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Livestock antibiotics may disrupt soil microbes

Researchers find that the effects of livestock antibiotics as well as heat caused by climate change can harm soil health
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Some soil microbes may be well-adapted to survive in high heat, others may be able to defend against antibiotic compounds and others may be able to handle both, but researchers say many microbial organisms will not be well-equipped to handle either stressor.

WESTERN PRODUCER — Soils are home to complex diversity of microbe communities that provide nutrients to plants, trap carbon, and hold water.

But soil health is subjected to stresses, including the effects of heat from climate change. When heat is combined with other stresses in the soil, such as livestock antibiotics, the impact can disrupt microbial communities.

As well, research from the Cary Institute of Ecosystem Studies in Millbrook, New York, has shown the impact of combined soil stresses that disrupt the soil’s microbial communities also leads to shifts in carbon and nitrogen.

“Our research group has been interested in how livestock-derived antibiotics are influencing soil,” said Jane Lucas, community ecologist at Cary Institute. “We know that many studies have examined how antibiotic compounds influence animal health, but far less is understood about how these active compounds influence the environment.”

She said that unused and active antibiotics can be eliminated through animal waste and enter the environment. Their previous research highlighted that these active compounds have the potential to change which microbes and invertebrates live in the soil with implications for soil function and nutrient cycling.

Researchers explored the interaction between antibiotics and temperature. They predicted that antibiotics could interact with temperature to create larger disturbances in soil communities or possibly the two could counteract each other.

Lucas said that warmer environments often help break down active antibiotics and support more microbial activity. However, antibiotics were expected to possibly decrease microbial activity, so they had an alternative prediction that rising temperature could help decrease some of the antibiotic effects.

Instead, the study recorded increased disruption with additional stressors.“I think this work is an important step in demonstrating that soil communities are capable of rebounding from some levels of stress, but the further we push them, the more difficult it may be for them to recover,” said Lucas. “This work also demonstrates that soil microbes respond to many different types of stressors and, because of their immense diversity, predicting which microbes will survive when faced with multiple stressors can be difficult.”

Heat and antibiotics can influence soils in a variety of ways. Some soil microbes may be well-adapted to survive in high heat, while others may be able to defend against antibiotic compounds. Still others may be able to handle both.

“But many microbial organisms will not be well-equipped to handle either of these stressors, which is why we saw a large drop in bacterial abundance when soils were in the warm, antibiotic-laden environments,” said Lucas. “Additionally, many of the mechanisms for how microbes defend against antibiotics are different from how they handle heat stress.”

In the study, the research team used Monensin, a common antibiotic used on cattle farms. While it is economical and easy to administer, it is poorly metabolized and much of it is still biologically active when excreted.

The researchers collected samples of prairie soil and vegetation from preserved land in northern Idaho free of grazing livestock. The samples were treated to either high, low or no doses of the antibiotic, heated at three different temperatures (15 C, 20 C, and 30 C) for seasonal variation and monitored for soil respiration, acidity, microbial composition and function, carbon and nitrogen cycling, and interactions among microbes.

When the rising heat combined with the antibiotic additions, bacteria collapsed, allowing fungi to dominate, which resulted in less microbial diversity.

Antibiotics alone increased bio-available carbon, while rising temperatures alone increased soil respiration and dissolved organic carbon. The net result of these changing carbon pools was a reduction in long-term carbon storage capacity.

“We saw real changes in soil microbe communities in both the low and high-dose additions,” said Lucas. “Rising temperature exacerbated these antibiotic effects, with distinct microbial communities emerging at each temperature tested. Within these assemblages, we saw reduced diversity and fewer micro-organisms overall. These changes could diminish soils’ resilience to future stress.”

She said that heat, in general, can be difficult for microbial organisms because all microbes have a thermal tolerance maximum. If they experience temperatures beyond that, they cannot survive.

“Soils are an amazing environment, and it takes a lot of energy to heat them to high temperatures, but when soils are exposed and experiencing unprecedented continuous warming, the soil microbiome will likely suffer. We often use heat as a way to kill microbial organisms (e.g., pasteurization), which emphasizes the susceptibility of microbial organisms to high temperatures.”

Soil is widely recognized as a carbon sink but, at the same time, it can be a carbon source, especially when factoring in stressed microbes. Soils produce and emit carbon while at the same time, act as an invaluable carbon store.

“However, we know that we are losing important topsoil and, particularly in croplands, topsoil is eroding 10 times faster than is being produced,” she said. “Ultimately, we need to do what we can to keep our soils intact and functioning as a long-term carbon store. This study highlights an additional way in which choices in agricultural management can have downstream effects that may hurt the long-term health and function of our soils. The next big question is how long are the effects of antibiotics and are there ways to recover from these introductions?”

In a domino effect, as antibiotics and rising soil temperatures disrupted microbe communities and their network structures, they cleared the way for a rise in fungal dominance and a change in soil nutrient reaction relationships.

“Our study found that fungi became dominant over bacteria, and also that the diversity of fungi decreased in high heat environments,” she said. “A likely reason for fungi to become more dominant was because the antibiotic in our study specifically targeted bacteria. This meant that many bacteria were killed, nutrients were released, and fungi had decreased competition. We often consider fungal-dominated soils as healthier and more efficient as fungi are able to build networks and forage for nutrients. That is not what we found in our study.

“Instead, even though fungi were able to increase, the overall microbial efficiency decreased, likely due to the stress of having to both defend against antibiotics and survive in high heat environments. Although fungi increased in abundance, the diversity of fungi was low at high heat, likely because only a subset of fungal species could handle the increased temperature.”

Lucas said researchers next plan to set up a long-term field experiment to examine how soils respond to multiple global change factors.

The research was published in Soil Biology and Biochemistry.