热带西太平洋深海沉积物微生物多样性及群落结构特征研究
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摘要
为研究热带西太平洋深海沉积物中微生物的多样性和群落结构特征,我们以PCR技术为基础分别构建了8个不同层位的细菌和古菌16S rRNA基因克隆文库。通过PCR扩增、基因测序、序列大于或等于97%相似度分析及在线杂合子检验,共得到691个细菌有效克隆,261种RFLP(Restriction Fragment Length Polymorphism)带型和181个OTUs(Operational Taxonomic Units);通过对古菌的研究最终获得719个古菌有效克隆,199种RFLP带型和104个OTUs。系统发育分析的结果表明,该研究中的细菌和古菌序列同来源于各种海洋环境的序列具有很好的同源性。细菌分为15个不同的类群,主要以绿弯菌门(Chloroflexi)、变形菌门(Proteobacteria)和浮霉菌门(Planctomycetes)为主,其中变形菌门又包括α-、γ-和δ-变形菌纲三个纲。古菌序列均从属于古菌的两个大的分支:Crenarchaeota泉古生菌(76%)和Euryarchaeota广古生菌(24%)。Deep-sea Archaeal Group (DSAG)和Miscellaneous Crenarchaeotic Group(MCG)是研究区域古菌的优势类群。香农威纳指数(H)、辛普森指数(1/D)、均匀度(J)及SChao 1、SACE等多样性指标表明,细菌克隆文库的3051bac4和3051bac8层位多样性最高,而古菌的TWP1层位具有较高的多样性;并且微生物的多样性随着深度的增加呈现一定的梯度变化,这种差异可能受热带西太平洋边界流以及频繁的火山、地震活动的影响。
通过系统发育分析和与其他地区的对比发现,热带西太平洋深海沉积物中的微生物类群无论在多样性、还是群落结构与组成上都与秘鲁边缘海1227位点处的微生物类群有很大的相似性,这两个区域虽然横跨东、西太平洋,但在相似的环境条件下也可能形成较为相近的微生物群落。另外,通过研究我们还发现,古菌DSAG和MCG可能是非水合物区某些层位处的优势类群,似乎比以前我们所想象的具有更广泛的生理适应性,它们的空间分布和群落结构可能因环境中地球化学梯度的不同而发生相应的变化。
To identify the diversity and community structure of microbes in deep subsurface sediments from the tropical Western Pacific, eight bacterial and archaeal 16S rRNA gene clone libraries were constructed by using a PCR-based cloning approach, respectively.
691 bacterial valid clones, 261 Restriction Fragment Length Polymorphism (RFLP) genotypes and 181 Operational Taxonomic Units (OTUs) were identified by using PCR amplicons, sequencing, chimera-check and 97% similarity analysis. Meanwhile, we obtained 719 archaeal clones, 199 RFLP genotypes and 181 OTUs.
Phylogenetic analysis of 16S rDNA sequences indicated the majority of members were most closely related to uncultivated groups and physiologically uncharacterized assemblages from various marine environments. 15 major bacterial lineages were obtained. Chloroflexi, Proteobacteria and Planctomycetes were the dominate phylotypes detected among the clone libraries. The division of contained three subdivisions includingα-,γ- andδ-Proteobateria subdivisions. In this study, all archaeal phylotypes were affiliated with Crenarchaeota (76%) and Euryarchaeota (24%), respectively. Deep-sea Archaeal Group (DSAG) and Miscellaneous Crenarchaeotic Group (MCG) belonging to Crenarchaeota were the most predominant archaeal 16S rDNA phylotypes in clone libraries. By means of the values of Shannon-Weiner (H), Simpson (1/D), and evenness (J) indices, the bacterial and archaeal communities observed in clone libraries obtained from the eight sediment layers were diverse and showed obviously stratified features. 3051bac4 and 3051bac8 layers had the highest diversity of the bacterial OTUs, and TWP1 clone library had the highest archaeal diversity. The difference might be caused by boundary currents of the tropical Western Pacific and frequent volcano and earthquake activities.
Phylotypes in this study shared high similarity with those in subsurface sediments from Peru Margin 1227 site in diversity and community structures, which indicated different geographical zones across the eastern and western Pacific might host similar members of archaeal populations based on similar sedimentary environments. In our study, members of DSAG and MCG seemed to dominate certain layers of the nonhydrate sediments, suggesting a wide ecophysiological adaptation than previously appreciated. The spatial distribution and community structure of these groups might vary with the different geochemical gradient of the environments.
通过系统发育分析和与其他地区的对比发现,热带西太平洋深海沉积物中的微生物类群无论在多样性、还是群落结构与组成上都与秘鲁边缘海1227位点处的微生物类群有很大的相似性,这两个区域虽然横跨东、西太平洋,但在相似的环境条件下也可能形成较为相近的微生物群落。另外,通过研究我们还发现,古菌DSAG和MCG可能是非水合物区某些层位处的优势类群,似乎比以前我们所想象的具有更广泛的生理适应性,它们的空间分布和群落结构可能因环境中地球化学梯度的不同而发生相应的变化。
To identify the diversity and community structure of microbes in deep subsurface sediments from the tropical Western Pacific, eight bacterial and archaeal 16S rRNA gene clone libraries were constructed by using a PCR-based cloning approach, respectively.
691 bacterial valid clones, 261 Restriction Fragment Length Polymorphism (RFLP) genotypes and 181 Operational Taxonomic Units (OTUs) were identified by using PCR amplicons, sequencing, chimera-check and 97% similarity analysis. Meanwhile, we obtained 719 archaeal clones, 199 RFLP genotypes and 181 OTUs.
Phylogenetic analysis of 16S rDNA sequences indicated the majority of members were most closely related to uncultivated groups and physiologically uncharacterized assemblages from various marine environments. 15 major bacterial lineages were obtained. Chloroflexi, Proteobacteria and Planctomycetes were the dominate phylotypes detected among the clone libraries. The division of contained three subdivisions includingα-,γ- andδ-Proteobateria subdivisions. In this study, all archaeal phylotypes were affiliated with Crenarchaeota (76%) and Euryarchaeota (24%), respectively. Deep-sea Archaeal Group (DSAG) and Miscellaneous Crenarchaeotic Group (MCG) belonging to Crenarchaeota were the most predominant archaeal 16S rDNA phylotypes in clone libraries. By means of the values of Shannon-Weiner (H), Simpson (1/D), and evenness (J) indices, the bacterial and archaeal communities observed in clone libraries obtained from the eight sediment layers were diverse and showed obviously stratified features. 3051bac4 and 3051bac8 layers had the highest diversity of the bacterial OTUs, and TWP1 clone library had the highest archaeal diversity. The difference might be caused by boundary currents of the tropical Western Pacific and frequent volcano and earthquake activities.
Phylotypes in this study shared high similarity with those in subsurface sediments from Peru Margin 1227 site in diversity and community structures, which indicated different geographical zones across the eastern and western Pacific might host similar members of archaeal populations based on similar sedimentary environments. In our study, members of DSAG and MCG seemed to dominate certain layers of the nonhydrate sediments, suggesting a wide ecophysiological adaptation than previously appreciated. The spatial distribution and community structure of these groups might vary with the different geochemical gradient of the environments.
引文
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