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。     

嗜酸氧化亚铁硫杆菌基因组学研究进展

嗜酸氧化亚铁硫杆菌(Acidithiobacillus ferrooxidan,A.ferrooxidans)广泛存在于酸性矿物废水中,与生物冶金和环境净化紧密相关。不同来源嗜酸氧化亚铁硫杆菌全基因组的测序,为我们利用比较基因组学和功能基因组学的方法去洞察嗜酸氧化亚铁硫杆菌功能基因,提供了坚实的研究基础和丰富的科研信息。简述了嗜酸氧化亚铁硫杆菌基因组学的基本特征;从比较基因组学和功能基因组学发现了嗜酸氧化亚铁硫杆菌菌株基因组水平的差异;通过生物信息学概述了该菌的铁和硫代谢机制,并从细菌的功能基因组学对其在生物冶金与环境治理等应用进行了展望。     

云南省蒙自酸性矿山排水微生物群落结构和功能

为探究酸性矿山排水生态系统不同环境中的微生物群落和功能,全面了解酸性矿山排水的形成和发展规律,采用高通量测序技术研究云南省蒙自某矿区酸矿水坑和周边溪水中的原核微生物群落组成,并结合样本理化特征分析影响群落结构的主要因素,进而解析菌群的环境功能。研究发现酸矿水坑中主要有广古菌门、变形菌门(包括α、γ和δ变形菌纲)、硝化螺菌门、厚壁菌门、放线菌门和酸杆菌门等类群,与周边溪水的群落结构具有明显差异。群落多样性与pH呈显著正相关,而热原体纲(Thermoplasmata)与pH呈负相关,可对群落结构起主导作用。酸矿水坑不同样本中均具有高丰度的亚铁原体属Ferroplasma (6.60%–86.34%),酸硫杆菌属Acidithiobacillus是酸矿水和沉积泥中主要的铁、硫氧化细菌,而专性铁氧化的钩端螺旋菌属Leptospirillum的丰度较低,铁卵形菌属Ferrovum几乎只存在于酸矿水中;此外,嗜酸或耐酸的异养菌广泛分布于酸矿水和沉积泥中,它们可促进铁、硫氧化菌的生长及催化矿石溶解。结果表明,pH通过影响微生物多样性和菌群分布而对酸性矿山排水环境微生物群落结构造成重大影响。     

硫对铅污染水稻土微生物活性及群落结构的影响

对含有不同浓度铅的水稻土添加硫代硫酸钠进行土培试验,研究硫作用下铅污染水稻土微生物活性及群落结构的变化.结果表明:添加硫底物后,土壤的氧化还原电位(Eh)升高,呼吸强度增强,硫氧化菌的数量显著增加.硫促进了土壤中硫氧化菌等微生物的生长并引起群落结构的变化,克隆测序表明,加硫处理下土壤微生物的特异性条带与拟杆菌、硫杆菌、β-变形菌和嗜酸菌具有很高的相似性.硫处理下土壤碳酸盐结合态及铁锰结合态铅含量发生了显著变化.     

冶金微生物的铁硫代谢多样性及其与矿物的相互作用

生物冶金是利用微生物铁硫元素代谢活性加速硫化矿物氧化溶解,并对其中有价金属加以提取回收的技术。冶金系统中微生物的代谢多样性及其耦合功能网络,尤其是以铁硫代谢途径为主的功能网络,在硫化矿物加速氧化溶解过程中承担了重要作用,是生物冶金技术理论研究的核心领域。本文归纳了冶金系统中多样化的微生物物种及其铁硫代谢途径,并从微生物代谢耦合角度探讨了微生物代谢多样性与矿物的相互作用。     

极端嗜酸硫杆菌高密度培养的研究进展

极端嗜酸硫杆菌属微生物在生物冶金、生物脱硫以及固体废弃物的处置中扮演重要作用,但该类微生物在培养过程中细胞浓度很低,限制了该类微生物的广泛应用。高密度培养是提高微生物生产效率的有效手段。高密度培养技术在嗜酸微生物中的应用能够显著减少微生物培养的生成成本,缩短生产周期,极端嗜酸硫杆菌微生物菌剂的输出速率。本文从菌种选育、培养条件、培养方式综述了极端嗜酸硫杆菌高密度培养的研究现状。     

