承德地区两温泉中古细菌基因型多样性分析

通过构建16S rDNA克隆文库,对承德地区两个不同温度的温泉中古细菌的基因型多样性进行了分子生态学研究。结果表明:山湾子温泉(A12)74.5℃热水中的古细菌主要分属泉古菌门(Crenarchaeota)和广古菌门(Euryarchaeota)两个门;七家温泉(A14)61.4℃热水中的古细菌则只属于泉古菌门,没有广古菌门微生物的分布。样品A12中的古细菌序列只可分为3种基因型,而A14中的古细菌序列可分为10种基因型。古细菌多样性的差异表明,温度是影响温泉中古细菌多样性水平的重要因素。样品A12中古细菌群落具有厌氧发酵乙酸产甲烷的生理功能,而A14中大多数古细菌均与氨氧化古菌有密切的亲缘关系,其主要生理功能为好氧氨氧化。     

贵州喀斯特地区碳酸盐岩表生古菌群落结构及多样性研究——以南江大峡谷为例

为了研究贵州喀斯特地区碳酸盐岩表生古菌群落结构的多样性,应用16S rDNA文库技术,对采集于贵州南江大峡谷的白云岩和石灰岩样品进行基因文库的构建和限制性片段长度多态性(RFLP)分析。用限制性核酸内切酶MspⅠ对两个文库中分别随机挑选的300个阳性克隆子进行酶切分型,白云岩和石灰岩16S rDNA基因文库各得到14和13个基因型,其覆盖率分别为95.4%和91.3%,香农指数分别为2.14和1.93。系统发育分析表明白云岩和石灰岩表生古菌克隆子全部归属于泉古菌门（Crenarchaeota）,代表性克隆与GenBank数据库已有16S rRNA序列的相似性为96%～100%,且最高相似性序列均来源于土壤及岩石环境的未可培养古菌序列。      

东海内陆架泥质区沉积物古菌群落垂向分布特征

为研究东海内陆架闽浙沿岸泥质区不同深度沉积物中古菌群落垂向分布特征, 利用古菌16S rDNA基因文库得到473个有效克隆、50个OTUs(Operational Taxonomic Units).16S rDNA序列系统进化和统计分析发现古菌分别归属于泉古生菌(Crenarchaeota)和广古生菌(Euryarchaeota), 其中以Miscellaneous Crenarchaeotic Group(MCG)为主, 仅含少量的Marine Benthic Group B(MBG-B)、South African Gold Mine Euryarchaeotic Group(SAGMEG)、Anaerobic Methanotrophs 3(ANME-3)、Marine Crenarchaeotic Group I(MG-I)和Marine Benthic Group D(MBG-D).该泥质区沉积物可能存在由ANME-3催化的甲烷厌氧氧化作用, 同源序列分析表明其古菌群落分布与周边环境有较大联系.UniFrac与沉积物环境因子分析表明该泥质区古菌群落垂向分布与沉积物有机质含量和粒度变化密切相关.      

http://www.sciencedirect.com/science/article/pii/S1674987111001307

South China Sea(SCS) is the largest Western Pacific marginal sea.However,microbial studies have never been performed in the cold seep sediments in the SCS.In 2004."SONNE" 177 cruise found two cold seep areas with different water depth in the northern SCS.Haiyang 4 area,where the water depth is around 3000 m.has already been confirmed for active seeping on the seafloor.such as microbial mats,authigenic carbonate crusts and bivalves.We investigated microbial abundance and diversity in a 5.55-111 sediment core collected from this cold seep area.An integrated approach was employed including geochemistry and 16S rRNA gene phylogenetic analyses.Here,we show that microbial abundance and diversity along with geochemistry profiles of the sediment core revealed a coupled reaction between sulphate reduction and methane oxidation.Acridine orange direct count results showed that microbial abundance ranges from 10~5 to 10~6 cells/g sediment(wet weight).The depth-related variation of the abundance showed the same trend as the methane concentration profile.Phylogenetic analysis indicated the presence of sulphate-reducing bacteria and anaerobic methane-oxidizing archaea.The diversity was much higher at the surface,but decreased sharply with depth in response to changes in the geochemical conditions of the sediments,such as methane,sulphate concentration and total organic carbon.Marine Benthic Group B.Chloroflexi and JSl were predominant phylotypes of the archaeal and bacterial libraries,respectively.     

