水稻土中铁还原菌多样性

微生物介导的异化Fe(III) 还原是非硫厌氧环境中Fe(III) 还原生成Fe(II) 的主要途径,然而相关的铁还原菌还不是很清楚,特别是在水稻土中.本文采用富集培养的方法,以乙酸和氢气作为电子供体,水铁矿和针铁矿作为电子受体,通过末端限制性片段长度多态性（T-RFLP）技术和16S rRNA基因克隆测序相结合的分子生物学方法研究了水稻土中铁还原菌的多样性.结果表明：无论是以乙酸或氢气为电子供体,水铁矿或针铁矿为电子受体,地杆菌（Geobacter）和梭菌（Clostridiales）是富集到的主要微生物群落;乙酸为电子供体时,富集到的主要微生物群落还包括红环菌（Rhodocyclaceae）;因此,除地杆菌外,梭菌和红环菌很可能也是水稻土中重要的铁还原菌.     

水稻土中硫酸盐还原微生物研究进展

硫是水稻必需的营养元素之一.硫酸盐还原是硫元素生物地球化学循环中的关键步骤,在稻田土壤表层和水稻根际都十分活跃.介导硫酸盐还原过程的硫酸盐还原菌(sulfate- reducing bacteria, SRB)是稻田土壤中重要的功能菌群.它们不仅是硫元素生物地球化学循环的重要参与者,也是土壤中有机污染物降解的主要力量之一,发挥着重要的生态和环境功能.综述了稻田土壤中微生物参与的硫酸盐还原过程、SRB的生物多样性以及目前研究稻田土壤SRB主要采用的分子生态学方法,如末端限制性片段长度多样性(T-RFLP)、变性梯度凝胶电泳(DGGE)、实时荧光定量PCR(real-time PCR)、荧光原位杂交(FISH),并对水稻土壤中SRB的分子生态学研究方向进行了展望.     

新疆低阶煤本源生物甲烷转化中微生物群落组成及变化

【目的】探究新疆低阶煤生物甲烷转化过程微生物群落组成及多样性。【方法】采用厌氧培养方法和末端限制性片段长度多态性技术(Terminal restriction fragment length polymorphism,T-RFLP)分析新疆低阶煤本源微生物对甲烷转化及有机酸含量的影响,分析新疆哈密大南湖长焰煤生物甲烷转化过程中微生物群落动态变化。【结果】研究表明长焰煤和褐煤对本源微生物产甲烷影响较小,随着低阶煤生物甲烷转化时间的延长,甲烷产量呈上升趋势,转化60 d后长焰煤甲烷产量高达10.28 m L/g,挥发性有机酸(VFA)浓度则最低;微生物多样性指数变化不明显,不同转化时间微生物主要类群为放线菌门(Actinobacteria),拟杆菌门(Bacteroidetes),厚壁菌门(Firmicutes),变形菌门(Proteobacteria);甲烷菌的群落结构相对于细菌较简单,在整个低阶煤生物转化产甲烷过程中共有古菌类群为甲烷八叠球菌属(Methanosarcina)、甲烷盐菌属(Methanohalobium)、甲烷叶菌属(Methanolobus)、甲烷食甲基菌属(Methanomethylovorans),它们是构成群落结构的基本菌群。【结论】低阶煤生物甲烷转化过程微生物群落具有丰富的多样性,且不同时期多样性有较大差异。甲烷菌群落结构相对于细菌较简单,共有类群明显。     