硫酸铁对嗜酸氧化亚铁硫杆菌铁代谢基因表达的影响

目的:探讨硫酸铁对嗜酸氧化亚铁硫杆菌生长及铁代谢基因表达的影响.方法:用血细胞计数板和重铬酸钾滴定法研究了不同浓度硫酸铁对嗜酸氧化亚铁硫杆菌生长的影响,采用实时荧光定量PCR技术研究了硫酸铁对嗜酸氧化亚铁硫杆菌铁代谢基因表达的影响.结果:硫酸铁对嗜酸氧化亚铁硫杆菌的生长有抑制作用,随着培养基中硫酸铁浓度的增加,抑制作用也越来越明显.实时定量PCR结果表明,用0.15 M硫酸铁刺激细菌后,实验中所涉及的铁代谢相关基因表现出相似的表达趋势.刺激10 min后,基因均发生明显的的表达上调,且表现为最大值.刺激时间延长,上调幅度逐渐减小.不同的操纵子基因表现出不同的上调幅度.结论:硫酸铁对嗜酸氧化亚铁硫杆菌的生长有明显的抑制作用,铁代谢相关基因对硫酸铁的刺激有积极的反应.     

嗜酸硫杆菌在工农业中的应用

嗜酸硫杆菌(属)(Acidithiobacillus spp.)能够氧化亚铁、硫或还原性无机硫化合物(reduced inorganic sulfur compounds,RISCs)获得能量,固定二氧化碳,是一类典型的嗜酸性化能自养微生物。嗜酸硫杆菌广泛分布于酸性矿水、热泉等酸性环境中,是地球生态系统硫和铁元素循环的主要推动者。嗜酸硫杆菌独特的生理代谢特征和极端环境适应性,使其广泛应用于生物浸出领域。本文综述了嗜酸硫杆菌的生理代谢特征和极端环境下的适应机制,阐述了嗜酸硫杆菌在工农业中的应用,讨论了面向国家重大需求,嗜酸硫杆菌在今后的主要研究方向和需要解决的关键科学问题,为嗜酸硫杆菌在生理代谢、环境适应和工农业应用的研究提供重要的线索和启示。     

铜蓝精矿的生物浸出

采用两种嗜酸硫杆菌(嗜酸氧化亚铁硫杆菌和喜温硫杆菌)对铜蓝进行生物浸出,实验在有或没有4 g/L硫酸亚铁pH 2．0、150转/分、35℃的三角瓶中进行。实验结果表明:用两种菌混合浸出的铜几乎等于嗜酸氧化亚铁硫杆菌单独浸出的铜;另外,亚铁的加入能提高铜的浸出。     

大庆盐碱地九种植物根际土壤微生物群落结构及功能多样性

盐碱土是陆地表面生态脆弱区域。它与荒漠化过程相伴而生,不但造成了资源的破坏、农业生产的巨大损失,而且还对生物圈和生态环境构成威胁。研究盐碱地植物根际土壤微生物群落的多样性,对于盐碱土壤的植被恢复和生态重建具有重要意义。运用PCR-DGGE技术和Biolog微平板法,对大庆盐碱地9种不同植物根际土壤微生物结构和功能的多样性进行了分析。结果表明,不同植物根际土壤微生物组成不同,同一科的植物具有相似的微生物组成。对11个克隆进行了序列测定,发现这一地区植物根际优势微生物菌群为变形菌门(Proteobacteria)和酸杆菌门(Acidobacteria)。利用Biolog微平板法分析了微生物群落功能多样性。结果表明,不同植物根际土壤细菌群落对底物碳源的代谢特征存在着一定的差异,其中豆科的野大豆根际土壤细菌对底物碳源的代谢能力最强。     

Diversity of the communities of acidophilic chemolithotrophic microorganisms in natural and technogenic ecosystems

The main representatives of acidophilic chemolithotrophs oxidizing sulfide minerals, ferrous iron, elemental sulfur, and reduced sulfur compounds and forming microbial communities in the natural and technogenic ecosystems with low pH values and high concentrations of heavy metal ions are listed. The species and strain diversity of the communities and environmental factors affecting their composition (temperature, pH value, energy substrate, mineralogical composition of sulfide ore concentrates, the presence of organic substances, and level of aeration) are analyzed. Involvement of mobile genetic elements (IS elements and plasmids) in the structural changes of the chromosomal DNA in the course of switching microbial metabolism to the oxidation of new energy substrates or under increased concentrations of metal ions is shown to be a probable mechanism responsible for the intraspecific genetic heterogeneity of the populations. Importance of determination of the dominant strains of different microbial species in the communities and of their physiological peculiarities for stabilization, optimization, and enhancement of efficiency of biotechnological processes for sulfide mineral oxidation is stressed.     

