The anammoxosome: an intracytoplasmic compartment in anammox bacteria

Anammox bacteria belong to the phylum Planctomycetes and perform anaerobic ammonium oxidation (anammox); they oxidize ammonium with nitrite as the electron acceptor to yield dinitrogen gas. The anammox reaction takes place inside the anammoxosome: an intracytoplasmic compartment bounded by a single ladderane lipid-containing membrane. The anammox bacteria, first found in a wastewater treatment plant in The Netherlands, have the potential to remove ammonium from wastewater without the addition of organic carbon. Very recently anammox bacteria were also discovered in the Black Sea where they are responsible for 30-50% of the nitrogen consumption. This review will introduce different forms of intracytoplasmic membrane systems found in prokaryotes and discuss the compartmentalization in anammox bacteria and its possible functional relation to catabolism and energy transduction.     

厌氧氨氧化菌的代谢途径及其关键酶的研究进展

作为新型生物脱氮工艺的代表,厌氧氨氧化反应的代谢功能菌——厌氧氨氧化(Anammox)菌也逐渐成为研究的热点。本文介绍了10种Anammox菌的发现过程,阐述了Anammox菌的关键酶的研究进展。通过对Candidatus"Brocadia anammoxidans"和Candidatus"Kuenenia stuttgartiensis"菌的代谢途径的分析和推理,综述了化学计量模型、生化反应模型和能量代谢模型,并提出了一种可能存在的基于关键酶的厌氧氨氧化菌微界面代谢新途径。     

厌氧氨氧化启动过程Anammox菌富集规律和差异分析

为明确厌氧氨氧化反应器启动过程中Anammox菌的富集规律,采用荧光原位杂交(FISH)和实时荧光定量PCR(q-PCR)分析技术,对未添加填料、添加多面空心球以及添加竹炭的3个UASB反应器厌氧氨氧化启动过程中Anammox菌的增长规律进行分析。研究表明,Anammox菌的相对数量和绝对数量均随着启动时间呈逐渐递增趋势,在稳定运行阶段的第123天,无填料、多面空心球和竹炭反应器中Anammox菌分别占总细菌的23.3%、32.6%和43.7%,单位VSS污泥中Anammox菌16S rRNA基因拷贝数分别为(25.64±2.76)×107、(47.12±2.76)×107和(577.99±27.25)×107拷贝数g–1 VSS。竹炭反应器中Anammox菌最大生长率和最短倍增时间分别为0.064 d?1和10.8 d,最大生长率分别是无填料和多面空心球反应器的1.78倍和1.88倍。因此,填料添加特别是竹炭的添加可极大地促进Anammox菌的选择性生长和繁殖。FISH和q-PCR分析技术均适用于Anammox菌的富集规律研究,但因其检测目标存在差异,造成两者表征结果有所不同。     

厌氧氨氧化细菌及其群落内细菌互作关系研究进展

厌氧氨氧化细菌具有的厌氧氨氧化反应是在厌氧条件下将氨氮和亚硝氮或一氧化氮转化为硝氮、生成氮气的过程,因其能够高效低能地处理低碳氮比废水而广受关注.目前,厌氧氨氧化细菌仍未实现纯培养,借助宏组学手段研究厌氧氨氧化细菌及其群落内细菌之间的互作关系是近年来的研究趋势.本文介绍了厌氧氨氧化细菌的种类和特性,综述了厌氧氨氧化细菌...     

铁矿物强化厌氧氨氧化效能及其微生物机制研究进展

自然界中的氮循环与铁循环相互交联,参与氮循环的厌氧氨氧化（anaerobic ammonium oxidation,anammox）菌的生长代谢及活性发挥也与铁元素紧密关联。自然界广泛存在的铁矿物因具有运行成本低廉、稳定性好、二次污染小等优势,在污水处理领域得到广泛应用。在厌氧氨氧化脱氮系统中引入适量铁矿物,不仅有助于促进anammox菌和铁还原菌的富集,提高功能基因丰度和相关酶活性,还可能通过影响污泥浓度、血红素c含量、胞外聚合物含量和颗粒化程度,改善污泥性能和提高厌氧氨氧化系统的稳定性。同时,铁矿物具有促进体系多种氮素转化途径（如anammox、铁自养反硝化、铁氨氧化、异化硝酸盐还原成铵和反硝化）相耦合的潜能,可以提高anammox污水处理系统的总氮去除率。本文基于铁矿物在促进污水生物脱氮方面的良好性能及其在anammox系统中的变化,从脱氮效能、污泥特性、微生物特征及酶活性等方面,系统综述了铁矿物对厌氧氨氧化系统的强化作用机制,并从anammox菌对铁矿物的利用及铁元素的摄取角度展望了后续的研究方向,以期为铁矿物强化厌氧氨氧化系统的实际应用提供理论和技术指导。     

