Mengke Song

Occurrence and risks of antibiotics in the coastal aquatic environment of the Yellow Sea, North China

Eleven antibiotics in three different categories were investigated in two types of coastal bays (a semi-enclosed bay and an open bay) of the Yellow Sea and in fresh water (rivers and sewage treatment plants [STP] effluents) that discharged into the bays. The results revealed the presence of three predominant antibiotics: dehydration erythromycin, sulfamethoxazole and trimethoprim. These antibiotics were detected in the seawater and fresh water with concentrations of <0.23-50.4 ng L(-1) and <0.25-663.1 ng L(-1), respectively. In terms of the regional distribution of the compounds within the two types of bays, higher concentrations (<0.23-50.4 ng L(-1)) and higher spatial variations (coefficients of variation: 98%-124%) were found in the semi-enclosed Jiaozhou Bay due to the poor water-exchange ability and to fresh-water inputs through rivers and/or STP effluents. In contrast, lower concentrations (<0.23-3.0 ng L(-1)) and lower spatial variations (coefficients of variation: 36%-75%) were present in the open Yantai Bays due to the strong water-exchange with the open sea. The source apportionment suggested that 1) fresh-water inputs were the primary source of macrolides in the coastal water, and 2) mariculture affected the relative pollution levels of trimethoprim, sulfamethoxazole and sulfathiazole in the bays. In addition, a risk assessment based on the calculated risk quotient (RQ) showed that the dehydrated erythromycin, sulfamethoxazole and clarithromycin detected at most of the sampling sites in Jiaozhou Bay could pose high (RQ>1) risks to the most sensitive aquatic microorganisms, such as Synechococcus leopoliensis and Pseudokirchneriella subcapitata, whilst in the Yantai Bays, the compounds could pose medium risks (1≥RQ>0.1) to the same aquatic microorganisms.

Anaerobic degradation of polychlorinated biphenyls (PCBs) and polychlorinated biphenyls ethers (PBDEs), and microbial community dynamics of electronic waste-contaminated soil.

Environmental contamination caused by electronic waste (e-waste) recycling is attracting increasing attention worldwide because of the threats posed to ecosystems and human safety. In the present study, we investigated the feasibility of in situ bioremediation of e-waste-contaminated soils. We found that, in the presence of lactate as an electron donor, higher halogenated congeners were converted to lower congeners via anaerobic halorespiration using ferrous ions in contaminated soil. The 16S rRNA gene sequences of terminal restriction fragments indicated that the three dominant strains were closely related to known dissimilatory iron-reducing bacteria (DIRB) and those able to perform dehalogenation upon respiration. The functional species performed the activities of ferrous oxidation to ferric ions and further ferrous reduction for dehalogenation. The present study links iron cycling to degradation of halogenated materials in natural e-waste-contaminated soil, and highlights the synergistic roles of soil bacteria and ferrous/ferric ion cycling in the dehalogenation of polychlorinated biphenyls (PCBs) and polybrominated biphenyl ethers (PBDEs).

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

ABSTRACT 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 13C 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.

Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil.

Information on microorganisms possessing the ability to metabolize different polycyclic aromatic hydrocarbons (PAHs) in complex environments helps in understanding PAHs behavior in natural environment and developing bioremediation strategies. In the present study, stable-isotope probing (SIP) was applied to investigate degraders of PAHs in a forest soil with the addition of individually (13)C-labeled phenanthrene, anthracene, and fluoranthene. Three distinct phylotypes were identified as the active phenanthrene-, anthracene- and fluoranthene-degrading bacteria. The putative phenanthrene degraders were classified as belonging to the genus Sphingomona. For anthracene, bacteria of the genus Rhodanobacter were the putative degraders, and in the microcosm amended with fluoranthene, the putative degraders were identified as belonging to the phylum Acidobacteria. Our results from DNA-SIP are the first to directly link Rhodanobacter- and Acidobacteria-related bacteria with anthracene and fluoranthene degradation, respectively. The results also illustrate the specificity and diversity of three- and four-ring PAHs degraders in forest soil, contributes to our understanding on natural PAHs biodegradation processes, and also proves the feasibility and practicality of DNA-based SIP for linking functions with identity especially uncultured microorganisms in complex microbial biota.

