念珠藻属植物hetR基因的适应性进化分析

以念珠藻属(Nostoc)及其近缘类群hetR基因的51条序列为研究对象,对hetR基因的编码蛋白进行生物信息学分析和系统发育分析,并使用分支模型、位点模型和分支-位点模型进行该基因位点的适应性进化研究。系统发育分析结果显示,51条hetR基因蛋白序列可分为4个大分支。适应性进化分析结果表明,在3种进化模型中,大多数分支及藻株都没有检测到统计学上具有显著性的正选择位点,说明检测的位点大多处于负选择压力下。但在普通念珠藻(Nostoc commune,CHAB2802)中检测到正选择位点(126T),提示念珠藻属植物hetR基因发生了适应性改变。     

洱海的浮游蓝藻布氏常丝藻及其分类学的讨论

常丝藻(Tychonema)是1988年由Anagnostidis和Komárek从颤藻属分离出来而新成立的蓝藻属,以纤细常丝藻(T.tenue)为模式种类。目前确认的常丝藻有纤细常丝藻、博多常丝藻(T.bornetii)和布氏常丝藻(T.bourrellyi)三个种类。我国已经有博多常丝藻的纪录,但是对模式种纤细常丝藻和它的相似种类布氏常丝藻却没有报道。在洱海中采集到布氏常丝藻(T.bourrellyi),研究并描述了该藻的藻丝颜色、藻细胞内含物的结构、藻体形态特征等。同时,通过藻种的分离培养技术,得到了布氏常丝藻的纯培养藻株,编号为CHAB663,并且测定了藻株的16S rRNA基因序列。测序结果表明,该藻株与T.bouurrellyi/T.tenue聚为一族。洱海分布的布氏常丝藻,是在欧洲以外首次发现此种藻类,也是我国的新纪录种。研究说明布氏常丝藻不仅仅分布在温带欧洲较为寒冷的水体中,在亚热带的水体中也可以存在。布氏常丝藻被认为是出现在轻微富营养化湖泊中,而我国洱海也被认为是富营养化的初级阶段的水体,这也表明,布氏常丝藻的出现对洱海的水环境状况起到了指示作用。此外,研究还对常丝藻属分类学问题进行了讨论。     

我国沿海拟菱形藻属的2新记录种及其产毒特征分析

为澄清我国沿海拟菱形藻属(Pseudo-nitzschia)的物种多样性,并确认中国海域拟菱形藻属是否具有产生多莫酸(Domoicacid)的能力,采用毛细管显微操作技术从我国沿海水体中分离、纯化拟菱形藻细胞,建立了单克隆培养株系,并基于核糖体转录间隔区ITS1-5.8S-ITS2 序列构建了分子系统树。结果表明,结合在光学显微镜和透射电镜下观察的形态学特征和分子系统发育分析数据,鉴定到我国拟菱形藻属的2新记录种:银河拟菱形藻(P. galaxiae Lundholm & Moestrup)和微孔拟菱形藻(P. micropora Priisholm, Moestrup & Lundholm),对其形态学特征进行了详细描述,并与相似种类进行了比较研究。利用高效液相色谱(HPLC)技术对多莫酸特征进行了检测,结果表明培养株系并不产生多莫酸。这些为我国拟菱形藻属物种多样性和产毒特征研究提供了基础数据。     

淡水刚毛藻目一新组合种及其系统发育分析

作者于2012-2014年先后在湖北省采集到4株刚毛藻目的丝状绿藻。经鉴定,其形态特征和莫拉瓦刚毛藻Cladophora moravica Gardavsk(1986)非常相似;但相较于刚毛藻属各个种的形态,4株藻体更接近黑孢藻科的分类特征。基于SSU和LSU rDNA序列构建的系统发育树显示,4株刚毛藻目的丝状绿藻均属于黑孢藻科拟湖球藻属(Aegagropilopsis)。据此,作者建议将该种名称作为一个新组合处理,即莫拉瓦拟湖球藻Aegagropilopsis moravica(Dvoˇrák)Zhao et Liu com.nov。拟湖球藻属仅含有3个种:莫拉瓦拟湖球藻、硬枝拟湖球藻和棒状拟湖球藻,其形态特征与湖球藻相近且易混淆,故采用核基因组序列分析方法区分二者是非常有效的。     

