一株兼性嗜冷产甲烷八叠球菌的分离鉴定及系统发育分析

为了提高低温条件下沼气发酵的效率,本文利用Hungate厌氧操作技术从新疆库尔勒越冬沼气池污泥中分离出一株生长温度范围为8～40℃的兼性嗜冷产甲烷菌株ZG-2。该菌株革兰氏染色为阳性,呈不规则球状叠放在一起,不运动,能够利用H。／C（]2混合物、甲醇、甲胺、乙酸盐作为单一碳源底物进行厌氧发酵生产甲烷。最适生长条件：温度为25～30℃,生长pH为6;NaCl浓度为0．2mol／L;不能耐受链霉素和卡那霉素。根据菌株形态特征和生理生化特性以及16SrDNA序列分析,初步认为菌株ZG-2为兼性嗜冷巴氏产甲烷八叠球菌（Methanosarcina barkeri）。     

Methane-consuming archaebacteria in marine sediments

Large amounts of methane are produced in marine sediments but are then consumed before contacting aerobic waters or the atmosphere. Although no organism that can consume methane anaerobically has ever been isolated, biogeochemical evidence indicates that the overall process involves a transfer of electrons from methane to sulphate and is probably mediated by several organisms, including a methanogen (operating in reverse) and a sulphate-reducer (using an unknown intermediate substrate). Here we describe studies of sediments related to a decomposing methane hydrate. These provide strong evidence that methane is being consumed by archaebacteria that are phylogenetically distinct from known methanogens. Specifically, lipid biomarkers that are commonly characteristic of archaea are so strongly depleted in carbon-13 that methane must be the carbon source, rather than the metabolic product, for the organisms that have produced them. Parallel gene surveys of small-subunit ribosomal RNA (16S rRNA) indicate the predominance of a new archael group which is peripherally related to the methanogenic orders Methanomicrobiales and Methanosarcinales.     

Isolation of a novel acidiphilic methanogen from an acidic peat bog

Acidic peatlands are among the largest natural sources of atmospheric methane and harbour a large diversity of methanogenic Archaea. Despite the ubiquity of methanogens in these peatlands, indigenous methanogens capable of growth at acidic pH values have resisted culture and isolation; these recalcitrant methanogens include members of an uncultured family-level clade in the Methanomicrobiales prevalent in many acidic peat bogs in the Northern Hemisphere. However, we recently succeeded in obtaining a mixed enrichment culture of a member of this clade. Here we describe its isolation and initial characterization. We demonstrate that the optimum pH for methanogenesis by this organism is lower than that of any previously described methanogen.     

珠江口海岸带沉积物甲烷相关古菌群落结构及多样性研究

用构建克隆文库的方法对珠江口沉积物中4个层位的甲烷相关古菌群落多样性特征进行研究.结果表明甲烷相关古菌群落结构主要可以分为3类,分别为Methanosaeta,Methanomicrobiales和Methanosarcinales/ANME,且其组成随沉积物深度的改变发生规律变化.Methanosaeta和Methanomicrobiales是属于乙酸和H2/CO2利用型甲烷产生菌,在克隆文库中的含量随沉积物深度的增加而减少;Methanosarcinales/ANME主要由甲烷氧化菌和甲基利用型甲烷产生菌组成,在克隆文库中的含量随沉积物深度的增加而增加.甲烷相关古菌群落结构的变化规律说明,在SMTZ区域及以上,甲烷产生以H2/CO2和乙酸型为主;在SMTZ区域以下,以甲基利用型为主;在SMTZ区域,主要是甲烷氧化过程,由古菌类群ANME-2a负责.     

Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree

How many primary lineages of life exist and what are their evolutionary relationships? These are fundamental but highly controversial issues. Woese and co-workers propose that archaebacteria, eubacteria and eukaryotes are the three primary lines of descent and their relationships can be represented by Fig. 1a (the 'archaebacterial tree') if one neglects the root of the tree. In contrast, Lake claims that archaebacteria are paraphyletic, and he groups eocytes (extremely thermophilic, sulphur-dependent bacteria) with eukaryotes, and halobacteria with eubacteria (the 'eocyte tree', Fig. 1b). Lake's view has gained considerable support as a result of an analysis of small subunit ribosomal RNA sequence data by a new approach, the evolutionary parsimony method. Here we report that analysis of small subunit data by the neighbour-joining and maximum parasimony methods favours the archaebacterial tree and that computer simulations using either the archaebacterial or the eocyte tree as a model tree show that the probability of recovering the model tree is very high (greater than 90 per cent) for both the neighbour-joining and maximum parsimony methods but is relatively low for the evolutionary parsimony method. Moreover, analysis of large subunit rRNA sequences by all three methods strongly favours the archaebacterial tree.     

