微生物浸出过程中胞外蛋白的作用及其机理研究进展

矿物-微生物-溶液多相界面是硫化矿生物浸出的关键场所,界面微生物胞外多聚物(EPS)关键组分胞外蛋白在生物膜形成、结构稳定和硫化矿溶解等方面起到关键作用。综述了生物浸出过程中EPS关键组分胞外蛋白的研究进展和胞外蛋白现有的研究方法及其对冶金微生物胞外蛋白研究的适用性,展望了浸矿微生物胞外蛋白研究的前景,旨为生物冶金领域研究EPS关键组分胞外蛋白结构及其作用机理提供重要的理论和方法支撑。     

微生物在矿物表面吸附的研究进展

微生物在矿物表面的吸附是微生物与矿物表面深度作用的前提, 也是生物药剂在选矿中的应用的基础研究。本文综述了影响微生物在矿物表面吸附的环境因素, 微生物细胞与矿物表面之间的相互作用, 微生物细胞表面基团、表面成分及其胞外聚合物对吸附过程的影响, 并提出了今后的研究方向。     

土壤矿物与微生物相互作用的机理及其环境效应

土壤矿物与微生物相互作用是地球表层系统中重要的生态过程.微生物或生物分子与矿物间的吸附(粘附)是两者相互作用的基础.吸附(粘附)是一个由分子间力、静电力、疏水作用力、氢键和空间位阻效应等多种作用力或作用因素共同决定、影响的物理化学过程.因此,微生物和矿物的表面性质如表面电荷、疏水性和它们所处的环境条件如pH、电解质浓度、温度等,都影响着矿物-微生物吸附(粘附)过程.微生物细胞或酶可吸附于矿物表面,其结果是细胞代谢或酶活性会发生明显变化,并进一步影响土壤中诸多相关的生态、环境过程.结合4种典型的初始吸附理论:表面自由能热力学理论、DLVO理论、吸附等温线理论和表面复合物理论及本课题组近年来的研究成果,对土壤矿物与微生物相互作用的类型、机理、作用力和现代研究技术等方面的最新研究进展进行了较为全面的论述,对土壤矿物-微生物相互作用的环境效应进行了讨论,并就该领域今后研究工作的特点及应关注的问题进行了展望.     

表面活性剂对土壤中多环芳烃生物有效性影响的研究进展

表面活性剂能够改变多环节烃(Polycyclic aromatic hydrocarbons,PAHs）在土壤中的溶解度、吸附/解吸平衡和与土壤微生物的相互作用,从而改变PAHs的生物有效性,表面活性剂主要通过降低土壤-水之间的界面张力,增加PAHs的溶解度、促进PAHs的运输等方式来加强PAHs的生物有效性,但由于表面活性剂本身对微生物的毒害作用或无毒的表面活性剂优先作为微生物的生长基质,可能会对PAHs的生物有效性起到抑制作用,另外,表面活性剂对土壤中不同形态的PAHs生物有效性的影响不同,表面活性剂、PAHs和土壤微生物的类型浓度以及土壤的物理化学条件等都对PAHs的生物有效性有影响。     

生物冶金中耐盐浸矿微生物的研究进展

耐盐浸矿微生物是指在发挥矿物浸出功能时对所处的含盐环境具有一定耐受能力的一类浸矿微生物。耐盐浸矿微生物因其可以适应不同浓度的氯化钠等盐,因而在淡水资源缺乏地区的生物冶金中具有广泛的应用价值。本文从耐盐浸矿微生物的种类、耐盐机制及其在矿物生物浸出中的应用现状进行了系统性综述,为耐盐浸矿微生物的研究和应用提供参考。     

强化产电微生物与电极间电子传递速率的研究进展

产电微生物是微生物燃料电池、电解池和电合成等微生物电化学技术(Microbial electrochemical technologies,METs)的研究基础。产电微生物与电极界面间的胞外电子传递(Extracellular electron transfer,EET)效率低以及生物被膜形成能力弱限制了METs在有机物降解、电能生产、海水淡化、生物修复和生物传感等方面的应用。因此,强化产电微生物与电极界面间的相互作用是过去几年的主要研究热点。针对近年的研究,本文系统概述了通过改造产电微生物来增强微生物-电极间相互作用的各种策略,重点分析了这些策略的适用性和局限性,并展望了强化产电微生物-电极界面作用在微生物电化学技术利用方面的研究前景。     

