The identification of vahlkampfiid amoebae by ITS sequencing

We have determined the internal transcribed spacer (ITS) sequences (including the 5.8S ribosomal DNA) of 30 strains of 14 species belonging to eight vahlkampfiid genera. Each previously described species has a specific ITS sequence, except for Tetramitus aberdonicus, Tetramitus thorntoni, and Tetramitus jugosus, which have identical ITS sequences. The latter three may therefore constitute a single species despite their apparent phenotypic differences. The ITS sequence appears to be conserved within a species. The species Willaertia magna appears to be ubiquitous. The 5.8S rDNA sequences of Singhamoeba horticola and Learamoeba waccamwensis indicate that they do not represent different genera, but both belong to the genus Tetramitus. The ITS sequences of 16 undescribed vahlkampfiid isolates were determined. Based on these sequences, seven isolates were identified as belonging to described species, while nine probably represent seven new species. Five of these presumed new species belong to the genus Tetramitus, and one each to the genera Vahlkampfia and Paravahlkampfia.     

基于28S rDNA D2基因片段与形态特征的矛茧蜂亚科系统发育研究（膜翅目：茧蜂科）

本研究选取矛茧蜂亚科Doryctinae（昆虫纲Insecta：膜翅目Hymenoptera：茧蜂科Braconidae）的6族15属18种做内群,茧蜂科其它7亚科11属11种做外群,首次结合同源核糖体28S rDNA D2基因序列片段和100个形态学和解剖学特征对该亚科进行了系统发育学研究。利用“非圆口类"的小腹茧蜂亚科Microgastrinae为根,以PAUP*4.0和MrBayes 3.0B4软件分别应用最大简约法（MP）和贝叶斯法对矛茧蜂亚科的分子数据和分子数据与非分子数据的结合体进行了运算分析;并以PAUP*4.0对矛茧蜂亚科的28S rDNA D2基因序列片段的碱基组成与碱基替代情况进行了分析。结果表明：矛茧蜂亚科的28S rDNA D2基因序列片段的GC含量在39.33%～48.28%之间变动,而对于碱基替代情况来讲,矛茧蜂亚科各成员间序列变异位点上颠换（transversion）大于转换（transition）。不同的分析算法所产生的系统发育树都表明矛茧蜂亚科是一个界限分明的单系群;在矛茧蜂亚科内,除了吉丁茧蜂族Siragrini为单系群外,其他族（矛茧蜂族Doryctini和方头茧蜂族Hecabolini）都是并系群。对于矛茧蜂亚科内各属之间的相互亲缘关系,不同算法所得的系统发育树的拓扑结构不完全一致,表明矛茧蜂亚科内（属及族）的系统发育关系还有待于进一步研究。     

基于16S rDNA和28S rDNA D2基因序列与形态特征联合分析的中国角顶叶蝉亚科系统发育研究（半翅目： 叶蝉科）

首次在国内利用28S rDNA D2区段和16S rDNA基因序列,结合50个形态特征对角顶叶蝉亚科(Deltocephalinae)［半翅目（Hemiptera）: 叶蝉科（Cicadellidae）］19个属进行系统发育分析研究。从无水乙醇浸泡保存的标本中提取基因组DNA并扩增了19个内群和1种外群Typhlocybinae［半翅目(Hemiptera): 叶蝉科(Cicadellidae)］种类的28S rDNA D2基因片段并测序,同时扩增了16S rDNA基因片段并测序11条,采用了GenBank中1个种类的16S rDNA同源序列。采用PAUP*4.0和MrBayes3.0两个分析软件和3种建树方法,利用同源28S D2 rDNA和16S rDNA两个基因序列与形态特征结合进行系统发育分析研究。分析结果表明,二叉叶蝉族Macrostelini是一个单系,并在角顶叶蝉亚科的系统发育中处于基部的位置,是内群中最原始的族;角顶叶蝉族Deltocephalini中除了纹翅叶蝉属Nakaharanus,其余各属构成单系;殃叶蝉族Euscelini内属的归属比较混乱,可能是一个并系群,属间差异有待进一步研究。隆额叶蝉族Paralimnini与顶带叶蝉族Athysanini是姐妹群。带叶蝉属Scaphoideus与纹翅叶蝉属Nakaharanus是姐妹群,二者与木叶蝉属Phlogotettix的关系最近,三者构成一个单系,建议将三者归为带叶蝉族Scaphoideini。研究结果还表明,小眼叶蝉族Xestocephalini和Balcluthini的系统发育位置不明,有待进一步研究。     