新疆醉马草内生菌群落结构

【目的】揭示醉马草不同组织内生细菌和内生真菌种群组成和分布。【方法】采用液氮研磨法分别提取醉马草种子、叶、茎、根组织总DNA,采用通用引物扩增内生细菌16S rDNA和真菌ITS,通过限制性内切酶HhaⅠ和RsaⅠ对16S rDNA PCR产物酶切,HhaeⅢ和HinfⅠ对真菌rDNA ITS PCR产物酶切得到不同的TRFs片段。TRFs经T-RFLP分析程序结合基因文库比对后,分析醉马草不同组织中内生细菌和内生真菌的群落组成及内生菌群落相似性。【结果】研究表明醉马草根部内生细菌多样性最高,而种子内生真菌多样性最为丰富。醉马草各组织内生细菌优势菌属均为Bacillus(29%以上),种子、叶、茎、根内生真菌优势菌属分别为Mycosphaerella(6.5%),Teratosphaeria(4.5%),Fragum(1.1%),Sebacina(11.3%)。聚类分析表明茎和叶内生细菌群落结构相似,种子和其他组织内生细菌群落结构相似性较远,而茎和种子内生真菌群落结构相似,叶和其他组织内生真菌群落结构相似性较远。醉马草内生菌多样性丰富且存在尚未认识的新类群。     

松江湿地沉积物细菌T-RFLP分析中PCR体系的建立与优化

细菌是微生物的重要组成部分,其对保持湿地生态系统平衡起着重要作用,在沉积物细菌T-RFLP(terminal restriction fragment length polymorphism)分析中建立与优化PCR体系对进一步研究沉积物细菌群落组成具有重要意义。此次研究以松江湿地沉积物细菌基因组DNA为模板,采用正交和单因素试验对PCR体系中各因素(模板DNA、Mg2+、dNTPs、引物、Taq酶)进行优化,系统分析各因素对PCR扩增结果的影响,建立最佳PCR反应体系。在20μL反应体系中,DNA模板30 ng、Mg2+2.0 mmol/L、dNTPs 0.2 mmol/L、引物0.2μmol/L、Taq酶0.5 U。该优化体系确保了沉积物细菌T-RFLP分析过程中PCR产物的质量与效果。     

黄河滩地和稻田土中铁还原菌、不产氧光合细菌分布机制

【目的】探讨沿黄流域土壤中铁还原菌(ferric reducing bacteria, Fe RB)、不产氧光合细菌(anoxygenic phototrophic bacteria, An PB)的分布机制。【方法】以沿黄流域(原阳段)为研究对象,采集黄河滩地和稻田土样,利用16Sr RNA基因高通量测序和实时荧光定量分析技术,结合统计学分析,揭示Fe RB、An PB菌群结构、丰度和主要环境影响因子。【结果】二者中的优势Fe RB在科(属)水平为Hydrogenophilaceae(Thiobacillus)、 Bacillaceae(Bacillus)、 Clostridiaceae、Rhodobactereace(Rhodobacter)、 Geobacteraceae(Geobacter),优势An PB为Rhodobactereace(Rhodobacter)、 Chloroflexaceae(Chloronema)、 Acetobacteraceae(Roseomonas)。An PB中Rhodobacteraceae与Fe RB中Bacillaceae、 Clostri...     

贵阳市湖泊沉积物中铁还原菌的季节分布

采用滚管计数法检测了贵阳市红枫湖、百花湖、阿哈湖沉积物不同季节铁还原菌(DIRB)含量,并分析了其pH及有机质等理化参数,检测了其沉积物孔隙水中铁、硫酸根含量。阿哈湖、百花湖和红枫湖沉积物中DIRB含量分别为1.09×104~8.83×105、1.05×104~3.43×105和4.80×103~4.47×105cells·g-1。暖季(6和9月)沉积物DIRB含量高于冬季(2月)1~2个数量级,且表层沉积物DIRB含量与界面水溶解氧含量呈显著相关(P0.05),表明沉积物DIRB含量受溶解氧和温度影响明显。由于受到沉积物中O2、SO42-等其他微生物可利用电子受体的控制,沉积物剖面上DIRB活动区域随着冬夏季节交替有向沉积物上部迁移的趋势。虽然阿哈湖长期受酸性煤矿废水污染,但各湖泊丰富的有机质(60~140 g·kg-1)及适宜的pH(6.2~7.1)为铁还原菌的生长提供了适宜的生长环境,使得水库之间沉积物铁还原菌在数量级上差异不大,但阿哈湖沉积物中铁还原菌生长峰值明显高于红枫湖、百花湖。     