A型口蹄疫病毒（FMDV）VP1基因遗传进化分析

对疑似感染FMDV的样本进行了FMDV VP1基因RT-PCR鉴定,测定了其中1个阳性样本序列(命名为HY).采用生物信息学软件比较了HY与参考序列的同源性,并构建VP1基因的分子系统树.结果表明:HY属A型FMDV亚洲拓扑型东南亚-97谱系,与我国近年来报道的A/GDMM/CHA/2013的序列相似性为99.1%,与AF/72疫苗株的相似性仅为79.0%.提示我国近年来报道的A型毒株与AF/72疫苗株的序列差异较大,应及时更换A型口蹄疫疫苗毒株.     

Chemolithoautotrophic metabolism of anaerobic extremely thermophilic archaebacteria

Several types of extremely thermophilic archaebacteria have recently been isolated from solfataric water holes, hot springs and hot sea floors. It has been shown that some of them can live using sulphur respiration of reduced carbon substrates as a source of energy, a type of metabolism previously described for the eubacterium Desulfuromonas. We report here that several extremely thermophilic archaebacteria can live with carbon dioxide as their sole carbon source, obtaining energy from the oxidation of hydrogen by sulphur, producing hydrogen sulphide. They are thus capable of a new type of anaerobic, purely chemolithoautotrophic metabolism, a possible primaeval mode of life.     

Novel major archaebacterial group from marine plankton.

Marine bacteria often dominate the plankton biomass and are responsible for much of the cycling of organic matter, but bacterial diversity is poorly understood because conventional identification methods (requiring culturing) miss about 99% of the organisms. Recent advances permit characterization of microbial communities by analysis of 16S ribosomal RNA gene sequences directly from biomass without the need to culture the organisms; such studies from surface ocean samples have found only eubacteria, not archaebacteria (or Archaea), which are profoundly different. Here we report 16S rRNA sequences obtained from Pacific Ocean bacterioplankton samples collected from depths of 100 m and 500 m. Among these we found sequences only distantly related to those of any organisms previously characterized by 16S rRNA sequences, with similarities to the nearest such relatives (extreme thermophiles) approximately the same as those between animals and plants. We suggest that these sequences are from a previously undescribed archaebacterial group that may have diverged from the ancestors of characterized organisms very early in evolution.     

Hydatellaceae identified as a new branch near the base of the angiosperm phylogenetic tree

Although the relationship of angiosperms to other seed plants remains controversial, great progress has been made in identifying the earliest extant splits in flowering-plant phylogeny, with the discovery that the New Caledonian shrub Amborella trichopoda, the water lilies (Nymphaeales), and the woody Austrobaileyales constitute a basal grade of lines that diverged before the main radiation in the clade. By focusing attention on these ancient lines, this finding has re-written our understanding of angiosperm structural and reproductive biology, physiology, ecology and taxonomy. The discovery of a new basal lineage would lead to further re-evaluation of the initial angiosperm radiation, but would also be unexpected, as nearly all of the approximately 460 flowering-plant families have been surveyed in molecular studies. Here we show that Hydatellaceae, a small family of dwarf aquatics that were formerly interpreted as monocots, are instead a highly modified and previously unrecognized ancient lineage of angiosperms. Molecular phylogenetic analyses of multiple plastid genes and associated noncoding regions from the two genera of Hydatellaceae identify this overlooked family as the sister group of Nymphaeales. This surprising result is further corroborated by evidence from the nuclear gene phytochrome C (PHYC), and by numerous morphological characters. This indicates that water lilies are part of a larger lineage that evolved more extreme and diverse modifications for life in an aquatic habitat than previously recognized.     

鲫鱼肠道温和气单胞菌的分离鉴定及药敏试验

从鲫鱼肠道分离纯化获得一株细菌,编号为XA-2,对其进行形态观察,并对理化特性、16S rDNA克隆测序及系统发育进化树构建等研究．结果表明,XA-2菌株为革兰氏阴性短杆菌,可发酵葡萄糖产气;进一步采用 PCR方法克隆16S rDNA序列,测得长度为1508 bp ;对系统发育进化树分析,发现XA-2菌株与温和气单胞菌（Aero-monas sobria）模式菌株NCIMB 12065的亲缘关系最近,同源性达99.73％,从而鉴定XA-2菌株为温和气单胞菌．采用27种抗生素进行药敏试验,结果显示该菌株对头孢噻吩、头孢噻肟、头孢克肟、头孢哌酮、新霉素、诺氟沙星、复方新诺明等药物敏感,对先锋霉素Ⅳ、阿莫西林、庆大霉素、卡那霉素、红霉素等药物不敏感．     