火丝菌科(盘菌目)部分属的系统学研究

本文以核糖体小亚基(SSUrDNA)为分子标记,对28个属60个种的71个序列片段进行序列分析,探讨火丝菌科的属间亲缘关系。研究结果支持广义的火丝菌科概念,表明该科是单起源的,显示5个主要分支。腐生或与植物共生形成菌根、囊盘被表面具有毛状物的15个属构成A分支,该分支中仅部分属之间的关系比较明确;与苔藓植物生长在一起的4个属构成B分支;C分支包括Otidea和Otideopsis两属,后者与Otidea的成员混杂在一起;D分支仅包括Acervus的成员;E分支由Geopyxis,Tarzetta,Paurocotylis等5个属组成。分子系统学的研究结果与形态学分类系统之间存在一定差异,依据形态特征和超微结构建立的亚科和族均未获得支持。     

大莲湖池杉林土壤细菌的季节性变化

应用稀释平板法对大莲湖池杉林湿地土壤细菌进行分离,采用16S rDNA序列分析法对所分离细菌进行鉴定。结果表明,池杉林不同季节土壤细菌种类和数量有差异。其中夏季土壤细菌数量和种类最多,春、秋季次之,冬季最少。四个季度共分离得到60株菌株,分属15个细菌种属,分别为芽胞杆菌(Bacillus),假单胞菌(Pseudomonas),黄杆菌(Flavobacterium),红球菌(Rhodococcus),北里孢菌(Kitasatosporia),金黄杆菌(Chryseobacterium),不动杆菌(Acinetobacter),鞘氨醇杆菌(Sphingobacterium),丛毛单胞菌(Comamonas),伯克霍尔德氏菌(Burkholderia),链霉菌(Streptomyces),沙雷氏菌(Serratia),肠杆菌(Enterobacter),窄食单胞菌(Stenotrophomonas)和节杆菌(Arthrobacter)。     

湛江红树林滩涂可培养真菌种群多样性分析

【目的】明确湛江地区红树林滩涂海洋真菌的种类及其分布,为海洋真菌的开发利用研究奠定基础。【方法】运用稀释平板法从湛江市高桥及特呈岛红树林滩涂不同的潮位带(低、中、高)和不同树种(白骨壤、桐花树、木榄、红海榄)采集淤泥样品550份,采用真菌形态学和ITS序列分析技术进行多样性研究【。结果】分离获得海洋真菌274株,共鉴定出19属39种真菌,以曲霉属Aspergillus、青霉属Penicillium和木霉属Trichoderma真菌分离频率高,为湛江红树林滩涂优势真菌种类,尤其在中潮位带真菌种类最多。此外,分离获得真菌Talaromyces helicus,为中国新记录种。【结论】湛江红树林滩涂海洋真菌的种类十分丰富,具有潜在的开发和利用前景。     

Phylogenetic relationships of the north-eastern Atlantic and Mediterranean blenniids

The phylogenetic relationships of 27 north-eastern Atlantic and Mediterranean blennioids are analysed based on a total of 1001 bp from a combined fragment of the 12S and 16S mitochondrial rDNA. The most relevant results with implications in current blenniid taxonomy are: (1) Lipophrys pholis and Lipophrys (=  Paralipophrys ) trigloides are included in a well-supported clade that by the rule of precedence must be named Lipophrys ; (2) the sister species of this clade are not the remaining species of the genus Lipophrys but instead a monotypic genus comprising Coryphoblennius galerita ; (3) the smaller species of Lipophrys were recovered in another well-supported and independent clade, which we propose to be recognized as Microlipophrys ; (4) although some authors included the genera Salaria and Lipophrys in a single group we have never recovered such a relationship. Instead, Salaria is more closely related to the genera Scartella and Parablennius ; (5) the genus Parablennius , which was never recovered as a monophyletic clade, is very diverse and may include several distinct lineages; (6) the relative position of Aidablennius sphynx casts some doubts on the currently recognized relationships between the different blenniid tribes. Meristic, morphological, behavioural and ecological characters support our results and are also discussed. The possible roles of the tropical West African coast and the Mediterranean in the diversification of blenniids are discussed.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 86 , 283–295.     

葡萄果粒表皮酵母菌多样性研究

从新疆、甘肃、陕西、宁夏、山东主要酿酒葡萄产区收集葡萄果粒并分离得到酵母258株,利用26S rDNA的D1/D2区序列分析并结合形态学、生理学特征对这些菌株进行了分类学研究,探讨了这些地区葡萄果粒表皮酵母的物种多样性及其分布.共鉴定出13属26种,其中优势属为汉逊酵母属Hanseniaspora(5种),假丝酵母属Candida(4种),毕赤酵母属Pichia(4种)和伊萨酵母属Issatchenkia(2种).对分离自不同地域的同种内不同菌株进行了D1/D2序列分析比较,以探讨不同地理起源地酵母种内序列稳定性及其变异.     