Novel phenanthrene-degrading bacteria identified by DNA-stable isotope probing

Microorganisms responsible for the degradation of phenanthrene in a clean forest soil sample were identified by DNA-based stable isotope probing (SIP). The soil was artificially amended with either 12C- or 13C-labeled phenanthrene, and soil DNA was extracted on days 3, 6 and 9. Terminal restriction fragment length polymorphism (TRFLP) results revealed that the fragments of 219- and 241-bp in HaeIII digests were distributed throughout the gradient profile at three different sampling time points, and both fragments were more dominant in the heavy fractions of the samples exposed to the 13C-labeled contaminant. 16S rRNA sequencing of the 13C-enriched fraction suggested that Acidobacterium spp. within the class Acidobacteria, and Collimonas spp. within the class Betaproteobacteria, were directly involved in the uptake and degradation of phenanthrene at different times. To our knowledge, this is the first report that the genus Collimonas has the ability to degrade PAHs. Two PAH-RHDα genes were identified in 13C-labeled DNA. However, isolation of pure cultures indicated that strains of Staphylococcus sp. PHE-3, Pseudomonas sp. PHE-1, and Pseudomonas sp. PHE-2 in the soil had high phenanthrene-degrading ability. This emphasizes the role of a culture-independent method in the functional understanding of microbial communities in situ.

Could Uptake and Acropetal Translocation of PBDEs by Corn Be Enhanced Following Cu Exposure? Evidence from a Root Damage Experiment.

Cocontamination by heavy metals and persistent organic pollutants (POPs) is ubiquitous in the environment. Fate of POPs within soil/water-plant system is a significant concern and an area where much uncertainty still exists when plants suffered cotoxicity from POPs and metals. This study investigated the fate of polybrominated diphenyl ethers (PBDEs) when copper (Cu) was present within the soil/water-plant system using pot and hydroponic experiments. The presence of Cu was found to induce damage to the root cell membranes of corn (Zea mays L. cv. Nongda 108) with increasing concentration in both shoots and roots. The PBDE congeners BDE209 and BDE47 in shoots were also enhanced with the increasing electrolytic leakage from root, attributed to Cu damage, and the highest shoot BDE209 and BDE47 levels were observed under the highest Cu dosage. In addition, positive correlations were observed between the PBDE content of corn shoots and the electrolytic leakage of corn roots. These results indicated that within a defective root system, more PBDEs will penetrate the roots and are acropetally translocated in the shoots. The potential ecological risk associated with the translocation and accumulation of POPs into plant shoots needs careful reconsideration in media cocontaminated with metals and POPs, whereas often ignored or underestimated in environmental risk assessments.

Biodegradation of Phenanthrene in Polycyclic Aromatic Hydrocarbon-Contaminated Wastewater Revealed by Coupling Cultivation-Dependent and -Independent Approaches

The indigenous microorganisms responsible for degrading phenanthrene (PHE) in polycyclic aromatic hydrocarbons (PAHs)-contaminated wastewater were identified by DNA-based stable isotope probing (DNA-SIP). In addition to the well-known PHE degraders Acinetobacter and Sphingobium, Kouleothrix and Sandaracinobacter were found, for the first time, to be directly responsible for indigenous PHE biodegradation. Additionally, a novel PHE degrader, Acinetobacter tandoii sp. LJ-5, was identified by DNA-SIP and direct cultivation. This is the first report and reference to A. tandoii involved in the bioremediation of PAHs-contaminated water. A PAH-RHDα gene involved in PHE metabolism was detected in the heavy fraction of 13C treatment, but the amplification of PAH-RHDα gene failed in A. tandoii LJ-5. Instead, the strain contained catechol 1,2-dioxygenase and the alpha/beta subunits of protocatechuate 3,4-dioxygenase, indicating use of the β-ketoadipate pathway to degrade PHE and related aromatic compounds. These findings add to our current knowledge on microorganisms degrading PHE by combining cultivation-dependent and cultivation-independent approaches and provide deeper insight into the diversity of indigenous PHE-degrading communities.

