Stable isotope probing （SIP） was used to identify microbes stimulated by ethanol addition in microcosms containing two sediments collected from the bioremediation test zone at the US Department of Energy Oak Ridge s...Stable isotope probing （SIP） was used to identify microbes stimulated by ethanol addition in microcosms containing two sediments collected from the bioremediation test zone at the US Department of Energy Oak Ridge site, TN, USA. One sample was highly bioreduced with ethanol while another was less reduced. Microcosms with the respective sediments were amended with ^13C labeled ethanol and incubated for 7 days for SIP. Ethanol was rapidly converted to acetate within 24h accompanied with the reduction of nitrate and sulfate. The accumulation of acetate persisted beyond the 7 d period. Aqueous U did not decline in the microcosm with the reduced sediment due to desorption of U but continuously declined in the less reduced sample. Microbial growth and concomitant 13C-DNA production was detected when ethanol was exhausted and abundant acetate had accumulated in both microcosms. This coincided with U（VI） reduction in the less reduced sample. I3C originating from ethanol was ultimately utilized for growth, either directly or indirectly, by the dominant microbial community members within 7 days of incubation. The microbial community was comprised predominantly of known denitrifiers, sulfate-reducing bacteria and iron （Ⅲ） reducing bacteria including Desulfovibrio, Sphingomonas, Ferribacterium, Rhodanobacter, Geothrix, Thiobacillus and others, including the known U（VI）-redueing bacteria Acidovorax, Anaeromyxobacter, Desulfovibrio, Geobac- ter and Desulfosporosinus. The findings suggest that ethanol biostimulates the U（VI）-reducing microbial com- munity by first serving as an electron donor for nitrate, sulfate, iron （IH） and U（VI） reduction, and acetate which then functions as electron donor for U（VI） reduction and carbon source for microbial growth.展开更多
Dissolved inorganic carbon(DIC) is an important source of carbon in aquatic ecosystems,especially under conditions of increased frequency of cyanobacterial bloom. However, the importance of bacteria in direct or indir...Dissolved inorganic carbon(DIC) is an important source of carbon in aquatic ecosystems,especially under conditions of increased frequency of cyanobacterial bloom. However, the importance of bacteria in direct or indirect utilization of DIC has been widely overlooked in eutrophic freshwater. To identify the functional bacteria that can actively utilize DIC in eutrophic freshwater during cyanobacterial bloom, stable-isotope probing(SIP) experiments were conducted on eutrophic river water with or without inoculation with cyanobacteria(Microcystis aeruginosa). Our 16 S rRNA sequencing results revealed the significance of Betaproteobacteria, with similar relative abundance as Alphaproteobacteria, in the active assimilation of H^(13)CO^(3-) into their DNA directly or indirectly, which include autotrophic genera Betaproteobacterial ammonia-oxidizing bacteria. Other bacterial groups containing autotrophic members, e.g. Planctomycetes and Nitrospira, also presented higher abundance among free-living bacteria in water without cyanobacteria. Microcystis aggregates showed a preference for some specific bacterial members that may utilize H^(13)CO^(3-) metabolized by Microcystis as organic matter, e.g. Bacteroidetes(Cytophagales, Sphingobacteriales), and microcystindegrading bacteria Betaproteobacteria(Paucibacter/Burkholderiaceae). This study provides some valuable information regarding the functional bacteria that can actively utilize DIC in eutrophic freshwater.展开更多
New ionization and detection techniques in mass spectrometry have been successfully applied for efficient analyses of complex biological systems. It is, however, still difficult to trace structural changes of a specif...New ionization and detection techniques in mass spectrometry have been successfully applied for efficient analyses of complex biological systems. It is, however, still difficult to trace structural changes of a specific molecular species in such systems. In the present study, a molecular probe strategy in combination with tandem electrospray ionization mass spectrometry has been examined using synthetic deuterium-labeled phosphatidylcholine hydroperoxide (PC-OOH/D3) and ethyl-labeled phosphatidylcholine having docosahexaenoic acid side chain (DHA-PC/Et). Administration of a