Green synthesis and characterization of Carica papaya leaf extract coated silver nanoparticles through X-ray diffraction,electron microscopy and evaluation of bactericidal properties

The evolution of nanotechnology and the production of nanomedicine from various sources had proven to be of intense value in the field of biomedicine. The smaller size of nanoparticles is gaining importance in research for the treatment of various diseases. Moreover the production of nanoparticles is eco-friendly and cost effective. In the present study silver nanoparticles were synthesized from Carica papaya leaf extract (CPL) and characterized for their size and shape using scanning electron microscopy and transmission electron microscopy, respectively. Fourier transform infrared spectroscopy (FTIR), Energy dispersive X-ray spectroscopy (EDS/EDX) and X-ray diffraction spectroscopy (XRD) were conducted to determine the concentration of metal ions, the shape of molecules. The bactericidal activity was evaluated using Luria Bertani broth cultures and the minimum inhibition concentration (MIC) and minimum bactericidal concentration (MBC) were estimated using turbidimetry. The data analysis showed size of 50–250 nm spherical shaped nanoparticles. The turbidimetry analysis showed MIC and MBC was >25 μg/mL against both Gram positive and Gram negative bacteria in Luria Bertani broth cultures. In summary the synthesized silver nanoparticles from CPL showed acceptable size and shape of nanoparticles and effective bactericidal activity.     

Characteristics and phylogenetic analysis of the facultative anaerobic dissimilatory azoreducing bacteria from activated sludge

Physiologically distinct facultative anaerobic microorganisms were isolated and investigated for their ability to oxidize different substrates with azo compounds as a terminal electron acceptor. Four strains of dissimilatory azoreducing bacteria (DARBs), isolated from activated sludge of a textile-printing wastewater treatment plant, could reduce azo compound by coupling oxidation of several of electron donors. Different strains preferred specific electron donor for azoreduction, such as hydrogen, formate or lactate. Evolutionary relationships among these DARBs were examined by phylogenetic analysis of 16S rDNA sequences. Members of the genera Citrobacter (AzoR-1), Acinetobacter (AzoR-3), and Pseudomonas (AzoR-9) formed a monophyletic group within the gamma subdivision of the class Proteobacteria, which was closely related to the member of the previously described Shewanella decolorationnis S12 that obtained its energy for growth by dissimilatory azoreduction process. The genus Bacillus (AzoR-6) made up a distinct branch within the Firmicutes cluster. The results of this study expanded the limited number of microbial isolates that are known to be capable of dissimilatory azoreduction and demonstrated that the ubiquity of azoreduction coupling with hydrogen or organic acids as an electron donor.     

Niche segregation of ammonia-oxidizing archaea and anammox bacteria in the Arabian Sea oxygen minimum zone

Ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing (anammox) bacteria have emerged as significant factors in the marine nitrogen cycle and are responsible for the oxidation of ammonium to nitrite and dinitrogen gas, respectively. Potential for an interaction between these groups exists; however, their distributions are rarely determined in tandem. Here we have examined the vertical distribution of AOA and anammox bacteria through the Arabian Sea oxygen minimum zone (OMZ), one of the most intense and vertically exaggerated OMZs in the global ocean, using a unique combination of intact polar lipid (IPL) and gene-based analyses, at both DNA and RNA levels. To screen for AOA-specific IPLs, we developed a high-performance liquid chromatography/mass spectrometry/mass spectrometry method targeting hexose-phosphohexose (HPH) crenarchaeol, a common IPL of cultivated AOA. HPH-crenarchaeol showed highest abundances in the upper OMZ transition zone at oxygen concentrations of ca. 5 μ, coincident with peaks in both thaumarchaeotal 16S rDNA and amoA gene abundances and gene expression. In contrast, concentrations of anammox-specific IPLs peaked within the core of the OMZ at 600 m, where oxygen reached the lowest concentrations, and coincided with peak anammox 16S rDNA and the hydrazine oxidoreductase (hzo) gene abundances and their expression. Taken together, the data reveal a unique depth distribution of abundant AOA and anammox bacteria and the segregation of their respective niches by >400 m, suggesting no direct coupling of their metabolisms at the time and site of sampling in the Arabian Sea OMZ.     

