不同降压过程对深海海水中可培养细菌群落组成的影响
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摘要
【目的】控制不同的压力变化过程,比较对深海水样中可培养细菌组成的影响,探讨马里亚纳海沟深海水样中可培养细菌在不同降压处理过程下的丰度变化和群落组成。【方法】利用保压技术采集无污染、深度6001 m的深海水样后,模拟缓慢降压和快速降压过程,通过2216E培养基及2216E加氧化三甲胺(TMAO)富集培养基,对分离得到的可培养菌株进行16S rRNA基因测序分析和丰度检测。【结果】通过缓慢降压和快速降压处理后,深海海水样品中可培养细菌的丰度和群落组成差异较大。其中,在缓慢降压处理的样品中,平均丰度约为190 CFU/mL,且种群组成单一,以Bacillus属为主(占总菌落数的96%);而快速降压处理的样品中,平均丰度约为437 CFU/mL,主要分布在4个属中:Bacillus (占总菌落数的27.8%)、Achromobacter (24.4%)、Microbacterium (34.4%)和Pseudomonas (13.7%)。值得一提的是,添加TMAO后,2种降压过程处理的样品中,可培养细菌的平均丰度均没有明显提升,但样品中的可培养细菌种类明显提升,部分种属的丰度也发生了明显的变化。此外,一些种属仅在特定的压力和底物存在的条件下出现。【结论】不同的降压方式能够影响深海海水中可培养细菌的丰度和群落组成,添加TMAO的富集实验表明可以增加分离到的细菌的种类,为下一步的深入研究提供良好的研究基础。
[Objective] The aim of this study was to compare the effect of pressure change styles on cultivable bacteria in deep-sea water sample by controlling the different pressure change process, and discuss the cultivable bacteria abundance and community composition of Mariana trench deep-sea water sample under different depressurization process. [Methods] We sampled the uncontaminated deep-sea water at the depth of 6001 m without depressurization. Then, samples were treated with short-time fast depressurization and long-time slow depressurization. After that, bacteria were enriched in the 2216 E or 2216 E media added trimethylamine N-oxide(TMAO). The 16 S rRNA gene of cultivable bacteria and their abundance were analyzed. [Results] Deep-sea water treated with slow and fast depressurization differed greatly in diversity and abundance of cultivable bacteria. In sample treated with slow depressurization process, the average abundance was approximately 190 CFU/mL and Bacillus was the dominant group(96% of total colonies). However, the average abundance of fast depressurized sample was approximately 437 CFU/mL, and diverse groups including Bacillus(27.8%), Achromobacter(24.4%),Microbacterium(34.4%) and Pseudomonas(13.7%) were observed. Noticeable, addition of TMAO had little effect on abundance of cultivable bacteria of both different depressurization samples, but the diversity of both samples increased and abundance of some species obviously changed. [Conclusion] Depressurization process could change the composition and abundance of cultivable bacteria in deep-sea water sample, addition of TMAO during the enrichment could increase the isolated bacterial species. These results made a solid foundation for further in-depth study of deep-sea bacteria.
[Objective] The aim of this study was to compare the effect of pressure change styles on cultivable bacteria in deep-sea water sample by controlling the different pressure change process, and discuss the cultivable bacteria abundance and community composition of Mariana trench deep-sea water sample under different depressurization process. [Methods] We sampled the uncontaminated deep-sea water at the depth of 6001 m without depressurization. Then, samples were treated with short-time fast depressurization and long-time slow depressurization. After that, bacteria were enriched in the 2216 E or 2216 E media added trimethylamine N-oxide(TMAO). The 16 S rRNA gene of cultivable bacteria and their abundance were analyzed. [Results] Deep-sea water treated with slow and fast depressurization differed greatly in diversity and abundance of cultivable bacteria. In sample treated with slow depressurization process, the average abundance was approximately 190 CFU/mL and Bacillus was the dominant group(96% of total colonies). However, the average abundance of fast depressurized sample was approximately 437 CFU/mL, and diverse groups including Bacillus(27.8%), Achromobacter(24.4%),Microbacterium(34.4%) and Pseudomonas(13.7%) were observed. Noticeable, addition of TMAO had little effect on abundance of cultivable bacteria of both different depressurization samples, but the diversity of both samples increased and abundance of some species obviously changed. [Conclusion] Depressurization process could change the composition and abundance of cultivable bacteria in deep-sea water sample, addition of TMAO during the enrichment could increase the isolated bacterial species. These results made a solid foundation for further in-depth study of deep-sea bacteria.
