Geochemical Differences, Source apportionment, and Origin Discrimination of Mineral Elements in Soil and Coffee Beans — A Case Study of Puer and Baoshan, the Largest Coffee Producing Regions in China

Background Yunnan, China, is one of the most important coffee-producing regions globally, yet little is known about how local soil mineral compositions influence bean quality and provenance. This study aims to explore the geochemical factors that control the source and bioavailability of mineral elements in coffee-growing soils. Furthermore, it investigates the extent to which soil elemental profiles can serve as reliable indicators for tracing the geographical origin of coffee beans. Methods We collected a total of 85 soil samples (Pu'er n = 31, Baoshan n = 54), 52 coffee bean samples (Pu'er n = 23, Baoshan n = 29), and 4 bedrock samples (2 per site). The concentrations of 11 mineral elements (Cr, Cu, Mn, Zn, Ca, K, Mg, Fe, Pb, Mo, and As) were measured using ICP-MS, along with soil pH and soil organic matter. Enrichment factor, bioconcentration factor, principal component analysis, and partial least squares regression were used to assess elemental mobility, sources, and traceability. Results The contents of As, Cr, and Pb in soils and beans were below national safety limits. K, Ca, Mg, Cu, and Mo showed high bioavailability, with higher uptake in Pu'er. Higher Pb and As accumulation was observed in Pu'er beans, whereas Zn and Mn were more enriched in Baoshan. Cr, Mo, and As originated from human activities, while Mg, Ca, and K stemmed from natural weathering. The elemental sources in Pu'er included weathering, industrial emissions, and agriculture; in Baoshan, coal combustion, mining, and agriculture were dominant. Three latent variables were extracted, with higher explanatory power in Pu'er (Xp: 78.07%, Yp: 38.69%) than in Baoshan (Xb: 46.26%, Yb: 29.49%). The LV1 axis enabled clear origin discrimination. Cr, Cu, Ca, and Mg were identified as key soil indicators for coffee origin traceability. Conclusion The concentrations of toxic elements remained within safety limits in both regions. However, notable regional differences were observed in element bioavailability and accumulation. Pu'er beans accumulated more Pb and As, while Baoshan showed greater enrichment of Zn and Mn. Source analysis revealed mixed natural and anthropogenic contributions, varying by region. PLSR effectively distinguished between coffee origins, with Cr, Cu, Ca, and Mg identified as core indicators for geographic traceability.