Bacterial polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenases (PAH-RHD) encoding genes in different soils from King George Bay, Antarctic Peninsula

Jurelevicius, Diogo; Alvarez, Vanessa Marques; Peixoto, Raquel S.; Rosado, Alexandre Soares; Seldin, Lucy

doi:10.1016/j.apsoil.2011.12.008

Cited by 59 publications

(27 citation statements)

References 34 publications

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“…However, it is well known that culture-independent approaches allow for a broader recognition of microbial populations responsible for PAH degradation in environments (Baldwin et al 2003;Jurelevicius et al 2012). 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).…”

Section: Introductionmentioning

confidence: 99%

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

Han

Liu

Zheng

et al. 2014

Environ Sci Pollut Res

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Soil pollution caused by polycyclic aromatic hydrocarbons (PAHs) is threatening human health and environmental safety. Investigating the relative prevalence of different PAH-degrading genes in PAH-polluted soils and searching for potential bioindicators reflecting the impact of PAH pollution on microbial communities are useful for microbial monitoring, risk evaluation, and potential bioremediation of soils polluted by PAHs. In this study, three functional genes, pdo1, nah, and C12O, which might be involved in the degradation of PAHs from a coke factory, were investigated by realtime quantitative PCR (qPCR) and clone library approaches. The results showed that the pdo1 and C12O genes were more abundant than the nah gene in the soils. There was a significantly positive relationship between the nah or pdo1 gene abundances and PAH content, while there was no correlation between C12O gene abundance and PAH content. Analyses of clone libraries showed that all the pdo1 sequences were grouped into Mycobacterium, while all the nah sequences were classified into three groups: Pseudomonas, Comamonas, and Polaromonas. These results indicated that the abundances of nah and pdo1 genes were positively influenced by levels of PAHs in soil and could be potential microbial indicators reflecting the impact of soil PAH pollution and that Mycobacteria were one of the most prevalent PAHs degraders in these PAH-polluted soils. Principal component analysis (PCA) and correlation analyses between microbial parameters and environmental factors revealed that total carbon (TC), total nitrogen (TN), and dissolved organic carbon (DOC) had positive effects on the abundances of all PAH-degrading genes. It suggests that increasing TC, TN, and DOC inputs could be a useful way to remediate PAH-polluted soils.

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Section: Introductionmentioning

confidence: 99%

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

Han

Liu

Zheng

et al. 2014

Environ Sci Pollut Res

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“…Terminal dioxygenase is the component of PAH-RHD, composed of large ␣-and small ␤-subunits. The genes coding for the mononuclear iron-containing catalytic domain (a conserved region) of PAH-RHD␣ (␣-subunit) have been widely used for studying RHD diversity and the PAH degradation potential by bacteria in the environment (11). In addition to the research on the genes involved in PAH degradation, studies using culture-dependent tools to investigate the degrading capacity of BaP degraders showed that rare bacteria were capable of metabolizing BaP without metabolic intermediate additives (9,10,13); in most cases, BaP degradation is stimulated by the addition of some intermediates produced during BaP metabolism (14,15).…”

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confidence: 99%

“…The functional PAH-RHD genes (encoding PAH-ring hydroxylating dioxygenase enzymes) have also been examined to understand BaP degradation mechanisms, such as nah, pah, arh, and phn genes in Gram-negative (GN) bacteria and the evolutionarily correlated nid, nir, phd, and nar genes in Gram-positive (GP) bacteria, which are responsible for the first step of PAHs (naphthalene, phenanthrene, anthracene, and pyrene) hydroxylation under aerobic conditions (11,12). Terminal dioxygenase is the component of PAH-RHD, composed of large ␣-and small ␤-subunits.…”

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confidence: 99%

Identification of Benzo[ a ]pyrene-Metabolizing Bacteria in Forest Soils by Using DNA-Based Stable-Isotope Probing

