Yue-Hui Hong

Characterization of a novel biosurfactant produced by marine hydrocarbon-degrading bacterium Achromobacter sp. HZ01.

To purify and characterize the biosurfactants produced by Achromobacter sp. HZ01.

Centennial-scale records of total organic carbon in sediment cores from the South Yellow Sea, China

Global carbon cycling is a significant factor that controls climate change. The centennial-scale variations in total organic carbon (TOC) contents and its sources in marginal sea sediments may reflect the influence of human activities on global climate change. In this study, two fine-grained sediment cores from the Yellow Sea Cold Water Mass of the South Yellow Sea were used to systematically determine TOC contents and stable carbon isotope ratios. These results were combined with previous data of black carbon and 210Pb dating from which we reconstructed the centennial-scale initial sequences of TOC, terrigenous TOC (TOCter) and marine autogenous TOC (TOCmar) after selecting suitable models to correct the measured TOC (TOCcor). These sequences showed that the TOCter decreased with time in the both cores while the TOCmar increased, particularly the rapid growth in core H43 since the late 1960s. According to the correlation between the Huanghe (Yellow) River discharge and the TOCcor, TOCter, or TOCmar, we found that the TOCter in the two cores mainly derived from the Huanghe River and was transported by it, and that higher Huanghe River discharge could strengthen the decomposition of TOCmar. The newly obtained initial TOC sequences provide important insights into the interaction between human activities and natural processes.

Synchronous response of sedimentary organic carbon accumulation on the inner shelf of the East China Sea to the water impoundment of Three Gorges and Gezhouba Dams

Coastal seas, located between continents and the open ocean, are an important active carbon pool. The sedimentary total organic carbon (TOC) in these areas is a mixture of terrestrial and marine sources, and can be a powerful proxy for tracing natural processes and human activities. In this study, one fine-grained sediment core (DH5-1) from the inner shelf of the East China Sea was systematically analyzed for TOC and black carbon (BC) contents and TOC stable carbon isotope ratios (δ13C). By combining these data with 210Pb dating, an improved carbon correction model and a two end-member mixing model, we reconstructed century-scale high-resolution sequences of corrected TOC, terrestrial TOC and marine TOC contents and identified two carbon depletion events in the DH5-1 record. The two events, shown as two minima in the TOC profiles, correspond temporally to 1985-1987 AD and 2003-2006 AD, which exactly matches the water impoundment of the Gezhouba Dam and Three Gorges Dam, respectively. In addition, the variations in TOC contents and δ13C values before, during or after the minima demonstrate a relationship between the depletion events and water impoundment of the dams on the Changjiang River. The TOC reductions may represent synchronous responses of sedimentary TOC and resultant ecological effects on the inner shelf of the East China Sea to the water impoundment of the dams. These new TOC records reflect the interaction between natural and anthropogenic processes and, accordingly, provide a deep insight and important references for assessing marine ecological effects resulting from water impoundment of largescale dams.

Fungus-larva relation in the formation of Cordyceps sinensis as revealed by stable carbon isotope analysis

For more than one thousand years, Cordyceps sinensis has been revered as a unique halidom in the Qinghai-Tibetan Plateau for its mysterious life history and predominant medicinal values. This mysterious fungus-larva symbiote also attracted the over-exploitation, while several problems on the initial colonization of Ophiocordyceps sinensis in the host larva have constrained artificial cultivation. In this work, stable carbon isotope analysis was employed to analyse the subsamples of C. sinensis from 5 representative habitats. The results demonstrated that these samples possessed similar δ13C profiles, i.e., a steady ascending trend from the top to the bottom of stroma, occurrence of the δ13C maximum at the head, a slight decrease from the head to the end of thorax, a sharply descent trend from the end of thorax to the forepart of abdomen, and maintenance of lower δ13C values in the rest parts of abdomen. Based on the data, we consider that the site near the head of the host larva may be the initial target attacked by O. sinensis, and the fungus growth is closely related to the digestive tract of its host larva. The growth stages of O. sinensis are accordingly speculated as the symptom-free, symptom-appearing, and stroma-germinating stages.