mixture of PC-OOH/D3 and DHA-PC/Et to human blood and human skin surface, followed by extraction and analysis with collision-induced tandem electrospray ionization mass spectrometry demonstrated that metabolites of both molecular probes can be detected simultaneously with strict selectivity. The present method is also found to be useful in tracing chemical changes of the unstable docosahexaenoyl group on the surface of processed fish. The activity of phospholipase A2 can also be assessed using a phospholipid molecular probe with a linoleoyl and a deuteriomethyl group via selective detection of the lyso-phospholipid product by mass spectrometry. The advantage of the present method is that no chromatographic separation is required and analysis can be performed under strictly the same condition for different molecular probes, affording multiple data by one experiment. The present strategy may be useful for tracing time-dependent phenomena in dynamic phospholipid biochemistry, and can be widely used for any biological and food systems.展开更多
不依赖于纯培养的分子生物技术已广泛应用于环境微生物的研究.综述了近年来在荧光原位杂交技术(Fluorescent in situ hybridization,FISH)和聚合酶链式反应技术(Polymerasechainreaction,PCR)基础上发展起来的几种新分子生物技术的基本...不依赖于纯培养的分子生物技术已广泛应用于环境微生物的研究.综述了近年来在荧光原位杂交技术(Fluorescent in situ hybridization,FISH)和聚合酶链式反应技术(Polymerasechainreaction,PCR)基础上发展起来的几种新分子生物技术的基本原理,包括FISH-MAR、FISH-microelectrodes、Clone-FISH、SIP、PCR-DGGE-cloning-sequencing、PCR-T-RFLP、Real-time fluorescent quantitative PCR和RT-PCR,以及其在污水生物处理系统内硝化菌群研究领域中的应用现状.通过这些分子生物技术,可以识别污水生物处理系统内的硝化菌群;建立硝化菌群动态变化与工艺运行参数之间的相关关系;从微生物学角度对系统运行状态给予最直接、最可靠的分析与证明,为污水生物处理系统的长期稳定运行奠定理论基础.最后对该领域的未来发展进行了展望.展开更多
稳定性同位素示踪复杂土壤中微生物DNA/RNA的技术难点是13C-DNA/RNA的鉴定。本研究针对我国六种典型水稻土,利用稳定性同位素13CH4示踪活性的甲烷氧化菌,超高速密度梯度离心获得不同浮力密度DNA/RNA后,以甲烷氧化菌独有的pmo A功能基因...稳定性同位素示踪复杂土壤中微生物DNA/RNA的技术难点是13C-DNA/RNA的鉴定。本研究针对我国六种典型水稻土,利用稳定性同位素13CH4示踪活性的甲烷氧化菌,超高速密度梯度离心获得不同浮力密度DNA/RNA后,以甲烷氧化菌独有的pmo A功能基因和16S r RNA特异基因作为分子标靶,通过半定量凝胶电泳技术评价了特异基因作为分子标靶判定13C-DNA/RNA的可行性,进一步利用克隆文库技术研究水稻土中的活性甲烷氧化菌群落结构。结果表明:甲烷氧化菌功能基因pmo A作为分子标靶,能够准确鉴别13C-DNA,而甲烷氧化菌特异的16S r RNA基因则能较好地区分12C和13C标记的RNA,但13C-RNA中的非目标微生物污染高于13C-DNA示踪技术。进一步以13C-DNA和13C-RNA为模板,分别构建了pmo A和16S r RNA基因的克隆文库,系统发育分析表明I型菌主导了土壤甲烷氧化过程,其中江西鹰潭和黑龙江五常土壤中活性甲烷氧化菌全部属于Ia型,而四川资阳、浙江嘉兴、江苏常熟和江都土壤中Ia型和Ib型甲烷氧化菌均有发现,并且后者比例较低。这些结果表明分子标靶基因能够有效判定复杂土壤中的甲烷氧化菌13C-DNA/RNA,在DNA和RNA水平的结果基本一致,我国典型水稻土中活性甲烷氧化菌可能存在一定的地理分异规律。展开更多
基金The authors thank Benli Chai for bioinformatic support and Anthony Gaca and Ami Smith for technical assistance in the laboratory. This study was funded by the US DOE Office of Science under grants DE-FG02-97ER62469, DE-FG02-97ER64398, AC05-00OR22725, and DE-SC0006783. Mary Beth Leigh was supported by a US National Science Foundation postdoctoral fellowship in Microbial Biology.
文摘Stable isotope probing （SIP） was used to identify microbes stimulated by ethanol addition in microcosms containing two sediments collected from the bioremediation test zone at the US Department of Energy Oak Ridge site, TN, USA. One sample was highly bioreduced with ethanol while another was less reduced. Microcosms with the respective sediments were amended with ^13C labeled ethanol and incubated for 7 days for SIP. Ethanol was rapidly converted to acetate within 24h accompanied with the reduction of nitrate and sulfate. The accumulation of acetate persisted beyond the 7 d period. Aqueous U did not decline in the microcosm with the reduced sediment due to desorption of U but continuously declined in the less reduced sample. Microbial growth and concomitant 13C-DNA production was detected when ethanol was exhausted and abundant acetate had accumulated in both microcosms. This coincided with U（VI） reduction in the less reduced sample. I3C originating from ethanol was ultimately utilized for growth, either directly or indirectly, by the dominant microbial community members within 7 days of incubation. The microbial community was comprised predominantly of known denitrifiers, sulfate-reducing bacteria and iron （Ⅲ） reducing bacteria including Desulfovibrio, Sphingomonas, Ferribacterium, Rhodanobacter, Geothrix, Thiobacillus and others, including the known U（VI）-redueing bacteria Acidovorax, Anaeromyxobacter, Desulfovibrio, Geobac- ter and Desulfosporosinus. The findings suggest that ethanol biostimulates the U（VI）-reducing microbial com- munity by first serving as an electron donor for nitrate, sulfate, iron （IH） and U（VI） reduction, and acetate which then functions as electron donor for U（VI） reduction and carbon source for microbial growth.
