Emission of 16 polycyclic aromatic hydrocarbons (PAHs) listed as U.S. Environmental Protection Agency (U.S. EPA) priority pollutants from major sources in China were compiled. Geographical distribution and temporal change of the PAH emission, as well as emission profiles, are discussed. It was estimated that the total PAH emission in China was 25,300 tons in 2003. The emission profile featured a relatively higher portion of high molecular weight (HMW) species with carcinogenic potential due to large contributions of domestic coal and coking industry. Among various sources, biomass burning, domestic coal combustion, and coking industry contributed 60%, 20%, and 16% of the total emission, respectively. Total emission, emission density, emission intensity, and emission per capita showed geographical variations. In general, the southeastern provinces were characterized by higher emission density, while those in western and northern China featured higher emission intensity and population-normalized emission. Although energy consumption in China went up continuously during the past two decades, annual emission of PAHs fluctuated depending on the amount of domestic coal consumption, coke production, and the efficiency of energy utilization.

RNA isolation with RNA in a high quantity is a basic analytical method in plant genetics, molecular biology and related physiological investigations. To understand the genetic and molecular biology of Chinese fir, sufficient high-quality total RNA must be obtained for cDNA library construction and other downstream molecular applications. However, extracting RNA from Chinese fir is difficult and often requires the modification of existing protocols. Chinese fir tissues containing large amounts of polysaccharides and polyphenol compounds and are one of the most difficult plant tissues for RNA isolation. Therefore, we developed a simple method for extracting high-quality RNA from Chinese fir tissues. RNA isolations were performed within two hours, RNA quality was measured for yield and purity. Total RNA obtained from this procedure was successfully used for cDNA library construction, RT-PCR and transcriptome sequencing. It was proven that extracted RNA was intact and suitable for downstream molecular applications, including RT-PCR and qPCR, and other downstream molecular applications. Thus, this protocol represents a simple, efficient, and low-cost method.

BackgroundMarine microorganisms are an important source of new drug leads. However, the discovery and sustainable production of these compounds are often hampered due to the unavailable expression of cryptic biosynthetic gene clusters or limited titer. Ribosome engineering and response surface methodology (RSM) integrated strategy was developed in this study to activate cryptic gene cluster in the deepsea-derived Streptomyces somaliensis SCSIO ZH66, and subsequently isolation, structural analysis, and the yield enhancement of the activated compound, anticancer drug lead Fredericamycin A (FDM A), were performed.ResultsIn order to discover novel natural products from marine Streptomyces strains by genome mining strategy, the deepsea-derived S. somaliensis SCSIO ZH66 was subject to ribosome engineering to activate the expression of cryptic gene clusters. A resistant strain ZH66-RIF1 was thereby obtained with 300 μg/mL rifampicin, which accumulated a brown pigment with cytotoxicity on MS plate while absent in the wild type strain. After screening of fermentation conditions, the compound with pigment was purified and identified to be FDM A, indicating that the activation of a cryptic FDM A biosynthetic gene cluster was taken place in strain ZH66-RIF1, and then it was identified to be ascribed to the mutation of R444H in the β subunit of RNA polymerase. To further improve the yield efficiently, nine fermentation medium components were examined for their significance on FDM A production by Plackett–Burman design and Box-Behnken design. The optimum medium composition was achieved by RSM strategy, under which the titer of FDM A reached 679.5 ± 15.8 mg/L after 7 days of fermentation, representing a 3-fold increase compared to the original medium. In terms of short fermentation time and low-cost fermentation medium, strain ZH66-RIF1 would be an ideal alternative source for FDM A production.ConclusionsOur results would hasten the efforts for further development of FDM A as a drug candidate. Moreover, this ribosome engineering and RSM integrated methodology is effective, fast and efficient; it would be applicable to genome mining for novel natural products from other strains.Electronic supplementary materialThe online version of this article (doi:10.1186/s12934-015-0244-2) contains supplementary material, which is available to authorized users.

Clarifying glycosyltrasferases (GTs) function is of significance for the development of GT inhibitors as drugs, and the use of GTs to glycodiversify small molecules in the search of drug leads. While many Actinomyces natural-product GTs had been functionally characterized, our understanding towards Bacillus natural-product GTs is so far very limited. Herein, genome-wide identification of macrolide GT genes from marine-derived Bacillus methylotrophicus B-9987 revealed the presence of three macrolide GT genes bmmGT1-3. While bmmGT1 was previously revealed to be involved in the biosynthesis of trans-acyltransferase (AT) polyketides compounds macrolactins (MLNs) and bacillaenes (BAEs), the functions of bmmGT2 and bmmGT3 were probed, demonstrating that they are capable to biochemically catalyze glycosylation of MLNs and BAEs as well but interestingly with different regioselectivity, affording four new MLNs analogs. Notably, further genome mining revealed that the orthologs of these three macrolide GT genes showed a regular distribution in the subtilis- and the cereus-clade Bacillus strains; interestingly, bmmGT1 orthologs only occurred in the subtilis-clade Bacillus, and they were also found in the genomes of Streptomyces strains, suggesting their close phylogenetic relationship. These results provide the first significant insight into the important roles of Bacillus macrolide GTs in the biology of the species.

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Exploration of unstable compounds is a rarely explored area of natural product research. We describe the integration of genomic and metabolomic analyses with bioassay-guided compound mining to effectively explore unstable bacillaenes. New bacillaene structures (2, 4, and 5) were identified from compound mixtures using the DANS-SVI (differential analysis of 2D NMR spectrum−single spectrum with variable intensities) method, which were further verified by the isolation of the pure compounds under strictly controlled conditions. Compound 1 exhibited antibacterial activity against multi-drug-resistant bacterial strains, while glycosylation decreased the activity of the bacillaene scaffold.

A Gram-stain-negative, motile, aerobic and rod-shaped bacterial strain, designated T17, was isolated from benthic sediment sampled at Jiaozhou Bay, Bohai Sea, China, and its taxonomic position was investigated. The 16S rRNA gene sequence of strain T17 exhibited the highest similarity values to those of the type strain Marinobacter lacisalsi FP2.5 (96.2 %) and Marinobacter koreensis DD-M3 (96.2 %). Strain T17 grew optimally at 35 °C, pH 7.0-8.0 and in the presence of 6.0-10.0 % (w/v) NaCl. The predominant ubiquinone in strain T17 was identified as Q-9. The major fatty acids of strain T17 were C12 : 0, C16 : 0 and C16 : 0 10-CH3. The major polar lipids of strain T17 were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidglycerol, an unidentified aminolipid and an unidentified phospholipid. The DNA G+C content of strain T17 was 63.0 mol%. The draft genome sequence of strain T17 includes 4 755 891 bp in total (N50=2 856 325 bp) with a medium read coverage of 100.0x and 11 scaffolds. In silico DNA-DNA hybridization with the three type strains showed 20.3, 19.7 and 19.9 % relatedness to Marinobacter santoriniensis NKSG1, Marinobacter segnicrescens SS11B1-4 and Marinobacter daqiaonensis CGMCC 1.9167, respectively. On the basis of the phenotypic, phylogenetic, genomic and chemotaxonomic properties, strain T17 is considered to represent a novel species within the genus Marinobacter, for which the name Marinobacterbohaiensis sp. nov. is proposed. The type strain is T17 (=KCTC 52710=MCCC 1K03282).

Using Illumine Hiseq sequencing assessed the diversity and distribution of fungal communities in seawater of the Mariana Trench, with depth ranging 1000–4000 meters.