Sequence-based identification of species belonging to the genus Debaryomyces

In the present study we assessed the identification by sequence analysis of the 15 species belonging to the genus Debaryomyces. We found that the following species can be identified both quickly and correctly by direct sequence comparison of the ribosomal 5.8S-ITS region: D. carsonii, D. etchelsii, D. maramus, D. melissophilus, D. occidentalis and D. yamadae. In contrast, the species D. castellii, D. coudertii, D. hansenii, D. nepalensis, D. polymorphus, D. pseudopolymorphus, D. robertsiae, D. udenii and D. vanrijiae showed high sequence similarity in ribosomal regions with one or several species. In these cases, sequence comparison of the ACT1 gene is proposed to ensure unequivocal strain designation.     

Bacterial diversity in surface sediments from the Pacific Arctic Ocean

In order to assess bacterial diversity within four surface sediment samples (0–5 cm) collected from the Pacific Arctic Ocean, 16S ribosomal DNA clone library analysis was performed. Near full length 16S rDNA sequences were obtained for 463 clones from four libraries and 13 distinct major lineages of Bacteria were identified (α, β, γ, δ and ε-Proteobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, Actinobacteria, Firmicutes, Planctomycetes, Spirochetes, and Verrucomicrobia). α, γ, and δ-Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria were common phylogenetic groups from all the sediments. The γ-Proteobacteria were the dominant bacterial lineage, representing near or over 50% of the clones. Over 35% of γ-Proteobacteria clones of four clone library were closely related to cultured bacterial isolates with similarity values ranging from 94 to 100%. The community composition was different among sampling sites, which potentially was related to geochemical differences.     

Molecular investigation of the distribution, abundance and diversity of the genus Pseudoalteromonas in marine samples

The genus Pseudoalteromonas has attracted interest because it has frequently been found in association with eukaryotic hosts, and because many Pseudoalteromonas species produce biologically active compounds. One distinct group of Pseudoalteromonas species is the antifouling subgroup containing Pseudoalteromonas tunicata and Ps. ulvae, which both produce extracellular compounds that inhibit growth and colonization by different marine organisms. PCR primers targeting the 16S rRNA gene of the genus Pseudoalteromonas and the antifouling subgroup were developed and applied in this study. Real-time quantitative PCR (qPCR) was applied to determine the relative bacterial abundance of the genus and the antifouling subgroup, and denaturing gradient gel electrophoresis (DGGE) was applied to study the diversity of the genus in 11 different types of marine samples from Danish coastal waters. The detection of Ps. tunicata that contain the antifouling subgroup was achieved through specific PCR amplification of the antibacterial protein gene (alpP). The Pseudoalteromonas species accounted for 1.6% of the total bacterial abundance across all samples. The Pseudoalteromonas diversity on the three unfouled marine organisms Ciona intestinalis, Ulva lactuca and Ulvaria fusca was found to be low, and Ps. tunicata was only detected on these three hosts, which all contain accessible cellulose polymers in their cell walls.     

猕猴桃属(Actinidia)植物的遗传多样性

猕猴桃属（Ａｃｔｉｎｉｄｉａ）植物全世界有６６个种、约１１８个种下分类单位（变种、变型）。中国有猕猴桃属６２个种,猕猴桃遗传资源极为丰富。本文就猕猴桃的遗传资源多样性主要特点作概要综述：１）形态性状多样性（重要的园艺及经济性状）;２）营养成分及风味多样性;３）性别变异;４）染色体倍性变异;５）同工酶水平遗传多样性;６）ＤＮＡ水平遗传多样性。     