Ammonia biofiltration and community analysis of ammonia-oxidizing bacteria in biofilters

Biological removal of ammonia was investigated using compost and sludge as packing materials in laboratory-scale biofilters. The aim of this study is to characterize the composition of ammonia-oxidizing bacteria (AOB) in two biofilters designed to remove ammonia. Experimental tests and measurements included analysis of removal efficiency and metabolic products. The inlet concentration of ammonia applied was 20–100 mg m⁻³. Removal efficiencies of BFC and BFS were in the range of 97–99% and 95–99%, respectively. Periodic analysis of the biofilter packing materials showed ammonia was removed from air stream by nitrification and by the improved absorption of NH₃ in the resultant acidity. Nitrate was the dominant product of NH₃ transformation. Changes in the composition of AOB were examined by using nested PCR, denaturing gradient gel electrophoresis (DGGE) and sequencing of DGGE bands. DGGE analysis of biofilter samples revealed that shifts in the community structure of AOB were observed in the experiment; however, the idle phase did not cause the structural shift of AOB. Phylogenetic analysis revealed the population of AOB showed Nitrosospira sp. remains the predominant population in BFC, while Nitrosomonas sp. is the predominant population in BFS.     

Hydrogenases in Desulfovibrio vulgaris Hildenborough: structural and physiologic characterisation of the membrane-bound [NiFeSe] hydrogenase

The genome of Desulfovibrio vulgaris Hildenborough (DvH) encodes for six hydrogenases (Hases), making it an interesting organism to study the role of these proteins in sulphate respiration. In this work we address the role of the [NiFeSe] Hase, found to be the major Hase associated with the cytoplasmic membrane. The purified enzyme displays interesting catalytic properties, such as a very high H₂ production activity, which is dependent on the presence of phospholipids or detergent, and resistance to oxygen inactivation since it is isolated aerobically in a Ni(II) oxidation state. Evidence was obtained that the [NiFeSe] Hase is post-translationally modified to include a hydrophobic group bound to the N-terminal, which is responsible for its membrane association. Cleavage of this group originates a soluble, less active form of the enzyme. Sequence analysis shows that [NiFeSe] Hases from Desulfovibrionacae form a separate family from the [NiFe] enzymes of these organisms, and are more closely related to [NiFe] Hases from more distant bacterial species that have a medial [4Fe4S]^2+/1+ cluster, but not a selenocysteine. The interaction of the [NiFeSe] Hase with periplasmic cytochromes was investigated and is similar to the [NiFe]₁ Hase, with the Type I cytochrome c ₃ as the preferred electron acceptor. A model of the DvH [NiFeSe] Hase was generated based on the structure of the Desulfomicrobium baculatum enzyme. The structures of the two [NiFeSe] Hases are compared with the structures of [NiFe] Hases, to evaluate the consensual structural differences between the two families. Several conserved residues close to the redox centres were identified, which may be relevant to the higher activity displayed by [NiFeSe] Hases. Electronic Supplementary Material Supplementary material is available for this article at     

