Microbial Diversity Responses to Lead Contamination Concentration in the Agricultural Soils, Lapindo Mudflow Area: Preliminary Bioremediation Study

Sample Collection and Processing: Soil samples were collected from two agricultural locations near the Lapindo Mud area in Sidoarjo, Indonesia. Sampling was done diagonally at depths of 0-15 cm, spaced 5 meters apart. Samples were homogenized and dried for analysis of physical (texture, moisture, permeability) and chemical characteristics (pH, CEC, organic carbon, total nitrogen, total phosphorus, and lead concentration). Analyzes took place at Brawijaya University from August 2023 to September 2024, with NGS conducted by a genetic science company.DNA Extraction and PCR: Chromosomal DNA was extracted using a modified Fast DNA Spin Kit. The DNA was purified, concentrated, and analyzed for quality via agarose gel electrophoresis. PCR amplification of 16S rDNA was performed, followed by purification of PCR products and library preparation for sequencing. Data quality was assessed using Qubit and Agilent systems.Analysis of Chromosomal DNA: DNA concentration was measured using NanoDrop and Qubit. Nanopore sequencing was performed, followed by base calling and quality filtering. Reads were classified using a Centrifuge classifier, and downstream analyses were conducted with tools like Pavian and RStudio to assess microbial diversity and taxonomy.Bioinformatics Workflow: The workflow included sample collection, DNA extraction, quality control, library preparation, and Nanopore sequencing. Data processing involved base calling, quality filtering, read classification, and downstream analysis, providing insights into microbial composition and potential for bioremediation of contaminated soils.