[Objective] The aim of this study is to understand the population composition of methanogens in rumen fluid of grazing Inner Mongolian cashmere goat. [Method] Total DNAs of various bacteria in rumen fluid were isolate...[Objective] The aim of this study is to understand the population composition of methanogens in rumen fluid of grazing Inner Mongolian cashmere goat. [Method] Total DNAs of various bacteria in rumen fluid were isolated for PCR amplification using the specifically designed primers based on conservative mcrA sequence of methanogens; then mcrA specific clone library was accordingly established. The restriction fragment length polymorphism(RFLP) of the library was further analyzed by digestion of restriction enzyme Taq I. [Result] One hundred and five randomly selected specific colonies were classified into six RFLP types, among which the dominant type accounts for 38%, and other types account for 27%, 18%, 5.5% and 4.5%, respectively. [Conclusion] There are at least six different methanogens in rumen fluid of grazing Inner Mongolian cashmere goat.展开更多
Anaerobic methanotrophic(ANME)microbes play a crucial role in the bioprocess of anaerobic oxidation of methane(AOM).However,due to their unculturable status,their diversity is poorly understood.In this study,we establ...Anaerobic methanotrophic(ANME)microbes play a crucial role in the bioprocess of anaerobic oxidation of methane(AOM).However,due to their unculturable status,their diversity is poorly understood.In this study,we established a microfluidics-based epicPCR(Emulsion,Paired Isolation,and Concatenation PCR)to fuse the 16S rRNA gene and mcrA gene to reveal thediversity of ANME microbes(mcrA gene hosts)in three sampling push-cores from the marine cold seep.A total of 372516Samplicon sequence variants(ASVs)of the mcrA gene hosts were detected,and classified into 78 genera across 23 phyla.Across all samples,the dominant phyla with high relative abundance(>10%)were the well-known Euryarchaeota,and somebacterial phyla such as Campylobacterota,Proteobacteria,and Chloroflexi;however,the specificity of these associations wasnot verified.In addition,the compositions of the mcrA gene hosts were significantly different in different layers,where thearchaeal hosts increased with the depths of sediments,indicating the carriers of AOM were divergent in depth.Furthermore,the consensus phylogenetic trees of the mcrA gene and the 16S rRNA gene showed congruence in archaea not in bacteria,suggesting the horizontal transfer of the mcrA gene may occur among host members.Finally,some bacterial metagenomeswere found to contain the mcrA gene as well as other genes that encode enzymes in the AOM pathway,which prospectivelypropose the existence of ANME bacteria.This study describes improvements for a potential method for studying the diversityof uncultured functional microbes and broadens our understanding of the diversity of ANMEs.展开更多
为了解天然放牧和舍饲条件下内蒙古绒山羊瘤胃中甲烷菌的种群组成。选取甲烷菌mcrA基因的特异性引物序列,利用PCR技术对从瘤胃液中抽提的细菌总DNA进行扩增,并建立了甲烷菌特异性的mcrA基因文库。用限制性内切酶Taq I对该文库特异性片...为了解天然放牧和舍饲条件下内蒙古绒山羊瘤胃中甲烷菌的种群组成。选取甲烷菌mcrA基因的特异性引物序列,利用PCR技术对从瘤胃液中抽提的细菌总DNA进行扩增,并建立了甲烷菌特异性的mcrA基因文库。用限制性内切酶Taq I对该文库特异性片段进行了限制性酶切片断长度多态性分析(Restriction fragment lengthpolymor-phism,RFLP)。放牧和舍饲内蒙古绒山羊瘤胃中甲烷菌的mcrA基因片段被分成6个不同的RFLP类型,并由此建立了DNA指纹图谱;系统发育树分析表明,其属于甲烷杆菌目和甲烷微菌目,且绒山羊瘤胃中的甲烷菌大部分属于甲烷短杆菌。放牧绒山羊瘤胃内甲烷菌种类比舍饲绒山羊更加丰富,6种甲烷菌所占比例均较高,而舍饲绒山羊只有两种优势菌比例较高,其他几种所占比例极低。展开更多
【目的】海洋沉积物中的古菌在全球生物地球化学循环中充当重要的角色,深入了解沉积物中古菌群落的结构及功能特征是探究海洋沉积物中古菌参与生物地球化学循环和生态学功能的基础。【方法】采用高通量测序技术,分别对南海北部陆坡不同...【目的】海洋沉积物中的古菌在全球生物地球化学循环中充当重要的角色,深入了解沉积物中古菌群落的结构及功能特征是探究海洋沉积物中古菌参与生物地球化学循环和生态学功能的基础。【方法】采用高通量测序技术,分别对南海北部陆坡不同海域(东部,西部和神狐海域的7个站位)沉积物中古菌16SrRNA基因进行Illumina Mi Seq测序。【结果】中国南海北部陆坡沉积物中古菌的主要门类是Bathyarchaeota、Thermoplasmata、Woesearchaeota(DHVEG-6)、Thaumarchaeota(Marine Group I)、Lokiarchaeota和Marine Hydrothermal Vent Group(MHVG),还存在少量的AK8、Marine Benthic Group A和Terrestrial Hot Spring Crenarchaeota Group(THSCG)等。在潜在水合物区沉积物中还发现了甲烷代谢相关古菌(Anaerobic methanotrophic archaea,ANME)类群,主要为ANME-1、ANME-2ab和ANME-2c等。甲烷代谢古菌的分布特征也从甲烷代谢保守功能基因mcr A(Methyl coenzyme-Mreductase A)的扩增中得到了验证。利用定量PCR对南海沉积物中的细菌、古菌的16SrRNA基因和mcrA基因进行了定量,发现细菌16SrRNA基因拷贝数为10~5-10~7 copies/g(湿重),古菌16SrRNA基因拷贝数为10~5-10~6 copies/g(湿重),潜在水合物区mcrA基因拷贝数为10~3-10~5 copies/g(湿重)。【结论】揭示了中国南海北部陆坡沉积物中具有丰富的微生物资源,其中古菌种类多样且丰度较高,同时发现冷泉特征古菌群落,为深入认识和理解南海沉积物中微生物丰度和古菌多样性,以及解析古菌地球化学功能奠定基础。展开更多
文摘[Objective] The aim of this study is to understand the population composition of methanogens in rumen fluid of grazing Inner Mongolian cashmere goat. [Method] Total DNAs of various bacteria in rumen fluid were isolated for PCR amplification using the specifically designed primers based on conservative mcrA sequence of methanogens; then mcrA specific clone library was accordingly established. The restriction fragment length polymorphism(RFLP) of the library was further analyzed by digestion of restriction enzyme Taq I. [Result] One hundred and five randomly selected specific colonies were classified into six RFLP types, among which the dominant type accounts for 38%, and other types account for 27%, 18%, 5.5% and 4.5%, respectively. [Conclusion] There are at least six different methanogens in rumen fluid of grazing Inner Mongolian cashmere goat.