家蚕肠道细菌群体调查与分析

目前,环境微生物中绝大部分是无法获得纯培养的。为了比较全面地了解家蚕肠道的细菌群体结构,研究采用了非培养法和传统培养法相结合的方法进行调查分析。非培养法是先直接提取家蚕肠道中的微生物群体基因组DNA,用PCR法扩增细菌16S rRNA基因,建立16S rDNA文库;再以限制性片段长度多态性(RFLP)方法从文库中筛选可能不同细菌来源的克隆,并测定其核苷酸序列。将所获得的序列与GenBank数据库进行BLAST比对分析,并通过系统发育分析,推测它们可能代表的细菌种属,以及对家蚕生长发育所起的作用。结果表明,家蚕肠道中的细菌主要是节杆菌属、乳杆菌属、大肠杆菌属、芽胞杆菌属、葡萄球菌属、假单胞菌属。它们在家蚕消化利用桑叶和疾病预防中可能有着重要意义。非培养法和培养法均有各自的长处和不足,两者具有较强的互补性。     

Structures of phosphate and trivanadate complexes of Bacillus stearothermophilus phosphatase PhoE: structural and functional analysis in the cofactor-dependent phosphoglycerate mutase superfamily

Bacillus stearothermophilus phosphatase PhoE is a member of the cofactor-dependent phosphoglycerate mutase superfamily possessing broad specificity phosphatase activity. Its previous structural determination in complex with glycerol revealed probable bases for its efficient hydrolysis of both large, hydrophobic, and smaller, hydrophilic substrates. Here we report two further structures of PhoE complexes, to higher resolution of diffraction, which yield a better and thorough understanding of its catalytic mechanism. The environment of the phosphate ion in the catalytic site of the first complex strongly suggests an acid-base catalytic function for Glu83. It also reveals how the C-terminal tail ordering is linked to enzyme activation on phosphate binding by a different mechanism to that seen in Escherichia coli phosphoglycerate mutase. The second complex structure with an unusual doubly covalently bound trivanadate shows how covalent modification of the phosphorylable His10 is accompanied by small structural changes, presumably to catalytic advantage. When compared with structures of related proteins in the cofactor-dependent phosphoglycerate mutase superfamily, an additional phosphate ligand, Gln22, is observed in PhoE. Functional constraints lead to the corresponding residue being conserved as Gly in fructose-2,6-bisphosphatases and Thr/Ser/Cys in phosphoglycerate mutases. A number of sequence annotation errors in databases are highlighted by this analysis. B. stearothermophilus PhoE is evolutionarily related to a group of enzymes primarily present in Gram-positive bacilli. Even within this group substrate specificity is clearly variable highlighting the difficulties of computational functional annotation in the cofactor-dependent phosphoglycerate mutase superfamily.     

Assessment of the validity of the double superhelix model for reconstituted high density lipoproteins: a combined computational-experimental approach

For several decades, the standard model for high density lipoprotein (HDL) particles reconstituted from apolipoprotein A-I (apoA-I) and phospholipid (apoA-I/HDL) has been a discoidal particle ∼100 Å in diameter and the thickness of a phospholipid bilayer. Recently, Wu et al. (Wu, Z., Gogonea, V., Lee, X., Wagner, M. A., Li, X. M., Huang, Y., Undurti, A., May, R. P., Haertlein, M., Moulin, M., Gutsche, I., Zaccai, G., Didonato, J. A., and Hazen, S. L. (2009) J. Biol. Chem. 284, 36605–36619) used small angle neutron scattering to develop a new model they termed double superhelix (DSH) apoA-I that is dramatically different from the standard model. Their model possesses an open helical shape that wraps around a prolate ellipsoidal type I hexagonal lyotropic liquid crystalline phase. Here, we used three independent approaches, molecular dynamics, EM tomography, and fluorescence resonance energy transfer spectroscopy (FRET) to assess the validity of the DSH model. (i) By using molecular dynamics, two different approaches, all-atom simulated annealing and coarse-grained simulation, show that initial ellipsoidal DSH particles rapidly collapse to discoidal bilayer structures. These results suggest that, compatible with current knowledge of lipid phase diagrams, apoA-I cannot stabilize hexagonal I phase particles of phospholipid. (ii) By using EM, two different approaches, negative stain and cryo-EM tomography, show that reconstituted apoA-I/HDL particles are discoidal in shape. (iii) By using FRET, reconstituted apoA-I/HDL particles show a 28–34-Å intermolecular separation between terminal domain residues 40 and 240, a distance that is incompatible with the dimensions of the DSH model. Therefore, we suggest that, although novel, the DSH model is energetically unfavorable and not likely to be correct. Rather, we conclude that all evidence supports the likelihood that reconstituted apoA-I/HDL particles, in general, are discoidal in shape.     

