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| 1 | Bacterial community in sediment from the Western Pacific 'Warm Pool' and its relationship to environment显示文摘Total DNAs were extracted from different sections of deep sea sediment core sample collected from the Western Pacific 'Warm Pool'. The bacterial 16S ribosomal DNA (rDNA) clone libraries were constructed and analyzed by PCR-restriction fragment length polymorphism (RFLP) and DNA sequencing. The bacterial communities in these samples and their relationship to environment were analyzed consequently. The results indicated that among eight main bacterial groups found in these sediments, members of the γ-Proteobacteria were most abundant in each section of sediment core sample and the genus Colwellia belonging to γ-Proteobacteria was dominant in this area. Members of the α-Proteobacteria were found commonly existing in these samples, while members belonging to β-Proteobacteria were seldom detected. The diversity of bacterial communities from different sections of sediment core sample was δ- and ε-Proteo- bacteria and the bacterial group including genera Cytopahga, Flexibacteria and Bacteroides (CFB group). These bacteria all were inversely proportional to the depth of sediment. Phylogenetic analysis showed that there were 18%-30% and 15%-25% of total bacterial communities related to methane and sulfur metabolism respectively in each section of core sample, implicating that the metabolism of sulfur and methane played an important role in the substance and energy cycles of the Western Pacific 'Warm Pool'. | ZENG Runying ZHAO Jing ZHANG Rui LIN Nianwei | 2005 | Science China Earth Sciences2005，48，2： | 21 |
| 2 | Characterization of an extreme alkaline-stable keratinase from the draft genome of feather-degrading Bacillus sp.JM7 from deep-sea显示文摘Bacillus sp. JM7, a strain isolated from the deep-sea of the South China Sea, was found to efficiently degrade 79.4% native chicken feather within 30 h. Scanning electron microscopy analysis showed that JM7 strain could gradually degrade feather by modifying the microstructure of feather keratin. A total of 25 protease genes were predicted from the draft genome of JM7 strain, among which a predicted subtilisin-like serine protease(designated as Ker02562) was further characterized for its keratinolytic activity. The recombinant Ker02562 functioned at a wide range of temperatures from 30℃ to 60℃, with an optimum at 40–50℃. Ker02562 was highly active at various pHs ranging from 5.0 to 13.0, with a maximum activity observed at pH 7.0–9.0. Remarkably, recombinant Ker02562 was stable in extreme alkaline environments(pH 10–13), which was much better than most other reported keratinases. Collectively, these favorable properties could make Bacillus sp. JM7 and Ker02562 attractive to be applied in the detergent formulation and feather bioconversion. | Min Jin Chen Chen Xiongfei He Runying Zeng | 2019 | Acta Oceanologica Sinica2019，38，2： | 2 |
| 3 | Phylogenetic analysis of bacterial community in deep-sea sediment from the western Pacific “warm pool”显示文摘A depth profile of bacterial community structure in one deep-sea sediment core of the western Pacific 'warm pool' (WP) was investigated and compared with that in a sediment sample from the eastern Pacific (EP) by phylogenetic analysis of 16S rDNA fragments. Five bacterial 16S rDNA clone libraries were constructed, and 133 clones with different restriction fragment length polymorphism (RFLP) patterns were sequenced. A phylogenetic analysis of these sequences revealed that the bacterial diversity in a sample from the WP was more abundant than that in the EP sample. The bacterial population in the sediment core of WP was composed of eight major lineages of the domain bacteria. Among them the γ-Proteobacteria was the predominant and most diverse group in each section of WP sediment core, followed by the α-Proteobacteria. The genus Colwellia belonging to γ-Proteobacteria was predominant in this sample. The shift of bacterial communities among different sections of the WP sediment core was δ-, ε-Proteobacteria, and Cytopahga-Flexibacteria-Bacteroides (CFB) group. The ratios between them in the bacterial communities all showed inversely proportional to the depth of sediment. The sequences related to sulphate reducing bacteria (SRB) were detected in every section. The bacterial community structure in this sediment core might be related to the environmental characteristics of the surface seawater of the western Pacific WP. | ZHAO Jing ZENG Runying | 2005 | Acta Oceanologica Sinica2005，24，5： | 2 |
| 4 | Cold-active serine alkaline protease from the psychrophilic bacterium Pseudomonas strain DY-A: enzyme purification and characterization显示文摘 | Runying Zeng Rui Zhang Jing Zhao Nianwei Lin | 2003 | Extremophiles2003，，4： | 1 |
