磷对地下水反硝化系统中细菌菌群结构的影响

采用16SrDNA克隆文库法研究了两根磷矿石含量不同的反硝化柱中细菌菌群结构的异同,每根反硝化柱中的样品随机测定了108个克隆子序列。研究结果表明,尽管两反硝化柱内的细菌均具有高度多样性,但是磷矿石的投加与否可明显引起菌群结构的变化。无磷矿石添加的反硝化柱内细菌分属14个类群,而有磷矿石添加的反硝化柱内细菌分属10个类群。两反硝化柱内的优势菌群均为β-proteobacteria和Bacte-roidetes,其相对含量存在着一定的差别,添加磷矿石的反硝化柱样品中β-proteobacteria和Bacteroidetes在文库中所占的比例分别为50.93%、15.74%,而无磷矿石添加的反硝化柱样品中β-proteobacteria和Bacteroidetes在文库中所占的比例分别为49.07%、12.04%。此外,β-proteobacteria类细菌内Rhodocyclales类菌属占据主导地位,包括Thauera sp.、Azospira restricta、Denitratisoma等具有反硝化功能的菌属。而且,Rhodocyclales类细菌在PC柱样品文库中所占的比例比其在ZC柱样品文库中的比例高9.2%。因此,磷矿石作为反硝化柱的固相磷源,可以影响细菌菌群结构,增加优势菌群的数量,最终提高硝酸盐的去除效率。     

甘肃西峰黄土中细菌16S rDNA 文库的构建与组成初步分析

对黄土高原西峰地区黄土沉积物中的有机质进行了总DNA 提取和PCR（聚合酶链式反应）扩增,通过克隆测序技 术构建了含有44 个克隆子的细菌16S rDNA 文库。对16S rDNA 系统发育的分析表明,西峰地区的黄土沉积物中细菌可分属 13 个类群,包括：酸杆菌（Acidobacteria）、变形菌（Proteobacteria）、放线菌（Actinobacteria）、绿弯菌（Chloroflexi）、厚壁菌（Firmicutes）、疣微菌（Verrucomicrobia）、浮霉菌（Planctomycetes）、芽单胞菌（Gemmatimonadetes）、异常球菌-栖热菌（Deinococcus-Thermus）、硝化螺旋菌（Nitrospirae）、蓝细菌（Cyanobacteria）、拟杆菌（Bacteroidetes）和Candidate divisionTG1。其中酸杆菌为最主要优势类群,变形菌为次优势类群,二者占黄土细菌总克隆数的70%,且大多为不可培养的基因型。     

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。     

黑潮源区沉积物古菌多样性调查及研究

为了研究西太平洋黑潮源区不同深度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MD06-3047进行基因文库的构建和分析,得到260个克隆,经分析处理后得到56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,西太平洋黑潮源区的本哈姆高原(Benham Rise)沉积物中有丰富多样的古菌群落,在1m内的沉积物中分布着9种古菌类群.古菌序列归属于泉古菌(Crenarchaeota)和广古菌(Euryarchaeota),并以泉古菌为主(占总序列的91.5％).其中,泉古菌包含MGI、MBG-B、MCG和UCII-b 4个类群,并且主要由MGI构成(占总序列的40.8％),而广古菌包含MBG-D、SAGMEG、DHVEG、MBG-E和VAL Ⅲ 5个类群,各类群所占总序列比例均较低(占总序列的0.4％～5.4％之间).研究结果对于理解西太平洋黑潮源区沉积物中古菌多样性有重要意义,并为今后研究古菌群落与环境之间的关系提供科学依据.     