The role of glycine residues 140 and 141 of subunit B in the functional ubiquinone binding site of the Na+-pumping NADH:quinone oxidoreductase from Vibrio cholerae

The Na(+)-pumping NADH:quinone oxidoreductase (Na(+)-NQR) is the main entrance for electrons into the respiratory chain of many marine and pathogenic bacteria. The enzyme accepts electrons from NADH and donates them to ubiquinone, and the free energy released by this redox reaction is used to create an electrochemical gradient of sodium across the cell membrane. Here we report the role of glycine 140 and glycine 141 of the NqrB subunit in the functional binding of ubiquinone. Mutations at these residues altered the affinity of the enzyme for ubiquinol. Moreover, mutations in residue NqrB-G140 almost completely abolished the electron transfer to ubiquinone. Thus, NqrB-G140 and -G141 are critical for the binding and reaction of Na(+)-NQR with its electron acceptor, ubiquinone.     

Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria

Metabolite balancing has turned out to be a powerful computational tool in metabolic engineering. However, the linear equation systems occurring in this analysis are often underdetermined. If it is difficult or impossible to find the missing constraints, it is nevertheless feasible in some cases to determine the values of a subset of the unknown rates. Here, a procedure for finding out which reaction rates can be uniquely calculated in underdetermined metabolic networks and computing these rates is given. The method is based on the null space to the stoichiometry matrix corresponding to the reactions with unknown rates. It is shown that this method is considerably easier to handle than an algorithm given previously (Van der Heijden et al., 1994a). Furthermore, a useful elementary representation of the null space is presented which is closely related with the elementary flux modes. This unique representation is central to a more general approach to observability/calculability analysis. In particular, it allows one to find, in an easy way, those sets of measurable rates that enable a calculation of a certain unknown rate. Besides, rates which are never calculable by metabolite balancing may be easily detected by this method. The applicability of these methods is illustrated by a model of the central metabolism in purple nonsulfur bacteria. The photoheterotrophic growth of these representatives of anoxygenic photosynthetic bacteria is stoichiometrically analyzed. Interesting metabolic constraints caused by the necessary balancing of NADPH can be detected in a highly underdetermined system. This is, to our knowledge, the first application of stoichiometric analysis to the metabolic network in this bacteria group using metabolite balancing techniques. A new software tool, the FluxAnalyzer, is introduced. It allows quantitative and structural analysis of metabolic networks in a graphical user interface.     

Cell cycle-dependent changes in Golgi stacks, vacuoles, clathrin-coated vesicles and multivesicular bodies in meristematic cells of Arabidopsis thaliana: A quantitative and spatial analysis

Cytokinesis in plants involves both the formation of a new wall and the partitioning of organelles between the daughter cells. To characterize the cellular changes that accompany the latter process, we have quantitatively analyzed the cell cycle-dependent changes in cell architecture of shoot apical meristem cells of Arabidopsis thaliana. For this analysis, the cells were preserved by high-pressure freezing and freeze-substitution techniques, and their Golgi stacks, multivesicular bodies, vacuoles and clathrin-coated vesicles (CCVs) characterized by means of serial thin section reconstructions, stereology and electron tomography techniques. Interphase cells possess ∼35 Golgi stacks, and this number doubles during G2 immediately prior to mitosis. At the onset of cytokinesis, the stacks concentrate around the periphery of the growing cell plate, but do not orient towards the cell plate. Interphase cells contain ∼18 multivesicular bodies, most of which are located close to a Golgi stack. During late cytokinesis, the appearance of a second group of cell plate-associated multivesicular bodies coincides with the onset of CCV formation at the cell plate. During this period a 4× increase in CCVs is paralleled by a doubling in number and a 4× increase in multivesicular bodies volume. The vacuole system also undergoes major changes in organization, size, and volume, with the most notable change seen during early telophase cytokinesis. In particular, the vacuoles form sausage-like tubular compartments with a 50% reduced surface area and an 80% reduced volume compared to prometaphase cells. We postulate that this transient reduction in vacuole volume during early telophase provides a means for increasing the volume of the cytosol to accommodate the forming phragmoplast microtubule array and associated cell plate-forming structures.     

