Complete genome sequence of "Thioalkalivibrio sulfidophilus" HL-EbGr7

"Thioalkalivibrio sulfidophilus" HL-EbGr7 is an obligately chemolithoautotrophic, haloalkaliphilic sulfur-oxidizing bacterium (SOB) belonging to the Gammaproteobacteria. The strain was found to predominate a full-scale bioreactor, removing sulfide from biogas. Here we report the complete genome sequence of strain HL-EbGr7 and its annotation. The genome was sequenced within the Joint Genome Institute Community Sequencing Program, because of its relevance to the sustainable removal of sulfide from bio- and industrial waste gases.     

Evaluating the Potential of Halothiobacillus Bacteria for Sulfur Oxidation and Biomass Production under Saline Soil

Abstract

Salinity negatively affects growth of sulfur-oxidizing bacteria (SOB) and their sulfate production ability, meanwhile decreases the available sulfate for plants in soil. The aim of this study was to isolate and characterize the bacteria of genus Halothiobacillus, as a salt-tolerant SOB, from saline and sulfidic habitats of Iran for the first time and evaluating the effect of salinity on their biomass and sulfate production during the oxidation of different sulfur sources. Isolation process and surveying the morphological, biochemical and 16S rRNA gene analysis resulted into identification of three species (eight strains) of Halothiobacillus genus including H. neapolitanus, H. hydrothermalis and H. halophilus. Salinity (0, 0.5, 1, 2 and 4?M NaCl) had a significant impact (p?≤?0.01) on bacterial biomass and sulfate production during the oxidation of thiosulfate and elemental sulfur. Biomass and sulfate production by strains was accompanied by a decrease in residual content of thiosulfate (RCT) in medium. The amount of produced biomass and sulfate in medium supplemented by thiosulfate was much higher than elemental sulfur. The highest amount of biomass and sulfate was produced by H. neapolitanus strain I19 at 0.5 and 1?M NaCl concentration. The results of this study could be the first step to focus on the application of these bacteria to increase sulfate storage of saline soils and crop production.     

Phylogeny of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Genes in Haloalkaliphilic Obligately Autotrophic Sulfur-Oxidizing Bacteria of the Genus <Emphasis Type="Italic">Thioalkalivibrio</Emphasis>

Fragments of genes of the “green-like” form I ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) of eight species of haloalkaliphilic obligately autotrophic sulfur-oxidizing bacteria of the genus Thioalkalivibrio have been revealed and sequenced using previously developed oligonucleotide primers. The data obtained are used for the construction of phylogenetic trees on the basis of nucleotide sequences of RuBisCO genes and their conceptual translations into amino acid sequences. Comparative analysis of the 16S rRNA and RuBisCO gene trees reveals discrepancies between their topologies. According to a RuBisCO gene analysis, the genus Thioalkalivibrio is not monophyletic, and its inner divergence conforms to the significant morphological differences observed between the species. Presumably, horizontal (interspecies) gene transfer was involved in the evolution of the genus Thioalkalivibrio.__________Translated from Mikrobiologiya, Vol. 74, No. 3, 2005, pp. 378–386.Original Russian Text Copyright © 2005 by Tourova, Spiridonova, Berg, Kuznetsov, Sorokin.     

Physiology of Organotrophic and Lithotrophic Growth of the Thermophilic Iron-Reducing Bacteria Thermoterrabacterium ferrireducens and Thermoanaerobacter siderophilus

Growth physiology of the iron-reducing bacteria Thermoterrabacterium ferrireducens and Thermoanaerobacter siderophilus was investigated. The stimulation of the organotrophic growth of T. ferrireducens and T. siderophilusin the presence of Fe(III) was shown to be due to the utilization of ferric iron as an electron acceptor in catabolic processes and not to the effect exerted on the metabolism by Fe(II) or by changes in the redox potential. It was established that Fe(III) reduction in T. ferrireducens is not a detoxication strategy. In T. siderophilus, this process is carried out to alleviate the inhibitory effect of hydrogen. T. ferrireducens was shown to be capable of lithoautotrophic growth with molecular hydrogen as an electron donor and amorphous ferric oxide as an electron acceptor, in the absence of any organic substances. The minimum threshold of H₂ consumption was 3 × 10^–5 vol % of H₂. The presence of CO dehydrogenase activity in T. ferrireducens suggests that CO₂ fixation in this organism involves the anaerobic acetyl-CoA pathway. T. siderophilus failed to grow under lithoautotrophic conditions. The fact that T. ferrireducens contains c-type cytochromes and T. siderophilus lacks them confirms the operation of different mechanisms of ferric iron reduction in these species.     

