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Composition and Function of Bacterial Communities of Bryophytes and Their Underlying Sediments in the Dajiuhu Peatland, Central China

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Journal of Earth Science 2023年第1期34卷 133-144页

作者： Xing Xiang Hongmei Wang Wen Tian Ruicheng Wang Linfeng Gong Ying Xu Baiying Man College of life science Shangrao Normal UniversityShangrao334001China state key laboratory of Biogeology and Environmental Geology China University of GeosciencesWuhan430074China state key laboratory breeding base of marine genetic resources Key Laboratory of Marine Genetic ResourcesThird Institute of OceanographySOAKey Laboratory of Marine Genetic Resources of Fujian ProvinceXiamen361005China

Symbiotic microbiomes of Sphagnum have been confirmed to play a fundamental role in carbon and nitrogen cycles, however, little is known about microbiomes associated with other bryophytes in subtropical peatland ecosystems. To explore the differences in community structure, metabolic potential and interaction relationship of bacterial microbiomes associated with different bryophytes species, the gametophytes of three bryophyte species(Sphagnum palustre, Aulacomnium androgynum, and Polytrichum commune) and their underlying peat sediments were collected from the subtropical Dajiuhu Peatland and subjected to Illumina high-throughout sequencing of 16S r RNA gene. Results showed that bacterial diversity was lowest in S. palustre, the dominant moss species, among the three moss species investigated in Dajiuhu Peatland. Bacterial communities from bryophytes clearly separated with those from sediments as indicated by both phylogenetic and taxonomical approaches. Linear discriminant analysis effect size(LEf Se) identified 30 and 36 indicator taxa in mosses and peat sediments. Bacteroidetes, Verrucomicrobia and Thermoleophilia significantly enriched in S. palustre, A. androgynum and P. commune, Chloroflexi, Proteobacteria and Acidobacteria subgroup 6 was indicator taxa for corresponding underlying sediments, respectively. Despite of these differences in compositions, bacterial functional structures were similar among all bryophytes, such as abundant aerobic heterotrophs, rare nitrifiers and denitrifiers. This phenomenon was also observed among the underlying sediments. Network analysis indicated that Proteobacteria and Acidobacteria located in the center of network and exerted strong interactions to other taxa. The sub-network of bacterial communities in sediments was more connected and microbial groups were more competitive than those in bryophytes subnetwork. Our results offer new insight into the community structure, ecological function and interaction pattern of bacterial

关键词： bryophytes bacteria bacterial microbiome indicator taxa co-occurrence network the Dajiuhu Peatland

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Metabolic tuning of a stable microbial community in the surface oligotrophic Indian Ocean revealed by integrated meta-omics

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marine Life Science & Technology 2022年第2期4卷 277-290页

作者： Zhang-Xian Xie Ke-Qiang Yan Ling-Fen Kong Ying-Bao Gai Tao Jin Yan-Bin He Ya-Yu Wang Feng Chen Lin Lin Zhi-Long Lin Hong-Kai Xu Zong-Ze Shao Si-Qi Liu Da-Zhi Wang state key laboratory of marine Environmental Science/College of the Environment and Ecology Xiamen UniversityXiamen361005China College of Ocean and Earth Sciences Xiamen UniversityXiamen361005China Southern marine Science and Engineering Guangdong laboratory(Zhuhai) Sun Yat-Sen UniversityZhuhai519082China BGI-Shenzhen Beishan Industrial Zone 11th BuildingShenzhen518083China BGI Education Center University of Chinese Academy of SciencesShenzhen518083China key laboratory of marine genetic resources Third Institute of OceanographyMinistry of Natural Resources of ChinaXiamen361005China state key laboratory breeding base of marine genetic resources/fujian key laboratory of marine genetic resources Xiamen361005China Institute of marine and Environmental Technology University of Maryland Center for Environmental ScienceBaltimoreMD21202USA