| 5 | Cold-adaptive alkaline protease from the psychrophilic Planomicrobium sp.547: enzyme characterization and gene cloning显示文摘A psychrophilic bacterium strain 547 producing cold-adaptive alkaline protease was isolated from the deep sea sediment of Prydz Bay,Antarctica.The organism was identified as a Planomicrobium species by 16S rRNA analysis.The optimal and highest growth temperatures for strain 547 were 15℃ and 30℃,respectively.The extracellular protease was purified by ammonium sulfate precipitation and DEAE cellulose-52 chromatography.The optimal temperature and pH for the activity of the purified enzyme were 35℃ and pH 9.0,respectively.The enzyme retained approximately 40% of its activity after 2 h of incubation at 50℃.The enzymatic activity was inhibited by 1 mmol/L phenylmethyl sulfonylfluoride (PMSF) and hydrochloride 4-(2-aminoethyl)-benzenesulfonyl fluoride (AEBSF),indicating that it was a serine protease.The presence of Ca2+ and Mn2+ increased the activity of the enzyme.The protease gene with a size of 1 269 bp was cloned from Planomicrobium sp.547 using primers designed based on the conserved sequences of proteases in GenBank.The Planomicrobium sp.547 protease contained a domain belonging to the peptidase S8 family,which has a length of 309 amino acid (AA) residues.The alignment and phylogenetic analysis of the AA sequence indicated that the protease belonged to the subtilisin family. | YANG XiangSheng CHEN XingLin XU XianZhong ZENG RunYing | 2011 | Chinese Journal of Polar Science2011，22，1： | 1 |
| 6 | Draft genome sequence of algal polysaccharides degradation bacterium, Flammeovirga sp. OC4显示文摘 | Yang Liu Zhiwei Yi Yaping Cai Runying Zeng | 2015 | Marine Genomics2015，，： | 1 |
| 7 | Phylogenetic diversity of TypeⅠpolyketide synthase genes from sediments of Ardley Island in Antarctica显示文摘The diversity of modular polyketide synthase (PKS) genes in sediments of Ardley Island in Antarctica, was studied by restriction fragment length polymorphism (RFLP) analysis. Phylogenetic analysis of 14 amino acid (AA) sequences indicates that the identified ketosynthase (KS) domains were clustered with those from diverse bacterial groups, including Cyanobacteria, γ-Proteobacteria, Actinobacteria, Firmicutes, and some unidentified microorganisms from marine sponge, bryozoan and other environmental samples. The obtained KS domains showed 43%-81% similarity at the AA level to reference sequences in GenBank. Six identified KS domains showed diverse sequences of the motif (VQTACSTS) that was used to identify the hybrid PKS/nonribosomal peptide synthetase (NRPS) enzyme complex, and formed a new branch. These results reveal a high diversity and novelty of PKS genes in antarctic sediments. | ZHAO Jing YANG Ning CHEN Xinglin JIANG Qingru ZENG Runying | 2011 | Acta Oceanologica Sinica2011，30，6： | 1 |
| 8 | Enhanced a novel β-agarase production in recombinant Escherichia coli BL21(DE3) through induction mode optimization and glycerol feeding strategy显示文摘Agarases are hydrolytic enzymes that act on the hydrolysis of agar and have a broad range of applications in food,cosmetics and pharmaceutical industries. In this study, a glycerol feeding strategy based on induction mode optimization for high cell density and β-agarase production was established, which could effectively control acetate yield. First, exponential feeding strategy of glycerol with different overall specific growth rates(μ) was applied in the pre-induction phase. The results showed that the low μ(μ=0.2) was suggested to be the optimal for cell growth and β-agarase production. Second, the effects of induction temperature and the inducer concentration on cell growth and β-agarase production were investigated in the post-induction phase. When induced by isopropyl-β-d-thiogalactoside(IPTG), the strategy of 0.8 mmol/L IPTG induction at 20℃ was found to be optimal for β-agarase production. When cultivation was induced by continuous lactose feeding strategy of 1.0 g/(L·h), the β-agarase activity reached 112.5 U/mL, which represented the highest β-agarase production to date.Furthermore, the β-agarase was capable of degrading G. lemaneiformis powder directly to produce neoagarooligosaccharide, and the hydrolysates were neoagarotetraose(NA4) and neoagarohexaose(NA6). The overall research may be useful for the industrial production and application of β-agarase. | CHAN Zhuhua CHEN Xinglin HOU Yanping GAO Boliang ZHAO Chungui YANG Suping ZENG Runying | 2018 | Acta Oceanologica Sinica2018，37，2： | 0 |
