Chromium pollution and its effects on soil health, microbial diversity, and sugarcane production in the Vellore sugarcane belt: a metagenomic and geochemical assessment

Disposal of tannery effluent has elevated soil chromium (Cr) across the Vellore sugarcane belt of southern India, yet its integrated consequences for soil health, bacterial communities and sugarcane productivity remain poorly characterised. Nine composite soil samples from a recognised tannery-affected belt were pre-stratified into High, Low and Near-threshold Cr sites. Soils and irrigation water were geochemically characterised for total and speciated heavy metals and profiled by full length (V1-V9) 16​S rRNA gene amplicon sequencing on an Oxford Nanopore GridION. Soil total Cr increased from 29.10 ± 0.14 to 180.51 ± 2.95 mg kg − 1 , the alkaline-extractable Cr (VI) fraction rising from 2.92 ± 0.09 to 52.07 ± 0.11 mg kg⁻¹ and co-occurring Cd and Ni increasing across strata. Soil pH shifted alkaline (7.74 to 8.48), organic carbon declined by up to 31.7% and exchangeable Ca and Mg by up to 40.4%. Tissue Cr followed root > shoot > leaf but peaked at Near-threshold rather than High Cr sites, indicating bioavailability-driven uptake. Cane and stalk fresh weight declined 25.8–31.3% at High Cr sites, whereas sucrose, Brix, purity and fibre remained largely unchanged. Alpha diversity followed a threshold structured rather than linear dose response, with observed richness in High Cr levels reduced to 74–76% that in Low Cr levels alongside parallel declines in Shannon diversity and Pielou’s evenness. NMDS resolved three non-overlapping community clusters. A Cr-resilient core ( Sphingomonas panacis , Nitrospira lenta ) persisted alongside elevated prediction of azoR/acpD and chrA abundance, defining a chromium-tolerance signature in tannery-impacted sugarcane soils.