Understanding the mechanisms,structuring microbial communities in oligotrophic ocean surface waters remains a major ecological *** redundancy and metabolic tuning are two mechanisms that have been proposed to shape microbial response to environmental ***,little is known about their roles in the oligotrophic surface ocean due to less integrative characterization of community taxonomy and ***,we applied an integrated meta-omics-based approach,from genes to proteins,to investigate the microbial community of the oligotrophic northern Indian *** spatial variabilities of both genomic and proteomic compositions indicated a stable microbial community that was dominated by Prochlorococcus,Synechococcus,and ***,fine tuning of some metabolic functions that are mainly driven by salinity and temperature was ***,a tuning divergence occurred between metabolic potential and activity in response to different environmental *** results indicate that metabolic tuning is an important mechanism for sustaining the stability of microbial communities in oligotrophic *** addition,integrated meta-omics provides a powerful tool to comprehensively understand microbial behavior and function in the ocean.

关键词： Microbial community Metabolic tuning Metaproteomics Metagenomics Oligotrophic ocean

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Temporal and Spatial Variations of Microbial Carbon Utilization in Water Bodies from the Dajiuhu Peatland, Central China

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Journal of Earth Science 2018年第4期29卷 969-976页

作者： Rui-Cheng Wang Hong-Mei Wang Xing Xiang Yu Gao Qing-Wei Song Lin-Feng Gong state key laboratory of Biogeology and Environmental Geology China University of Geosciences Wuhan 430074 China state key laboratory breeding base of marine genetic resources Key Laboratory of Marine Genetic Resources Third Institute of Oceanography SOA Key Laboratory of Marine Genetic Resources of Fujian Province Xiamen 361005 China

To investigate the microbial utilization of organic carbon in peatland ecosystem, water samples were collected from the Dajiuhu Peatland and nearby lakes, central China across the year of 2014. The acridine orange （AO） staining and Biolog Eco microplates were used to numerate microbial counts and determine the carbon utilization of microbial communities. Meanwhile, physicochemical characteristics were measured for subsequent analysis of the correlation between microbial carbon utilization and environmental factors. Results indicated that total microbial counts were between 106107 cells/L. Microbial diversities and carbon utilization rates showed a similar pattern, highest in September and lowest in November. Microbial communities in the peat pore waters preferred to utilize N-bearing carbon sources such as amines and amino acids compared with microbial communities in lakes. The network analysis of microbial utilization of 31 carbon substrates clearly distinguished microbial communities from peat pore waters and those from lakes. Redundancy analysis （RDA） showed the total organic nitrogen content （P=-0.03, F=2.5） and daily average temperature （P=0.034, F=2.4） significantly controlled microbial carbon utilization throughout the sampling period. Our report is the first one to address the temporal and spatial variations of carbon uti- lization of microbial communities which are closely related to the decomposition of organic matter in the Dajiuhu Peatland in context of climate warming.

关键词： carbon source microbial carbon utilization average temperature Dajiuhu Peatland.

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A novel beta-galactose-specific lectin of the tubeworm,Ridgeia piscesae,from the hydrothermal vent

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Acta Oceanologica Sinica 2017年第6期36卷 61-67页

作者： RUAN Lingwei XU Haipeng LIN Wenyang SHI Hong CUI Zhizhong XU Xun state key laboratory breeding base of marine genetic resources Xiamen 361005China key laboratory of marine genetic resources of state Oceanic Administration Third Institute of OceanographyState Oceanic AdministrationXiamen 361005China fujian key laboratory of marine genetic resources Xiamen 361005China Animal Science and Technology College Shandong Agricultural UniversityTai'an 271018China

