Comparative genomics reveal unique markers to monitor by routine PCR assay bioinoculant of Sphingobium indicum B90A in hexachlorocyclohexane (HCH) contaminated soils

• Published in: Indian journal of microbiology 2024-09, Vol.64 (3), p.1266-1277
• Main Authors: Phian, Sonika, Verma, Helianthous, Singh, Durgesh Narain, Singh, Yogendra, Lal, Rup, Rawat, Charu Dogra
• Format: Article
• Language: English
• Subjects: Amplification; Biomarkers; Biomedical and Life Sciences; Bioremediation; Decontamination; DNA sequencing; Gardens & gardening; Gene sequencing; Genes; Genomes; Hexachlorocyclohexane; Life Sciences; Medical Microbiology; Microbiology; Nucleotide sequence; Original Research Article; Polymerase chain reaction; Similarity; Soil contamination; Soil pollution; Soils; Sphingobium indicum; Tracking; Uniqueness
• ISSN: 0046-8991; 0973-7715
• DOI: 10.1007/s12088-024-01321-7

Bioinoculants of Sphingobium indicum B90A have been used to decontaminate hexachlorocyclohexane (HCH)-contaminated soils in the past. There is no selective or convenient method available to track the added B90A in HCH-contaminated soils in the presence of several native sphingomonads. Here, we describe a method, BioMarkTrack, for tracking B90A bioinoculant by simple amplification of the B90A specific biomarker genes. Whole-genome sequence data of 120 different genera of sphingomonads ( Sphingobium , Novosphingobium , Sphingomonas , Sphingopyxis , and Sphingosinicella ) were retrieved from the NCBI database and annotated. Intra- and inter-genus similarity searches, including the genome of B90A as a reference was conducted. 122 unique gene sequences were identified in strain B90A, out of which 45 genes were selected that showed no similarity with the NCBI non-redundant (NR) database or gene sequences in the publicly available database. Primers were designed for amplification of 4 biomarkers. To validate the biomarkers B90A tracking efficacy in bioaugmented soils, a microcosm study was conducted in which sterile garden and HCH-contaminated dumpsite soils were amended with strain B90A. Amplification of the biomarker was observed both in sterile garden soil and HCH-contaminated dumpsite soil but not in control (lacking B90A) samples. Further, the primer set was used to track B90A in a bioremediation field trial soil, demonstrating the convenience and efficiency of the simple PCR-based method, which can be employed for tracking B90A in bioaugmented soils. The approach as presented here can be employed on different bioinoculants to identify unique biomarkers and then tracking these organisms during bioremediation.