云南色球藻科新分类群

在对云南石林国家级风景区碳酸盐岩表面的气生蓝藻类进行研究时,发现色球藻科中的1个新 种和3个新变种。其中石林肾胞藻是中国特有属——肾胞藻属中至今发现的第2个种;3个变种均属于星球藻属。     

华北太行山北段高于庄组微古植物的新发现

长城群高于庄组主要分布于我国华北地区,地质年龄约在14－16亿年。主要描述了华北太行山北段灵邱县境内高于组白云岩中的层状和扁豆状透镜体燧石及穹隆式叠层石的黑色燧石中的颤藻、念珠藻和色球藻植物的8个新种和3个未定种,其中还有两个新修订属。这些新的促群再加上前人在高于庄组地层中已报道的汇成了近100个种生物组合,进一步证明高于庄组地地球上中元代微化石类群最丰富的产地之一。以下是该 新发现和新修订的分类类群：颤藻科（Oscillatoriaceae): Eophormkidium orculiformis sp. nov., E. sp., Siphonophycus caudataceous sp. nov., Palaeolyngbya complanata sp. nov., P. capitata sp. nvo., P. sp., Oscilaltoriopsis sp.;念珠藻科（Nosto-caceae):Veteronostiocale vaginata sp.nov.;色球藻科（Chroococcaceae):Maculosphaera giganta sp.nov.,Gloeotheceopsis grandis sp.nov.;分类位置未定的类群：Myxococcoides limpida sp.nov.。     

囊裸藻属与陀螺藻属囊壳微细结构及元素组成比较

对采自自然水体中囊裸藻属(Trachelomonas)的8种和陀螺藻属(Strombomonas)的两种藻类的囊壳微细结构和元素组成进行了比较分析,并探讨了这两个属的系统演化关系。结果表明：组成囊壳的矿质元素主要是铁和硅,在陀螺藻和表面粗糙的囊裸藻中,硅的含量较高,铁的含量相对较低;在大多数囊裸藻中,尤其是表面致密、光滑的种类中,铁的含量较高,硅的含量较低,矿质元素的组成与囊壳的颜色无直接关系。建议将陀螺藻属(Strombomonas)撤消,原陀螺藻属的种作为囊裸藻属(Trachelomonas)中的一个种组(Group),它们是裸藻科中最原始的具囊壳的类群。     

囊裸藻属与陀螺藻属囊壳微细结构及元素组成比较

对采自自然水体中囊裸藻属(Trachelomonas)的8种和陀螺藻属(Strombomonas)的两种藻类的囊壳微细结构和元素组成进行了比较分析,并探讨了这两个属的系统演化关系.结果表明:组成囊壳的矿质元素主要是铁和硅,在陀螺藻和表面粗糙的囊裸藻中,硅的含量较高,铁的含量相对较低;在大多数囊裸藻中,尤其是表面致密、光滑的种类中,铁的含量较高,硅的含量较低,矿质元素的组成与囊壳的颜色无直接关系.建议将陀螺藻属(Strombomonas)撤消,原陀螺藻属的种作为囊裸藻属(Trachelomonas)中的一个种组(Group),它们是裸藻科中最原始的具囊壳的类群.     

我国鱼腥藻的新记录种——粘质鱼腥藻

蓝藻是淡水水体的重要组成类群,而鱼腥藻又是水华蓝藻的一个重要种属.但由于该属种类较多,国内文献报导的不到世界分布的四分之一.该文利用染色和显微镜镜检方法对采自广东省高州水库蓝藻水华的样品进行观察,经鉴定,确认一个我国鱼腥藻属的新记录种--粘质鱼腥藻Anabaena mucosa, J. Komarkova-Legnerova & P. Eloranta ,1992 .对该属及该属一个新记录种的主要形态学特征进行了描述,提供了相应的形态照片,并对相似种进行了形态学比较研究.     

