Pesticides are xenobiotic molecules necessary to control pests in agriculture, home, and industry. However, water and soil can become contaminated as a consequence of their extensive use. Therefore, because of its eco-friendly characteristics and efficiency, bioremediation of contaminated sites is a powerful tool with advantages over other kinds of treatments. For an efficient pesticides bioremediation, it is necessary to take into account different aspects related to the microbial metabolism and physiology. In this respect, OMICs studies such as genomics, transcriptomics, proteomics, and metabolomics are essential to generate relevant information about the genes and proteins involved in pesticide degradation, the metabolites generated by microbial pesticide degradation, and the cellular strategies to contend against stress caused by pesticide exposition. Pesticides as organochlorines and organophosphorus are the more commonly studied using OMIC approaches. To date, many genomes of microorganisms capable of degrading pesticides have been published, mainly bacterial strains from Burkholderia, Pseudomonas, and Rhodococcus genera. Following the genomic reports, transcriptomic studies, using microarrays and more recently next-generation sequencing technology RNA-Seq, in pesticide microbial degradation are the most numerous. Proteomics, metabolomics, as well as studies that combine different OMIC are gained interest. This review aims to describe a brief overview of pesticide biodegradation mechanisms; new tools to study microorganisms in natural environments; basic concepts of the OMICs approaches; as well as advances in methodologies associated with the analysis of that tools. Additionally, the most recent reports on genomics, transcriptomics, proteomics, and metabolomics during the degradation of pesticides are also analyzed.

Omics Approaches to Pesticide Biodegradation.

Ciprofloxacin-degrading Paraclostridium sp. isolated from sulfate-reducing bacteria-enriched sludge: Optimization and mechanism.

Biotechnological tools to elucidate the mechanism of pesticide degradation in the environment.

Herbicide bioremediation: from strains to bacterial communities

Biochar has caught great attention over the last decade with the loose and porous structure, and carbon stability provides suitable living conditions for the growth and activity of microorganisms. This review provided a comprehensive summary of biochar immobilization microbe (BIM) in water and soil decontamination. Firstly, the bacterial immobilization techniques including adsorption, entrapping, and covalence methods were exhibited. Secondly, the applications of BIM in water and soil environmental remediation were introduced, mainly including the treatment of organic pollutants, heavy metals, and N/P, among which the most frequently immobilized microorganism was Bacillus. Then, the mechanisms of adsorption, redox, and degradation were analyzed. Finally, pertinent questions for future research of BIM technology were proposed. The purpose of this paper is to provide useful background information for the selection of better biochar fixation microorganisms for water and soil remediation. 

Immobilization of microbes on biochar for water and soil remediation: A review.

Transcriptomic analysis of Chlorimuron-ethyl degrading bacterial strain Klebsiella jilinsis 2N3.

Klebsiella pneumoniae 2N3 is a strain of gram-negative bacteria that can degrade chlorimuron-ethyl and grow with chlorimuron-ethyl as the sole nitrogen source. The complete genome of Klebsiella pneumoniae 2N3 was sequenced using third generation high-throughput DNA sequencing technology. The genomic size of strain 2N3 was 5.32 Mb with a GC content of 57.33% and a total of 5156 coding genes and 112 non-coding RNAs predicted. Two hydrolases expressed by open reading frames (ORFs) 0934 and 0492 were predicted and experimentally confirmed by gene knockout to be involved in the degradation of chlorimuron-ethyl. Strains of ΔORF 0934, ΔORF 0492, and wild type (WT) reached their highest growth rates after 8-10 hours in incubation. The degradation rates of chlorimuron-ethyl by both ΔORF 0934 and ΔORF 0492 decreased in comparison to the WT during the first 8 hours in culture by 25.60% and 24.74%, respectively, while strains ΔORF 0934, ΔORF 0492, and the WT reached the highest degradation rates of chlorimuron-ethyl in 36 hours of 74.56%, 90.53%, and 95.06%, respectively. This study provides scientific evidence to support the application of Klebsiella pneumoniae 2N3 in bioremediation to control environmental pollution.

https://www.mdpi.com/1422-0067/20/12/3053/pdf

Whole Genome Sequencing and Analysis of Chlorimuron-Ethyl Degrading Bacteria Klebsiella pneumoniae 2N3

Glutathione-S-transferase (GST) catalyzes the degradation of Chlorimuron-ethyl by Klebsiella jilinsis 2N3.

Klebsiella jilinsis 2N3 promotes maize growth and induces resistance to northern corn leaf blight

Microbial degradation is one of the effective methods to remove thifensulfuron-methyl (TSM) in soil and water environments. In this study, a high-efficiency TSM degrading strain Serratia marcecens N80 was used. The abandoned fungus substrate was converted to biochars at various pyrolysis temperatures (300, 450 and 600 °C). Biochar made at 600 °C (BC600) showed the best TSM adsorption capacity, while strain N80 adsorption efficiency reached the maximum up to 81.08%. Therefore, BC600, polyvinyl alcohol (PVA), and sodium alginate (SA) were chosen to establish an immobilized system for strain N80. The immobilized N80 beads (IN80) showed significantly improved reusability and storage stability. Under the optimal condition (pH 7.0, 35 °C, 1.5 × 10 8  cfu/mL), TSM (50 mg/L) degradation rates by free N80 and IN80 were 83.47 and 89.37% within 48 h, respectively. Free N80 and IN80 accelerated TSM degradation in soil, reducing its half-life to 6.13 d and 4.36 d, respectively. However, immobilized material beads (IM) slightly delayed the soil TSM degradation. TSM activated catalase and dehydrogenase but inhibited invertase and urease. IN80 treatment accelerated the recovery of invertase and urease. Moreover, IN80 accelerated the recovery of bacterial and fungal populations; the beneficial genera inhibited by TSM such as Sphingomonas, Lysobacter, Massilia, Rhodanobacter, and Gemmatimonas also increased to varying degrees. Meanwhile, IN80 showed an excellent inhibitory effect on pathogenic fungi (Fusarium and Alternaria), while increased the relative abundance of Mortierella, and the soil resistance to diseases. This study offers a potential in situ remediation strategy to improve the quality of the soil environment.

Cheng Zhang

Papers

Transcriptomic analysis of Chlorimuron-ethyl degrading bacterial strain Klebsiella jilinsis 2N3.

Whole Genome Sequencing and Analysis of Chlorimuron-Ethyl Degrading Bacteria Klebsiella pneumoniae 2N3

Glutathione-S-transferase (GST) catalyzes the degradation of Chlorimuron-ethyl by Klebsiella jilinsis 2N3.

Klebsiella jilinsis 2N3 promotes maize growth and induces resistance to northern corn leaf blight

Degradation characteristics and soil remediation of thifensulfuron-methyl by immobilized Serratia marcecens N80 beads