蕙兰根内可培养细菌的物种多样性

以MS基本培养基添加蕙兰菌根浸出液制成的培养基进行分离培养的方法,从野生蕙兰（Cymbidium faberi）根部首次分离到内生细菌。经过分离纯化培养获得纯菌株27株。经过16S rDNA基因序列测序,并与GenBank数据比对,其相似性均在98%以上,分析鉴定结果表明,存活的22株菌可分为8属14种。分别隶属于伯克氏菌属（Burkholderia）、假单胞菌属（Pseudomonas）、芽胞杆菌属（Bacillus）、Leifsonia属、贪食菌属（Variovorax）、欧文氏菌属（Erwinia）、Duganella属和不动杆菌属（Acinetobacter）。对这些菌株进行分离培养及鉴定有助于理解兰花与微生物之间的相互作用关系,为开发利用这些微生物开辟新的思路。     

葡萄果粒表皮酵母菌多样性研究

从新疆、甘肃、陕西、宁夏、山东主要酿酒葡萄产区收集葡萄果粒并分离得到酵母258株, 利用26S rDNA的D1/D2区序列分析并结合形态学、生理学特征对这些菌株进行了分类学研究, 探讨了这些地区葡萄果粒表皮酵母的物种多样性及其分布。共鉴定出13属26种, 其中优势属为汉逊酵母属Hanseniaspora(5种), 假丝酵母属Candida(4种), 毕赤酵母属Pichia(4种)和伊萨酵母属Issatchenkia(2种)。对分离自不同地域的同种内不同菌株进行了D1/D2序列分析比较, 以探讨不同地理起源地酵母种内序列稳定性及其变异。     

石河子不同树龄蟠桃土壤中可培养酵母多样性分析及功能酵母的筛选

为了探究新疆本土蟠桃园可培养酵母菌多样性,并挖掘功能酵母资源,本研究以新疆石河子蟠桃园3年、8年、15年树龄的根际和非根际土壤以及桃树叶片为材料,经过传统的分离培养方法获得可培养的酵母菌菌株,并进行形态学、生理生化以及26S r DNA的D1/D2区序列分析,共获得可培养酵母菌129株,从属于12个属17个种,其中子囊菌酵母为优势菌群,占分离属的88%,分布于威克汉姆酵母属(Wickerhamomyces),Vanrija属,Barnettozyma属和有孢圆酵母属(Torulaspora)等11个属的15个种。担子菌占分离属的12%,分布于隐球酵母属(Cryptococcus)的2个种。其中优势属威克汉姆酵母属,包括异常威克汉姆酵母(W. anomalus)和W. pijperi两个种,占总比例的33%,优势种异常威克汉姆酵母所占总株数比例为17%。从可培养酵母中共筛选出23株功能酵母,其中富硒酵母21株,优势种为白地霉(Galactomyces candidum),产蛋白酶酵母2株均属于隐球酵母属的Cryptococcus albidus。结果表明,新疆桃园中蕴含丰富的酵母菌资源,非根际土壤中的酵母多样性大于根际及叶片酵母多样性,且分离得到富硒酵母及产蛋白酶酵母。本研究挖掘了新疆本土可培养酵母菌资源,同时也为功能酵母的开发和利用提供理论指导。     

Phylogenetic Analysis of the Genus Bifidobacterium and Related Genera Based on 16S rDNA Sequences

The 16S rRNA gene sequences were determined for type strains of 21 Bifidobacterium species. A phylogenetic tree was constructed using the determined sequences and sequences from DNA databases, which contain the sequences of 11 type strains of Bifidobacterium species and 11 strains of related genera. All species of the genus Bifidobacterium and Gardnerella vaginalis ATCC 14018 belonged to a cluster phylogenetically distinct from the other genera. The cluster was divided into two subclusters: subcluster 1 composed of most species of Bifidobacterium and G. vaginalis, and subcluster 2 consisting of two species, B. denticolens and B. inopinatum; both of which were isolated from human dental caries. In the genus Bifidobacterium, four groups of species are known to be moderately to highly related by DNA-DNA hybridization. The four groups of species exhibited more than 99% similarity among their 16S rDNA sequences within each group. These results indicated that species with around 99% or more similarity in their 16S rDNA sequences should be confirmed for species identities.     