西太平洋暖池核心区Ontong Java 海台古菌多样性研究

为了研究西太平洋暖池核心区表层古菌群落结构及多样性,应用16S rDNA文库技术对KX08-973-22站位(取名为CWP)水体样构建基因文库,得到了561个克隆,经分析处理后得到50个OUT(Operational Taxonimic Units).通过对16S rRNA基因序列的同源性比较,构建系统发育树分析及统计...     

Anaerobic Metabolism in Tidal Freshwater Wetlands: II. Effects of Plant Removal on Archaeal Microbial Communities

The interaction of plant and microbial communities are known to influence the dynamics of methane emission in wetlands. Plant manipulations were conducted in an organic rich (JB-organic) and a mineral rich (JB-mineral) site in a tidal freshwater wetland to determine if plant removal impacted archaeal populations. In concert, a suite of process-based measurements also determined the effects of plant removal on rates of methanogenesis and Fe-reduction. The microbial populations were analyzed with clone libraries of the SSU ribosomal RNA (rRNA) gene from selected plots, and terminal restriction length polymorphism (tRFLP) of the SSU rRNA and the methyl-coenzyme M reductase (mcrA) gene. Overall, methanogenesis dominated anaerobic carbon mineralization at both sites during the most active growing season. A total of 114 SSU rRNA clones from four different plots revealed a diversity of Euryarchaeota including representatives of the Methanomicrobiales, Methanosarcinales and Thermoplasmatales. The clone libraries were dominated by the Thaumarchaeota, accounting for 65 % of clones, although their diversity was low. A total of 112 tRFLP profiles were generated from 56 samples from 25 subplots; the patterns for both SSU rRNA and mcrA showed little variation between sites, either with plant treatment or with the growing season. Overall these results suggest that wetland soil archaeal populations were resilient to changes in the associated surface plant communities. The work also revealed the presence of novel, mesophilic Thaumarchaeota of unknown metabolic function.     

http://www.sciencedirect.com/science/article/pii/S1674987111001290

The Three Gorges Dam(TGD) of the Yangtze River.China,is one of the largest irrigation and hydroelectric engineering projects in the world.The effects of huge man-made projects like TGD on fauna and macrophyte are obvious,mainly through changes of water dynamics and flow pattern;however, it is less clear how microorganisms respond to such changes.This research was aimed to examine differences in microbial diversity at different seasons and locations(in front of and behind the TGD).In addition, differences between particle-attached and free-living communities were also examined.The community structures of total and potentially active microorganisms in the water columns behind and in front of the TGD were analyzed with the DNA- and RNA-based 16S rRNA gene phylogenetic approaches over three different seasons.Clone libraries of 16S rRNA genes were prepared after amplification from extracted DNA and.for some samples,after preparing cDNA from extracted rRNA.Differences were observed between sites at different seasons and between free-living and particle-attached communities.Both bacterial and archaeal communities were more diverse in summer than in winter, due to higher nutrient levels and warmer temperature in summer than in winter.Particle-attached microorganisms were more diverse than free-living communities,possibly because of higher nutrient levels and heterogeneous geochemical micro-environments in particles.Spatial variations in bacterial community structure were observed,i.e..the water reservoir behind the TGD(upstream) hosted more diverse bacterial populations than in front of the dam(downstream),because of diverse sources of sediments and waters from upstream to the reservoir.These results have important implications for our understanding of responses of microbial communities to environmental changes in river ecosystems affected by dam construction.     