长白山小天池和长白瀑布水体典型样本的细菌多样性比较

水体中微生物对环境的改变有着敏感的响应。16S rRNA基因克隆文库可以同时反映标本中的细菌种类和各种细菌的相对比例。本研究构建环境样品16S rRNA基因的克隆文库,解析长白山小天池入水口和长白瀑布下水潭两个典型水体样本中的细菌种属多样性特征,并探讨其与水体性质的关系。小天池文库共获得89条16S rRNA基因序列,分别属于10个类群,其中Betaproteobacteria是主要类群(占总数的23.6%)。长白瀑布文库共获得88条序列,分别属于8个类群,以Betaproteobacteria为主要类群(占总数的35.2%)。Bacteroidetes、Betaproteobacteria、Alphaproteobacteria和Gammaproteobacteria是两个样本共有的优势类群,而Deltaproteobacteria、Acidobacteria和Armatimonadetes只在小天池入水口处检出。长白瀑布水潭中的细菌群落多样性明显偏低,种群均匀度指数也较低,但两样本的地理距离极短,认为人类活动可能是导致这种差异的原因。     

玉米根际土壤细菌群落对不同程度镉污染的响应：以甘肃省白银市四龙镇地区为例

为了研究玉米根际土壤细菌群落对土壤Cd污染的响应,本研究基于Illumina MiSeq高通量测序平台,对取自甘肃省白银市四龙镇地区的4组不同Cd污染程度的土壤样品进行16S rDNA扩增子测序分析。结果显示：4组不同Cd污染程度的玉米根际土壤细菌样品的Chao1指数和Shannon指数差异性不明显(p>0.05),表明Cd污染对土壤细菌多样性的影响不显著。4组样品的细菌丰富度相似,优势类群大致相同。4组样品的优势门均为变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)、酸杆菌门(Acidobacteria)、绿弯菌门(Chloroflexi)和浮霉菌门(Planctomycetes),优势菌属为Ohtaekwangia、GP4、GP6、硝化螺旋菌属(Nitrospira)和芽单胞菌属(Gemmatimonas)等。Ohtaekwangia和芽单胞菌属的细菌抗逆性较强,随着环境中Cd含量的增加,其细菌相对丰度增加,而GP4和GP6的细菌抗逆性较差,其相对丰度会随土壤Cd含量的降低而降低。Cd污染会引起土壤中细菌的多样性变化,但细菌多样性与土壤中Cd含...     

北京莲花池趋磁细菌的群落多样性研究

趋磁细菌是一类在细胞内合成磁铁矿(Fe_3O_4)或胶黄铁矿(Fe_3S_4)磁小体的微生物,广泛分布在水环境和沉积环境,在铁、硫、碳、氮、磷等元素的生物地球化学循环中发挥重要作用.趋磁细菌培养条件苛刻,目前对环境趋磁细菌的多样性和生理代谢特征等还有待系统深入的研究.本研究综合利用电子显微镜、能谱分析和分子生态学等技术方法,对北京地区莲花池沉积物中趋磁细菌的形态多样性、细胞元素分布特征和系统发育多样性等进行了系统分析.光学显微镜观察和电子显微镜分析显示莲花池中存在大量趋磁细菌(～10~3～10~4细胞/mL),从形态上主要分为球形和弧形两种,在细胞内富含铁、硫、镁等元素.基于16S rRNA基因的系统发育研究共发现了7个新类群,分别属于(Proteobacteria)中的α-变形菌纲和γ-变形菌纲,其中属于α-变形菌纲的5个类群与已知趋磁细菌序列最相似(≥91%).本研究结果有助于更好地认识自然界趋磁细菌的群落多样性和地质环境功能.     

冻融循环对青藏高原腹地不同生态系统土壤细菌群落结构的影响

通过构建16S rRNA基因克隆文库,研究了冻融循环对青藏高原腹地北麓河的高寒沼泽草甸和高寒沙化草原两种不同生态系统土壤细菌群落结构的影响. 结果表明: α-、 β-、 γ- 和δ-变形菌门(α-、 β-、 γ- 和δ-Proteobacteria)、 酸杆菌门(Acidobacteria)、 放线菌门(Actinobacteria)、 拟杆菌门(Bacteroidetes)和浮霉菌门(Planctomycetes)为两个生态系统土壤共有的细菌类群, 其中, 变形菌门、 酸杆菌门及浮霉菌门细菌为研究区域优势菌, 而厚壁菌门(Firmicutes)为高寒沼泽草甸土壤所特有, 疣微菌门(Verrucomicrobia)和绿弯菌门(Chloroflexi)细菌是高寒沙化草原土壤特有的细菌类群, 表明青藏高原腹地两种生态系统土壤具有丰富的细菌多样性. 冻融循环会降低区域土壤的细菌多样性, 随冻融循环, 高寒沼泽草甸和高寒沙化草原生态系统土壤放线菌门丰度均呈现下降趋势, 但大部分细菌随冻融循环的变化在两种生态类型中呈现不同的变化规律, 结果说明冻融循环对于不同生态系统土壤细菌群落结构的影响既存在相似性, 也存在着较大的差异.     