水稻土中铁氧化物对产甲烷古菌群落结构的影响

产甲烷菌广泛分布在淹水水稻土等各种厌氧环境中,在全球气候变化、碳循环和能源等领域都发挥着重要的作用。研究发现,厌氧条件下,水稻土中铁氧化物的生物还原会抑制产甲烷菌的甲烷合成作用。然而,目前关于铁氧化物对产甲烷菌群落结构的影响报道较少。通过泥浆厌氧培养实验,向采集的水稻土中添加甲酸盐作为甲烷合成的底物(Control,CK处理),并设置添加水铁矿作为体系中唯一电子受体的处理组(Ferrihydrite,Fh处理)。培养结束后,与CK相比,添加水铁矿显著降低了古菌在总微生物群落中的占比,但对古菌群落的物种多样性和均一度没有显著影响;且两组处理中优势种均为操作分类单元(Operational taxonomic unit,OTU)2056和OTU 911(76%—80%)。这说明碳源相同时,产甲烷菌的群落结构不受铁氧化物的影响。本研究为探索土壤中微生物铁还原与碳循环耦合的分子机制奠定基础。     

DGGE和T-RFLP在堆肥微生物群落结构研究中的应用

对堆肥微生物种群分布及其动态变化的研究进行了分析,论述了分子生物技术中的变性梯度凝胶电泳和末端标记限制性片段长度多态性的原理和特点,以及用于研究堆肥微生物的群落结构演变规律,为分析和筛选堆肥中的微生物提供更加有效、快速的信息,促进堆肥技术的发展。     

Enumeration of Fe(II)-oxidizing and Fe(III)-reducing bacteria in the root zone of wetland plants: Implications for a rhizosphere iron cycle

Iron plaque occurs on the roots of most wetland and submersed aquatic plant species and is a large pool of oxidized Fe(III) in some environments. Because plaque formation in wetlands with circumneutral pH has been largely assumed to be an abiotic process, no systematic effort has been made to describe plaque-associated microbial communities or their role in plaque deposition. We hypothesized that Fe(II)-oxidizing bacteria (FeOB) and Fe(III)-reducing bacteria (FeRB) are abundant in the rhizosphere of wetland plants across a wide range of biogeochemical environments. In a survey of 13 wetland and aquatic habitats in the Mid-Atlantic region, FeOB were present in the rhizosphere of 92% of the plant specimens collected (n = 37), representing 25 plant species. In a subsequent study at six of these sites, bacterial abundances were determined in the rhizosphere and bulk soil using the most probable number technique. The soil had significantly more total bacteria than the roots on a dry mass basis (1.4 × 10⁹ cells/g soil vs. 8.6 × 10⁷ cells/g root; p < 0.05). The absolute abundance of aerobic, lithotrophic FeOB was higher in the soil than in the rhizosphere (3.7 × 10⁶/g soil vs. 5.9 × 10⁵/g root; p < 0.05), but there was no statistical difference between these habitats in terms of relative abundance (1% of the total cell number). In the rhizosphere, FeRB accounted for an average of 12% of all bacterial cells while in the soil they accounted for < 1% of the total bacteria. We concluded that FeOB are ubiquitous and abundant in wetland ecosystems, and that FeRB are dominant members of the rhizosphere microbial community. These observations provide a strong rationale for quantifying the contribution of FeOB to rhizosphere Fe(II) oxidation rates, and investigating the combined role of FeOB and FeRB in a rhizosphere iron cycle.     