A membrane-bound nitrate reductase encoded by the narGHJI operon is responsible for anaerobic respiration in Halomonas maura

The halophilic bacterium Halomonas maura is capable of anaerobic respiration on nitrates. By insertional mutagenesis with the minitransposon Tn-5 we obtained the mutant Tc62, which was incapable of anaerobic respiration on nitrates. An analysis of the regions adjacent to the transposon allowed us to characterize the membrane-bound anaerobic-respiratory nitrate reductase narGHJI gene cluster in H. maura. We identified consensus sequences for fumarate and nitrate reductase regulator (FNR)-like protein-binding sites in the promoter regions of the nar genes and consensus sequences corresponding to the NarL binding sites upstream of the nar genes. RT-PCR analysis showed that the narGHJI operon was expressed in response to anaerobic conditions when nitrate was available as electron acceptor. This membrane-bound nitrate reductase is the only enzyme responsible for anaerobic respiration on nitrate in H. maura. In this article we discuss the possible relationship between this enzyme and a dissimilatory nitrate-reduction-to-ammonia process (DNRA) in H. maura and its role in the colonization of the rhizosphere.     

Utilization of arylaliphatic nitriles by haloalkaliphilic Halomonas nitrilicus sp. nov. isolated from soda soils

An enrichment culture from saline soda soils, using acetate as carbon and energy source and 2-phenylpropionitrile as nitrogen source (PPN) at pH 10, resulted in the isolation of strain ANL-αCH3. The strain was identified as a representative of the genus Halomonas in the Gammaproteobacteria. The bacterium was capable of PPN utilization as a nitrogen source only, while phenylacetonitrile (PAN) served both as carbon, energy and nitrogen source. This capacity was not described previously for any other haloalkaliphilic bacteria. Apart from the nitriles mentioned above, resting cells of ANL-αCH3 also hydrolyzed mandelonitrile, benzonitrile, acrylonitrile, and phenylglycinonitrile, presumably using nitrilase pathway. Neither nitrile hydratase nor amidase activity was detected. The isolate showed a capacity to grow with benzoate and salicylate as carbon and energy source and demonstrated the ability to completely mineralize PAN. These clearly indicated a potential to catabolize aromatic compounds. On the basis of unique phenotype and distinct phylogeny, strain ANL-αCH3 is proposed as a novel species of the genus Halomonas—Halomonas nitrilicus sp. nov. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Tolerance to Various Toxicants by Marine Bacteria Highly Resistant to Mercury

Bacteria highly resistant to mercury isolated from seawater and sediment samples were tested for growth in the presence of different heavy metals, pesticides, phenol, formaldehyde, formic acid, and trichloroethane to investigate their potential for growth in the presence of a variety of toxic xenobiotics. We hypothesized that bacteria resistant to high concentrations of mercury would have potential capacities to tolerate or possibly degrade a variety of toxic materials and thus would be important in environmental pollution bioremediation. The mercury-resistant bacteria were found to belong to Pseudomonas, Proteus, Xanthomonas, Alteromonas, Aeromonas, and Enterobacteriaceae. All these environmental bacterial strains tolerant to mercury used in this study were capable of growth at a far higher concentration (50 ppm) of mercury than previously reported. Likewise, their ability to grow in the presence of toxic xenobiotics, either singly or in combination, was superior to that of bacteria incapable of growth in media containing 5 ppm mercury. Plasmid-curing assays done in this study ascertained that resistance to mercury antibiotics, and toxic xenobiotics is mediated by chromosomally borne genes and/or transposable elements rather than by plasmids.     