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.     

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。     

Bacterial Community Dynamics in a Seagrass (<Emphasis Type="Italic">Posidonia oceanica</Emphasis>) Meadow Sediment

Some traits of the bacterial community dynamics associated to the rhizosphere of the Mediterranean seagrass Posidonia oceanica, growing in carbonate sediments, were analyzed during a 2-year period in an enclosed bay of the Balearic Islands. The diversity of the bacterial community was studied by the construction of 16S rDNA clone library. For testing temporal and vertical differences in the abundance of total cells and active Bacteria, we used 4′,6-diamidino-2-phenylindole (DAPI) staining and fluorescence in situ hybridization (FISH). Moreover, some relevant groups of sulfate-reducing bacteria (SRB) were occasionally assessed by FISH. Despite the observed decrease in the total DAPI-stained cells, bacterial counts, and sulfate reduction rates throughout the sampling time, we found an increase in both the pore-water sulfide concentration and the proportion of SRB. Overall, the results revealed a very high bacterial diversity and indicated shifts in bacterial dynamics that could not be related to temperature-dependent factors, suggesting a link between the documented regression of the seagrass meadow and the decline of the microbial community, likely due to large organic matter inputs to the bay.     

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。     

Principal component analysis for interaction of nitrifiers and wastewater environments at a full-scale activated sludge plant

This study investigated the relationship between wastewater environments and the nitrifiers at a full-scale plant using principal component analysis. Ammonia-oxidizing bacteria and nitrite-oxidizing bacteria were detected by florescent in situ hybridization, polymerase chain reaction, phylogenetic analysis, real-time quantitative polymerase chain reaction. Pyrosequencing was also used in profiling the ammonia monooxygenase locus of ammonia-oxidizing bacteria community. It was found that the dominant ammonia-oxidizing bacteria sequences were related to uncultured ammonia-oxidizing bacterium, uncultured Nitrosomonadaceae bacterium, Nitrosomonas sp., and uncultured bacterium. In addition, Nitrobacter clones were related to uncultured alpha proteobacterium, uncultured bacterium, uncultured Nitrobacter sp., and uncultured Bradyrhizobium sp., whereas Nitrospira clones were similar to uncultured bacterium, Candidatus Nitrospira defluvii, uncultured Nitrospira sp., and uncultured Nitrospirae bacterium. The ammonia-oxidizing bacteria and nitrite-oxidizing bacteria ranged 2.83 × 10⁸–1.33 × 10¹⁰ and 1.25 × 10¹⁰–1.13 × 10¹¹ copies L^?1, respectively, equivalent to nitrite-oxidizing bacteria: ammonia-oxidizing bacteria ratio of 10:1. The first three parts of the principal components analysis accounted for 76.8% of the explained variance. The first principal component (44.4%) designated that ammonia-oxidizing bacteria and Nitrospira were mainly influenced by seasonal variations, followed by chemical oxygen demand concentration and nitrogen species (i.e., ammonia, nitrite, and nitrate). The second principal component (19.1%) showed no information about the nitrifiers’ interaction with environmental factors, whereas Nitrobacter demonstrated a high correlation with ammonia on the third principal component (13.3%). These results revealed that the species of Nitrobacter were less influenced by environmental conditions than ammonia-oxidizing bacteria and Nitrospira spp.     