Distributions and compositions of old and emerging flame retardants in the rhizosphere and non-rhizosphere soil in an e-waste contaminated area of South China

We investigated rhizosphere effects on the distributions and compositions of polybrominated diphenyl ethers (PBDEs), novel brominated flame retardants (NBFRs), and dechlorane plus (DPs) in rhizosphere soils (RS) and non-rhizosphere soils (NRS) in an e-waste recycling area in South China. The concentrations of PBDEs, NBFRs, and DPs ranged from 13.9 to 351, 11.6 to 70.8, and 0.64 to 8.74 ng g(-1) in RS and 7.56 to 127, 8.98 to 144, and 0.38 to 8.45 ng g(-1) in NRS, respectively. BDE-209 and DBDPE were the dominant congeners of PBDEs and NBFRs, respectively. PBDEs, NBFRs, and DPs were more enriched in RS than NRS in most vegetables species. Further analysis suggested that the differentiation of the rhizosphere effect on halogenated flame retardants (HFRs) was not solely controlled by the octanol-water coefficients. This difference was also reflected by the correlations between total organic carbon (TOC) and PBDEs, NBFRs, or DPs, which indicated that organic carbon was a more pivotal controlling factor for PBDEs and DPs than for NBFRs in soil. We also found significant positive correlations between PBDEs and their replacement products, which indicated a similar emission pattern and environmental behaviour.

Characterisation of the phenanthrene degradation-related genes and degrading ability of a newly isolated copper-tolerant bacterium

A copper-tolerant phenanthrene (PHE)-degrading bacterium, strain Sphingobium sp. PHE-1, was newly isolated from the activated sludge in a wastewater treatment plant. Two key genes, ahdA1b-1 encoding polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHDɑ) and xyLE encoding catechol-2,3-dioxygenase (C23O), involved in the PHE metabolism by strain PHE-1 were identified. The PAH-RHD gene cluster showed 96% identity with the same cluster of Sphingomonas sp. P2. Our results indicated the induced transcription of xylE and ahdA1b-1 genes by PHE, simultaneously promoted by Cu(II). For the first time, high concentration of Cu(II) is found to encourage the expression of PAH-RHDɑ and C23O genes during PHE degradation. Applying Sphingomonas PHE-1 in PHE-contaminated soils for bioaugmentation, the abundance of xylE gene was increased by the planting of ryegrass and the presence of Cu(II), which, in turn, benefited ryegrass growth. The best performance of PHE degradation and the highest abundance of xylE genes occurred in PHE-copper co-contaminated soils planted with ryegrass.

Exploring the Influence of Environmental Factors on Bacterial Communities within the Rhizosphere of the Cu-tolerant plant, Elsholtzia splendens

Bacterial communities of rhizospheric soils play an important role in the tolerance and uptake of metal-tolerant/hyperaccumulating plants to metals, e.g. the Cu-tolerant Elsholtzia splendens native to China. In this work, pyrosequencing of the bacterial 16S rRNA gene was firstly applied to investigate the rhizospheric bacterial community of E. splendens grown at Cu contaminated sites. The 47 phyla including 11 dominant phyla (>1%) in E. splendens rhizosphere were presented. The effects of Cu and other environmental factors (total organic carbon, total nitrogen and pH) on the rhizospheric bacterial community were studied comprehensively. The phyla abundances were affected by the environmental factors to different extent, and we found pH, instead of Cu concentration, influenced UniFrac distance significantly and was identified as the most important environmental factor affecting bacterial community. In addition, the influence of environmental factors on gene profiles was explored according to the predicted metagenomes obtained by PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states). Our study illustrates a view about Cu-tolerant E. splendens rhizospheric bacterial communities (composition, diversity and gene profiles) and their influencing factors, giving a hand for the understanding on bacterial community is formed and affected in rhizosphere.