基金supported by the National Key Research and Development Program of China(No.2017YFD0800101)the State Natural Science Foundation of China(Nos.31600419,41571458,41471415)
文摘Dissolved inorganic carbon(DIC) is an important source of carbon in aquatic ecosystems,especially under conditions of increased frequency of cyanobacterial bloom. However, the importance of bacteria in direct or indirect utilization of DIC has been widely overlooked in eutrophic freshwater. To identify the functional bacteria that can actively utilize DIC in eutrophic freshwater during cyanobacterial bloom, stable-isotope probing(SIP) experiments were conducted on eutrophic river water with or without inoculation with cyanobacteria(Microcystis aeruginosa). Our 16 S rRNA sequencing results revealed the significance of Betaproteobacteria, with similar relative abundance as Alphaproteobacteria, in the active assimilation of H^(13)CO^(3-) into their DNA directly or indirectly, which include autotrophic genera Betaproteobacterial ammonia-oxidizing bacteria. Other bacterial groups containing autotrophic members, e.g. Planctomycetes and Nitrospira, also presented higher abundance among free-living bacteria in water without cyanobacteria. Microcystis aggregates showed a preference for some specific bacterial members that may utilize H^(13)CO^(3-) metabolized by Microcystis as organic matter, e.g. Bacteroidetes(Cytophagales, Sphingobacteriales), and microcystindegrading bacteria Betaproteobacteria(Paucibacter/Burkholderiaceae). This study provides some valuable information regarding the functional bacteria that can actively utilize DIC in eutrophic freshwater.
文摘New ionization and detection techniques in mass spectrometry have been successfully applied for efficient analyses of complex biological systems. It is, however, still difficult to trace structural changes of a specific molecular species in such systems. In the present study, a molecular probe strategy in combination with tandem electrospray ionization mass spectrometry has been examined using synthetic deuterium-labeled phosphatidylcholine hydroperoxide (PC-OOH/D3) and ethyl-labeled phosphatidylcholine having docosahexaenoic acid side chain (DHA-PC/Et). Administration of a mixture of PC-OOH/D3 and DHA-PC/Et to human blood and human skin surface, followed by extraction and analysis with collision-induced tandem electrospray ionization mass spectrometry demonstrated that metabolites of both molecular probes can be detected simultaneously with strict selectivity. The present method is also found to be useful in tracing chemical changes of the unstable docosahexaenoyl group on the surface of processed fish. The activity of phospholipase A2 can also be assessed using a phospholipid molecular probe with a linoleoyl and a deuteriomethyl group via selective detection of the lyso-phospholipid product by mass spectrometry. The advantage of the present method is that no chromatographic separation is required and analysis can be performed under strictly the same condition for different molecular probes, affording multiple data by one experiment. The present strategy may be useful for tracing time-dependent phenomena in dynamic phospholipid biochemistry, and can be widely used for any biological and food systems.
文摘稳定性同位素示踪复杂土壤中微生物DNA/RNA的技术难点是13C-DNA/RNA的鉴定。本研究针对我国六种典型水稻土,利用稳定性同位素13CH4示踪活性的甲烷氧化菌,超高速密度梯度离心获得不同浮力密度DNA/RNA后,以甲烷氧化菌独有的pmo A功能基因和16S r RNA特异基因作为分子标靶,通过半定量凝胶电泳技术评价了特异基因作为分子标靶判定13C-DNA/RNA的可行性,进一步利用克隆文库技术研究水稻土中的活性甲烷氧化菌群落结构。结果表明:甲烷氧化菌功能基因pmo A作为分子标靶,能够准确鉴别13C-DNA,而甲烷氧化菌特异的16S r RNA基因则能较好地区分12C和13C标记的RNA,但13C-RNA中的非目标微生物污染高于13C-DNA示踪技术。进一步以13C-DNA和13C-RNA为模板,分别构建了pmo A和16S r RNA基因的克隆文库,系统发育分析表明I型菌主导了土壤甲烷氧化过程,其中江西鹰潭和黑龙江五常土壤中活性甲烷氧化菌全部属于Ia型,而四川资阳、浙江嘉兴、江苏常熟和江都土壤中Ia型和Ib型甲烷氧化菌均有发现,并且后者比例较低。这些结果表明分子标靶基因能够有效判定复杂土壤中的甲烷氧化菌13C-DNA/RNA,在DNA和RNA水平的结果基本一致,我国典型水稻土中活性甲烷氧化菌可能存在一定的地理分异规律。