青藏高原多年冻土区土壤需氧可培养细菌多样性及群落功能研究

以青藏高原腹地不同植被类型多年冻土区土壤细菌为研究对象, 分析了可培养菌群数量、 多样性和生理代谢功能的变化及其与环境因子间的关系. 结果显示: 从沼泽草甸到高寒荒漠, 土壤水分、 总碳、 总氮含量逐渐降低, pH值升高, 可培养细菌数量在2.97×10⁶~2.88×10⁷ CFU·g^-1, 与含水量、 总碳、 总氮显著正相关; Actinobacteria(51.4%)和γ-Proteobacteria(31.7%)为优势菌群, α-protebacteria仅在沼泽草甸中有分布, β-protebacteria、 Bacterioidetes丰度与含水量、 总碳、 总氮间显著正相关; 自沼泽到荒漠, 菌群代谢活性和Shannon功能多样性指数降低, pH与Shannon指数显著负相关, 继氨基酸类碳源之后, 多聚物逐渐成为被细菌群落主要利用的碳源种类. 研究表明, 伴随冻土退化地上植被逆向演替的过程, 青藏高原多年冻土地下土壤微生物群落丰度、 遗传和代谢功能多样性均发生了不同程度的响应.     

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。      

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.     

Comparison of microbial communities in petroleum-contaminated groundwater using genetic and metabolic profiles at Kyonggi-Do,South Korea

This research has been performed to determine the differences in microbial communities according to physicochemical properties such as concentrations of volatile aromatic hydrocarbons such as benzene, toluene, ethylbenzene, and xylene (BTEX), dissolved oxygen (DO), electron acceptors, etc., in oil-contaminated groundwaters at Kyonggi-Do, South Korea. The properties of bacterial and microbial communities were analyzed by 16S polymerase chain reaction (PCR) denaturing gradient gel electrophoresis (DGGE) fingerprinting method and community-level physiological profiling (CLPP) using Eco-plate, respectively. Based on the DGGE fingerprints, the similarities of bacterial community structures were high with similar DO levels, and low with different DO levels. Whereas the dominant bacterial groups in GW13 (highest BTEX and lowest DO) were acidobacteria, α-proteobacteria, β-proteobacteria, γ-proteobacteria, δ-proteobacteria, and spirochetes, those in GW7 (highest BTEX and highest DO) were actinobacteria, α-proteobacteria, β-proteobacteria, γ-proteobacteria, δ-proteobacteria, and sphingobacteria. Based on the CLPP results, the groundwater samples were roughly divided into three groups: above 4 mg/L in DO (group 1: GW3 and GW7), below 4 mg/L in DO (group 2: GW8, W1, W2, W3, and BH10), and highly contaminated with BTEX (group 3: GW13). Shannon index showed that the microbial diversities and equitabilities were higher in shallower aquifer samples. Overall, this study verified that the greatest influencing factors on microbial/bacterial communities in groundwaters were DO and carbon sources, although BTEX concentration was one of the major factors.     

青藏高原疏勒河上游不同类型冻土可培养细菌多样性特征研究

在气候变暖及人类活动的双重干扰下,疏勒河上游冻土发生了显著退化,如活动层厚度加大、植被退化等,而冻土退化对微生物的影响一直是科研人员关注的热点话题。以疏勒河上游不同季节（4月、6月、9月）、不同退化程度冻土为研究对象,研究了可培养细菌多样性特征。通过16S rDNA基因测序及构建系统发育树表明,研究区域可培养细菌归类为27个属,分属于α-变形菌门,γ-变形菌门,放线菌门,厚壁菌门和拟杆菌门,其中放线菌门为优势类群。从属水平来讲,可培养细菌以节杆菌属和微球菌属为主,其含量随冻土退化程度加深分别呈下降和升高趋势。土壤细菌多样性与环境因子的相关性分析表明,可培养细菌多样性与土壤含水量、总氮极显著正相关,与有机碳显著正相关。这些结果表明,伴随着冻土退化而发生的地上植被逆向演替过程中,青藏高原不同类型冻土间已产生较大的环境异质性如土壤碳氮及含水量,进一步可能导致冻土微生物多样性分异。研究结果为利用微生物综合评价青藏高原不同类型冻土的生态环境提供了数据基础。