黑潮源区沉积物微生物多样性初步研究

从黑潮源区采集上层沉积物,进行DNA提取,以细菌和古菌的16S rDNA通用引物PCR扩增黑潮源区沉积物中细菌和古菌群落的16S rDNA,并构建细菌和古菌的16S rDNA文库,经限制性片段长度多态性分析(Restriction Fragment Length Polymorphism,RFLP),DNA序列测定和系统发育分析,对黑潮源区表层沉积物的细菌和古菌多样性进行了研究。研究结果表明:黑潮源区细菌包括了变形杆菌(Proteobacteria)、酸杆菌(Acidbacterium)、浮霉菌(Planctanycene)、疣微菌(Verrucomicro-bia)和Candidate division OP8和拟杆菌(Bacteroidetes)共6个类群,其中变形杆菌是优势类群。古菌包括了泉古菌(Crenarchaeota)和广古菌(Euryarchaeota),其中泉古菌占优势;泉古菌包括MCG、C3、MBGA和MGI 4个类群,而广古菌包括SAGMEG、MBGE和MEG 3个类群,其中MBGE是优势类群。     

苏禄海深海沉积物古菌群落结构多样性研究

为了研究热带西太平洋深海沉积物中古菌群落结构的多样性,应用16S rDNA文库技术,对IMAGES ⅪⅤ航次采集的岩芯MD3 059进行基因文库的构建和分析,选取得到543个克隆,处理获得137个OTUs(Operational Taxonomic Units).基于16s rRNA序列的同源性比较,绘制系统进化树,进行统计学分析.研究结果显示,热带西太平洋苏禄海沉积物中有丰富多样的古菌群落,在不足5 m的沉积物中垂直分布着11种古菌类群.古菌序列归属于泉古菌(Crenarchaeota)和广古菌(Euryarchaeota),其中,前者主要由Miscellaneous Crenarchaeotic Group(MCG)构成(占总古菌克隆序列的50%以上),而后者主要由Marine Benthic Group D(MBG-D)、South Africa Gold Mine Euryarchaeotic Group(SAGMEG)和Marine Benthic Group B(MBG-B)等种属构成(占总古菌克隆序列的30%以上).研究结果对于理解热带西太平洋深海沉积物中微生物多样性和未来开发利用微生物资源具有重要意义.     

http://www.sciencedirect.com/science/article/pii/S1674987114000668

Microbial diversity in the hydrate-containing (sites SH3B and SH7B) and-free (sites SH1B, SH5B, SH5C) sediments collected from the Shenhu area of the South China Sea (SCS) was investigated using 16S rR...     

Distributions and assemblages of microbial communities along a sediment core retrieved from a potential hydrate-bearing region offshore southwestern Taiwan

Assessing the impacts of methane released from hydrate-bearing environments on global carbon cycling would require detailed insights into the distributions and capacities of microbial communities at different horizons of sediment column. In this study, we conducted geochemical, gene abundance and diversity analyses for a sediment core retrieved from a potential hydrate-bearing region off southwestern Taiwan. Geochemical profiles were characterized by a sulfate-to-methane transition with decreasing total organic carbon and nitrogen in sediments, and increasing dissolved inorganic carbon, ammonium and total sulfur in sediments. Bacterial and archaeal 16S rRNA and amoA gene abundances decreased with depth. In contrast, ANME-1 and -2 16S rRNA gene abundances increased significantly across the sulfate-to-methane transition and peaked at different horizons below this interface. A total of 124,379 bacterial and 130,351 archaeal reads were recovered through tag-pyrosequencing of 16S rRNA genes and categorized into 9014 bacterial and 6394 archaeal operational taxonomic units on the basis of 97% sequence similarity, respectively. Major bacterial phyla/divisions and archaeal groups (>5% of the total reads) detected included Chloroflexi, Planctomycetes, OP9, Deltaproteobacteria, BHI80-139, MBG-B, Halobacteria, MCG, Thermoplasmata, ANME-1 and MG-I. The abundance variations of most major OTUs (>0.5% of the total reads) were statistically correlated with those of geochemical parameters. These lines of evidence suggest that the populations represented by the major OTUs or detected by group-specific primers were compartmentalized into different horizons and involved directly or indirectly in the cycling of methane, sulfate, organic carbon and nitrogen. Overall, this study demonstrates that the deep sequencing coverage combined with the quantification of gene abundance and geochemical characterization would enable to uncover the detailed distributions and potential metabolic capabilities of specific groups from complexly structured microbial communities in methane-rich marine sediments.     

