喜温嗜酸硫杆菌SM-1的ROS防护机制

【目的】从基因组水平探讨生物冶金微生物——喜温嗜酸硫杆菌(Acidithiobacillus caldus)的活性氧类物质(Reactive oxygen species,ROS)防护机制。【方法】采用罗氏454 GS FLX测序平台对喜温嗜酸硫杆菌SM-1进行全基因组测序,利用NCBI非冗余蛋白数据库、Uniport蛋白数据库对全基因组序列进行功能注释,并采用基因组百科全书数据库(KEGG)进行基因组代谢途径重构,通过比较基因组学方法分析SM-1基因组中参与ROS防护相关的基因及可能的分子机制。【结果】SM-1细胞内的酶促抗氧化系统可用于清除细胞内产生的ROS物质,而非酶促抗氧化系统可用于维持细胞内的还原性内环境;细胞内的DNA损伤修复系统可用于修复DNA的氧化损伤从而保持个体遗传物质的稳定性。此外,SM-1基因组中大量的转座元件可能会增加基因组的可塑性以适应极端冶金环境。【结论】SM-1基因组序列的获得为从整体水平揭示喜温嗜酸硫杆菌适应生物冶金环境ROS氧化损伤的防护机制提供了帮助,对于SM-1的ROS防护机制的认知也为进一步通过遗传改造、提升其在高浓度重金属离子冶金环境中的抗性、提高冶金效率提供了理论指导。     

一株嗜酸硫杆菌M4-422-6的分离及其全基因组测序和比较基因组学分析

【目的】开展具有硫氧化能力的嗜酸硫杆菌属(Acidithiobacillus)的分离及其比较基因组学分析,不仅可以丰富硫氧化细菌菌种资源,而且有助于加深理解嗜酸硫杆菌的分子进化与生态适应机制。【方法】利用以硫代硫酸钠为唯一能源的培养基分离具有硫氧化能力的细菌;利用Illumina HiSeq X和Oxford Nanopore测序平台对一株嗜酸硫杆菌M4-422-6进行全基因组测序;利用相关生物信息学分析软件对原始数据进行组装和基因组注释,并与一株亲缘关系最近的菌株Igneacidithiobacillus copahuensis VAN18-1进行比较基因组学分析。【结果】分离获得一株具有硫氧化能力的嗜酸硫杆菌M4-422-6。基因组注释结果显示,菌株M4-422-6基因组由1个染色体和2个质粒组成,基因组大小为2 917 823 bp,G+C含量为58.54%,共编码2 925个蛋白。16S rRNA基因和基因组系统发育树显示,菌株M4-422-6代表嗜酸硫杆菌属的一个潜在新种。功能基因注释结果显示,菌株Acidithiobacillus sp. M4-422-6拥有与菌株特性相关的众多基因,包括硫氧化相关基因、CO₂固定相关基因和耐酸相关基因。比较基因组学分析发现,虽然菌株M4-422-6与VAN18-1的亲缘关系最近,但两者仍拥有众多的差异基因,主要包括噬菌体抗性相关基因和移动元件编码基因。【结论】菌株M4-422-6代表嗜酸硫杆菌属的一个潜在新种,该菌株具有同种内菌株所不具有的特有基因,并据此推测嗜酸硫杆菌种内分化可归因于对特定生态位的适应。     