鄱阳湖的中国水华蓝藻新记录属气丝藻属

2012年4月和10月在江西省鄱阳湖进行野外调查时, 发现一种浮游的丝状蓝藻。通过分离纯培养, 获得了6个纯化藻株。根据藻株主要形态学特征及其16S rRNA基因序列与比较, 鄱阳湖这些藻株与老挝的2株Aerosakkonema funiforme较为相近, 其中16S rRNA基因序列的相似度达到98%。鉴于这些藻株不同于颤藻目中其他属的藻株, 因此确定为我国一水华蓝藻新记录属气丝藻属Aerosakkonema Nanda Watanabe 2012, 模式种为索状气丝藻Aerosakkonema funiforme Nanda Watanabe 2012。       

Gene transfer to the desiccation-tolerant cyanobacterium Chroococcidiopsis

The coccoid cyanobacterium Chroococcidiopsis dominates microbial communities in the most extreme arid hot and cold deserts. These communities withstand constraints that result from multiple cycles of drying and wetting and/or prolonged desiccation, through mechanisms which remain poorly understood. Here we describe the first system for genetic manipulation of Chroococcidiopsis. Plasmids pDUCA7 and pRL489, based on the pDU1 replicon of Nostoc sp. strain PCC 7524, were transferred to different isolates of Chroococcidiopsis via conjugation and electroporation. This report provides the first evidence that pDU1 replicons can be maintained in cyanobacteria other than Nostoc and Anabaena. Following conjugation, both plasmids replicated in Chroococcidiopsis sp. strains 029, 057, and 123 but not in strains 171 and 584. Both plasmids were electroporated into strains 029 and 123 but not into strains 057, 171, and 584. Expression of P(psbA)-luxAB on pRL489 was visualized through in vivo luminescence. Efficiencies of conjugative transfer for pDUCA7 and pRL489 into Chroococcidiopsis sp. strain 029 were approximately 10(-2) and 10(-4) transconjugants per recipient cell, respectively. Conjugative transfer occurred with a lower efficiency into strains 057 and 123. Electrotransformation efficiencies of about 10(-4) electrotransformants per recipient cell were achieved with strains 029 and 123, using either pDUCA7 or pRL489. Extracellular deoxyribonucleases were associated with each of the five strains. Phylogenetic analysis, based upon the V6 to V8 variable regions of 16S rRNA, suggests that desert strains 057, 123, 171, and 029 are distinct from the type species strain Chroococcidiopsis thermalis PCC 7203. The high efficiency of conjugative transfer of Chroococcidiopsis sp. strain 029, from the Negev Desert, Israel, makes this a suitable experimental strain for genetic studies on desiccation tolerance.     

<Emphasis Type="Italic">Arthrobacter soli</Emphasis> sp. nov., a novel bacterium isolated from wastewater reservoir sediment

A novel Gram-positive bacterium, designated SYB2T, was isolated from wastewater reservoir sediment, and a polyphasic taxonomic study was conducted based on its morphological, physiological, and biochemical features, as well as the analysis of its 16S rRNA gene sequence. During the phylogenetic analysis of the strain SYB2T, results of a 16S rRNA gene sequence analysis placed this bacterium in the genus Arthrobacter within the family Micrococcaceae. SYB2T and Arthrobacter protophormiae ATCC 19271T, the most closely related species, both exhibited a 16S rRNA gene sequence similarity of 98.99%. The genomic DNA G+C content of the novel strain was found to be 62.0 mol%. The predominant fatty acid composition was anteiso-C15:0, anteiso-C17:0, iso-C16:0, and iso-C15:0. Analysis of 16S rRNA gene sequences and DNA-DNA relatedness, as well as physiological and biochemical tests, showed genotypic and phenotypic differences between strain SYB2T and other Arthrobacter species. The type strain of the novel species was identified as SYB2T (= KCTC 19291T= DSM 19449T).     

A bridge too far in naming species: a total evidence approach does not support recognition of four species in Desertifilum (Cyanobacteria)

A population of Desertifilum (Cyanobacteria, Oscillatoriales) from an oligotrophic desertic biotope was isolated and characterized using a polyphasic approach including molecular, morphological, and ecological information. The population was initially assumed to be a new species based on ecological and biogeographic separation from other existing species, however, phylogenetic analyses based on sequences of the 16S rRNA gene and 16S–23S ITS region, placed this strain clearly within the type species, Desertifilum tharense. Comparative analysis of morphology, 16S rRNA gene similarity, 16S–23S ITS secondary structure, and percent dissimilarity of the ITS regions for all characterized strains supports placing the six Desertifilum strains (designated as PD2001/TDC17, UAM‐C/S02, CHAB7200, NapGTcm17, IPPAS B‐1220, and PMC 872.14) into D. tharense. The recognition of Desertifilum salkalinema and Desertifilum dzianense is not supported, although our analysis does support continued recognition of Desertifilum fontinale. Pragmatic criteria for recognition of closely related species are proposed based on this study and others, and more rigorous review of future taxonomic papers is recommended.     

