Researchers led by Yasunori Ichihashi at the RIKEN Center for Sustainable Resource Science (CSRS) in Japan recently examined how different kinds of pesticides and fertilizers affect mandarin oranges across Japan. Advanced statistical analysis showed that while reducing pesticides enhanced the diversity of microbes in the soil, it also led to an increase in fruit disease caused by leaf pathogens. The real-world data from commercial farms thus indicate a trade-off above ground with potential ecological benefits below ground. The study offers important insights for the advancement of sustainable agricultural technologies and future policy development.

Typical agricultural research is done in controlled conditions in laboratories or in test fields. This leads to a gap between experimental findings and what happens in real-world farms. In an effort to bridge this gap, Ichihashi and his team collected fruit and soil samples from mandarin orange orchards across 12 prefectures in Japan. Unlike in a controlled experiment, farmers choose the type of pesticides and fertilizers that they want to use. These biases, along with variable environmental factors, make it difficult to discern the real effects.

To overcome this problem, the researchers turned to a statistical method that is often used in academic fields such as economics, where controlled experiments are impractical or unethical. There are many variables that affect fruit and soil, such as the cultivar category, tree age, annual temperature, amount of rain, duration of sunshine, and soil type. The statistical method adjusts these co-varying factors using a technique called inverse probability weighting. After the adjustment, the researchers were able to control for these factors and see how pesticide and fertilizer types affect soil properties, microbial communities, and fruit quality.

Farmers in Japan vary in their use of pesticides and fertilizers. The study showed that the most common practice is to use chemical pesticides with chemical and organic fertilizers. However, some farms used organic pesticides, and some used only organic fertilizer. The frequency of use also varied, with some farms applying pesticides and fertilizer less often than the standard frequency. Complicating the situation, the researchers found that factors such as climate and tree age varied across these different cultivation methods. “These data indicate that simple comparisons between methods can lead to biased conclusions,” says first author Fuki Fujiwara. “This underscores the necessity of using advanced statistical techniques, as was done in this study, to accurately evaluate the effects of cultivation practices.”

Analysis showed that reducing chemical pesticides led to more fruit diseases caused by leaf pathogens. At the same time, it enhanced soil microbial diversity and reduced the number of soil pathogens. Carbon content in the soil was improved by reducing chemical input, not by the use of organic fertilizers. This challenges the common assumption that adding organic fertilizers directly increases carbon storage. Instead, it indicates that reducing fertilizers—nitrogen input—may be more important.

“In the short-term,” explains Fujiwara, “this study offers immediate feedback to the agricultural community by scientifically demonstrating how the types of pesticides and fertilizers affect fruit quality and soil conditions.” Farmers can use these insights to improve their cultivation methods and make informed decisions that balance sustainability with productivity. For policymakers and agricultural extension services, the findings provide valuable evidence for designing support programs that align with real-world farming practices.

“In the long-term this study lays the foundation for more evidence-based decision-making in agriculture by utilizing real-world data and robust statistical methods,” says Fujiwara. The next steps for the laboratory will include applying their methods to other crops and regions, as well as feedback to farmers.

Ichihashi says that by collaborating closely with agricultural producers, they aim to return their scientific findings to the field and strengthen the link between research and practice. “We hope to enhance partnerships with farmers, private companies, and local governments to improve data collection and practical implementation of research findings.”