Large-scale analysis of real-world production data from mandarin orange orchards: Soil can be improved through reduction of pesticides and fertilizers

Special Postdoctoral Researcher Fuki Fujiwara and Team Director Yasunori Ichihashi from the Holobiont and Resilience Research Team at the RIKEN Center for Sustainable Resource Science and Professor Naoto Nihei, Associate Professor Yukari Okano, and Associate Professor Daisuke Takata from the Faculty of Food and Agricultural Sciences at Fukushima University, in collaboration with the University of Tokyo, Hokkaido University, and the Research Institute of Environment, Agriculture, and Fisheries, Osaka Prefecture, announced that they have clarified the possibility that reducing the use of pesticides and fertilizers can lead to environmental conservation effects and reduce soil pathogenic fungi. They did this by analyzing real-world data gathered from mandarin oranges and their orchards across Japan. They collected oranges and soil from mandarin orange orchards across the country, converted them into data, and conducted large-scale analysis. This is expected to contribute to sustainable agriculture. The results were published in Plant Biotechnology on December 25.

Maintaining agricultural production while reducing the environmental burden of pesticides and fertilizers has become an important challenge in sustainable agriculture. To achieve this, an understanding of the agricultural ecosystem formed by crops and microorganisms is essential, but it is difficult to reproduce actual, varying conditions in experimental orchards and laboratories. In particular, fruit trees such as mandarin oranges require a long time until they can be harvested and obtaining and analyzing experimental data has been difficult.

Therefore, in this study, the research group focused on real-world data obtained directly from producers' orchards. They compared and examined data that has previously been difficult to compare by applying statistical methods from cohort studies.

The researchers themselves collected a total of 206 fruit and soil sample sets from 11 prefectures, including major production areas (Ehime, Hiroshima, Kagawa, Kanagawa, Kumamoto, Mie, Osaka, Saga, Shizuoka, Tokushima, and Wakayama Prefectures). They then conducted multi-omics analysis.

The cultivation methods behind each sample were classified based on the types and amounts of pesticides and fertilizers used. The samples included "conventional cultivation" using common chemical pesticides and chemical and organic fertilizers, "special cultivation" in which these were reduced by half, "organic cultivation" using organic-certified pesticides but not chemical pesticides and with no limit on the amount of organic fertilizer, and "natural cultivation" using neither fertilizers nor pesticides.

As a result, in addition to gaining fruit quality data, the group constructed a multi-layered dataset that included soil chemical properties, elemental composition in soil extracts, soil microbial (bacterial and fungal) composition, and soil microbial functional composition. They successfully converted the agricultural ecosystem of mandarin orange orchards into data.

Furthermore, statistical adjustments were made to account for the possibility that varieties and environmental conditions might be biased in each cultivation method group. Specifically, differences in background conditions such as meteorological conditions, soil classification, variety, and tree age for each sample were expressed as "propensity scores," and, based on these, variations in background conditions were corrected using "inverse probability weighting."

Then, they used the multi-omics data to compare conventional cultivation and other cultivation methods. As a result, they found that the carbon content in the soil increased significantly in environmentally friendly cultivation methods such as the "special cultivation" and "natural cultivation" of mandarin oranges. Carbon content has been reported to contribute to improved soil fertility and mitigation of climate change.

Additionally, zinc and other heavy metals in the soil, which are sources of environmental pollution risk, were significantly reduced in the groups that reduced pesticide use. Interestingly, in "organic cultivation" where the amount of organic fertilizer was not limited, the soil carbon content did not increase. This suggests that reducing the "amount" of fertilizer may contribute more to increasing soil carbon content than changing the type of fertilizer.

In conventional cultivation using normal amounts of chemically synthesized pesticides, the degree of disease (citrus black spot disease) observed in harvested products was significantly suppressed compared with other methods. On the other hand, the proportion of pathogenic bacteria and fungi in the soil increased. This suggests that chemically synthesized pesticides may increase non-target pathogens through the reduction of microbial diversity.

Ichihashi commented: "Our research approach of using cohort study methods in this study can be applied to various studies related to agriculture and can also be applied to other crops. We will continue to focus on real-world data and aim to advance its application to the evaluation of a wide range of agricultural technologies, including biotechnology and compounds with functions that help plant growth called bio stimulants."

Journal Information
Publication: Plant Biotechnology
Title: A cohort study of sustainable cultivation methods in mandarin orange orchards across Japan
DOI: 10.5511/plantbiotechnology.25.0605a