Hydrogen metabolism of the unicellular cyanobacterium Chroococcidiopsis thermalis ATCC29380

Abstract Hydrogenase was induced in the unicellular cyanobacterium Chroococcidiopsis thermalis ATCC29380 when grown aerobically in a medium lacking combined nitrogen. Nitrogenase, however, was only observed after incubation of cells in a microaerobic environment. Hydrogen evolution could not be detected under aerobic conditions, but upon transfer of cells to dark anaerobic conditions, large amounts of hydrogen were immediately produced. This hydrogen evolution was sensitive to light and oxygen but not to inhibitors of protein synthesis. The enzyme activity catalyzing the formation of hydrogen was not membrane-bound; some functional properties were characterized in cell-free extracts.     

Streptacidiphilus jiangxiensis sp. nov., a novel actinomycete isolated from acidic rhizosphere soil in China

The taxonomic position of three acidophilic actinomycetes isolated from acidic rhizosphere soil was established using a polyphasic approach. The morphological and chemical properties of the isolates were found to be consistent with their assignment to the genus Streptacidiphilus. Almost complete 16S rRNA gene sequences determined for the strains were aligned with corresponding sequences of representatives of the genera Kitasatospora, Streptacidiphilus and Streptomyces and phylogenetic trees inferred using three tree-making algorithms. The organisms formed a distinct subclade within the Streptacidiphilus 16S rRNA gene tree. They also shared nearly identical phenotypic profiles and rep-PCR fingerprint patterns that readily distinguished them from representatives of the established species of Streptacidiphilus. It is evident from the genotypic and phenotypic data that the three isolates form a new species in the genus Streptacidiphilus. The name proposed for this new species is Streptacidiphilus jiangxiensis, the type strain is isolate 33214T (= AS 4.1857T = JCM 12277T).     

Use of rpoB gene analysis for identification of nitrogen-fixing Paenibacillus species as an alternative to the 16S rRNA gene

AIM: To avoid the limitations of 16S rRNA-based phylogenetic analysis for Paenibacillus species, the usefulness of the RNA polymerase beta-subunit encoding gene (rpoB) was investigated as an alternative to the 16S rRNA gene for taxonomic studies. METHODS AND RESULTS: Partial rpoB sequences were generated for the type strains of eight nitrogen-fixing Paenibacillus species. The presence of only one copy of rpoB in the genome of P. graminis strain RSA19(T) was demonstrated by denaturing gradient gel electrophoresis and hybridization assays. A comparative analysis of the sequences of the 16S rRNA and rpoB genes was performed and the eight species showed between 91.6-99.1% (16S rRNA) and 77.9-97.3% (rpoB) similarity, allowing a more accurate discrimination between the different species using the rpoB gene. Finally, 24 isolates from the rhizosphere of different cultivars of maize previously identified as Paenibacillus spp. were assigned correctly to one of the nitrogen-fixing species. CONCLUSIONS, SIGNIFICANCE AND IMPACT OF THE STUDY: The data obtained in this study indicate that rpoB is a powerful identification tool, which can be used for the correct discrimination of the nitrogen-fixing species of agricultural and industrial importance within the genus Paenibacillus.     

Evolutionary relationships among members of the genus Chlamydia based on 16S ribosomal DNA analysis.

Nucleotide sequences from strains of the four species currently in the genus Chlamydia, C. pecorum, C. pneumoniae, C. psittaci, and C. trachomatis were investigated. In vitro-amplified RNA genes of the ribosomal small subunit from 30 strains of C. pneumoniae and C. pecorum were subjected to solid-phase DNA sequencing of both strands. The human isolates of C. pneumoniae differed in only one position in the 16S rRNA gene, indicating genetic homogeneity among these strains. Interestingly, horse isolate N16 of C. pneumoniae was found to be closely related to the human isolates of this species, with a 98.9% nucleotide similarity between their 16S rRNA sequences. The type strain and koala isolates of C. pecorum were also found to be very similar to each other, possessing two different 16S rRNA sequences with only one-nucleotide difference. Furthermore, the C. pecorum strains truncated the 16S rRNA molecule by one nucleotide compared to the molecules of the other chlamydial species. This truncation was found to result in loss of a unilaterally bulged nucleotide, an attribute present in all other eubacteria. The phylogenetic structure of the genus Chlamydia was determined by analysis of 16S rRNA sequences. All phylogenetic trees revealed a distinct line of descent of the family Chlamydiaceae built of two main clusters which we denote the C. pneumoniae cluster and the C. psittaci cluster. The clusters were verified by bootstrap analysis of the trees and signature nucleotide analysis. The former cluster contained the human isolates of C. pneumoniae and equine strain N16. The latter cluster consisted of C. psittaci, C. pecorum, and C. trachomatis. The members of the C. pneumoniae cluster showed tight clustering and strain N16 is likely to be a subspecies of C. pneumoniae since these strains also share some antigenic cross-reactivity and clustering of major outer membrane protein gene sequences. C. psittaci and strain N16 branched early out of the respective cluster, and interestingly, their inclusion bodies do not stain with iodine. Furthermore, they also share less reliable features like normal elementary body morphology and plasmid content. Therefore, the branching order presented here is very likely a true reflection of evolution, with strain N16 of the species C. pneumoniae and C. psittaci forming early branches of their respective cluster and with C. trachomatis being the more recently evolved species within the genus Chlamydia.     