Lectins are sugar-specific binding proteins or glycoproteins that play important physiological roles in cellular recognition and regulation. And they are also valuable in medicine and pharmacy. Tubeworm is the representative species around the hydrothermal vent in the deep sea. They have developed unique mechanisms to adapt to the harsh environment. In this study, a 1 092 bp cDNA, designed as rpgal, was first cloned and characterized from the tubeworm Ridgeia piscesae. Sequence analysis showed that RPGAL had low homology with the known galectin. And it had two homologous carbohydrate-recognition domains, which is the characteristic of the tandem-repeat type galectins. The RPGAL was successfully recombinant expressed in Escherichia coli and purified. Analysis of biological activity revealed that RPGAL was metal ion independent and it could agglutinate all the vertebrate erythrocytes tested. It was stable at 10-50℃ and pH 5-10. And the hemagglutinating activity of RPGAL was strongly inhibited by D-Lactose and lipopolysaccharide. Although RPGAL had no effect on the microorganisms tested, it showed anti-tumor activity towards HeLa cells and HT1080 cells, which was accomplished by apoptosis. The study demonstrated that RPGAL was a novel galectin and provided a potential candidate for therapy of anti-tumor.

关键词： galectin antitumor apoptosis tubeworm Ridgeia piscesae

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Simultaneous nitrification and denitrification conducted by Halomonas venusta MA-ZP17-13 under low temperature conditions

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Acta Oceanologica Sinica 2021年第9期40卷 94-104页

作者： Guizhen Li Qiliang Lai Guangshan Wei Peisheng Yan Zongze Shao School of Environment Harbin Institute of TechnologyHarbin 150090China key laboratory of marine genetic resources Third Institute of OceanographyMinistry of Natural ResourcesXiamen 361005China state key laboratory breeding base of marine genetic resources Xiamen 361005China fujian key laboratory of marine genetic resources Xiamen 361005China Sourthem marine Science and Engineering Guangdong laboratory(Zhuhai) Zhuhai 519080China

Nitrification is a key step in the global nitrogen *** with autotrophic nitrification,heterotrophic nitrification remains poorly *** this study,Halomonas venusta MA-ZP17-13,isolated from seawater in shrimp aquaculture (Penaeus vannamei),could simultaneously undertake nitrification and *** the initial ammonium concentration at 100 mg/L,the maximum ammonium-nitrogen removal rate reached98.7%under the optimal conditions including C/N concentration ratio at 5.95,p H at 8.93,and Na Cl at 2.33%.The corresponding average removal rate was 1.37 mg/(L·h)(according to nitrogen) in 3 d at 11.2℃.By whole genome sequencing and analysis,nitrification-and denitrification-related genes were identified,including ammonia monooxygenase,nitrate reductase,nitrite reductase,nitric oxide dioxygenase and nitric oxide synthase;while no gene encoding hydroxylamine oxidase was identified,it implied the existence of a novel nitrification pathway from hydroxylamine to *** results indicate heterotrophic bacterium *** MA-ZP17-13 can undertake simultaneous nitrification and denitrification at low temperature and has potential for NH_(4)^(+)-N/NH_(3)-N removal in marine aquaculture systems.

关键词： Halomonas heterotrophic nitrification denitrification ammonia oxidization ammonia removal

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Molecular characteristics of three thymosin-repeat proteins from Marsupenaeus japonicus and their responses to WSSV infection

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Acta Oceanologica Sinica 2016年第4期35卷 44-50页

作者： MA Jinyou RUAN Lingwei XU Xun GAO Zhaoming College of Animal Sciences Henan Institute of Science and Technology Xinxiang 453003 China state key laboratory breeding base of marine genetic resources Xiamen 361005 China key laboratory of marine genetic resources of state Oceanic Administration Third Institute of Oceanography State Oceanic Administration Xiamen 361005 China