Genome Sequencing Reveals the Potential of Achromobacter sp. HZ01 for Bioremediation

Petroleum pollution is a severe environmental issue. Comprehensively revealing the genetic backgrounds of hydrocarbon-degrading microorganisms contributes to developing effective methods for bioremediation of crude oil-polluted environments. Marine bacterium Achromobacter sp. HZ01 is capable of degrading hydrocarbons and producing biosurfactants. In this study, the draft genome (5.5 Mbp) of strain HZ01 has been obtained by Illumina sequencing, containing 5,162 predicted genes. Genome annotation shows that “amino acid metabolism” is the most abundant metabolic pathway. Strain HZ01 is not capable of using some common carbohydrates as the sole carbon sources, which is due to that it contains few genes associated with carbohydrate transport and lacks some important enzymes related to glycometabolism. It contains abundant proteins directly related to petroleum hydrocarbon degradation. AlkB hydroxylase and its homologs were not identified. It harbors a complete enzyme system of terminal oxidation pathway for n-alkane degradation, which may be initiated by cytochrome P450. The enzymes involved in the catechol pathway are relatively complete for the degradation of aromatic compounds. This bacterium lacks several essential enzymes for methane oxidation, and Baeyer-Villiger monooxygenase involved in the subterminal oxidation pathway and cycloalkane degradation was not identified. These results suggest that strain HZ01 degrades n-alkanes via the terminal oxidation pathway, degrades aromatic compounds primarily via the catechol pathway and cannot perform methane oxidation or cycloalkane degradation. Additionally, strain HZ01 possesses abundant genes related to the metabolism of secondary metabolites, including some genes involved in biosurfactant (such as glycolipids and lipopeptides) synthesis. The genome analysis also reveals its genetic basis for nitrogen metabolism, antibiotic resistance, regulatory responses to environmental changes, cell motility, and material transport. The obtained genome data provide us with a better understanding of hydrocarbon-degrading bacteria, which may contribute to the future design of rational strategies for bioremediation of petroleum-polluted marine environments.

Molecular characterization and gene expression of cathepsin L in Nile tilapia (Oreochromis niloticus)

Abstract Cathepsin L (CatL) has been widely known for its involvement in the innate immunity. However, it still remains poorly understand how CatL modulates the immune system of teleosts. Moreover, the CatL of Nile tilapia (NtCatL) has not been cloned or characterized. In this study, the gene encoding NtCatL was cloned, and was characterized by bioinformatics analysis, heterologous expression and protease activity assay. The coding sequence of NtCatL is 1017 bp in length and encodes 338 amino acid residues with a predicted molecular weight of 38.487 kDa and a theoretical isoelectric point of 5.79. NtCatL possesses the features of a typical cathepsin L, including one signal peptide, one propeptide region, and one papain family cysteine protease domain containing four active site residues (Gln135, Cys141, His281, and Asn305). The prediction of protein‐protein interaction shows that NtCatL may interact with some functional proteins for realizing an immune function. Real‐time quantitative PCR revealed the widespread transcriptional expression of NtCatL in six tissues of healthy Nile tilapia, and the NtCatL mRNA is significantly up‐regulated after Streptococcus agalactiae challenge. These results suggest that NtCatL is likely to be involved in the immune reaction of Nile tilapia. Recombinant proteins from the mature domain (residues 117–337) of NtCatL were obtained by heterologous expression using pET28a and Rosetta (DE3) competent cells. A protein product with the high purity was obtained by using TALON Superflow purification rather than adopting HisTrap HP columns. The protease activity of the recombinant protein was verified by using a substrate hydrolyzing assay. This work has cloned and characterized the CatL from Nile tilapia for the first time, and contributes to elucidating the immunological functions of CatL. HighlightsThe CatL of Nile tilapia has been cloned and characterized for the first time.The expression level of NtCatL was revealed in six tissues of Nile tilapia.NtCatL may involve in the innate immune system of Nile tilapia.The protease activity of the recombinant protein from NtCatL was verified.

Characterization of the transcriptome of Achromobacter sp. HZ01 with the outstanding hydrocarbon-degrading ability.