嗜酸硫杆菌属物种的比较基因组学分析

[目的]对喜温嗜酸硫杆菌和氧化亚铁嗜酸硫杆菌菌株的基因组数据进行比较分析和数据挖掘。[方法]采用Blast程序、MUMmer软件以及Artemis比对软件对4株嗜酸硫杆菌的基因组序列和蛋白质组序列进行同源比对分析以及可视化呈现,并通过RT-PCR对缺失基因进行验证。[结果]与喜温嗜酸硫杆菌相比,氧化亚铁嗜酸硫杆菌不含有鞭毛编码基因,并且含有较少的转座元件(26和41个);喜温嗜酸硫杆菌主要采用SOX系统(clusterⅠ和clusterⅡ)进行无机硫化合物的氧化;除硝酸盐还原外,氧化亚铁嗜酸硫杆菌还可以通过固氮酶(AFE1522-1515和Lferr_1240-1233)固定氮气获得氮源。此外,插入序列造成硫氧化还原酶基因的缺失以及7个功能基因失活等现象表明冶金微生物基因组存在不稳定性。[结论]比较基因组学为更好地挖掘嗜酸硫杆菌属物种的基因组数据信息、揭示其基因组结构特征以及冶金性状等差异提供了重要支持。     

GWAS研究大肠杆菌和金黄色葡萄球菌种间互作进化机制

【目的】通过实验室培养模拟自然环境微生物相互作用,进而找到影响细菌基因型和表型的基因。【方法】将大肠杆菌和金黄色葡萄球菌在实验室条件下进行单独培养和两两混合培养并连续转接,通过得到的数量表型与最大生长速率表型做全基因组关联分析(GWAS),对得到的与表型相关的SNP进行注释与分析。【结果】162个SNP位点影响到大肠杆菌原始菌株与共培养菌株的生长,36个SNP位点影响大肠杆菌菌株在单独培养和共同培养的生长。总共有85个SNP位点影响金黄色葡萄球菌的原始菌株与单独培养。其中5个基因在之前文献中已有报道。对影响不同时间点细菌数量变化形状的SNP位点进行功能注释,大肠杆菌中有706个与生长性能相关。金黄色葡萄球菌中,129个和不同的生长性能相关。大肠杆菌SNP位点的13个基因在之前的研究中已有报道。【结论】混合培养和单独培养都检测到与生长相关的显著基因,本研究表明了GWAS在研究细菌互作进化机制方面的潜力。     

基于比较基因组学解析耐酸乳杆菌G10的多碳源利用特征

【背景】耐酸乳杆菌（Lactobacillus acetotolerans）是白酒发酵过程中的优势乳酸菌,对白酒发酵具有重要作用。L. acetotolerans G10是分离自芝麻香型白酒发酵酒醅的一株能够利用多种碳源的菌株。【目的】基于全基因组测序,解析菌株G10多碳源利用机制。【方法】通过三代测序平台Oxford Nanopore完成菌株G10全基因组测序,分别利用Circlator和Prodigal对测序数据进行组装和基因预测;通过细菌基因组分析工具（bacterial pan genome analysis tool,BPGA）进行泛基因组分析。【结果】G10能够利用22种糖类及糖类衍生物,其全基因组大小为1 627 828 bp,含有1 878个编码基因;基于Koyto Encyclopedia of Genes and Genomes （KEGG）数据库注释获得292个碳源代谢相关基因,基于Carbohydrate-Active Enzymes （CAZy）数据库注释获得44个CAZy家族的编码基因。与其他发酵食品来源的耐酸乳杆菌相比,G10基因组最小,但其总基因数量以及...     

鸡源暹罗芽孢杆菌CML548的益生特性及全基因组分析

【背景】芽孢杆菌是用于动物微生态制剂的重要菌株之一。暹罗芽孢杆菌因具有较强的抑菌活性,近年来受到广泛关注。【目的】对实验室前期分离的鸡源暹罗芽孢杆菌CML548的益生特性进行评价,通过全基因组测序及生物信息学分析,探究其抑菌及潜在的益生机制。【方法】通过牛津杯法、稀释涂布平板法分别对菌株CML548的抑菌和产酶特性、酸和胆盐的耐受性进行研究。使用IlluminaHiSeq2500测序平台进行全基因组测序,并通过多种生物信息学工具和数据库对基因组进行注释和分析。【结果】体外实验表明该菌株具有优良的益生性状：能够有效抑制致病性大肠杆菌、鼠伤寒沙门氏菌、产气荚膜梭菌的生长;能够同时产生蛋白酶、淀粉酶和纤维素酶;具有较高的酸和胆盐耐受性。全基因组测序分析表明菌株CML548的基因组大小为4061741bp,GC含量为46.07%,预测到3 961个编码基因。分别有1 693、2 704、3 413、186、67、1、5个基因被GO、KEGG、COG、CAZy、DBAASP、CARD、VFDB数据库注释;通过antiSMASH预测到16个与次级代谢产物合成相关的基因簇。此外,还发现其含有抗菌活性...     

