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Genome organization & proteomics of HCH degrading bacteria chalked

Rapid fire

  • Use of in-situ consortium best bioremediation of HCH degradation
  • Bio-stimulation would be a better approach
  • Ten draft genome announcements, comparative genomics, metagenomics, taxonomical characterizations & bioremediation studies from project
  • Thirty four research papers
  • More than 40 students trained

Lindane, or Hexachlorocyclohexane (HCH), a toxic agricultural chemical is difficult to remove from the environment on account of the poor understanding HCH degraders in relation to condition prevailing at such natural dumpsites.

A DBT supported study chalked out genome organization and proteomics of HCH degrading bacteria and metagenomics, metatranscriptomics analysis at the HCH dumpsite.

The study was an attempt to develop a better understanding of the microbes involved in HCH degradation in pure culture conditions and also at the dumpsite.

Sphingobium indicum B90A was sequenced and further sequencing gaps were filled. This led to designation of the assembled sequence data into respective replicons, i.e., chromosome and plasmids. Further, the genomes of the HCH degraders were sequenced and annotated to reveal their genomic ability to survive in high HCH concentrations (450mg/g) and to metabolize different HCH isomers.

The information so obtained was utilized to perform comparative genomics of Sphingobium spp., which revealed the ongoing evolution of HCH degradation pathway among HCH degraders.

Hexachlorocyclohexane (HCH) also known as lindane has been used extensively for the control of agricultural pests leading to serious contamination of our environment.

Regardless of the stereochemistry, stability and persistence of HCH isomers, they have been known to damage the environment, toxic to mammals as they cause mutations, disrupt endocrine system and cause cancer.

One ton purification of lindane from technical HCH produces 10 tons of HCH muck consisting of α-, β- and δ- HCH. During the past 60 years, large quantity of lindane has been used worldwide leading to the formation of 4-7 million tons of HCH muck that is scattered at different places round the globe.

Several efforts to develop a bioremediation technology for the decontamination of this HCH muck have been made in the past but these have not been fruitful yet.

As of today, no technology exists that can aid in complete decontamination of HCH isomers. Poor understanding of these HCH degraders in relation to condition prevailing at such natural dumpsites is a major limiting factor for developing bioremediation technology.

This study showed the abundance of sphingomonads spp. at the HCH dumpsite, which are well known for their role in HCH degradation. In addition, the data was utilized for reconstruction of the last common ancestor of Sphingobium spp. whereby linA and linC were found to be environment specific traits whereas linB, linDER were found integrated in the predicted ancestor. The metatranscriptomics analysis also showed the abundance of Lin genes at the dumpsite and proteomics study identified the enhanced expression of Lin genes under treatment with HCH isomers. The potential HCH degraders were used to perform the biodegradation trials using pot scale study, which revealed a maximum of 51.7% degradation using a combination of biostimulation and bioaugmentation.

The study also highlighted the role of IS6100 elements in Lin genes acquisition and their differential variation in close vicinity of Lin genes. Culture-based studies revealed enrichment of Pseudomonas genotypes along with Sphingomonads followed by isolation of a HCH tolerant strain, Pseudomonas sp. Further, in an effort to reveal the unculturable diversity at the HCH dumpsite metagenomic analysis was performed on the soil samples obtained from the dumpsite, 1Km and 5Km away from the dumpsite.

The work carried out under this project was published in peer reviewed journals consisting of 10 draft genome announcements, comparative genomics, metagenomics, taxonomical characterizations and bioremediation studies. In the last 4 years, thirty four (34) research papers have been published in the peer reviewed scientific journals. More than 40 students got trained.

Investigators have used multiple strategies to study HCH degradation and precisely concluded that use of in-situ consortium will be best option for bioremediation of HCH degradation and biostimulation would be a better approach. Results obtained in metagenomic analysis also revealed that it’s a community which is working in bioremediation of HCH. In future further community analysis and bio-stimulation studies needs to be attempted for development of bioremediation strategy for HCH degradation.

Slider Image : Comparative genome map of Sphingobium spp. S. japonicum UT26S used as a reference genome over which other strains were mapped. Genes for HCH, Phenol/Toluene, Chlorophenol, Anthranilate and Homogentisate degradation pathways were identified in the outermost region of the figure. Outermost circle1: Orthologous genes, circle 2: S. lactosutens DS20, circle 3: S. baderi LL03, circle 4: S. quisquilarium P25, circle 5: S. ummariense RL3, circle 6: Sphingobium sp. HDIPO4, circle 7: S. chinhatense IP26, circle 8 (innermost circle): S.indicum B90A. (Darker color intensity represents higher percentage identity).
Slider Image : Comparative genome map of Sphingobium spp. S. japonicum UT26S used as a reference genome over which other strains were mapped. Genes for HCH, Phenol/Toluene, Chlorophenol, Anthranilate and Homogentisate degradation pathways were identified in the outermost region of the figure. Outermost circle1: Orthologous genes, circle 2: S. lactosutens DS20, circle 3: S. baderi LL03, circle 4: S. quisquilarium P25, circle 5: S. ummariense RL3, circle 6: Sphingobium sp. HDIPO4, circle 7: S. chinhatense IP26, circle 8 (innermost circle): S.indicum B90A. (Darker color intensity represents higher percentage identity).