Taxonomy of oxalotrophic <Emphasis Type="Italic">Methylobacterium</Emphasis> strains

Most of the oxalotrophic bacteria are facultative methylotrophs and play important ecological roles in soil fertility and cycling of elements. This study gives a detailed picture of the taxonomy and diversity of these bacteria and provides new information about the taxonomical variability within the genus Methylobacterium. Twelve mesophilic, pink-pigmented, and facultatively methylotrophic oxalate-oxidizing strains were included in this work that had been previously isolated from the soil and some plant tissues by the potassium oxalate enrichment method. The isolates were characterized using biochemical tests, cellular lipid profiles, spectral characteristics of carotenoid pigments, G+C content of the DNA, and 16S rDNA sequencing. The taxonomic similarities among the strains were analyzed using the simple matching (S _SM) and Jaccard (S _J) coefficients, and the UPGMA clustering algorithm. The phylogenetic position of the strains was inferred by the neighbor-joining method on the basis of the 16S rDNA sequences. All isolates were Gram-negative, facultatively methylotrophic, oxidase and catalase positive, and required no growth factors. Based on the results of numerical taxonomy, the strains formed four closely related clusters sharing ≥85% similarity. Analysis of the 16S rDNA sequences demonstrated that oxalotrophic, pink-pigmented, and facultatively methylotrophic strains could be identified as members of the genus Methylobacterium. Except for M. variabile and M. aquaticum, all of the Methylobacterium type strains tested had the ability of oxalate utilization. Our results indicate that the capability of oxalate utilization seems to be an uncommon trait and could be used as a valuable taxonomic criterion for differentiation of Methylobacterium species.     

Microbial diversity of soil bacteria in agricultural field contaminated with heavy metals

In this study we evaluated the bacterial diversity in a soil sample from a site next to a chemical industrial factory previously contaminated with heavy metals. Analysis of 16S rDNA sequences amplified from DNA directly extracted from the soil revealed 17 different bacterial types （genera and/or species）. They included Polyangium spp., Sphingomonas spp., Variovorax spp., Hafina spp., Clostridia, Acidobacteria, the enterics and some uncultured strains. Microbes able to tolerate high concentrations of cadmium （500μmol/L and above） were also isolated from the soil. These isolates included strains of Acinetobacter （strain CD06）, Enterobacter sp. （strains CD01, CD03, CD04 and CD08） （similar strains also identified in culture-independent approach） and a strain of Stenotrophomonas sp. The results indicated that the species identified from direct analysis of 16S rDNA of the soil can be quite different from those strains obtained from enrichment cultures and the microbial activities for heavy metal resistance might be more appropriately addressed by the actual isolates.     

石油污染地下水中细菌多样性研究

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10个细菌类群,分别为γ-Proteobacteria(49.1%)、α-Proteobacteria(12.9%)、β-Proteobacteria(11.1%)、Bacteroidetes(9.2%)、Verrucomicrobia(6.7%)、Acidobacteria(2.5%)、δ-Proteobacteria(1.2%)、Actinobacteria(1.2%)、Planctomycetes(0.6%)、Unidentifiedbacteria(5.5%).在这一生态系统中,γ-Proteobacteria类细菌占据主导地位,接近50%,尤其是假单胞菌属(Pseudomonas)微生物在文库中的比例达35.6%.该石油污染地下水样品中细菌与许多其它已知的降解菌亲缘关系较近,如鞘胺醇单胞菌(Sphingomonas)、红球菌(Rhodococcus)和短波单胞菌(B...     

北极新奥尔松地区土壤及沉积物中可培养细菌多样性及分布特征分析

以2010年中国北极黄河站科学考察从新奥尔松地区采集的2个土壤和8个不同类型的沉积物样品为研究对象,采用分离培养方法及16S rRNA基因序列测定分析可培养细菌的多样性。对从10个站位分离出的343株细菌进行菌落特征分析,选取47株代表性细菌进行16S rRNA基因的分子鉴定并构建系统发育树,结果表明47株细菌归属于4个门,6个纲,18个属和29个种。在属水平上,芽孢杆菌纲细菌的多样性最为丰富,共6个属;在菌株数量上,γ-变形菌纲属于优势类群,共27株,分属于13个种。北极新奥尔松地区可培养细菌在海洋沉积物、湖泊沉积物、河流沉积物及土壤中的种属构成存在差异,其中海洋沉积物中细菌多样性最为丰富,而湖泊沉积物中细菌多样性次之。     

