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

Identification of Benzo[a]pyrene-metabolizing bacteria in forest soils by using DNA-based stable-isotope probing

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

Concentrations, seasonal variations, and outflow of atmospheric polycyclic aromatic hydrocarbons (PAHs) at Ningbo site, Eastern China

AbstractThirty six pairs of gas and particle (PM2.5) atmospheric samples were collected by high-volume samplers from July 2009 to March 2010 at an eastern background site in Ningbo and analyzed for polycyclic aromatic hydrocarbons (PAHs). The total (gas+particle) air concentrations of 16 PAHs ranged from 11.0 to 103ng m−3, with an average of 46.0α23.4ng m−3. Seasonal trends of PAH concentrations were observed with high concentrations in winter and low in summer, mainly due to regional sources and meteorological conditions. The association with other airborne pollutants and diagnostic ratio analysis indicated that PAHs in Eastern China background were predominantly from coal/biomass combustion. Coal combustion controlled atmospheric PAHs in winter, whilst biomass burning became important in summer and autumn. Located at eastern coastal areas, Ningbo site was chosen to estimate the atmospheric outflow of PAHs. Transport fluxes were characterized by elevated values in spring and winter. Southward transport fluxes dominated during the sampling period, presenting the transport from northern to southern China

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 13C-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

The impact on the soil microbial community and enzyme activity of two earthworm species during the bioremediation of pentachlorophenol-contaminated soils

The ecological effect of earthworms on the fate of soil pentachlorophenol (PCP) differs with species. This study addressed the roles and mechanisms by which two earthworm species (epigeic Eisenia fetida and endogeic Amynthas robustus E. Perrier) affect the soil microbial community and enzyme activity during the bioremediation of PCP-contaminated soils. A. robustus removed more soil PCP than did E. foetida. A. robustus improved nitrogen utilisation efficiency and soil oxidation more than did E. foetida, whereas the latter promoted the organic matter cycle in the soil. Both earthworm species significantly increased the amount of cultivable bacteria and actinomyces in soils, enhancing the utilisation rate of the carbon source (i.e. carbohydrates, carboxyl acids, and amino acids) and improving the richness and evenness of the soil microbial community. Additionally, earthworm treatment optimized the soil microbial community and increased the amount of the PCP-4-monooxygenase gene. Phylogenic classification revealed stimulation of indigenous PCP bacterial degraders, as assigned to the families Flavobacteriaceae, Pseudomonadaceae and Sphingobacteriacea, by both earthworms. A. robustus and E. foetida specifically promoted Comamonadaceae and Moraxellaceae PCP degraders, respectively

Antibiotics in the offshore waters of the Bohai Sea and the Yellow Sea in China: Occurrence, distribution and ecological risks

The ocean is an important sink of land-based pollutants. Previous studies showed that serious antibiotic pollution occurred in the coastal waters, but limited studies focused on their presence in offshore waters. In this study, eleven antibiotics in three different categories were investigated in offshore waters of the Bohai Sea and the Yellow Sea in China. The results indicated that three antibiotics dehydration erythromycin, sulfamethoxazole and trimethoprim occurred throughout the offshore waters at concentrations of 0.10-16.6 ng L-1 and they decreased exponentially from the rivers to the coastal and offshore waters. The other antibiotics all presented very low detection rates (<10%) and concentrations (<0.51 ng L-1). Although the concentrations were very low, risk assessment based on the calculated risk quotients (RQs) showed that sulfamethoxazole, dehydration erythromycin and clarithromycin at most of sampling sites posed medium or low ecological risks (0.01 < RQ < 1) to some sensitive aquatic organisms, including Synechococcus leopoliensis and Pseudokirchneriella subcapitata. (C) 2012 Elsevier Ltd. All rights reserved.The ocean is an important sink of land-based pollutants. Previous studies showed that serious antibiotic pollution occurred in the coastal waters, but limited studies focused on their presence in offshore waters. In this study, eleven antibiotics in three different categories were investigated in offshore waters of the Bohai Sea and the Yellow Sea in China. The results indicated that three antibiotics dehydration erythromycin, sulfamethoxazole and trimethoprim occurred throughout the offshore waters at concentrations of 0.10-16.6 ng L-1 and they decreased exponentially from the rivers to the coastal and offshore waters. The other antibiotics all presented very low detection rates (<10%) and concentrations (<0.51 ng L-1). Although the concentrations were very low, risk assessment based on the calculated risk quotients (RQs) showed that sulfamethoxazole, dehydration erythromycin and clarithromycin at most of sampling sites posed medium or low ecological risks (0.01 < RQ < 1) to some sensitive aquatic organisms, including Synechococcus leopoliensis and Pseudokirchneriella subcapitata. (C) 2012 Elsevier Ltd. All rights reserved

