Comparative Genomics of a Paddy Field Bacterial Isolate Ochrobactrum sp. CPD-03: Analysis of Chlorpyrifos Degradation Potential

Unleashing potential of Pseudomonas aeruginosa RNC3 and Stenotrophomonas maltophilia RNC7 for chlorpyrifos biodegradation by genome analysis and kinetic studies

Chlorpyrifos (CP) is an extensively used organophosphate (OP) pesticide that inhibits the biogeochemical cycle with subsequent loss of soil fertility. In this view, indigenous soil bacteria with significant CP degradation capacity were identified as Pseudomonas aeruginosa RNC3 and Stenotrophomonas maltophilia RNC7 through 16 S rRNA. The optimum values of independent variables for CP degradation were found to be 30 ℃, pH 7, 100 mgL-1 of CP, and 1 OD600 cell culture. RNC3 and RNC7 showed 82.5 mgL-1 and 77.1 mgL-1 CP degradation within 5 days. A Michaelis-Menten kinetic model estimated the degradation rate (Vmax) and substrate binding affinity (Ks) for RNC3 were 1.23 mgL-1h-1 and 123 mgL-1 whereas for RNC7 as 1.19 mgL-1h -1 and 124.3 mgL-1, respectively. The major metabolites 3,5,6-trichloro-2-pyridinol (TCP) and 2-hydroxy pyridine were identified during CP degradation by RNC3 whereas, only TCP by RNC7 using GC-MS. Key enzymes encoded by opd and opch2 genes were annotated in the genomes of RNC3 and RNC7 along with the set of putative degradation genes (tcp, yieH, pho, prp). Protein-ligand docking between OPCH2 and CP found - 7.9 kcal mol -1 as a high binding affinity with the conserved catalytic triad (Ser155-Asp251-His281) in the active site. The study suggests that RNC3 can completely mineralize CP, whereas both strains have shown robust degradation ability of OP group of pesticides. The potential of rapid acclimatization to natural soil environment and non-virulent nature of the selected strains are beneficial for in situ application. Thus, selected indigenous strains can be applied for the bioremediation of OP-contaminated soil.

An insights of organochlorine pesticides categories, properties, eco-toxicity and new developments in bioremediation process

Organochlorine pesticides (OCPs) have been used in agriculture, increasing crop yields and representing a serious and persistent global contaminant that is harmful to the environment and human health. OCPs are typically bioaccumulative and persistent chemicals that can spread over long distances. The challenge is to reduce the impacts caused by OCPs, which can be achieved by treating OCPs in an appropriate soil and water environment. Therefore, this report summarizes the process of bioremediation with commercially available OCPs, considering their types, impacts, and characteristics in soil and water sources. The methods explained in this report were considered to be an effective and environmentally friendly technique because they result in the complete transformation of OCPs into a non-toxic end product. This report suggests that the bioremediation process can overcome the challenges and limitations of physical and chemical treatment for OCP removal. Advanced methods such as biosurfactants and genetically modified strains can be used to promote bioremediation of OCPs.

Genomic Characteristics and Functional Analysis of Brucella sp. Strain WY7 Isolated from Antarctic Krill

Antarctic krill (Euphausia superba) is a key species of the Antarctic ecosystem whose unique ecological status and great development potential have attracted extensive attention. However, the genomic characteristics and potential biological functions of the symbiotic microorganisms of Antarctic krill remain unknown. In this study, we cultured and identified a strain of Brucella sp. WY7 from Antarctic krill using whole-genome sequencing and assembly, functional annotation, and comparative genomics analysis. First, based on 16S rDNA sequence alignment and phylogenetic tree analysis, we identified strain WY7 as Brucella. The assembled genome of strain WY7 revealed that it has two chromosomes and a plasmid, with a total genome length of 4,698,850 bp and an average G + C content of 57.18%. The DNA-DNA hybridization value and average nucleotide identity value of strain WY7 and Brucella anthropi ATCC® 49188TM, a type strain isolated from human clinical specimens, were 94.8% and 99.07%, respectively, indicating that strain WY7 is closely related to Brucella anthropi. Genomic island prediction showed that the strain has 60 genomic islands, which may produce HigB and VapC toxins. AntiSMASH analysis results showed that strain WY7 might produce many secondary metabolites, such as terpenes, siderophores and ectoine. Moreover, the genome contains genes involved in the degradation of aromatic compounds, suggesting that strain WY7 can use aromatic compounds in its metabolism. Our work will help to understand the genomic characteristics and metabolic potential of bacterial strains isolated from Antarctic krill, thereby revealing their roles in Antarctic krill and marine ecosystems.

Combined biostimulation and bioaugmentation for chlorpyrifos degradation in laboratory microcosms

Chlorpyrifos (CP) is a persistent organophosphorus pesticide (OP) used in soil ecosystem for insect control. Bioremediation process has been proven promising in degrading these toxic molecules and restoring the physio-chemical properties of soil. This work reports a laboratory microcosm study in both non-sterile & sterile conditions, conducted over a period of 56 days to examine the combined effect of additional supplements like biostimulants (BSs) such as N, P, and K in the presence of suitable carrier materials (compost, wheat straw, and corncob) along with bioaugmentation by a Ochrobactrum sp. CPD-03 on CP degradation from the contaminated soil. CP degradation was thoroughly monitored at an interval of 7 days over a period of 56 days. Results showed biostimulation and bioaugmentation along with compost as carrier material had shown higher CP degradation efficiency of 76 ± 2.8 and 74 ± 1.6% in non-sterile and sterile microcosms over a period of 56 days. Moreover, bacterial community profiling (16s rRNA and opd gene) demonstrated increased microbial counts, corroborating the efficiency of the bioremediation process. The survival of CPD-03 at the end of the assay validated its ability of colonizing modified soils. By this integrated method with compost as carrier material, bioremediation process could be enhanced for restoration CP-contaminated soils.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02980-9.

Myco-remediation of Chlorinated Pesticides: Insights Into Fungal Metabolic System

Synthetic chemicals including organochlorine pesticides pose environment and health hazard due to persistent and bio-accumulation property. Majority of them are recognized as endocrine disruptors. Fungi are ubiquitous in nature and employs efficient enzymatic machinery for the biotransformation and degradation of toxic, recalcitrant pollutants. This review critically discusses the organochlorine biotransformation process mediated by fungi and highlights the role of enzymatic system responsible for biotransformation, especially distribution of dehalogenase homologs among fungal classes. It also explores the potential use of fungal derived biomaterial, mainly chitosan as an adsorbing biomaterial for pesticides and heavy metals removal. Further, prospects of employing fungus to over-come the existing bioremediation limitations are discussed. The study highlights the potential scope of utilizing fungi for initial biotransformation purposes, preceding final biodegradation by bacterial species under environmental conditions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-021-00940-8.