沉水植物茎叶微界面特性研究进展

沉水植物茎叶-水界面是浅水湖泊的重要界面之一,对湖泊生物地球化学循环和水环境质量具有重要影响。富营养化水体中,大量的附着物常富集在沉水植物茎叶表面,形成了特殊的生物-水微界面。对该微界面特性进行深入研究,有助于揭示沉水植物在微环境层面对富营养化水体中物质循环的调控过程和机制。沉水植物茎叶微界面具有促进水体养分转化、改变环境因子及可溶性物质的空间分布,增加物质运输的阻力和距离、降低植物光合作用、调控重金属等生态功能;微界面结构及环境因子受水体营养盐浓度、沉水植物种类及生长阶段等因素的影响。对微界面结构功能的主要研究方法进行了分析总结,并对沉水植物茎叶微界面的研究前沿进行了展望。     

土壤铁矿物形态转化影响有机碳固定研究进展

铁是地壳中丰度第四高的元素,其可通过多种方式影响土壤有机碳累积,尤其铁氧化物与土壤有机碳相互作用形成的稳定有机-矿物复合物,被认为是土壤可溶性有机碳长期固定的关键地球化学机制。促进土壤固定有机碳不仅可以提高土壤质量和肥力,还是应对全球气候变化的主要策略之一。然而,铁活跃的氧化还原反应和多样化的赋存形态,使其转化过程对土壤有机碳累积和稳定性的影响结果受到诸多生物和非生物因素调控。从不同角度,结合多学科的研究成果,综述了近年来国内外关于铁矿物形态转化影响土壤有机碳固定的相关研究,包括铁矿物形态转化过程、土壤有机碳固定机制、铁矿物形态转化影响土壤有机碳固定的机制及其主要影响因素（各种环境条件、自身的铁矿物性质、碳源质量等方面）,强调铁在土壤有机碳固定过程中的重要作用。对铁固定土壤有机碳的相关研究提出了建议,为今后研究提供相关参考。     

生物破乳菌形态、表面性质和物质特征研究方法与进展

生物破乳菌在石油开采与加工行业的研究已经引起各界的广泛关注,然而由于生物破乳菌菌体形态、表面性质和表面物质的复杂性,使菌体的破乳活性特征尚未被揭示。本文介绍了生物破乳剂的来源、合成及破乳机制;归纳了影响生物破乳菌破乳活性的菌体形态、表面性质和表面物质三方面因素的研究进展,特别是总结了相关研究的方法;最后在此基础上对今后研究方向提出展望。     

2020年地质微生物学专刊序言

中国微生物学会地质微生物学专业委员会第八届地质微生物学研讨会于2019年6月13-15日在青岛举行,来自国内外127所高校和科研院所的600余位专家学者齐聚此次会议,围绕地质微生物学领域相关的最新研究进展进行了深入交流和研讨。为展示与会学者的部分最新研究成果,特组织这期地质微生物专刊。
本期《微生物学报》专刊以地质微生物学为主题,选取了第八届地质微生物学学术会议报导的地质微生物学研究新技术、极端环境微生物、微生物与元素生物地球化学循环、微生物-矿物相互作用、地质微生物应用、以及环境微生物生态与进化等领域的19篇文章,与读者共享。在“地质微生物学研究新技术”专栏,提出了单细胞拉曼光谱在研究代谢过程、分选活细胞以及揭示细胞对物质利用等方面的应用前景;在“极端环境微生物”专栏,报导了贵州兴义喀斯特洞穴中的微生物多样性及抗菌活性,综述了嗜盐菌中甘氨酸甜菜碱的合成途径及其生物学功能;在“微生物与元素生物地球化学循环”专栏,报导了海洋异养细菌、好氧甲烷氧化耦合反硝化细菌、与农田土壤中丛枝菌根真菌-根际细菌及其在碳氮磷循环过程中作用,综述了海洋氮循环过程及基于基因组代谢网络模型预测研究进展、以及湖泊微生物参与硝化、反硝化与硫循环过程的研究进展;在“微生物-矿物相互作用”专栏,报导了铁还原菌与砷还原菌与矿物相互作用及其对元素循环的影响;在“地质微生物应用”专栏,报导了典型油气藏上方土壤甲烷氧化菌群落特征及其勘探意义与煤灰分和无机矿物对生物产气的影响;在“环境微生物生态与进化”专栏,报导了我国南海、东海与黄河三角洲沉积物微生物群落结构特征,综述了候选门级辐射类群（CPR）细菌与古菌ESCRT系统研究进展。
希望通过本专刊,进一步扩大地质微生物学在国内的影响、并促进地质微生物学相关学科的发展和融合。     

