Metagenomic characterization of bacterial community in hypersaline Lake Tuz for halogenated pollutants degradation

Abstract

The use of microbes to degrade pollutants is the prevailing, low-cost green technology to treat different kinds of polluted environments. As a result of the unethical dumping of industrial effluents into these environments, many naturally existing hypersaline areas are becoming progressively polluted. This study, therefore, aim to evaluate microbial diversity, characterize novel pollutants degrading-bacteria from hypersaline Lake Tuz in Turkey and conduct in-silico assessment of dehalogenase gene. In this study, metagenomics analysis was done using 16S rRNA amplicon sequencing. Bacteria identification was performed using 16S rRNA amplification and whole genomic sequencing. The study also includes assessment and interaction of dehalogenase (DehH2) gene in respect to salt tolerance with pollutants haloacetates, haloacids and chlorpyrifos, by substrate docking, MD simulation and MM-PBSA. In the present study, metagenomic analysis revealed that Firmicutes, Fusobacteria and Proteobacteria were the most abundant phyla and functional genes related to adaptation and bioremediation potential. The isolated Bacillus subtilis strain H1 and Bacillus thuringiensis strain H2 were capable of degrading haloalkanoic acids, haloacetates and chlorpyrifos. Strains H1 and H2 were optimally utilized 2,2- dichloropropionic acid (2,2-DCP), 2,3-dichloropropionic acid (2,3-DCP), L-2- chloropropionic acid (L-2-CP), D-2-chloropropionic acid (D-2-CP), 3- chloropropionic acid (3CP), monochloroacetate (MCA), trichloroacetate (TCA) and organophosphate (chlorpyrifos) as their carbon source under similar growth conditions (pH 8.0, 30 ?C), except the latter preferred a higher concentration of halogenated compound (30 mM) as well as salinity (35%). Dehalogenase from strain H2 (DehH2) was found belongs to Group II dehalogenase with a 63.71% sequence identity to PH0459 haloacid dehalogenase of hyperthermophilic Pyrococcus horikoshii OT3 (PDB ID 1X42). The MD simulations revealed that haloacids and haloacetates were preferentially degraded by the DehH2 (-6.3 to -4.7 kcal/mol and -3.3 to -4.6 kcal/mol) at 35 % NaCl and without NaCl respectively, through three or four hydrogen bonds to the catalytic triad, Asp125, Arg201, and Lys202. Data of MD simulation corroborated earlier molecular docking results, in which the complexes were observed to reach equilibrium at short period of time RMSD (? 0.13 – 0.189 nm) and have the minimum number of fluctuations (0.05 – 0.25 nm). The MM-PBSA calculations revealed that haloacetates and haloacids gave the lowest free binding energies (?Gbinding) (– 45.14 to – 7.62 Kcal/mol). The exception was chlorpyrifos in which RMSD (? 0.295 to unstable), RMSF values (0.05 – 0.59 nm) were the largest, while chlorpyrifos was unable to spontaneously bind to DehH2 (+180.57 kcal/mol) at both salinity conditions (35% and 0% NaCl). Whole genomic sequencing analysis such as Multi locus sequence alignment (MLSA), average nucleotide identity (ANI) and core genome phylogenetic analysis re-identified Bacillus thuringiensis H2 as Bacillus megaterium. Several genes involved in pollutants degradation and adaptation are found in the genome sequence. Based on the findings, it was apparent that hypersaline Lake Tuz inhabit novel pollutant-degrading bacteria which could be used for wastewater treatment.