16S rRNA gene and 16S-23S rRNA gene internal transcribed spacer sequences analysis of the genus Myxococcus.

Phylogenetic relationships of the species belonging to the genus Myxococcus were elucidated based on the sequences of 16S rRNA genes and 16S-23S rRNA gene internal transcribed spacer (ITS) regions. The Myxococcus species were consequently classified into four distinct groups. The type strain of Myxococcus coralloides occupied an independent position (Group 1); it has been recently reclassified as Corallococcus coralloides. Group 2 comprised the type strains of both Myxococcus virescens and Myxococcus xanthus, and some strains assigned to Myxococcus flavescens. The type strain of M. flavescens was contained in Group 3 along with the strains of Myxococcus fulvus. Group 4 included the strains belonging to C. coralloides, M. fulvus, and M. stipitatus. The type strain of M. fulvus that was allocated outside Group 4 in the 16S rRNA gene tree belonged to Group 3 in the ITS tree. These results strongly suggest that the morphological characteristics of Myxococcus species are not consistent with the phylogenetic relationships. The Myxococcus species must therefore be redefined according to the phylogenetic relationships revealed in this study.     

8种贵州药用植物内生放线菌的分离及多样性研究

【背景】药用植物内生菌能产生多种活性较好的次级代谢产物,是新抗生素发现的重要来源。目前,药用植物内生菌的研究主要集中在内生真菌,内生放线菌研究相对较少,是一个尚未充分开发的新领域。【目的】研究贵州药用植物内生放线菌多样性,以期发现新种放线菌或产新活性物质的放线菌,为微生物药物研究奠定基础。【方法】药用植物样品表面消毒后用粉碎机粉碎,采用9种不同分离培养基分离放线菌;通过提取放线菌基因组DNA,PCR扩增16S rRNA基因序列,测定序列并提交EzBioCloud数据库进行序列比对,构建系统进化树,进行内生放线菌多样性分析。【结果】通过形态特征初步排重,从8种药用植物样品中共分离得到内生菌62株,测定其16S rRNA基因序列,序列比对结果表明其中的57株菌分布于放线菌域的5目8科16属,分别是短小杆菌属(Curtobacterium)、链霉菌属(Streptomyces)、微杆菌属(Microbacterium)、纤维单胞菌属(Cellulomonas)、植物杆菌属(Plantibacter)、原小单孢菌属(Promicromonospora)、动球菌属(Kineococcus)、壤球菌属(Agrococcus)、沼杆菌属(Patulibacter)、气微菌属(Aeromicrobium)、拉贝达氏菌属(Labedella)、叶居菌属(Frondihabitans)、冷杆菌属(Frigoribacterium)、节杆菌属(Arthrobacter)、动孢菌属(Kineosporia)、Amnibacterium属,其中短小杆菌属(Curtobacterium)为优势菌属,菌株M8JJ-5和M2KJ-4的16S rRNA基因序列分别与有效发表菌株AmnibacteriumkyonggienseKSL51201-037T(FJ527819)和Aeromicrobiumfastidiosum DSM10552T (Z78209)的相似性最高,相似性分别为97.29%和98.95%,可能为潜在新物种。【结论】贵州药用植物中蕴藏着多样性丰富的放线菌且具有从中发现新放线菌的潜力,能为新抗生素的发现提供菌种储备,也为今后对该地区放线菌资源的认识和开发利用提供理论依据。