四川海螺沟冰川土样芽胞杆菌资源分析

【背景】芽胞杆菌(Bacillus-like)是一类能形成具有强抗性芽胞且可在多种极端环境下存活的细菌,其产生的多种功能代谢产物在多种领域具有重要研究价值。由于冰川低温、寡营养的独特生态环境,其存在的芽胞杆菌可能具有特殊性,因此研究冰川芽胞杆菌有利于发掘新基因、丰富芽胞杆菌多样性。【目的】了解四川海螺沟冰川土壤芽胞杆菌资源,为挖掘芽胞杆菌新资源提供基础。【方法】采用纯培养法分离获得冰川土壤芽胞杆菌资源,利用16S r RNA基因进行系统发育分析,测定代表性菌株的生理生化特性并采用类平均法和欧氏距离模型进行聚类分析。【结果】共筛选到可培养细菌44株,经16S r RNA基因鉴定确定其中36株为芽胞杆菌,隶属于4个属的19个种,分别为芽胞杆菌属(Bacillus)11个种24株、类芽胞杆菌属(Paenibacillus)2个种3株、短芽胞杆菌属(Brevibacillus)4个种5株和赖氨酸芽胞杆菌属(Lysinibacillus)2个种4株,其中以芽胞杆菌属(Bacillus)为优势属。分离菌中仅3株芽胞杆菌可在4°C生存,7株能在50°C生长,大部分菌株在30°C下生长良好;有74%菌株能耐碱,有37%菌株能在无盐条件下生长。根据生理生化结果,采用类平均法和欧氏距离模型进行聚类分析,可分为3组,分别包含7种、4种和6种芽胞杆菌。第1组均可以水解七叶灵和利用葡萄糖,第2组均不能水解七叶灵和利用葡萄糖,第3组仅能共同利用葡萄糖。【结论】四川海螺沟冰川土壤蕴藏着较为丰富的芽胞杆菌资源,为芽胞杆菌新资源挖掘提供了资源保障。     

Arctic plant diversity in the Early Eocene greenhouse

For the majority of the Early Caenozoic, a remarkable expanse of humid, mesothermal to temperate forests spread across Northern Polar regions that now contain specialized plant and animal communities adapted to life in extreme environments. Little is known on the taxonomic diversity of Arctic floras during greenhouse periods of the Caenozoic. We show for the first time that plant richness in the globally warm Early Eocene (approx. 55-52 Myr) in the Canadian High Arctic (76° N) is comparable with that approximately 3500 km further south at mid-latitudes in the US western interior (44-47° N). Arctic Eocene pollen floras are most comparable in richness with today's forests in the southeastern United States, some 5000 km further south of the Arctic. Nearly half of the Eocene, Arctic plant taxa are endemic and the richness of pollen floras implies significant patchiness to the vegetation type and clear regional richness of angiosperms. The reduced latitudinal diversity gradient in Early Eocene North American plant species demonstrates that extreme photoperiod in the Arctic did not limit taxonomic diversity of plants.     

Mitochondrial DNA diversity in an apomictic Daphnia complex from the Canadian High Arctic

Cyclic parthenogenesis is the ancestral mode of reproduction in the cladoceran crustacean, Daphnia pulex, but some populations have made the transition to obligate parthenogenesis and this is the only mode of reproduction known to occur in arctic populations. Melanism and polyploidy are also common in arctic populations of this species. Prior allozyme studies of arctic D. pulex revealed substantial levels of clonal diversity on a regional scale. Clonal groupings based on cluster analysis of allozyme genotypes do not conform to groupings based on the presence/absence of melanin or on ploidy level. In order to further elucidate genetic relationships among arctic D. pulex clones, mitochondrial DNA (mtDNA) variation was examined in 31 populations from two Canadian high-arctic sites. The data were also compared to a previous study of mtDNA variation in populations from a Canadian low-arctic site. Cladistic analysis of restriction site variation of the entire mitochondrial genome and nucleotide sequence variation of the mitochondrial control region was used to construct genetic relationships among mitochondrial genotypes. Three distinct mitochondrial lineages were detected. One lineage was associated with diploid, nonmelanic clones and is the same as the lineage that is found in temperate populations of D. pulex. The other two lineages (A & B) were associated with polyploid, melanic clones. Sequence divergence between the A and B lineages was 2.4%. Sequence divergence between D. pulex and either of these two lineages exceeded 3%. It is suggested that the melanic, polyploid clones are hybrids between males of D. pulex (and/or a closely related congener, D. pulicaria) and females of either of two ancestral melanic species that have mitochondrial lineages A and B. Geographic patterns of mitochondrial diversity in ‘melanic’ lineage B support the hypothesis of an high-arctic refuge for the ancestral species during the last glacial period.     

