新型淡水微囊藻噬藻体vB＿MweS-yong2的分离与基因组分析

【目的】蓝藻(cyanobacteria)水华频繁暴发,引起水质恶化,使水生生物大量死亡,给水产养殖业造成巨大的经济损失;其代谢产物藻毒素具有肝毒性、神经毒性、生殖毒性、遗传毒性和肿瘤促进作用,并可在水生生物中富集,造成饮用水安全风险和水产品食用安全风险。噬藻体(cyanophages)是一类特异性侵染蓝藻的病毒,参与调控蓝藻的种群密度和丰度,被认为是极具潜力的蓝藻水华生物防控工具。以往的研究报道多集中于海水噬藻体,有关淡水噬藻体的报道寥寥无几,迄今尚无惠氏微囊藻(Microcystis wesenbergii)噬藻体的研究报道。本研究的目的在于分离、鉴定惠氏微囊藻噬藻体。【方法】以惠氏微囊藻FACHB-1112为指示宿主,采用双层平板法从淡水中分离出噬藻体vB＿MweS-yong2,对其进行全基因组测序、基因功能注释和系统进化分析。【结果】vB＿MweS-yong2的基因组长44 530 bp,G+C含量为71.6%,有61个开放阅读框(ORF)、1个tRNA基因。成对序列比较(pairwise sequence comparison,PASC)表明,vB＿MweS-yong2与所有...     

聚球藻(Synechococcus leopoliensis 625)藻胆体-类囊体膜光谱特性和光能传递的研究

聚球藻(Synechococcus leopoliensis 625)属于蓝藻。       

也西湖噬藻体的分离与鉴定

【背景】噬藻体是一类特异性侵染蓝藻的病毒,广泛存在于淡水和海水水体中,参与调控宿主蓝藻的丰度和种群密度,被认为是潜在的蓝藻水华生物防控工具。但目前的研究多集中于海洋噬藻体,对淡水噬藻体的生物学特性和结构生物学等研究较少。【目的】分离更多种类的淡水噬藻体,为研究淡水噬藻体的三维结构、侵染机制、与宿主的共进化关系,及其在蓝藻水华防治中的应用提供理论基础。【方法】采集中国科学技术大学西校区内景观湖也西湖水华暴发水域的水样,利用液体培养基和双层固体平板法对17种宿主蓝藻进行筛选,通过NaCl-PEG沉淀法和氯化铯密度梯度离心分离和纯化噬藻体,并利用负染电镜观察噬藻体的形态,同时采用梯度稀释法测定裂解液的效价。【结果】发现也西湖的水样可特异性侵染本实验室分离自巢湖的一株拟鱼腥藻Pan。侵染后的裂解液中存在4株形态各异的噬藻体,包括1株短尾噬藻体和3株长尾噬藻体,其中包括首次发现的1株含有非典型长轴状头部结构的淡水噬藻体。【结论】也西湖作为巢湖流域的一个小型水体,具有与巢湖类似的水华蓝藻及其噬藻体分布谱,因此可以用于模拟大型湖泊进行相关分子生态学和生物防控的研究。     

噬藻斑扩大及噬藻体吸附率与宿主生长期的关系

蓝藻是地球上最重要的初级生产者之一,它们在北极水域等极端环境下均可生存,固氮贡献巨大1,而噬藻体是重要的具物种特异性的蓝藻致死者,在控制蓝藻种群的结构中无疑起着重要作用:噬藻体不但在海水中大量存在2,而且在控制水体初级生产力方面起关键作用.       