全基因组测序揭示两株泡菜源植物乳杆菌基因型差异和潜在益生特性北大核心

【目的】为了探究植物乳杆菌(Lactiplantibacillus plantarum)基因型差异和潜在益生特性,采用全基因组测序技术对其进行测序并解析基因组序列及生物特性。【方法】本研究基于HiSeq和PacBio测序平台,对团队前期从四川多代泡菜中分离获得、体外益生特性评价良好的潜在益生菌菌株L.plantarum Eden-Star PC06和L.plantarum Eden-Star PC108的全基因组进行测序。利用相关生物信息学软件对原始数据进行组装及其后续的功能注释、分子进化、菌株安全性、次级代谢产物合成基因簇以及益生特性相关基因进行分析。【结果】通过基因组装得到了2株植物乳杆菌的全基因组信息,L.plantarum Eden-Star PC06和Eden-Star PC108基因组大小分别为3163902 bp和3205054 bp;GC含量分别为44.68%和44.67%;分别包含3161个和3197个DNA编码序列;功能基因数据库比对结果显示2株菌在碳水化合物利用、氨基酸利用和糖基转移酶等基因上得到大量注释;通过比对数据库,在2株植物乳杆菌全基因组上发现了4个与肠液耐受相关的胆盐水解酶基因、完整的植物乳杆菌细菌素合成相关基因簇和抵御多种胁迫的益生相关基因。【结论】本研究通过全基因组测序在基因水平上探究了L.plantarum Eden-Star PC06和Eden-Star PC108基因型差异和益生特性基因,证明L.plantarum Eden-Star PC06和Eden-Star PC108是2株有应用前景的益生菌菌株,以期为筛选优良益生菌菌株和评价其益生特性提供遗传学基础。     

好客嗜酸两面菌W1寡营养酸性热泉环境的适应机制

【目的】从基因组水平揭示好客嗜酸两面菌(Acidianus hospitalis)W1对寡营养酸性热泉环境的适应机制。【方法】使用NCBI非冗余蛋白数据库、Uniport蛋白数据库以及Sulfolobus数据库对好客嗜酸两面菌W1基因组序列进行功能注释,使用KEGG数据库对基因组进行In slico代谢途径重构,在此基础之上,采用比较基因组学方法对代谢途径进行鉴定和完善。【结果】好客嗜酸两面菌W1具备多样化的代谢方式以适应寡营养酸性热泉环境。W1菌株通过3-羟基丙酸/4-羟基丁酸和乙二酸-4-羟基丁酸循环进行CO2固定、通过氧化还原型无机硫化物(Reduced inorganic sulfur compounds,RISCs)获取能量营自养型生长。但W1菌株与模式菌株Acidianus ambivalens的硫代谢方式不同,W1基因组中缺少编码亚硫酸-受体氧化还原酶(SAOR)、腺苷硫酸(APS)还原酶、硫酸腺苷酰转移酶(SAT)和腺苷硫酸:磷酸腺苷转移酶(APAT)的基因。此外,W1菌株可以通过非磷酸化的分支的ED途径和TCA循环进行葡萄糖代谢,糖类和氨基酸转运蛋白以及相应水解酶的存在表明W1能够利用部分有机物营兼性自养型生长。与A.ambivalens不同,W1菌株不能利用H2作为电子供体。【结论】多样化的代谢方式为好客嗜酸两面菌W1更好地适应寡营养酸性热泉环境提供了重要保障,对于W1菌株特有代谢方式的揭示也丰富了对于嗜酸两面菌(Acidianus)属物种代谢多样性的认知。     