趋磁细菌的地域分布特征

通过对来自目前GenBank中趋磁细菌的16S rDNA序列分析,并进行系统进化树的构建,比较不同区域趋磁细菌的差异.目前,GenBank中共有239条趋磁细菌16S rDNA序列,相似性分析后有137条不同的序列(海洋55条,淡水82条),分属于变形菌门和硝化螺菌门.全长序列的系统进化分析显示,全球趋磁细菌的分布具有一定的区域性,海洋与淡水趋磁细菌区分明显.不同地域的趋磁细菌的系统进化分析显示,近海与大洋的趋磁细菌有明显的差别;而同为海洋或淡水的环境中,如巴西和美国近海、德国和中国的淡水湖泊,趋磁细菌相似性较高,即相同生境中的趋磁细菌相似性较高,表明趋磁细菌的类型与生境条件有很大关联性.基于16S rDNA序列分析,推测趋磁细菌起源可能是多源的,环境条件可能作为重要的进化压力在趋磁细菌长期演化过程中扮演重要角色.     

超声波促进好氧/缺氧污泥消化过程中细菌群落结构分析

应用基于16S rDNA的PCR-DGGE对超声波-好氧/缺氧污泥消化过程中微生物种群的多样性进行研究.通过SDS细胞裂解法提取不同时期污泥中的基因组DNA,采用通用引物进行V3区域PCR扩增,长约190 bp的PCR产物经DGGE分离后,获得污泥微生物群落的DNA特征指纹图谱,对条带进行切胶测序,使用序列数据进行同源性分析并建立系统发育树.DGGE图谱表明,在反应器运行的不同时期,微生物群落结构发生动态演替.5、10、15、20、25 d微生物相似性与0 d相比分别为61.2%、48.2%、46.4%、42.6%、41.7%,总细菌Shannon指数经历了一个从逐渐减少到趋于稳定的过程,这表明超声波改变污泥内部性质,导致微生物多样性的降低.UPGMA聚类分析将DGGE图谱区分为三大族群并对应于不同运行时期.测序结果表明,超声波-好氧/缺氧污泥消化中微生物群落主要为Firmicute、Genuscitrobacter、Bacilli、α-Proteobacteria、β-Proteobacteria.     

Shinella zoogloeoides BC026对吡啶的降解特性研究

从首钢焦化厂的污水处理系统中分离1株能以吡啶为唯一碳、氮源的细菌BC026,它具有自絮凝特性,对卡那霉素、氨苄青霉素和壮观霉素具有抗性,可在阿须贝无氮培养基中良好生长.通过16S rRNA序列分析和Biolog微生物鉴定系统鉴定,确定该菌为Shinella zoogloeoides.纯菌对单基质的降解实验表明,在30℃、180 r/min和pH为7的条件下,当投菌量为0.1 g/L时,BC026可在17 h内将400 mg/L吡啶完全降解;在吡啶初始浓度为99～1 806 mg/L的无机盐培养基中,BC026均能保持降解活性,较高初始浓度的吡啶对BC026的生长产生一定抑制,但BC026在适应后对吡啶的降解速率较快;降解最适温度为30～35℃,最适pH为8.BC026对吡啶的代谢途径研究表明：降解的第一步是断开吡啶的2条C—N链,生成氨氮和戊二醛,随后戊二醛被氧化为戊二酸,并最终转化为二氧化碳和水;吡啶中的氮有59.5%转化成氨氮.     