噬藻体研究进展

噬藻体（Cyanophage）是以蓝藻为寄主的浮游病毒类群,因其能特异性地感染蓝藻而具有重要的生态地位,是蓝藻＂水华＂潜在的控制因子。噬藻体的生物学、生态学特征是了解噬藻体的一扇窗,分子生物学研究仍将是主要的研究方向之一。同时,噬藻体研究手段也在不断更新。该文从这几个方面综述了噬藻体相关研究进展。     

噬藻体光合作用基因研究

感染原绿球藻和聚球藻的噬藻体基因组中普遍存在与psbA、psbD和hli等同源的基因,这些基因编码的蛋白参与光合作用,是光合成反应中心II(photosystem II,PSII)的重要组成成分,在噬藻体感染蓝藻过程中可能发挥着重要的作用。一些假说认为这些基因可能来自于宿主并发生共进化。因此,光合作用基因的功能、起源与演变及基因多样性分布引起了人们的关注。     

聚球藻(Synechococcus leopoliensis625)藻胆体-类囊体膜光化学活性和亚显微结构的研究

聚球藻藻胆体-类囊体膜吸收光谱中有五个吸收峰,它们位于420nm,438nm,490nm,624nm 和678nm。放氧速率为161—179mol O2/mg Chl.hr.电镜照片中显示在类囊体膜上有大量藻胆体。     

噬藻体生物多样性的研究动态

噬藻体(Cyanophage)是感染原核生物蓝藻(Cyanobacteria)的病毒,广泛分布于各种水生态系统中,对调控初级生产力、蓝藻种群密度及结构演替、微生物间基因转移以及全球生物地理化学循环等方面有重大影响。关注噬藻体的生物多样性,发现其感染相关基因,阐明噬藻体与宿主蓝藻的相互作用,将为藻华控制及认识病毒在复杂水环境中的功能提供重要信息。本文就噬藻体生物多样性,包括生态系统多样性、物种多样性及遗传多样性研究动态做一综述。     

Crystal structure of a novel fold protein Gp72 from the freshwater cyanophage Mic1

Cyanophages, widespread in aquatic systems, are a class of viruses that specifically infect cyanobacteria. Though they play important roles in modulating the homeostasis of cyanobacterial populations, little is known about the freshwater cyanophages, especially those hypothetical proteins of unknown function. Mic1 is a freshwater siphocyanophage isolated from the Lake Chaohu. It encodes three hypothetical proteins Gp65, Gp66, and Gp72, which share an identity of 61.6% to 83%. However, we find these three homologous proteins differ from each other in oligomeric state. Moreover, we solve the crystal structure of Gp72 at 2.3 Å, which represents a novel fold in the α + β class. Structural analyses combined with redox assays enable us to propose a model of disulfide bond mediated oligomerization for Gp72. Altogether, these findings provide structural and biochemical basis for further investigations on the freshwater cyanophage Mic1.     

The unicellular freshwater cyanobacterium Synechococcus and mixotrophic flagellates: evidence for a functional association in an oligotrophic, subalpine lake

1. We applied Reynolds's approach to the study of phytoplankton ecology through functional associations of species to identify possible algal species, which associate with the freshwater cyanobacterium Synechococcus. Previously an association among Synechococcus spp. and small‐celled chlorophytes (association Z) has been recognised by evaluating phytoplankton associations according to functional criteria. 2. Biomass data for phytoplankton and picocyanobacteria from Lago Maggiore spanning more years were organised in a matrix and a cluster analysis was performed. The results showed four groups separated at a linkage distance of 0.20. Mixotrophic species which clustered with Synechococcus spp. were Ceratium hirundinella, Chrysochromulina parva, Cryptomonas erosa, Cryptomonas ovata, Dinobryon bavaricum, Dinobryon sociale, Rhodomonas minuta and Uroglena americana. The redundancy analysis (RDA) consolidated the association of Synechococcus with C. hirundinella and R. minuta showing greater probability of occurrence than random aggregates of species. 3. The association Synechococcus spp. –C. hirundinella also appeared from temporal variation of their biomass. In early summer both these species increased at the same time; later, the peak of C. hirundinella (potential predator) coincided with a minimum of Synechococcus spp. suggesting a possible predator‐prey interaction. This implied that phytoplankton assemblages which form a functional group cannot only have similar adaptations and requirements but can also exhibit trophic interactions. 4. We propose to enlarge the association Z and create an association Z_MX (where _MX stands for mixotrophs) which would include Synechococcus spp. and C. hirundinella as the most representative of the mixotrophic species found in the oligotrophic Lago Maggiore.     