南海西沙海槽沉积物细菌多样性初步研究

对来自南海西沙海槽的深海沉积物进行总DNA提取,并构建细菌16S rDNA文库。细菌16S rDNA系统发育分析表明沉积物中细菌分属4个类群：变形杆菌(Proteobacteria)、浮霉菌(Planctomycene)、低G+C含量革兰氏阳性菌和放线菌(Actinobacteria),它们分别占总体的49%、22%、22%和7%。Proteobacteria类群又以δ Proteobacteria亚群占优势,其他分属α 和γ Proteobacteria亚群。Planctomycene和低G+C含量革兰氏阳性菌两个常见于浅海的类群,在西沙海槽沉积物的丰度高于其他深海沉积物,可能是随沉积物被浊流搬运至海槽。     

Abundance and diversity of snow bacteria in two glaciers at the Tibetan Plateau

Snow bacterial abundance and diversity at the Guoqu Glacier and the East Rongbuk Glacier located in the central and southern Tibetan Plateau were investigated using a 16S rRNA gene clone library and flow cytometry approach. Bacterial abundance was observed to show seasonal variation, with different patterns, at the two glaciers. High bacterial abundance occurs during the monsoon season at the East Rongbuk Glacier and during the non-monsoon season at the Guoqu Glacier. Seasonal variation in abundance is caused by the snow bacterial growth at the East Rongbuk Glacier, but by bacterial input from the dust at the Guoqu Glacier. Under the influence of various atmospheric circulations and temperature, bacterial diversity varies seasonally at different degrees. Seasonal variation in bacterial diversity is more distinct at the Guoqu Glacier than at the East Rongbuk Glacier. Bacterial diversity at the two glaciers exhibits different responses to various environmental conditions. More bacteria at the Guoqu Glacier are connected with those from a soil environment, while more bacteria affiliated with a marine environment occur at the East Rongbuk Glacier.     

Distribution characteristics and factors influencing microbial communities in the core soils of a seawater intrusion area in Longkou City,China

Microbes live throughout the soil profile. Microbial communities in subsurface horizons are impacted by a saltwater–freshwater transition zone formed by seawater intrusion (SWI) in coastal regions. The main purpose of this study is to explore the changes in microbial communities within the soil profile because of SWI. The study characterizes the depth-dependent distributions of bacterial and archaeal communities through high-throughput sequencing of 16S rRNA gene amplicons by collecting surface soil and deep core samples at nine soil depths in Longkou City, China. The results showed that although microbial communities were considerably impacted by SWI in both horizontal and vertical domains, the extent of these effects was variable. The soil depth strongly influenced the microbial communities, and the microbial diversity and community structure were significantly different (p < 0.05) at various depths. Compared with SWI, soil depth was a greater influencing factor for microbial diversity and community structure. Furthermore, soil microbial community structure was closely related to the environmental conditions, among which the most significant environmental factors were soil depth, pH, organic carbon, and total nitrogen.

     

Increased Variability of Microbial Communities in Restored Salt Marshes nearly 30?Years After Tidal Flow Restoration

We analyzed microbial diversity and community composition from four salt marsh sites that were impounded for 40?C50?years and subsequently restored and four unimpounded sites in southeastern Connecticut over one growing season. Community composition and diversity were assessed by terminal restriction fragment length polymorphism (TRFLP) and sequence analysis of 16S ribosomal RNA (rRNA) genes. Our results indicated diverse communities, with sequences representing 14 different bacterial divisions. Proteobacteria, Bacteroidetes, and Planctomycetes dominated clone libraries from both restored and unimpounded sites. Multivariate analysis of the TRFLP data suggest significant site, sample date, and restoration status effects, but the exact causes of these effects are not clear. Composition of clone libraries and abundance of bacterial 16S rRNA genes were not significantly different between restored sites and unimpounded sites, but restored sites showed greater temporal and spatial variability of bacterial communities based on TRFLP profiles compared with unimpounded sites, and variability was greatest at sites more recently restored. In summary, our study suggests there may be long-lasting effects on stability of bacterial communities in restored salt marshes and raises questions about the resilience and ultimate recovery of the communities after chronic disturbance.     

