Biodegradation of pyrene and catabolic genes in contaminated soils cultivated with Lolium multiflorum L

Abstract

Background, aim, and scope In the soil environment, polycyclic aromatic hydrocarbons (PAHs) and heavy metals (HMs) are of great environmental and human health concerns due to their widespread occurrence, persistence, and carcinogenic properties. Bioremediation of contaminated soil is a cost-effective, environmentally friendly, and publicly acceptable approach to address the removal of environmental contaminants. However, bioremediation of contaminants depends on plant-microbe interactions in the rhizosphere. The microorganisms that can mineralize various PAHs have PAH dioxygenase genes like nahAc, phnAc, and pdo1. To understand the fate of pyrene in rhizospheric and non-rhizospheric soils in the presence or absence of Pb, pyrene biodegradation, bacterial community structure, and dioxygenase genes were investigated in a pot experiment. Methods Soil was amended with Pb (a representative heavy metal), pyrene, and a Pb/pyrene mixture. After 8 weeks of aging, one set of pot microcosms was cultivated with rye grass (Lolium multiflorum L) seedlings, while another set was not cultivated for the purpose of comparing rhizosphere and non-rhizosphere pyrene degradation. Pyrene was extracted from freeze-dried soil and plant samples using a Soxhlet extraction method and the extracts were dried to 1 mL under gentle nitrogen flow and analyzed using gas chromatograph mass spectrometry (Agilent 6890, USA). Soil DNA was extracted from triplicate samples and the DGGE was performed using a Bio-Rad Dcode™ Universal Mutation Detection System (Bio-Rad, USA). PAH dioxygenase genes, including nahAc, phnAc, and pdo1, were detected using PCR amplification. Similarly, pyrene degraders were also investigated using plate counting technique. Results Biodegradation rates recorded over an 18-week period showed that rye grass promoted significant (P<0.05) pyrene degradation. Pyrene removal efficiency from rhizospheric soils was 59.1±2.1% and 68.7±2.3% in pyreneand Pb/pyrene-amended soils, respectively. The results indicate that pyrene dissipation was significantly (P<0.05) higher in Pb/pyrene-amended soils than only-pyreneamended soils. The plant growth promoted the degradation of pyrene and accounted for 12.1% to 17.0% of dissipation enhancement in the rhizospheric soils. In this study, the DGGE profiles revealed a shift in soil bacterial community structure in all amended soils, with a higher number and greater complexity of banding patterns in Pb/pyreneamended samples than in either Pb-or pyrene-amended samples. In the control and Pb-amended soil, pdo1 and nahAc genes were not detected throughout the incubation period but were detected in the pyrene-and Pb/pyreneamended soils. However, phnAc genes were not detected in either amended or non-amended soils throughout the incubation period. The addition of pyrene had a dramatic effect on the number of pyrene degraders. Discussion Plants contribute to the degradation of PAHs by increasing the size of microbial population, promoting microbial activity, and modifying microbial community

Insight into the Modulation of Dissolved Organic Matter on Microbial Remediation of PAH-Contaminated Soils

“…The information of PAH degraders can be expressed by abundance and community composition of PAH degrading-related genes using molecular ecology techniques. Pdo1, nah, and C12O are three important PAH-degrading genes which are widespread in soils near a coking plant [20][21][22] and encode the pyrene dioxygenase [23], naphthalene dioxygenase [24], and catechol 1,2-dioxygenase [25], respectively. In this study, abundance and community composition of the above PAH-degrading genes and the removal efficiency of different PAHs were monitored during the bioremediation of aging PAH-contaminated soils amended with the DOM derived from various agricultural wastes.…”

Response of bacterial pdo1, nah, and C12O genes to aged soil PAH pollution in a coke factory area

“…Recently, the abundance and composition of PAHdegrading microbial populations present in PAH-polluted environments have been investigated to some extent through direct extraction of DNA from the environment and analysis of PAH-degrading genes (Singleton et al 2005;Lillis et al 2010;Paissé et al 2012). pdo1, nah, and C12O are three important PAH-degrading genes which have been detected widely from environments polluted by aromatic compounds or bacteria isolated from those environments (Baldwin et al 2003;Johnsen et al 2006;Khan et al 2009;Tuan et al 2011). The pdo1 gene encodes the pyrene dioxygenases associated with degradation of high-molecular weight (HMW) PAHs (Johnsen et al 2006), the nah gene encodes naphthalene dioxygenases associated with degradation of low-molecular weight (LMW) PAHs (Baldwin et al 2003), and the C12O gene encodes catechol 1,2-dioxygenase associated with cleavage of the last aromatic ring in the degradative pathway of PAHs (Sei et al 1999).…”

Phytoremediation for soils contaminated by phenanthrene and pyrene with multiple plant species

“…A broad range of plant species have been tested for their abilities to promote the degradation of PAHs in soils (Huang et al 2004;Lee et al 2008;Khan et al 2009;Wang and Oyaizua 2009). The mechanisms of phytoremediation for soils polluted by PAHs involve direct plant uptake, microbial degradation stimulated by plant roots, co-metabolism of contaminants in the rhizosphere, and adsorption to humic or organic matter (Schnoor et al 1995;Reilley et al 1996;Chen et al 2003).…”

“…However, the importance of each process has not been evaluated, and few reports dealt with the efficiency of phytoremediation of soil PAHs pollution in relation to the properties of PAHs and plant species (Macek et al 2000;Chiou et al 2001;Toner and Lceyval 2003;Gao and Zhu 2005). Besides most of the research concerning the remediation of soils contaminated by PAHs only based on single plant species, multi-species phytoremediation was scarcely reported (Khan et al 2009;Wang and Oyaizua 2009). In this article, three plant species, rape (Brassica campestris), a widely cultured oil crop, and alfalfa (Medicago sativa), and white clover (Trifolium repens), as green manure and/or forage crops, were selected to investigate the potential of multi-species phytoremediation in decontaminating PAHs contaminated soil and to evaluate the relative importance of possible pathways for the removal of PAHs from soils under single or mixed cropping patterns.…”