Non‐homogeneous biofilm modeling applied to bioleaching processes

A two‐dimensional non‐homogeneous biofilm model is proposed for the first time to study chemical and biochemical reactions at the microorganism scale applied to biological metal leaching from mineral ores. The spatial and temporal relation between these reactions, microorganism growth and the morphological changes of the biofilm caused by solid inorganic precipitate formation were studied using this model. The model considers diffusion limitations due to accumulation of inorganic particles over the mineral substratum, and allows the study of the effect of discrete phases on chemical and microbiological mineral solubilization. The particle‐based modeling strategy allowed representation of contact reactions between the microorganisms and the insoluble precipitates, such as those required for sulfur attack and solubilization. Time‐dependent simulations of chemical chalcopyrite leaching showed that chalcopyrite passivation occurs only when an impervious solid layer is formed on the mineral surface. This mineral layer hinders the diffusion of one kinetically determinant mineral‐attacking chemical species through a nearly irreversible chemical mechanism. Simulations with iron and sulfur oxidizing microorganisms revealed that chemolithoautotrophic biofilms are able to delay passivation onset by formation of corrosion pits and increase of the solid layer porosity through sulfur dissolution. The model results also show that the observed flat morphology of bioleaching biofilms is favored preferentially at low iron concentrations due to preferential growth at the biofilm edge on the surface of sulfur‐forming minerals. Flat biofilms can also be advantageous for chalcopyrite bioleaching because they tend to favor sulfur dissolution over iron oxidation. The adopted modeling strategy is of great interest for the numerical representation of heterogeneous biofilm systems including abiotic solid particles. Biotechnol. Bioeng. 2010;106: 660–676. © 2010 Wiley Periodicals, Inc.     

Investigation of energy gene expressions and community structures of free and attached acidophilic bacteria in chalcopyrite bioleaching

In order to better understand the bioleaching mechanism, expression of genes involved in energy conservation and community structure of free and attached acidophilic bacteria in chalcopyrite bioleaching were investigated. Using quantitative real-time PCR, we studied the expression of genes involved in energy conservation in free and attached Acidithiobacillus ferrooxidans during bioleaching of chalcopyrite. Sulfur oxidation genes of attached A. ferrooxidans were up-regulated while ferrous iron oxidation genes were down-regulated compared with free A. ferrooxidans in the solution. The up-regulation may be induced by elemental sulfur on the mineral surface. This conclusion was supported by the results of HPLC analysis. Sulfur-oxidizing Acidithiobacillus thiooxidans and ferrous-oxidizing Leptospirillum ferrooxidans were the members of the mixed culture in chalcopyrite bioleaching. Study of the community structure of free and attached bacteria showed that A. thiooxidans dominated the attached bacteria while L. ferrooxidans dominated the free bacteria. With respect to available energy sources during bioleaching of chalcopyrite, sulfur-oxidizers tend to be on the mineral surfaces whereas ferrous iron-oxidizers tend to be suspended in the aqueous phase. Taken together, these results indicate that the main role of attached acidophilic bacteria was to oxidize elemental sulfur and dissolution of chalcopyrite involved chiefly an indirect bioleaching mechanism.     