PCR-DGGE分析啤酒废水生物处理工艺的微生物区系

应用基于16s rDNA的PER-DGGE(变性梯度凝胶电泳)技术对啤酒废水"水解酸化 SBR"工艺的微生物多样性进行研究.分别取水解酸化池与SBR池中不同深度以及不同处理时段的活性污泥,提取样品总DNA,通过PER扩增、变性梯度凝胶电泳,将16S rDNA(V3区)的PER扩增片段割胶克隆测序确定样品中的微生物群落,与筛选出的高效菌株进行对比分析.结果表明,水解酸化池中的微生物群落随深度的改变,在结构组成和种群数量上均有较大差异,2 m深处微生物群落相对丰富,优势条带突出;SBR池不同深度微生物种群结构一致,沉淀期、进水期和曝气期不同处理时段的微生物种类一致,但优势菌群不同;所测序列v2、23、25、31、h5和15号分别与菌株uncultured Thermotogales sp.Comamonas sp.WT OTU1、Agrobaaerium tumefaciens、Bacillus subtilis、Bdellovibrio bacteriovorus、Comamonas testosteroni有高度同源性,活性污泥样品中的优势条带与高效菌株的序列不同,表明筛选出的高效菌并非为实际处理过程中的优势菌.     

Characterization and phylogenetic analysis of a phenanthrene-degrading strain isolated from oil-contaminated soil

Bacterium strain EVA17 was isolated from an oil-contaminated soil, and identified as Sphingomonas sp.based on analysis of 16S rDNA sequence, cellular fatty acid composition and physiological-chemical tests. The salicylate hydroxylase and catechol 2, 3-dioxygenase (C23O) were detected in cell-free lysates, suggesting a pathway for phenanthrene catabolism via salicylate and catechol. Alignment showed that both of the C23O and GST genes of the strain EVA17 had high similarity with homologues of strains from genus Sphingomonas. The phylogenetic analysis based on 16S rDNA and C23O gene sequence indicated that EVA17 should be classified into genus Sphingomonas, although the two phylogenetic trees were slightly different from each other. The results of co-amplification and sequence determination indicated that GST gene should be located upstream of the C230 gene.     

饮用水深度处理活性炭池中微生物群落分布研究

采集2种炭龄饮用水深度处理活性炭池表面生物膜,提取微生物总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,5 a炭龄炭样克隆文库中阳性克隆的16S rDNA序列分属11个细菌类群,分别为α-Proteobacteria(26....     

北部湾卡盾藻(Chattonella spp.)种类鉴定

2018年9月在北部湾海域分离得到3株卡盾藻,采用光学显微镜对其进行形态学初步鉴定,并通过核糖体大亚基LSU rDNA和ITS基因进行系统进化分析。结果表明,卡盾藻北部湾株符合海洋卡盾藻形态学典型特征:藻体黄褐色,细胞呈纺锤形,无黏液泡,尾部具尖端,细胞平均长（57.8±9.1）μm。系统发育树上北部湾卡盾藻分别以96%（LSU rDNA）和99%（ITS）的自展支持率与不同来源的海洋卡盾藻、古老卡盾藻、卵圆卡盾藻、小型卡盾藻聚在同一大分支上。通过遗传距离分析发现,北部湾3株卡盾藻与不同来源的海洋卡盾藻、古老卡盾藻、卵圆卡盾藻、小型卡盾藻亲缘关系较近,LSU和ITS遗传距离分别为0.0000~0.0016和0.0000~0.0235;而与盐生卡盾藻亲缘关系较远,遗传距离分别为0.0415~0.0490和0.0733~0.0750。因此,综合形态学和分子生物学结果可以确定北部湾3株卡盾藻为海洋卡盾藻/海洋卡盾藻的变种。研究结果可为我国卡盾藻藻华藻种库的构建和卡盾藻北部湾株生理生态学的研究提供基础数据。     

祁连山七一冰川及融水中细菌多样性的研究

通过荧光显微镜测定细菌密度,利用分离培养和16S rDNA序列分析细菌种类多样性,对祁连山七一冰川雪及融水中的细菌数量和多样性进行了研究.结果表明,七一冰川雪及融水中微生物总数为103~105cells.mL-1,可培养细菌数为0~600cfu.mL-1.恢复出的22株不同种类的细菌隶属于Bacteroidetes、Actinobacteria、Firmicutes和a,β,γ-Proteobacteria共6个类群,其中Bacteroidetes占总类群的80%,为优势类群;Pedobacter和Pseudomonas属为优势菌,占可培养细菌数量的90%.与青藏高原、南北极冰雪中微生物的比较分析发现Pantoea、Providencia、Terrabacter及Aerococcus这4个属和Oxalobacteraceae细菌是七一冰川的地方种类,在其它低温环境中未被发现.     