| 9 | Enhanced cold active lipase production by metagenomic library recombinant clone CALIP3 with a step-wise temperature and dissolved oxygen level control strategy显示文摘A metagenomic library recombinant clone CAPL3, an Escherichia coli strain generated by transformed with metagenomic library from deep-sea sediments, can efficiently produce cold active lipase. The effects of both temperature and dissolved oxygen(DO) on cold active lipase production by batch culture of metagenomic library recombinant clone(CAPL3) from deep-sea sediment were investigated. First, a two-stage temperature control strategy was developed, in which the temperature was kept at 34 °C for the first 15 h, and then switched to30 °C. The cold active lipase activity and productivity reached 315.2 U·ml^(-1)and 8.08 U·ml^(-1)·h^(-1), respectively,increased by both 14.5% compared to the results obtained with temperature controlled at 30°C. In addition, different DO control modes were conducted, based on the data obtained from the different DO control strategies and analysis of kinetics parameters at different DO levels. A step-wise temperature and DO control strategy were developed to improve lipase production, i.e., temperature and DO level were controlled at 34 °C, 30% during 0–15 h;30 °C, 30% during 15–18 h, and 30 °C, 20% during 18–39 h. With this strategy, the maximum lipase activity reached 354.6 U·ml^(-1)at 39 h, which was 28.8% higher than that achieved without temperature and DO control(275.3 U·ml^(-1)). | Zhuhua Chan Runping Wang Fan Yang Runying Zeng | 2016 | Chinese Journal of Chemical Engineering2016，24，9： | 0 |
| 10 | Phylogenetically diverse,acetaldehyde-degrading bacterial community in the deep sea water of the West Pacific Ocean显示文摘As a major aldehyde pollutant widely existing in industry and our daily life, acetaldehyde is more and more harmful to human health. As characteristic habitat niche, bacteria from deep sea environments are abundant and distinctive in heredity, physiology and ecological functions. Thus, the development of acetaldehyde-degrading bacteria from deep sea provides a new method to harness acetaldehyde pollutant. Firstly, in this study,acetaldehyde-degrading bacteria in the deep sea water of the West Pacific Ocean were enriched in situ and in the laboratory respectively, and then the diversity of uncultured bacteria was studied by using 16 S r RNA genes. Then acetaldehyde-degrading strains were isolated from two samples, including enrichment in situ and enrichment in laboratory samples of deep sea water from the West Pacific Ocean using acetaldehyde as the sole carbon source,and then the ability of acetaldehyde degradation was detected. Our results showed that the main uncultured bacteria of two samples with different enrichment approaches were similar, including Proteobacteria,Actinobacteria, Firmicutes, Cyanobacteria, but the structure of bacterial community were significant different.Four subgroups, α, γ, δ and ε, were found in Proteobacteria group. The γ-Proteobacteria was dominant(63.5%clones in laboratory enriched sample, 75% clones in situ enriched sample). The species belonged to γ-Proteobacteria and their proportion was nearly identical between the two enrichment samples, and Vibrio was the predominant genus(45% in laboratory enriched sample, 48.5% in situ enriched sample), followed by Halomonas(9% in situ enriched sample) and Streptococcus(6% in laboratory enriched sample). A total of 12 acetaldehyde-degrading strains were isolated from the two samples, which belonged to Vibrio, Halomonas,Pseudoalteromonas, Pseudomonas and Bacillus of γ-Proteobacteria. Strains ACH-L-5, ACH-L-8 and ACH-S-12,belonging to Vibrio and Halomonas, have strong ability of acetaldehyde degradation, which could tolerate 1.5 g/L acetaldehyde and degrade 350 mg/L acetaldehyde within 24 hours. Our results indicated that bacteria of γ-Proteobacteria may play an important role in carbon cycle of deep sea environments, especial the bacteria belonging to Vibrio and Halomonas and these strains was suggested for their potentials in government of aldehyde pollutants. | GAO Boliang SHANG Xiexie LI Li DI Wenjie ZENG Runying | 2018 | Acta Oceanologica Sinica2018，37，8： | 0 |
| 11 | Transient Expression of VHB and GLUT1 in the Green Alga Haematococcus pluvialis Using Agrobacteriummediated Transformation显示文摘The first successful Agrobacterium-mediated transformation of the green alga Haematococcus pluvialis using the vectors hosting the genes coding for VHB(Vitreoscilla hemoglobin) and GLUT1(glucose transporter 1) is reported here.The greenish yellow fluorescence of EGFP was observed when the zeocin-resistant cells were viewed with a fluorescent microscope.The functional expression of EGFP showed that the Agrobacterium-mediated transformation could efficiently transfer the exogenous gene into H.pluvialis.RT-PCR was used to successfully amplify the mRNA of VHB and GLUT1 genes from transformed cells,while Southern blots indicated the integration of VHB and GLUT1 genes into the genome of H.pluvialis.Transferring VHB and GLUT1 genes into this alga would pave the way for manipulation of many important pathways relevant to the food,pharmaceutical,and nutraceutical industries. | Jinfei YAN Zhaokai WANG Zhiwei YI Runying ZENG | 2016 | Agricultural Biotechnology2016，5，2： | 0 |