一株冠突散囊菌的分离鉴定、基因组成及其枇杷花发酵特性分析

【背景】冠突散囊菌LYEC03是从陕西泾阳茯砖茶中分离得到的主要发酵菌株。【目的】研究冠突散囊菌LYEC03菌株的基因组信息及其发酵枇杷花产品的特性,从分子水平阐明冠突散囊菌的发酵机制。【方法】应用形态和显微形态观察、ITS序列鉴定、重测序及框架图测序对所分离的菌株LYEC03进行鉴定和基因组信息解析,采用所分离的菌株LYEC03发酵枇杷花,研究冠突散囊菌对枇杷花主要功效成分及抗氧化性能的影响。【结果】陕西泾阳茯砖茶中分离得到的主要发酵菌株LYEC03确定为冠突散囊菌。菌株LYEC03与参考基因组覆盖率高,含有丰富的纤维素酶、蛋白酶、氧化酶和脂肪酶相关基因;基因组相关整体变异较小,其中假设蛋白、碳水化合物激酶、纤维素酶家族糖基水解酶、位点2蛋白酶家族蛋白、多酚氧化酶和谷胱甘肽过氧化物酶等与菌株生长、能量代谢调节、产纤维酶、产蛋白酶和产氧化酶相关的基因发生了变异。菌株LYEC03基因组序列长度30 623 602 bp、GC含量51.70%、编码13 033个基因、编码基因占比55.74%,参与了碳水化合物代谢、氨基酸代谢、外源生物降解代谢、能量代谢、脂质代谢与萜类化合物和聚酮类化合物的...     

生防菌解淀粉芽孢杆菌 SQ-2 全基因组测序及生物信息学分析

【背景】解淀粉芽孢杆菌SQ-2是从市售豆瓣酱中分离得到的一株益生菌,实验表明菌株SQ-2具有较强的抑制植物病原真菌的能力,说明SQ-2具有较好的生物防治能力,有作为生物农药的潜力。【目的】研究菌株SQ-2的遗传信息并揭示其抑菌机制。【方法】在Illumina MiSeq X10平台上对菌株SQ-2进行全基因组测序,使用Trim Galore V.0.4.0清理原始数据,并使用FastQC检查质量;使用SOAPdenovo2进行从头组装,使用antiSMASH鉴定负责次级代谢产物生物合成的基因。【结果】解淀粉芽孢杆菌SQ-2基因组大小为3 486 537 bp,GC含量为46.63%,共编码4298个基因,共发现11个与次级代谢产物生物合成相关的基因簇,其中6个被确定为抗真菌物质合成簇,分别编码bacillaene、bacilysin、butirosin、fengycin、bacillibactin和surfactin。基因组框架测序数据提交至NCBI获得GenBank登录号为JAHXSB000000000。超高液相色谱/质谱联用分析表明产生了儿茶酚型嗜铁素、多烯类和表面活性肽。【结论】...     

Foreign exploration for Scirtothrips perseae Nakahara (Thysanoptera: Thripidae) and associated natural enemies on avocado (Persea americana Miller)

Scirtothrips perseae Nakahara was discovered attacking avocados in California, USA, in 1996. Host plant surveys in California indicated that S. perseae has a highly restricted host range with larvae being found only on avocados, while adults were collected from 11 different plant species. As part of a management program for this pest, a “classical” biological control program was initiated and foreign exploration was conducted to delineate the home range of S. perseae, to survey for associated natural enemies and inventory other species of phytophagous thrips on avocados grown in Mexico, Guatemala, Costa Rica, the Dominican Republic, Trinidad, and Brazil. Foreign exploration efforts indicate that S. perseae occurs on avocados grown at high altitudes (>1500 m) from Uruapan in Mexico south to areas around Guatemala City in Guatemala. In Costa Rica, S. perseae is replaced by an undescribed congener as the dominant phytophagous thrips on avocados grown at high altitudes (>1300 m). No species of Scirtothrips were found on avocados in the Dominican Republic, Trinidad, or Brazil. In total, 2136 phytophagous thrips were collected and identified, representing over 47 identified species from at least 19 genera. The significance of these species records is discussed. Of collected material 4% were potential thrips biological control agents. Natural enemies were dominated by six genera of predatory thrips (Aeolothrips, Aleurodothrips, Franklinothrips, Leptothrips, Scolothrips, and Karnyothrips). One genus each of parasitoid (Ceranisus) and predatory mite (Balaustium) were found. Based on the results of our sampling techniques, prospects for the importation of thrips natural enemies for use in a “classical” biological control program in California against S. perseae are not promising.     