砾间接触氧化反应器中填料表面细菌多样性及其主要功能

采用分子生物学手段,通过构建16S rDNA基因文库,对新型剩余污泥减量化处理系统—生物砾间接触氧化反应器 (GCOR) 中载体表面附着细菌多样性进行了系统发育分析,并讨论了多种细菌共存对剩余污泥减量化的贡献。结果表明,附着细菌可分为好氧呼吸菌群、兼性厌氧菌群、厌氧水解发酵菌群和生长缓慢菌群等4大类。其中,优势菌群分别是以兼具呼吸/发酵代谢方式的β变形菌、嗜水气单胞菌及以发酵为主要代谢方式的拟杆菌属。此外,好氧菌群中还发育有假单胞菌属、硝化螺菌属细菌和黄杆菌属细菌等。慢速生长菌群包括Caldimonas taiwanensis strain On 1和Ideonella sp.。填料表面生物膜微生态环境复杂,微生物多样性较高,好氧、厌氧菌群以及慢速生长菌群等多种细菌共同作用,为在降解污水有机物的同时,达到剩余污泥减量化做出巨大贡献。结果分析表明,细菌的主要功能可归纳为：能量解偶联、共代谢作用、生物溶胞作用和慢性生长种群的影响。     

祁连山冻土区天然气水合物DK一2钻孔微生物群落

对青海省祁连山永久冻土区天然气水合物DK一2钻孔的11件样品进行分析,通过微生物群落分析来探寻水合物层样品与非水合物层样品的差别。在11件样品中均发现了细菌16SrDNA,未检测到海洋天然气水合物地区常见的古菌16SrDNA、mc以（I,Ⅱ）、pmoA、mmoX和mxaF。分析得到的细菌16SrDNA分属5个门,包括变形杆菌门、放线菌门、拟杆菌门、厚壁菌门和异常球菌一栖热菌门,随着样品深度的增加,细菌多样性有降低的趋势。对非水合物层样品DK2—19和水合物层样品DK2—25进行细菌系统发育树分析,发现这2个样品群落结构相差较大。水合物层样品与非水合物层样品细菌群落对比后发现,水合物层样品中叫一变形杆菌的比例低于非水合物层样品中1一变形杆菌的比例,而Arthrobacter属多发现于非水合物层的样品中。     

http://www.sciencedirect.com/science/article/pii/S1674987111001344

The Rehai Geothermal Field,located in Tengcbong County,in central-western Yunnan Province, is the largest and most intensively studied geothermal held in China.A wide physicochemical diversity of springs(ambient to ~97℃;pH from≤.8 to≥9.3) provides a multitude of niches for extremophilic microorganisms.A variety of studies have focused on the cultivation,identification,basic physiology,taxonomy,and biotechnological potential of thermophilic microorganisms from Rehai.Thermophilic bacteria isolated from Rehai belong to the phyla Firmicutes and Deinococcus-Thenmts. Firmicutes include neutrophilic or alkaliphilic Anoxybacillus,Bacillus,Caldalkalibacillus.Caldanaerobacier, Laceyella,and Geobacillus,as well as thermoacidophilic Alicyclobacillus and Sulfobacillus. Isolates from the Deinococcus-Thermus phylum include several Meiothermus and Thennus species.Many of these bacteria synthesize thermostable polymer-degrading enzymes that may be useful for biotechnology. The thermoacidophilic archaea Acidianus.Melal/osp/utera.and Suljolobus have also been isolated and studied.A few studies have reported the isolation of thermophilic viruses belonging to Siphoviridae(TTSP4 and TTSPIO) and Fuselloviridae(STSVl) infecting Thennus spp.and Suljolobus spp..respectively.More recently,cultivation-independent studies using 16S rRNA gene sequences, shotgun metagenomics,or "functional gene" sequences have revealed a much broader diversity of microorganisms than represented in culture.Studies of the gene and mRNA encoding the large subunit of the ammonia monooxygenase(imioA) of ammonia-oxidizing Archaea(AOA) and the tetraether lipid erenarchaeol. a potential biomarker for AOA.suggest a wide diversity,but possibly low abundance,of thermophilic AOA in Rehai.Finally,we introduce the Tengchong Partnerships in International Research and Education(PIRE) project,an international collaboration between Chinese and U.S.scientists with the goal of promoting international and interdisciplinary cooperation to gain a more holistic and global view of life in terrestrial geothermal springs.     