基金supported by the NationalNatural Science Foundation of China(Nos.32001092,91851106,and 91951103).
文摘Anaerobic methanotrophic(ANME)microbes play a crucial role in the bioprocess of anaerobic oxidation of methane(AOM).However,due to their unculturable status,their diversity is poorly understood.In this study,we established a microfluidics-based epicPCR(Emulsion,Paired Isolation,and Concatenation PCR)to fuse the 16S rRNA gene and mcrA gene to reveal thediversity of ANME microbes(mcrA gene hosts)in three sampling push-cores from the marine cold seep.A total of 372516Samplicon sequence variants(ASVs)of the mcrA gene hosts were detected,and classified into 78 genera across 23 phyla.Across all samples,the dominant phyla with high relative abundance(>10%)were the well-known Euryarchaeota,and somebacterial phyla such as Campylobacterota,Proteobacteria,and Chloroflexi;however,the specificity of these associations wasnot verified.In addition,the compositions of the mcrA gene hosts were significantly different in different layers,where thearchaeal hosts increased with the depths of sediments,indicating the carriers of AOM were divergent in depth.Furthermore,the consensus phylogenetic trees of the mcrA gene and the 16S rRNA gene showed congruence in archaea not in bacteria,suggesting the horizontal transfer of the mcrA gene may occur among host members.Finally,some bacterial metagenomeswere found to contain the mcrA gene as well as other genes that encode enzymes in the AOM pathway,which prospectivelypropose the existence of ANME bacteria.This study describes improvements for a potential method for studying the diversityof uncultured functional microbes and broadens our understanding of the diversity of ANMEs.
文摘为了解天然放牧和舍饲条件下内蒙古绒山羊瘤胃中甲烷菌的种群组成。选取甲烷菌mcrA基因的特异性引物序列,利用PCR技术对从瘤胃液中抽提的细菌总DNA进行扩增,并建立了甲烷菌特异性的mcrA基因文库。用限制性内切酶Taq I对该文库特异性片段进行了限制性酶切片断长度多态性分析(Restriction fragment lengthpolymor-phism,RFLP)。放牧和舍饲内蒙古绒山羊瘤胃中甲烷菌的mcrA基因片段被分成6个不同的RFLP类型,并由此建立了DNA指纹图谱;系统发育树分析表明,其属于甲烷杆菌目和甲烷微菌目,且绒山羊瘤胃中的甲烷菌大部分属于甲烷短杆菌。放牧绒山羊瘤胃内甲烷菌种类比舍饲绒山羊更加丰富,6种甲烷菌所占比例均较高,而舍饲绒山羊只有两种优势菌比例较高,其他几种所占比例极低。
文摘【目的】海洋沉积物中的古菌在全球生物地球化学循环中充当重要的角色,深入了解沉积物中古菌群落的结构及功能特征是探究海洋沉积物中古菌参与生物地球化学循环和生态学功能的基础。【方法】采用高通量测序技术,分别对南海北部陆坡不同海域(东部,西部和神狐海域的7个站位)沉积物中古菌16SrRNA基因进行Illumina Mi Seq测序。【结果】中国南海北部陆坡沉积物中古菌的主要门类是Bathyarchaeota、Thermoplasmata、Woesearchaeota(DHVEG-6)、Thaumarchaeota(Marine Group I)、Lokiarchaeota和Marine Hydrothermal Vent Group(MHVG),还存在少量的AK8、Marine Benthic Group A和Terrestrial Hot Spring Crenarchaeota Group(THSCG)等。在潜在水合物区沉积物中还发现了甲烷代谢相关古菌(Anaerobic methanotrophic archaea,ANME)类群,主要为ANME-1、ANME-2ab和ANME-2c等。甲烷代谢古菌的分布特征也从甲烷代谢保守功能基因mcr A(Methyl coenzyme-Mreductase A)的扩增中得到了验证。利用定量PCR对南海沉积物中的细菌、古菌的16SrRNA基因和mcrA基因进行了定量,发现细菌16SrRNA基因拷贝数为10~5-10~7 copies/g(湿重),古菌16SrRNA基因拷贝数为10~5-10~6 copies/g(湿重),潜在水合物区mcrA基因拷贝数为10~3-10~5 copies/g(湿重)。【结论】揭示了中国南海北部陆坡沉积物中具有丰富的微生物资源,其中古菌种类多样且丰度较高,同时发现冷泉特征古菌群落,为深入认识和理解南海沉积物中微生物丰度和古菌多样性,以及解析古菌地球化学功能奠定基础。