异化Fe(Ⅲ)还原微生物研究进展

铁是地壳中含量第四丰富的元素,微生物介导的异化铁还原是自然界中Fe(Ⅲ)还原的主要途径。介绍了Fe(Ⅲ)还原菌的分类及多样性,总结了Fe(Ⅲ)还原菌还原铁氧化物机制及其产能代谢机制,概述了Fe(Ⅲ)还原菌的生态环境意义,并对未来Fe(Ⅲ)还原菌的分子生态学研究方向提出了探索性的建议。     

Isolation and Characterization of Pseudomonas stutzeri Capable of Reducing Fe(III) and Nitrate from Skarn-type Copper Mine Tailings

Nitrate and Fe(III) are two terminal electron acceptors in anaerobic respiration by microorganisms growing in the anoxic soil or sediment environment. In the current paper a facultative anaerobic dissimilatory Fe(III)- and nitrate-reducing bacterium was isolated from the Linchong tailings, a skarn-type copper mine tailings, located in Anhui. Skarn often formed at the contact zone between intrusions of granitic magma bodies into contact with carbonate sedimentary rocks. This made the tailings possessed strong acid neutralizing capacity and pH of the pore water was 6.8–8.6. The isolate, which was designated strain CW (CCTCC AB 2013114), was a gram-negative rod bacterium and belonged to the gamma subgroup p of the proteobacteria, closely (99.0%) related to Pseudomonas stutzeri. In defined medium, strain CW was shown to grow anaerobically with the acetate using the ferric iron or nitrate as the electron acceptors. Results also showed that strain CW could not grow in the presence of ferrous iron and nitrite.     

Microbial Communities Involved in Fe Reduction and Mobility During Soil Organic Matter (SOM) Mineralization in Two Contrasted Paddy Soils

Lowland rice fields of West Africa (Ivory Coast) and South Asia (Thailand) are affected by ferrous toxicity or salinity, respectively, and their soil waters contain large amounts of ferrous iron, depending on reducing irrigation condition and suggesting occurrence of bacterial reducing processes. To determine the involvement, dynamic and activities of bacterial communities in Fe(III) reduction and mobilization during anaerobic degradation and mineralization of soil organic matter (SOM), different experiments and analyses have been performed. Results demonstrated that the utilization of SOM as sole carbon, nutrient and energy sources favored the presence of large bacterial communities: facultative anaerobic and anaerobic bacteria, Fe(III)-reducing bacteria (FeRB) (fermentative and Fe respiring), sulfate reducing bacteria (SRB) which are involved in carbon, nitrogen, iron and sulfur cycling. The larger functional diversity is observed in the Ivory Coast paddy soils containing larger amounts of organic matter and sulfur compounds. These communities contained complementary populations (chemoorganotrophic, chemolitotrophic, aerobic, facultative anaerobic and anaerobic) that can be active at different steps of iron solubilization with simultaneous organic matter mineralization. Our results indicate that the pH controlled by bacterial activity, the nature much more than the content of organic matter, and consequently the structure and activity of bacterial communities influence significantly the availability and dynamic of iron in paddy fields which affect the soil quality.     

海洋沉积物中铁还原细菌组成及异化铁还原与产氢性质分析

[背景]一些铁还原细菌具有异化铁还原与产氢的能力,该类细菌在环境污染修复的同时能够解决能源问题.[目的]从海洋沉积物中富集获得异化铁还原菌群,明确混合菌群组成、异化铁还原及产氢性质.获得海洋沉积物中异化铁还原混合菌群组成,分析菌群异化铁还原和产氢性质.[方法]利用高通量测序技术分析异化铁还原菌群的优势菌组成,在此基础上...     

