A Trench Plate-Based Approach for the Selective Isolation of Metal-Cycling Bacteria

Microbes play a vital role in biogeochemical cycling by transforming key elements such as iron, nitrogen, and selenium in natural environments. This study introduces and evaluates a novel Trench Plate Method, a magnetically guided enrichment approach designed to selectively isolate metal-cycling, magnetotactic-like bacteria from estuarine sediments of the Narmada River, India. The method enabled the enrichment of bacteria exhibiting directional motility toward magnetic poles, demonstrating its effectiveness as a behaviour-based isolation technique. Taxonomic identification through 16S rRNA sequencing and whole-genome sequencing revealed the isolate to be Escherichia coli, a surprising finding given the targeted selection. However, genomic analysis confirmed the presence of key metabolic genes involved in iron, selenium and nitrogen cycling, alongside magnetosome-like structures observed via transmission electron microscopy. These findings suggest an unexpected functional potential in E. coli, reflecting adaptive mechanisms in sedimentary metal-rich environments. The integration of behaviour-based enrichment with genomic profiling provides a powerful strategy for uncovering functionally relevant microbes, regardless of traditional taxonomy, with implications for biogeochemical studies and bioremediation.