Distinct Biogeography of Different Fungal Guilds and Their Associations With Plant Species Richness in Forest Ecosystems

Plant pathogens are increasingly considered as important agents in promoting plant coexistence, while plant symbionts like ectomycorrhizal fungi (EMF) can facilitate plant dominance by helping conspecific individuals to defend against plant pathogens. However, we know little about their relationships with plants at large scales. Here, using soil fungal data collected from 28 forest reserves across China, we explored the latitudinal diversity gradients of overall fungi and different fungal functional guilds, including putative plant pathogens, EMF, and saprotrophic fungi. We further linked the spatial patterns of alpha diversities of putative plant pathogens and EMF to the variation of plant species richness. We found that the relationships between latitude and alpha diversities of putative plant pathogens and EMF were region-dependent with sharp diversity shifts around the mid-latitude (similar to 35 degrees N), which differed from the unimodal diversity distributions of the overall and saprotrophic fungi. The variations in the diversities of putative plant pathogens and EMF were largely explained by the spatial regions (south vs. north/subtropical zone vs. temperate zone). Additionally, the alpha diversities of these two fungal guilds exhibited opposing trends across latitude. EMF could alter the relationship between diversities of putative plant pathogens and plants in the south/subtropical region, but not vice versa. We also found that the ratio of their alpha diversities (EMF to putative plant pathogens) was negatively related to plant species richness across the spatial regions (north to south), and explained similar to 10% of the variation of plant species richness. Overall, our findings suggest that plant-microbe interactions not only shape the local plant diversity but also may have non-negligible contributions to the large-scale patterns of plant diversity in forest ecosystems.National Natural Science Foundation of China [31600403, 31800422, 41673111, U1501232, 41622106]; Natural Science Foundation of Guangdong Province, China [2016A030312003]; U.S. National Science Foundation MacroSystems Biology program [NSF EF-1065844]; Candidates at Sun Yat-Sen UniversityOpen access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Spectrochemical determination of unique bacterial responses following long-term low-level exposure to antimicrobials

Agents arising from engineering or pharmaceutical industries may have significant environmental impacts. Particularly, antimicrobials not only act as efficient eliminators of certain microbes but also facilitate the propagation of organisms with antimicrobial resistance, giving rise to critical health issues, e.g., the bloom of multidrug-resistant bacteria. Although many investigations have examined microbial responses to antimicrobials and characterized relevant mechanisms, they have focused mainly on high-level and short-term exposures, instead of simulating real-world scenarios in which the antimicrobial exposure is at a low-level for long periods. Herein, we developed a spectrochemical tool, attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy, as a high-throughput and nondestructive approach to interrogate the long-term effects of low-level antimicrobial exposure in bacterial cells. Post-exposure to nanoparticulate silver (AgNP), tetracycline or their mixtures for 12 days, Gram-positive (Mycobacterium vanbaalenii PYR-1) and Gram-negative (Pseudomonas fluorescens) bacteria exhibited distinct IR spectral alterations. Multivariate analysis coupled with multivariate regression trees (MRT) indicates nutrient depletion and exposure time as the primary factors in bacterial behaviour, followed by exposure category and bacterial type. Nutrient depletion and starvation during long-term exposure drives bacterial cells into a dormant state or to exhibit additional cellular components (e.g., fatty acids) in response to antimicrobials, consequently causing a broader range of spectral alterations compared to short-term exposure. This work is the first report highlighting the more important roles of exposure duration and nutrient depletion, instead of treatment regimens of antimicrobials, in microbial responses to low-level and prolonged environmental exposures