高温菌的生理生化及其16S rDNA序列分析

利用高温菌耐热嗜热的特性和有机物好氧分解的基本原理,从厨余垃圾处理系统中分离筛选到6株在65℃能产生淀粉酶、脂肪酶、蛋白质酶及纤维素酶的高温高效菌种,并对其生理生化和16S rDNA进行了分析。结果表明:筛选出的6株高温菌,经鉴定都有芽孢,并具有兼氧性;对其进行16S rDNA区段序列测定显示,6株高温菌属于Geobacillus thermog lucosidasius菌种中的不同亚种;分离筛选出的高温菌经过2h的迟缓期后很快进入对数生长期,且持续时间较长,生长速度尤以HB6最快;6株高温菌株全部具有淀粉、纤维素、蛋白质降解活性,5株有脂肪降解活性。可见高温菌具有更高的有机物降解活性和更快的代谢速率,可提高有机物质的降解速率,缩短工艺运行时间,有利于工业化生产,在厨余资源化利用上具有广泛的应用前景。     

青藏铁路沿线土壤可培养微生物种群多样性分析

选择青藏铁路沿线不同海拔高度的10个地点采集土壤样品,采用3种不同的培养基分离培养其中的微生物;提取各土壤样品可培养微生物菌体基因组DNA,进行16S rDNA的PCR扩增,对可培养微生物种群多样性进行分析.结果表明,该地区可培养微生物的数量为1×106～8×106 CFU/g.16S rDNA序列分析发现,分离培养的微生物主要包括厚壁菌门(Firmicutes)、放线菌门(Actinobacteria)和变形菌门γ亚群(Gammaproteobacteria) 3个类群,分别占菌株总数的53.1%,29.6%和16.0%.其中,Bacillus sp.为优势菌属,占菌株总数的29.6%;Bacillus simplex为优势种,占菌株总数的12.3%.      

Phylogenetic diversity and specificity of bacteria associated with Microcystis aeruginosa and other cyanobacteria

Interactions between bacteria and cyanobacteria have been suggested to have a potential to influence harmful algal bloom dynamics; however, little information on these interactions has been reported. In this study, the bacterial communities associated with five strains of Microcystis aeruginosa, three species of other Microcystis spp., and four representative species of non-Microcystis cyanobacteria were compared. Bacterial 16S rDNA fragments were amplified and separated by denaturing gradient gel electrophoresis (DGGE) followed by DNA sequence analysis. The similarities among bacterial communities associated with these cyanobacteria were compared to the digitized DGGE profiles using the cluster analyses. The bacterial community structure of all cyanobacterial cultures di ered. Cluster analysis showed that the similarity values among M. aeruginosa cultures were higher than those of other cyanobacterial cultures. Sequence analysis of DGGE fragments indicated the presence of bacteria including, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacteroidetes and Actinobacteria in the cyanobacterial cultures. Members of the Sphingomonadales were the prevalent group among the Microcystis-associated bacteria. The results provided further evidence for species-specific associations between cyanoabcteria and heterotrophic bacteria, which are useful for understanding interactions between Microcystis and their associated bacteria.     

抚顺西露天油页岩可培养微生物的分离与鉴定

为了解油页岩中可培养微生物的多样性,利用稀释平板培养法对我国抚顺盆地西露天组油页岩中可培养微生物进行分离纯化,并对所获菌株进行16S rDNA(细菌)和rDNA ITS(真菌)序列测定和系统发育树分析.以营养琼脂培养基分离到8株细菌,以马铃薯葡萄糖琼脂培养基分离到4株真菌.16S rDNA序列测定结果表明细菌菌株属于芽孢杆菌属(Bacillus),赖氨酸芽孢杆菌属(Lysinibacillus),短杆菌属(Brevibacillus),类芽胞杆菌属(Paenibacillus)和红球菌属(Rhodococcus); rDNA ITS序列测定结果显示真菌菌株分别属于芽枝霉属(Cladosporium),曲霉属(Aspergillus),犁头霉属(Absidia)和正青霉属(Eupenicillium). 2株细菌(ZK4和ZK5)能够在以油页岩为唯一碳源和氮源的固体培养基上连续生长5代以上,且长势良好, 可作为油页岩生物转化的潜力菌株进行深入研究.     

