Dynamic changes in functional gene copy numbers and microbial communities during degradation of pyrene in soils

Peng, Jingjing; Cai, Chao; Qiao, Min; Li, Hong; Zhu, Yan

doi:10.1016/j.envpol.2010.06.020

Cited by 51 publications

(25 citation statements)

References 44 publications

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“…The microbial community changes at sites A1 and A2 were similar to previous reports that xenobiotic pollutants can influence the microbial community significantly Liu et al 2011b). However, the microbial community change at site A3 was quite similar to a previous report showing no obvious difference in the bacterial community between the pyrene-spiked soil and the control (Peng et al 2010). It appears that some potential BDE 209 degradation bacteria may account for that phenomenon.…”

Section: Discussionsupporting

confidence: 87%

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Microbial community shift with decabromodiphenyl ether (BDE 209) in sediments of the Pearl River estuary, China

Wang

Sun

et al. 2013

Biologia

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Abstract:To compare the effect of decabromodiphenyl ether (BDE 209) on microbial community from the Pearl River estuary, the microbial community at three in situ sites and the responses of microbial community to BDE-209 stressor were investigated. Denaturing gradient gel electrophoresis analysis of 16S rRNA gene showed that microbial community at site A2 has less diversity than sites A1 and A3. Physicochemical parameters (NH4-N, salinity and SiO3-Si) could significantly impact the microbial community composition in this estuary. In laboratory-incubated experiments, results indicated high concentration of BDE 209 (100 mg/kg) could increase the microbial diversity at sites A1 and A2, whereas reduced the microbial diversity at site A3. The unweighted pair group method with arithmetic means cluster analysis and principal component analysis demonstrated that the community structure changes at sites A1 and A2 were driven by the BDE 209 concentration, whereas at site A3 they depended on the incubation time. Thirty-five days after the addition of 100 mg/kg BDE 209, Firmicutes were found to be the dominant bacteria at sites A1 and A2. These data suggest the BDE 209 may have different effects on the microbial community in the Pearl River estuary.

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Section: Discussionsupporting

confidence: 87%

“…Cluster analysis and phylogenetic analysis of microbial community under BDE 209 stressor In a laboratory-incubated experiment, xenobiotic pollutant concentrations and incubation times were the two key factors to influence the microbial community structure (Zhou et al 2008;Wang et al 2009;Peng et al 2010;Liu et al 2011b).…”

Section: Discussionmentioning

confidence: 99%

Microbial community shift with decabromodiphenyl ether (BDE 209) in sediments of the Pearl River estuary, China

Wang

Sun

et al. 2013

Biologia

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“…1). Compared with previous findings (Chen and Ding 2012;Peng et al 2010;Xu et al 2006), pyrene dissipation in both soils was relatively more rapid in this study. It was likely due to the rapid enrichment of activated indigenous degraders in response to the presence of pyrene, which would result in higher pyrene degradation (>96 %) in 1-month incubation (Hamdi et al 2007).…”

Section: Dissipation Of Pyrenecontrasting

confidence: 96%

“…This result indicates that there was no significant change in the overall population density of the total bacteria in soils exposed to pyrene. This observation is similar to previous studies showing that 16S rDNA gene copy numbers were not affected by the addition of PAHs including pyrene, phenanthrene, and naphthalene (Park and Crowley 2006;Peng et al 2010;Niepceron et al 2014). However, the relatively constant density for the bacterial biomass did not rule out variations in the species composition of the bacterial community.…”

Section: Enrichment Of Functional Microbes During Pyrene Degradationsupporting

confidence: 92%

Enrichment of functional microbes and genes during pyrene degradation in two different soils