Tag-encoded pyrosequencing analysis of bacterial diversity within different alpine grassland ecosystems of the Qinghai-Tibet Plateau,China

The Qinghai-Tibet Plateau is sensitive to climate change, with ecosystems that are important with respect to scientific research. Here high-throughput DNA pyrosequencing was used to assess bacterial diversity within different alpine grassland ecosystems of the Qinghai-Tibet Plateau, China. In total, 34,759 sequences were obtained for the three ecosystems––alpine cold swamp meadow (ASM), alpine cold meadow (AM), alpine sandy grassland (ASG), and 31 phyla and a small number of unclassified bacteria were detected. The bacterial community structures were different for each alpine grassland ecosystem. The Proteobacteria and Acidobacteria were the predominant phyla in all three ecosystems. Besides this, Actinobacteria and Chloroflexi were abundant in ASM, Bacteroidetes, Gemmatimonadetes and Verrucomicrobia were abundant in AM, and Actinobacteria were abundant in ASG. In addition, the functional bacterial genera also differed with each alpine grassland ecosystem. The ASM contained more nitrifying bacteria, methane-oxidizing bacteria and sulfur- and sulfate-reducing bacteria, whereas the ASG ecosystem contained more nitrogen-fixing bacteria. Pyrosequencing provided a greater insight into bacterial diversity within different alpine grassland ecosystems than previously possible, and gave key data for the involvement of bacteria in the protection of alpine grassland ecosystems of the Qinghai-Tibet Plateau, China.     

石油污染地下水中细菌分子生态学研究

采集了某废弃炼油厂的石油污染地下水样品,提取水中微生物总DNA,构建细菌16S rDNA克隆文库,并通过16S rDNA序列的系统发育分析,对样品中的细菌种群多样性以及群落结构进行了研究。结果表明,文库中阳性克隆的16S rDNA序列分属11个细菌类群,分别为Betaproteobacteria(381％),Alphaproteobacteria(353％),Gamaproteobacteria(51％),Deltaroteobacteria(52％),Bacteroidetes(40％),Verrucomicrobia(25％),Epsilonproteobacteria(19％),Nitrospira(13％),Planctomycetes(13％),Candidate Division OD1(13％),Unclassified Bacteria(38％)。在这一生态系统中,Betaproteobacteria和Alphaproteobacteria类细菌占据主导地位,二者所占比例均在三分之一以上。群落中最主要的降解菌是噬氢菌属(Hydrogenophaga)和鞘氨醇单胞菌属(Sphingomonas)细菌,它们在文库中所占比例达239％和195％。该石油污染地下水样品中细菌与许多其他已知的降解菌亲缘关系较近,如Sulfuricurvum kujiense、Trichlorobacter thiogenes、Rhodoferax ferrireducens以及红细菌属(Rhodobacter)、甲基单胞菌属(Methylomonas)和涅瓦菌属(Nevskia)细菌等。此外,文库中克隆的16S rDNA序列与许多类似的污染场地中发现的环境克隆相似性很高,如煤焦油污染的地下水、苯污染的地下水、原油污染的土壤、溴甲烷和氯甲烷污染的土壤、抗生素生产废水以及活性污泥等,证明该石油污染地下水中有大量降解菌群的存在。石油污染物的种类对降解菌群的组成有一定的选择作用。