Taxonomic status of the species of the green algal genusNeochloris

Komárek has recently reviewed the various species assigned to the green algal genusNeochloris Starr (Chlorococcales, Chlorococcaceae) and removed those with uninucleate vegetative cells to a new genus,Ettlia. Watanabe & Floyd, unaware ofKomárek's work, also reviewed the species ofNeochloris and distributed them among three genera—Neochloris, Chlorococcopsis gen. nov., andParietochloris gen. nov.—on the basis of details of the covering of the zoospore and the arrangement of the basal bodies of the flagellar apparatus. This paper reconciles these two treatments and makes additional recommendations at the ranks of genus, family, order, and class.     

Phylogeny of cardinalfishes (Teleostei: Gobiiformes: Apogonidae) and the evolution of visceral bioluminescence

The cardinalfishes (Apogonidae) are a diverse clade of small, mostly reef-dwelling fishes, for which a variety of morphological data have not yielded a consistent phylogeny. We use DNA sequence to hypothesize phylogenetic relationships within Apogonidae and among apogonids and other acanthomorph families, to examine patterns of evolution including the distribution of a visceral bioluminescence system. In conformance with previous studies, Apogonidae is placed in a clade with Pempheridae, Kurtidae, Leiognathidae, and Gobioidei. The apogonid genus Pseudamia is recovered outside the remainder of the family, not as sister to the superficially similar genus Gymnapogon. Species sampled from the Caribbean and Western Atlantic (Phaeoptyx, Astrapogon, and some Apogon species) form a clade, as do the larger-bodied Glossamia and Cheilodipterus. Incidence of visceral bioluminescence is found scattered throughout the phylogeny, independently for each group in which it is present. Examination of the fine structure of the visceral bioluminescence system through histology shows that light organs exhibit a range of morphologies, with some composed of complex masses of tubules (Siphamia, Pempheris, Parapriacanthus) and others lacking tubules but containing chambers formed by folds of the visceral epithelium (Acropoma, Archamia, Jaydia, and Rhabdamia). Light organs in Siphamia, Acropoma, Pempheris and Parapriacanthus are distinct from but connected to the gut; those in Archamia, Jaydia, and Rhabdamia are simply portions of the intestinal tract, and are little differentiated from the surrounding tissues. The presence or absence of symbiotic luminescent bacteria does not correlate with light organ structure; the tubular light organs of Siphamia and chambered tubes of Acropoma house bacteria, those in Pempheridae and the other Apogonidae do not.     

Die GattungKarschia — Bindeglied zwischen bitunicaten Ascomyceten und lecanoralen Flechtenpilzen?

The genusKarschia, in the earlier sense, including saprophytes and parasites on lichens, has been thought to be a non-lichenized parallel genus of the lichen genusBuellia. Modern workers included it on the one hand inBuellia, on the other hand combined it with bitunicate ascomycetes. It is now proved thatKarschia is heterogeneous and contains but superficially similar members both of the genusBuellia of theLecanorales and of typical or masked bitunicateAscomycetes. Therefore, it can not be regarded as a link betweenLecanorales andDothideales. The type species ofKarschia belongs to theDothideales.

