Journal of Advances in Microbiology

Background: Sponge iron industries release heavy metals and other industrial pollutants that can alter soil physicochemical properties and disrupt native microbial communities. These changes may influence microbial diversity, ecological interactions and functional processes. However, the combined diversity and functional adaptation of bacterial, fungal and viral communities in sponge iron industry-contaminated soils remain insufficiently characterised, highlighting the need for an integrated metagenomic investigation.

Aims: To investigate the taxonomic composition, functional potential, and multi-kingdom ecological adaptation of microbial communities in sponge iron industry-impacted soil using whole-genome shotgun metagenomic sequencing, with a focus on identifying microbial taxa and metabolic pathways associated with tolerance to heavy-metal stress and ecological resilience.

Study Design: An observational, cross-sectional, culture-independent metagenomic study integrating physicochemical characterisation, whole-genome shotgun sequencing, and bioinformatics analyses.

Place and Duration of Study: Soil affected by the sponge iron industry in Barjora, West Bengal, India. Laboratory investigations, sequencing, and computational analyses were conducted during the study period.

Methodology: Soil physicochemical properties and concentrations of heavy metals, including Fe, Pb, Cd, and As, were assessed. Illumina whole-genome shotgun sequencing generated approximately 51.199 million raw reads, with 44.257 million cleaned reads reported after quality filtering. Bacterial, fungal, and viral communities were characterised through taxonomic profiling. Functional annotation was performed using KEGG Orthology (KO), Enzyme Commission (EC), and Pfam databases to investigate metabolic pathways, functional enrichment, and microbial diversity.

Results: Bacterial communities were dominated by Proteobacteria (58.78%) and Actinobacteria (21.32%), whereas Acidobacteria accounted for only 0.86%. Ascomycota dominated the fungal communities (87.49%), particularly Thermothielavioides terrestris and Thermothelomyces thermophilus. Viral communities were predominantly represented by Caudovirales bacteriophages, including Siphoviridae and Myoviridae. Functional annotation revealed enrichment of fatty acid metabolism, β-oxidation, aldehyde detoxification, and ABC and MFS transport systems, suggesting adaptive responses associated with oxidative-stress management and cellular homeostasis. Rarefaction analyses indicated greater bacterial and viral richness than fungal richness.

Conclusion: The findings indicate multi-kingdom microbial restructuring and functional adaptation under chronic industrial contamination. The proposed Multi-Kingdom Adaptation Workflow (MKAW) provides a systems-level framework for understanding microbial resilience and identifying potential bioindicators and functional targets for industrial soil bioremediation.