外来杂草入侵的化学机制

由外来杂草入侵引发的严重生态和经济问题已倍受关注,外来杂草在新生境成功入侵,除了具备一些基本的生物生态学特征外,还应具备一些特有的入侵机制,阐明外来杂草的各种入侵机制可以为入侵杂草的预测和控制提供科学依据。外来杂草只有在新生境中与原产地生物种间的相互作用中取得优势,才能定植并扩增种群而成功入侵．在这些外来杂草和原产地生物种间的相互作用关系中,化学关系是不可忽视的方面．目前研究已经证实：植物的化感作用在外来杂草成功入侵中发挥着重要的作用．事实上,植物也可以通过合成和释放特定的化学物质防御或抑制新生境的动物、植物和微生物．外来杂草入侵的化学机制涉及到植物化学生态学的各个方面。因此,外来杂草的化学生态学特征应作为入侵种预测的重要指标之一,外来杂草入侵的化学机制应是今后重要的研究方向。     

Effects of L-cysteine on Ni-Cu sulfide and marmatite bioleaching by Acidithiobacillus caldus

The effect of L-cysteine in different concentrations on the bioleaching of Ni-Cu sulfide and marmatite were studied with a moderately thermophilic, sulfur-oxidizing bacterium, strain of Acidithiobacillus caldus. X-ray diffraction (XRD) observations showed the change of bioleached solid residues and the effect of L-cysteine on the surface charges of minerals. It was found that adding certain amounts of L-cysteine to the leaching system of Ni-Cu sulfide largely enhanced the leaching rate, while L-cysteine inhibited the bioleaching of marmatite by A. caldus. The mechanism of L-cysteine interaction with mineral surfaces was studied by means of zeta potential determination and IR spectra.     

矿物电子能量协同微生物胞外电子传递与生长代谢

矿物是无机自然界吸收与转化能量的重要载体,其与微生物的胞外电子传递过程体现出矿物电子能量对微生物生长代谢与能量获取方式的影响。根据电子来源与产生途径,以往研究表明矿物中变价元素原子最外层或次外层价电子与半导体矿物导带上的光电子是微生物可以利用的两种不同胞外电子能量形式,其产生及传递方式与微生物胞外电子传递的电子载体密切相关。在协同微生物胞外电子传递过程中,矿物不同电子能量形式之间既有相似性亦存在着差异。反过来,微生物胞内-胞外电子传递途径也影响对矿物电子能量的吸收与获取,进而对微生物生长代谢等生命活动产生影响。本文在阐述矿物不同电子能量形式产生机制及其参与生物化学反应的共性和差异性特征基础上,综述了微生物获取矿物电子能量所需的不同电子载体类型与传递途径,探讨了矿物不同电子能量形式对微生物生长代谢等生命活动的影响,展望了自然条件下微生物利用矿物电子能量调节其生命活动、调控元素与能量循环的新方式。     

Surface alteration of realgar (As4S4) by Acidithiobacillus ferrooxidans

The chemical and physical characteristics of realgar (an arsenic sulfide mineral that occurs in several crystalline forms) in the presence of Acidithiobacillus ferrooxidans BY-3 were investigated in this work. Grains of the mineral were incubated for 10, 20, and 30 days with A. ferrooxidans cultured in 9K medium at 30 °C and at 150 rpm agitation. Abiotic control experiments were conducted in identical solutions. The effect of bioleaching on the surface properties of realgar was characterized by scanning electron microscopy (SEM), energy-dispersive spectroscopy (EDS), inductively coupled plasma atomic emission spectroscope (ICP-AES), X-ray diffraction (XRD), and Raman spectroscopy. SEM and EDS analyses confirmed the ability of A. ferrooxidans to modify surfaces of realgar and to efficiently enhance its dissolution. ICP-AES showed the dissolution and precipitation of realgar during bioleaching. Based on the XRD pattern and the Raman spectra, the decrease in arsenic in the liquid phase was due to co-precipitation of the mineral with Fe(III) or Fe(III) compounds (e.g., jarosite or goethite). Thus, not only did Fe(III) alter the surface of realgar, but it also promoted its dissolution during bioleaching.     