Geomicrobiology of extremely acidic subsurface environments

Extreme acidophiles (microorganisms with pH optima of 相似文献   

Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center

Microbial processes within deep-sea hydrothermal plumes affect ocean biogeochemistry on global scales. In rising hydrothermal plumes, a combination of microbial metabolism and particle formation processes initiate the transformation of reduced chemicals like hydrogen sulfide, hydrogen, methane, iron, manganese and ammonia that are abundant in hydrothermal vent fluids. Despite the biogeochemical importance of this rising portion of plumes, it is understudied in comparison to neutrally buoyant plumes. Here we use metagenomics and bioenergetic modeling to describe the abundance and genetic potential of microorganisms in relation to available electron donors in five different hydrothermal plumes and three associated background deep-sea waters from the Eastern Lau Spreading Center located in the Western Pacific Ocean. Three hundred and thirty one distinct genomic ‘bins'' were identified, comprising an estimated 951 genomes of archaea, bacteria, eukarya and viruses. A significant proportion of these genomes is from novel microorganisms and thus reveals insights into the energy metabolism of heretofore unknown microbial groups. Community-wide analyses of genes encoding enzymes that oxidize inorganic energy sources showed that sulfur oxidation was the most abundant and diverse chemolithotrophic microbial metabolism in the community. Genes for sulfur oxidation were commonly present in genomic bins that also contained genes for oxidation of hydrogen and methane, suggesting metabolic versatility in these microbial groups. The relative diversity and abundance of genes encoding hydrogen oxidation was moderate, whereas that of genes for methane and ammonia oxidation was low in comparison to sulfur oxidation. Bioenergetic-thermodynamic modeling supports the metagenomic analyses, showing that oxidation of elemental sulfur with oxygen is the most dominant catabolic reaction in the hydrothermal plumes. We conclude that the energy metabolism of microbial communities inhabiting rising hydrothermal plumes is dictated by the underlying plume chemistry, with a dominant role for sulfur-based chemolithoautotrophy.     

微生物生态学理论框架

微生物是生态系统的重要组成部分,直接或间接地参与所有的生态过程。微生物生态学是基于微生物群体的科学,利用微生物群体DNA/RNA等标志物,重点研究微生物群落构建、组成演变、多样性及其与环境的关系,在生态学理论的指导和反复模型拟合下由统计分析得出具有普遍意义的结论。其研究范围从基因尺度到全球尺度。分子生物学技术的发展,使人们可以直接从基因水平上考查其多样性,从而使得对微生物空间分布格局及其成因的深入研究成为可能。进而可以从方法学探讨微生物生物多样性、分布格局、影响机制及其对全球变化的响应等。在微生物生态学研究中,群落构建与演化、分布特征(含植物-微生物相互关系)、执行群体功能的机理(生物地球化学循环等)、对环境变化的响应与反馈机理是今后需要关注的重点领域。概述了微生物生态学的概念,并初步提出其理论框架,在对比宏观生态学基础理论和模型的基础上,分析微生物多样性的研究内容、研究方法和群落构建的理论机制,展望了今后研究的重点领域。     

Risk Assessment,Microbial Communities,and Pollution-Induced Community Tolerance

Until recently, parameters from microorganisms were generally not included in risk assessment at a comparable level to animals and plants. However, the major part of global biomass, biodiversity, and ecosystem processes is present in the microbial world and microbiological techniques applicable to risk assessment are becoming available. Two microbial indicators are described based on the usage of multiwell plates with different substrates and a redox indicator for monitoring mineralisation. With both techniques autochthonous microbial communities are analysed. Producing functional fingerprints of the microbial community gives insights into the composition of different functions. This is equivalent to observations of ecological abundance and species composition. When lack of reference sites or reference data renders risk assessment difficult, measurement of the pollution-induced community tolerance (PICT) can provide useful information.     

Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau

Permafrost represents an important understudied genetic resource. Soil microorganisms play important roles in regulating biogeochemical cycles and maintaining ecosystem function. However, our knowledge of patterns and drivers of permafrost microbial communities is limited over broad geographic scales. Using high‐throughput Illumina sequencing, this study compared soil bacterial, archaeal and fungal communities between the active and permafrost layers on the Tibetan Plateau. Our results indicated that microbial alpha diversity was significantly higher in the active layer than in the permafrost layer with the exception of fungal Shannon–Wiener index and Simpson's diversity index, and microbial community structures were significantly different between the two layers. Our results also revealed that environmental factors such as soil fertility (soil organic carbon, dissolved organic carbon and total nitrogen contents) were the primary drivers of the beta diversity of bacterial, archaeal and fungal communities in the active layer. In contrast, environmental variables such as the mean annual precipitation and total phosphorus played dominant roles in driving the microbial beta diversity in the permafrost layer. Spatial distance was important for predicting the bacterial and archaeal beta diversity in both the active and permafrost layers, but not for fungal communities. Collectively, these results demonstrated different driving factors of microbial beta diversity between the active layer and permafrost layer, implying that the drivers of the microbial beta diversity observed in the active layer cannot be used to predict the biogeographic patterns of the microbial beta diversity in the permafrost layer.     