引文
[1]Fang JS,Zhang L,Bazylinski DA.Deep-sea piezosphere and piezophiles:geomicrobiology and biogeochemistry.Trends in Microbiology,2010,18(9):413-422.
[2]Abe F,Kato C,Horikoshi K.Pressure-regulated metabolism in microorganisms.Trends in Microbiology,1999,7(11):447-453.
[3]Orcutt BN,Sylvan JB,Knab NJ,Edwards KJ.Microbial ecology of the dark ocean above,at,and below the seafloor.Microbiology and Molecular Biology Reviews,2011,75(2):361-422.
[4]Simonato F,Campanaro S,Lauro FM,Vezzi A,D’Angelo M,Vitulo N,Valle G,Bartlett DH.Piezophilic adaptation:a genomic point of view.Journal of Biotechnology,2006,126(1):11-25.
[5]Oger PM,Jebbar M.The many ways of coping with pressure.Research in Microbiology,2010,161(10):799-809.
[6]Kamjam M,Sivalingam P,Deng ZX,Hong K.Deep sea actinomycetes and their secondary metabolites.Frontiers in Microbiology,2017,8:760.
[7]Azam F,Malfatti F.Microbial structuring of marine ecosystems.Nature Reviews Microbiology,2007,5(10):782-791.
[8]Li XG,Xu J,Xiao X.High pressure adaptation of deep-sea microorganisms and biogeochemical cycles.Microbiology China,2013,40(1):59-70.(in Chinese).李学恭,徐俊,肖湘.深海微生物高压适应与生物地球化学循环.微生物学通报,2013,40(1):59-70.
[9]Zeng X,Birrien JL,Fouquet Y,Cherkashov G,Jebbar M,Querellou J,Oger P,Cambon-Bonavita MA,Xiao X,Prieur D.Pyrococcus CH1,an obligate piezophilic hyperthermophile:extending the upper pressure-temperature limits for life.The ISME Journal,2009,3(7):873-876.
[10]Kato C,Li L,Nogi Y,Nakamura Y,Tamaoka J,Horikoshi K.Extremely barophilic bacteria isolated from the Mariana Trench,Challenger Deep,at a depth of 11,000 meters.Applied and Environmental Microbiology,1998,64(4):1510-1513.
[11]Kim S-J,Kato C.Sampling,isolation,cultivation,and characterization of piezophilic microbes//Timmis KN.Handbook of Hydrocarbon and Lipid Microbiology.Berlin,Heidelberg:Springer,2010:3869-3881.
[12]Tamburini C,Garcin J,Ragot M,Bianchi A.Biopolymer hydrolysis and bacterial production under ambient hydrostatic pressure through a 2000 m water column in the NWMediterranean.Deep Sea Research Part II:Topical Studies in Oceanography,2002,49(11):2109-2123.
[13]Parkes RJ,Martin D,Amann H,Anders E,Holland M,Schultheiss PJ,Wang XW,Dotchev K.Technology for high-pressure sampling and analysis of deep-sea sediments,associated gas hydrates,and deep-biosphere processes//Collett T,Johnson A,Knapp C,Boswell R.Natural Gas Hydrates-Energy Resource Potential and Associated Geologic Hazards.AAPG Memoir,2009.
[14]Song W,Zhu SQ.Design of hydraulic system for autonomous sampler at deep-sea//Proceedings of 2015 International Conference on Fluid Power and Mechatronics(FPM).Harbin,China:IEEE,2015:643-648.
[15]Edgcomb VP,Taylor C,Pachiadaki MG,Honjo S,Engstrom I,Yakimov M.Comparison of Niskin vs.in situ approaches for analysis of gene expression in deep Mediterranean Sea water samples.Deep Sea Research Part II:Topical Studies in Oceanography,2016,129:213-222.
