The catabolic pathways of in situ rhizosphere PAH degraders and the main factors driving PAH rhizoremediation in oil‐contaminated soil

Abstract

Catalysis rhizospheric treatments supplemented with these two substances, further confirming their key roles in PAH removal and in situ PAH rhizoremediation. Our study offers novel insights into the mechanisms of in situ rhizoremediation at PAH-contaminated sites.

DNA stable isotope probing on soil treated by plant biostimulation and flooding revealed the bacterial communities involved in PCB degradation

“…Altogether this information pointed out that Actinobacteria and Betaproteobacteria are the key bacterial targets to be enriched in a plant biostimulation-based approach aimed at the on-site bioremediation of the highly and historically PCB-polluted site considered in our study. Future research perspectives include in situ-SIP coupled with metagenomic analysis 49 and will allow to deepen the investigation of plant-microbiome interactions and increase the knowledge of the metabolic reactions occurring during the PCB biodegradation in the field.…”

In Situ Discrimination and Cultivation of Active Degraders in Soils by Genome-Directed Cultivation Assisted by SIP-Raman-Activated Cell Sorting

“…DNA was extracted from each sample using the PowerSoil DNA Isolation Kit (MO BIO, Carlsbad, CA), according to the manufacturer’s instructions. After detection with a NanoDrop 2000 spectrophotometer, DNA from the 12 C_Toluene and 13 C_Toluene microcosms was used for the CsCl gradient ultracentrifugation as previously described. , Briefly, approximately 5 μg of DNA was mixed with tris EDTA/CsCl solution at a buoyancy density (BD) value of ∼1.77 g/mL and transferred to the Quick-Seal polyallomer tubes (13 × 51 mm, 5.1 mL, Beckman Coulter, Pasadena, CA, USA). Ultracentrifugation was conducted in a Beckman Coulter L-100XP ultracentrifuge at 47,500 rpm for 48 h at 20 °C.…”

“…To explore the toluene metabolic pathways of functional microorganisms, the assembled metagenomes were binned using MaxBin2 and metaBAT2, evaluated by CheckM (comp ≥80%, cont ≤10%) to generate high-quality bins. Assembled contigs of the target bins related to toluene degradation were used for protein sequence prediction and annotation using Prokka v1.1, while KEGG pathways were inferred using HUMAnN2 . As 16S rRNA genes are difficult to assemble into the metagenome-assembled genomes, the gyrB gene that encodes the B subunit protein of DNA gyrase (topoisomerase type II) and has a single copy was chosen as a molecular classification marker .…”

“…Assembled contigs of the target bins related to toluene degradation were used for protein sequence prediction and annotation using Prokka v1.1, while KEGG pathways were inferred using HUMAnN2. 36 As 16S rRNA genes are difficult to assemble into the metagenome-assembled genomes, the gyrB gene that encodes the B subunit protein of DNA gyrase (topoisomerase type II) and has a single copy was chosen as a molecular classification marker. 47 Furthermore, we confirmed whether the assembled bins represented the genomes of the SIPidentified active degraders using whole-genome comparisons based on average nucleotide identities (ANI).…”

Sphingomonas Relies on Chemotaxis to Degrade Polycyclic Aromatic Hydrocarbons and Maintain Dominance in Coking Sites

“…Combining molecular ecology network analysis with metagenomics helps to identify microorganisms that play important ecological functions in PAH-contaminated soils and elucidate their functional potential and metabolic pathways. There has been excellent work combining metagenomics and molecular ecology network analysis to clarify the degradation and metabolic pathways of PAHs by in situ rhizosphere microorganisms [17]. However, the identification of key microorganisms that have an important impact on the microbial community structure and their ecological functions in PAH-contaminated sites still needs further exploration.…”