Microbiological analysis of the population of extremely haloalkaliphilic sulfur-oxidizing bacteria dominating in lab-scale sulfide-removing bioreactors

Thiopaq biotechnology for partial sulfide oxidation to elemental sulfur is an efficient way to remove H₂S from biogases. However, its application for high-pressure natural gas desulfurization needs upgrading. Particularly, an increase in alkalinity of the scrubbing liquid is required. Therefore, the feasibility of sulfide oxidation into elemental sulfur under oxygen limitation was tested at extremely haloalkaline conditions in lab-scale bioreactors using mix sediments from hypersaline soda lakes as inoculum. The microbiological analysis, both culture dependent and independent, of the successfully operating bioreactors revealed a domination of obligately chemolithoautotrophic and extremely haloalkaliphilic sulfur-oxidizing bacteria belonging to the genus Thioalkalivibrio. Two subgroups were recognized among the isolates. The subgroup enriched from the reactors operating at pH 10 clustered with Thioalkalivibrio jannaschii–Thioalkalivibrio versutus core group of the genus Thioalkalivibrio. Another subgroup, obtained mostly with sulfide as substrate and at lower pH, belonged to the cluster of facultatively alkaliphilic Thioalkalivibrio halophilus. Overall, the results clearly indicate a large potential of the genus Thiolalkalivibrio to efficiently oxidize sulfide at extremely haloalkaline conditions, which makes it suitable for application in the natural gas desulfurization. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Nucleotide sequence accession numbers: The GenBank/EMBL accession numbers of the 16S rRNA gene sequence determined in this study are EU709849–EU709878.     

Metabolism of Inorganic N Compounds by Ammonia-Oxidizing Bacteria

ABSTRACT

Ammonia oxidizing bacteria extract energy for growth from the oxidation of ammonia to nitrite. Ammonia monooxygenase, which initiates ammonia oxidation, remains enigmatic given the lack of purified preparations. Genetic and biochemical studies support a model for the enzyme consisting of three subunits and metal centers of copper and iron. Knowledge of hydroxylamine oxidoreductase, which oxidizes hydroxylamine formed by ammonia monooxygenase to nitrite, is informed by a crystal structure and detailed spectroscopic and catalytic studies. Other inorganic nitrogen compounds, including NO, N₂O, NO₂, and N₂ can be consumed and/or produced by ammonia-oxidizing bacteria. NO and N₂O can be produced as byproducts of hydroxylamine oxidation or through nitrite reduction. NO₂ can serve as an alternative oxidant in place of O₂ in some ammonia-oxidizing strains. Our knowledge of the diversity of inorganic N metabolism by ammonia-oxidizing bacteria continues to grow. Nonetheless, many questions remain regarding the enzymes and genes involved in these processes and the role of these pathways in ammonia oxidizers.     

Dissimilatory Oxidation and Reduction of Elemental Sulfur in Thermophilic Archaea

The oxidation and reduction of elemental sulfur and reduced inorganic sulfur species are some of the most important energy-yielding reactions for microorganisms living in volcanic hot springs, solfataras, and submarine hydrothermal vents, including both heterotrophic, mixotrophic, and chemolithoautotrophic, carbon dioxide-fixing species. Elemental sulfur is the electron donor in aerobic archaea like Acidianus and Sulfolobus. It is oxidized via sulfite and thiosulfate in a pathway involving both soluble and membrane-bound enzymes. This pathway was recently found to be coupled to the aerobic respiratory chain, eliciting a link between sulfur oxidation and oxygen reduction at the level of the respiratory heme copper oxidase. In contrast, elemental sulfur is the electron acceptor in a short electron transport chain consisting of a membrane-bound hydrogenase and a sulfur reductase in (facultatively) anaerobic chemolithotrophic archaea Acidianus and Pyrodictium species. It is also the electron acceptor in organoheterotrophic anaerobic species like Pyrococcus and Thermococcus, however, an electron transport chain has not been described as yet. The current knowledge on the composition and properties of the aerobic and anaerobic pathways of dissimilatory elemental sulfur metabolism in thermophilic archaea is summarized in this contribution.     

Modeling of recycling oxic and anoxic treatment system for swine wastewater using neural networks

A recycling reactor system operated under sequential anoxic and oxic conditions for the treatment of swine wastewater has been developed, in which piggery slurry is fermentatively and aerobically treated and then part of the effluent is recycled to the pigsty. This system significantly removes offensive smells (at both the pigsty and the treatment plant), BOD and others, and may be cost effective for small-scale farms. The most dominant heterotrophic were, in order,Alcaligenes faecalis, Brevundimonas diminuta andStreptococcus sp., while lactic acid bacteria were dominantly observed in the anoxic tank. We propose a novel monitoring system for a recycling piggery slurry treatment system through the use of neural networks. In this study, we tried to model the treatment process for each tank in the system (influent, fermentation, aeration, first sedimentation and fourth sedimentation tanks) based upon the population densities of the heterotrophic and lactic acid bacteria. Principal component analysis (PCA) was first applied to identify a relationship between input and output. The input would be microbial densities and the treatment parameters, such as population densities of heterotrophic and lactic acid bacteria, suspended solids (SS), COD, NH₄ ⁺-N, or-tho-phosphorus (o-P), and total-phosphorus (T-P). Then multi-layer neural networks were employed to model the treatment process for each tank. PCA filtration of the input data as microbial densities was found to facilitate the modeling procedure for the system monitoring even with a relatively lower number of input. Neural networks independently trained for each treatment tank and their subsequent combined data analysis allowed a successful prediction of the treatment system for at least two days.     