水圈微生物：推动地球重要元素循环的隐形巨人

正生活在水圈环境中的微生物数量巨大、遗传与代谢方式极为多样,它们驱动着地球上重要元素的循环。水圈微生物研究已经成为生命科学与地球科学的研究热点。国家自然科学基金委员会于2017年启动了"水圈微生物驱动地球元素循环的机制"重大研究计划(简称"水圈微生物"计划)。"水圈微生物"计划拟选择典型水圈生境,通过多学科交叉研究,借助新技术、新方法,揭示水圈微生物在物种、群落和生态水平驱动碳氮硫循环的机制及其环境响应,     

单细胞稳定同位素标记技术在固氮微生物中的应用研究

生物固氮是指固氮微生物将大气中氮气还原为生物可利用氨的过程,是环境中新氮的主要来源,调控初级生产力并影响氮储库的收支平衡。由于环境中大部分固氮微生物不可纯培养,不依赖培养且具有高空间分辨率水平的单细胞技术,成为研究固氮微生物的有力手段。~(15)N_2稳定同位素标记技术,以微生物对~(15)N的同化量或速率为依据,是表征微生物固氮活性的最直接手段。本文对~(15)N_2稳定同位素标记结合两种单细胞技术,即纳米二次离子质谱(Nano SIMS)和单细胞拉曼光谱,用于固氮微生物研究的最新进展进行了综述,内容包括揭示环境中高活性固氮微生物、空间分布、与其他生物的共生关系、细胞生理状态等,并进一步对近期发展的基于单细胞拉曼光谱的固氮微生物研究进行了展望。     

盐城滨海滩涂湿地典型植物群落土壤微生物组成与结构特征

土壤微生物是生态系统维持正常结构与功能的重要组成部分,为探究盐城滩涂典型湿地土壤微生物群落结构特征,以江苏盐城滩涂互花米草、藨草、盐地碱蓬、芦苇及淤泥质光滩5种典型群落为对象,采用16S rRNA高通量测序技术分析0—10 cm(表层)、10—30 cm(中层)、30—60 cm(深层)土壤微生物多样性及群落结构。结果表明：(1)几种植物群落间,土壤微生物群落结构差异较大,主要体现在细菌群落结构的差异性,古菌群落结构差异相对较小。光滩与植物群落间,在土壤细菌种类及相对丰度上差异相对较大,互花米草群落与本土植物群落间,在微生物群落的细菌种类组成上存在较大差异;藨草群落土壤表层微生物群落结构与互花米草群落相似,深层与盐地碱蓬、芦苇群落相似。(2)同一群落不同层次土壤微生物群落结构相似,差异小于不同群落间土壤微生物群落的结构差异性;不同群落对应层次间,表深层土壤中五种群落土壤微生物多样性存在显著差异,中层土壤中五种群落微生物多样性差异不显著。总体上,植物群落类型对土壤微生物群落结构的影响大于土壤深度;与本土植物群落相比,互花米草群落土壤主要优势门微生物种类差异较小,但部分优势门微生物相对丰度...     

Plant Communities, Soil Microorganisms, and Soil Carbon Cycling: Does Altering the World Belowground Matter to Ecosystem Functioning?

Soil microorganisms mediate many critical ecosystem processes. Little is known, however, about the factors that determine soil microbial community composition, and whether microbial community composition influences process rates. Here, we investigated whether aboveground plant diversity affects soil microbial community composition, and whether differences in microbial communities in turn affect ecosystem process rates. Using an experimental system at La Selva Biological Station, Costa Rica, we found that plant diversity (plots contained 1, 3, 5, or > 25 plant species) had a significant effect on microbial community composition (as determined by phospholipid fatty acid analysis). The different microbial communities had significantly different respiration responses to 24 labile carbon compounds. We then tested whether these differences in microbial composition and catabolic capabilities were indicative of the ability of distinct microbial communities to decompose different types of litter in a fully factorial laboratory litter transplant experiment. Both microbial biomass and microbial community composition appeared to play a role in litter decomposition rates. Our work suggests, however, that the more important mechanism through which changes in plant diversity affect soil microbial communities and their carbon cycling activities may be through alterations in their abundance rather than their community composition.