Microbial remediation has become one of the most important strategies for eliminating petroleum pollutants. Revealing the transcript maps of microorganisms with the hydrocarbon-degrading ability contributes to enhance the degradation of hydrocarbons and further improve the effectiveness of bioremediation. In this study, we characterized the transcriptome of hydrocarbon-degrading Achromobacter sp. HZ01 after petroleum treatment for 16h. A total of 38,706,280 and 38,954,413 clean reads were obtained by RNA-seq for the petroleum-treated group and control, respectively. By an effective de novo assembly, 3597 unigenes were obtained, including 3485 annotated transcripts. Petroleum treatment had significantly influenced the transcriptional profile of strain HZ01, involving 742 differentially expressed genes. A part of genes were activated to exert specific physiological functions, whereas more genes were down-regulated including specific genes related to cell motility, genes associated with glycometabolism, and genes coding for ribosomal proteins. Identification of genes related to petroleum degradation revealed that the fatty acid metabolic pathway and a part of monooxygenases and dehydrogenases were activated, whereas the TCA cycle was inactive. Additionally, terminal oxidation might be a major aerobic pathway for the degradation of n-alkanes in strain HZ01. The newly obtained data contribute to better understand the gene expression profiles of hydrocarbon-degrading microorganisms after petroleum treatment, to further investigate the genetic characteristics of strain HZ01 and other related species and to develop cost-effective and eco-friendly strategies for remediation of crude oil-polluted environments.

Century-scale high-resolution black carbon records in sediment cores from the South Yellow Sea, China

Black carbon (BC) has received increasing attention in the last 20 years because it is not only an absorbent of toxic pollutants but also a greenhouse substance, preserving fire-history records, and more importantly, acting as an indicator of biogeochemical cycles and global changes. By adopting an improved chemothermal oxidation method (WXY), this study reconstructed the century-scale high-resolution records of BC deposition from two fine-grained sediment cores collected from the Yellow Sea Cold Water Mass in the South Yellow Sea. The BC records were divided into five stages, which exhibited specific sequences with three BC peaks at approximately 1891, 1921, and 2007 AD, representing times at which the first heavy storms appeared just after the termination of long-term droughts. The significant correlation between the times of the BC peaks in the cores and heavy storms in the area of the Huanghe (Yellow) River demonstrated that BC peaks could result from markedly strengthened sedimentation due to surface runoff, which augmented the atmospheric deposition. Stable carbon isotope analysis indicated that the evident increase in carbon isotope ratios of BC in Stage 5 might have resulted from the input of weathered rock-derived graphitic carbon cardinally induced by the annual anthropogenic modulation of water-borne sediment in the Huanghe River since 2005 AD. Numerical calculations demonstrated that the input fraction of graphitic carbon was 22.97% for Stage 5, whereas no graphitic carbon entered during Stages 1 and 3. The obtained data provide new and important understanding of the source-sink history of BC in the Yellow Sea.

Stable Carbon Isotope Composition of the Lipids in Natural Ophiocordyceps sinensis from Major Habitats in China and Its Substitutes

Ophiocordyceps sinensis is one rare medicinal fungus produced in the Qinghai-Tibetan Plateau. Its quality and price varies hugely with different habitat, and its numerous substitutes have sprung up in functional food markets. This paper aims to discriminate the geographic origin of wild O. sinensis and its substitutes via element analyzer–isotope ratio mass spectrometry and gas chromatography–isotope ratio mass spectrometry. The δ13C values of major fatty acids in the lipids of O. sinensis are characterized unanimously by the variation relation C18:0 < C18:2 ≈ C16:0 < C18:1, while their fluctuation intervals are notably different between those of neutral and polar lipids. The comparative analysis of the δ13C ratios of major fatty acids in lipids of O. sinensis suggests that the δ13C patterns may be sensitive potential indicators to discriminate its geographical origin. The δ13C values of individual major fatty acids of lipids from the cultivated stromata of Cordyceps militaris (SCM), the fermented mycelia of Hirsurella sinensis (FMH) and Paecilomyces epiali (FMP) range from −31.2‰ to −29.7‰, −16.9‰ to −14.3‰, and −26.5‰ to −23.9‰, respectively. Their δ13C pattern of individual major fatty acids may be used as a potential indicator to discriminate the products of natural O. sinensis and its substitutes.

Publisher Correction: Fungus-larva relation in the formation of Cordyceps sinensis as revealed by stable carbon isotope analysis

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