| 12 | Coextraction of microbial metagenomic DNA and RNA from deep-sea sediment显示文摘A protocol to coextract the microbial metagenomic DNA and RNA from deep-sea sediment was developed for the microbiological study of environmental samples.The obtained pure metagenomic DNA with the size larger than 23 kb and stable RNA could be used directly for PCR and reverse transcription-PCR(RT-PCR)respectively.The direct lysis including the treatments of SDS,proteinase and lysozyme was applied to acquiring the metagenomic DNA and RNA furthest.Prior to the lysis treatment,the glass bead and denaturing solution were added to enhance the lysis efficiency and keep the integrity of RNA respectively.Denaturing gradient gel electrophoresis(DGGE)was applied in accessing the microbial 16S rRNA diversity by PCR and RT-PCR amplification from a single extraction.The pattern obtained by this analysis revealed some differences between them,indicating the efficiency of the protocol in extracting the metagenomic DNA and total RNA from deep-sea sediment. | ZHAO Jing YANG Xiangsheng ZENG Runying | 2007 | Acta Oceanologica Sinica2007，26，6： | 0 |
| 13 | Particle size shapes the prokaryotic microbial communities in mangrove sediments:A case study of Sanya,China显示文摘The prokaryotic microbial communities in the sediments play crucial roles in the ecological functions of mangrove ecosystems.Therefore,the environmental factors that affect the structures of these prokaryotic microbial communities could indirectly participate in the regulation of mangrove functions,which is of great value for mangrove studies.The particle size(PS)of soils is recently demonstrated as a key environmental factor for shaping the microbial communities;however,this hypothesis has rarely been tested for mangrove environments.A case study of three tropical mangroves from Sanya,China was performed in this work to assess the influence of PS on the prokaryotic microbial community structures of bacteria,archaea,diazotrophs,and denitrifiers in the sediments.Results showed the variability in the spatial scale and the stability in the temporal scale for the prokaryotic communities,indicating that the tropical mangrove sediments could be a versatile but stable environment.Among the collected environmental factors,PS,salinity,and humidity had the greatest impacts,and PS mostly affected the structures of these prokaryotic communities based on its highest R^2 values of canonical correspondence analysis,Mental test,and linear fitting(p≤0.05).Furthermore,PS was positively correlated with the diversity and abundance of diazotrophic communities and negatively correlated with the abundances of methanogenic communities including Methanobacteriaceae,Methanospirillaceae,Methanoregulaceae,and Methanosaetaceae.Former studies show the increasing trend of PS caused by the rise of sea level and the intensification of human activities.Therefore,our findings indicate that PS could be a potential intermediate that links climate change and human activities with the possible ecological function migration of mangroves;meanwhile,the increase of PS could in turn release the stress of these environmental changes by increasing the abundance and diversity of the diazotrophic community and decreasing the abundances of methanogens. | Wu Qu Michael Vicent Shija Jie Wu Min Jin Jianxin Wang Runying Zeng Zhuhua Chan | 2022 | Acta Oceanologica Sinica2022，41，8： | 0 |
| 14 | Characterization of Bacillus phage Gxv1,a novel lytic Salasvirus phage isolated from deep-sea seamount sediments显示文摘Seamounts are hotspots for marine life,but to date,no bacteriophages have been reported.Here,a novel Bacillus podophage(named as Bacillus phage Gxv1)was isolated from deep-sea seamount sediments of the western Pacifc Ocean(~5790 m).Phage Gxv1 has a hexameric head~42–53 nm in diameter and a short tail of~30 nm long,which is a typical feature of the Podoviridae family.One-step curve analysis showed that Gxv1 is a lytic phage that can initiate host lysis within 3.5 h postinfection,and has a relatively large burst size.The 21,781-bp genome contains 34 predicted genes,and the G+C content of phage Gxv1 is 39.69%.Whole-genome comparison of phage Gxv1 with known bacteriophages,using BlastN analysis against the IMG/VR database,revealed that phage Gxv1 is closely related to Bacillus phage phi29 that infects Bacillus subtilis,and their genome-wide similarity is 93.62%.Phylogenetic analysis based on DNA polymerase showed that phage Gxv1 belongs to the Salasvirus genus.Multiple genome alignment showed that phage Gxv1 shares a high level of sequence similarity and common gene order with Bacillus phage phi29.However,some sequences are unique to phage Gxv1,and this region contains genes encoding DNA packing protein,DNA replication protein,and unknown protein.These sequences exhibit low sequence similarity to known bacteriophages,highlighting an unknown origin of these sequences.This study will help improve our understanding of the Salasvirus genus and phage diversity in deep-sea seamounts. | Xun Guo Tianyou Zhang Min Jin Runying Zeng | 2021 | Marine Life Science & Technology2021，3，1： | 0 |
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