[16]Petrov E,Rohde PR,Cornell B,Martinac B.The protective effect of osmoprotectant TMAO on bacterial mechanosensitive channels of small conductance Msc S/Msc K under high hydrostatic pressure.Channels,2012,6(4):262-271.
[17]He HL,Chen XL,Zhang XY,Sun CY,Zou BC,Zhang YZ.Novel use for the osmolyte trimethylamine N-oxide:retaining the psychrophilic characters of cold-adapted protease deseasin MCP-01 and simultaneously improving its thermostability.Marine Biotechnology,2009,11(6):710-716.
[18]Saad-Nehme J,Silva JL,Meyer-Fernandes JR.Osmolytes protect mitochondrial F0F1-ATPase complex against pressure inactivation.Biochimica et Biophysica Acta(BBA)-Protein Structure and Molecular Enzymology,2001,1546(1):164-170.
[19]Zhang SD,Santini CL,Zhang WJ,Barbe V,Mangenot S,Guyomar C,Garel M,Chen HT,Li XG,Yin QJ,Zhao Y,Armengaud J,Gaillard JC,Martini S,Pradel N,Vidaud C,Alberto F,Médigue C,Tamburini C,Wu LF.Genomic and physiological analysis reveals versatile metabolic capacity of deep-sea Photobacterium phosphoreum ANT-2200.Extremophiles,2016,20(3):301-310.
[20]Barrett EL,Kwan HS.Bacterial reduction of Trimethylamine oxide.Annual Review of Microbiology,1985,39:131-149.
[21]Yin QJ,Zhang WJ,Qi XQ,Zhang SD,Jiang T,Li XG,Chen Y,Santini CL,Zhou H,Chou IM,Wu LF.High hydrostatic pressure inducible trimethylamine N-oxide reductase improves the pressure tolerance of piezosensitive bacteria Vibrio fluvialis.Frontiers in Microbiology,2018,8:2646.
[22]Yin QJ,Zhang WJ,Li XG,Zhou LH,Qi XQ,Zhang C,Wu LF.Contribution of trimethylamine N-oxide on the growth and pressure tolerance of deep-sea bacteria.CJOL,2018,1(2).
[23]Yancey PH,Gerringer ME,Drazen JC,Rowden AA,Jamieson A.Marine fish may be biochemically constrained from inhabiting the deepest ocean depths.Proceedings of the National Academy of Sciences of the United States of America,2014,111(12):4461-4465.
[2]Abe F,Kato C,Horikoshi K.Pressure-regulated metabolism in microorganisms.Trends in Microbiology,1999,7(11):447-453.
[3]Orcutt BN,Sylvan JB,Knab NJ,Edwards KJ.Microbial ecology of the dark ocean above,at,and below the seafloor.Microbiology and Molecular Biology Reviews,2011,75(2):361-422.
[4]Simonato F,Campanaro S,Lauro FM,Vezzi A,D’Angelo M,Vitulo N,Valle G,Bartlett DH.Piezophilic adaptation:a genomic point of view.Journal of Biotechnology,2006,126(1):11-25.
[5]Oger PM,Jebbar M.The many ways of coping with pressure.Research in Microbiology,2010,161(10):799-809.
[6]Kamjam M,Sivalingam P,Deng ZX,Hong K.Deep sea actinomycetes and their secondary metabolites.Frontiers in Microbiology,2017,8:760.
[7]Azam F,Malfatti F.Microbial structuring of marine ecosystems.Nature Reviews Microbiology,2007,5(10):782-791.
[8]Li XG,Xu J,Xiao X.High pressure adaptation of deep-sea microorganisms and biogeochemical cycles.Microbiology China,2013,40(1):59-70.(in Chinese).李学恭,徐俊,肖湘.深海微生物高压适应与生物地球化学循环.微生物学通报,2013,40(1):59-70.
[9]Zeng X,Birrien JL,Fouquet Y,Cherkashov G,Jebbar M,Querellou J,Oger P,Cambon-Bonavita MA,Xiao X,Prieur D.Pyrococcus CH1,an obligate piezophilic hyperthermophile:extending the upper pressure-temperature limits for life.The ISME Journal,2009,3(7):873-876.