一株高产抗菌活性物质链霉菌的初步分类鉴定

对一株土壤中筛选出的可以产抗菌活性物质的链霉菌进行了研究，测定了该菌的抗菌谱，发现该菌株对多种植物病原性真菌及细菌有拮抗作用，但对植物病原性真菌的抑制效果低于植物病原性细菌.通过形态特征、培养特征、生理生化特性及抑菌谱等系列比较，发现该链霉菌菌株与链霉菌属的黑胡桃链霉菌(Streptomyces nogalater)的特征基本相符；通过16S?rDNA序列比对，发现该菌株16S?rDNA与黑胡桃链霉菌的16S?rDNA同源性达99％.根据多项分类原则和系统进化树的构建分析，将该菌株暂归入黑胡桃链霉菌类.     

A ubiquitous thermoacidophilic archaeon from deep-sea hydrothermal vents

Deep-sea hydrothermal vents are important in global biogeochemical cycles, providing biological oases at the sea floor that are supported by the thermal and chemical flux from the Earth's interior. As hot, acidic and reduced hydrothermal fluids mix with cold, alkaline and oxygenated sea water, minerals precipitate to form porous sulphide-sulphate deposits. These structures provide microhabitats for a diversity of prokaryotes that exploit the geochemical and physical gradients in this dynamic ecosystem. It has been proposed that fluid pH in the actively venting sulphide structures is generally low (pH < 4.5), yet no extreme thermoacidophile has been isolated from vent deposits. Culture-independent surveys based on ribosomal RNA genes from deep-sea hydrothermal deposits have identified a widespread euryarchaeotal lineage, DHVE2 (deep-sea hydrothermal vent euryarchaeotic 2). Despite the ubiquity and apparent deep-sea endemism of DHVE2, cultivation of this group has been unsuccessful and thus its metabolism remains a mystery. Here we report the isolation and cultivation of a member of the DHVE2 group, which is an obligate thermoacidophilic sulphur- or iron-reducing heterotroph capable of growing from pH 3.3 to 5.8 and between 55 and 75 degrees C. In addition, we demonstrate that this isolate constitutes up to 15% of the archaeal population, providing evidence that thermoacidophiles may be key players in the sulphur and iron cycling at deep-sea vents.     

Was the universal common ancestry proved?

The question of whether or not all life on Earth shares a single common ancestor has been a central problem of evolutionary biology since Darwin. Although the theory of universal common ancestry (UCA) has gathered a compelling list of circumstantial evidence, as given in ref. 2, there has been no attempt to test statistically the UCA hypothesis among the three domains of life (eubacteria, archaebacteria and eukaryotes) by using molecular sequences. Theobald recently challenged this problem with a formal statistical test, and concluded that the UCA hypothesis holds. Although his attempt is the first step towards establishing the UCA theory with a solid statistical basis, we think that the test of Theobald is not sufficient enough to reject the alternative hypothesis of the separate origins of life, despite the Akaike information criterion (AIC) of model selection giving a clear distinction between the competing hypotheses.     

A molecular chaperone from a thermophilic archaebacterium is related to the eukaryotic protein t-complex polypeptide-1

There is evidence to suggest that components of archaebacteria are evolutionarily related to cognates in the eukaryotic cytosol. We postulated that the major heat-shock protein of the thermophilic archaebacterium, Sulfolobus shibatae, is a molecular chaperone and that it is related to an as-yet unidentified chaperone component in the eukaryotic cytosol. Acquired thermotolerance in S. shibatae correlates with the predominant synthesis of this already abundant protein, referred to as thermophilic factor 55 (TF55). TF55 is a homo-oligomeric complex of two stacked 9-membered rings, closely resembling the 7-membered-ring complexes of the chaperonins, groEL, hsp60 and Rubisco-binding protein. The TF55 complex binds unfolded polypeptides in vitro and has ATPase activity-features consistent with its being a molecular chaperone. The primary structure of TF55, however, is not significantly related to the chaperonins. On the other hand, it is highly homologous (36-40% identity) to a ubiquitous eukaryotic protein, t-complex polypeptide-1 (TCP1). In Saccharomyces cerevisiae, TCP1 is an essential protein that may play a part in mitotic spindle formation. We suggest that TF55 in archaebacteria and TCP1 in the eukaryotic cytosol are members of a new class of molecular chaperones.     