不同地区人初乳中细菌多样性研究

初乳中的微生物在婴儿生长发育过程中具有多种有益作用。【目的】本研究分析了影响初乳微生物组成的多个因素,为后续探讨人初乳菌群的相关研究提供新思路。【方法】通过PacBio SMRT测序技术对37份采集自湖北恩施地区人初乳样本中细菌16S rRNA基因序列进行测序,并结合公共数据库中已公布的来自内蒙古、海南、广西、河北、黑龙江和江苏等地区的62份人初乳中微生物组数据,探究不同地区人初乳中菌群组成与结构特点。【结果】99份人初乳样本共注释到345个属,937个种,其中乳酸乳球菌(Lactococcuslactis)、Ralstoniainsidiosa、溶血孪生球菌(Gemella haemolysans)等是人初乳中的优势菌种。基于jaccard距离的主坐标分析(principal coordinate analysis, PCoA)显示,不同地区之间的人初乳菌群呈现显著分离趋势。同时比较影响初乳微生物组成因素的R2大小发现：地区>婴儿喂养方式>妊娠期健康状态>分娩方式>胎次。【结论】本研究通过比较多个因素对人初乳中细菌菌群的影响,发现不同地区是影响人初乳微生物组成...     

Microbial diversity in Cenozoic sediments recovered from the Lomonosov Ridge in the Central Arctic Basin

The current understanding of microbes inhabiting deeply buried marine sediments is based largely on samples collected from continental shelves in tropical and temperate latitudes. The geographical range of marine subsurface coring was expanded during the Integrated Ocean Drilling Program Arctic Coring Expedition (IODP ACEX). This expedition to the ice-covered central Arctic Ocean successfully cored the entire 428 m sediment stack on the Lomonosov Ridge during August and September 2004. The recovered cores vary from siliciclastic sediment low in organic carbon (< 0.2%) to organic rich (∼3%) black sediments that rapidly accumulated in the early middle Eocene. Three geochemical environments were characterized based on chemical analyses of porewater: an upper ammonium oxidation zone, a carbonate dissolution zone and a deep (> 200 m below sea floor) sulfate reduction zone. The diversity of microbes within each zone was assessed using 16S rRNA phylogenetic markers. Bacterial 16S rRNA genes were successfully amplified from each of the biogeochemical zones, while archaea was only amplified from the deep sulfate reduction zone. The microbial communities at each zone are phylogenetically different and are most closely related to those from other deep subsurface environments.     

Plasmid diversity within the genus Chlamydia

Examination of 12 Chlamydia psittaci strains recovered from nine different host species (three avian and six mammalian) revealed the presence of a 7.5 kb plasmid in all isolates except two ovine abortion strains, the human strain IOL207 and the Cal 10 strain. Restriction mapping analysis distinguished four different plasmids that were associated with avian, feline, equine and guinea-pig C. psittaci isolates, respectively. The restriction maps of these four C. psittaci plasmid types all differed from that of the plasmid recovered from C. trachomatis L2/434. Despite this plasmid diversity, which is likely to be of taxonomic importance, all four plasmids identified within the species C. psittaci were found to share some sequence homology, which was mapped to two separate regions in the plasmid molecules. One region, which showed a high degree of homology between C. psittaci plasmids and also detectable homology with the C. trachomatis plasmid, may represent a common replication control region for plasmids of this genus.     

智利海洋沉积物中放线菌多样性

【目的】认识智利海洋沉积物中放线菌的多样性。【方法】分别采用选择性分离培养和非培养的基于16SrRNA基因序列系统发育分析方法,对来自智利南部海域海洋沉积物中放线菌多样性进行研究。采用6种选择性分离培养基分离放线菌;利用放线菌特异性引物对样品总DNA进行16SrRNA基因序列扩增并构建了16SrRNA基因克隆文库。分别挑选不同培养特征的22株放线菌和59个基因克隆进行16SrRNA基因序列的系统进化分析;测定分离的放线菌对海水的依赖性及产生抗菌活性化合物的能力。【结果】共分离到328株放线菌;挑选的22株放线菌分别属于小单孢菌属、多形孢菌属、链霉菌属、迪茨氏菌属、气微菌属和短状杆菌属;挑取的59个克隆属于40个分类单元,其中60%分类单元属于放线菌门放线菌亚纲、酸微菌亚纲和红色杆菌亚纲,另外40%的分类单元在放线菌内形成几个独立的进化分支,有可能代表放线菌新类群。22株放线菌有19株具有抗菌活性,50%的生长依赖海水的放线菌也具有抗菌活性。【结论】智利海域沉积物存在丰富的放线菌系统发育多样性并能产生活性次级代谢产物,而且还蕴藏丰富的新类型的放线菌资源。     

A new eocene triprojectate pollen genus from the Canadian Arctic, Novemprojectus

A new triprojectate pollen genus, Novemprojectus, is described from a middle Eocene sample from the Eureka Sound Formation on Kanguk Peninsula of Axel Heiberg Island, the Canadian Arctic. The type species of the genus is Novemprojectus traversii.     

