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Organic amendments are usually carried out at field-scale for efficient remediation of organic pollutants; however, their effects on pollutant distribution and the corresponding microbial mechanisms were rarely discussed. The main aim of this study was to compare the fate of benz[a]anthracene in soil amended by several bioremediation materials and underlying microbial mechanisms. In this study, the potential for biotransformation of polycyclic aromatic hydrocarbon in a farmland soil was investigated in microcosms spiked with 14C-benz[a]anthracene as the tracer. A series of organic amendments including lignin, straw, mushroom culture waste, and cow manure, as well as a fungal inoculum of Pleurotus ostreatus, were compared. Illumina sequencing was introduced to reveal the bacterial community in different amendments. The metagenomic function was predicted with the bioinformatics tool of phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt). From the results, the lignin-contained substrates (lignin, straw, mushroom culture waste) showed increase trend in the dissipation of benz[a]anthracene, while Pleurotus ostreatus and cow manure resulted in opposite trends. Specifically, mushroom culture waste mainly increased 14C to the formation of humin-bound residue (39.5 ± 6.8%); lignin amendment significantly (P

Laccases are capable of rapidly oxidizing benzo[a]pyrene. It is thought that the metabolites with an increase in water solubility caused by the oxidation of benzo[a]pyrene may stimulate the subsequent mineralization. However, to date, there has been no experimental evidence to support this. In this study, the fate of benzo[a]pyrene in soil affected by laccase amendment and the resulting soil bacterial responses were investigated. Laccase amendment promoted benzo[a]pyrene dissipation (15.6%) from soil, accompanied by trace mineralization (0.58 ± 0.02%) and substantial bound residue formation (∼80%). An increase of ∼15% in the bound residue fraction was observed by laccase amendment, which mainly resulted from covalent binding of the residues to humin fraction. During the incubation, the abundance of bacterial 16S rRNA and polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase genes did not change markedly. In contrast, benzo[a]pyrene treated with laccase resulted in a smaller shift in the bacterial community composition, indicating a reduced disturbance to the soil microbial communities. These results here suggest that benzo[a]pyrene contaminated soil can be detoxified by laccase amendment mainly due to the enhanced bound residue formation to soil organic matter via covalent binding.

Bioremediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil is often limited by inadequate microbial activity and/or low PAH bioavailability. A pot experiment was performed with an aged contaminated arable soil to explore the remediation potential of ryegrass and lignin, which are believed to improve microbial degradation, as well as the biosurfactant rhamnolipid. On average, the concentration of 15 priority PAHs was reduced by 41.7% in the combined ryegrass, lignin and rhamnolipid treatment after 90 days. In contrast, there was no reduction in PAH concentration when each treatment was used alone. The rhamnolipid was beneficial for successful remediation, as shown by the lack of PAH transformation in all non-rhamnolipid treatments. The total amount of PAHs that accumulated in ryegrass biomass was less than 0.1% of the initial amount in the pot. When the theoretical estimate of plant uptake was considered, it suggested that rhizoremediation rather than direct uptake contributed to PAH dissipation. High-throughput sequencing analysis demonstrated that lignin addition substantially changed the fungal and bacterial communities; however, there was no indication that lignin selected for known bacterial PAH degraders. Nevertheless, a [14C]benz(a)anthracene-spiked microcosm experiment showed that lignin amendment led to enhanced PAH mineralization and nonextractable residue formation. Taken together, these findings highlight the importance of selecting bioremediation treatments that can simultaneously stimulate microbial activity and increase PAH bioavailability to achieve remediation effectively. Treatments incorporating rhizoremediation, biostimulation and biosurfactant addition hold promise for detoxifying aged PAH-contaminated agricultural soil.

Thaumarchaeota is an ecologically relevant archaeal phylum which may significantly contribute to global nitrogen cycling. Thaumarchaeotal abundance, composition, and activity can be changed by soil pH and pollutants such as toxic metals. This study aims to examine the responses of thaumarchaeotal community to soil pH variation and polycyclic aromatic hydrocarbon (PAH) pollution which may co-occur in agricultural soils. Field soil samples were collected from agricultural land impacted by both acidification and PAH contamination. Thaumarchaeotal abundance and composition were assessed using molecular approaches targeting 16S rRNA or amoA genes and were linked to environmental factors by correlation and canonical correspondence analysis (CCA). To evaluate the short-term responses of Thaumarchaeota to PAHs, additional soil microcosms amended with either three selected PAHs were established. Changes in thaumarchaeotal communities during the incubation were monitored. A significant correlation between thaumarchaeotal gene abundance and soil pH was observed within field samples, with the I.1a-associated group enriched when pH

Bacteria able to degrade pyrene play a critical role in the biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons (PAHs). However, the traditional isolation procedure only obtains strains related to the genus Mycobacterium. The aim of the present study was to develop a modified method to isolate taxonomically distinct pyrene-degrading strains. The results indicated that replacing pyrene with phenanthrene in the isolation step improved the isolation efficiency. Using the modified method, six PAH degraders belonging to the genera Bosea, Arthrobacter, Paenibacillus, Bacillus, and Rhodococcus were obtained. They were capable of effectively utilizing pyrene (∼100%) as their sole carbon source, and could co-metabolize the degradation of benzo [a]pyrene (26.9-71.5%). In contrast, a small amount of pyrene (5.6%) and benzo [a]pyrene (8.6%) were degraded by a phenanthrene-degrading Sphingobium sp. NS7 under the same conditions. The difference in PAHs degradation between agar plate culture and liquid culture may lead to the low isolation efficiency in the traditional procedure. Hereditary stability analysis showed that PAH degradation capability of the Bosea, Paenibacillus, and Rhodococcus strains were easily lost without PAH pressure, which may partly explain why those strains were difficult to obtain using the traditional method.