Physicochemical and Enzymatic Properties of ATP: Nucleotide Pyrophosphotransferase

The molecular weight determined by the sedimentation equilibrium and SDS Polyacrylamide gel electrophoresis was 29,000 and 28,000, respectively. Isoelectric point of the enzyme was determined as pH 7.7. This enzyme contained large amounts of alanine, aspartic acid, glutamic acid and serine, and no cysteine residue was found. The enzyme was inhibited by SDS, KMnO₄, EDTA and tetracycline. GTP and GDP were the most active as pyrophosphate acceptor to the enzyme. The apparent Km for ATP was 2.2×10^?4 m and that for GTP was 2.1×10^?4m in the reaction of ATP+GTP→AMP+pppGpp. On the other hand, in the reaction of 2ATP→AMP+pppApp, the apparent Km for donor and acceptor ATP was 1.7×10^?3m. Effects of pH and metal ions on the enzymatic synthesis of pppGpp were also studied.     

Modes of Biomineralization of Magnetite by Microbes

Biomineralization processes have traditionally been grouped into two distinct modes; biologically induced mineralization (BIM) and biologically controlled mineralization (BCM). In BIM, microbes cause mineral formation by sorbing solutes onto their cell surfaces or extruded organic polymers and/or releasing reactive metabolites which alter the saturation state of the solution proximal to the cell or polymer surface. Such mineral products appear to have no specific recognized functions. On the other hand, in BCM microbes exert a great degree of chemical and genetic control over the nucleation and growth of mineral particles, presumably because the biominerals produced serve some physiological function. Interestingly, there are examples where the same biomineral is produced by both modes in the same sedimentary environment. For example, the magnetic mineral magnetite (Fe ₃ O ₄ ) is generated extracellularly in the bulk pore waters of sediments by various Fe(III)-reducing bacteria under anaerobic conditions, while some other anaerobic and microaerophilic bacteria and possibly protists form magnetite intracellularly within preformed vesicles. Differences in precipitation mechanisms might be caused by enzymatic activity at specific sites on the surface of the cell. Whereas one type of microbe might facilitate the transport of dissolved Fe(III) into the cell, another type will express its reductive enzymes and cause the reduction of Fe(III) external to the cell. Still other microbes might induce magnetite formation indirectly through the oxidation of Fe(II), followed by the reaction of dissolved Fe(II) with hydrolyzed Fe(III). The biomineralization of magnetite has significant effect on environmental iron cycling, the magnetization of sediments and thus the geologic record, and on the use of biomarkers as microbial fossils.     

微生物燃料电池中产电微生物的研究进展

产电微生物是微生物燃料电池系统的核心组成, 本文从生物学角度介绍了几种产电微生物的分类学地位、形态特征、生理生化特征及在微生物燃料电池中的产电机理和产电能力, 分析了利用产电微生物进行废水处理同时生物发电的应用前景, 提出产电微生物在MFC系统中的进一步研究方向为微生物的富集、驯化、改造和多种菌种优化组合等。     

Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen-suppressive soil

Soil that is suppressive to disease caused by fungal pathogens is an interesting source to target for novel chitinases that might be contributing towards disease suppression. In this study, we screened for chitinase genes, in a phytopathogen-suppressive soil in three ways: (1) from a metagenomic library constructed from microbial cells extracted from soil, (2) from directly extracted DNA and (3) from bacterial isolates with antifungal and chitinase activities. Terminal restriction fragment length polymorphism (T-RFLP) of chitinase genes revealed differences in amplified chitinase genes from the metagenomic library and the directly extracted DNA, but approximately 40% of the identified chitinase terminal restriction fragments (TRFs) were found in both sources. All of the chitinase TRFs from the isolates were matched to TRFs in the directly extracted DNA and the metagenomic library. The most abundant chitinase TRF in the soil DNA and the metagenomic library corresponded to the TRF¹⁰³ of the isolate Streptomyces mutomycini and/or Streptomyces clavifer . There were good matches between T-RFLP profiles of chitinase gene fragments obtained from different sources of DNA. However, there were also differences in both the chitinase and the 16S rRNA gene T-RFLP patterns depending on the source of DNA, emphasizing the lack of complete coverage of the gene diversity by any of the approaches used.