一株产抗菌物质链霉菌的筛选及鉴定

从土壤中分离到一株对棉花黄萎病菌(Verticillium dahliae)有较强拮抗作用的链霉菌菌株HCCB10124,研究其拮抗性表明,对10种常见的病原真菌和部分细菌有拮抗作用,但对植物病原性真菌的抑制效果高于细菌.其形态特征、培养特性、生理生化特性、细胞壁组分与链霉菌属中的白网链霉菌(Streptomyces albireticuli)相同,16S rDNA序列的同源性达99%.根据多项分类原则和系统进化树的构建分析,将该菌株初步归属于白网链霉菌.     

一株高产谷氨酰胺合成酶的LNU 0165菌的鉴定

谷氨酰胺合成酶是应用广泛的生物酶类,以LNU0165为实验出发菌株,对不同pH、温度条件下产谷氨酰胺合成酶的最佳发酵条件进行了研究,通过测定其谷氨酰胺合成酶酶活力,确定LNU0165为高产菌株.从分子水平上对该菌株进行16S rRNA序列分析及同源性比较,以及生理生化的鉴定．根据LNU0165菌株16SrRNA与GenBank数据库中Arthrobacter globiformis的16S rRNA的序列具有99％的同源性,确定LNU0165为球形节杆菌（Arthrobacter globiformis）．     

GPU下的二叉树定价模型

针对二叉树定价模型算法计算量大、耗时长的问题,利用CUDA架构对该模型进行了并行改造,在GPU上对该算法进行了加速测试与相应的性能分析.实验结果表明:在单个GTX295节点上,对于数据规模为16 K的期权,GPU相对于其4核Xeon E5520的加速比已达约200倍,GPU每s所能处理的期权数量达到了24 852个,符合实时商业引擎的要求.另外,通过衡量一些关键指标,考察了该算法在GPU上的扩展性及其计算精度对结果的影响.     

黄土高原沙棘根际氢氧化细菌的分离与种属分布

目的研究陕西黄土高原沙棘(Hippophae rhamnoides)根际氢氧化细菌种属分布。方法利用持续通H2的气体循环培养体系分离纯化细菌。通过TTC(2,3,5-氯化三苯基四氮唑)试验和氧化H2能力测定筛选含有氢化酶的菌株。根据其培养特征、形态特征和生理生化特征进行菌株鉴定。用16S rRNA基因序列分析法对氧化氢能力最强的优势菌株构建系统发育树。结果筛选出6株菌初步确定为氢氧化细菌,并划分为4个属:芽孢杆菌属(Bacillus)、气单胞菌属(Aeromonas)、假单胞菌属(Pseudomonas)和微球菌属(Micrococcus)。其中菌株FS2的16S rRNA基因序列(Gen-Bank登录号为GU084156)与芽孢杆菌属相似性为99%,在系统发育树上位于同一分支,因此将菌株FS2归为芽孢杆菌属(Bacillus)。结论说明氢氧化细菌在自然界分布广泛,并为分析氢氧化细菌的种群结构特征提供基础材料。     

中华绒螯蟹弧菌病及病原检验

对一起自然发生的中华绒螯蟹（Eriocheir sinensis H．Milne-Edwards）病例进行了检验,结果表明该病是由鳗利斯顿氏菌（Listonella anguillarum）所引起的病害。对从病（死）蟹肝胰腺中分离做纯培养的6株菌（HF010522-1至HF010522-6）进行了形态特征、主要理化特性等方面的鉴定;同时,选择代表菌株（HF010522-1）对健康蟹进行了人工感染试验,结果显示出较强的致病作用;另外,测定了HF010522-1菌株的16S rRNA基因序列、构建了系统发育树;选用37种抗菌类药物对3株菌做药敏试验,结果均表现对头孢噻肟等31种药物呈现敏感或高度敏感、对头孢拉啶低度敏感、对青霉素G等5种耐药。     

一株拮抗稻瘟病内生霉菌OsiSh-10的筛选与鉴定

从湖南浏阳大围山种植的湘矮早7号水稻中,筛选到一株对水稻稻瘟病菌有显著抑制效果的水稻内生放线菌OsiSh-10菌株.由拮抗菌包覆种子和喷晒水稻叶面的实验表明将该菌喷晒于水稻叶面可以对叶瘟起到明显的控制效果,且喷一次的效果比喷两次的效果好,包覆种子反而使病情指数升高.根据形态特征、培养特征、生理生化、16s rRNA序列比对及进化树构建鉴定OsiSh-10菌株属于白色链霉菌(Streptomyces albus).OsiSh-10是一株具有稻瘟病生防潜力的菌株.