The fate of polycyclic aromatic hydrocarbons (PAHs) determines their potential risk in soil, which may be directly affected by abiotic conditions and indirectly through the changes in decomposer communities. In comparison, the indirect effects on the fate remain largely elusive. In this study, the fate of phenanthrene and benzo[a]pyrene and the corresponding bacterial changes were investigated in three contaminated farmland soils using a 14C tracer method and Miseq sequencing. The results showed that most benzo[a]pyrene was consistently extractable with dichloromethane (DCM) after the 60-day incubation (60.4%–78.2%), while phenanthrene was mainly mineralized to CO2 during the 30-day incubation (40.4%–58.7%). Soils from Guangzhou (GZ) showed a different distribution pattern of 14C-PAHs exemplified by low mineralization and disparate bound residue formation. The PAH fate in the Shenyang (SY) and Nanjing (NJ) soils were similar to each other than to that in the GZ soil. The fate in the GZ soil seemed to be linked to the distinct edaphic properties, such as organic matter content, however soil microbial community could have influenced the distribution pattern of PAHs. This potential role of microorganisms was reflected by the unique changes in the copy numbers of Gram positive RHDα gene, and by the distinct shifts in bacterial community composition during the incubation. A quite different shift in bacterial communities was found in the GZ microcosms which may influence PAH mineralization and non-extractable residue (NER) formation.

Acidification and pollution are two major threats to agricultural ecosystems; however, microbial community responses to co-existed soil acidification and pollution remain less explored. In this study, arable soils of broad pH (4.26–8.43) and polycyclic aromatic hydrocarbon (PAH) gradients (0.18–20.68 mg kg−1) were collected from vegetable farmlands. Bacterial community characteristics including abundance, diversity and composition were revealed by quantitative PCR and high-throughput sequencing. The bacterial 16S rRNA gene copies significantly correlated with soil carbon and nitrogen contents, suggesting the control of nutrients accessibility on bacterial abundance. The bacterial diversity was strongly related to soil pH, with higher diversity in neutral samples and lower in acidic samples. Soil pH was also identified by an ordination analysis as important factor shaping bacterial community composition. The relative abundances of some dominant phyla varied along the pH gradient, and the enrichment of a few phylotypes suggested their adaptation to low pH condition. In contrast, at the current pollution level, PAH showed marginal effects on soil bacterial community. Overall, these findings suggest pH was the primary determinant of bacterial community in these arable soils, indicative of a more substantial influence of acidification than PAH pollution on bacteria driven ecological processes.

Ring-hydroxylating dioxygenases (RHDs) play a critical role in the biodegradation of polycyclic aromatic hydrocarbons (PAHs). In this study, genes pdoAB encoding a dioxygenase capable of oxidizing various PAHs with up to five-ring benzo[a]pyrene were cloned from Mycobacterium sp. NJS-P. The α-subunit of the PdoAB showed 99% and 93% identity to that from Mycobacterium sp. S65 and Mycobacterium sp. py136, respectively. An Escherichia coli expression experiment revealed that the enzyme is able to oxidize anthracene, phenanthrene, pyrene and benzo[a]pyrene, but not to fluoranthene and benzo[a]anthracene. Furthermore, the results of in silico analysis showed that PdoAB has a large substrate-binding pocket satisfying for accommodation of HMW PAHs, and suggested that the binding energy of intermolecular interaction may predict the substrate conversion of RHDs towards HMW PAHs, especially those may have steric constraints on the substrate-binding pocket, such as benzo[a]pyrene and benzo[a]anthracene.

Bacterial laccase CueO from Escherichia coli can oxidize polycyclic aromatic hydrocarbons (PAHs); however, its application in the remediation of PAH-contaminated soil mainly suffers from a low oxidation rate and copper dependence. It was reported that a laccase with a higher redox potential tended to have a higher oxidation rate; thus, the present study investigated the oxidation of PAHs using another bacterial laccase CotA from Bacillus subtilis with a higher redox potential (525 mV) than CueO (440 mV). Recombinant CotA was overexpressed in E. coli and partially purified, exhibiting a higher laccase-specific activity than CueO over a broad pH and temperature range. CotA exhibited moderate thermostability at high temperatures. CotA oxidized PAHs in the absence of exogenous copper. Thereby, secondary heavy metal pollution can be avoided, another advantage of CotA over CueO. Moreover, this study also evaluated some unexplained phenomena in our previous study. It was observed that the oxidation of PAHs with bacterial laccases can be promoted by copper. The partially purified bacterial laccase oxidized only two of the 15 tested PAHs, i.e., anthracene and benzo[a]pyrene, indicating the presence of natural redox mediators in crude cell extracts. Overall, the recombinant CotA oxidizes PAHs with high laccase activity and copper independence, indicating that CotA is a better candidate for the remediation of PAHs than CueO. Besides, the findings here provide a better understanding of the oxidation of PAHs using bacterial laccases.