Demineralization of coal by stepwise bioleaching: a comparative study of three Indian coals by fourier transform infra red and X-ray diffraction techniques

A method was devised for the removal of deleterious minerals and metals from high ash-containing Indian coals. A selective enriched mixed culture developed for this purpose was used for stepwise aerobic bioleaching of two high ash Indian bituminous coals (Topa coal and Godavari coal) and Neyveli lignite. The process of bioleaching resulted in the removal of more than 50% of the mineral matter in five repeated steps and thus produced relatively demineralized, clean coal. Various parameters were optimized for bioleaching in order to maximize the removal of mineral matter. Based on the above studies a two-step pilot experiment was conducted under optimum conditions. The results obtained indicated removal of 75% of the mineral matter from one of the coals. The changes in mineral matter composition of these coals were evaluated using Fourier Transform Infra Red (FTIR) spectroscopy and X-ray diffraction (XRD) techniques. The results indicated a decrease in the intensity of many peaks when seen in combination with the amount of mineral matter removed from the bioleached coals. The mechanism of the bioleaching process is discussed and many uses of the clean coal produced are suggested.     

Field- and Lab-Based Potentiometric Titrations of Microbial Mats from the Fairmont Hot Spring,Canada

Potentiometric titrations are an effective tool to constrain the protonation constants and site concentrations for microbial surface ligands. Protonation models developed from these experiments are often coupled with data from metal adsorption experiments to calculate microbial ligand-metal binding constants. Ultimately, the resulting surface complexation models can be used to predict metal immobilization behavior across diverse chemical conditions. However, most protonation and metal-ligand thermodynamic constants have been generated in laboratory experiments that use cultured microbes which may differ in their chemical reactivity from environmental samples. In this study, we investigate the use of in situ field potentiometric titrations of microbial mats at a carbonate hot spring located at Fairmont Hot Springs, British Columbia, with the aim to study microbial reactivities in a natural field system. We found that authigenic carbonate minerals complicated the potentiometric titration process due to a “carbonate spike” introduced by the contribution of inorganic carbonate mineral dissolution and subsequent carbonate speciation changes during the transition from low to high pH. This inhibits the determination of microbial surface ligand variety and concentrations. Our preliminary study also highlights the need for developing novel probes to quantify in situ microbial mat reactivity in future field investigations.     

Biomineralization at hot springs and mineral springs, and their significance in relation to the Earth's history]

Recently, there is strong interest on microbe-mineral interactions. This is related also to recent expanded knowledges on extremely severe environments in which microbes live. Interaction between microbes and minerals contains biomineralization processes. Varieties of biomineralization products are found not only in various geologic materials and processes in the earth's history but also in present surface environments. Some hot springs represent such environments similar to those of unique and extremely severe environments for life. In this short review, the author briefly shows some examples of biomineralizations at some hot springs and mineral springs, Japan. In such environments, iron ore was formed and some varieties of growing stromatolites were found. The varieties of stromatolite are siliceous, calcic and manganese types. Cyanobacteria and the other bacteria are related to form the stromatolite structure. In the Gunma iron ore, sedimentary iron ores were mineralogically described in order to evaluate the role of microorganisms and plants in ore formation. The iron ore is composed of nanocrystalline goethite. Algal fossils are clearly preserved in some ores. Various products of biomineralization are found in the present pH 2-3, Fe2(+)- and SO4(2-)-rich streams. Bacterial precipitation had variations from amorphous Fe-P-(S) precipitates near the outlet of mineral spring, to Fe-P-S precipitates and to Fe-S-(P) precipitates. Mosses and green algae are also collecting Fe precipitates in and around the living and dead cells. The Gunma Iron Ore can be said as Biologically Induced Iron Ore. At Onikobe and Akakura hot springs, growing stromatolites of siliceous and calcareous types, were found, respectively. At Onikobe, The stromatolites grow especially near the geyser. Cyanobacterial filaments in stromatolite were well preserved in the siliceous and calcic stromatolites. The filaments oriented in two directions which form the layered structures were found. At Yunokoya hot spring, black and brittle stromatolitic structures which were composed of amorphous Mn minerals are growing. The form of these structures are hemispherical. Many bacteria that were coated with amorphous Mn minerals were found on these structures. Furthermore, Precambrian (Proterozoic : Wittenoom-Chichester region, western Australia) manganese stromatolite was briefly shown in comparison. The black stromatolite has been clarified to be composed of todorokite. Small spotty and donuts-like shaped todorokite aggregates which are very similar to biologically induced Mn-precipitates were found in massive dolomite layers.