三株寡养单胞菌对苯噻草胺的降解及系统发育分析

从污水处理厂好氧活性污泥中分离和纯化到3个能降解苯噻草胺的细菌菌株。这些菌株均为革兰氏阴性、好氧、不形成芽孢的杆菌。根据其形态特征、生理生化性状和16SrDNA序列分析结果表明。分离菌株Y2、Y3和Y5均为寡养单胞菌（stenotrophomonas spp．）。     

Bacterial diversity in soils around a lead and zinc mine

Five samples of soil collected from a lead and zinc mine were used to assess the effect of combined contamination of heavy metals on soil bacterial communities using a polyphasic approach including characterization of isolates by culture method, community level catabolic profiling in BIOLOG GN microplates, and genetic community fingerprinting by denaturing gradient gel electrophoresis of 16S rDNA fragments amplified by PCR from community DNA （PCR-DGGE）. The structure of the bacterial community was affected to a certain extent by heavy metals. The PCR-DGGE analysis of 16S rRNA genes showed that there were significant differences in the structure of the microbial community among the soil samples, which were related to the contamination levels. The number of bacteria and the number of denaturing gradient gel electrophoresis （DGGE） bands in the soils increased with increasing distance from the lead and zinc mine tailing, whereas the concentration of lead （Pb） and cadmium （Cd） was decreased. Heavily polluted soils could be characterized by a community that differs from those of lightly polluted soils in richness and structure of dominating bacterial populations. The clustering analysis of the DGGE profiles showed that the bacteria in all the five samples of soil belonged to three clusters. The data from the BIOLOG analysis also showed the same result. This study showed that heavy metal contamination decreased both the biomass and diversity of the bacterial community in soil.     

啤酒废水处理系统高效菌株的分离筛选与分析

从啤酒废水处理系统SBR池中取得的水样,分离纯化得到菌株35株,分别以进站原水和水解酸化池出水作为污水培养基,进行COD降解试验,复筛后分别得到3株COD降解率高且降解效果稳定的细菌12#,15#,23#与15#,25#,31#。将高效菌株与SBR池的活性污泥混合,考察其对啤酒废水的处理效果,结果表明,23#与活性污泥交互作用时在原水污水培养基中摇床培养16h COD降解率达到75.13%;25#与活性污泥交互作用处理水解酸化池出水120h时降解率达到82.40%。对4株高效菌株15#,23#,25#,31#进行16S rDNA序列测定,将所得序列与GenBank中已登录的相近细菌种群的DNA序列对比,得到高度同源性的细菌菌种。     

PCR-DGGE研究处理垃圾渗滤液序批式生物膜反应器(SBBR)中的细菌多样性

为了研究序批式生物膜反应器中的细菌多样性及其脱氮的微生物学机理,为工艺改进提供依据,从同步高效去除垃圾渗滤液中高氨氮和高COD的SBBR生物膜和渗滤液原水中采集微生物样品并提取微生物总DNA,使用细菌通用引物对（GC341F/907R）从总DNA中成功扩增出目标16S rDNA片段,然后对扩增的16S rDNA进行DGGE,对凝胶染色并进行条带统计分析和切胶测序,使用序列数据进行同源性分析并建立了系统发育树.结果表明,该驯化后的SBBR生物膜和渗滤液原水中都有比较丰富的细菌多样性,驯化的生物膜细菌主要来自渗滤液原水,而且生物膜细菌在反应器正常运行时不会出现明显的群落结构变化;在该SBBR中有多种硝化细菌与反硝化细菌、好氧反硝化细菌和厌氧氨氧化细菌共存,说明该反应器中可能同时存在全程硝化反硝化、同步硝化反硝化和厌氧氨氧化3种脱氮方式.研究结果为SBBR脱氮微生物机理研究提供了一些有价值的参考依据.