[10]Kato C,Li L,Nogi Y,Nakamura Y,Tamaoka J,Horikoshi K.Extremely barophilic bacteria isolated from the Mariana Trench,Challenger Deep,at a depth of 11,000 meters.Applied and Environmental Microbiology,1998,64(4):1510-1513.
[11]Kim S-J,Kato C.Sampling,isolation,cultivation,and characterization of piezophilic microbes//Timmis KN.Handbook of Hydrocarbon and Lipid Microbiology.Berlin,Heidelberg:Springer,2010:3869-3881.
[12]Tamburini C,Garcin J,Ragot M,Bianchi A.Biopolymer hydrolysis and bacterial production under ambient hydrostatic pressure through a 2000 m water column in the NWMediterranean.Deep Sea Research Part II:Topical Studies in Oceanography,2002,49(11):2109-2123.
[13]Parkes RJ,Martin D,Amann H,Anders E,Holland M,Schultheiss PJ,Wang XW,Dotchev K.Technology for high-pressure sampling and analysis of deep-sea sediments,associated gas hydrates,and deep-biosphere processes//Collett T,Johnson A,Knapp C,Boswell R.Natural Gas Hydrates-Energy Resource Potential and Associated Geologic Hazards.AAPG Memoir,2009.
[14]Song W,Zhu SQ.Design of hydraulic system for autonomous sampler at deep-sea//Proceedings of 2015 International Conference on Fluid Power and Mechatronics(FPM).Harbin,China:IEEE,2015:643-648.
[15]Edgcomb VP,Taylor C,Pachiadaki MG,Honjo S,Engstrom I,Yakimov M.Comparison of Niskin vs.in situ approaches for analysis of gene expression in deep Mediterranean Sea water samples.Deep Sea Research Part II:Topical Studies in Oceanography,2016,129:213-222.
[16]Petrov E,Rohde PR,Cornell B,Martinac B.The protective effect of osmoprotectant TMAO on bacterial mechanosensitive channels of small conductance Msc S/Msc K under high hydrostatic pressure.Channels,2012,6(4):262-271.
[17]He HL,Chen XL,Zhang XY,Sun CY,Zou BC,Zhang YZ.Novel use for the osmolyte trimethylamine N-oxide:retaining the psychrophilic characters of cold-adapted protease deseasin MCP-01 and simultaneously improving its thermostability.Marine Biotechnology,2009,11(6):710-716.
[18]Saad-Nehme J,Silva JL,Meyer-Fernandes JR.Osmolytes protect mitochondrial F0F1-ATPase complex against pressure inactivation.Biochimica et Biophysica Acta(BBA)-Protein Structure and Molecular Enzymology,2001,1546(1):164-170.
[19]Zhang SD,Santini CL,Zhang WJ,Barbe V,Mangenot S,Guyomar C,Garel M,Chen HT,Li XG,Yin QJ,Zhao Y,Armengaud J,Gaillard JC,Martini S,Pradel N,Vidaud C,Alberto F,Médigue C,Tamburini C,Wu LF.Genomic and physiological analysis reveals versatile metabolic capacity of deep-sea Photobacterium phosphoreum ANT-2200.Extremophiles,2016,20(3):301-310.
[20]Barrett EL,Kwan HS.Bacterial reduction of Trimethylamine oxide.Annual Review of Microbiology,1985,39:131-149.
[21]Yin QJ,Zhang WJ,Qi XQ,Zhang SD,Jiang T,Li XG,Chen Y,Santini CL,Zhou H,Chou IM,Wu LF.High hydrostatic pressure inducible trimethylamine N-oxide reductase improves the pressure tolerance of piezosensitive bacteria Vibrio fluvialis.Frontiers in Microbiology,2018,8:2646.
[22]Yin QJ,Zhang WJ,Li XG,Zhou LH,Qi XQ,Zhang C,Wu LF.Contribution of trimethylamine N-oxide on the growth and pressure tolerance of deep-sea bacteria.CJOL,2018,1(2).
[23]Yancey PH,Gerringer ME,Drazen JC,Rowden AA,Jamieson A.Marine fish may be biochemically constrained from inhabiting the deepest ocean depths.Proceedings of the National Academy of Sciences of the United States of America,2014,111(12):4461-4465.
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