基于能源代谢分析的南昌市能源消费碳排放综合生态效率研究

有关能源消费的代谢机理及生态效率研究是当前生态经济研究领域中的重点和难点,也是政府决策部门、相关行业及人群关注的热点。基于能源代谢分析理念,构建了基于相对变量的城市能源消费碳排放综合生态效率度量模型,对2000—2013年南昌市能源消费结构、碳排放量及其生态效率进行了测算与分析。结果表明:(1)南昌市在2000—2013年,能源消费量和碳排放量整体上呈"N"型曲线上升的一致性变化特征,主要经历了快速增长、短暂下降、恢复平稳增长3个阶段,且煤炭是南昌市能源消费和碳排放的主要来源,短时期内难以改变;(2)南昌市的能源消费效率和碳排放效率整体上在不断优化;(3)南昌市能源消费碳排放综合生态效率经历了较大的波动变化,整体上的生态效率分值并不高;仍需要加大节能减排力度,全面优化南昌市能源消费结构。     

Isolation and phylogenetic analysis of cultivable manganese bacteria in sediments from the Arctic Ocean

Isolation, molecular identification and phylogenetic analysis were carried out to investigate the biodiversity of manganese bacteria in sediments which were collected from the Arctic Ocean during the 2^nd Chinese Arctic Scientific Expedition. 21 and 19 species of cultivable strains were isolated from sediments at Stations P11 and S11, respectively, according to their distinct morphological character on the screening plate of manganese medium. Molecular identification and phylogenetic analysis showed that the cultivable manganese bacteria from Station P11 were basically composed of γ-Proteobacteria (γ subgroup of the Proteobacteria branch of the domain Bacteria) and Actinobacteria, which accounted for 86% and 14%, respectively. The isolates of γ-Proteobacteria mainly included Psychrobacter, Shewanella, Acinetobacter and Marinobacter, of which Psychrobacter was the major genus, which accounted for 67% of the γ-Proteobacteria. The cultivable manganese bacteria from Station S11 included α-Proteobacteria, γ-Proteobacteria and Flavobacteria of Bacteroides. The γ-Proteobacteria mainly included Shewanella, Marinomonas and Alteromonas. The majority of α-Proteobacteria was Sphingomonas. The phylogenetic analysis indicated that bacteria from sediments at Stations P11 and S11 had different cultivable manganese microbial communities. All tested strains had higher resistance to Mn²⁺, of which Marinomonas sp. S11-S-4 had the highest resistant ability.     

北极海洋沉积物中锰细菌的分离与系统发育

对中国第二次北极科学考察采集的北极海洋沉积物中的锰细菌进行了筛选、分离和系统发育分析。根据其在筛选平板上菌落的形态学特征,分别从站位P11和S11采集的沉积物中分离到了21株和19株锰细菌。系统发育分析表明,两个站位的锰细菌群落组成有着明显的差别。站位P11分离的可培养锰细菌主要由细菌域（Bacteria）中变形杆菌门的γ-变形杆菌纲（γ-Proteobacteria）和放线菌纲（Actinobacteria）组成,二者分别占86％和14％;γ-变形杆菌纲主要包括嗜冷杆菌属（Psychrobacter）、希瓦氏菌属（Shewanella）、假交替单胞菌属（Pseudoaheromonas）、不动杆菌属（Acinetobacter）、海杆菌属（Marinobacter）,其中以嗜冷杆菌属为主,其比例可达67％。从站位S11分离到的可培养锰细菌主要包括细菌域中变形杆菌门的α-变形杆菌纲（α-Proteobacteria）和γ-变形杆菌纲以及拟杆菌门（Bacteroides）中的黄杆菌纲（Flavobaeteria）;γ-变形杆菌纲主要包括希瓦氏菌属、海单胞菌属（Marinomonas）和交替单胞菌属（Aheromonas）,α-变形杆菌纲主要为鞘氨醇单胞菌属（Sphingomonas）。实验菌株均对Mn^2＋有着较强的抗性,其中以菌株Marinomonas sp．S11-S-4耐受性最高。