Soil altered by livestock antibiotics

The overuse and misuse of antibiotics in medical settings is often credited for our rising rates of antibiotic resistance, yet it is not the only factor contributing to its rise. A surprising statistic for most is that in the U.S., the vast majority (80%) of antibiotics produced are used in livestock systems. This amounts to 33 million pounds of antibiotics provided to livestock annually. These antibiotics often pass through the animal and enter the environment via urine or manure. In the U.S., nearly 30 million pounds of antibiotics enter the environment in this manner annually.

Carl Wepking

Jane Lucas

Whether this antibiotic-laden manure is applied to fields as fertilizer or ends up in pastures, soils and the microbes that inhabit them are typically the front lines for exposure. Because soil microbes drive many critical soil functions, the introduction of antibiotics may be affecting both soil and human health.

A recent study found that prolonged exposure to manure from livestock given antibiotics changes the soil microbial communities and their physiology, as well as how carbon and nitrogen move through these terrestrial systems. Researchers in this study collected manure from cattle given one of two antibiotics, pirlimycin and cephapirin, and compared the effects to manure from untreated cows.

They found that antibiotic-laden manure increased the relative amount of fungi compared to bacteria, and bacterial groups of human health concern also increased. Fungi-to-bacteria ratios can be used as an indicator of soil health, with fungal-dominated soils considered to be more typical of undisturbed soil. With this in mind, an increased ratio of fungi to bacteria is thought to be a positive effect. However, in this case, the increase in the ratio of fungi to bacteria is likely to be attributed not to beneficial soil practices but instead to the diminishment of bacteria given the activity of antibiotics.

Evidence from this study also emphasizes the harmful influence antibiotic inputs can have on soil function. While both antibiotics changed the function of the soil, the reason for the changes was unique to each antibiotic. Cephapirin changed the physiology of the microbial community, leading to a decrease in microbial efficiency, an effect also observed in previous research. Pirlimycin, by contrast, changed the composition of the microbial community, leading certain bacterial taxa to play a more dominant role as compared to control manure. These differing effects highlight the compound-specific influence antibiotics can have on the ecological role soils play.

Ecologically, these changes in soil and terrestrial ecosystem function may be the tip of the iceberg. Microbes are important symbionts for all walks of life, and they are highly susceptible to antibiotic exposure. But microbes are not the only organisms affected by antibiotics. Additional studies have shown that insects and some of the processes they govern are harmed by antibiotic exposure. The influence of antibiotics on soil microbes and other soil organisms suggests that antibiotic introductions could cause effects on the entire soil food web, with repercussions on the functions we rely on from soils.

One of the key findings of this research is that not all manures are created equal. The amount of carbon sequestered in soils exposed to manure from cattle given antibiotics was less than that of plots exposed to control manure. If accumulating carbon in your soil is a goal of manure additions, then the source of your manure should be considered.

Additionally, while human health considerations were not the focus of our research, the topic of antibiotics cannot be mentioned without acknowledging the elephant in the room: The current arsenal of antibiotics struggles to deal with antibiotic-resistant pathogens. Previous work on this topic showed hundredsfold and even thousandsfold increases in certain antibiotic resistance genes with exposure to manure from cattle administered antibiotics compared to adjacent reference sites.

As genetic material can be transferred vertically (from parent-cell to offspring) and horizontally (from one bacterial cell to a neighboring bacterial cell), increasing the genetic material which codes for antibiotic resistance is a major concern.

One Health – the idea that environmental health and human health are intrinsically linked – is best encapsulated by the problem of growing antibiotic resistance and, as the concept suggests, this is a problem that must be considered holistically in order to find a solution. However, problems associated with antibiotics are emblematic of the many challenges facing our agricultural system. Monetary benefits of the prophylactic use of antibiotics in livestock are dwarfed by the downstream costs of antibiotic resistance.

Similarly, unintended consequences of some other agricultural practices cause reverberations far beyond farms. A dramatic example of one such reverberation is the dead zone created around the mouth of the Mississippi River in the Gulf of Mexico, which is estimated to cost over $80 million by way of seafood and tourism. To boot, rural communities are struggling; work by the Union of Concerned Scientists has shown that around 40% of farm income this year will be through some form of government assistance, while farm bankruptcies in 2019 were up by 25% from the previous year.

Perhaps the time has come to reimagine our agricultural system and find a model that emphasizes profitability, resiliency and sustainability, thus allowing rural communities to thrive while also providing key ecosystem services that society relies on from land. The unintended consequences of antibiotic use provides a glimpse into the challenges facing our current agricultural model and, when considered as part of the larger picture, can hopefully foster discussions leading to transformational change.