Microbial diversity responses to lead contamination concentration in agricultural soils, Lapindo mudflow area: Preliminary bioremediation study

¹ Doctoral Biology program, Faculty of Natural Science and Mathematics, University of Brawijaya, Jl. Veteran, Malang City 65145, East Java, Indonesia.
² Department of Biology, Faculty of Natural Science and Mathematics, University of Brawijaya, Jl. Veteran, Malang City 65145, East Java, Indonesia.
³ Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Malaysia.
⁴ Department of Chemistry, Faculty of Natural Science and Mathematics, University of Brawijaya, Jl. Veteran, Malang City 65145, East Java, Indonesia

^* Corresponding author: This email address is being protected from spambots. You need JavaScript enabled to view it.

Abstract

Lead (Pb) contamination resulting from the Lapindo mudflow in Indonesia has generated long-lasting heavy metal stress in nearby agricultural soils, persisting for over 20 years. Microbial community responses to such environmental-geological contamination remain poorly characterized within the region. This study was designed as an exploratory investigation of the impact of Lead (Pb) contamination on bacterial diversity and community composition, in order to establish baseline ecological data for future large-scale bioremediation assessments. Soil samples were collected from three locations with differing Pb contamination levels: Location 1: Glagah Arum, Location 2: Polo Gunting, and Location 3: Pond epicenter-P025A. Physicochemical parameters were analyzed, and bacterial communities were characterized using Oxford Nanopore full-length 16S rRNA gene sequencing. Alpha-diversity metrics (Shannon, Simpson, and Chao1 indices) were computed from normalized operational taxonomic unit (OTU) data to assess microbial richness and evenness. Preliminary observations suggest that the physicochemical parameters are as follows: Location 1 (low, 2.85 mg/kg), Location 2 (moderate, 3.08 mg/kg), and Location 3 (high, 11.38 mg/kg). Diversity decreased by about 30–40% with increasing Pb concentration. Community composition appeared to shift progressively from Pseudomonadota dominance in low Pb soils to Bacillota and Thermodesulfobacteriota in moderately contaminated sites, and to Cyanobacteriota (Oscillatoriales) in highly contaminated soils. A resilient core microbiome of 425 taxa was detected across all sites. Redundancy analysis indicated Pb concentration as the dominant environmental filter, with soil organic matter and moisture providing secondary influences. This study provides an exploratory assessment of community composition under Pb contamination, excluding functional genes and an actual bioremediation assay, which may inform future bioremediation and ecological restoration.