Psychrobacter nivimaris sp. nov., a heterotrophic bacterium attached to organic particles isolated from the South Atlantic (Antarctica)

An aggregate-attached bacterium, strain 88/2-7, was isolated from samples of the Southern Ocean and investigated in a polyphasic approach. The novel marine isolate is an aerobic, Gram-negative, oxidase- and catalase-positive, non-motile short rod and grows in form of cream-colored colonies. Growth was observed at 5-35 degrees C. The bacterium tolerated concentrations of 0-13% (w/v) NaCl and utilized a relatively restricted spectrum of carbon sources. The analysis of the fatty acids revealed 18:1 cis 9 (18:1omega9c) as main fatty acid. The G+C content of the DNA was approximately 42 mol%. The sequence of the 16S rDNA assigned strain 88/2-7 to the gamma-subclass of Proteobacteria with a similarity of 99.65% to Psychrobacter proteolyticus (DSM 13887T). A DNA-DNA-hybridization study showed only 26.8% renaturation to the respective strain. Based on the morphological, physiological and molecular properties of the new isolate, the name Psychrobacter nivimaris sp. nov. (type strain 88/2-7T) is proposed.     

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。     

Oxidation of ethylene by cotyledon extracts from Vicia faba L.

Improved rates of ethylene oxidation by cell-free preparations from cotyledons of Vicia faba L. have been obtained using cryogenic storage techniques and by developing a method for the hydrolysis of ethylene oxide. Gel permeation chromatography showed that a low-molecular-size fraction was required for activity; accordingly, the kinetics of ethylene oxidation in the presence of this fraction were studied. Reduced pyridine nucleotides could substitute for the low-molecular-size fraction. Activity under a nitrogen atmosphere was 60% lower than in air. The need for reduced nicotinamide adenine dinucleotide phosphate (NADPH) and oxygen indicated that the enzyme might be a mixed-function oxidase. Using sufficient NADPH to approach saturation, the apparent Michaelis constant (K _m) for ethylene was 1.94±0.38 · 10^-8 M (aqueous phase), and when ethylene was saturating, the K _m for NADPH was 3.7 · 10^-5 M. Carbon monoxide was found to inhibit by competing with ethylene, and the inhibitor constant was 5.97 · 10^-7 M in solution. In the presence of excess ethylene and NADPH, activity was highest in phosphate-buffered medium pH 7.9. The bulk of the activity was found in a microsomal fraction.Abbreviations Epps N-2-hydroxyethylpiperazine-N-3-propane sulphinic acid - Tris 2-amino-2-(hydroxymethyl)-1,3-porpanediol     

罗氏沼虾(Macrobrachium rosenbergii)养殖池塘沉积物中细菌、硫酸盐还原菌和硫氧化菌的垂直分布特征

沉积物中微生物介导的硫循环在有机物分解和养分循环中发挥重要作用,但目前我们对水产养殖生态系统中的参与硫酸盐还原和硫氧化过程的微生物多样性及其调控机制仍知之甚少。【目的】探究硫酸盐还原菌(sulfate-reducing bacteria,SRB)和硫氧化菌(sulfur-oxidizing bacteria,SOB)的垂直分布特征及其主要的环境驱动因素。【方法】本研究利用高通量测序和荧光定量PCR (qPCR)分析了罗氏沼虾(Macrobrachium rosenbergii)养殖池塘沉积物表层(0–1 cm)、中层(10–11 cm)和底层(20–21 cm)中的细菌、SRB和SOB的丰度、多样性和群落组成。【结果】细菌(16S rRNA)、硫酸盐还原菌(dsrB)和硫氧化菌(soxB)的基因拷贝数呈现着从表层到中层急剧骤降的趋势(ANOVA,P<0.05),但中层和底层样品之间的差异却并不显著(P>0.05),以及α多样性分析显示3个群体的物种丰富度和均匀度都随深度而逐步降低,这都说明硫循环过程主要发生于沉积物的表层。γ-、δ-和β-变形菌分别是细菌、SRB和SOB的优势类群;其中SRB以Desulfobacca属和脱硫八叠球菌属(Desulfosarcina)为主,前者在表层有着最低的比重,而后者却与之相反;硫杆菌(Thiobacillus)作为细菌和SOB的优势属,更广泛地分布于中层沉积物中。RDA分析和Mantel检验揭示了影响细菌群落的主要环境因子是NO₃^–、SO₄^2–、TOC和TON,而SRB的群落变异主要是由As、TON、NO₃^–和Pb所驱动,以及SOB的群落变化则主要响应了TC、NO₂^–、NH₄⁺和TON浓度。【结论】养殖池塘底栖的细菌、SRB和SOB的丰度、多样性和群落结构的垂直分布特征可能受到多种环境因素共同的影响。     