2015

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Purpose Stimulating microbial degradation is a promising strategy for the remediation of soils contaminated with polycyclic aromatic hydrocarbons (PAHs). To better understand the functional microbial populations and processes involved in pyrene biodegradation in situ, the dynamics of pyrene degradation and functional microbial abundance were monitored during pyrene incubation in soils. We hope our findings will provide new insights into in situ pyrene biodegradation in soils and help to identify functional microbes from soils. Materials and methods Pyrene (60 mg kg −1 ) was incubated with two different soils, one is lower PAH-containing agricultural soil (LS), and the other is higher PAH-containing industrial soil (HS). During incubation, triplicate samples were collected on days 0, 3, 7, 14, and 35. Pyrene in soil samples was analyzed using an Agilent gas chromatograph (7890A) equipped with a mass-selective detector (model 5897). DNA in soils was extracted with a FastDNA Spin kit for soil (Bio101, USA). The abundance of functional microbes and genes was monitored by a Taqman or SYBR Green based realtime PCR quantification using an iCycler iQ5 themocycler (Bio-Rad, USA). The diversity of PAH-RHDα GP genes was evaluated by constructing clone libraries and sequencing.Results and discussion In both soils, more than 80 % of the added pyrene was degraded within 35 days. After 35-day incubation, there was a significant enrichment of Gram-positive bacteria harboring PAH-ring hydroxylation dioxygenase ( PA H -R H D α G P ) g e n e s , a n d t h e a b u n d a n c e o f Mycobacterium increased significantly. In PAH-RHD α GP clone libraries from two soils, Mycobacterium was detected, while most sequences were closely related to uncultured Gram-positive bacteria. In addition, two pyrene catabolic pathways might be involved in pyrene degradation, as pyrene dioxygenase genes, nidA and nidA3, were dramatically enriched during incubation. Moreover, the abundance and diversity of potential degraders in two soils showed significantly difference in responding to pyrene stress. This result indicates that soil condition can significantly affect functional microbial populations and biological process for pyrene biodegradation. Conclusions These results revealed that Mycobacterium as well as uncultured Gram-positive PAH-RHD α genotypes may be the important group of pyrene degraders in soils, and two pyrene catabolic pathways, targeted by nidA and nidA3, might potentially contribute to in situ biodegradation of pyrene. This study characterized the response pattern of potential pyrene degraders to pyrene stress in two different soils, which would increase our understanding of the indigenous processes of pyrene biodegradation in soil environment.

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“…Crystalline pyrene (L08162, Alfa Aesar, Lancaster, USA) was dissolved in acetone and uniformly sprayed onto soil to produce sub-samples with pyrene levels of 0 (pyrene-free, with acetone only), 20,50,100,200,400,700,1000,2000 and 5000 mg kg À1 dry weight soil (Brinch et al, 2002;Peng et al, 2010). These subsamples were homogenized by continuous hand shaking in 1000 mL glass bottles and the bottles were closed for 5 min to let the solvent disperse, followed by storage at 25 C in the dark for 16 h. When acetone was evaporated off, sub-samples were mixed with non-spiked soil at the ratio of 1:9 and shaken thoroughly, generating final pyrene levels of 0 (non-spiked control), 2,5,10,20,40,70,100,200 and 500 mg kg À1 dry weight soil (denoted as Pr2, Pr5, Pr10, Pr20, Pr40, Pr70, Pr100, Pr200 and Pr500, respectively).…”

Section: Spiking Of Soil With Pyrenementioning

confidence: 99%

Effect of pyrene on denitrification activity and abundance and composition of denitrifying community in an agricultural soil

Guo

Deng

Qiao

et al. 2011

Environmental Pollution

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a b s t r a c tToxicity of pyrene on the denitrifiers was studied by spiking an agricultural soil with pyrene to a series of concentrations (0e500 mg kg À1 ) followed by doseeresponse and dynamic incubation experiments. Results showed a positive correlation between potential denitrification activity and copy numbers of denitrifying functional genes (nirK, nirS and nosZ), and were both negatively correlated with pyrene concentrations. Based on the comparison of EC 50 values, denitrifiers harboring nirK, nirS or nosZ gene were more sensitive than denitrification activity, and denitrifiers harboring nirS gene were more sensitive than that harboring nirK or nosZ genes. Seven days after spiking with EC 50 concentration of pyrene, denitrifiers diversity decreased and community composition changed in comparison with the control. Phylogenetic analyses of three genes showed that the addition of pyrene increased the proportion of Bradyrhizobiaceae, Rhodospirillales, Burkholderiales and Pseudomonadales. Some species belonging to these groups were reported to be able to degrade PAHs.

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Dynamic changes in functional gene copy numbers and microbial communities during degradation of pyrene in soils

Cited by 51 publications

References 44 publications

Microbial community shift with decabromodiphenyl ether (BDE 209) in sediments of the Pearl River estuary, China

Microbial community shift with decabromodiphenyl ether (BDE 209) in sediments of the Pearl River estuary, China

Enrichment of functional microbes and genes during pyrene degradation in two different soils

Effect of pyrene on denitrification activity and abundance and composition of denitrifying community in an agricultural soil

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