet another question: Can specific bacterial and fungal communities serve to indicate certain ecosystem functions? As Acosta-Martinez observed from the beginning, microbes are generally more sensitive to management changes than total SOC or other soil properties—suggesting microbial dynamics could signal larger changes to come. When farmers adopt a new practice, for instance, the appearance of a particular microbial assemblage could offer early reassurance that SOC is accumulating. “Or if there’s a disturbance, and we see an immediate decline in a certain group of organisms, maybe we can predict a decline in a certain associated function,” Moore-Kucera says.

Being able to make such forecasts will only become more critical as the region’s fortunes evolve, adds Acosta-Martinez. “We want to know how we can be more prepared for all that is coming: changes in climate and the transition here into dryland agriculture.”

One such change is the rise in sorghum production in the High Plains, says ASA and CSSA Fellow Chuck West, a Texas Tech forage agronomist who now directs the ICL program. That’s why he and Texas Tech animal scientist Sara Trojan are now designing a new ICL experiment focused on the water-frugal plants, and the pair will work with Acosta-Martinez and Moore-Kucera to monitor their impact on the soil. Meanwhile, the two microbiologists have another grant to study whether microbial communities can signal ecosystem-level changes in Conservation Reserve Program (CRP) grasslands that have recently been converted into dryland cropping systems.

Bottom image: Water-stable macro-aggregates (2–8 mm) collected during a size fractionation procedure. Photo by Dr. Lisa Fultz. Green circles: Scanning electron micrograph of Burkholderia cepacia.

Photo by Janice Haney Carr, CDC.

“The sites we’re looking at are very sandy, very low in organic matter. So are the benefits that perennial grasses provide to these soils maintained with this transition, or do they decrease as we shift back to annual cropping?” Moore-Kucera asks. “Or maybe there’s some kind of rotation—a compromise between keeping land in CRP for 25 years and just taking it out completely.”

Perhaps the biggest shift on everyone’s minds, though, is the one that’s happening in climate. In 2011, west Texas recorded its worst drought ever, with conditions harkening back to the Dust Bowl days. Just five inches of rain fell all year—two-thirds less than normal—and temperatures soared repeatedly above 100 degrees. Crop losses were huge, and many pastures and hay meadows never greened up that spring, including those of the ICL experiment.

“It was the first time ever in my entire career that I wasn’t able to put any livestock on research plots,” Allen says. “There wasn’t any grass there to put them on. There was nothing.”

Curious about what the soil microbes were doing under such barren conditions, Acosta-Martinez took soil samples from the experiment during the drought. And while her findings are still preliminary, they have her concerned. Expecting to see less microbial enzyme activity due to the lack of water, she observed instead higher-than-normal levels. It suggests to her that reserves of SOC built up over the course of the experiment are now being degraded as the drought lingers because little else is available for the microbes to work on.

“So, it’s something to keep in perspective,” she says. “If we are losing in droughts like this so much of the organic matter, then it’s important to know how we can recover from that.”

The result is troubling, but it also shows the potential for microbial information to inform decisions about agroecosystems—especially in places, like the Texas High Plains, where the best way forward is hard to know and the costs of making a wrong choice are high.

“I think what we’re doing is providing a pathway to the future, so that we can go more knowledgeably toward solutions instead of haphazardly,” Allen says. “Because the one given out there is that it’s changing.”




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