Decomposition of Organic Mercurial Compounds by Mercury-resistant Bacteria

Isopentyl isovalerate and anisic acid were first isolated and identified from the Japanese peppermint oil. The former compound possesses characteristic apple-like oder. α-Bourbonene, menthofurolactone, and β-caryophyllene epoxide were also isolated and identified from the oil of Shubi, a newly registered Japanese peppermint.     

美洲大蠊内生菌的分离鉴定及酶活性、抑菌作用测定

分离美洲大蠊内生细菌并测定菌体的淀粉、纤维素降解酶活性及抑菌特性。对虫体表面消毒,以LB和高氏一号培养基分离虫体内部细菌并进行16S rRNA基因序列分析。变色圈法测定降解酶活性,抑菌圈法测定抑菌活性。结果共分离到11株细菌,4株属于链霉菌属(Streptomyces),6株分别属于肠杆菌属(Enterbacter)、变形菌属(Proteus）、肠球菌属（Enterococcus）、沙雷氏菌属（Serratia）、芽胞杆菌属（Bacillus）和漫游球菌属（Vagococcus）。另有1株菌在NCBI中与肠杆菌的相似度最高, 为95%,可能代表着一个潜在的新种。4株链霉菌均有淀粉和纤维素降解能力。有3株菌对青枯雷尔氏菌有抑制效果。研究结果表明,美洲大蠊内生菌具有某些功能,甚至含有尚未发现的新菌种,是重要的菌种资源。     

Isolation of Marine Bacteria by In Situ Culture on Media-Supplemented Polyurethane Foam

Polyurethane foam (PUF) supplemented with various agar media was used in situ to trap marine bacteria and it consequently provided a substrate on which they could be cultivated while exposed to natural seawater in the coral reef area. The bacterial population on the PUF blocks was analyzed by denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rDNA fragments. Changing the composition of the cultivation medium in the PUF blocks and selecting different sampling sites resulted in different bacteria being detected on the PUF blocks. For example, iron-utilizing (IU) bacteria, siderophore-producing (SP) bacteria, and petroleum-degrading (PD) bacteria were isolated from PUF blocks and it was discovered that IU and SP contained iron and PD contained hydrocarbon. This method opens up the possibility for isolating novel and useful marine bacteria.     

Production of Resting Forms by the Gram-Negative Chemolithoautotrophic Bacteria Thioalkalivibrio versutusand Thioalkalimicrobium aerophilum

The haloalkaliphilic chemolithoautotrophic gram-negative bacteria Thioalkalivibrio versutus, strain AL2, and Thioalkalimicrobium aerophilum, strain AL3, were shown to possess the capacity to produce resting forms, namely cystlike refractile cells (CRC), whose production was controlled by the level of the d₁ extracellular factors exhibiting the function of anabiosis autoinducers. The conditions were elucidated that promote the formation of CRC in the developmental cycles of the cultures studied, in condensed cell suspensions undergoing autolysis, and under the action of exogenously introduced chemical analogues of anabiosis autoinducers (alkylhydroxybenzenes). The peculiarities of the fine structure of the resting cells obtained were studied. Distinctions were revealed (with respect to viability and thermotolerance) between the CRC formed under different conditions. The relationship between the growth strategy and survival strategy of extremophilic bacteria is discussed taking into account the effect of the d₁ autoregulatory factors. A new model of CRC formation is proposed: CRC production in the life cycle of bacteria developing under conditions of increased concentration of anabiosis autoinducers.