Structure and assembly pattern of a freshwater short-tailed cyanophage Pam1

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AS-1 cyanophage infection inhibits the photosynthetic electron flow of photosystem II in Synechococcus sp. PCC 6301, a cyanobacterium

In Synechococcus sp. cells AS-1 cyanophage infection gradually inhibits the photosystem II mediated photosynthetic electron flow whereas the activity of photosystem I is apparently unaffected by the cyanophage infection. Transient fluorescence induction and flash-induced delayed luminescence decay studies revealed that the inhibition may occur at the level of the secondary acceptor, Q_B of photosystem II. In addition, the breakdown of D₁-protein is inhibited, comparable to DCMU-induced protection of D₁-protein turnover, in AS-1-infected cells.     

粪肠球菌噬菌体vB_EfaP_IME195的生物学特性及其全基因组分析

【目的】以粪肠球菌为宿主菌,从医院的污水中筛选出相应的粪肠球菌噬菌体v B_Efa P_IME195,简称IME195,研究其生物学特性;并通过高通量测序得到其全基因组,深入研究其基因组学特征。【方法】以临床的耐药粪肠球菌为宿主菌,利用医院污水筛选噬菌体并纯化;对噬菌体IME195生物学特性进行了深入研究,包括电镜观察噬菌体形态、最佳感染复数、一步生长曲线、噬菌体IME195对紫外线的敏感度、对温度的耐受程度、对p H的耐受程度、对氯仿是否敏感;通过蛋白酶K/SDS法提取噬菌体IME195全基因组;Ion Torrent高通量测序;测序后进行噬菌体全基因组序列组装、注释、进化分析和比较分析。【结果】通过噬菌体梯度稀释,双层培养基平板法得到噬菌斑边缘分明、斑体透明的裂解性噬菌体IME195,最佳感染复数为0.01,一步生长曲线显示IME195的潜伏期为30 min,暴发量为11。该噬菌体对紫外线比较敏感,对5%浓度的氯仿不敏感,噬菌体对高温比较敏感,该噬菌体在p H 6.0-8.0范围内具有良好的裂解活性;电镜观察结果显示该噬菌体属于尾病毒目短尾噬菌体科;全基因组分析表明:噬菌体IME195基因组大小只有18 607 bp(Gen Bank登录号为KT932700),G+C含量仅为33%。BLASTn比对结果表明,该噬菌体和Gen Bank中的噬菌体v B_Efae230P-4只有82%的相似性。对噬菌体IME195进行了全基因组功能注释和进化分析。【结论】分离鉴定了一株粪肠球菌噬菌体,进行了生物学特性、全基因组测序和生物信息学深入分析,为噬菌体治疗多重耐药细菌奠定了基础。     

Photosynthetic genes in viral populations with a large genomic size range from Norwegian coastal waters

This study reports the diversity of uncultured environmental viruses harbouring photosynthetic genes (psbA and psbD) in samples from cold seawater (latitude above 60 degrees ). The viral community in coastal Norwegian waters was separated according to genome size using pulse field gel electrophoresis. Viral populations within a wide genome size range (31-380 kb) were investigated for the presence of the psbA and psbD genes using PCR, combined with cloning and sequencing. The results show the presence of photosynthetic genes in viral populations from all size ranges. Thus, valuable information could be obtained about the size class to which viral particles that encode photosynthesis genes belong. The wide genomic size range detected implies that a different cyanophage profile has been observed than has been reported previously. Thus, the method of phage gene detection applied here may represent a truer picture of phage diversity in general or that there is a larger range of size profile for viruses with psbA and psbD in higher latitudes than for the better-studied lower latitudes. Alternatively, a picture of diversity based on a different set of biases than that from either isolation-based research or from conventional metagenomic approaches may be observed.     

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。