16S rDNA sequence analysis of bacterial isolates from biodeteriorated mural paintings in the Servilia tomb (Necropolis of carmona, Seville, Spain)

Bacteria were isolated from damaged mural paintings of the Servilia tomb (necropolis of Carmona, Seville, Spain). Selected strains, representative for different clusters of isolates with similar fatty acid profiles, were analysed by 16S rDNA sequence analysis. Bacillus is the dominant genus among the isolates: members of the rRNA species complexes of B. megaterium, B. pumilus and B. firmus were found as well as several other Bacillus species. One group of halotolerant isolates falls in the Bacillus sensu lato group, with closest relatedness to the genera Salibacillus and Virgibacillus. Other genera found are Artbrobacter, Micrococcus, Streptomyces, Sphingomonas, Paenibacillus, and a genus closely related to Paracraurococcus. Many isolates showed low 16S rDNA sequence similarities with the closest related database entries, a strong indication for the presence of several new species among the isolates.     

基于28S rDNA D1-D2基因片段与16S rDNA部分序列联合分析的叶肢介系统发育研究

叶肢介(Conchostraca)的系统发育问题一直是甲壳动物研究中颇具争议的一个课题.本研究测定了我国2种叶肢介(Eocyzicus mongolianus,Eoc yzicus orientalis)的28S rDNA D1-D2区基因序列和16S rDNA E-G区序列,并与GenBank中的20种叶肢介序列一起...     

The evolutionary history of the Chydoridae (Crustacea: Cladocera)

Although much is known about the evolutionary history of the pelagic 'cladocerans', there is little information on benthic families such as the Chydoridae. In this study, we examine the phylogenetic history of 37 chydorid species using sequence variation in two mitochondrial genes, COI and 16S rDNA, and one nuclear gene, 18S rDNA. The four recognized subfamilies of chydorids (Eurycercinae, Saycinae, Aloninae and Chydorinae) were well supported, being separated by large sequence divergences of 14.3–16.4%. By contrast, the existing taxonomic system appears to be less clear at a generic level, since many genera (e.g. Alona , Chydorus , Pleuroxus ) consist of an amalgam of distantly related species. However, among those genera which are monophyletic, levels of divergence are very high, suggesting that they originated somewhere in the mid-Palaeozoic. The factors involved in promoting diversification in this group are discussed.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79, 629–643.     

Molecular systematics of sponges (Porifera)

The first application of molecular systematics to sponges was in the 1980s, using allozyme divergence to dis-criminate between conspecific and congeneric sponge populations. Since this time, a fairly large database has been accumulated and, although the first findings seemed to indicate that sponge species were genetically more divergent than those of other marine invertebrates, a recent review of the available dataset indicates that levels of interspecific gene identities in most sponges fall within the normal range found between species of other invertebrates. Nevertheless, some sponge genera have species that are extremely divergent from each other, suggesting a possible polyphyly of these genera. In the 1990s, molecular studies comparing sequences of ribosomal RNA have been used to reappraise the phylogenetic relationships among sponge genera, families, orders and classes. Both the 18S small subunit and the 28S large subunit rRNA genes have been sequenced (41 complete or partial and 75 partial sequences, respectively). Sequences of 18S rRNA show good support for Porifera being true Metazoa, but they are not informative for resolving relationships among genera, families or orders. 28S rRNA domains D1 and D2 appear to be more informative for the terminal nodes and provide resolution for internal topologies in sufficiently closely related species, but the deep nodes between orders or classes cannot be resolved using this molecule. Recently, a more conserved gene, Hsp70, has been used to try to resolve the relationships in the deep nodes. Metazoan monophyly is very well supported. Nevertheless, the divergence between the three classes of Porifera, as well as the divergence between Porifera, Cnidaria and Ctenophora, is not resolved. Research is in progress using other genes such as those of the homeodomain, the tyrosine kinase domain, and those coding for the aggregation factor. For the moment the dataset for these genes is too restricted to resolve the phylogenetic relationships of these phyla. However, whichever the genes, the phylogenies obtained suggest that Porifera could be paraphyletic and that the phylogenetic relationships of most of the families and orders of the Demospongiae have to be reassessed. The Calcarea and Hexactinellida are still to be studied at the molecular level.     