Song

Luo

Jiang

et al. 2015

Appl Environ Microbiol

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c DNA-based stable-isotope probing (DNA-SIP) was used in this study to investigate the uncultivated bacteria with benzo[a]pyrene (BaP) metabolism capacities in two Chinese forest soils (Mt. Maoer in Heilongjiang Province and Mt. Baicaowa in Hubei Province). We characterized three different phylotypes with responsibility for BaP degradation, none of which were previously reported as BaP-degrading microorganisms by SIP. In Mt. Maoer soil microcosms, the putative BaP degraders were classified as belonging to the genus Terrimonas (family Chitinophagaceae, order Sphingobacteriales), whereas Burkholderia spp. were the key BaP degraders in Mt. Baicaowa soils. The addition of metabolic salicylate significantly increased BaP degradation efficiency in Mt. Maoer soils, and the BaP-metabolizing bacteria shifted to the microorganisms in the family Oxalobacteraceae (genus unclassified). Meanwhile, salicylate addition did not change either BaP degradation or putative BaP degraders in Mt. Baicaowa. Polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHD) genes were amplified, sequenced, and quantified in the DNA-SIP 13 C heavy fraction to further confirm the BaP metabolism. By illuminating the microbial diversity and salicylate additive effects on BaP degradation across different soils, the results increased our understanding of BaP natural attenuation and provided a possible approach to enhance the bioremediation of BaP-contaminated soils. P olycyclic aromatic hydrocarbons (PAHs), a class of persistent organic pollutants (POPs), enter the environment through both natural and anthropogenic pathways. PAHs are released into the environment by means of natural processes, such as forest fires and direct biosynthesis under the action of microbes and plants (1). The primary artificial source of PAHs is the incomplete combustion of organic matter at high temperatures caused by human activities (2). Their presence in the environment poses a severe threat to public and ecosystem health because of their known acute toxicity and mutagenic, teratogenic, and carcinogenic features; they are therefore classified as priority pollutants by the U.S. Environmental Protection Agency (3). Furthermore, the persistence and genotoxicity of PAHs increase with molecular weight, and the presence of high-molecular-weight (HMW) PAHs in the environment is of greater concern. Benzo[a]pyrene (BaP), a representative HMW PAH with a five-ring structure, is a widespread pollutant with potent mutagenic and carcinogenic properties (4, 5). BaP is therefore identified as the first class of "human carcinogens" according to the report of the World Health Organization (WHO) International Agency for Research on Cancer (6). Generally, in soils with no industrial contamination, BaP concentrations vary from 3.5 to 3,700 g/kg, with a median concentration of 16 g/kg of soil; in contaminated soils and sediments, BaP concentrations range from 82 to 536 mg/kg (7).Bacteria possessing the ability of BaP utilization are readily isolated from contaminated soils or se...

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“…As described in previous research, strains ascribed to Bacillus sp. have been reported to be the efficient degraders of PAHs [13,14]. Also Pseudomonas sp.…”

Section: Resultsmentioning

confidence: 99%

Phenanthrene and Pyrene Modify the Composition and Structure of the Cultivable Endophytic Bacterial Community in Ryegrass (Lolium multiflorum Lam)

Zhu

Sun

et al. 2016

IJERPH

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This study provides new insights into the dynamics of bacterial community structure during phytoremediation. The communities of cultivable autochthonous endophytic bacteria in ryegrass exposed to polycyclic aromatic hydrocarbons (PAHs) were investigated with regard to their potential to biodegrade PAHs. Bacterial counts and 16S rRNA gene sequence were used in the microbiological evaluation. A total of 33 endophytic bacterial strains were isolated from ryegrass plants, which represented 15 different genera and eight different classes, respectively. Moreover, PAH contamination modified the composition and structure of the endophytic bacterial community in the plants. Bacillus sp., Pantoea sp., Pseudomonas sp., Arthrobacter sp., Pedobacter sp. and Delftia sp. were only isolated from the seedlings exposed to PAHs. Furthermore, the dominant genera in roots shifted from Enterobacter sp. to Serratia sp., Bacillus sp., Pantoea sp., and Stenotrophomonas sp., which could highly biodegrade phenanthrene (PHE). However, the diversity of endophytic bacterial community was decreased by exposure to the mixture of PAHs, and increased by respective exposure to PHE and pyrene (PYR), while the abundance was increased by PAH exposure. The results clearly indicated that the exposure of plants to PAHs would be beneficial for improving the effectiveness of phytoremediation of PAHs.

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Bacterial polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenases (PAH-RHD) encoding genes in different soils from King George Bay, Antarctic Peninsula

Cited by 59 publications

References 34 publications

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

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

Identification of Benzo[ a ]pyrene-Metabolizing Bacteria in Forest Soils by Using DNA-Based Stable-Isotope Probing

Phenanthrene and Pyrene Modify the Composition and Structure of the Cultivable Endophytic Bacterial Community in Ryegrass (Lolium multiflorum Lam)

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