Genetic diversity of the genus Lactobacillus bacteria from the human gastrointestinal microbiome

The species and strain genetic diversity of bacterial cultures belonging to the genus Lactobacillus, which were isolated from the gastrointestinal microbiome of the human population living in the former Soviet Union in the years 1960-1980, was studied. The bacteria demonstrated probiotic characteristics. Phylogenetic analysis of sequences of the gene coding for 16S rRNA detected earlier by us, showed that the gene found in bacteria isolated from the intestinal content of healthy adults and represented by species L. plantarum, L. helveticus, L. casei/paracasei, L. rhamnosus, and L. fermentum has high homology (97-100%) with this gene in type representatives of the species. The genotypic and strain diversity of cultures was studied using RAPD-PCR and nonspecific primers. This method with the use of the ERIC-1 primer gave reliable and reproducible results as compared that using with M13 and MSP primers and allowed the identification of examined bacteria belonging to the genus Lactobacillus at the level of species and certification at the strain level.     

Plasmid occurrence and diversity in the genus Paracoccus

The results of screening for the occurrence of plasmids in several strains representing 11 out of 13 species of the genus Paracoccus are presented. We show that plasmids (ranging in size from 2.7 to above 450 kb) are widely distributed in this genus. Only one tested strain (P. alkenifer) appears to be plasmid-free. The majority of the strains harbour at least two plasmids, one of which usually fits into the class of megaplasmids.     

Biochemical diversity and evolution in the genus Mus

Thirteen biochemical groups of wild mice from Europe, Asia, and Africa belonging to the genus Mus are analyzed at 22–42 protein loci. Phylogenetic trees are proposed and patterns of biochemical evolution are discussed, as well as the possible contribution of wild mice to the genetic diversity of laboratory stocks.     

Exploring bacterial diversity from contaminated soil samples from river Yamuna

The Yamuna is the source of key water supply in the national capital region of India. Due to its immense importance, the pollution of Yamuna has become an imperative issue of study. Various initiatives have been taken by the Indian Government to decontaminate this river, but so far no possible outcome has been obtained. Therefore bioremediation may seem to be a promising approach. To assess the bioremediation potential of the microbes at river Yamuna, study of microbial diversity was carried out. Escherichia, Pseudomonas, Bacillus, Thermomicrobium, Azoarcus, Nitrosomonas and Shigella were the dominant genera present at the contaminated river coastal zone. The presence of Escherichia and Shigella indicated the sewage contamination in the river. On the other hand, the presence of Pseudomonas and Bacillus indicated the existence of indigenous bacterial communities capable of de-polluting the river, thus providing a promising approach to decontaminate Yamuna by natural means.     

Phylogenetic and physiological diversity of microorganisms isolated from a deep greenland glacier ice core

We studied a sample from the GISP 2 (Greenland Ice Sheet Project) ice core to determine the diversity and survival of microorganisms trapped in the ice at least 120,000 years ago. Previously, we examined the phylogenetic relationships among 16S ribosomal DNA (rDNA) sequences in a clone library obtained by PCR amplification from genomic DNA extracted from anaerobic enrichments. Here we report the isolation of nearly 800 aerobic organisms that were grouped by morphology and amplified rDNA restriction analysis patterns to select isolates for further study. The phylogenetic analyses of 56 representative rDNA sequences showed that the isolates belonged to four major phylogenetic groups: the high-G+C gram-positives, low-G+C gram-positives, Proteobacteria, and the Cytophaga-Flavobacterium-Bacteroides group. The most abundant and diverse isolates were within the high-G+C gram-positive cluster that had not been represented in the clone library. The Jukes-Cantor evolutionary distance matrix results suggested that at least 7 isolates represent new species within characterized genera and that 49 are different strains of known species. The isolates were further categorized based on the isolation conditions, temperature range for growth, enzyme activity, antibiotic resistance, presence of plasmids, and strain-specific genomic variations. A significant observation with implications for the development of novel and more effective cultivation methods was that preliminary incubation in anaerobic and aerobic liquid prior to plating on agar media greatly increased the recovery of CFU from the ice core sample.