Phylogenetic Relationships of Scenedesmus and Scenedesmus-like Coccoid Green Algae as Inferred from ITS-2 rDNA Sequence Comparisons

Abstract: Analyses of ITS-2 ribosomal DNA from Scenedesmus and Scenedesmus-like strains showed that this molecule is well suited for resolving evolutionary relationships at various taxo-nomic levels. The analyses clearly suggested the separation of the investigated strains into two groups which corresponded to the "subgenera" Desmodesmus and Scenedesmus/Acutodesmus . No clear distinction between Acutodesmus and Scenedesmus was seen. It is proposed to regard both groups as distinct genera, Desmodesmus gen. nov. and Scenedesmus sensu strictu , and to merge Acutodesmus into Scenedesmus . Monophyly of both genera, Scenedesmus and Desmodesmus , is further supported by certain secondary structure features of ITS-2. The relationships resolved by the ITS-2 analyses are congruent with findings from cell wall ultrastructure, but not with those from other morphological features such as cell wall surface structures or cell shape. Didymocystis inermis and Dicloster acuatus , though somewhat similar in vegetative cell morphology to species of Scenedesmus and Desmodesmus , were seen as members of independent genera because of substantial differences in primary structure and length variations in ITS-2 when compared with each other and the latter two genera.     

Phylogeny of the families Pyuridae and Styelidae (Stolidobranchiata, Ascidiacea) inferred from mitochondrial and nuclear DNA sequences

The Order Stolidobranchiata comprises the families Pyuridae, Styelidae and Molgulidae. Early molecular data was consistent with monophyly of the Stolidobranchiata and also the Molgulidae. Internal phylogeny and relationships between Styelidae and Pyuridae were inconclusive however. In order to clarify these points we used mitochondrial and nuclear sequences from 31 species of Styelidae and 25 of Pyuridae. Phylogenetic trees recovered the Pyuridae as a monophyletic clade, and their genera appeared as monophyletic with the exception of Pyura. The Styelidae, on the other hand, appeared as a paraphyletic group split into several clades. One of them was formed by solitary oviparous species, of which the Pyuridae were a sister group. A second clade included the colonial genera Botryllus, Botrylloides and Symplegma. The remaining colonial and solitary genera formed several poorly resolved clades. One of the more species genus, Polycarpa, was shown to be polyphyletic, and the species Styela plicata grouped into two genetically distant clades suggesting the existence of two cryptic species. The internal phylogeny of Styelidae has bearings on the origin of coloniality in this family. We suggest to abandon the traditional division of colonial forms into social and compound species and use instead the categories of aggregated colonies that do not have common vascular systems, and integrated colonies, that do possess such systems. Our molecular results indicate that there have been several independent acquisitions of coloniality in the Styelidae, and that viviparity may be a pre-adaptation for a colonial life-style.     

粒毛盘菌属及其相关属的分子系统学研究*

晶杯菌科的分类目前主要基于子囊盘外囊盘被表面毛状物的形态学特征,在系统演化关系上十分不清楚。本研究利用18SrRNA基因核苷酸序列分析方法探讨该科粒毛盘菌属及其相关属间的系统发育关系。以Saccharomycescerevisiae为外群的严格合意树和最简约树表明,粒毛盘菌属与其相关的属形成三个分支。Lachnumhyalopus,L.nudipes和L.virgineum代表一个分支。L.brasiliense,L.sclerotii,L.singerianum,Albotrichaguangxiensis,Calycellinapopulina.,Cistellagrevillei,Hyaloscyphaaureliella,Lachnellulacalyciformis,Parachnopezizaguangxiensis和Trichopezizasulphurea聚在一起(支持率为57%),为另一个分支。上述两个姊妹分支的支持强度为76%。与Lachnum在形态上有些相似的Cistella和Lachnum聚在一起的支持强度为51%。传统上纳入Arachnopezizoideae的Parachnopeziza与该亚科的模式属Arachnopeziza的关系较远。Arachnopezizaaurata是供试的14个种中距离最远的一个,位于系统发育树的最外侧,与上述两个分支的亲缘关系较远,这对Arachnopezizoideae在晶杯菌科中的地位提出了质疑。     

秦岭地区子囊菌酵母物种多样性研究

从陕西秦岭地区的果实和叶等不同基物上分离得到子囊菌酵母262株,利用26SrDNA的D1/D2区域序列分析并结合形态学特征对这些菌株进行了分类学研究,探讨了该地区子囊菌酵母的物种多样性及其分布。共鉴定出10属31种,其中优势属为假丝酵母属Candida,12种,(其中新种2个,另文发表)、酿酒酵母属Saccharomyces,5种、毕赤酵母属Pichia,5种和有孢汉逊酵母属Hanseniaspora,3种。对分离自陕西秦岭不同地区与海拔的同一个种的不同菌株进行了D1/D2序列分析比较,以探讨子囊菌酵母种内序列稳定性和变异幅度。