     

Biological control of three floating water weeds,<Emphasis Type="Italic">Eichhornia crassipes,Pistia stratiotes</Emphasis>, and <Emphasis Type="Italic">Salviniamolesta</Emphasis> in the Republic of Congo

Since 1999, four specific weevils (Coleoptera, Curculionidae) were released in the Republic of Congo against three exotic floating water weeds: Neochetina eichhorniae Warner and N. bruchi Hustache against water hyacinth, Neohydronomus affinis Hustache against water lettuce, and Cyrtobagous salviniae Calder and Sands against water fern. Recoveries of exotic weevils were made from all 24 release sites except one, and all four species have established and spread (up to 800 km for water hyacinth weevils). Within a few years of releases, control of water fern and water lettuce was such that fishing and navigation could be resumed, while reductions of water hyacinth populations were only beginning.     

A molecular phylogeny of Hebeloma species from Europe

In order to widen the scope of existing phylogenies of the ectomycorrhizal agaric genus Hebeloma a total of 53 new rDNA ITS sequences from that genus was generated, augmented by sequences retrieved from GenBank, and analysed using Bayesian, strict consensus and neighbour joining methods. The lignicolous Hebelomina neerlandica, Gymnopilus penetrans, and two species of Galerina served as outgroup taxa. Anamika indica, as well as representatives of the genera Hymenogaster and Naucoria, were included to test the monophyly of Hebeloma, which is confirmed by the results. Hebeloma, Naucoria, Hymenogaster and Anamika indica cluster in a strongly supported monophyletic hebelomatoid clade. All trees largely reflect the current infrageneric classification within Hebeloma, and divide the genus into mostly well-supported monophyletic groups surrounding H. crustuliniforme, H. velutipes, H. sacchariolens, H. sinapizans, and H. radicosum, with H. sarcophyllum being shown at an independent position; however this is not well supported. The section Indusiata divides with strong support into three groups, the position of the pleurocystidiate Hebeloma cistophilum suggests the possible existence of a third subsection within sect. Indusiata. Subsection Sacchariolentia is raised to the rank of section.     

Systematic significance of mature embryo of bamboos

The mature embryo of seven species belonging to five genera of Indian bamboos is described. In all these the basic pattern of embryo organisation is same: the scutellar and coleoptilar bundles are not separated by an internode, the epiblast is absent, the lower portion of the scutellum and the coleorhiza are separated by a cleft and the margins of embryonic leaves overlap. The features unique to fleshy fruited bamboos are: presence of a massive scutellum, the juxtaposition of plumule and radicle and the occurrence of a bud in the axil of the coleoptile. The fleshy fruit bearing bamboos should be classified into one group, the tribeMelocanneae. Evidence is provided to recognise additional groups in the subfamilyBambusoideae.     

Demographic characteristics of an intertidal bay goby (Lepidogobius lepidus)

Synopsis In a fourteen month study (May 1976 – June 1977) I examined the following characteristics of an intertidal bay goby (Lepidogobius lepidus) in Morro Bay, California, U.S.A.: annual and seasonal patterns of abundance, age composition and growth rates, survivorship and mortality patterns, and the reproductive cycle for female gobies. Fishes were collected with the aid of quinaldine and otoliths and ovaries removed. Age and growth rates were estimated from otolith annuli using a back calculation formula and a Brody-Bertalanffy growth curve. Mortality rates were derived using the methods of Heincke (1913), Robson & Chapman (1960), mean age, and a catch curve (Ricker 1975). A gonad index was used to describe the annual reproductive cycle. Results indicated that abundance fluctuated seasonally and that these fluctuations appeared to be caused by reproductive emigrations. Bay gobies reached an age of 7+ and a standard length of 87 mm. Growth was relatively constant (6 mm yr⁻¹) until age 5, at which point it began to decline. The mean rates of survivorship, mortality, and instantaneous mortality were 0.75, 0.25, and 0.29 respectively. Mortality rates for individual age classes ranged from 0.13 to 0.51 and increased with age. This stock appears to reproduce mainly during the winter.