β-thymosins, a family of highly conserved peptides, play a vital role in wound-healing, angiogenesis,antimicrobial process and antiviral immunity. Three novel β-thymosin-repeat proteins, named mjthm4, mjthm3 and mjthm2, were cloned from Marsupenaeus japonicus using expressed sequence tags（EST） from suppression subtractive hybridization. The mjthm4, mjthm3 and mjthm2 c DNAs possessed open reading frames that encoded166, 128 and 90 amino acid residue polypeptides and contained four, three and two β-thymosin actin binding modules, respectively. Blast analysis demonstrated that mjthm4, mjthm3 and mjthm2 shared high homology with known invertebrate multi-repeat β-thymosins. These proteins are ubiquitously expressed in all of the examined tissues, and the transcriptional levels were highest in the intestine. Further investigation revealed that mjthm4,mjthm3 and mjthm2 were remarkably up-regulated 6 h after WSSV infection. Moreover, while mjthm4 transcriptional levels displayed no changes, mjthm3 and mjthm2 levels decreased in the virus-resistant *** results indicate that mjthm4, mjthm3 and mjthm2 are novel multi-repeat β-thymosin homologues, have a close relationship with WSSV infection, and might contribute to a better understanding of host defense and/or virus invasion interactions in shrimps.

关键词： β-thymosin thymosin-repeat proteins white spot syndrome virus(WSSV) Marsupenaeus japonicus

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Characterization of an extreme alkaline-stable keratinase from the draft genome of feather-degrading Bacillus ***7 from deep-sea

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Acta Oceanologica Sinica 2019年第2期38卷 87-95页

作者： Min Jin Chen Chen Xiongfei He Runying Zeng state key laboratory breeding base of marine genetic Resource Third Institute of Oceanography Ministry of Natural Resources South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center fujian Collaborative Innovation Center for Exploitation and Utilization of marine Biological resources

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.

关键词： Bacillus deep-sea feather-degradation keratinases feather bioconversion alkaline-stable

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Characterization of Bacillus phage Gxv1,a novel lytic Salasvirus phage isolated from deep-sea seamount sediments

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marine Life Science & Technology 2021年第1期3卷 13-19页

作者： Xun Guo Tianyou Zhang Min Jin Runying Zeng state key laboratory breeding base of marine genetic Resource Ministry of Natural ResourcesThird Institute of OceanographyXiamen 361005China Southern marine Science and Engineering Guangdong laboratory(Zhuhai) Zhuhai 519000China

Seamounts are hotspots for marine life,but to date,no bacteriophages have been ***,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 ***-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 *** 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 *** genome alignment showed that phage Gxv1 shares a high level of sequence similarity and common gene order with Bacillus phage ***,some sequences are unique to phage Gxv1,and this region contains genes encoding DNA packing protein,DNA replication protein,and unknown *** sequences exhibit low sequence similarity to known bacteriophages,highlighting an unknown origin of these *** study will help improve our understanding of the Salasvirus genus and phage diversity in deep-sea seamounts.

关键词： Seamount Deep sea Salasvirus Bacillus phage Characterization

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Phylogenetically diverse,acetaldehyde-degrading bacterial community in the deep sea water of the West Pacific Ocean

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Acta Oceanologica Sinica 2018年第8期37卷 54-64页

作者： GAO Boliang SHANG Xiexie LI Li DI Wenjie ZENG Runying School of Life Sciences Xiamen UniversityXiamen 361102China state key laboratory breeding base of marine genetic Resource Third Institute of OceanographyState Oceanic AdministrationXiamen 361005China fujian Collaborative Innovation Center for Exploitation and Utilization of marine Biological resources Xiamen 361005China

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 *** 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 degr

关键词： acetaldehyde-degrading bacteria ALDH deep sea in situ

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Enhanced a novel β-agarase production in recombinant Escherichia coli BL21(DE3) through induction mode optimization and glycerol feeding strategy

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Acta Oceanologica Sinica 2018年第2期37卷 110-118页

作者： CHAN Zhuhua CHEN Xinglin HOU Yanping GAO Boliang ZHAO Chungui YANG Suping ZENG Runying Department of Bioengineering and Biotechnology Huaqiao University state key laboratory breeding base of marine genetic Resource Third Institute of Oceanography State Oceanic Administration School of Life Sciences Xiamen University

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 ***, 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.

关键词： β-agarase Escherichia coli process optimization glycerol feeding strategy neoagarooligosaccharide

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